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  • Wiley  (17,850)
  • Institute of Physics  (7,656)
  • Cell Press
  • International Union of Crystallography (IUCr)
  • National Academy of Sciences
  • 2020-2023  (141)
  • 1950-1954  (17,671)
  • 1935-1939  (10,645)
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  • 1
    Publication Date: 2022-03-11
    Description: As the Arctic coast erodes, it drains thermokarst lakes, transforming them into lagoons and, eventually, integrates them into subsea permafrost. Lagoons represent the first stage of a thermokarst lake transition to a marine setting and possibly more saline and colder upper boundary conditions. In this research, borehole data, electrical resistivity surveying, and modelling of heat and salt diffusion were carried out at Polar Fox Lagoon on the Bykovsky Peninsula, Siberia. Polar Fox Lagoon is a seasonally isolated water body connected to Tiksi Bay through a channel, leading to hypersaline waters under the ice cover. The boreholes in the centre of the lagoon revealed floating ice and a saline cryotic bed underlain by a saline cryotic talik, a thin ice‐bearing permafrost layer, and unfrozen ground. The bathymetry showed that most of the lagoon was ice‐grounded in spring. In bedfast ice areas, the electrical resistivity profiles suggest that an unfrozen saline layer was underlain by a thick layer of refrozen talik. The modelling suggests thermokarst lake taliks refreeze when submerged in saltwater with mean annual bottom water temperatures below or slightly above 0 °C. This occurs, because the top‐down chemical degradation of newly formed ice‐bearing permafrost is slower than the cooling of the talik. Hence, lagoons may pre‐condition taliks with a layer of ice‐bearing permafrost before encroachment by the sea and this frozen layer may act as a cap on gas migration out of the underlying talik.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 2
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    Wiley
    In:  EPIC3Journal of Geophysical Research-Atmospheres, Wiley, 127(3), pp. 1-18, ISSN: 0148-0227
    Publication Date: 2022-02-28
    Description: Fram Strait in the northern North Atlantic is a key region for marine cold air outbreaks (MCAOs), southward discharges of polar air under northerly air flow, which have a strong impact on air-sea heat fluxes, boundary layer processes and severe weather. This study investigates climatologies and decadal trends of Fram Strait MCAOs of different intensity classes based on the ERA5 reanalysis product for 1979–2020. Among striking interannual variability, it is shown that the main MCAO season is December through March, when MCAOs occur around 2/3 of the time. We report on significant decadal MCAO decreases in December and January, and a significant increase in March. While the mid-winter decrease is mainly related to the different paces of warming between the surface and the lower atmosphere, the increase in March can be related to changes in synoptic circulation patterns. As an explanation for the latter, a possible feedback between retreating Barents Sea sea ice, enhanced cyclonic activity and Fram Strait MCAOs is postulated. Exemplifying the trend toward stronger MCAOs during March, the study details the recordbreaking MCAO season in early 2020, and an observational case study of an extreme MCAO event in March 2020 is conducted. Thereby, radiosonde observations are combined with kinematic air back-trajectories to provide rare observational evidence for the diabatic cooling and drying during the MCAO preconditioning phase.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 3
    Publication Date: 2022-03-07
    Description: Fjords are recognized as hotspots of organic carbon (OC) burial in the coastal ocean. In fjords with glaciated catchments, glacier discharge carries large amounts of suspended matter. This sedimentary load includes OC from bedrock and terrigenous sources (modern vegetation, peat, soil deposits), which is either buried in the fjord or remineralized during export, acting as a potential source of CO2 to the atmosphere. In sub-Antarctic South Georgia, fjord-terminating glaciers have been retreating during the past decades, likely as a response to changing climate conditions. We determine sources of OC in surface sediments of Cumberland Bay, South Georgia, using lipid biomarkers and the bulk 14C isotopic composition, and quantify OC burial at present and for the time period of documented glacier retreat (between 1958 and 2017). Petrogenic OC is the dominant type of OC in proximity to the present-day calving fronts (60.4 ± 1.4% to 73.8 ± 2.6%) and decreases to 14.0 ± 2.7% outside the fjord, indicating that petrogenic OC is effectively buried in the fjord. Beside of marine OC, terrigenous OC comprises 2.7 ± 0.5% to 7.9 ± 5.9% and is mostly derived from modern plants and Holocene peat and soil deposits that are eroded along the flanks of the fjord, rather than released by the retreating fjord glaciers. We estimate that the retreat of tidewater glaciers between 1958 and 2017 led to an increase in petrogenic carbon accumulation of 22% in Cumberland West Bay and 6.5% in Cumberland East Bay, suggesting that successive glacier retreat does not only release petrogenic OC into the fjord, but also increases the capacity of OC burial.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
    Publication Date: 2022-04-24
    Description: Hillaire‐Marcelet al. bring forward several physical and geochemical arguments against our finding of an Arctic glaciolacustrine system in the past. In brief, we find that a physical approach to further test our hypothesis should additionally consider the actual bathymetry of the Greenland–Scotland Ridge (GSR), the density maximum of freshwater at 3–4°C, the sensible heat flux from rivers, and the actual volumes that are being mixed and advected. Their geochemical considerations acknowledge our original argument, but they also add a number of assumptions that are neither required to explain the observations, nor do they correspond to the lithology of the sediments. Rather than being additive in nature, their arguments of high particle flux, low particle flux, export of 230Th and accumulation of 230Th, are mutually exclusive. We first address the arguments above, before commenting on some misunderstandings of our original claim in their contribution, especially regarding our dating approach.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
    Publication Date: 2022-04-22
    Description: Integrated electron microprobe analyses (EMPAs) on glass and Sr–Nd isotope analyses have been performed on 17 tephras from the Middle Pleistocene Mercure lacustrine succession, southern Apennines. Two 40Ar/39Ar ages and the recognition of four relevant tephras from Colli Albani, Sabatini and possibly Roccamonfina volcanoes allowed us to ascribe the investigated succession to the late Marine Isotope Stage (MIS) 15–12 interval (560–440 ka). The Sr–Nd isotopes and major element glass compositions allowed us to attribute 10 out of the other 13 tephras to a poorly known activity of the Roccamofina volcano, whereas two layers were tentatively attributed to previously unknown Middle Pleistocene activity of Ponza Island or Campanian volcanoes, and one to Salina Island. The tephrostratigraphic correlation of the Mercure tephras with the Acerno lacustrine pollen record (Campania) also allowed us to evaluate the climatostratigraphic position of the tephras within the framework of the MIS 15–12 climatic variability. These results were obtained by combining the Sr–Nd isotope ratio with EMPA and 40Ar/39Ar geochronological data. This confirms the notable consistency of this approach for studying the Mediterranean Middle Pleistocene tephrostratigraphy, which, despite its great potential for both volcanology and Quaternary studies, has been hitherto barely explored.
    Description: Published
    Description: 232–248
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: 4V. Processi pre-eruttivi
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Keywords: 40Ar/39Ar dating; EMPA glass compositions ; Middle Pleistocene; ; peri-Tyrrhenian explosive volcanisms ; Sr isotopes.
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
    Publication Date: 2022-05-03
    Description: Shallow seabed depressions attributed to focused fluid seepage, known as pock- marks, have been documented in all continental margins. In this study, we dem- onstrate how pockmark formation can be the result of a combination of multiple factors— fluid type, overpressures, seafloor sediment type, stratigraphy and bot- tom currents. We integrate multibeam echosounder and seismic reflection data, sediment cores and pore water samples, with numerical models of groundwa- ter and gas hydrates, from the Canterbury Margin (off New Zealand). More than 6800 surface pockmarks, reaching densities of 100 per km2, and an undefined number of buried pockmarks, are identified in the middle to outer shelf and lower continental slope. Fluid conduits across the shelf and slope include shal- low to deep chimneys/pipes. Methane with a biogenic and/or thermogenic origin is the main fluid forming flow and escape features, although saline and fresh- ened groundwaters may also be seeping across the slope. The main drivers of fluid flow and seepage are overpressure across the slope generated by sediment loading and thin sediment overburden above the overpressured interval in the outer shelf. Other processes (e.g. methane generation and flow, a reduction in hydrostatic pressure due to sea- level lowering) may also account for fluid flow and seepage features, particularly across the shelf. Pockmark occurrence coin- cides with muddy sediments at the seafloor, whereas their planform is elongated by bottom currents.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 7
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Romagnoni, G., Kvile, K. o., Dagestad, K., Eikeset, A. M., Kristiansen, T., Stenseth, N. C., & Langangen, O. Influence of larval transport and temperature on recruitment dynamics of North Sea cod (Gadus morhua) across spatial scales of observation. Fisheries Oceanography, (2020): 1-16, doi:10.1111/fog.12474.
    Description: The survival of fish eggs and larvae, and therefore recruitment success, can be critically affected by transport in ocean currents. Combining a model of early‐life stage dispersal with statistical stock–recruitment models, we investigated the role of larval transport for recruitment variability across spatial scales for the population complex of North Sea cod (Gadus morhua ). By using a coupled physical–biological model, we estimated the egg and larval transport over a 44‐year period. The oceanographic component of the model, capable of capturing the interannual variability of temperature and ocean current patterns, was coupled to the biological component, an individual‐based model (IBM) that simulated the cod eggs and larvae development and mortality. This study proposes a novel method to account for larval transport and success in stock–recruitment models: weighting the spawning stock biomass by retention rate and, in the case of multiple populations, their connectivity. Our method provides an estimate of the stock biomass contributing to recruitment and the effect of larval transport on recruitment variability. Our results indicate an effect, albeit small, in some populations at the local level. Including transport anomaly as an environmental covariate in traditional stock–recruitment models in turn captures recruitment variability at larger scales. Our study aims to quantify the role of larval transport for recruitment across spatial scales, and disentangle the roles of temperature and larval transport on effective connectivity between populations, thus informing about the potential impacts of climate change on the cod population structure in the North Sea.
    Description: G.R. was supported by the Norden Top‐level Research Initiative sub‐programme “Effect Studies and Adaptation to Climate Change” through the Nordic Centre for Research on Marine Ecosystems and Resources under Climate Change (NorMER). K.Ø.K. was supported by the WHOI John H. Steele Post‐doctoral Scholar award and VISTA – a basic research program in collaboration between The Norwegian Academy of Science and Letters, and Equinor. We thank an anonymous referee for valuable comments that substantially improved the article.
    Keywords: Atlantic cod ; biophysical model ; larval transport ; North Sea ; populations ; stock–recruitment ; temperature
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2022-03-16
    Description: Tectono-stratigraphic interpretation and sequential restoration modelling was performed over two high-resolution seismic profiles crossing the Western Ionian Basin of southern Italy. This analysis was undertaken in order to provide greater insights and a more reliable assessment of the deformation rate affecting the area. Offshore seismic profiling illuminates the sub-seafloor setting where a belt of active normal faults slice across the foot of the Malta Escarpment, a regional-scale structural boundary inherited from the Permo-Triassic palaeotectonic setting. A sequential restoration workflow was established to back-deform the entire investigated sector with the primary aim of analysing the deformation history of the three major normal faults affecting the area. Restoration of the tectono-stratigraphic model reveals how deformation rates evolved through time. In the early stage, the studied area experienced a significant deformation with the horizontal component prevailing over the vertical element. In this context, the three major faults contribute to only one third of the total deformation. The overall throw and extension then notably reduced through time towards the present day and, since the middle Pliocene, ongoing crustal deformation is accommodated almost entirely by the three major normal faults. Unloading and decompaction indicate that when compared to the unrestored seismic sections, a revision and a reduction of roughly one third of the vertical displacement of the faults offset is required. This analysis ultimately allows us to better understand the seismic potential of the region.
    Description: Published
    Description: 321-341
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
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    Wiley
    In:  EPIC3Limnology and Oceanography Letters, Wiley, 7(2), pp. 167-174, ISSN: 2378-2242
    Publication Date: 2022-03-25
    Description: The end of the polar night with the concurrent onset of photosynthetic biomass production ultimately leads to the spring bloom, which represents the most important event of primary production for the Arctic marine ecosystem. This dataset shows, for the first time, significant in situ biomass accumulation during the dark–light transition in the high Arctic, as well as the earliest recorded positive net primary production rates together with constant chlorophyll a-normalized potential for primary production through winter and spring. The results indicate a high physiological capacity to perform photosynthesis upon re-illumination, which is in the same range as that observed during the spring bloom. Put in context with other data, the results of this study indicate that also active cells originating from the low winter standing stock in the water column, rather than solely resting stages from the sediment, can seed early spring bloom assemblages.
    Repository Name: EPIC Alfred Wegener Institut
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  • 10
    Publication Date: 2022-02-17
    Description: Free access at https://onlinelibrary.wiley.com/doi/10.1111/1755-6724.14824
    Description: Earthquake is a sudden release of energy due to fault motions. The severity of the damages can be minimized by development of a culture of prevention which includes the Seismic Hazard Assessment, microzonation studies and appropriate building codes. Earthquake risk assessment methods require seismo tectonic information usually organized in earthquake catalogues utilized in Probabilistic Seismic Hazard Assessment (PSHA) based on initial work by Cornell (1968), where probability distributions for magnitudes and source site distances reported in earthquake catalogues were utilized for the first time. In following years the method furtherly improved reporting an upper bound on the earthquake magnitude in each region avoiding the inclusion of unrealistically big earthquakes. A different approach has been followed in Countries characterized by significant incompletenesses in available earthquake catalogues. In these places the Deterministic Seismic Hazard Assessment (DSHA) methods have been often utilized. In particular the DSHA takes into account the maximum possible earthquake to evaluate the intensity of seismic ground motion distribution at a site by taking account the seismotectonic setup of the area. A deepening in the knowledge of seismotectonics and of morphostructural features of the studied area has been carried out in pattern recognition studies (Gelfand et al., 1976 and references therein). More updated applications named Neo-Deterministic Seismic Hazard Assessment (NDSHA) proposed by Wang et al. (2021) also consider morphostructural zoning which, in turn, considers nodes (fractured areas), lineaments and topographical features like the maximal elevation and the minimal elevation of the studied area. The steepness of topographic surfaces and sharp variations in morphostructural parameters indicate high tectonic activity. Some geological features are also presently utilized in PSHA methods in some Countries and considers basic parameters like the top and the bottom of seismogenic layers deduced by faults geometry within the frame of the Earthquake Rupture Forecasting (Bird and Liu, 2007).
    Description: Published
    Description: 31-33
    Description: 9T. Geochimica dei fluidi applicata allo studio e al monitoraggio di aree sismiche
    Description: JCR Journal
    Keywords: probabilistic seismic hazard assessment, deterministic seismic hazard assessment, helium isotopes, geochemical prospection, earthquake precursors ; seismic hazard estimation by geochemical methods
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
    Publication Date: 2022-02-21
    Description: Relative sea‐level (RSL) evolution during Marine Isotopic Stage (MIS) 5 in the Mediterranean basin is still not fully understood despite a plethora of morphological, stratigraphic and geochronological studies carried out on highstand deposits of this area. In this review we assembled a database of 323 U/Th‐dated samples (e.g. corals, molluscs, speleothems) which were used to chronologically constrain RSL evolution within MIS 5. The application of strict geochemical criteria to the U/Th samples indicates that only ~33% of data available for the Mediterranean Sea can be considered ‘reliable’. Most of these data (~65%) refer to the MIS 5e highstand, while only ~17% could be related to the MIS 5a. No attribution to MIS 5c can be unequivocally supported. Nevertheless, the resulting framework does not allow us to define a satisfactory RSL trend during the MIS 5e highstand and subsequent MIS 5 substages. Overall, the proposed selection of reliable/unreliable data would be useful for detecting areas where MIS 5 substage attributions are not supported by confident U/Th chronological data and thus the related reconstructions need to be revised. In this regard, the resulting framework calls for a reappraisal and re‐examination of the Mediterranean records with advanced geochronological methodologies.
    Description: Published
    Description: 1174-1189
    Description: 5A. Ricerche polari e paleoclima
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
    Publication Date: 2022-02-25
    Description: The Apennines are a retreating collisional belt where the foreland basin system, across large domains, is floored by a subaerial forebulge unconformity developed due to forebulge uplift and erosion. This unconformity is overlain by a diachronous sequence of three lithostratigraphic units made of (a) shallow-water carbonates, (b) hemipelagic marls and shales and (c) siliciclastic turbidites. Typically, the latter two have been interpreted regionally as the onset of syn-orogenic deposition in the foredeep depozone, whereas little attention has been given to the underlying unit. Accordingly, the rate of migration of the central-southern Apennine fold-thrust beltforeland basin system has been constrained, so far, exclusively considering the age of the hemipelagites and turbidites, which largely post-date the onset of foredeep depozone. In this work, we provide new high-resolution ages obtained by strontium isotope stratigraphy applied to calcitic bivalve shells sampled at the base of the first syn-orogenic deposits overlying the Eocene-Cretaceous pre-orogenic substratum. Integration of our results with published data indicates progressive rejuvenation of the strata sealing the forebulge unconformity towards the outer portions of the foldthrust belt. In particular, the age of the forebulge unconformity linearly scales with the pre-orogenic position of the analysed sites, pointing to an overall constant migration velocity of the forebulge wave in the last 25 Myr.
    Description: Published
    Description: 2817-2836
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Keywords: central-southern Apennines (Italy) ; fold-thrust belt ; forebulge ; foredeep
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
    Publication Date: 2022-01-04
    Description: We present a novel method to estimate dynamic ice loss of Greenland's three largest outlet glaciers: Jakobshavn Isbræ, Kangerlussuaq Glacier, and Helheim Glacier. We use Global Navigation Satellite System (GNSS) stations attached to bedrock to measure elastic displacements of the solid Earth caused by dynamic thinning near the glacier terminus. When we compare our results with discharge, we find a time lag between glacier speedup/slowdown and onset of dynamic thinning/thickening. Our results show that dynamic thinning/thickening on Jakobshavn Isbræ occurs 0.87 ± 0.07 years before speedup/slowdown. This implies that using GNSS time series we are able to predict speedup/slowdown of Jakobshavn Isbræ by up to 10.4 months. For Kangerlussuaq Glacier the lag between thinning/thickening and speedup/slowdown is 0.37 ± 0.17 years (4.4 months). Our methodology and results could be important for studies that attempt to model and understand mechanisms controlling short-term dynamic fluctuations of outlet glaciers in Greenland.
    Repository Name: EPIC Alfred Wegener Institut
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  • 14
    Publication Date: 2021-11-29
    Description: This work presents a novel empirical Ground Motion prediction Model (GMM) for vertical-to-horizontal (VH) response spectral amplitudes up to 10 s, peak ground acceleration and velocity for shallow crustal earthquakes in Italy. Being calibrated on the most up-to-date strong motion dataset for Italian crustal earthquakes (ITA18), the model is consistent with the ITA18 GMM for the horizontal ground motion. This property makes the model useful in probabilistic seismic hazard assessment for Italy to derive compatible vertical and horizontal response spectra. To account for the increase of VH ratios in the proximity of the seismic source, an adjustment term is introduced to improve the prediction capability of the model in near-source conditions, relying on the worldwide NEar-Source Strong motion dataset (NESS). The proposed model uses a simple functional form restricted to a limited number of predictor variables, namely, magnitude, source-to-site distance, focal mechanism, and site effects, and the variability associated with both VH and V models is provided.
    Description: Published
    Description: 4121-4141
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
    Publication Date: 2021-12-16
    Description: Diffusive gradients in thin fi lms (DGT) have been tested in CO2-rich, metal-bearing fl uids from springs in the Campo de Calatrava region in Central Spain, to assess their applicability as a monitoring tool in onshore CO2 storage projects. These fi lms are capable of adsorbing metals and recording changes in their concentration in water, sediments, and soils. Considering that CO2 dissolution promotes metal solubilization and transport, the use of these fi lms could be valuable as a monitoring tool of early leakage. A number of DGT have been deployed in selected springs with constant metal concentration. The studied waters show high concentrations of Fe, as high as 1 × 104 μg·L–1, Ni, Co, Zn, Cu, and Mn. Comparing re-calculated metal concentration in DGT with metal water concentration, two different metal behaviors are observed: (i) metals with sorption consistent with the metal concentration (i.e. plotting close to the 1:1 line in a [Me]DGT: [Me]water plot), and (ii) metals with non–linear sorption, with some data showing metal enrichment in DGT compared with the concentration in water. Metals in the fi rst group include Fe, Mn, Co, Ni, and U, and metals in the second group are Zn, Pb, Cr, Cu, and Al. From this research, it is concluded that the metals in the fi rst group can be used to monitor potential leakage by using DGT, providing effective leakage detection even considering low variations of concentrations, episodic metal release, and reducing costs compared with conventional, periodic water sampling.
    Description: Published
    Description: 163-175
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Keywords: Campo de Calatrava ; CO2 storage and leakage ; DGT ; metal leakage ; metal transport ; trace metals ; 03.04. Chemical and biological ; 05.04. Instrumentation and techniques of general interest
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 16
    Publication Date: 2021-12-22
    Description: We present a new geometrical method capable of quantifying and illustrating the outcomes of a three-component mixing dynamics. In a three-component mixing sce nario, classical algebraic equations and endmember mixing analysis (EMMA) can be used to quantify the contributions from each fraction. Three-component mixing of natural waters, either in an element–element plot or by using the EMMA mixing sub space is described by a triangular shaped distribution of sample points where each endmember is placed on an apex, while each side corresponds to the mixing function of the two endmembers placed at the apex, considering the third endmembers' con tribution equal to zero. Along each side, the theoretical mixing fractions can be com puted using mass balance equations. Samples with contributions from three endmembers will plot inside the triangle, while the homogeneous barycentric coordi nate projections can be projected onto the three sides. The geochemistry observed in the mineralized Ferrarelle aquifer system (southern Italy) results from three component mixing of groundwater, each with diagnostic geochemical compositions. The defined boundary conditions allow us to parameterize and validate the proce dures for modelling mixing, including selection of suitable geochemical tracer
    Description: Published
    Description: e14409
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
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  • 17
    Publication Date: 2022-01-11
    Description: Mt Etna has made headlines over the last weeks and months with spectacular eruptions, some of them highly explosive. This type of paroxysmal eruptive behaviour is characteristic of Etna’s activity over the past few decades and so it is no surprise that Etna is among the most active volcanoes worldwide. Etna is well-known for its extraordinary geology and due to its repeated eruptive activity it provides a continuous supply of new scientific opportunities to understand the inner workings of large basaltic volcanic systems. In addition to its scientific value, Etna is also a world famous tourist attraction and has been listed as a UNESCO World Heritage site in 2013 for its geological and cultural value and not least for its fine agricultural products. Etna’s status as an iconic volcano is not a recent phenomenon; in fact, Etna has been a literary fixture for at least 3000 years, giving rise to many ancient myths and legends that mark it as a special place, deserving of human respect. From the ancient eruptions to the latest events in February–April 2021, people try to explain and understand the processes that occur within and beneath the volcano. In this article, we briefly summarize the recent eruptive activity of Etna as well as the ancient myths and legends that surround this volcano, from the underground forge of Hephaestus to the adventures of Odysseus, all the way to the benefits and dangers the volcano provides to those living on its flanks today.
    Description: Published
    Description: 141-149
    Description: 2TM. Divulgazione Scientifica
    Description: N/A or not JCR
    Keywords: Etna, mythology, 2021 paroxysms, economy ; 04.08. Volcanology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 18
    Publication Date: 2022-07-04
    Description: Collapse of permafrost coasts delivers large quantities of particulate organic carbon (POC) to arctic coastal areas. With rapidly‐changing environmental conditions, sediment and organic carbon (OC) mobilization and transport pathways are also changing. Here, we assess the sources and sinks of POC in the highly‐dynamic nearshore zone of Herschel Island ‐ Qikiqtaruk (Yukon, Canada). Our results show that POC concentrations sharply decrease, from 15.9 to 0.3 mg L‐1, within the first 100 – 300 meters offshore. Simultaneously, radiocarbon ages of POC drop from 16,400 to 3,600 14C years, indicating rapid settling of old permafrost POC to underlying sediments. This suggests that permafrost OC is, apart from a very narrow resuspension zone (〈5 m water depth), predominantly deposited in nearshore sediments. While long‐term storage of permafrost OC in marine sediments potentially limits biodegradation and its subsequent release as greenhouse gas, resuspension of fine‐grained, OC‐rich sediments in the nearshore zone potentially enhances OC turnover.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed , info:eu-repo/semantics/article
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  • 19
    Publication Date: 2022-06-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suca, J., Ji, R., Baumann, H., Pham, K., Silva, T., Wiley, D., Feng, Z., & Llopiz, J. Larval transport pathways from three prominent sand lance habitats in the Gulf of Maine. Fisheries Oceanography, 31(3), (2022): 333– 352, https://doi.org/10.1111/fog.12580.
    Description: Northern sand lance (Ammodytes dubius) are among the most critically important forage fish throughout the Northeast US shelf. Despite their ecological importance, little is known about the larval transport of this species. Here, we use otolith microstructure analysis to estimate hatch and settlement dates of sand lance and then use these measurements to parametrize particle tracking experiments to assess the source–sink dynamics of three prominent sand lance habitats in the Gulf of Maine: Stellwagen Bank, the Great South Channel, and Georges Bank. Our results indicate the pelagic larval duration of northern sand lance lasts about 2 months (range: 50–84 days) and exhibit a broad range of hatch and settlement dates. Forward and backward particle tracking experiments show substantial interannual variability, yet suggest transport generally follows the north to south circulation in the Gulf of Maine region. We find that Stellwagen Bank is a major source of larvae for the Great South Channel, while the Great South Channel primarily serves as a sink for larvae from Stellwagen Bank and Georges Bank. Retention is likely the primary source of larvae on Georges Bank. Retention within both Georges Bank and Stellwagen Bank varies interannually in response to changes in local wind events, while the Great South Channel only exhibited notable retention in a single year. Collectively, these results provide a framework to assess population connectivity among these sand lance habitats, which informs the species' recruitment dynamics and impacts its vulnerability to exploitation.
    Description: Funding came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (Woods Hole Sea Grant, Woods Hole Oceanographic Institution, NA18OAR4170104, Project No. R/O-57; RJ, HB, and JKL), the Bureau of Ocean Energy Management (IA agreement M17PG0019; DNW, HB, and JKL) including a subaward via the National Marine Sanctuary Foundation (18-11-B-203), and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE 1655686; RJ and JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship program.
    Keywords: Gulf of Maine ; larval retention ; otolith microstructure ; particle tracking ; population connectivity ; sand lance
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  • 20
    Publication Date: 2022-05-24
    Description: We have reinterpreted the causative fault parameters of the 2005 Zarand earthquake in the light of a new imagery study using Interferometric Synthetic Aperture Radar (InSAR). By conducting a joint inversion of two InSAR datasets, we can characterize the rupture as it relates to complex local structures. At first, the mainshock ruptured a nearly pure reverse fault, dipping ~65° NNW in the basement below the southeastern area of Zarand. Two more fault segments were subsequently activated: an oblique‐normal fault segment parallel to the first segment, dipping 61° to the south, and a normal‐oblique fault segment at the eastern termination of the rupture zone. The first fault segment ruptured the surface, while slip along the other two segments was confined to the lower sedimentary strata.
    Description: Published
    Description: 274-283
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 21
    Publication Date: 2022-08-31
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fay, R., Hamel, S., van de Pol, M., Gaillard, J.-M., Yoccoz, N. G., Acker, P., Authier, M., Larue, B., Le Coeur, C., Macdonald, K. R., Nicol-Harper, A., Barbraud, C., Bonenfant, C., Van Vuren, D. H., Cam, E., Delord, K., Gamelon, M., Moiron, M., Pelletier, F., Rotella, J., Teplitsky, C., Visser, M. E., Wells, C. P., Wheelwright, N. T., Jenouvrier, S., & Saether, B.-E. Temporal correlations among demographic parameters are ubiquitous but highly variable across species. Ecology Letters, 25(7), (2022): 1640-1654, https://doi.org/10.1111/ele.14026.
    Description: Temporal correlations among demographic parameters can strongly influence population dynamics. Our empirical knowledge, however, is very limited regarding the direction and the magnitude of these correlations and how they vary among demographic parameters and species’ life histories. Here, we use long-term demographic data from 15 bird and mammal species with contrasting pace of life to quantify correlation patterns among five key demographic parameters: juvenile and adult survival, reproductive probability, reproductive success and productivity. Correlations among demographic parameters were ubiquitous, more frequently positive than negative, but strongly differed across species. Correlations did not markedly change along the slow-fast continuum of life histories, suggesting that they were more strongly driven by ecological than evolutionary factors. As positive temporal demographic correlations decrease the mean of the long-run population growth rate, the common practice of ignoring temporal correlations in population models could lead to the underestimation of extinction risks in most species.
    Description: This project was funded by the CNRS, including a long-term support by the OSU-OREME. Data collection for Weddell seals was supported by the National Science Foundation, Division of Polar Programs under grant number ANT-1640481 to J.J. Rotella, R.A. Garrott and D.B. Siniff and prior NSF Grants to R. A. Garrott, J. J. Rotella, D. B. Siniff and J. Ward Testa. Stéphanie Jenouvrier acknowledges the support of the NSF 1840058.
    Keywords: capture-recapture ; demographic correlation ; demography ; environmental stochasticity ; slow-fast continuum ; stochastic population dynamics ; temporal covariation
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  • 22
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Peredo, E. L., & Cardon, Z. G. Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae. Proceedings of the National Academy of Sciences of the United States of America, 117(29), 1(2020): 7438-17445, doi:10.1073/pnas.1906904117.
    Description: Among green plants, desiccation tolerance is common in seeds and spores but rare in leaves and other vegetative green tissues. Over the last two decades, genes have been identified whose expression is induced by desiccation in diverse, desiccation-tolerant (DT) taxa, including, e.g., late embryogenesis abundant proteins (LEA) and reactive oxygen species scavengers. This up-regulation is observed in DT resurrection plants, mosses, and green algae most closely related to these Embryophytes. Here we test whether this same suite of protective genes is up-regulated during desiccation in even more distantly related DT green algae, and, importantly, whether that up-regulation is unique to DT algae or also occurs in a desiccation-intolerant relative. We used three closely related aquatic and desert-derived green microalgae in the family Scenedesmaceae and capitalized on extraordinary desiccation tolerance in two of the species, contrasting with desiccation intolerance in the third. We found that during desiccation, all three species increased expression of common protective genes. The feature distinguishing gene expression in DT algae, however, was extensive down-regulation of gene expression associated with diverse metabolic processes during the desiccation time course, suggesting a switch from active growth to energy-saving metabolism. This widespread downshift did not occur in the desiccation-intolerant taxon. These results show that desiccation-induced up-regulation of expression of protective genes may be necessary but is not sufficient to confer desiccation tolerance. The data also suggest that desiccation tolerance may require induced protective mechanisms operating in concert with massive down-regulation of gene expression controlling numerous other aspects of metabolism.
    Description: Dr. Louise Lewis (University of Connecticut) provided F. rotunda and A. deserticola. Suzanne Thomas and Jordan Stark provided expert technical assistance. This work was supported by the NSF, Division of Integrative Organismal Systems (1355085 to Z.G.C.), and an anonymous donor (to Z.G.C.).
    Keywords: Aquatic green algae ; Desert-evolved green algae ; Extremophiles ; Microbiotic ; Crusts ; Scenedesmaceae
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  • 23
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Criswell, K. E., Roberts, L. E., Koo, E. T., Head, J. J., & Gillis, J. A. Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences of the United States of America, 118(51), (2021): e2114563118, https://doi.org/10.1073/pnas.2114563118.
    Description: The axial skeleton of tetrapods is organized into distinct anteroposterior regions of the vertebral column (cervical, trunk, sacral, and caudal), and transitions between these regions are determined by colinear anterior expression boundaries of Hox5/6, -9, -10, and -11 paralogy group genes within embryonic paraxial mesoderm. Fishes, conversely, exhibit little in the way of discrete axial regionalization, and this has led to scenarios of an origin of Hox-mediated axial skeletal complexity with the evolutionary transition to land in tetrapods. Here, combining geometric morphometric analysis of vertebral column morphology with cell lineage tracing of hox gene expression boundaries in developing embryos, we recover evidence of at least five distinct regions in the vertebral skeleton of a cartilaginous fish, the little skate (Leucoraja erinacea). We find that skate embryos exhibit tetrapod-like anteroposterior nesting of hox gene expression in their paraxial mesoderm, and we show that anterior expression boundaries of hox5/6, hox9, hox10, and hox11 paralogy group genes predict regional transitions in the differentiated skate axial skeleton. Our findings suggest that hox-based axial skeletal regionalization did not originate with tetrapods but rather has a much deeper evolutionary history than was previously appreciated.
    Description: This research was funded by a Natural Environment Research Council Grant (to J.J.H., J.A.G., and K.E.C.: NE/S000739/1) and a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377), and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) (to J.A.G.).
    Keywords: Hox genes ; Regionalization ; Chondrichthyan ; Vertebral column
    Repository Name: Woods Hole Open Access Server
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  • 24
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kuehn, E., Clausen, D. S., Null, R. W., Metzger, B. M., Willis, A. D., & Ozpolat, B. D. Segment number threshold determines juvenile onset of germline cluster expansion in Platynereis dumerilii. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, (2021.): 1-16, https://doi.org/10.1002/jez.b.23100.
    Description: Development of sexual characters and generation of gametes are tightly coupled with growth. Platynereis dumerilii is a marine annelid that has been used to study germline development and gametogenesis. P. dumerilii has germ cell clusters found across the body in the juvenile worms, and the clusters eventually form the gametes. Like other segmented worms, P. dumerilii grows by adding new segments at its posterior end. The number of segments reflect the growth state of the worms and therefore is a useful and measurable growth state metric to study the growth-reproduction crosstalk. To understand how growth correlates with progression of gametogenesis, we investigated germline development across several developmental stages. We discovered a distinct transition period when worms increase the number of germline clusters at a particular segment number threshold. Additionally, we found that keeping worms short in segment number, by manipulating environmental conditions or via amputations, supported a segment number threshold requirement for germline development. Finally, we asked if these clusters in P. dumerilii play a role in regeneration (as similar free-roaming cells are observed in Hydra and planarian regeneration) and found that the clusters were not required for regeneration in P. dumerilii, suggesting a strictly germline nature. Overall, these molecular analyses suggest a previously unidentified developmental transition dependent on the growth state of juvenile P. dumerilii leading to substantially increased germline expansion.
    Description: Research reported in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R35GM138008 (to BDÖ) and R35GM133420 (to ADW) and Hibbitt Startup Funds (to BDÖ).
    Keywords: Annelida ; Critical size ; Developmental transition ; Gametogenesis ; Sexual reproduction
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  • 25
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Meaders, J. L., de Matos, S. N., & Burgess, D. R. A pushing mechanism for microtubule aster positioning in a large cell type. Cell Reports, 33(1), (2020): 108213, doi:10.1016/j.celrep.2020.108213.
    Description: After fertilization, microtubule (MT) sperm asters undergo long-range migration to accurately position pronuclei. Due to the large sizes of zygotes, the forces driving aster migration are considered to be from pulling on the astral MTs by dynein, with no significant contribution from pushing forces. Here, we re-investigate the forces responsible for sperm aster centration in sea urchin zygotes. Our quantifications of aster geometry and MT density preclude a pulling mechanism. Manipulation of aster radial lengths and growth rates, combined with quantitative tracking of aster migration dynamics, indicates that aster migration is equal to the length of rear aster radii, supporting a pushing model for centration. We find that dynein inhibition causes an increase in aster migration rates. Finally, ablation of rear astral MTs halts migration, whereas front and side ablations do not. Collectively, our data indicate that a pushing mechanism can drive the migration of asters in a large cell type.
    Description: We would like to thank Dr. Jesse Gatlin for sending us the Tau-mCherry fusion protein for imaging live MTs. We would also like to thank Dr. Timothy Mitchison, Dr. Christine Field, and Dr. James Pelletier for supplying us with CA4, p150-CC1, and EB1-GFP peptides, as well as for fruitful discussions. Finally, we would like to thank Dr. Charles Shuster and Leslie Toledo-Jacobo for constructive feedback when preparing the manuscript. We thank Bret Judson and the Boston College Imaging Core for infrastructure and support. This material is based upon work supported by NSF grant no. 124425 to D.R.B.
    Keywords: Dynein ; Aster ; Microtubule ; Centrosome ; Pronucleus ; Fertilization ; Aster position
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  • 26
    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stolp, Z. D., Kulkarni, M., Liu, Y., Zhu, C., Jalisi, A., Lin, S., Casadevall, A., Cunningham, K. W., Pineda, F. J., Teng, X., & Hardwick, J. M. Yeast cell death pathway requiring AP-3 vesicle trafficking leads to vacuole/lysosome membrane permeabilization. Cell Reports, 39(2), (2022): 110647, https://doi.org/10.1016/j.celrep.2022.110647.
    Description: Unicellular eukaryotes have been suggested as undergoing self-inflicted destruction. However, molecular details are sparse compared with the mechanisms of programmed/regulated cell death known for human cells and animal models. Here, we report a molecular cell death pathway in Saccharomyces cerevisiae leading to vacuole/lysosome membrane permeabilization. Following a transient cell death stimulus, yeast cells die slowly over several hours, consistent with an ongoing molecular dying process. A genome-wide screen for death-promoting factors identified all subunits of the AP-3 complex, a vesicle trafficking adapter known to transport and install newly synthesized proteins on the vacuole/lysosome membrane. To promote cell death, AP-3 requires its Arf1-GTPase-dependent vesicle trafficking function and the kinase Yck3, which is selectively transported to the vacuole membrane by AP-3. Video microscopy revealed a sequence of events where vacuole permeability precedes the loss of plasma membrane integrity. AP-3-dependent death appears to be conserved in the human pathogenic yeast Cryptococcus neoformans.
    Description: Funding sources: National Institutes of Health, United States grants AI144373 and NS127076 (J.M.H.), AI115016 and AI153414 (K.W.C.), and AI052733, AI152078, and HL059842 (A.C.); National Natural Science Foundation of China 31970550; and the Priority Academic Program Development of the Jiangsu Higher Education Institutes (X.T.).
    Keywords: Yeast ; Programmed cell death ; Vesicle trafficking ; AP-3 ; Vacuole ; Cryptococcus ; Yck3 ; Regulated cell death ; Lysosome ; Vacuolar membrane permeabilization
    Repository Name: Woods Hole Open Access Server
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  • 27
    Publication Date: 2022-10-31
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Northcutt, A. J., Kick, D. R., Otopalik, A. G., Goetz, B. M., Harris, R. M., Santin, J. M., Hofmann, H. A., Marder, E., & Schulz, D. J. Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis. Proceedings of the National Academy of Sciences of the United States of America, 116 (52) (2019): 26980-26990, doi: 10.1073/pnas.1911413116.
    Description: Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: If cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell-type classification, we performed 2 forms of transcriptional profiling—RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from 2 small crustacean neuronal networks: The stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally defined neuron types can be classified by expression profile alone. The results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post hoc grouping, so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between 2 or more cell types. Therefore, this study supports the general utility of cell identification by transcriptional profiling, but adds a caution: It is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology, or innervation target can neuronal identity be unambiguously determined.
    Description: We thank members of the D.J.S., H.A.H., and E.M. laboratories for helpful discussions. We thank the Genomic Sequencing and Analysis Facility (The University of Texas [UT] at Austin) for library preparation and sequencing and the bioinformatics consulting team at the UT Austin Center for Computational Biology and Bioinformatics for helpful advice. This work was supported by National Institutes of Health grant R01MH046742-29 (to E.M. and D.J.S.) and the National Institute of General Medical Sciences T32GM008396 (support for A.J.N.) and National Institute of Mental Health grant 5R25MH059472-18 and the Grass Foundation (support for Neural Systems and Behavior Course at the Marine Biological Laboratory).
    Keywords: qPCR ; RNA-seq ; Stomatogastric ; Expression profiling
    Repository Name: Woods Hole Open Access Server
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  • 28
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Long, M. H., Rheuban, J. E., McCorkle, D. C., Burdige, D. J., & Zimmerman, R. C. Closing the oxygen mass balance in shallow coastal ecosystems. Limnology and Oceanography, 64(6), (2019): 2694-2708, doi: 10.1002/lno.11248.
    Description: The oxygen concentration in marine ecosystems is influenced by production and consumption in the water column and fluxes across both the atmosphere–water and benthic–water boundaries. Each of these fluxes has the potential to be significant in shallow ecosystems due to high fluxes and low water volumes. This study evaluated the contributions of these three fluxes to the oxygen budget in two contrasting ecosystems, a Zostera marina (eelgrass) meadow in Virginia, U.S.A., and a coral reef in Bermuda. Benthic oxygen fluxes were evaluated by eddy covariance. Water column oxygen production and consumption were measured using an automated water incubation system. Atmosphere–water oxygen fluxes were estimated by parameterizations based on wind speed or turbulent kinetic energy dissipation rates. We observed significant contributions of both benthic fluxes and water column processes to the oxygen mass balance, despite the often‐assumed dominance of the benthic communities. Water column rates accounted for 45% and 58% of the total oxygen rate, and benthic fluxes accounted for 23% and 39% of the total oxygen rate in the shallow (~ 1.5 m) eelgrass meadow and deeper (~ 7.5 m) reef site, respectively. Atmosphere–water fluxes were a minor component at the deeper reef site (3%) but a major component at the shallow eelgrass meadow (32%), driven by diel changes in the sign and strength of atmosphere–water gradient. When summed, the measured benthic, atmosphere–water, and water column rates predicted, with 85–90% confidence, the observed time rate of change of oxygen in the water column and provided an accurate, high temporal resolution closure of the oxygen mass balance.
    Description: This work was substantially improved by comments from two anonymous reviewers. We thank Victoria Hill, David Ruble, Jeremy Bleakney, and Brian Collister for assistance in the field and the staff of the Bermuda Institute of Ocean Sciences and the Anheuser‐Busch Coastal Research Center for logistical support. This work was supported by NSF OCE grants 1657727 (to M.H.L. and D.C.M.), 1635403 (to R.C.Z. and D.J.B.), and 1633951 (to M.H.L.).
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  • 29
    Publication Date: 2022-05-26
    Description: Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry, Geophysics, Geosystems XX (2019): Tyne, R. L., Barry, P. H., Hillegonds, D. J., Hunt, A. G., Kulongoski, J. T., Stephens, M. J., Byrne, D. J., & Ballentine, C. J. A novel method for the extraction, purification, and characterization of noble gases in produced fluids. Geochemistry Geophysics Geosystems, 20, (2019): 5588-5597, doi: 10.1029/2019GC008552.
    Description: Hydrocarbon systems with declining or viscous oil production are often stimulated using enhanced oil recovery (EOR) techniques, such as the injection of water, steam, and CO2, in order to increase oil and gas production. As EOR and other methods of enhancing production such as hydraulic fracturing have become more prevalent, environmental concerns about the impact of both new and historical hydrocarbon production on overlying shallow aquifers have increased. Noble gas isotopes are powerful tracers of subsurface fluid provenance and can be used to understand the impact of EOR on hydrocarbon systems and potentially overlying aquifers. In oil systems, produced fluids can consist of a mixture of oil, water and gas. Noble gases are typically measured in the gas phase; however, it is not always possible to collect gases and therefore produced fluids (which are water, oil, and gas mixtures) must be analyzed. We outline a new technique to separate and analyze noble gases in multiphase hydrocarbon‐associated fluid samples. An offline double capillary method has been developed to quantitatively isolate noble gases into a transfer vessel, while effectively removing all water, oil, and less volatile hydrocarbons. The gases are then cleaned and analyzed using standard techniques. Air‐saturated water reference materials (n = 24) were analyzed and results show a method reproducibility of 2.9% for 4He, 3.8% for 20Ne, 4.5% for 36Ar, 5 .3% for 84Kr, and 5.7% for 132Xe. This new technique was used to measure the noble gas isotopic compositions in six produced fluid samples from the Fruitvale Oil Field, Bakersfield, California.
    Description: This work was supported by a Natural Environment Research Council studentship to R. L. Tyne (grant NE/L002612/1) and the USGS (grant 15‐080‐250), as part of the California State Water Resource Control Board's, Oil and Gas Regional Groundwater Monitoring Program (RMP). Data can be accessed in Tables 1 and 2 and in the data release from Gannon et al. (2018). We thank the owners and operators at the Fruitvale Oil Field for access to wells. We thank Stuart Gilfillan and an anonymous reviewer for their constructive reviews as well as Marie Edmonds for editorial handling. We also thank Matthew Landon and Myles Moor from the USGS who provided helpful comments on an earlier version of the manuscript. Any use of trade, firm or product names are for descriptive purposes only and do not imply endorsement by the U.S. Government.
    Description: 2020-04-14
    Keywords: Noble Gas ; Methods ; Produced Fluids
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  • 30
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chapman, A. S. A., Beaulieu, S. E., Colaco, A., Gebruk, A. V., Hilario, A., Kihara, T. C., Ramirez-Llodra, E., Sarrazin, J., Tunnicliffe, V., Amon, D. J., Baker, M. C., Boschen-Rose, R. E., Chen, C., Cooper, I. J., Copley, J. T., Corbari, L., Cordes, E. E., Cuvelier, D., Duperron, S., Du Preez, C., Gollner, S., Horton, T., Hourdez, S., Krylova, E. M., Linse, K., LokaBharathi, P. A., Marsh, L., Matabos, M., Mills, S. W., Mullineaux, L. S., Rapp, H. T., Reid, W. D. K., Rybakova (Goroslavskaya), E., Thomas, T. R. A., Southgate, S. J., Stohr, S., Turner, P. J., Watanabe, H. K., Yasuhara, M., & Bates, A. E. sFDvent: a global trait database for deep-sea hydrothermal-vent fauna. Global Ecology and Biogeography, 28(11), (2019): 1538-1551, doi: 10.1111/geb.12975.
    Description: Motivation Traits are increasingly being used to quantify global biodiversity patterns, with trait databases growing in size and number, across diverse taxa. Despite growing interest in a trait‐based approach to the biodiversity of the deep sea, where the impacts of human activities (including seabed mining) accelerate, there is no single repository for species traits for deep‐sea chemosynthesis‐based ecosystems, including hydrothermal vents. Using an international, collaborative approach, we have compiled the first global‐scale trait database for deep‐sea hydrothermal‐vent fauna – sFDvent (sDiv‐funded trait database for the Functional Diversity of vents). We formed a funded working group to select traits appropriate to: (a) capture the performance of vent species and their influence on ecosystem processes, and (b) compare trait‐based diversity in different ecosystems. Forty contributors, representing expertise across most known hydrothermal‐vent systems and taxa, scored species traits using online collaborative tools and shared workspaces. Here, we characterise the sFDvent database, describe our approach, and evaluate its scope. Finally, we compare the sFDvent database to similar databases from shallow‐marine and terrestrial ecosystems to highlight how the sFDvent database can inform cross‐ecosystem comparisons. We also make the sFDvent database publicly available online by assigning a persistent, unique DOI. Main types of variable contained Six hundred and forty‐six vent species names, associated location information (33 regions), and scores for 13 traits (in categories: community structure, generalist/specialist, geographic distribution, habitat use, life history, mobility, species associations, symbiont, and trophic structure). Contributor IDs, certainty scores, and references are also provided. Spatial location and grain Global coverage (grain size: ocean basin), spanning eight ocean basins, including vents on 12 mid‐ocean ridges and 6 back‐arc spreading centres. Time period and grain sFDvent includes information on deep‐sea vent species, and associated taxonomic updates, since they were first discovered in 1977. Time is not recorded. The database will be updated every 5 years. Major taxa and level of measurement Deep‐sea hydrothermal‐vent fauna with species‐level identification present or in progress. Software format .csv and MS Excel (.xlsx).
    Description: We would like to thank the following experts, who are not authors on this publication but made contributions to the sFDvent database: Anna Metaxas, Alexander Mironov, Jianwen Qiu (seep species contributions, to be added to a future version of the database) and Anders Warén. We would also like to thank Robert Cooke for his advice, time, and assistance in processing the raw data contributions to the sFDvent database using R. Thanks also to members of iDiv and its synthesis centre – sDiv – for much‐valued advice, support, and assistance during working‐group meetings: Doreen Brückner, Jes Hines, Borja Jiménez‐Alfaro, Ingolf Kühn and Marten Winter. We would also like to thank the following supporters of the database who contributed indirectly via early design meetings or members of their research groups: Malcolm Clark, Charles Fisher, Adrian Glover, Ashley Rowden and Cindy Lee Van Dover. Finally, thanks to the families of sFDvent working group members for their support while they were participating in meetings at iDiv in Germany. Financial support for sFDvent working group meetings was gratefully received from sDiv, the Synthesis Centre of iDiv (DFG FZT 118). ASAC was a PhD candidate funded by the SPITFIRE Doctoral Training Partnership (supported by the Natural Environmental Research Council, grant number: NE/L002531/1) and the University of Southampton at the time of submission. ASAC also thanks Dominic, Lesley, Lettice and Simon Chapman for their support throughout this project. AEB and VT are sponsored through the Canada Research Chair Programme. SEB received support from National Science Foundation Division of Environmental Biology Award #1558904 and The Joint Initiative Awards Fund from the Andrew W. Mellon Foundation. AC is supported by Program Investigador (IF/00029/2014/CP1230/CT0002) from Fundação para a Ciência e a Tecnologia (FCT). This study also had the support of Fundação para a Ciência e a Tecnologia, through the strategic project UID/MAR/04292/2013 granted to marine environmental sciences centre. Data compiled by AVG and EG were supported by Russian science foundation Grant 14‐50‐00095. AH was supported by the grant BPD/UI88/5805/2017 awarded by CESAM (UID/AMB/50017), which is financed by FCT/Ministério da Educação through national funds and co‐funded by fundo Europeu de desenvolvimento regional, within the PT2020 Partnership Agreement and Compete 2020. ERLL was partially supported by the MarMine project (247626/O30). JS was supported by Ifremer. Data on vent fauna from the East Scotia Ridge, Mid‐Cayman Spreading Centre, and Southwest Indian Ridge were obtained by UK natural environment research council Grants NE/D01249X/1, NE/F017774/1 and NE/H012087/1, respectively. REBR's contribution was supported by a Postdoctoral Fellowship at the University of Victoria, funded by the Canadian Healthy Oceans Network II Strategic Research Program (CHONe II). DC is supported by a post‐doctoral scholarship (SFRH/BPD/110278/2015) from FCT. HTR was supported by the Research Council of Norway through project number 70184227 and the KG Jebsen Centre for Deep Sea Research (University of Bergen). MY was partially supported by grants from the Research Grants Council of the Hong Kong Special Administrative Region, China (project codes: HKU 17306014, HKU 17311316).
    Keywords: biodiversity ; collaboration ; conservation ; cross‐ecosystem ; database ; deep sea ; functional trait ; global‐scale ; hydrothermal vent ; sFDvent
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  • 31
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Weber, L., González-Díaz, P., Armenteros, M., Ferrer, V. M., Bretos, F., Bartels, E., Santoro, A. E., & Apprill, A. Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys. Environmental Microbiology, 22(1), (2019): 499-519, doi: 10.1111/1462-2920.14870.
    Description: There are a few baseline reef‐systems available for understanding the microbiology of healthy coral reefs and their surrounding seawater. Here, we examined the seawater microbial ecology of 25 Northern Caribbean reefs varying in human impact and protection in Cuba and the Florida Keys, USA, by measuring nutrient concentrations, microbial abundances, and respiration rates as well as sequencing bacterial and archaeal amplicons and community functional genes. Overall, seawater microbial composition and biogeochemistry were influenced by reef location and hydrogeography. Seawater from the highly protected ‘crown jewel’ offshore reefs in Jardines de la Reina, Cuba had low concentrations of nutrients and organic carbon, abundant Prochlorococcus, and high microbial community alpha diversity. Seawater from the less protected system of Los Canarreos, Cuba had elevated microbial community beta‐diversity whereas waters from the most impacted nearshore reefs in the Florida Keys contained high organic carbon and nitrogen concentrations and potential microbial functions characteristic of microbialized reefs. Each reef system had distinct microbial signatures and within this context, we propose that the protection and offshore nature of Jardines de la Reina may preserve the oligotrophic paradigm and the metabolic dependence of the community on primary production by picocyanobacteria.
    Description: We thank Justin Ossolinski, Sean McNally, Tom Lankiewicz, Lázaro García, and the crew from R/V Felipe Poey for assistance with sample collection and processing. We thank Marlin Nauticas and Marinas for the use of their dive facilities. We thank Chris Wright, Mark Band, and staff at the University of Illinois W. M. Keck Center for Comparative and Functional Genomics for sequencing assistance, Karen Selph for training in flow cytometry, Krista Longnecker for TOC and TN analyses, and Joe Jennings for nutrient analyses. Funding was provided to A.A. and A.E.S. by a Dalio Explore award from the Dalio Foundation (now 'OceanX') and analysis time was supported with the NSF Graduate Research Fellowship award to L.W. and NSF award OCE 1736288 to A.A. Research was conducted under the LH112 AN (25) 2015 licence granted by the Cuban Center for Inspection and Environmental Control.
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  • 32
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Staudinger, M. D., Goyert, H., Suca, J. J., Coleman, K., Welch, L., Llopiz, J. K., Wiley, D., Altman, I., Applegate, A., Auster, P., Baumann, H., Beaty, J., Boelke, D., Kaufman, L., Loring, P., Moxley, J., Paton, S., Powers, K., Richardson, D., Robbins, J., Runge, J., Smith, B., Spiegel, C., & Steinmetz, H. The role of sand lances (Ammodytes sp.) in the Northwest Atlantic ecosystem: a synthesis of current knowledge with implications for conservation and management. Fish and Fisheries, 00, (2020): 1-34, doi:10.1111/faf.12445.
    Description: The American sand lance (Ammodytes americanus, Ammodytidae) and the Northern sand lance (A. dubius, Ammodytidae) are small forage fishes that play an important functional role in the Northwest Atlantic Ocean (NWA). The NWA is a highly dynamic ecosystem currently facing increased risks from climate change, fishing and energy development. We need a better understanding of the biology, population dynamics and ecosystem role of Ammodytes to inform relevant management, climate adaptation and conservation efforts. To meet this need, we synthesized available data on the (a) life history, behaviour and distribution; (b) trophic ecology; (c) threats and vulnerabilities; and (d) ecosystem services role of Ammodytes in the NWA. Overall, 72 regional predators including 45 species of fishes, two squids, 16 seabirds and nine marine mammals were found to consume Ammodytes. Priority research needs identified during this effort include basic information on the patterns and drivers in abundance and distribution of Ammodytes, improved assessments of reproductive biology schedules and investigations of regional sensitivity and resilience to climate change, fishing and habitat disturbance. Food web studies are also needed to evaluate trophic linkages and to assess the consequences of inconsistent zooplankton prey and predator fields on energy flow within the NWA ecosystem. Synthesis results represent the first comprehensive assessment of Ammodytes in the NWA and are intended to inform new research and support regional ecosystem‐based management approaches.
    Description: This manuscript is the result of follow‐up work stemming from a working group formed at a two‐day multidisciplinary and international workshop held at the Parker River National Wildlife Refuge, Massachusetts in May 2017, which convened 55 experts scientists, natural resource managers and conservation practitioners from 15 state, federal, academic and non‐governmental organizations with interest and expertise in Ammodytes ecology. Support for this effort was provided by USFWS, NOAA Stellwagen Bank National Marine Sanctuary, U.S. Department of the Interior, U.S. Geological Survey, Northeast Climate Adaptation Science Center (Award # G16AC00237), an NSF Graduate Research Fellowship to J.J.S., a CINAR Fellow Award to J.K.L. under Cooperative Agreement NA14OAR4320158, NSF award OCE‐1325451 to J.K.L., NSF award OCE‐1459087 to J.A.R, a Regional Sea Grant award to H.B. (RNE16‐CTHCE‐l), a National Marine Sanctuary Foundation award to P.J.A. (18‐08‐B‐196) and grants from the Mudge Foundation. The contents of this paper are the responsibility of the authors and do not necessarily represent the views of the National Oceanographic and Atmospheric Administration, U.S. Fish and Wildlife Service, New England Fishery Management Council and Mid‐Atlantic Fishery Management Council. This manuscript is submitted for publication with the understanding that the United States Government is authorized to reproduce and distribute reprints for Governmental purposes. Any use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
    Keywords: Ammodytes ; ecosystem‐based management ; forage fish ; life history ; sand lance ; trophic ecology
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  • 33
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lebrato, M., Garbe-Schönberg, D., Müller, M. N., Blanco-Ameijeiras, S., Feely, R. A., Lorenzoni, L., Molinero, J. C., Bremer, K., Jones, D. O. B., Iglesias-Rodriguez, D., Greeley, D., Lamare, M. D., Paulmier, A., Graco, M., Cartes, J., Barcelos E Ramos, J., de Lara, A., Sanchez-Leal, R., Jimenez, P., Paparazzo, F. E., Hartman, S. E., Westernströer, U., Küter, M., Benavides, R., da Silva, A. F., Bell, S., Payne, C., Olafsdottir, S., Robinson, K., Jantunen, L. M., Korablev, A., Webster, R. J., Jones, E. M., Gilg, O., Bailly du Bois, P., Beldowski, J., Ashjian, C., Yahia, N. D., Twining, B., Chen, X. G., Tseng, L. C., Hwang, J. S., Dahms, H. U., & Oschlies, A. Global variability in seawater Mg:Ca and Sr:Ca ratios in the modern ocean. Proceedings of the National Academy of Sciences of the United States of America, 117(36), (2020): 22281-22292, doi:10.1073/pnas.1918943117.
    Description: Seawater Mg:Ca and Sr:Ca ratios are biogeochemical parameters reflecting the Earth–ocean–atmosphere dynamic exchange of elements. The ratios’ dependence on the environment and organisms' biology facilitates their application in marine sciences. Here, we present a measured single-laboratory dataset, combined with previous data, to test the assumption of limited seawater Mg:Ca and Sr:Ca variability across marine environments globally. High variability was found in open-ocean upwelling and polar regions, shelves/neritic and river-influenced areas, where seawater Mg:Ca and Sr:Ca ratios range from ∼4.40 to 6.40 mmol:mol and ∼6.95 to 9.80 mmol:mol, respectively. Open-ocean seawater Mg:Ca is semiconservative (∼4.90 to 5.30 mol:mol), while Sr:Ca is more variable and nonconservative (∼7.70 to 8.80 mmol:mol); both ratios are nonconservative in coastal seas. Further, the Ca, Mg, and Sr elemental fluxes are connected to large total alkalinity deviations from International Association for the Physical Sciences of the Oceans (IAPSO) standard values. Because there is significant modern seawater Mg:Ca and Sr:Ca ratios variability across marine environments we cannot absolutely assume that fossil archives using taxa-specific proxies reflect true global seawater chemistry but rather taxa- and process-specific ecosystem variations, reflecting regional conditions. This variability could reconcile secular seawater Mg:Ca and Sr:Ca ratio reconstructions using different taxa and techniques by assuming an error of 1 to 1.50 mol:mol, and 1 to 1.90 mmol:mol, respectively. The modern ratios’ variability is similar to the reconstructed rise over 20 Ma (Neogene Period), nurturing the question of seminonconservative behavior of Ca, Mg, and Sr over modern Earth geological history with an overlooked environmental effect.
    Description: We thank the researchers, staff, students, and volunteers in all the expeditions around the world for their contributions. One anonymous referee and Bernhard Peucker-Ehenbrink, Woods Hole Oceanographic Institution, contributed significantly to the final version of the manuscript. This study was developed under a grant from the Federal Ministry of Education and Research to D.G.-S. under contract 03F0722A, by the Kiel Cluster of Excellence “The Future Ocean” (D1067/87) to A.O. and M.L., and by the “European project on Ocean Acidification” (European Community’s Seventh Framework Programme FP7/2007-2013, grant agreement 211384) to A.O. and M.L. Additional funding was provided from project DOSMARES CTM2010-21810-C03-02, by the UK Natural Environment Research Council, to the National Oceanography Centre. This is Pacific Marine Environmental Laboratory contribution number 5046.
    Keywords: global ; seawater ; Mg:Ca ; Sr:Ca ; biogeochemistry
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  • 34
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chakraborty, A., Ruff, S. E., Dong, X., Ellefson, E. D., Li, C., Brooks, J. M., McBee, J., Bernard, B. B., & Hubert, C. R. J. Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres. Proceedings of the National Academy of Sciences of the United States of America, 117(20), (2020): 11029-11037, doi: 10.1073/pnas.2002289117.
    Description: Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence the composition of the seabed microbiome and if they transport deep subsurface life up to the surface. Here we analyzed 172 marine surficial sediments from the deep-water Eastern Gulf of Mexico to assess whether hydrocarbon fluid migration is a mechanism for upward microbial dispersal. While 132 of these sediments contained migrated liquid hydrocarbons, evidence of continuous advective transport of thermogenic alkane gases was observed in 11 sediments. Gas seeps harbored distinct microbial communities featuring bacteria and archaea that are well-known inhabitants of deep biosphere sediments. Specifically, 25 distinct sequence variants within the uncultivated bacterial phyla Atribacteria and Aminicenantes and the archaeal order Thermoprofundales occurred in significantly greater relative sequence abundance along with well-known seep-colonizing members of the bacterial genus Sulfurovum, in the gas-positive sediments. Metabolic predictions guided by metagenome-assembled genomes suggested these organisms are anaerobic heterotrophs capable of nonrespiratory breakdown of organic matter, likely enabling them to inhabit energy-limited deep subseafloor ecosystems. These results point to petroleum geofluids as a vector for the advection-assisted upward dispersal of deep biosphere microbes from subsurface to surface environments, shaping the microbiome of cold seep sediments and providing a general mechanism for the maintenance of microbial diversity in the deep sea.
    Description: We wish to thank Jody Sandel as well as the crew of R/V GeoExplorer for collection of piston cores, onboard core processing, sample preservation, and shipment. Cynthia Kwan and Oliver Horanszky are thanked for assistance with amplicon library preparation. We also wish to thank Jayne Rattray, Daniel Gittins, and Marc Strous for valuable discussions and suggestions, and Rhonda Clark for research support. Collaborations with Andy Mort from the Geological Survey of Canada, and Richard Hatton from Geoscience Wales are also gratefully acknowledged. This work was financially supported by a Mitacs Elevate Postdoctoral Fellowship awarded to A.C.; an Alberta Innovates-Technology Futures/Eyes High Postdoctoral Fellowship to S.E.R.; and a Natural Sciences and Engineering Research Council Strategic Project Grant, a Genome Canada Genomics Applications Partnership Program grant, a Canada Foundation for Innovation grant (CFI-JELF 33752) for instrumentation, and Campus Alberta Innovates Program Chair funding to C.R.J.H.
    Keywords: Deep biosphere ; Microbiome ; Dispersal
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  • 35
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in MBL Hernandez, C. M., van Daalen, S. F., Caswell, H., Neubert, M. G., & Gribble, K. E. A demographic and evolutionary analysis of maternal effect senescence. Proceedings of the National Academy of Sciences of the United States of America, 17(28), (2020):16431-16437, doi: 10.1073/pnas.1919988117.
    Description: Maternal effect senescence—a decline in offspring survival or fertility with maternal age—has been demonstrated in many taxa, including humans. Despite decades of phenotypic studies, questions remain about how maternal effect senescence impacts evolutionary fitness. To understand the influence of maternal effect senescence on population dynamics, fitness, and selection, we developed matrix population models in which individuals are jointly classified by age and maternal age. We fit these models to data from individual-based culture experiments on the aquatic invertebrate, Brachionus manjavacas (Rotifera). By comparing models with and without maternal effects, we found that maternal effect senescence significantly reduces fitness for B. manjavacas and that this decrease arises primarily through reduced fertility, particularly at maternal ages corresponding to peak reproductive output. We also used the models to estimate selection gradients, which measure the strength of selection, in both high growth rate (laboratory) and two simulated low growth rate environments. In all environments, selection gradients on survival and fertility decrease with increasing age. They also decrease with increasing maternal age for late maternal ages, implying that maternal effect senescence can evolve through the same process as in Hamilton’s theory of the evolution of age-related senescence. The models we developed are widely applicable to evaluate the fitness consequences of maternal effect senescence across species with diverse aging and fertility schedule phenotypes.
    Description: K.E.G. was supported by Grant 5K01AG049049 from the National Institute on Aging and by the Bay and Paul Foundations. H.C. and S.F.v.D. were supported by the European Research Council through Advanced Grants 322829 and 788195 and by the Dutch Research Council through Grant ALWOP.2015.100. C.M.H. was supported by a National Science Foundation Graduate Research Fellowship. M.G.N. received funding from The Paul MacDonald Fye Chair for Excellence in Oceanography at the Woods Hole Oceanographic Institution.
    Keywords: Aging ; Demography ; Fitness ; Maternal effects ; Selection gradients
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  • 36
    Publication Date: 2022-10-27
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ritschard, E. A., Whitelaw, B., Albertin, C. B., Cooke, I. R., Strugnell, J. M., & Simakov, O. Coupled genomic evolutionary histories as signatures of organismal innovations in cephalopods: co-evolutionary signatures across levels of genome organization may shed light on functional linkage and origin of cephalopod novelties. BioEssays, 41, (2019): 1900073, doi: 10.1002/bies.201900073.
    Description: How genomic innovation translates into organismal organization remains largely unanswered. Possessing the largest invertebrate nervous system, in conjunction with many species‐specific organs, coleoid cephalopods (octopuses, squids, cuttlefishes) provide exciting model systems to investigate how organismal novelties evolve. However, dissecting these processes requires novel approaches that enable deeper interrogation of genome evolution. Here, the existence of specific sets of genomic co‐evolutionary signatures between expanded gene families, genome reorganization, and novel genes is posited. It is reasoned that their co‐evolution has contributed to the complex organization of cephalopod nervous systems and the emergence of ecologically unique organs. In the course of reviewing this field, how the first cephalopod genomic studies have begun to shed light on the molecular underpinnings of morphological novelty is illustrated and their impact on directing future research is described. It is argued that the application and evolutionary profiling of evolutionary signatures from these studies will help identify and dissect the organismal principles of cephalopod innovations. By providing specific examples, the implications of this approach both within and beyond cephalopod biology are discussed.
    Description: E.A.R. and O.S. are supported by the Austrian Science Fund (Grant No. P30686‐B29). E.A.R. is supported by Stazione Zoologica Anton Dohrn (Naples, Italy) PhD Program. The authors wish to thank Graziano Fiorito (SZN, Italy), Hannah Schmidbaur (University of Vienna, Austria), Thomas Hummel (University of Vienna, Austria) for many insightful comments and reading of the draft manuscript. The authors would like to apologize to all colleagues whose work has been omitted due to space constraints.
    Keywords: Cephalopod ; Gene duplication ; Genome rearrangement ; Novel gene ; Organismal innovation
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  • 37
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Arenas Gómez, Claudia M., Sabin, K. Z., & Echeverri, K. Wound healing across the animal kingdom: Crosstalk between the immune system and the extracellular matrix. Developmental Dynamics, (2020): 1-13, doi:10.1002/dvdy.178.
    Description: Tissue regeneration is widespread in the animal kingdom. To date, key roles for different molecular and cellular programs in regeneration have been described, but the ultimate blueprint for this talent remains elusive. In animals capable of tissue regeneration, one of the most crucial stages is wound healing, whose main goal is to close the wound and prevent infection. In this stage, it is necessary to avoid scar formation to facilitate the activation of the immune system and remodeling of the extracellular matrix, key factors in promoting tissue regeneration. In this review, we will discuss the current state of knowledge regarding the role of the immune system and the interplay with the extracellular matrix to trigger a regenerative response.
    Description: The research in the Echeverri lab is supported NIH NCID R01 to Karen Echeverri and start‐up funds from the MBL. Keith Z. Sabin has been supported by an NIH T32 GM113846 grant.
    Keywords: Extracellular matrix ; Immune system ; Regeneration ; Wound healing
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  • 38
    Publication Date: 2022-10-27
    Description: Author Posting. © National Academy of Sciences, 2021. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 118(11), (2021): e2020025118, https://doi.org/10.1073/pnas.2020025118.
    Description: For organisms to have robust locomotion, their neuromuscular organization must adapt to constantly changing environments. In jellyfish, swimming robustness emerges when marginal pacemakers fire action potentials throughout the bell’s motor nerve net, which signals the musculature to contract. The speed of the muscle activation wave is dictated by the passage times of the action potentials. However, passive elastic material properties also influence the emergent kinematics, with time scales independent of neuromuscular organization. In this multimodal study, we examine the interplay between these two time scales during turning. A three-dimensional computational fluid–structure interaction model of a jellyfish was developed to determine the resulting emergent kinematics, using bidirectional muscular activation waves to actuate the bell rim. Activation wave speeds near the material wave speed yielded successful turns, with a 76-fold difference in turning rate between the best and worst performers. Hyperextension of the margin occurred only at activation wave speeds near the material wave speed, suggesting resonance. This hyperextension resulted in a 34-fold asymmetry in the circulation of the vortex ring between the inside and outside of the turn. Experimental recording of the activation speed confirmed that jellyfish actuate within this range, and flow visualization using particle image velocimetry validated the corresponding fluid dynamics of the numerical model. This suggests that neuromechanical wave resonance plays an important role in the robustness of an organism’s locomotory system and presents an undiscovered constraint on the evolution of flexible organisms. Understanding these dynamics is essential for developing actuators in soft body robotics and bioengineered pumps.
    Description: This research was funded by the NSF Division of Mathematical Sciences, under Faculty Early Career Development Program Grant 1151478 (to L.A.M.).
    Description: 2021-09-16
    Keywords: Jellyfish ; Propulsion ; Neuromechanics ; Fluid-structure interaction ; Maneuverability
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  • 39
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kanso, E. A., Lopes, R. M., Strickler, J. R., Dabiri, J. O., & Costello, J. H. Teamwork in the viscous oceanic microscale. Proceedings of the National Academy of Sciences of the United States of America, 118(29), (2021): e2018193118, https://doi.org/10.1073/pnas.2018193118.
    Description: Nutrient acquisition is crucial for oceanic microbes, and competitive solutions to solve this challenge have evolved among a range of unicellular protists. However, solitary solutions are not the only approach found in natural populations. A diverse array of oceanic protists form temporary or even long-lasting attachments to other protists and marine aggregates. Do these planktonic consortia provide benefits to their members? Here, we use empirical and modeling approaches to evaluate whether the relationship between a large centric diatom, Coscinodiscus wailesii, and a ciliate epibiont, Pseudovorticella coscinodisci, provides nutrient flux benefits to the host diatom. We find that fluid flows generated by ciliary beating can increase nutrient flux to a diatom cell surface four to 10 times that of a still cell without ciliate epibionts. This cosmopolitan species of diatom does not form consortia in all environments but frequently joins such consortia in nutrient-depleted waters. Our results demonstrate that symbiotic consortia provide a cooperative alternative of comparable or greater magnitude to sinking for enhancement of nutrient acquisition in challenging environments.
    Description: We are grateful to Y. Garcia for help with organism sampling and sorting. E.A.K. is funded by NSF-2100209, NSF RAISE IOS-2034043 and NIH R01 HL 153622-01A1. R.M.L. is a CNPq research fellow (grant # 310642/2017-5). J.H.C. and J.O.D. are funded by Grant NSF-2100705.
    Keywords: Phytoplankton ; Nutrient limitation ; Symbiosis ; Diffusion limitation ; Cell size
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  • 40
    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sanders‐DeMott, R., Eagle, M., Kroeger, K., Wang, F., Brooks, T., Suttles, J., Nick, S., Mann, A., & Tang, J. Impoundment increases methane emissions in Phragmites‐invaded coastal wetlands. Global Change Biology, 28(15), (2022): 4539– 4557. https://doi.org/10.1111/gcb.16217.
    Description: Saline tidal wetlands are important sites of carbon sequestration and produce negligible methane (CH4) emissions due to regular inundation with sulfate-rich seawater. Yet, widespread management of coastal hydrology has restricted tidal exchange in vast areas of coastal wetlands. These ecosystems often undergo impoundment and freshening, which in turn cause vegetation shifts like invasion by Phragmites, that affect ecosystem carbon balance. Understanding controls and scaling of carbon exchange in these understudied ecosystems is critical for informing climate consequences of blue carbon restoration and/or management interventions. Here, we (1) examine how carbon fluxes vary across a salinity gradient (4–25 psu) in impounded and natural, tidally unrestricted Phragmites wetlands using static chambers and (2) probe drivers of carbon fluxes within an impounded coastal wetland using eddy covariance at the Herring River in Wellfleet, MA, United States. Freshening across the salinity gradient led to a 50-fold increase in CH4 emissions, but effects on carbon dioxide (CO2) were less pronounced with uptake generally enhanced in the fresher, impounded sites. The impounded wetland experienced little variation in water-table depth or salinity during the growing season and was a strong CO2 sink of −352 g CO2-C m−2 year−1 offset by CH4 emission of 11.4 g CH4-C m−2 year−1. Growing season CH4 flux was driven primarily by temperature. Methane flux exhibited a diurnal cycle with a night-time minimum that was not reflected in opaque chamber measurements. Therefore, we suggest accounting for the diurnal cycle of CH4 in Phragmites, for example by applying a scaling factor developed here of ~0.6 to mid-day chamber measurements. Taken together, these results suggest that although freshened, impounded wetlands can be strong carbon sinks, enhanced CH4 emission with freshening reduces net radiative balance. Restoration of tidal flow to impounded ecosystems could limit CH4 production and enhance their climate regulating benefits.
    Description: This project was supported by USGS-NPS Natural Resources Preservation Program #2021-07, U.S. Geological Survey Coastal & Marine Hazards and Resources Program and the USGS Land Change Science Program's LandCarbon program, and NOAA National Estuarine Research Reserve Science Collaborative NA14NOS4190145. R Sanders-DeMott was supported by a USGS Mendenhall Fellowship and partnership with Restore America's Estuaries.
    Keywords: Blue carbon ; Coastal wetland ; Dike ; Eddy covariance ; Impoundment ; Methane ; Net ecosystem exchange ; Phragmites ; Restoration ; Static chambers
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  • 41
    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tsakalakis, I., Follows, M. J., Dutkiewicz, S., Follett, C. L., & Vallino, J. J. Diel light cycles affect phytoplankton competition in the global ocean. Global Ecology and Biogeography, 31(9), (2022): 1838-1849, https://doi.org/10.1111/geb.13562.
    Description: Aim Light, essential for photosynthesis, is present in two periodic cycles in nature: seasonal and diel. Although seasonality of light is typically resolved in ocean biogeochemical–ecosystem models because of its significance for seasonal succession and biogeography of phytoplankton, the diel light cycle is generally not resolved. The goal of this study is to demonstrate the impact of diel light cycles on phytoplankton competition and biogeography in the global ocean. Location Global ocean. Major taxa studied Phytoplankton. Methods We use a three-dimensional global ocean model and compare simulations of high temporal resolution with and without diel light cycles. The model simulates 15 phytoplankton types with different cell sizes, encompassing two broad ecological strategies: small cells with high nutrient affinity (gleaners) and larger cells with high maximal growth rate (opportunists). Both are grazed by zooplankton and limited by nitrogen, phosphorus and iron. Results Simulations show that diel cycles of light induce diel cycles in limiting nutrients in the global ocean. Diel nutrient cycles are associated with higher concentrations of limiting nutrients, by 100% at low latitudes (−40° to 40°), a process that increases the relative abundance of opportunists over gleaners. Size classes with the highest maximal growth rates from both gleaner and opportunist groups are favoured by diel light cycles. This mechanism weakens as latitude increases, because the effects of the seasonal cycle dominate over those of the diel cycle. Main conclusions Understanding the mechanisms that govern phytoplankton biogeography is crucial for predicting ocean ecosystem functioning and biogeochemical cycles. We show that the diel light cycle has a significant impact on phytoplankton competition and biogeography, indicating the need for understanding the role of diel processes in shaping macroecological patterns in the global ocean.
    Description: Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems supported M.J.F. and S.D. on CBIOMES grant #549931; C.L.F. on CBIOMES grants #827829 and #553242; and J.J.V. and I.T. on CBIOMES grant #549941. The National Science Foundation supported I.T. and J.J.V. on award #1558710 and J.J.V. on awards #1637630, #1655552 and #1841599.
    Keywords: Biogeography ; Diel light cycle ; Global ocean ; Modelling ; Nutrient cycles ; Phytoplankton ; Resource competition
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  • 42
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2020. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 117(22), (2020): 12215-12221, doi: 10.1073/pnas.1918439117.
    Description: Picophytoplankton are the most abundant primary producers in the ocean. Knowledge of their community dynamics is key to understanding their role in marine food webs and global biogeochemical cycles. To this end, we analyzed a 16-y time series of observations of a phytoplankton community at a nearshore site on the Northeast US Shelf. We used a size-structured population model to estimate in situ division rates for the picoeukaryote assemblage and compared the dynamics with those of the picocyanobacteria Synechococcus at the same location. We found that the picoeukaryotes divide at roughly twice the rate of the more abundant Synechococcus and are subject to greater loss rates (likely from viral lysis and zooplankton grazing). We describe the dynamics of these groups across short and long timescales and conclude that, despite their taxonomic differences, their populations respond similarly to changes in the biotic and abiotic environment. Both groups appear to be temperature limited in the spring and light limited in the fall and to experience greater mortality during the day than at night. Compared with Synechococcus, the picoeukaryotes are subject to greater top-down control and contribute more to the region’s primary productivity than their standing stocks suggest.
    Description: We thank E. T. Crockford, E. E. Peacock, J. Fredericks, Z. Sandwith, the MVCO Operations Team, and divers of the Woods Hole Oceanographic Institution diving program. This work was supported by NSF Grants OCE-0119915 (to R.J.O. and H.M.S.) and OCE-1655686 (to M.G.N., R.J.O., A.R.S., and H.M.O.); NASA Grants NNX11AF07G (to H.M.S.) and NNX13AC98G (to H.M.S.); Gordon and Betty Moore Foundation Grant GGA#934 (to H.M.S.); and Simons Foundation Grant 561126 (to H.M.S.).
    Description: 2020-11-15
    Keywords: Picoeukaryotes ; Flow cytometry ; Matrix model ; Primary productivity
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  • 43
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Munoz, S. E., Porter, T. J., Bakkelund, A., Nusbaumer, J., Dee, S. G., Hamilton, B., Giosan, L., & Tierney, J. E. Lipid biomarker record documents hydroclimatic variability of the Mississippi River Basin during the common era. Geophysical Research Letters, 47(12), (2020): e2020GL087237, doi:10.1029/2020GL087237.
    Description: Floods and droughts in the Mississippi River basin are perennial hazards that cause severe economic disruption. Here we develop and analyze a new lipid biomarker record from Horseshoe Lake (Illinois, USA) to evaluate the climatic conditions associated with hydroclimatic extremes that occurred in this region over the last 1,800 years. We present geochemical proxy evidence of temperature and moisture variability using branched glycerol dialkyl glycerol tetraethers (brGDGTs) and plant leaf wax hydrogen isotopic composition (δ2Hwax) and use isotope‐enabled coupled model simulations to diagnose the controls on these proxies. Our data show pronounced warming during the Medieval era (CE 1000–1,600) that corresponds to midcontinental megadroughts. Severe floods on the upper Mississippi River basin also occurred during the Medieval era and correspond to periods of enhanced warm‐season moisture. Our findings imply that projected increases in temperature and warm‐season precipitation could enhance both drought and flood hazards in this economically vital region.
    Description: This project was supported by grants to S. E. M and L. G. (NSF EAR‐1804107), T. J. P. (NSERC Discovery Grant), and S. G. D. (NOAA‐NA18OAR4310427).
    Keywords: Lipid biomarker ; Leaf wax ; BrGDGT ; Common Era ; Paleoclimate ; Hydroclimate
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  • 44
    Publication Date: 2022-10-26
    Description: © The Author(s), 202. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in McDermott, J. M., Sylva, S. P., Ono, S., German, C. R., & Seewald, J. S. Abiotic redox reactions in hydrothermal mixing zones: decreased energy availability for the subsurface biosphere. Proceedings of the National Academy of Sciences of the United States of America, 117(34), (2020): 20453-20461, doi:10.1073/pnas.2003108117.
    Description: Subseafloor mixing of high-temperature hot-spring fluids with cold seawater creates intermediate-temperature diffuse fluids that are replete with potential chemical energy. This energy can be harnessed by a chemosynthetic biosphere that permeates hydrothermal regions on Earth. Shifts in the abundance of redox-reactive species in diffuse fluids are often interpreted to reflect the direct influence of subseafloor microbial activity on fluid geochemical budgets. Here, we examine hydrothermal fluids venting at 44 to 149 °C at the Piccard hydrothermal field that span the canonical 122 °C limit to life, and thus provide a rare opportunity to study the transition between habitable and uninhabitable environments. In contrast with previous studies, we show that hydrocarbons are contributed by biomass pyrolysis, while abiotic sulfate (SO42−) reduction produces large depletions in H2. The latter process consumes energy that could otherwise support key metabolic strategies employed by the subseafloor biosphere. Available Gibbs free energy is reduced by 71 to 86% across the habitable temperature range for both hydrogenotrophic SO42− reduction to hydrogen sulfide (H2S) and carbon dioxide (CO2) reduction to methane (CH4). The abiotic H2 sink we identify has implications for the productivity of subseafloor microbial ecosystems and is an important process to consider within models of H2 production and consumption in young oceanic crust.
    Description: Financial support was provided by the National Aeronautics and Space Administration (NASA) Astrobiology program (Awards NNX09AB75G and 80NSSC19K1427 to C.R.G. and J.S.S.) and the NSF (Award OCE-1061863 to C.R.G. and J.S.S.). Ship and vehicle time for cruise FK008 was provided by the Schmidt Ocean Institute. We thank the ROV Jason II and HROV Nereus groups, and the captain, officers, and crew of R/V Atlantis (AT18-16) and R/V Falkor (FK008) for their dedication to skillful operations at sea. We thank our scientific colleagues from both cruises, as well as Meg Tivey, Frieder Klein, and Scott Wankel for insightful discussions. We are grateful to the editor and two anonymous reviewers for providing helpful comments and suggestions.
    Keywords: Hydrothermal vent ; Subsurface biosphere ; Bioenergetics ; Biogeochemistry
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  • 45
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bowen, J. C., Ward, C. P., Kling, G. W., & Cory, R. M. Arctic amplification of global warming strengthened by sunlight oxidation of permafrost carbon to CO2. Geophysical Research Letters, 47(12), (2020): e2020GL087085, doi:10.1029/2020GL087085.
    Description: Once thawed, up to 15% of the ∼1,000 Pg of organic carbon (C) in arctic permafrost soils may be oxidized to carbon dioxide (CO2) by 2,100, amplifying climate change. However, predictions of this amplification strength ignore the oxidation of permafrost C to CO2 in surface waters (photomineralization). We characterized the wavelength dependence of permafrost dissolved organic carbon (DOC) photomineralization and demonstrate that iron catalyzes photomineralization of old DOC (4,000–6,300 a BP) derived from soil lignin and tannin. Rates of CO2 production from photomineralization of permafrost DOC are twofold higher than for modern DOC. Given that model predictions of future net loss of ecosystem C from thawing permafrost do not include the loss of CO2 to the atmosphere from DOC photomineralization, current predictions of an average of 208 Pg C loss by 2,299 may be too low by ~14%.
    Description: This research was supported by National Science Foundation (NSF) CAREER 1351745 (R.M.C.), DEB 1637459 and 1754835 (G.W.K.), the Camille and Henry Dreyfus Postdoctoral Program in Environmental Chemistry (R.M.C. and C.P.W.), the Frank and Lisina Hock Endowed Fund (C.P.W.), and the NOSAMS Graduate Student Internship Program (J.C.B.).
    Keywords: Photochemistry ; Permafrost ; Arctic ; Carbon cycling ; Dissolved organic carbon
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  • 46
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Reysenbach, A. L., St John, E., Meneghin, J., Flores, G. E., Podar, M., Dombrowski, N., Spang, A., L'Haridon, S., Humphris, S. E., de Ronde, C. E. J., Caratori Tontini, F., Tivey, M., Stucker, V. K., Stewart, L. C., Diehl, A., & Bach, W. Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities. Proceedings of the National Academy of Sciences of the United States of America, 117(51), (2020): 202019021, doi:10.1073/pnas.2019021117.
    Description: Hydrothermally active submarine volcanoes are mineral-rich biological oases contributing significantly to chemical fluxes in the deep sea, yet little is known about the microbial communities inhabiting these systems. Here we investigate the diversity of microbial life in hydrothermal deposits and their metagenomics-inferred physiology in light of the geological history and resulting hydrothermal fluid paths in the subsurface of Brothers submarine volcano north of New Zealand on the southern Kermadec arc. From metagenome-assembled genomes we identified over 90 putative bacterial and archaeal genomic families and nearly 300 previously unknown genera, many potentially endemic to this submarine volcanic environment. While magmatically influenced hydrothermal systems on the volcanic resurgent cones of Brothers volcano harbor communities of thermoacidophiles and diverse members of the superphylum “DPANN,” two distinct communities are associated with the caldera wall, likely shaped by two different types of hydrothermal circulation. The communities whose phylogenetic diversity primarily aligns with that of the cone sites and magmatically influenced hydrothermal systems elsewhere are characterized predominately by anaerobic metabolisms. These populations are probably maintained by fluids with greater magmatic inputs that have interacted with different (deeper) previously altered mineral assemblages. However, proximal (a few meters distant) communities with gene-inferred aerobic, microaerophilic, and anaerobic metabolisms are likely supported by shallower seawater-dominated circulation. Furthermore, mixing of fluids from these two distinct hydrothermal circulation systems may have an underlying imprint on the high microbial phylogenomic diversity. Collectively our results highlight the importance of considering geologic evolution and history of subsurface processes in studying microbial colonization and community dynamics in volcanic environments.
    Description: We thank the captain and crew of the R/V Thompson and the engineers from Woods Hole Oceanographic Institution for the successful operation of ROV Jason. The project was funded by NSF grants OCE‐1558356 (Principal Investigator S.E.H.) and OCE-1558795 (Principal Investigator A.-L.R.). S.L. received a grant from the University of Brest to work in the A.-L.R. laboratory. A travel fund from Interridge enabled A.D. to participate on the R/V Thompson cruise. Funding for this work for C.E.J.d.R., F.C.T., V.K.S., and L.C.S. was provided by the New Zealand government. A.S. was supported by the Swedish Research Council (Vetenskapsrådet starting grant 2016-03559 to A.S.) and the Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Dutch Research Council) Foundation of the Netherlands Organization for Scientific Research (Women In Science Excel [WISE] fellowship to A.S.). A.-L.R. and E.S.J. thank Rika Anderson for helpful methodological discussions and Sean Sylva for assistance in shipboard geochemical analysis.
    Keywords: Metagenomics ; Deep-sea hydrothermal ; Thermophiles ; Archaea ; Volcanics
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  • 47
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coesel, S. N., Durham, B. P., Groussman, R. D., Hu, S. K., Caron, D. A., Morales, R. L., Ribalet, F., & Armbrust, E. V. Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proceedings of the National Academy of Sciences of the United States of America, 118(6), (2021): e2011038118, https://doi.org/10.1073./pnas.2011038118.
    Description: The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.
    Description: This work was supported by a grant from the Simons Foundation (SCOPE Award 329108 [to E.V.A.]) and XSEDE Grant Allocation OCE160019 (to R.D.G.).
    Keywords: Photoreceptors ; Microbial eukaryotes ; Oligotrophic gyre ; Diel cycles ; Metatranscriptomics
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  • 48
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Jin, D., Hoagland, P., & Ashton, A. D. Risk averse choices of managed beach widths under environmental uncertainty. Natural Resource Modeling, (2021): e12324, https://doi.org/10.1111/nrm.12324.
    Description: Applying a theoretical geo-economic approach, we examined key factors affecting decisions about the choice of beach width when eroded coastal beaches are being nourished (i.e., when fill is placed to widen a beach). Within this geo-economic framework, optimal beach width is positively related to its values for hazard protection and recreation and negatively related to nourishment costs and the discount rate. Using a dynamic modeling framework, we investigated the time paths of beach width and nourishment that maximized net present value under an accelerating sea level. We then analyzed how environmental uncertainty about expected future beach width, arising from natural shoreline dynamics, intermittent large storms, or sea-level rise, leads to economic choices favoring narrower beaches. Risk aversion can affect a coastal property owner's choice of beach width in contradictory ways: the expected benefits of hazard protection must be balanced against the expected costs of repeated nourishment actions.
    Description: Support for this study was provided by NSF Grant No. ARG 1518503, WHOI Sea Grant (NOAA Award Number: NA18OAR4170104), and the J. Seward Johnson Fund in Support of the Marine Policy Center.
    Keywords: Beach nourishment ; Beach width ; Coastal protection ; Risk management ; Shoreline change
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  • 49
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Farrell, U. C., Samawi, R., Anjanappa, S., Klykov, R., Adeboye, O. O., Agic, H., Ahm, A.-S. C., Boag, T. H., Bowyer, F., Brocks, J. J., Brunoir, T. N., Canfield, D. E., Chen, X., Cheng, M., Clarkson, M. O., Cole, D. B., Cordie, D. R., Crockford, P. W., Cui, H., Dahl, T. W., Mouro, L. D., Dewing, K., Dornbos, S. Q., Drabon, N., Dumoulin, J. A., Emmings, J. F., Endriga, C. R., Fraser, T. A., Gaines, R. R., Gaschnig, R. M., Gibson, T. M., Gilleaudeau, G. J., Gill, B. C., Goldberg, K., Guilbaud, R., Halverson, G. P., Hammarlund, E. U., Hantsoo, K. G., Henderson, M. A., Hodgskiss, M. S. W., Horner, Tristan J., Husson, J. M., Johnson, B., Kabanov, P., Brenhin K. C., Kimmig, J., Kipp, M. A., Knoll, A. H., Kreitsmann, T., Kunzmann, M., Kurzweil, F., LeRoy, M. A., Li, C., Lipp, A. G., Loydell, D. K., Lu, X., Macdonald, F. A., Magnall, J. M., Mänd, K., Mehra, A., Melchin, M. J., Miller, A. J., Mills, N. T., Mwinde, C. N., O'Connell, B., Och, L. M., Ossa Ossa, F., Pagès, A., Paiste, K., Partin, C. A., Peters, S. E., Petrov, P., Playter, T. L., Plaza-Torres, S., Porter, Susannah M., Poulton, S. W., Pruss, S. B., Richoz, S., Ritzer, S. R., Rooney, A. D., Sahoo, S. K., Schoepfer, S. D., Sclafani, J. A., Shen, Y., Shorttle, O., Slotznick, S. P., Smith, E. F., Spinks, S., Stockey, R. G., Strauss, J. V., Stüeken, E. E., Tecklenburg, S., Thomson, D., Tosca, N. J., Uhlein, G. J., Vizcaíno, M. N., Wang, H., White, T., Wilby, P. R., Woltz, C. R., Wood, R. A., Xiang, L., Yurchenko, I. A., Zhang, T., Planavsky, N. J., Lau, K. V., Johnston, D. T., Sperling, E. A., The Sedimentary Geochemistry and Paleoenvironments Project. Geobiology. 00, (2021): 1– 12,https://doi.org/10.1111/gbi.12462.
    Description: Geobiology explores how Earth's system has changed over the course of geologic history and how living organisms on this planet are impacted by or are indeed causing these changes. For decades, geologists, paleontologists, and geochemists have generated data to investigate these topics. Foundational efforts in sedimentary geochemistry utilized spreadsheets for data storage and analysis, suitable for several thousand samples, but not practical or scalable for larger, more complex datasets. As results have accumulated, researchers have increasingly gravitated toward larger compilations and statistical tools. New data frameworks have become necessary to handle larger sample sets and encourage more sophisticated or even standardized statistical analyses. In this paper, we describe the Sedimentary Geochemistry and Paleoenvironments Project (SGP; Figure 1), which is an open, community-oriented, database-driven research consortium. The goals of SGP are to (1) create a relational database tailored to the needs of the deep-time (millions to billions of years) sedimentary geochemical research community, including assembling and curating published and associated unpublished data; (2) create a website where data can be retrieved in a flexible way; and (3) build a collaborative consortium where researchers are incentivized to contribute data by giving them priority access and the opportunity to work on exciting questions in group papers. Finally, and more idealistically, the goal was to establish a culture of modern data management and data analysis in sedimentary geochemistry. Relative to many other fields, the main emphasis in our field has been on instrument measurement of sedimentary geochemical data rather than data analysis (compared with fields like ecology, for instance, where the post-experiment ANOVA (analysis of variance) is customary). Thus, the longer-term goal was to build a collaborative environment where geobiologists and geologists can work and learn together to assess changes in geochemical signatures through Earth history.
    Description: We thank the donors of The American Chemical Society Petroleum Research Fund for partial support of SGP website development (61017-ND2). EAS is funded by National Science Foundation grant (NSF) EAR-1922966. BGS authors (JE, PW) publish with permission of the Executive Director of the British Geological Survey, UKRI.
    Keywords: Consortium ; Database ; Earth history ; Geochemistry ; Website
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  • 50
    Publication Date: 2022-10-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Dommain, R., Riedl, S., Olaka, L. A., deMenocal, P., Deino, A. L., Owen, R. B., Muiruri, V., Müller, J., Potts, R., & Strecker, M. R. Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients. Proceedings of the National Academy of Sciences of the United States of America, 119(28),(2022): e2121388119, https://doi.org/10.1073/pnas.2121388119.
    Description: East Africa is a global biodiversity hotspot and exhibits distinct longitudinal diversity gradients from west to east in freshwater fishes and forest mammals. The assembly of this exceptional biodiversity and the drivers behind diversity gradients remain poorly understood, with diversification often studied at local scales and less attention paid to biotic exchange between Afrotropical regions. Here, we reconstruct a river system that existed for several millennia along the now semiarid Kenya Rift Valley during the humid early Holocene and show how this river system influenced postglacial dispersal of fishes and mammals due to its dual role as a dispersal corridor and barrier. Using geomorphological, geochronological, isotopic, and fossil analyses and a synthesis of radiocarbon dates, we find that the overflow of Kenyan rift lakes between 12 and 8 ka before present formed a bidirectional river system consisting of a “Northern River” connected to the Nile Basin and a “Southern River,” a closed basin. The drainage divide between these rivers represented the only viable terrestrial dispersal corridor across the rift. The degree and duration of past hydrological connectivity between adjacent river basins determined spatial diversity gradients for East African fishes. Our reconstruction explains the isolated distribution of Nilotic fish species in modern Kenyan rift lakes, Guineo-Congolian mammal species in forests east of the Kenya Rift, and recent incipient vertebrate speciation and local endemism in this region. Climate-driven rearrangements of drainage networks unrelated to tectonic activity contributed significantly to the assembly of species diversity and modern faunas in the East African biodiversity hotspot.
    Description: R.D. was funded by a Smithsonian Human Origins Postdoctoral Fellowship and by Geo.X—the Research Network for Geosciences in Berlin and Potsdam. Fig. 1 D, E, and G and SI Appendix, Figs. S1 and S3 are based on the TanDEM-X Science DEM granted to L.A.O. and S.R. by the German Aerospace Center (DLR) in 2017. L.A.O. acknowledges the Volkswagen Foundation for funding this study with Grant No. 89369. M.R.S. and S.R. were supported by funds from Potsdam University and the Geothermal Development Company of Kenya, and R.B.O. and V.M. were supported by the Hong Kong General Research Fund. We acknowledge support from the National Museums of Kenya and the Kenya Government permission granted by the Ministry of Sports, Culture and the Arts, and by the National Commission for Science, Technology and Innovation (NACOSTI) Permits P/14/7709/683 (to R.P.) and P/16/11924/11448 (to L.A.O.). This work is a contribution of the Olorgesailie Drilling Project, for which support from the National Museums of Kenya, the Oldonyo Nyokie Group Ranch, the Peter Buck Fund for Human Origins Research (Smithsonian Institution), the William H. Donner Foundation, the Ruth and Vernon Taylor Foundation, Whitney and Betty MacMillan, and the Smithsonian Human Origins Program is gratefully acknowledged. LacCore is acknowledged for support in drilling and core storage.
    Keywords: East Africa ; Biogeography ; Biodiversity ; Hydrological connectivity ; Holocene
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  • 51
    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Umanzor, S., Li, Y., Bailey, D., Augyte, S., Huang, M., Marty-Rivera, M., Jannink, J., Yarish, C., & Lindell, S. Comparative analysis of morphometric traits of farmed sugar kelp and skinny kelp, Saccharina spp., strains from the Northwest Atlantic. Journal of the World Aquaculture Society, (2021), https://doi.org/10.1111/jwas.12783.
    Description: Our team has initiated a selective breeding program for regional strains of sugar kelp, Saccharina latissima, to improve the competitiveness of kelp farming in the United States. Within our breeding program, we also include an endemic putative species, Saccharina angustissima, locally referred to as skinny kelp. We crossed uniclonal gametophyte cultures derived from 37 wild‐collected blades representing five sugar kelp strains and one skinny kelp strain to produce 104 unique crosses. Each cross was outplanted on a near‐shore research farm located in the Gulf of Maine (GOM). After the first farming season, our results indicated that sugar kelp and skinny kelp were interfertile, and produced mature and reproductively viable sporophytes. Morphological traits of individual blades varied depending on the parental contribution (sugar vs. skinny), with significant differences found in progeny blade length, width, thickness, and in stipe length and diameter. Despite these differences, wet weight and blade density per plot showed no statistical differences regardless of the cross. Given their published genetic similarity and their interfertility shown here, S. angustissima and S. latissima may not be different species, and may each contribute genetic diversity to breeding programs aimed at meeting ocean farming and market needs.
    Description: Funding was provided by the U.S. Department of Energy, ARPAe MARINER project contract number DE‐AR0000915 and DE‐AR0000911, AgCore Technologies of Rhode Island, and the Massachusetts Clean Energy Center, AmplifyMass Program.
    Keywords: Morphometrics ; Phenotyping ; Saccharina angustissima ; Saccharina latissima ; Seaweed aquaculture ; Selective breeding
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  • 52
    Publication Date: 2022-10-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Walter, J. A., Castorani, M. C. N., Bell, T. W., Sheppard, L. W., Cavanaugh, K. C., & Reuman, D. C. Tail-dependent spatial synchrony arises from nonlinear driver-response relationships. Ecology Letters, 25, (2022): 1189– 1201, https://doi.org/10.1111/ele.13991.
    Description: Spatial synchrony may be tail-dependent, that is, stronger when populations are abundant than scarce, or vice-versa. Here, ‘tail-dependent’ follows from distributions having a lower tail consisting of relatively low values and an upper tail of relatively high values. We present a general theory of how the distribution and correlation structure of an environmental driver translates into tail-dependent spatial synchrony through a non-linear response, and examine empirical evidence for theoretical predictions in giant kelp along the California coastline. In sheltered areas, kelp declines synchronously (lower-tail dependence) when waves are relatively intense, because waves below a certain height do little damage to kelp. Conversely, in exposed areas, kelp is synchronised primarily by periods of calmness that cause shared recovery (upper-tail dependence). We find evidence for geographies of tail dependence in synchrony, which helps structure regional population resilience: areas where population declines are asynchronous may be more resilient to disturbance because remnant populations facilitate reestablishment.
    Description: This research was supported by NSF-OCE awards 2023555, 2023523, 2140335, 2023474, and the James S McDonnell Foundation. This project used data developed through the Santa Barbara Coastal Long Term Ecological Research project, funded through NSF-OCE 1831937.
    Keywords: Copula ; Disturbance ; Giant kelp ; Macrocystis pyrifera ; Nutrients ; Stability ; Synchrony ; Waves
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  • 53
    Publication Date: 2022-10-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Rypkema, N., Schmidt, H., & Fischell, E. Synchronous-clock range-angle relative acoustic navigation: a unified approach to multi-AUV localization, command, control, and coordination. Journal of Field Robotics, 2(1), (2022): 774–806, https://doi.org/10.55417/fr.2022026.
    Description: This paper presents a scalable acoustic navigation approach for the unified command, control, and coordination of multiple autonomous underwater vehicles (AUVs). Existing multi-AUV operations typically achieve coordination manually by programming individual vehicles on the surface via radio communications, which becomes impractical with large vehicle numbers; or they require bi-directional intervehicle acoustic communications to achieve limited coordination when submerged, with limited scalability due to the physical properties of the acoustic channel. Our approach utilizes a single, periodically broadcasting beacon acting as a navigation reference for the group of AUVs, each of which carries a chip-scale atomic clock and fixed ultrashort baseline array of acoustic receivers. One-way travel-time from synchronized clocks and time-delays between signals received by each array element allow any number of vehicles within receive distance to determine range, angle, and thus determine their relative position to the beacon. The operator can command different vehicle behaviors by selecting between broadcast signals from a predetermined set, while coordination between AUVs is achieved without intervehicle communication by defining individual vehicle behaviors within the context of the group. Vehicle behaviors are designed within a beacon-centric moving frame of reference, allowing the operator to control the absolute position of the AUV group by repositioning the navigation beacon to survey the area of interest. Multiple deployments with a fleet of three miniature, low-cost SandShark AUVs performing closed-loop acoustic navigation in real-time provide experimental results validated against a secondary long-baseline positioning system, demonstrating the capabilities and robustness of our approach with real-world data.
    Description: This work was partially supported by the Office of Naval Research, the Defense Advanced Research Projects Agency, Lincoln Laboratory, and the Reuben F. and Elizabeth B. Richards Endowed Funds at WHOI.
    Keywords: Underwater robotics ; Navigation ; Multirobot systems ; Localization ; Marine robotics
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  • 54
    Publication Date: 2022-10-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Castorani, M. C. N., Bell, T. W., Walter, J. A., Reuman, D. C., Cavanaugh, K. C., & Sheppard, L. W. Disturbance and nutrients synchronise kelp forests across scales through interacting Moran effects. Ecology Letters, 25(8), (2022): 1854-1868, https://doi.org/10.1111/ele.14066.
    Description: Spatial synchrony is a ubiquitous and important feature of population dynamics, but many aspects of this phenomenon are not well understood. In particular, it is largely unknown how multiple environmental drivers interact to determine synchrony via Moran effects, and how these impacts vary across spatial and temporal scales. Using new wavelet statistical techniques, we characterised synchrony in populations of giant kelp Macrocystis pyrifera, a widely distributed marine foundation species, and related synchrony to variation in oceanographic conditions across 33 years (1987–2019) and 〉900 km of coastline in California, USA. We discovered that disturbance (storm-driven waves) and resources (seawater nutrients)—underpinned by climatic variability—act individually and interactively to produce synchrony in giant kelp across geography and timescales. Our findings demonstrate that understanding and predicting synchrony, and thus the regional stability of populations, relies on resolving the synergistic and antagonistic Moran effects of multiple environmental drivers acting on different timescales.
    Description: This study was funded by the U.S. National Science Foundation (NSF) through linked NSF-OCE awards 2023555, 2023523, 2140335, and 2023474 to M.C.N.C., K.C.C., T.W.B., and D.C.R., respectively. The research was initiated during a synthesis working group at the Long Term Ecological Research Network Office and National Center for Ecological Analysis and Synthesis funded under NSF-DEB award 1545288. D.C.R. and L.W.S. were also partly supported by NSF award 1714195, the McDonnell Foundation, and the California Department of Fish and Wildlife Delta Science Program. This project used data developed through the Santa Barbara Coastal Long Term Ecological Research project, funded through NSF-OCE award 1831937.
    Keywords: Coherence ; Disturbance ; Moran effect ; Nitrate ; North Pacific Gyre Oscillation ; Oceanography ; Population dynamics ; Remote sensing ; Spatial synchrony ; Wavelet transforms
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  • 55
    Publication Date: 2022-10-20
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Martins, M. C. I., Miller, C., Hamilton, P., Robbins, J., Zitterbart, D. P., & Moore, M. Respiration cycle duration and seawater flux through open blowholes of humpback (Megaptera novaeangliae) and North Atlantic right (Eubalaena glacialis) whales. Marine Mammal Science, (2020): 1-20, doi:10.1111/mms.12703.
    Description: Little is known about the dynamics of baleen whale respiratory cycles, especially the mechanics and activity of the blowholes and their interaction with seawater. In this study, the duration of complete respiration cycles (expiration/inhalation events) were quantified for the first time in two species: North Atlantic right whale (NARW) and humpback whale (HW) using high resolution, detailed imagery from an unoccupied aerial system (UAS). The mean duration of complete respiration cycles (expiration/inhalation event) in the NARW and HW were 3.07 s (SD = 0.503, n = 15) and 2.85 s (SD = 0.581, n = 21), respectively. Furthermore, we saw no significant differences in respiration cycle duration between age and sex classes in the NARW, but significant differences were observed between age classes in the HW. The observation of seawater covering an open blowhole was also quantified, with NARW having 20% of all breaths with seawater presence versus 90% in HW. Seawater incursion has not been described previously and challenges the general consensus that water does not enter the respiratory tract in baleen whales. Prevalent seawater has implications for the analysis and interpretation of exhaled respiratory vapor/mucosa samples, as well as for the potential inhalation of oil in spills.
    Description: Samples were collected under NMFS NOAA Permits 17355, 17355‐01, and 21371, and with approval from the Woods Hole Oceanographic Institution Institutional Animal Care and Use Committee. Funding by Ocean Life Institute of the Woods Hole Oceanographic Institution, NOAA NA14OAR4320158 and University College London Master of Research in Biodiversity, Evolution and Conservation program.
    Keywords: Humpback whale ; North Atlantic right whale ; Respiratory cycle ; Respiratory health ; Unoccupied aerial systems
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  • 56
    Publication Date: 2022-10-20
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Caruso, F., Hickmott, L., Warren, J. D., Segre, P., Chiang, G., Bahamonde, P., Español-Jiménez, S., Li, S., & Bocconcelli, A. Diel differences in blue whale (Balaenoptera musculus) dive behavior increase nighttime risk of ship strikes in northern Chilean Patagonia. Integrative Zoology, (2020): 1-18, doi:10.1111/1749-4877.12501.
    Description: The northern Chilean Patagonia region is a key feeding ground and a nursing habitat in the southern hemisphere for blue whales (Balaenoptera musculus). From 2014 to 2019, during 6 separate research cruises, the dive behavior of 28 individual blue whales was investigated using bio‐logging tags (DTAGs), generating ≈190 h of data. Whales dove to significantly greater depths during the day compared to nighttime (day: 32.6 ± 18.7 m; night: 6.2 ± 2.7 m; P 〈 0.01). During the night, most time was spent close to the surface (86% ± 9.4%; P 〈 0.01) and at depths of less than 12 m. From 2016 to 2019, active acoustics (scientific echosounders) were used to record prey (euphausiids) density and distribution simultaneously with whale diving data. Tagged whales appeared to perform dives relative to the vertical migration of prey during the day. The association between diurnal prey migration and shallow nighttime dive behavior suggests that blue whales are at increased risk of ship collisions during periods of darkness since the estimated maximum ship draft of vessels operating in the region is also ≈12 m. In recent decades, northern Chilean Patagonia has seen a large increase in marine traffic due to a boom in salmon aquaculture and the passenger ship industry. Vessel strike risks for large whales are likely underestimated in this region. Results reported in this study may be valuable for policy and mitigation decisions regarding conservation of the endangered blue whale.
    Description: This work was conducted under Chilean research permit PINV 38–2014 Ballena Azul, Golfo Corcovado, from the Ministerio de Economia, Fomento y Turismo, Subsecreteria de Pesca y Acuicultura. We would like to thank the crews of the vessels Centinela, Khronos and Solidaridad for their involvement in the fieldwork. Special thanks to Rafaela Landea‐Briones, Gloria Howes, Esteban Tapia Brunet, Pepe Montt, Thomas Montt, and Daniel Casado for helping and welcoming us in Patagonia. Thanks to MERI Foundation and their students Carlos Cantergiani, Andrea Hirmas and Elvira Vergara for their support and contributions to field efforts. We extend our gratitude to our collaborators Laela Sayigh, Michael Moore, Daniel Zitterbart, Frants Jensen, Aran Mooney, John Durban, Jeremy Goldbogen, and Dave Cade. Thanks to WHOI for financial and technical support. The data analysis and paper writing was financially supported by the National Key Research and Development Program of China (Grant number 2016YFC0300802); the biodiversity investigation, observation and assessment program (2019‐2023) of the Ministry of Ecology and Environment of China; and Indian Ocean Ninety‐east Ridge Ecosystem and Marine Environment Monitoring and Protection, supported by the China Ocean Mineral Resources R&D Association (no. DY135‐E2‐4). Additionally, FC thanks the President's International Fellowship Initiative (PIFI) of the Chinese Academy of Sciences.
    Keywords: Bio‐logging tags ; Blue whale ; Diving profile ; Ocean conservation ; Prey distribution
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  • 57
    Publication Date: 2022-10-20
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bell, T. W., & Siegel, D. A. Nutrient availability and senescence spatially structure the dynamics of a foundation species. Proceedings of the National Academy of Sciences of the United States of America, 119(1), (2021): e2105135118, https://doi.org/10.1073/pnas.2105135118.
    Description: Disentangling the roles of the external environment and internal biotic drivers of plant population dynamics is challenging due to the absence of relevant physiological and abundance information over appropriate space and time scales. Remote observations of giant kelp biomass and photosynthetic pigment concentrations are used to show that spatiotemporal patterns of physiological condition, and thus growth and production, are regulated by different processes depending on the scale of observation. Nutrient supply was linked to regional scale (〉1 km) physiological condition dynamics, and kelp forest stands were more persistent where nutrient levels were consistently high. However, on local scales (〈1 km), internal senescence processes related to canopy age demographics determined patterns of biomass loss across individual kelp forests despite uniform nutrient conditions. Repeat measurements of physiology over continuous spatial fields can provide insights into complex dynamics that are unexplained by the environmental drivers thought to regulate abundance. Emerging remote sensing technologies that provide simultaneous estimates of abundance and physiology can quantify the roles of environmental change and demographics governing plant population dynamics for a wide range of aquatic and terrestrial ecosystems.
    Description: This work was supported by the US NSF (Grants OCE 1232779 and 1831937), by the US Department of Energy (Cooperative Agreement DE-AR0000922), and by NASA (Grant NNX14AR62A) and the NASA Earth and Space Sciences Fellowship program in support of T.W.B.
    Keywords: Physiology ; Population ; Biomass ; Hyperspectral ; Giant kelp
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  • 58
    Publication Date: 2022-10-20
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Billings, G., Walter, M., Pizarro, O., Johnson-Roberson, M., & Camilli, R. Towards automated sample collection and return in extreme underwater environments. Journal of Field Robotics, 2(1), (2022): 1351–1385, https://doi.org/10.55417/fr.2022045.
    Description: In this report, we present the system design, operational strategy, and results of coordinated multivehicle field demonstrations of autonomous marine robotic technologies in search-for-life missions within the Pacific shelf margin of Costa Rica and the Santorini-Kolumbo caldera complex, which serve as analogs to environments that may exist in oceans beyond Earth. This report focuses on the automation of remotely operated vehicle (ROV) manipulator operations for targeted biological sample-collection-and-return from the seafloor. In the context of future extraterrestrial exploration missions to ocean worlds, an ROV is an analog to a planetary lander, which must be capable of high-level autonomy. Our field trials involve two underwater vehicles, the SuBastian ROV and the Nereid Under Ice (NUI) hybrid ROV for mixed initiative (i.e., teleoperated or autonomous) missions, both equipped seven-degrees-of-freedom hydraulic manipulators. We describe an adaptable, hardware-independent computer vision architecture that enables high-level automated manipulation. The vision system provides a three-dimensional understanding of the workspace to inform manipulator motion planning in complex unstructured environments. We demonstrate the effectiveness of the vision system and control framework through field trials in increasingly challenging environments, including the automated collection and return of biological samples from within the active undersea volcano Kolumbo. Based on our experiences in the field, we discuss the performance of our system and identify promising directions for future research.
    Description: This work was funded under a NASA PSTAR grant, number NNX16AL08G, and by the National Science Foundation under grants IIS-1830660 and IIS-1830500. The authors would like to thank the Costa Rican Ministry of Environment and Energy and National System of Conservation Areas for permitting research operations at the Costa Rican shelf margin, and the Schmidt Ocean Institute (including the captain and crew of the R/V Falkor and ROV SuBastian) for their generous support and making the FK181210 expedition safe and highly successful. Additionally, the authors would like to thank the Greek Ministry of Foreign Affairs for permitting the 2019 Kolumbo Expedition to the Kolumbo and Santorini calderas, as well as Prof. Evi Nomikou and Dr. Aggelos Mallios for their expert guidance and tireless contributions to the expedition.
    Keywords: Underwater robotics ; Mobile manipulation ; Marine robotics ; Exploration
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  • 59
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Huynh, A., Maktabi, B., Reddy, C. M., O'Neil, G. W., Chandler, M., & Baki, G. Evaluation of alkenones, a renewably sourced, plant-derived wax as a structuring agent for lipsticks. International Journal of Cosmetic Science, (2020), doi:10.1111/ics.12597.
    Description: OBJECTIVE Waxes are used as structuring agents in lipsticks. There are a variety of waxes combined in a single lipstick to provide good stability, pleasant texture and good pay‐off. Due to a significant growth for natural, green and sustainable products, there is a constant search for alternatives to animal‐derived and petroleum‐derived ingredients. In this study, a green, non‐animalderived wax, namely long‐chain ketones (referred to as alkenones), sourced from marine microalgae was formulated into lipsticks and evaluated as a structuring agent. METHODS Alkenones were used as a substitute for microcrystalline wax, ozokerite and candelilla wax, typical structuring agents. In total, 384 lipsticks were formulated: L1 (control, no alkenones), L2 (alkenones as a substitute for ozokerite), L3 (alkenones as a substitute for microcrystalline wax) and L4 (alkenones as a substitute for candelilla wax). Products were tested for hardness (bending force), stiffness, firmness (needle penetration), pay‐off (using a texture analyser and a consumer panel), friction, melting point and stability for 12 weeks at 25 and 45°C. RESULTS Alkenones influenced each characteristic evaluated. In general, lipsticks with alkenones (L2‐L4) became softer and easier to bend compared to the control (L1). In terms of firmness, lipsticks were similar to the control, except for L4, which was significantly (P 〈 0.05) firmer. The effect on pay‐off was not consistent. L2 and L3 had higher pay‐off to skin and fabric than L1. In addition, L4 had the lowest amount transferred, but it still had the highest colour intensity on skin. Alkenones influenced friction (glide) positively; the average friction decreased for L2‐L4. The lowest friction (i.e. best glide) was shown in L4. Melting point of the lipsticks was lower when alkenones were present. Overall, L4, containing 7% of 4 alkenones in combination with microcrystalline wax, ozokerite and carnauba wax, was found to have the most desirable attributes, including ease of bending, high level of firmness, low pay‐off in terms of amount, high colour intensity on skin and low friction (i.e. better glide). Consumers preferred L4 the most overall. CONCLUSION Results of this study indicate that alkenones offer a sustainable, non‐animal and non‐petroleum‐derived choice as a structuring agent for lipsticks.
    Description: The authors would like to thank Texture Technologies for the technical assistance provided during this project. This research was funded by the Washington Research Foundation and a private donor from friends of the Woods Hole Oceanographic Institution, grant number N‐127244.
    Keywords: Colour cosmetics ; Formulation/stability ; Statistics ; Alkenones ; Lipstick
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  • 60
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2020. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences (2020): 201913625, doi: 10.1073/pnas.1913625117.
    Description: Oceanic transform faults display a unique combination of seismic and aseismic slip behavior, including a large globally averaged seismic deficit, and the local occurrence of repeating magnitude (M) ∼6 earthquakes with abundant foreshocks and seismic swarms, as on the Gofar transform of the East Pacific Rise and the Blanco Ridge in the northeast Pacific Ocean. However, the underlying mechanisms that govern the partitioning between seismic and aseismic slip and their interaction remain unclear. Here we present a numerical modeling study of earthquake sequences and aseismic transient slip on oceanic transform faults. In the model, strong dilatancy strengthening, supported by seismic imaging that indicates enhanced fluid-filled porosity and possible hydrothermal circulation down to the brittle–ductile transition, effectively stabilizes along-strike seismic rupture propagation and results in rupture barriers where aseismic transients arise episodically. The modeled slow slip migrates along the barrier zones at speeds ∼10 to 600 m/h, spatiotemporally correlated with the observed migration of seismic swarms on the Gofar transform. Our model thus suggests the possible prevalence of episodic aseismic transients in M ∼6 rupture barrier zones that host active swarms on oceanic transform faults and provides candidates for future seafloor geodesy experiments to verify the relation between aseismic fault slip, earthquake swarms, and fault zone hydromechanical properties.
    Description: We thank Joan Gomberg, Ruth Harris, Steve Hickman, Shane Detweiler, Mike Diggles, and two anonymous external reviewers for their thoughtful comments that helped to improve the manuscript. This study was supported by Natural Sciences and Engineering Research Council of Canada Discovery Grants RGPIN/418338-2012 and RGPIN-2018-05389; and NSF Grants OCE-10-61203 and OCE-18-33279.
    Description: 2020-10-28
    Keywords: Oceanic transform faults ; Earthquake rupture segmentation ; Aseismic transients ; Seismic swarms
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  • 61
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Patrick, S. C., Martin, J. G. A., Ummenhofer, C. C., Corbeau, A., & Weimerskirch, H. Albatrosses respond adaptively to climate variability by changing variance in a foraging trait. Global Change Biology, (2021), https://doi.org/10.1111/gcb.15735.
    Description: The ability of individuals and populations to adapt to a changing climate is a key determinant of population dynamics. While changes in mean behaviour are well studied, changes in trait variance have been largely ignored, despite being assumed to be crucial for adapting to a changing environment. As the ability to acquire resources is essential to both reproduction and survival, changes in behaviours that maximize resource acquisition should be under selection. Here, using foraging trip duration data collected over 7 years on black-browed albatrosses (Thalassarche melanophris) on the Kerguelen Islands in the southern Indian Ocean, we examined the importance of changes in the mean and variance in foraging behaviour, and the associated effects on fitness, in response to the El Niño Southern Oscillation (ENSO). Using double hierarchical models, we found no evidence that individuals change their mean foraging trip duration in response to a changing environment, but found strong evidence of changes in variance. Younger birds showed greater variability in foraging trip duration in poor conditions as did birds with higher fitness. However, during brooding, birds showed greater variability in foraging behaviour under good conditions, suggesting that optimal conditions allow the alteration between chick provisioning and self-maintenance trips. We found weak correlations between sea surface temperature and the ENSO, but stronger links with sea-level pressure. We suggest that variability in behavioural traits affecting resource acquisition is under selection and offers a mechanism by which individuals can adapt to a changing climate. Studies which look only at effects on mean behaviour may underestimate the effects of climate change and fail to consider variance in traits as a key evolutionary force.
    Description: The authors thank the Institut Polaire Français Paul Emile Victor (IPEV, programme 109 to HW) for providing financial and logistical support for the field work at Kerguelen, and to the Terres Australes et Antarctique Francaises (TAAF). The usage of the following data sets is gratefully acknowledged: SOI, NCEP/NCAR SLP and NOAA OISST v2, all provided by NOAA/OAR/ESRL PSD, Boulder, Colorado, USA, through https://www.esrl.noaa.gov/psd. CCU acknowledges support from the Joint Initiative Awards Fund from the Andrew W. Mellon Foundation and the James E. and Barbara V. Moltz Fellowship for Climate-Related Research.
    Keywords: Bet-hedging ; Intra-individual variability ; Resource acquisition ; Salt-water immersion logger ; Seabirds ; Southern Oscillation Index
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  • 62
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Buesseler, K. O., Boyd, P. W., Black, E. E., & Siegel, D. A. Metrics that matter for assessing the ocean biological carbon pump. Proceedings of the National Academy of Sciences of the United States of America, (2020): 201918114, doi: 10.1073/pnas.1918114117.
    Description: The biological carbon pump (BCP) comprises wide-ranging processes that set carbon supply, consumption, and storage in the oceans’ interior. It is becoming increasingly evident that small changes in the efficiency of the BCP can significantly alter ocean carbon sequestration and, thus, atmospheric CO2 and climate, as well as the functioning of midwater ecosystems. Earth system models, including those used by the United Nation’s Intergovernmental Panel on Climate Change, most often assess POC (particulate organic carbon) flux into the ocean interior at a fixed reference depth. The extrapolation of these fluxes to other depths, which defines the BCP efficiencies, is often executed using an idealized and empirically based flux-vs.-depth relationship, often referred to as the “Martin curve.” We use a new compilation of POC fluxes in the upper ocean to reveal very different patterns in BCP efficiencies depending upon whether the fluxes are assessed at a fixed reference depth or relative to the depth of the sunlit euphotic zone (Ez). We find that the fixed-depth approach underestimates BCP efficiencies when the Ez is shallow, and vice versa. This adjustment alters regional assessments of BCP efficiencies as well as global carbon budgets and the interpretation of prior BCP studies. With several international studies recently underway to study the ocean BCP, there are new and unique opportunities to improve our understanding of the mechanistic controls on BCP efficiencies. However, we will only be able to compare results between studies if we use a common set of Ez-based metrics.
    Description: We thank the many scientists whose ideas and contributions over the years are the foundation of this paper. This includes A. Martin, who led the organization of the BIARRITZ group (now JETZON) workshop in July 2019, discussions at which helped to motivate this article. We thank D. Karl for pointing us in the right direction for this paper format at PNAS and two thoughtful reviewers who through their comments helped to improve this manuscript. Support for writing this piece is acknowledged from several sources, including the Woods Hole Oceanographic Institution’s Ocean Twilight Zone project (K.O.B.); NASA as part of the EXport Processes in the global Ocean from RemoTe Sensing (EXPORTS) program (K.O.B. and D.A.S.). E.E.B. was supported by a postdoctoral fellowship through the Ocean Frontier Institute at Dalhousie University. P.W.B. was supported by the Australian Research Council through a Laureate (FL160100131).
    Keywords: Biological carbon pump ; Twilight zone ; Particle flux
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  • 63
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Anderson, D. M., Fachon, E., Pickart, R. S., Lin, P., Fischer, A. D., Richlen, M. L., Uva, V., Brosnahan, M. L., McRaven, L., Bahr, F., Lefebvre, K., Grebmeier, J. M., Danielson, S. L., Lyu, Y., & Fukai, Y. Evidence for massive and recurrent toxic blooms of Alexandrium catenella in the Alaskan Arctic. Proceedings of the National Academy of Sciences of the United States of America, 118(41) (2021): e2107387118, https://doi.org/10.1073/pnas.2107387118.
    Description: Among the organisms that spread into and flourish in Arctic waters with rising temperatures and sea ice loss are toxic algae, a group of harmful algal bloom species that produce potent biotoxins. Alexandrium catenella, a cyst-forming dinoflagellate that causes paralytic shellfish poisoning worldwide, has been a significant threat to human health in southeastern Alaska for centuries. It is known to be transported into Arctic regions in waters transiting northward through the Bering Strait, yet there is little recognition of this organism as a human health concern north of the Strait. Here, we describe an exceptionally large A. catenella benthic cyst bed and hydrographic conditions across the Chukchi Sea that support germination and development of recurrent, locally originating and self-seeding blooms. Two prominent cyst accumulation zones result from deposition promoted by weak circulation. Cyst concentrations are among the highest reported globally for this species, and the cyst bed is at least 6× larger in area than any other. These extraordinary accumulations are attributed to repeated inputs from advected southern blooms and to localized cyst formation and deposition. Over the past two decades, warming has likely increased the magnitude of the germination flux twofold and advanced the timing of cell inoculation into the euphotic zone by 20 d. Conditions are also now favorable for bloom development in surface waters. The region is poised to support annually recurrent A. catenella blooms that are massive in scale, posing a significant and worrisome threat to public and ecosystem health in Alaskan Arctic communities where economies are subsistence based.
    Description: Funding for D.M.A., R.S.P., E.F., P.L., A.D.F., V.U., M.L.B., L.M., F.B., and M.L.R. was provided by grants from the NSF Office of Polar Programs (Grants OPP-1823002 and OPP-1733564) and the National Ocanic and Atmospheric Administration (NOAA) Arctic Research program (through the Cooperative Institute for the North Atlantic Region [CINAR; Grants NA14OAR4320158 and NA19OAR4320074]), for J.M.G. through CINAR 22309.07 UMCES (University of Maryland Center for Environmental Science), and for D.M.A. and K.L. through NOAA’s Center for Coastal and Ocean Studies Ecology and Oceanography of Harmful Algal Blooms (ECOHAB) Program (NA20NOS4780195). Funding for D.M.A., M.L.R., M.L.B., E.F., V.U., and A.D.F. was also provided by NSF (Grant OCE-1840381) and NIH (Grant 1P01-ES028938-01) through the Woods Hole Center for Oceans and Human Health. S.L.D. was supported by North Pacific Research Board IERP Grants A91-99a and A91-00a. This is IERP publication ArcticIERP-41 and ECOHAB Contribution No. ECO983.
    Keywords: Harmful algal bloom ; HAB ; Alexandrium ; Alaskan Arctic ; Climate
    Repository Name: Woods Hole Open Access Server
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  • 64
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2021. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 118(8), (2021): e1918605118, https://doi.org/10.1073/pnas.1918605118.
    Description: Changes in chromium (Cr) isotope ratios due to fractionation between trivalent [Cr(III)] and hexavalent [Cr(VI)] are being utilized by geologists to infer oxygen conditions in past environments. However, there is little information available on Cr in the modern ocean to ground-truth these inferences. Transformations between the two chromium species are important processes in oceanic Cr cycling. Here we present profiles of hexavalent and trivalent Cr concentrations and stable isotope ratios from the eastern tropical North Pacific (ETNP) oxygen-deficient zone (ODZ) which support theoretical and experimental studies that predict that lighter Cr is preferentially reduced in low-oxygen environments and that residual dissolved Cr becomes heavier due to removal of particle-reactive Cr(III) on sinking particles. The Cr(III) maximum dominantly occurs in the upper portion of the ODZ, implying that microbial activity (dependent on the sinking flux of organic matter) may be the dominant mechanism for this transformation, rather than a simple inorganic chemical conversion between the species depending on the redox potential.
    Description: We thank chief scientist Gabrielle Rocap for accommodating us on cruises Roger Revelle 1804-5 and Kilo Moana 19-20 (sponsored by NSF Grant DEB-1542240 to G. Rocap, A. Devol, R. Kiel, and C. Deutch), Jim Moffett for helping with sampling on these cruises, and Mark Altabet and Frank Stewart for collecting the samples from station 2T on cruise New Horizon 1410. This research was supported by NSF Grant OCE-1736996 (to E.A.B.) and by a fellowship from the Massachusetts Institute of Technology/Woods Hole Oceanographic Institution Joint Program in Oceanography.
    Keywords: Chromium isotopes ; Oxygen-deficient zones ; Trace elements ; Trivalent chromium ; Hexavalent ; Chromium
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  • 65
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Jenouvrier, S., Judy, C.-C., Wolf, S., Holland, M., Labrousse, S., LaRue, M., Wienecke, B., Fretwell, P., Barbraud, C., Greenwald, N., Stroeve, J., & Trathan, P. N. The call of the emperor penguin: legal responses to species threatened by climate change. Global Change Biology, 27, (2021): 5008– 5029, https://doi.org/10.1111/gcb.15806.
    Description: Species extinction risk is accelerating due to anthropogenic climate change, making it urgent to protect vulnerable species through legal frameworks in order to facilitate conservation actions that help mitigate risk. Here, we discuss fundamental concepts for assessing climate change risks to species using the example of the emperor penguin (Aptenodytes forsteri), currently being considered for protection under the US Endangered Species Act (ESA). This species forms colonies on Antarctic sea ice, which is projected to significantly decline due to ongoing greenhouse gas (GHG) emissions. We project the dynamics of all known emperor penguin colonies under different GHG emission scenarios using a climate-dependent meta-population model including the effects of extreme climate events based on the observational satellite record of colonies. Assessments for listing species under the ESA require information about how species resiliency, redundancy and representation (3Rs) will be affected by threats within the foreseeable future. Our results show that if sea ice declines at the rate projected by climate models under current energy system trends and policies, the 3Rs would be dramatically reduced and almost all colonies would become quasi-extinct by 2100. We conclude that the species should be listed as threatened under the ESA.
    Description: We acknowledge support of NASA (80NSSC20K1289) to SJ, MH, and of NSF—OPP (1744794) to SJ, ML.
    Keywords: climate risk assessments ; Endangered Species Act ; foreseeable future ; population projections ; resiliency, redundancy and representation (3Rs) ; sea ice projections ; species distribution ; treatment of scientific uncertainty
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  • 66
    Publication Date: 2022-05-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Jenouvrier, S., Long, M. C., Coste, C. F. D., Holland, M., Gamelon, M., Yoccoz, N., & Saether, B.-E. Detecting climate signals in populations across life histories. Global Change Biology, 28, (2022): 2236– 2258, https://doi.org/10.1111/gcb.16041.
    Description: Climate impacts are not always easily discerned in wild populations as detecting climate change signals in populations is challenged by stochastic noise associated with natural climate variability, variability in biotic and abiotic processes, and observation error in demographic rates. Detection of the impact of climate change on populations requires making a formal distinction between signals in the population associated with long-term climate trends from those generated by stochastic noise. The time of emergence (ToE) identifies when the signal of anthropogenic climate change can be quantitatively distinguished from natural climate variability. This concept has been applied extensively in the climate sciences, but has not been explored in the context of population dynamics. Here, we outline an approach to detecting climate-driven signals in populations based on an assessment of when climate change drives population dynamics beyond the envelope characteristic of stochastic variations in an unperturbed state. Specifically, we present a theoretical assessment of the time of emergence of climate-driven signals in population dynamics (ToEpop). We identify the dependence of (ToEpop)on the magnitude of both trends and variability in climate and also explore the effect of intrinsic demographic controls on (ToEpop). We demonstrate that different life histories (fast species vs. slow species), demographic processes (survival, reproduction), and the relationships between climate and demographic rates yield population dynamics that filter climate trends and variability differently. We illustrate empirically how to detect the point in time when anthropogenic signals in populations emerge from stochastic noise for a species threatened by climate change: the emperor penguin. Finally, we propose six testable hypotheses and a road map for future research.
    Description: We acknowledge the support of NASA 80NSSC20K1289 to SJ, ML, and MH; NSF OPP 1744794 to SJ and NSF OPP 2037561 to SJ and MH.
    Keywords: climate change ; emperor penguin ; life histories ; population trend ; population variability ; signal to noise ; time of emergence
    Repository Name: Woods Hole Open Access Server
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  • 67
    Publication Date: 2022-07-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Carson, M., Doberneck, D., Hart, Z., Kelsey, H., Pierce, J., Porter, D., Richlen, M., Schandera, L., & Triezenberg, H. A strategic framework for community engagement in oceans and human health, Community Science, 1(1), (2022): e2022CSJ000001, https://doi.org/10.1029/2022csj000001.
    Description: Over the past two decades, scientific research on the connections between the health and resilience of marine ecosystems and human health, well-being, and community prosperity has expanded and evolved into a distinct “metadiscipline” known as Oceans and Human Health (OHH), recognized by the scientific community as well as policy makers. OHH goals are diverse and seek to improve public health outcomes, promote sustainable use of aquatic systems and resources, and strengthen community resilience. OHH research has historically included some level of community outreach and partner involvement; however, the increasing disruption of aquatic environments and urgency of public health impacts calls for a more systematic approach to effectively identify and engage with community partners to achieve project goals and outcomes. Herein, we present a strategic framework developed collaboratively by community engagement personnel from the four recently established U.S. Centers for Oceans and Human Health (COHH). This framework supports researchers in defining levels of community engagement and in aligning partners, purpose, activities, and approaches intentionally in their community engagement efforts. Specifically, we describe: (a) a framework for a range of outreach and engagement approaches; (b) the need for identifying partners, purpose, activities, and approaches; and (c) the importance of making intentional alignment among them. Misalignment across these dimensions may lead to wasting time or resources, eroding public trust, or failing to achieve intended outcomes. We illustrate the framework with examples from current COHH case studies and conclude with future directions for strategic community engagement in OHH and other environmental health contexts.
    Description: This publication was prepared by Heather Triezenberg and the team under award NA180AR4170102 from the National Oceanic and Atmospheric Administration, U.S. Department of Commerce through the Regents of the University of Michigan, and supported by funding from the NIH (1P01ES028939-01) and the NSF (1840715) to the Bowling Green State University Great Lakes Center for Fresh Waters and Human Health. Funding for M. L. Richlen was provided by the NSF (OCE1840381) and NIH (1P01-ES028938-01) through the Woods Hole Center for Oceans and Human Health. Research at the Center for Oceans and Human Health and Climate Change Interactions (OHHC2I) at the University of South Carolina is supported by the NIH Award Number P01ES028942, granted to Principal Investigators Geoffrey Scott and Paul Sandifer. M. A. Carson, Z. Hart, H. Kelsey, D. E. Porter, and L. Schandera are Community Engagement Core investigators at this Center. Funding for J. Pierce is provided by the NSF (grant number OCE-1841811) and the NIH (P01ES028949) through the Greater Caribbean Center for Ciguatera Research at the Florida Gulf Coast University.
    Keywords: harmful algal blooms ; human health ; pollutants ; ocean health
    Repository Name: Woods Hole Open Access Server
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  • 68
    Publication Date: 2022-08-15
    Description: The sinking of carbon fixed via net primary production (NPP) into the ocean interior is an important part of marine biogeochemical cycles. NPP measurements follow a log-normal probability distribution, meaning NPP variations can be simply described by two parameters despite NPP's complexity. By analyzing a global database of open ocean particle fluxes, we show that this log-normal probability distribution propagates into the variations of near-seafloor fluxes of particulate organic carbon (POC), calcium carbonate, and opal. Deep-sea particle fluxes at subtropical and temperate time-series sites follow the same log-normal probability distribution, strongly suggesting the log-normal description is robust and applies on multiple scales. This log-normality implies that 29% of the highest measurements are responsible for 71% of the total near-seafloor POC flux. We discuss possible causes for the dampening of variability from NPP to deep-sea POC flux, and present an updated relationship predicting POC flux from mineral flux and depth.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 69
    Publication Date: 2022-08-15
    Description: The attenuation coefficient b is one of the most common ways to describe how strong the carbon flux is attenuated throughout the water column. Therefore, b is an essential input variable in many carbon flux and climate models. Marsay et al. (2015, https://doi.org/10.1073/pnas.1415311112) proposed that the median surface water temperature (0–500 m) may be a predictor of b, but our observations from Arctic waters challenge this hypothesis. We found a highly variable attenuation coefficient (b = 0.43–1.84) in cold Arctic waters (〈4.1 °C). Accordingly, we suggest that water temperature is not a globally valid predictor of the attenuation coefficient. We advocate instead that the phytoplankton composition and especially the relative abundance of diatoms can be used to parametrize the carbon flux attenuation in local and global carbon flux models.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 70
    Publication Date: 2022-08-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Womersley, F. C., Humphries, N. E., Queiroz, N., Vedor, M., da Costa, I., Furtado, M., Tyminski, J. P., Abrantes, K., Araujo, G., Bach, S. S., Barnett, A., Berumen, M. L., Bessudo Lion, S., Braun, C. D., Clingham, E., Cochran, J. E. M., de la Parra, R., Diamant, S., Dove, A. D. M., Dudgeon, C. L., Erdmann, M. V., Espinoza, E., Fitzpatrick, R., González Cano, J., Green, J. R., Guzman, H. M., Hardenstine, R., Hasan, A., Hazin, F. H. V., Hearn, A. R., Hueter, R. E., Jaidah, M. Y., Labaja, J., Ladinol, F., Macena, B. C. L., Morris Jr., J. J., Norman, B. M., Peñaherrera-Palmav, C., Pierce, S. J., Quintero, L. M., Ramırez-Macías, D., Reynolds, S. D., Richardson, A. J., Robinson, D. P., Rohner, C. A., Rowat, D. R. L., Sheaves, M., Shivji, M. S., Sianipar, A. B., Skomal, G. B., Soler, G., Syakurachman, I., Thorrold, S. R., Webb, D. H., Wetherbee, B. M., White, T. D., Clavelle, T., Kroodsma, D. A., Thums, M., Ferreira, L. C., Meekan, M. G., Arrowsmith, L. M., Lester, E. K., Meyers, M. M., Peel, L. R., Sequeira, A. M. M., Eguıluz, V. M., Duarte, C. M., & Sims, D. W. Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark. Proceedings of the National Academy of Sciences of the United States of America, 119(20), (2022): e2117440119, https://doi.org/10.1073/pnas.2117440119.
    Description: Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (〉300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial “cryptic” lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.
    Description: Funding for data analysis was provided by the UK Natural Environment Research Council (NERC) through a University of Southampton INSPIRE DTP PhD Studentship to F.C.W. Additional funding for data analysis was provided by NERC Discovery Science (NE/R00997/X/1) and the European Research Council (ERC-AdG-2019 883583 OCEAN DEOXYFISH) to D.W.S., Fundação para a Ciência e a Tecnologia (FCT) under PTDC/BIA/28855/2017 and COMPETE POCI-01–0145-FEDER-028855, and MARINFO–NORTE-01–0145-FEDER-000031 (funded by Norte Portugal Regional Operational Program [NORTE2020] under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund–ERDF) to N.Q. FCT also supported N.Q. (CEECIND/02857/2018) and M.V. (PTDC/BIA-COM/28855/2017). D.W.S. was supported by a Marine Biological Association Senior Research Fellowship. All tagging procedures were approved by institutional ethical review bodies and complied with all relevant ethical regulations in the jurisdictions in which they were performed. Details for individual research teams are given in SI Appendix, section 8. Full acknowledgments for tagging and field research are given in SI Appendix, section 7. This research is part of the Global Shark Movement Project (https://www.globalsharkmovement.org).
    Keywords: ship strike ; marine megafauna ; conservation ; movement ecology ; human impact
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  • 71
    Publication Date: 2022-08-30
    Description: Most tropical corals live in symbiosis with Symbiodiniaceae algae whose photosynthetic production of oxygen (O2) may lead to excess O2 in the diffusive boundary layer (DBL) above the coral surface. When flow is low, cilia-induced mixing of the coral DBL is vital to remove excess O2 and prevent oxidative stress that may lead to coral bleaching and mortality. Here, we combined particle image velocimetry using O2-sensitive nanoparticles (sensPIV) with chlorophyll (Chla)-sensitive hyperspectral imaging to visualize the microscale distribution and dynamics of ciliary flows and O2 in the coral DBL in relation to the distribution of Symbiodiniaceae Chla in the tissue of the reef building coral, Porites lutea. Curiously, we found an inverse relation between O2 in the DBL and Chla in the underlying tissue, with patches of high O2 in the DBL above low Chla in the underlying tissue surrounding the polyp mouth areas and pockets of low O2 concentrations in the DBL above high Chla in the coenosarc tissue connecting neighboring polyps. The spatial segregation of Chla and O2 is related to ciliary-induced flows, causing a lateral redistribution of O2 in the DBL. In a 2D transport-reaction model of the coral DBL, we show that the enhanced O2 transport allocates parts of the O2 surplus to areas containing less chla, which minimizes oxidative stress. Cilary flows thus confer a spatially complex mass transfer in the coral DBL, which may play an important role in mitigating oxidative stress and bleaching in corals.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 72
    Publication Date: 2022-06-22
    Description: Silicic calderas are volcanic systems whose unrest evolution is more unpredictable than other volcano types because they often do not culminate in an eruption. Their complex structure strongly influences the post-collapse volcano-tectonic evolution, usually coupling volcanism and ground deformation. Among such volcanoes, the Campi Flegrei caldera (southern Italy) is one of the most studied. Significant long- and short-term ground deformations characterize this restless volcano. Several studies performed on the marinecontinental succession exposed in the central sector of the Campi Flegrei caldera provided a reconstruction of ground deformation during the last 15 kyr. However, considering that over one-third of the caldera is presently submerged beneath the Pozzuoli Gulf, a comprehensive stratigraphic on-land-offshore framework is still lacking. This study aims at reconstructing the offshore succession through analysis of high-resolution single and multichannel reflection seismic profiles and correlates the resulting seismic stratigraphic framework with the stratigraphy reconstructed on-land. Results provide new clues on the causative relations between the intra-caldera marine and volcaniclastic sedimentation and the alternating phases of marine transgressions and regressions originated by the interplay between ground deformation and sea-level rise. The volcano-tectonic reconstruction, provided in this work, connects the major caldera floor movements to the large Plinian eruptions of Pomici Principali (12 ka) and Agnano Monte Spina (4.55 ka), with the onset of the first post-caldera doming at ~10.5 ka. We emphasize that ground deformation is usually coupled with volcanic activity, which shows a self-similar pattern, regardless of its scale. Thus, characterizing the long-term deformation history becomes of particular interest and relevance for hazard assessment and definition of future unrest scenarios.
    Description: Published
    Description: 855-882
    Description: 1V. Storia eruttiva
    Description: JCR Journal
    Keywords: offshore stratigraphy ; seismic units ; La Starza succession ; volcanism, ; 04.08. Volcanology ; 04.04. Geology ; 04.07. Tectonophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 73
    Publication Date: 2022-06-29
    Description: Rapid and profound climatic and environmental changes have been predicted for the Antarctic Peninsula with so far unknown impact on the biogeochemistry of the continental shelves. In this study, we investigate benthic carbon sedimentation, remineralization and iron cycling using sediment cores retrieved on a 400 mile transect with contrasting sea ice conditions along the eastern shelf of the Antarctic Peninsula. Sediments at comparable water depths of 330-450 m showed sedimentation and remineralization rates of organic carbon, ranging from 2.5-13 and 1.8-7.2 mmol C m-2 d-1, respectively. Both rates were positively correlated with the occurrence of marginal sea ice conditions (5-35% ice cover) along the transect, suggesting a favorable influence of the corresponding light regime and water column stratification on algae growth and sedimentation rates. From south to north, the burial efficiency of organic carbon decreased from 58% to 27%, while bottom water temperatures increased from -1.9 to -0.1 °C. Net iron reduction rates, as estimated from pore-water profiles of dissolved iron, were significantly correlated with carbon degradation rates and contributed 0.7-1.2% to the total organic carbon remineralization. Tightly coupled phosphate-iron recycling was indicated by significant covariation of dissolved iron and phosphate concentrations, which almost consistently exhibited P/Fe flux ratios of 0.26. Iron efflux into bottom waters of 0.6-4.5 µmol Fe m-2 d-1 was estimated from an empirical model. Despite the deep shelf waters, a clear bentho-pelagic coupling is indicated, shaped by the extent and duration of marginal sea ice conditions during summer, and likely to be affected by future climate change.
    Repository Name: EPIC Alfred Wegener Institut
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  • 74
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    Wiley
    In:  EPIC3Journal of Geophysical Research-Oceans, Wiley, 126(12), pp. e2021JC017633, ISSN: 0148-0227
    Publication Date: 2022-06-29
    Description: The transient climate response (TCR) is 20% higher in the Alfred Wegener Institute Climate Model (AWI-CM) compared to the Max Planck Institute Earth System Model (MPI-ESM) whereas the equilibrium climate sensitivity (ECS) is by up to 10% higher in AWI-CM. These results are largely independent of the two considered model resolutions for each model. The two coupled CMIP6 models share the same atmosphere-land component ECHAM6.3 developed at the Max Planck Institute for Meteorology (MPI-M). However, ECHAM6.3 is coupled to two different ocean models, namely the MPIOM sea ice-ocean model developed at MPI-M and the FESOM sea ice-ocean model developed at the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI). A reason for the different TCR is related to ocean heat uptake in response to greenhouse gas forcing. Specifically, AWI-CM simulations show stronger surface heating than MPI-ESM simulations while the latter accumulate more heat in the deeper ocean. The vertically integrated ocean heat content is increasing slower in AWI-CM model configurations compared to MPI-ESM model configurations in the high latitudes. Weaker vertical mixing in AWI-CM model configurations compared to MPI-ESM model configurations seems to be key for these differences. The strongest difference in vertical ocean mixing occurs inside the Weddell and Ross Gyres and the northern North Atlantic. Over the North Atlantic, these differences materialize in a lack of a warming hole in AWI-CM model configurations and the presence of a warming hole in MPI-ESM model configurations. All these differences occur largely independent of the considered model resolutions.
    Repository Name: EPIC Alfred Wegener Institut
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  • 75
    Publication Date: 2022-06-24
    Description: A variety of tectonic processes spread along the circum-Mediterranean orogenic belts driven by the convergence of major plates, episodes of slab retreat and lateral and vertical mantle flows. Here, we provide an updated view of crustal stress and strain-rate fields for the Albanides belt in the eastern Adria-Eurasia convergence boundary. We framed a new geodetic-based source model for the 2019 Mw6.4 Durrёs earthquake in light of the regional deformation, propending for a transpressional west-dipping seismogenic fault. Our results highlight a fault-scale complexity which mirrors the long-time scale deformation of the Albanides plate boundary, where the rotation induced by the fast Hellenic rollback is accommodated also by transpression on inherited structures.
    Description: Published
    Description: 244–252
    Description: 3T. Fisica dei terremoti e Sorgente Sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 76
    Publication Date: 2022-05-24
    Description: Pyroclastic currents are described as gravity currents, and the classic conceptual model gives a first-order importance to the density of such currents. This directs quantitative models to assume specific flow structures (shallow water or equilib rium turbulent boundary layer), which may apply to restricted volcanic areas inde pendently of source dynamics or may correspond to source dynamics separate from topographic interaction. The recent introduction of two end-members of pyroclastic currents, inertial and forced, is further developed here, leading to a global conceptual model in which source dynamics and topographic interaction are both taken into account. The concept of energy facies is defined here as the ensemble of the first order indicators of pyroclastic currents (topological aspect ratio, competence ratio and emplacement temperature) that are proxies of the energy of such currents. Nine energy facies are introduced with general applicability and with the goal to globally characterize pyroclastic currents from vent to deposit.
    Description: Published
    Description: 1-11
    Description: 4V. Processi pre-eruttivi
    Description: 5V. Processi eruttivi e post-eruttivi
    Description: JCR Journal
    Keywords: Energy facies ; pyroclastic currents
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 77
    Publication Date: 2022-06-22
    Description: Thirteen samples of mortar collected from different masonry structures of the Curia of Pompey the Great and from three mixtilinear basins located within the Sacred Area of Largo Argentina were studied. Despite the use of the same volcanic deposit, known as "Pozzolane Rosse", to produce the fine aggregate in all these mortars, it was possible to highlight some distinctive features through the combination of geochemical analyses on selected trace elements and petrographic analysis under an optical microscope, allowing us to distinguish among the three groups of mortars. These types of mortars reflect a perfect coincidence between the diversity of the volcanic materials used and the different construction phases identified and documented by the analysis of the stratigraphic units: a first construction phase of Pompeian age, a second one of Augustan age and, finally, one of the medieval period. Furthermore, it was possible to ascertain two phases of construction of the basins, the second coeval with the interventions of the Augustan period. Finally, this study increases the knowledge on the methods of exploitation and selection of volcanic materials used to produce mortars in Roman times, identifying additional elements useful to establish their origin and chronology of use.
    Description: Published
    Description: 597-610
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 78
    Publication Date: 2022-07-10
    Description: The bacterial communities of Caulerpa lentillifera were studied during an outbreak of an unknown disease in a sea grape farm from Vietnam. Clear differences between healthy and diseased cases were observed at the order, genus, and Operational Taxonomic Unit (OTU) level. A richer diversity was detected in the diseased thalli of C. lentillifera, as well as the dominance of the orders Flavobacteriales (phylum Bacteroidetes) and Phycisphaerales (Planctomycetes). Aquibacter, Winogradskyella, and other OTUs of the family Flavobacteriaceae were hypothesized as detrimental bacteria, this family comprises some well-known seaweed pathogens. Phycisphaera together with other Planctomycetes and Woeseia were probably saprophytes of C. lentillifera. The Rhodobacteraceae and Rhodovulum dominated the bacterial community composition of healthy C. lentillifera. The likely beneficial role of Bradyrhizobium, Paracoccus, and Brevundimonas strains on nutrient cycling and phytohormone production was discussed. The bleaching of diseased C. lentillifera might not only be associated with pathogens but also with an oxidative response. This study offers pioneering insights on the co-occurrence of C. lentillifera-attached bacteria, potential detrimental or beneficial microbes, and a baseline for understanding the C. lentillifera holobiont. Further applied and basic research is urgently needed on C. lentillifera microbiome, shotgun metagenomic, metatranscriptomic, and metabolomic studies as well as bioactivity assays are recommended.
    Repository Name: EPIC Alfred Wegener Institut
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  • 79
    Publication Date: 2022-09-15
    Description: Phytoplankton stand at the base of the marine food-web, and play a major role in global carbon cycling. Rising CO2 levels and temperatures are expected to enhance growth and alter carbon:nutrient stoichiometry of marine phytoplankton, with possible consequences for the functioning of marine food-webs and the oceanic carbon pump. To date, however, the consistency of phytoplankton stoichiometric responses remains unclear. We therefore performed a meta-analysis on data from experimental studies on stoichiometric responses of marine phytoplankton to elevated pCO2 and 3–5° warming under nutrient replete and limited conditions. Our results demonstrate that elevated pCO2 increased overall phytoplankton C:N (by 4%) and C:P (by 9%) molar ratios under nutrient replete conditions, as well as phytoplankton growth rates (by 6%). Nutrient limitation amplified the CO2 effect on C:N and C:P ratios, with increases to 27% and 17%, respectively. In contrast to elevated pCO2, warming did not consistently alter phytoplankton elemental composition. This could be attributed to species- and study-specific increases and decreases in stoichiometry in response to warming. While our observed moderate CO2-driven changes in stoichiometry are not likely to drive marked changes in food web functioning, they are in the same order of magnitude as current and projected estimations of oceanic carbon export. Therefore, our results may indicate a stoichiometric compensation mechanism for reduced oceanic carbon export due to declining primary production in the near future.
    Repository Name: EPIC Alfred Wegener Institut
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  • 80
    Publication Date: 2022-09-14
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Thomas, M., Jensen, F. H., Averly, B., Demartsev, V., Manser, M. B., Sainburg, T., Roch, M. A., & Strandburg-Peshkin, A. A practical guide for generating unsupervised, spectrogram-based latent space representations of animal vocalizations. The Journal of Animal Ecology, 91(8), (2022): 1567– 1581, https://doi.org/10.1111/1365-2656.13754.
    Description: 1. Background: The manual detection, analysis and classification of animal vocalizations in acoustic recordings is laborious and requires expert knowledge. Hence, there is a need for objective, generalizable methods that detect underlying patterns in these data, categorize sounds into distinct groups and quantify similarities between them. Among all computational methods that have been proposed to accomplish this, neighbourhood-based dimensionality reduction of spectrograms to produce a latent space representation of calls stands out for its conceptual simplicity and effectiveness. 2. Goal of the study/what was done: Using a dataset of manually annotated meerkat Suricata suricatta vocalizations, we demonstrate how this method can be used to obtain meaningful latent space representations that reflect the established taxonomy of call types. We analyse strengths and weaknesses of the proposed approach, give recommendations for its usage and show application examples, such as the classification of ambiguous calls and the detection of mislabelled calls. 3. What this means: All analyses are accompanied by example code to help researchers realize the potential of this method for the study of animal vocalizations.
    Description: This work was supported by HFSP Research Grant RGP0051/2019 to ASP, MBM and MAR, and funded by the Deutsche Forschungsgemeinschaft (DFG) under Germany's Excellence Strategy (EXC-2117-422037984). ASP received additional funding from the Gips-Schüle Stiftung, the Zukunftskolleg at the University of Konstanz and the Max-Planck-Institute of Animal Behaviour. VD was funded by the Minerva Stiftung and Alexander von Humboldt Foundation.
    Keywords: animal sounds ; animal vocalizations ; bioacoustics ; call classification ; dimensionality reduction ; spectrogram ; UMAP ; unsupervised learning
    Repository Name: Woods Hole Open Access Server
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  • 81
    Publication Date: 2022-06-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Acker, M., Hogle, S. L., Berube, P. M., Hackl, T., Coe, A., Stepanauskas, R., Chisholm, S. W., & Repeta, D. J. Phosphonate production by marine microbes: exploring new sources and potential function. Proceedings of the National Academy of Sciences of the United States of America, 119(11), (2022): e2113386119, https://doi.org/10.1073/pnas.2113386119.
    Description: Phosphonates are organophosphorus metabolites with a characteristic C-P bond. They are ubiquitous in the marine environment, their degradation broadly supports ecosystem productivity, and they are key components of the marine phosphorus (P) cycle. However, the microbial producers that sustain the large oceanic inventory of phosphonates as well as the physiological and ecological roles of phosphonates are enigmatic. Here, we show that phosphonate synthesis genes are rare but widely distributed among diverse bacteria and archaea, including Prochlorococcus and SAR11, the two major groups of bacteria in the ocean. In addition, we show that Prochlorococcus can allocate over 40% of its total cellular P-quota toward phosphonate production. However, we find no evidence that Prochlorococcus uses phosphonates for surplus P storage, and nearly all producer genomes lack the genes necessary to degrade and assimilate phosphonates. Instead, we postulate that phosphonates are associated with cell-surface glycoproteins, suggesting that phosphonates mediate ecological interactions between the cell and its surrounding environment. Our findings indicate that the oligotrophic surface ocean phosphonate pool is sustained by a relatively small fraction of the bacterioplankton cells allocating a significant portion of their P quotas toward secondary metabolism and away from growth and reproduction.
    Description: This work was supported in part by grants from the NSF (OCE-1153588 and DBI-0424599 to S.W.C.; OCE-1335810 and OIA-1826734 to R.S.; and OCE-1634080 to D.J.R.), the Gordon and Betty Moore Foundation (no. 6000 to D.J.R.), and the Simons Foundation (Life Sciences Project Award IDs 337262 and 647135 to S.W.C.; 510023 to R.S.; and Simons Collaboration on Ocean Processes and Ecology [SCOPE] Award ID 329108 to S.W.C. and D.J.R.).
    Keywords: phosphonate ; Prochlorococcus ; marine ; biogeochemistry ; phosphorus
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  • 82
    Publication Date: 2022-07-20
    Description: The Antarctic krill (Euphausia superba Dana) is a keystone species in the Southern Ocean that uses an arsenal of hydrolases for biomacromolecule decomposition to effectively digest its omnivorous diet. The present study builds on a hybrid-assembled transcriptome (13,671 ORFs) combined with comprehensive proteome profiling. The analysis of individual krill compartments allowed detection of significantly more different proteins compared to that of the entire animal (1,464 vs. 294 proteins). The nearby krill sampling stations in the Bransfield Strait (Antarctic Peninsula) yielded rather uniform proteome datasets. Proteins related to energy production and lipid degradation were particularly abundant in the abdomen, agreeing with the high energy demand of muscle tissue. A total of 378 different biomacromolecule hydrolysing enzymes were detected, including 250 proteases, 99 CAZymes, 14 nucleases and 15 lipases. The large repertoire in proteases is in accord with the protein-rich diet affiliated with E. superba’s omnivorous lifestyle and complex biology. The richness in chitin-degrading enzymes allows not only digestion of zooplankton diet, but also the utilization of the discharged exoskeleton after moulting.
    Repository Name: EPIC Alfred Wegener Institut
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  • 83
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sosa, O. A., Burrell, T. J., Wilson, S. T., Foreman, R. K., Karl, D. M., & Repeta, D. J. Phosphonate cycling supports methane and ethylene supersaturation in the phosphate-depleted western North Atlantic Ocean. Limnology and Oceanography, (2020), doi:10.1002/lno.11463.
    Description: In oligotrophic ocean regions, dissolved organic phosphorus (DOP) plays a prominent role as a source of phosphorus (P) to microorganisms. An important bioavailable component of DOP is phosphonates, organophosphorus compounds with a carbon‐phosphorus (C‐P) bond, which are ubiquitous in high molecular weight dissolved organic matter (HMWDOM). In addition to being a source of P, the degradation of phosphonates by the bacterial C‐P lyase enzymatic pathway causes the release of trace hydrocarbon gases relevant to climate and atmospheric chemistry. In this study, we investigated the roles of phosphate and phosphonate cycling in the production of methane (CH4) and ethylene (C2H4) in the western North Atlantic Ocean, a region that features a transition in phosphate concentrations from coastal to open ocean waters. We observed an inverse relationship between phosphate and the saturation state of CH4 and C2H4 in the water column, and between phosphate and the relative abundance of the C‐P lyase marker gene phnJ . In phosphate‐depleted waters, methylphosphonate and 2‐hydroxyethylphosphonate, the C‐P lyase substrates that yield CH4 and C2H4, respectively, were readily degraded in proportions consistent with their abundance and bioavailability in HMWDOM and with the concentrations of CH4 and C2H4 in the water column. We conclude that phosphonate degradation through the C‐P lyase pathway is an important source and a common production pathway of CH4 and C2H4 in the phosphate‐depleted surface waters of the western North Atlantic Ocean and that phosphate concentration can be an important control on the saturation state of these gases in the upper ocean.
    Description: We thank the captain and crew of the R/V Neil Armstrong and chief scientist Benjamin Van Mooy for supporting and leading research at sea. Chiara Santinelli and Eric Grabowski provided analyses of dissolved organic carbon. This research was funded by NSF Chemical Oceanography award OCE‐1634080 to D.J.R. Additional support was provided by the Gordon and Betty Moore Foundation grant 3794 to D.M.K. and grant 6000 to D.J.R., and the Simons Collaboration on Ocean Processes and Ecology (SCOPE) program grant 329108 to D.M.K., E.F.D., and D.J.R.
    Repository Name: Woods Hole Open Access Server
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  • 84
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2021. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Journal of Phycology, doi:10.1111/jpy.13135.
    Description: Gymnodinium gracile, described from the coasts of Denmark in 1881, is one of the first described unarmored dinoflagellates. Individuals which morphologically fit with the original description were isolated from the English Channel (North‐East Atlantic). The SSU rRNA gene sequences were identical to the sequences identified as Balechina pachydermata and Gymnodinium amphora from the Mediterranean Sea and Brazil. We propose the transfer of Gymnodinium gracile into the genus Balechina as B. gracilis comb. nov. These sequences constitute an independent lineage, clustering with numerous environmental sequences from polar to tropical waters. The widespread distribution, the high plasticity in size, shape and coloration and the difficulties in discerning the fine longitudinal striae have contributed to the description of numerous synonyms: Amphidinium vasculum, Balechina pachydermata (=Gymnodinium pachydermatum), Gymnodinium achromaticum, G. abbreviatum, G. amphora, G. dogielii, G. lohmannii (=G. roseum sensu Lohmann 1908), G. situla and Gyrodinium cuneatum (=G. gracile sensu Pouchet 1885).
    Description: F.G. was supported by the convention #2101893310 between CNRS INSU and the French Ministry of Ecology (MTES) for the implementation of the Monitoring Program of the European Marine Strategy Framework directive (MSFD) for pelagic habitats and the descriptor ‘biodiversity’. Samples were collected during the ECOPEL Manche 2018 spring and summer cruises (CNRS-LOG) onboard R/V "Antea" (IRD, Institut de Recherche pour le Développement) in the frame of the cited convention and the CPER ‘Hauts de France’ project MARCO supported by the French state, the ‘Hauts de France’ French Region and the European Regional Development Founds (ERDF).
    Keywords: Dinophyta ; naked Dinoflagellata ; Gymnodiniales ; new combination ; taxonomy ; molecular phylogenetics
    Repository Name: Woods Hole Open Access Server
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  • 85
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Reusch, S., Biswas, A., Hirst, W. G., & Reber, S. Affinity purification of label-free tubulins from xenopus egg extracts. STAR Protocols, 1(3), (2020): 100151, doi:10.1016/j.xpro.2020.100151.
    Description: Cytoplasmic extracts from unfertilized Xenopus eggs have made important contributions to our understanding of microtubule dynamics, spindle assembly, and scaling. Until recently, these in vitro studies relied on the use of heterologous tubulin. This protocol allows for the purification of physiologically relevant Xenopus tubulins in milligram yield, which are a complex mixture of isoforms with various post-translational modifications. The protocol is applicable to any cell or tissue of interest. For complete details on the use and execution of this protocol, please refer to Hirst et al. (2020).
    Description: This article was prompted by our stay at the Marine Biological Laboratory (MBL), Woods Hole, MA, in the summer of 2016 funded by the Princeton-Humboldt Strategic Partnership Grant together with the lab of Sabine Petry (Princeton University). We are grateful to the National Xenopus Resource (NXR) for supplying frogs. For mass spectrometry, we would like to acknowledge the assistance of Benno Kuropka and Chris Weise from the Core Facility BioSupraMol supported by the Deutsche Forschungsgemeinschaft (DFG). We thank the Protein Expression Purification and Characterization (PEPC) facility at the MPI-CBG; in particular, we thank Aliona Bogdanova and Barbara Borgonovo. We thank all former and current members of the Reber lab for discussions and helpful advice, in particular Christoph Hentschel and Soma Zsoter for technical assistance. S.R. acknowledges funding from the IRI Life Sciences (Humboldt-Universität zu Berlin, Excellence Initiative/DFG). W.H. was supported by the Alliance Berlin Canberra co-funded by a grant from the Deutsche Forschungsgemeinschaft (DFG) for the International Research Training Group (IRTG) 2290 and the Australian National University.
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  • 86
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sakinan, S., Lawson, G. L., Wiebe, P. H., Chu, D., & Copley, N. J. Accounting for seasonal and composition-related variability in acoustic material properties in estimating copepod and krill target strength. Limnology and Oceanography-Methods, 17, (2019): 607-625, doi: 10.1002/lom3.10336.
    Description: Estimation of abundance or biomass, using acoustic techniques requires knowledge of the frequency dependent acoustic backscatter characteristics, or target strength, of organisms. Target strength of zooplankton is typically estimated from physics‐based models that involve multiple parameters, notably including the acoustic material properties (i.e., the contrasts in density and sound speed between the animal and surrounding seawater). In this work, variability in the acoustic material properties of two zooplankton species in the Gulf of Maine, the copepod (Calanus finmarchicus) and krill (Meganyctiphanes norvegica), was investigated relative to changing season as well as, for the copepod, temperature and depth. Increases in the density and sound speed contrasts of these species from fall to spring were observed. Target strength predictions based on these measurements varied between fall and spring by 2‐3 dB in krill. Measurements were also conducted on C. finmarchicus lipid extract at changing temperature and pressure. The density contrast of the extract varied negatively with temperature, while the sound speed contrast changed by more than 10 % over the temperature and pressure ranges that the organism expected to occupy. C. finmarchicus target strength predictions showed that the combined effect of temperature and pressure can be significant (more than 10 dB) due to the varying response of lipids. The large vertical migration ranges and lipid accumulation characteristics of these species (e.g., the diapause behaviour of Calanus copepods) suggest that it is necessary for seasonal and environmental variability in material properties to be taken into account to achieve reliable measurements.
    Description: We thank Captain Ken Houtler and Mate Ian Hanley on the R/V Tioga for assistance at sea. Al Bradley kindly loaned and provided assistance with the pressure chamber. We would also like to thank Phil Alatalo and Taylor Crockford for their assistance with at‐sea sampling, Dave Kulis and Jennifer Johnson for their assistance in the laboratory, and Andone Lavery for advice and loaning of the data acquisition system. Special thanks to Alex Bergan for general logistics and overall support. Funding was provided by the WHOI Ocean Life Institute. S.S. was supported by TUBITAK 2219 ‐ International Postdoctoral Research Fellowship Program.
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  • 87
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Weber, L., Gonzalez-Diaz, P., Armenteros, M., & Apprill, A. The coral ecosphere: a unique coral reef habitat that fosters coral-microbial interactions. Limnology and Oceanography, 64(6), (2019): 2373-2388, doi: 10.1002/lno.11190.
    Description: Scleractinian corals are bathed in a sea of planktonic and particle‐associated microorganisms. The metabolic products of corals influence the growth and composition of microorganisms, but interactions between corals and seawater microorganisms are underexplored. We conducted a field‐based survey to compare the biomass, diversity, composition, and functional capacity of microorganisms in small‐volume seawater samples collected adjacent to five coral species with seawater collected 〉 1 m away from the reef substrate on the same reefs. Seawater collected close to corals generally harbored copiotrophic‐type bacteria and its bacterial and archaeal composition was influenced by coral species as well as the local reef environment. Trends in picoplankton abundances were variable and either increased or decreased away from coral colonies based on coral species and picoplankton functional group. Genes characteristic of surface‐attached and potentially virulent microbial lifestyles were enriched in near‐coral seawater compared to reef seawater. There was a prominent association between the coral Porites astreoides and the coral symbiont Endozoicomonas, suggesting recruitment and/or shedding of these cells into the surrounding seawater. This evidence extends our understanding of potential species‐specific and reef site‐influenced microbial interactions that occur between corals and microorganisms within this near‐coral seawater environment that we propose to call the “coral ecosphere.” Microbial interactions that occur within the coral ecosphere could influence recruitment of coral‐associated microorganisms and facilitate the transfer of coral metabolites into the microbial food web, thus fostering reef biogeochemical cycling and a linkage between corals and the water column.
    Description: This project was funded by the Dalio Foundation through the Dalio Ocean Initiative, which helped establish a new partnership between U.S. and Cuban scientists. Data analysis and manuscript preparation support was provided by NSF GRFP award to L. W. and NSF OCE‐1736288 to A. A. Special thanks to our colleague Alyson Santoro (University of California, Santa Barbara) for project advice and discussion, Fernando Bretos (The Ocean Foundation) for cruise conceptualization and organization, and Justin Ossolinski, Sean McNally, Thomas Lankiewicz, as well as the fellow scientists on the missions for field assistance. Thanks to the crew of the R/V Felipe Poey as well as the La Reina vessel and the Avalon diving center. We are grateful for Karen Selph of the University of Hawai‘i School of Ocean and Earth Science and Technology for training in flow cytometry methods and Chris Wright and the University of Illinois W. M. Keck Center for Comparative and Functional Genomics for sequencing support. We would also like to thank Greg Fournier, Elizabeth Kujawinski, and Stefan Sievert for comments on this manuscript.
    Repository Name: Woods Hole Open Access Server
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  • 88
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hunter-Cevera, K. R., Neubert, M. G., Olson, R. J., Shalapyonok, A., Solow, A. R., & Sosik, H. M. Seasons of Syn. Limnology and Oceanography. (2019), doi: 10.1002/lno.11374.
    Description: Synechococcus is a widespread and important marine primary producer. Time series provide critical information for identifying and understanding the factors that determine abundance patterns. Here, we present the results of analysis of a 16‐yr hourly time series of Synechococcus at the Martha's Vineyard Coastal Observatory, obtained with an automated, in situ flow cytometer. We focus on understanding seasonal abundance patterns by examining relationships between cell division rate, loss rate, cellular properties (e.g., cell volume, phycoerythrin fluorescence), and environmental variables (e.g., temperature, light). We find that the drivers of cell division vary with season; cells are temperature‐limited in winter and spring, but light‐limited in the fall. Losses to the population also vary with season. Our results lead to testable hypotheses about Synechococcus ecophysiology and a working framework for understanding the seasonal controls of Synechococcus cell abundance in a temperate coastal system.
    Description: We would like to thank E. T. Crockford, E. E. Peacock, J. Fredericks, Z. Sandwith, the MVCO Operations Team, divers of the WHOI diving program, and captain Houtler and first mate Hanley of the R/V Tioga for logistical support; S. Laney for assistance with radiometer data processing; and P. Henderson of the Woods Hole Oceanographic Institution (WHOI) Nutrient Analytical Facility for analytical support. This work was supported by U.S. NSF grants OCE‐0119915, OCE‐0530830, OCE‐1031256, OCE‐1655686, DEB‐1145017, and DEB‐1257545; NASA grants NNX11AF07G and NNX13AC98G; Gordon and Betty Moore Foundation grant GGA#934; the Investment in Science Fund, given primarily by WHOI Trustee and Corporation Members; Simons Foundation award 561126; National Defense Science and Engineering graduate fellowship from the U.S. Department of Defense, and the Hibbitt Early Career Fellowship at the Marine Biological Laboratory.
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  • 89
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bhatnagar, S., Cowley, E. S., Kopf, S. H., Pérez Castro, S., Kearney, S., Dawson, S. C., Hanselmann, K., & Ruff, S. E. Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom. Environmental Microbiome, 15(1),(2020): 3, doi:10.1186/s40793-019-0348-0.
    Description: Background: Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosystem releases hydrogen sulfide particularly upon physical disturbance, causing blooms of anoxygenic sulfur-oxidizing phototrophs. To study the habitat, microbial community structure, assembly and function we carried out in situ experiments investigating the bloom dynamics over time. Results: Phototrophic microbial mats and permanently or seasonally stratified water columns commonly contain multiple phototrophic lineages that coexist based on their light, oxygen and nutrient preferences. We describe similar coexistence patterns and ecological niches in estuarine planktonic blooms of phototrophs. The water column showed steep gradients of oxygen, pH, sulfate, sulfide, and salinity. The upper part of the bloom was dominated by aerobic phototrophic Cyanobacteria, the middle and lower parts by anoxygenic purple sulfur bacteria (Chromatiales) and green sulfur bacteria (Chlorobiales), respectively. We show stable coexistence of phototrophic lineages from five bacterial phyla and present metagenome-assembled genomes (MAGs) of two uncultured Chlorobaculum and Prosthecochloris species. In addition to genes involved in sulfur oxidation and photopigment biosynthesis the MAGs contained complete operons encoding for terminal oxidases. The metagenomes also contained numerous contigs affiliating with Microviridae viruses, potentially affecting Chlorobi. Our data suggest a short sulfur cycle within the bloom in which elemental sulfur produced by sulfide-oxidizing phototrophs is most likely reduced back to sulfide by Desulfuromonas sp. Conclusions: The release of sulfide creates a habitat selecting for anoxygenic sulfur-oxidizing phototrophs, which in turn create a niche for sulfur reducers. Strong syntrophism between these guilds apparently drives a short sulfur cycle that may explain the rapid development of the bloom. The fast growth and high biomass yield of Chlorobi-affiliated organisms implies that the studied lineages of green sulfur bacteria can thrive in hypoxic habitats. This oxygen tolerance is corroborated by oxidases found in MAGs of uncultured Chlorobi. The findings improve our understanding of the ecology and ecophysiology of anoxygenic phototrophs and their impact on the coupled biogeochemical cycles of sulfur and carbon.
    Description: This work was carried out at the Microbial Diversity summer course at the Marine Biological Laboratory in Woods Hole, MA. The course was supported by grants from National Aeronautics and Space Administration, the US Department of Energy, the Simons Foundation, the Beckman Foundation, and the Agouron Institute. Additional funding for SER was provided by the Marine Biological Laboratory.
    Keywords: Microbial succession ; Green sulfur bacteria ; Prosthecochloris ; Syntrophy ; Brackish coastal ecosystem ; Anoxygenic phototrophy ; Microviridae ; Sulfur cycling ; CRISPR-Cas ; Resilience
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  • 90
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2020. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 117(26), (2020): 14618-14621, doi:10.1073/pnas.2008009117.
    Description: Plastic pollution is one of the most visible and complex environmental issues today. Interested and concerned parties include researchers, governmental agencies, nongovernmental organizations, industry, media, and the general public. One key assumption behind the issue and the public outcry is that plastics last indefinitely in the environment, resulting in chronic exposure that harms animals and humans. But the data supporting this assumption are scant.
    Description: We thank Briana Prado, Cassia Armstrong, and Anna Walsh for their help with the review, Kenneth Kostel, Katie Linehan, Daniel Ward, and Rose Cory for feedback on an earlier version of this piece, John Furfey for assistance with tracking down the original sources of the environmental lifetime estimates, and Natalie Reiner for help with Fig. 1. We acknowledge financial support from Woods Hole Oceanographic Institution (Woods Hole, MA) and the Seaver Institute (Los Angeles, CA).
    Description: 2020-12-10
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  • 91
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Addamo, A. M., Miller, K. J., Haussermann, V., Taviani, M., & Machordom, A. Global-scale genetic structure of a cosmopolitan cold-water coral species. Aquatic Conservation: Marine and Freshwater Ecosystems, (2020): 1-14, doi:10.1002/aqc.3421.
    Description: 1. When considering widely distributed marine organisms with low dispersal capabilities, there is often an implication that the distribution of cosmopolitan species is an artefact of taxonomy, constrained by the absence of characters for delimiting either sibling or cryptic species. Few studies have assessed the relationship among populations across the global range of the species' distribution, and the presence of oceanographic barriers that might influence gene flow among populations are underestimated. 2. In this study, evolutionary and ecological drivers of connectivity patterns have been inferred among populations of the cold‐water coral Desmophyllum dianthus, a common and widespread solitary scleractinian species, whose reproduction strategy and larval dispersal are still poorly unknown. 3. The genetic structure of D. dianthus was explored using 30 microsatellites in 347 specimens from 13 localities distributed in the Mediterranean Sea and Atlantic and Pacific Oceans. 4. Results clearly reveal genetically differentiated populations in the Northern and Southern Hemispheres (FST = 0.16, FSC = 0.01, FCT = 0.15, P‐values highly significant), and Chilean and New Zealand populations with independent genetic profiles. 5. Marine connectivity patterns at different spatial scales are discussed to characterize larval dispersal and gene flow through the Northern and Southern Hemispheres.
    Description: This research was supported by the Spanish Ministry of Science and Innovation (CGL2011‐23306), and EU CoCoNET—“Towards COast to COast NETworks of marine protected areas (from the shore to the high and deep sea), coupled with sea‐based wind energy potential”—from FP7‐KKBE of the European Commission (project ID: 287844). This scientific contribution commits to EESF Cocarde, Italian Flag Ritmare, and Region Apulia Biomap programmes. This is scientific publication no. 1888 Ismar‐CNR Bologna. Funding to VH was partially provided through Fondecyt project nos. 1131039 and 1161699. This is publication no. 179 of Huinay Scientific Field Station.
    Keywords: cold‐water corals ; cosmopolitan species ; gene flow ; larval dispersal ; microsatellite ; molecular ecology ; population structure
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  • 92
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ralston, D. K., Yellen, B., Woodruff, J. D., & Fernald, S. Turbidity hysteresis in an estuary and tidal river following an extreme discharge event. Geophysical Research Letters, 47(15), (2020): e2020GL088005, doi:10.1029/2020GL088005.
    Description: Nonlinear turbidity‐discharge relationships are explored in the context of sediment sourcing and event‐driven hysteresis using long‐term (≥12‐year) turbidity observations from the tidal freshwater and saline estuary of the Hudson River. At four locations spanning 175 km, turbidity generally increased with discharge but did not follow a constant log‐log dependence, in part due to event‐driven adjustments in sediment availability. Following major sediment inputs from extreme precipitation and discharge events in 2011, turbidity in the tidal river increased by 20–50% for a given discharge. The coherent shifts in the turbidity‐discharge relationship along the tidal river over the subsequent 2 years suggest that the 2011 events increased sediment availability for resuspension. In the saline estuary, changes in the sediment‐discharge relationship were less apparent after the high discharge events, indicating that greater background turbidity due to internal sources make event‐driven inputs less important in the saline estuary at interannual time scales.
    Description: This work was sponsored by the National Estuarine Research Reserve System Science Collaborative, funded by the National Oceanic and Atmospheric Administration and managed by the University of Michigan Water Center (NAI4NOS4190145), with additional support to Yellen and Woodruff from USGS Cooperative Agreement No. G19AC00091.
    Repository Name: Woods Hole Open Access Server
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  • 93
    Publication Date: 2022-12-12
    Description: Author Posting. © The Author(s), 2022. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in . Journal of Phycology (2022), https://doi.org/10.1111/jpy.13230.
    Description: The marine green alga Brilliantia kiribatiensis gen. et sp. nov. is described from samples collected from the coral reefs of the Southern Line Islands, Republic of Kiribati, Pacific Ocean. Phylogenetic analysis of sequences of the large- and small-subunit rDNA and the rDNA internal transcribed spacer region revealed that Brilliantia is a member of the Boodleaceae (Cladophorales), containing the genera Apjohnia, Boodlea, Cladophoropsis, Chamaedoris, Phyllodictyon, and Struvea. Within this clade it formed a distinct lineage, sister to Struvea elegans, but more distantly related to the bona fide Struvea species (including the type S. plumosa). Brilliantia differs from the other genera by having a very simple architecture forming upright, unbranched, single-celled filaments attached to the substratum by a rhizoidal mat. Cell division occurs by segregative cell division only at the onset of reproduction. Based on current sample collection, B. kiribatiensis seems to be largely restricted to the Southern Line Islands, although it was also observed on neighboring islands, including Orona Atoll in the Phoenix Islands of Kiribati, and the Rangiroa and Takapoto Atolls in the Tuamotus of French Polynesia. This discovery highlights the likeliness that there is still much biodiversity yet to be discovered from these remote and pristine reefs of the central Pacific.
    Description: National Geographic Society
    Description: 2022-12-12
    Keywords: 18S nuclear ribosomal DNA ; Chlorophyta ; Cladophorales ; Molecular phylogeny ; Siphonocladales ; Ulvophyceae
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 94
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Repeta, D. J. Unifying chemical and biological perspectives of carbon accumulation in the environment. Proceedings of the National Academy of Sciences of the United States of America, 118(11), (2021); e2100935118, https://doi.org/10.1073/pnas.2100935118.
    Description: Heterotrophic microorganisms are fiendishly clever at degrading all shapes and sizes of organic compounds to extract the energy they need to build biomass. Every year marine phytoplankton fix ∼50 billion tons of carbon dioxide into organic matter, and every year marine heterotrophs respire nearly all of this organic matter back to carbon dioxide (1). Nearly all, but not all. With each spin of this carbon cycle, a small amount of organic matter escapes respiration and becomes sequestered in seawater, sediments, and soils. Over time, this small “leak” in the system leads to the accumulation of a vast reservoir of carbon; some 5 × 1019 kg of organic matter are thought to be sequestered in sedimentary rocks (2). This carbon sequestration has immense consequences for life on Earth, as illustrated by the change in climate we are now experiencing due in part to the transfer of a minute portion of this inventory from geologic reservoirs into the atmosphere.
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  • 95
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sequeira, A. M. M., O'Toole, M., Keates, T. R., McDonnell, L. H., Braun, C. D., Hoenner, X., Jaine, F. R. A., Jonsen, I. D., Newman, P., Pye, J., Bograd, S. J., Hays, G. C., Hazen, E. L., Holland, M., Tsontos, V. M., Blight, C., Cagnacci, F., Davidson, S. C., Dettki, H., Duarte, C. M., Dunn, D. C., Eguiluz, V. M., Fedak, M., Gleiss, A. C., Hammerschlag, N., Hindell, M. A., Holland, K., Janekovic, I., McKinzie, M. K., Muelbert, M. M. C., Pattiaratchi, C., Rutz, C., Sims, D. W., Simmons, S. E., Townsend, B., Whoriskey, F., Woodward, B., Costa, D. P., Heupel, M. R., McMahon, C. R., Harcourt, R., & Weise, M. A standardisation framework for bio-logging data to advance ecological research and conservation. Methods in Ecology and Evolution, 12, (2021): 996–1007, https://doi.org/10.1111/2041-210X.13593.
    Description: 1. Bio-logging data obtained by tagging animals are key to addressing global conservation challenges. However, the many thousands of existing bio-logging datasets are not easily discoverable, universally comparable, nor readily accessible through existing repositories and across platforms, slowing down ecological research and effective management. A set of universal standards is needed to ensure discoverability, interoperability and effective translation of bio-logging data into research and management recommendations. 2. We propose a standardisation framework adhering to existing data principles (FAIR: Findable, Accessible, Interoperable and Reusable; and TRUST: Transparency, Responsibility, User focus, Sustainability and Technology) and involving the use of simple templates to create a data flow from manufacturers and researchers to compliant repositories, where automated procedures should be in place to prepare data availability into four standardised levels: (a) decoded raw data, (b) curated data, (c) interpolated data and (d) gridded data. Our framework allows for integration of simple tabular arrays (e.g. csv files) and creation of sharable and interoperable network Common Data Form (netCDF) files containing all the needed information for accuracy-of-use, rightful attribution (ensuring data providers keep ownership through the entire process) and data preservation security. 3. We show the standardisation benefits for all stakeholders involved, and illustrate the application of our framework by focusing on marine animals and by providing examples of the workflow across all data levels, including filled templates and code to process data between levels, as well as templates to prepare netCDF files ready for sharing. 4. Adoption of our framework will facilitate collection of Essential Ocean Variables (EOVs) in support of the Global Ocean Observing System (GOOS) and inter-governmental assessments (e.g. the World Ocean Assessment), and will provide a starting point for broader efforts to establish interoperable bio-logging data formats across all fields in animal ecology.
    Description: We are thankful to ONR and UWA OI for funding the workshop, and to ARC for DP210103091. A.M.M.S. was funded by a 2020 Pew Fellowship in Marine Conservation, and also supported by AIMS. C.R. was the recipient of a Radcliffe Fellowship at the Radcliffe Institute for Advanced Study, Harvard University.
    Keywords: bio-logging template ; data accessibility and interoperability ; data standards ; metadata templates ; movement ecology ; sensors ; telemetry ; tracking
    Repository Name: Woods Hole Open Access Server
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  • 96
    Publication Date: 2022-05-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, Mark L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S-M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A., Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M. Thomas P., Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J-H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O’Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D., Zhang, G. The Earth BioGenome Project 2020: starting the clock. Proceedings of the National Academy of Sciences of the United States of America, 119(4), (2022): e2115635118, https://doi.org/10.1073/pnas.2115635118.
    Description: November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP’s major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP.
    Repository Name: Woods Hole Open Access Server
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  • 97
    Publication Date: 2022-05-25
    Description: Ecological stability under environmental change is determined by both interspecific and intraspecific processes. Particularly for planktonic microorganisms, it is challenging to follow intraspecific dynamics over space and time. We propose a new method, microsatellite PoolSeq barcoding (MPB), for tracing allele frequency changes in protist populations. We successfully applied this method to experimental community incubations and field samples of the diatom Thalassiosira hyalina from the Arctic, a rapidly changing ecosystem. Validation of the method found compelling accuracy in comparison with established genotyping approaches within different diversity contexts. In experimental and environmental samples, we show that MPB can detect meaningful patterns of population dynamics, resolving allelic stability and shifts within a key diatom species in response to experimental treatments as well as different bloom phases and years. Through our novel MPB approach, we produced a large dataset of populations at different time‐points and locations with comparably little effort. Results like this can add insights into the roles of selection and plasticity in natural protist populations under stable experimental but also variable field conditions. Especially for organisms where genotype sampling remains challenging, MPB holds great potential to efficiently resolve eco‐evolutionary dynamics and to assess the mechanisms and limits of resilience to environmental stressors.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 98
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Barone, B., Nicholson, D., Ferron, S., Firing, E., & Karl, D. The estimation of gross oxygen production and community respiration from autonomous time-series measurements in the oligotrophic ocean. Limnology and Oceanography-Methods, 17, (2019): 650-664, doi: 10.1002/lom3.10340.
    Description: Diel variations in oxygen concentration have been extensively used to estimate rates of photosynthesis and respiration in productive freshwater and marine ecosystems. Recent improvements in optical oxygen sensors now enable us to use the same approach to estimate metabolic rates in the oligotrophic waters that cover most of the global ocean and for measurements collected by autonomous underwater vehicles. By building on previous methods, we propose a procedure to estimate photosynthesis and respiration from vertically resolved diel measurements of oxygen concentration. This procedure involves isolating the oxygen variation due to biological processes from the variation due to physical processes, and calculating metabolic rates from biogenic oxygen changes using linear least squares analysis. We tested our method on underwater glider observations from the surface layer of the North Pacific Subtropical Gyre where we estimated rates of gross oxygen production and community respiration both averaging 1.0 mmol O2 m−3 d−1, consistent with previous estimates from the same environment. Method uncertainty was computed as the standard deviation of the fitted parameters and averaged 0.6 and 0.5 mmol O2 m−3 d−1 for oxygen production and respiration, respectively. The variability of metabolic rates was larger than this uncertainty and we were able to discern covariation in the biological production and consumption of oxygen. The proposed method resolved variability on time scales of approximately 1 week. This resolution can be improved in several ways including by measuring turbulent mixing, increasing the number of measurements in the surface ocean, and adopting a Lagrangian approach during data collection.
    Description: This study would not have been possible without the skilled contribution of Steve Poulos (University of Hawaii) who directed glider operations including deployments, recoveries, and piloting. We thank Steve and all the other people involved in these activities including Sarah Searson, Gabe Foreman, Jim Burkitt, and Blake Watkins (University of Hawaii). We thank Henry Bittig (Laboratoire d'Océanographie de Villefranche) for his advice on the inverse filtering correction. We thank Saulo Soares, Andrei Natarov, and Kelvin Richards (University of Hawaii) for their comments on an early draft of this manuscript. We also thank Sam Wilson, Tara Clemente, Dan Sadler, Susan Curless, and Walt Deppe (University of Hawaii) for leading the oceanographic cruises used for glider deployments and recoveries. We thank the HOT‐SCOPE team for measuring the Winkler O2 concentration used for optode calibration. We thank Jesse M. Wilson for providing us the period of the CR measurements reported in Wilson et al. (2014). Finally, we thank captains and crews of R/V Kilo Moana and R/V Ka'imikai‐O‐Kanaloa, and the Ocean Technology Group of the University of Hawaii for their assistance at sea. Glider data used in this article are available on the ftp server of the School of Ocean and Earth Science and Technology of the University of Hawaii (ftp://ftp.soest.hawaii.edu/pilot/). Blended Sea Winds are distributed by NOAA‐NCDC and are available at https://www.ncdc.noaa.gov. Sea‐level pressure from the NCEP/NCAR reanalysis is available at https://www.esrl.noaa.gov/psd/data/gridded/data.ncep.reanalysis.surface.html. Satellite PAR is distributed by NASA and available at https://oceandata.sci.gsfc.nasa.gov. This research was supported by the 2015 Balzan Prize to D.M.K., the Simons Foundation (SCOPE award 329108 to D.M.K. and E.F. DeLong), the Gordon and Betty Moore Foundation (grant #3794 to D.M.K.), and the National Science Foundation through grants to C‐MORE (EF‐0424599 to D.M.K.) and HOT (OCE‐1260164 to D.M.K). D.N. was supported by NSF (OCE‐1129644) and an Independent Study Award from the Woods Hole Oceanographic Institution.
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  • 99
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gadol, O., Tibor, G., ten Brink, U., Hall, J. K., Groves-Gidney, G., Bar-Ann, G., Huebscher, C., & Makovsky, Y. Semi-automated bathymetric spectral decomposition delineates the impact of mass wasting on the morphological evolution of the continental slope, offshore Israel. Basin Research, (2019): 1-28, doi: 10.1111/bre.12420.
    Description: Understanding continental‐slope morphological evolution is essential for predicting basin deposition. However, separating the imprints and chronology of different seafloor shaping processes is difficult. This study explores the utility of bathymetric spectral decomposition for separating and characterizing the variety of interleaved seafloor imprints of mass wasting, and clarifying their role in the morphological evolution of the southeastern Mediterranean Sea passive‐margin slope. Bathymetric spectral decomposition, integrated with interpretation of seismic profiles, highlights the long‐term shape of the slope and separates the observed mass transport elements into several genetic groups: (1) a series of ~25 km wide, now‐buried slide scars and lobes; (2) slope‐parallel bathymetric scarps representing shallow faults; (3) slope‐perpendicular, open slope slide scars; (4) bathymetric roughness representing debris lobes; (5) slope‐confined gullies. Our results provide a multi‐scale view of the interplay between sediment transport, mass transport and shallow faulting in the evolution of the slope morphology. The base of the slope and focused disturbances are controlled by ~1 km deep salt retreat, and mimic the Messinian base of slope. The top of the open‐slope is delimited by faults, accommodating internal collapse of the margin. The now‐buried slides were slope‐confined and presumably cohesive, and mostly nucleated along the upper‐slope faults. Sediment accumulations, infilling the now‐buried scars, generated more recent open‐slope slides. These latter slides transported ~10 km3 of sediments, depositing a significant fraction (~3 m in average) of the sediments along the base of the studied slope during the past 〈 50 ka. South to north decrease in the volume of the open‐slope slides highlight their role in counterbalancing the northwards diminishing sediment supply and helping to maintain a long‐term steady‐state bathymetric profile. The latest phase slope‐confined gullies were presumably created by channelling of bottom currents into slide‐scar depressions, possibly establishing incipient canyon headword erosion.
    Description: Funding for this study was provided by the State of Israel Ministry of Science and Technology grant 3–9145. Omri Gadol studies were supported by the State of Israel Ministry of Energy grants program, the Dr. Moses Strauss Department of Marine Geosciences and the Hatter Department of Marine Technologies. We thank the Oil Commissioner Office, State of Israel Ministry of Energy, Delek Drilling, Adira Energy and Modiin Energy for data sharing and permitting; and Emerson‐Paradigm for sponsoring their software. We also thank Alexander Surdyaev, AMEL, for his constant support; and David Mosher, Glen Sherman and Jason Chaytor for their valuable reviews.
    Keywords: landslide volume ; Levant Basin ; mass transport complexes ; morphometric analyses ; semi‐automated mapping ; slope confined gullies ; submarine slide ; thin skin faulting
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  • 100
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Blakeslee, A. M. H., Manousaki, T., Vasileiadou, K., & Tepolt, C. K. An evolutionary perspective on marine invasions. Evolutionary Applications, 13, (2020): 479-485, doi:10.1111/eva.12906.
    Description: Species distributions are rapidly changing as human globalization increasingly moves organisms to novel environments. In marine systems, species introductions are the result of a number of anthropogenic mechanisms, notably shipping, aquaculture/mariculture, the pet and bait trades, and the creation of canals. Marine invasions are a global threat to human and non‐human populations alike and are often listed as one of the top conservation concerns worldwide, having ecological, evolutionary, and social ramifications. Evolutionary investigations of marine invasions can provide crucial insight into an introduced species’ potential impacts in its new range, including: physiological adaptation and behavioral changes to exploit new environments; changes in resident populations, community interactions, and ecosystems; and severe reductions in genetic diversity that may limit evolutionary potential in the introduced range. This special issue focuses on current research advances in the evolutionary biology of marine invasions and can be broadly classified into a few major avenues of research: the evolutionary history of invasive populations, post‐invasion reproductive changes, and the role of evolution in parasite introductions. Together, they demonstrate the value of investigating marine invasions from an evolutionary perspective, with benefits to both fundamental and applied evolutionary biology at local and broad scales.
    Description: We thank the organizers of Marine Evolution 2018 for bringing together a dynamic group of researchers working in all aspects of marine evolutionary biology and for facilitating the discussion of evolution in marine invasion. We also thank Evolutionary Applications for providing an avenue to share the results of this meeting more broadly and hope it will encourage continued research and discussion of this topic.
    Keywords: adaptation ; estuarine ; evolutionary history ; host–parasite interactions ; introduction ; non‐native ; reproduction ; sea
    Repository Name: Woods Hole Open Access Server
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