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  • Articles  (179,292)
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  • 1
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    Sub-seasonal thaw slump mass wasting is not consistently energy limited at the landscape scale (2017)
    Copernicus
    In:  EPIC3The Cryosphere Discussions, Copernicus, 2017, pp. 1-24
    Details
    Publication Date: 2017-08-30
    Description: Predicting future thaw slump activity requires a sound understanding of the atmospheric drivers and geomorphic controls on mass wasting across a range of time scales. On sub-seasonal time scales, sparse measurements indicate that mass wasting at active slumps is often limited by the energy available for melting ground ice, but other factors such as rainfall or the formation of an insulating veneer may also be relevant. To study the sub-seasonal drivers, we derive topographic changes from single-pass radar interferometric data acquired by the TanDEM-X satellite (12 m resolution). The high vertical precision (around 30 cm), frequent observations (11 days) and large coverage (5000 km2) allow us to track volume losses as drivers such as the available energy change during summer in two study regions. We find that thaw slumps in the Tuktoyaktuk coastlands, Canada, are not energy limited in June, as they undergo limited mass wasting (height loss of around 0 cm/day) despite the ample available energy, indicating the widespread presence of an insulating snow or debris veneer. Later in summer, height losses generally increase (around 3 cm/day), but they do so in distinct ways. For many slumps, mass wasting tracks the available energy, a temporal pattern that is also observed at coastal yedoma cliffs on the Bykovsky Peninsula, Russia. However, the other two common temporal trajectories are asynchronous with the available energy, as they track strong precipitation events or show a sudden speed-up in late August, respectively. The observed temporal patterns are poorly related to slump characteristics like the slump area. The contrasting temporal behaviour of nearby thaw slumps highlights the importance of complex local and temporally varying controls on mass wasting.
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  • 2
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    Oxygenated volatile organic carbon in the western Pacific convective centre: ocean cycling, air–sea gas exchange and atmospheric transport. (2017)
    Copernicus
    In:  EPIC3Atmos. Chem. Phys. Discuss., Copernicus, acp-20, ISSN: 1680-7375
    Details
    Publication Date: 2017-11-06
    Description: A suite of oxygenated volatile organic compounds (OVOCs – acetaldehyde, acetone, propanal, butanal and butanone) were measured concurrently in the surface water and atmosphere of the South China Sea and Sulu Sea in November 2011. A strong correlation was observed between all OVOC concentrations in the surface seawater along the entire cruise track, except for acetaldehyde, suggesting similar sources and sinks in the surface ocean. Additionally, several phytoplankton groups, such as haptophytes or pelagophytes, were also correlated to all OVOCs indicating that phytoplankton may be an important source for marine OVOCs in the South China and Sulu Seas. Humic and protein like fluorescent dissolved organic matter (FDOM) components seemed to be additional precursors for butanone and acetaldehyde. The atmospheric OVOC mixing ratios were relative high compared with literature values, suggesting the coastal region of North Borneo as a local hot spot for atmospheric OVOCs. The flux of atmospheric OVOCs was largely into the ocean for all 5 gases, with a few important exceptions near the coast of Borneo. The calculated amount of OVOCs entrained into the ocean seemed to be an important source of OVOCs to the surface ocean. When the fluxes were out of the ocean, marine OVOCs were found to be enough to control the local measured OVOC distribution in the atmosphere. Based on our model calculations, at least 0.4 ppb of marine derived acetone and butanone can reach the upper troposphere, where they may have an important influence on hydrogen oxide radical formation over the western Pacific Ocean.
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  • 3
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    The Extrapolar SWIFT model (version 1.0): fast stratospheric ozone chemistry for global climate models (2017)
    Copernicus
    In:  EPIC3Geoscientific Model Development, Copernicus, 11, pp. 753-769
    Details
    Publication Date: 2018-03-28
    Description: The Extrapolar SWIFT model is a fast ozone chemistry scheme for interactive calculation of the extrapolar stratospheric ozone layer in coupled general circulation models (GCMs). In contrast to the widely used prescribed ozone, the SWIFT ozone layer interacts with the model dynamics and can respond to atmospheric variability or climatological trends. The Extrapolar SWIFT model employs a repro-modelling approach, where algebraic functions are used to approximate the numerical output of a full stratospheric chemistry and transport model (ATLAS). The full model solves a coupled chemical differential equations system with 55 initial and boundary conditions (mixing ratio of various chemical species and atmospheric parameters). Hence the rate of change of ozone over 24  h is a function of 55 variables. Using covariances between these variables, we can find linear combinations in order to reduce the parameter space to the following nine basic variables: latitude, pressure altitude, temperature, local ozone column, mixing ratio of ozone and of the ozone depleting families (Cly, Bry, NOy and HOy). We will show that these 9 variables are sufficient to characterize the rate of change of ozone. An automated procedure fits a polynomial function of fourth degree to the rate of change of ozone obtained from several simulations with the ATLAS model. One polynomial function is determined per month which yields the rate of change of ozone over 24 h. A key aspect for the robustness of the Extrapolar SWIFT model is to include a wide range of stratospheric variability in the numerical output of the ATLAS model, also covering atmospheric states that will occur in a future climate (e.g. temperature and meridional circulation changes or reduction of stratospheric chlorine loading). For validation purposes, the Extrapolar SWIFT model has been integrated into the ATLAS model replacing the full stratospheric chemistry scheme. Simulations with SWIFT in ATLAS have proven that the systematic error is small and does not accumulate during the course of a simulation. In the context of a 10 year simulation, the ozone layer, simulated by SWIFT, shows a stable annual cycle, with inter-annual variations comparable to the ATLAS model. The application of Extrapolar SWIFT requires the evaluation of polynomial functions with 30–100 terms. Nowadays, computers can calculate such polynomial functions at thousands of model grid points in seconds. SWIFT provides the desired numerical efficiency and computes the ozone layer 104 times faster than the chemistry scheme in the ATLAS CTM.
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  • 4
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    Winter sea ice export from the Laptev Sea preconditions the local summer sea ice cover and fast ice decay (2017)
    Copernicus
    In:  EPIC3The Cryosphere, Copernicus, 11(5), pp. 2383-2391
    Details
    Publication Date: 2017-10-24
    Description: Ice retreat in the eastern Eurasian Arctic is a consequence of atmospheric and oceanic processes and regional feedback mechanisms acting on the ice cover, both in winter and summer. A correct representation of these processes in numerical models is important, since it will improve predictions of sea ice anomalies along the Northeast Passage and beyond. In this study, we highlight the importance of winter ice dynamics for local summer sea ice anomalies in thickness, volume and extent. By means of airborne sea ice thickness surveys made over pack ice areas in the south-eastern Laptev Sea, we show that years of offshore-directed sea ice transport have a thinning effect on the late-winter sea ice cover. To confirm the preconditioning effect of enhanced offshore advection in late winter on the summer sea ice cover, we perform a sensitivity study using a numerical model. Results verify that the preconditioning effect plays a bigger role for the regional ice extent. Furthermore, they indicate an increase in volume export from the Laptev Sea as a consequence of enhanced offshore advection, which has far-reaching consequences for the entire Arctic sea ice mass balance. Moreover we show that ice dynamics in winter not only preconditions local summer ice extent, but also accelerate fast-ice decay.
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  • 5
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    Deglacial Subarctic Pacific Oxygenation Changes: Causes and Links to Northern Hemisphere Climate (2018)
    Copernicus
    In:  EPIC3European Geosciences Union EGU General Assembly, Vienna, Austria, 2018-04-08-2018-04-13Copernicus
    Details
    Publication Date: 2018-06-18
    Description: We use a comprehensive suite of partially laminated high-resolution sediment cores from the Bering Sea, covering a depth transect from 1100 m to 2700 m to study deglacial surface ocean warming patterns, associated changes in biological productivity, oxygen minimum zone dynamics and continent-ocean links through Yukon river runoff. We apply a combination of planktic and benthic isotopes, x-ray fluorescence (XRF)-derived ele- mental ratios and a multi-proxy assessment of changes in upper ocean temperatures. Severe oxygen depletions occurred during the Bølling/Allerød (B/A) and early Holocene, which is in accordance with other locations in the North Pacific, especially the Alaska margin. Detailed analysis of the timing of lamination occurrence between the different sediment cores revealed that the onset of severe anoxia at the beginning of the B/A and early Holocene is a near-synchronous event, while the disappearance of laminations is a diachronic process. The deglacial Oxygen Minimum Zone(OMZ) strengthening is mainly driven by increased export production, visible in XRF-derived elemental ratios, and corresponding high accumulation rates of biogenic components. The export production in turn is a response to rising sea surface temperatures, decreased sea ice cover and increased thermal stratification, while a major nutrient source was the eastern continental shelf, which was flooded during the deglacial global sea level rise. It is discussed controversially whether oxygenation variations in the deglacial subarctic Pacific were coupled to changes in mid-depth water chemistry, or rather a response to physical processes like deep-intermediate ocean or mixed layer warming, or stratification changes. However, knowledge of the driving forcing mechanism for OMZ strengthening is of particular importance, as these are tightly coupled to the regional marine carbon budget, e.g. via the strength and efficiency of the biological pump. Here, our laminated sediments provided the opportunity to study ocean dynamics in exceptional detail, possible on decadal to annual timescales. Due to the correlation patterns of our records to the NGRIP oxygen isotope record through layer counts we presume that (i) the presence of laminations is tightly coupled to submillennial, short-term warm phases, especially during the Bølling-Allerød (B/A), (ii) that the laminations represent annual layered sediments (varves). The latter point in conjunction with our geochemical proxies strongly supports an atmospheric teleconnection between SE Asia, the North Atlantic and the North Pacific, with observed changes in mid-depth ocean dynamics occurring on fast, nearly decadal timescales. Thus, the Bering Sea OMZ is a highly sensitive system reacting almost instantaneously to small temperature changes and therefore has the potential to influence the global carbon budget on short timescales, in particular during episodes of rapidly warming climate.
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  • 6
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    Radiative impact of an extreme Arctic biomass-burning event (2018)
    Copernicus
    In:  EPIC3Atmos. Chem. Phys., Copernicus, 18, pp. 8829-8848
    Details
    Publication Date: 2020-03-05
    Description: The aim of the presented study was to investigate the impact on the radiation budget of a biomass-burning plume, transported from Alaska to the High Arctic region of Ny-Ålesund, Svalbard, in early July 2015. Since the mean aerosol optical depth increased by the factor of 10 above the average summer background values, this large aerosol load event is considered particularly exceptional in the last 25 years. In situ data with hygroscopic growth equations, as well as remote sensing measurements as inputs to radiative transfer models, were used, in order to estimate biases associated with (i) hygroscopicity, (ii) variability of single-scattering albedo profiles, and (iii) plane-parallel closure of the modelled atmosphere. A chemical weather model with satellite-derived biomass-burning emissions was applied to interpret the transport and transformation pathways. The provided MODTRAN radiative transfer model (RTM) simulations for the smoke event (14:00 9 July–11:30 11 July) resulted in a mean aerosol direct radiative forcing at the levels of −78.9 and −47.0 W m ^-2 at the surface and at the top of the atmosphere, respectively, for the mean value of aerosol optical depth equal to 0.64 at 550 nm. This corresponded to the average clear-sky direct radiative forcing of −43.3 W/m ^2, estimated by radiometer and model simulations at the surface. Ultimately, uncertainty associated with the plane-parallel atmosphere approximation altered results by about 2 W m^−2. Furthermore, model-derived aerosol direct radiative forcing efficiency reached on average −126 W m^−2/τ550 and −71 W^m−2/τ550 at the surface and at the top of the atmosphere, respectively. The heating rate, estimated at up to 1.8 K day^−1 inside the biomass-burning plume, implied vertical mixing with turbulent kinetic energy of 0.3 m^2s^−2
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  • 7
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    A synthesis dataset of permafrost-affected soil thermal conditions for Alaska, USA (2018)
    Copernicus
    In:  EPIC3Earth System Science Data, Copernicus, 10(4), pp. 2311-2328, ISSN: 1866-3516
    Details
    Publication Date: 2020-09-06
    Description: Recent observations of near-surface soil temperatures over the circumpolar Arctic show accelerated warming of permafrost-affected soils. The availability of a comprehensive near-surface permafrost and active layer dataset is critical to better understanding climate impacts and to constraining permafrost thermal conditions and its spatial distribution in land system models. We compiled a soil temperature dataset from 72 monitoring stations in Alaska using data collected by the US Geological Survey, the National Park Service, and the University of Alaska Fairbanks permafrost monitoring networks. The array of monitoring stations spans a large range of latitudes from 60.9 to 71.3 N and elevations from near sea level to~ 1300 m, comprising tundra and boreal forest regions. This dataset consists of monthly ground temperatures at depths up to 1 m, volumetric soil water content, snow depth, and air temperature during 1997–2016. These data have been quality controlled in collection and processing. Meanwhile, we implemented data harmonization evaluation for the processed dataset. The final product (PF-AK, v0. 1) is available at the Arctic Data Center (https://doi. org/10.18739/A2KG55).
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  • 8
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    Scaling-up permafrost thermal measurements in western Alaska using an ecotype approach (2016)
    Copernicus
    In:  EPIC3The Cryosphere, Copernicus, 10(5), pp. 2517-2532, ISSN: 1994-0424
    Details
    Publication Date: 2020-09-06
    Description: Permafrost temperatures are increasing in Alaska due to climate change and in some cases permafrost is thawing and degrading. In areas where degradation has already occurred the effects can be dramatic, resulting in changing ecosystems, carbon release, and damage to infrastructure. However, in many areas we lack baseline data, such as subsurface temperatures, needed to assess future changes and potential risk areas. Besides climate, the physical properties of the vegetation cover and subsurface material have a major influence on the thermal state of permafrost. These properties are often directly related to the type of ecosystem overlaying permafrost. In this paper we demonstrate that classifying the landscape into general ecotypes is an effective way to scale up permafrost thermal data collected from field monitoring sites. Additionally, we find that within some ecotypes the absence of a moss layer is indicative of the absence of near-surface permafrost. As a proof of concept, we used the ground temperature data collected from the field sites to recode an ecotype land cover map into a map of mean annual ground temperature ranges at 1 m depth based on analysis and clustering of observed thermal regimes. The map should be useful for decision making with respect to land use and understanding how the landscape might change under future climate scenarios.
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  • 9
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    Antarctic climate variability on regional and continental scales over the last 2000 years (2017)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 13(11), pp. 1609-1634, ISSN: 1814-9332
    Details
    Publication Date: 2017-12-19
    Description: Climate trends in the Antarctic region remain poorly characterized, owing to the brevity and scarcity of direct climate observations and the large magnitude of interannual to decadal-scale climate variability. Here, within the framework of the PAGES Antarctica2k working group, we build an enlarged database of ice core water stable isotope records from Antarctica, consisting of 112 records. We produce both unweighted and weighted isotopic (δ18O) composites and temperature reconstructions since 0 CE, binned at 5- and 10-year resolution, for seven climatically distinct regions covering the Antarctic continent. Following earlier work of the Antarctica2k working group, we also produce composites and reconstructions for the broader regions of East Antarctica, West Antarctica and the whole continent. We use three methods for our temperature reconstructions: (i) a temperature scaling based on the δ18O–temperature relationship output from an ECHAM5-wiso model simulation nudged to ERA-Interim atmospheric reanalyses from 1979 to 2013, and adjusted for the West Antarctic Ice Sheet region to borehole temperature data, (ii) a temperature scaling of the isotopic normalized anomalies to the variance of the regional reanalysis temperature and (iii) a composite-plus-scaling approach used in a previous continent-scale reconstruction of Antarctic temperature since 1 CE but applied to the new Antarctic ice core database. Our new reconstructions confirm a significant cooling trend from 0 to 1900 CE across all Antarctic regions where records extend back into the 1st millennium, with the exception of the Wilkes Land coast and Weddell Sea coast regions. Within this long-term cooling trend from 0 to 1900 CE, we find that the warmest period occurs between 300 and 1000 CE, and the coldest interval occurs from 1200 to 1900 CE. Since 1900 CE, significant warming trends are identified for the West Antarctic Ice Sheet, the Dronning Maud Land coast and the Antarctic Peninsula regions, and these trends are robust across the distribution of records that contribute to the unweighted isotopic composites and also significant in the weighted temperature reconstructions. Only for the Antarctic Peninsula is this most recent century-scale trend unusual in the context of natural variability over the last 2000 years. However, projected warming of the Antarctic continent during the 21st century may soon see significant and unusual warming develop across other parts of the Antarctic continent. The extended Antarctica2k ice core isotope database developed by this working group opens up many avenues for developing a deeper understanding of the response of Antarctic climate to natural and anthropogenic climate forcings. The first long-term quantification of regional climate in Antarctica presented herein is a basis for data–model comparison and assessments of past, present and future driving factors of Antarctic climate.
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  • 10
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    Arctic Ocean CO2 uptake: an improved multiyear estimate of the air–sea CO2 flux incorporating chlorophyll a concentrations (2018)
    Copernicus
    In:  EPIC3Biogeosciences, Copernicus, 15(6), pp. 1643-1661, ISSN: 1726-4189
    Details
    Publication Date: 2018-04-05
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  • 11
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    Estimates of late Cenozoic climate change relevant to Earth surface processes in tectonically active orogens (2018)
    Copernicus
    In:  EPIC3Earth Surface Dynamics, Copernicus, 6(2), pp. 271-301, ISSN: 2196-632X
    Details
    Publication Date: 2018-04-16
    Description: The denudation history of active orogens is often interpreted in the context of modern climate gradients. Here we address the validity of this approach and ask what are the spatial and temporal variations in palaeoclimate for a latitudinally diverse range of active orogens? We do this using high-resolution (T159, ca. 80 × 80 km at the Equator) palaeoclimate simulations from the ECHAM5 global atmospheric general circulation model and a statistical cluster analysis of climate over different orogens (Andes, Himalayas, SE Alaska, Pacific NW USA). Time periods and boundary conditions considered include the Pliocene (PLIO, ∼3Ma), the Last Glacial Maximum (LGM, ∼21ka), mid-Holocene (MH, ∼6ka), and pre-industrial (PI, reference year 1850). The regional simulated climates of each orogen are described by means of cluster analyses based on the variability in precipitation, 2 m air temperature, the intra-annual amplitude of these values, and monsoonal wind speeds where appropriate. Results indicate the largest differences in the PI climate existed for the LGM and PLIO climates in the form of widespread cooling and reduced precipitation in the LGM and warming and enhanced precipitation during the PLIO. The LGM climate shows the largest deviation in annual precipitation from the PI climate and shows enhanced precipitation in the temperate Andes and coastal regions for both SE Alaska and the US Pacific Northwest. Furthermore, LGM precipitation is reduced in the western Himalayas and enhanced in the eastern Himalayas, resulting in a shift of the wettest regional climates eastward along the orogen. The cluster-analysis results also suggest more climatic variability across latitudes east of the Andes in the PLIO climate than in other time slice experiments conducted here. Taken together, these results highlight significant changes in late Cenozoic regional climatology over the last ∼3Myr. Comparison of simulated climate with proxy-based reconstructions for the MH and LGM reveal satisfactory to good performance of the model in reproducing precipitation changes, although in some cases discrepancies between neighbouring proxy observations highlight contradictions between proxy observations themselves. Finally, we document regions where the largest magnitudes of late Cenozoic changes in precipitation and temperature occur and offer the highest potential for future observational studies that quantify the impact of climate change on denudation and weathering rates.
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  • 12
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    Moisture transport and Antarctic sea ice: austral spring 2016 event (2018)
    Copernicus
    In:  EPIC3Earth System Dynamics, Copernicus, 9(3), pp. 939-954, ISSN: 2190-4979
    Details
    Publication Date: 2018-07-09
    Description: In austral spring 2016 the Antarctic region experienced anomalous sea ice retreat in all sectors, with sea ice extent in October and November 2016 being the lowest in the Southern Hemisphere over the observational period (1979–present). The extreme sea ice retreat was accompanied by widespread warming along the coastal areas as well as in the interior of the Antarctic continent. This exceptional event occurred along with a strong negative phase of the Southern Annular Mode (SAM) and the moistest and warmest spring on record, over large areas covering the Indian Ocean, the Ross Sea and the Weddell Sea. In October 2016, the positive anomalies of the totally integrated water vapor (IWV) and 2 m air temperature (T2m) over the Indian Ocean, western Pacific, Bellingshausen Sea and southern part of Ross Sea were unprecedented in the last 39 years. In October and November 2016, when the largest magnitude of negative daily sea ice concentration anomalies was observed, repeated episodes of poleward advection of warm and moist air took place. These results suggest the importance of moist and warm air intrusions into the Antarctic region as one of the main contributors to this exceptional sea ice retreat event.
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  • 13
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    Promising Oldest Ice sites in East Antarctica based on thermodynamical modelling (2018)
    Copernicus
    In:  EPIC3The Cryosphere Discussions, Copernicus, pp. 1-22, ISSN: 1994-0440
    Details
    Publication Date: 2018-08-20
    Description: To resolve the mechanisms behind the major climate reorganisation which occurred between 0.9 and 1.2Ma, the recovery of a suitable 1.5 million-year-old ice core is fundamental. The quest for such an Oldest Ice core requires a number of key boundary conditions, of which the poorly known basal geothermal heat flux (GHF) is lacking. We use a transient thermodynamical 1D vertical model that solves for the rate of change of temperature in the vertical, with surface temperature and modelled GHF as boundary conditions. For each point on the ice sheet, the model is forced with variations in atmospheric conditions over the last 2Ma, and modelled ice-thickness variations. The process is repeated for a range of GHF values to determine the value of GHF that marks the limit between frozen and melting conditions over the whole ice sheet, taking into account 2Ma of climate history. These threshold values of GHF are statistically compared to existing GHF data sets. The new probabilistic GHF fields obtained for the ice sheet thus provide the missing boundary conditions in the search for Oldest Ice. High spatial resolution radar data are examined locally in the Dome Fuji and Dome C regions, as these represent the ice core community's primary drilling sites. GHF, bedrock variability, ice thickness and other essential criteria combined highlight a dozen major potential Oldest Ice sites in the vicinity of Dome Fuji and Dome C, where GHF allows for Oldest Ice.
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  • 14
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    Water stable isotope spatio-temporal variability in Antarctica in 1960–2013: observations and simulations from the ECHAM5-wiso atmospheric general circulation model (2018)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 14(6), pp. 923-946, ISSN: 1814-9332
    Details
    Publication Date: 2018-09-10
    Description: Polar ice core water isotope records are commonly used to infer past changes in Antarctic temperature, motivating an improved understanding and quantification of the temporal relationship between δ18O and temperature. This can be achieved using simulations performed by atmospheric general circulation models equipped with water stable isotopes. Here, we evaluate the skills of the high-resolution water-isotope-enabled atmospheric general circulation model ECHAM5-wiso (the European Centre Hamburg Model) nudged to European Centre for Medium-Range Weather Forecasts (ECMWF) reanalysis using simulations covering the period 1960–2013 over the Antarctic continent. We compare model outputs with field data, first with a focus on regional climate variables and second on water stable isotopes, using our updated dataset of water stable isotope measurements from precipitation, snow, and firn–ice core samples. ECHAM5-wiso simulates a large increase in temperature from 1978 to 1979, possibly caused by a discontinuity in the European Reanalyses (ERA) linked to the assimilation of remote sensing data starting in 1979. Although some model–data mismatches are observed, the (precipitation minus evaporation) outputs are found to be realistic products for surface mass balance. A warm model bias over central East Antarctica and a cold model bias over coastal regions explain first-order δ18O model biases by too strong isotopic depletion on coastal areas and underestimated depletion inland. At the second order, despite these biases, ECHAM5-wiso correctly captures the observed spatial patterns of deuterium excess. The results of model–data comparisons for the inter-annual δ18O standard deviation difer when using precipitation or ice core data. Further studies should explore the importance of deposition and post-deposition processes affecting ice core signals and not resolved in the model. These results build trust in the use of ECHAM5-wiso outputs to investigate the spatial, seasonal, and inter-annual δ18O–temperature relationships. We thus make the first Antarctica-wide synthesis of prior results. First, we show that local spatial or seasonal slopes are not a correct surrogate for inter-annual temporal slopes, leading to the conclusion that the same isotope–temperature slope cannot be applied for the climatic interpretation of Antarctic ice core for all timescales. Finally, we explore the phasing between the seasonal cycles of deuterium excess and δ18O as a source of information on changes in moisture sources affecting the δ18O–temperature relationship. The few available records and ECHAM5-wiso show different phase relationships in coastal, intermediate, and central regions. This work evaluates the use of the ECHAM5-wiso model as a tool for the investigation of water stable isotopes in Antarctic precipitation and calls for extended studies to improve our understanding of such proxies.
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  • 15
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    Solar and volcanic forcing of North Atlantic climate inferred from a process-based reconstruction (2018)
    Copernicus
    In:  EPIC3Climate of the Past, Copernicus, 14(8), pp. 1179-1194, ISSN: 1814-9332
    Details
    Publication Date: 2018-09-10
    Description: The effect of external forcings on atmospheric circulation is debated. Due to the short observational period, the analysis of the role of external forcings is hampered, making it difficult to assess the sensitivity of atmospheric circulation to external forcings, as well as persistence of the effects. In observations, the average response to tropical volcanic eruptions is a positive North Atlantic Oscillation (NAO) during the following winter. However, past major tropical eruptions exceeding the magnitude of eruptions during the instrumental era could have had more lasting effects. Decadal NAO variability has been suggested to follow the 11-year solar cycle, and linkages have been made between grand solar minima and negative NAO. However, the solar link to NAO found by modeling studies is not unequivocally supported by reconstructions, and is not consistently present in observations for the 20th century. Here we present a reconstruction of atmospheric winter circulation for the North Atlantic region covering the period 1241–1970 CE. Based on seasonally resolved Greenland ice core records and a 1200-year-long simulation with an isotope-enabled climate model, we reconstruct sea level pressure and temperature by matching the spatiotemporal variability in the modeled isotopic composition to that of the ice cores. This method allows us to capture the primary (NAO) and secondary mode (Eastern Atlantic Pattern) of atmospheric circulation in the North Atlantic region, while, contrary to previous reconstructions, preserving the amplitude of observed year-to-year atmospheric variability. Our results show five winters of positive NAO on average following major tropical volcanic eruptions, which is more persistent than previously suggested. In response to decadal minima of solar activity we find a high-pressure anomaly over northern Europe, while a reinforced opposite response in pressure emerges with a 5-year time lag. On centennial timescales we observe a similar response of circulation as for the 5-year time-lagged response, with a high-pressure anomaly across North America and south of Greenland. This response to solar forcing is correlated to the second mode of atmospheric circulation, the Eastern Atlantic Pattern. The response could be due to an increase in blocking frequency, possibly linked to a weakening of the subpolar gyre. The long-term anomalies of temperature during solar minima shows cooling across Greenland, Iceland and western Europe, resembling the cooling pattern during the Little Ice Age (1450–1850 CE). While our results show significant correlation between solar forcing and the secondary circulation pattern on decadal (r = 0.29, p 〈 0.01) and centennial timescales (r = 0.6, p 〈 0.01), we find no consistent relationship between solar forcing and NAO. We conclude that solar and volcanic forcing impacts different modes of our reconstructed atmospheric circulation, which can aid in separating the regional effects of forcings and understanding the underlying mechanisms.
    Repository Name: EPIC Alfred Wegener Institut
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    Global Carbon Budget 2018 (2018)
    Copernicus
    In:  EPIC3Earth System Science Data Discussions, Copernicus, pp. 1-3, ISSN: 1866-3591
    Details
    Publication Date: 2018-10-08
    Repository Name: EPIC Alfred Wegener Institut
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    A modelling assessment from glacial North Pacific deep water to modern intermediate water formation process (2018)
    Copernicus
    In:  EPIC3European Geosciences Union (EGU) General Assembly, Vienna, Austria, 2018-04-08-2018-04-13Copernicus
    Details
    Publication Date: 2018-06-18
    Description: North Pacific Intermediate water (NPIW) is a dominant water mass controlling ∼400-1200m depth North Pacific Ocean, meanwhile there is a cessation of North Pacific deep water (NPDW) formation in in modern observations. In contrast, paleoceanographic evidences have recorded NPDW formations during last glacial periods. This sug- gests either a rapid or gradual shutting down process of NPDW formation during the last deglaciation. Here, we use an Earth System Model to diagnose the physical and corresponding biogeochemical evolutions in the North Pacific Ocean before and after the last deglaciation, as well as potential changes during rapid climate shifts of the last deglaciation. Linked to different background climate conditions and varying Atlantic Meridional Over- turning Circulation states, we characterize the modelled NPIW and NPDW changes and builds up linkages to marine records. Our results further develop our understanding about the deglacial switch from NPDW to modern NPIW-only formation process.
    Repository Name: EPIC Alfred Wegener Institut
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    A global monthly climatology of total alkalinity: a neural network approach (2018)
    Copernicus
    In:  EPIC3Earth System Science Data Discussions, Copernicus, pp. 1-31, ISSN: 1866-3591
    Details
    Publication Date: 2018-10-29
    Repository Name: EPIC Alfred Wegener Institut
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  • 19
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    Presence of rapidly degrading permafrost plateaus in south-central Alaska (2016)
    Copernicus
    In:  EPIC3The Cryosphere, Copernicus, 10(6), pp. 2673-2692, ISSN: 1994-0424
    Details
    Publication Date: 2016-11-16
    Description: Permafrost presence is determined by a complex interaction of climatic, topographic, and ecological conditions operating over long time scales. In particular, vegetation and organic layer characteristics may act to protect permafrost in regions with a mean annual air temperature (MAAT) above 0°C. In this study, we document the presence of residual permafrost plateaus in the western Kenai Peninsula lowlands of south-central Alaska, a region with a MAAT of 1.5+/-1 °C (1981–2010). Continuous ground temperature measurements between 16 September 2012 and 15 September 2015, using calibrated thermistor strings, documented the presence of warm permafrost (-0.04 to -0.08 °C). Field measurements (probing) on several plateau features during the fall of 2015 showed that the depth to the permafrost table averaged 1.48m but at some locations was as shallow as 0.53 m. Late winter surveys (augering, coring, and GPR) in 2016 showed that the average seasonally frozen ground thickness was 0.45 m, overlying a talik above the permafrost table. Measured permafrost thickness ranged from 0.33 to 〉6.90 m. Manual interpretation of historic aerial photography acquired in 1950 indicates that residual permafrost plateaus covered 920 ha as mapped across portions of four wetland complexes encompassing 4810 ha. However, between 1950 and ca. 2010, permafrost plateau extent decreased by 60.0 %, with lateral feature degradation accounting for 85.0% of the reduction in area. Permafrost loss on the Kenai Peninsula is likely associated with a warming climate, wildfires that remove the protective forest and organic layer cover, groundwater flow at depth, and lateral heat transfer from wetland surface waters in the summer. Better understanding the resilience and vulnerability of ecosystem-protected permafrost is critical for mapping and predicting future permafrost extent and degradation across all permafrost regions that are currently warming. Further work should focus on reconstructing permafrost history in south-central Alaska as well as additional contemporary observations of these ecosystem-protected permafrost sites south of the regions with relatively stable permafrost.
    Repository Name: EPIC Alfred Wegener Institut
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  • 20
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    Three-dimensional imaging from laser scanner, photogrammetric and acoustic non-destructive techniques in the characterization of stone building materials (2018)
    Copernicus
    Details
    Publication Date: 2019-03-26
    Description: Abstract. When combined, the three-dimensional imaging of different physical properties of architectural monumen- tal structures acquired through different methodologies can highlight with efficiency the characteristics of the stone building materials. In this work, we compound high res- olution Digital Color Images (DCI) and Terrestrial Laser Scanner (TLS) data for a dense 3-D reconstruction of an ancient pillar in a nineteenth century building in the town of Cagliari, Italy. The TLS technique was supported by a digital photogrammetry survey in order to obtain a natural color texturized 3-D model of the studied pillar. Geometri- cal anomaly maps showing interesting analogies were com- puted both from the 3-D model derived from the TLS ap- plication and from the high resolution 3-D model detected with the photogrammetry. Starting from the 3-D reconstruc- tion from previous techniques, an acoustic tomography in a sector of prior interest of the investigated architectural ele- ment was planned and carried out. The ultrasonic tomogra- phy proved to be an effective tool for detecting internal decay or defects, locating the position of the anomalies and estimat- ing their sizes, shapes, and characteristics in terms of elastic- mechanical properties. Finally, the combination of geophysi- cal and petrographical data sets represents a powerful method for understanding the quality of the building stone materials in the shallow and inner parts of the investigated architectural structures.
    Description: Regione Autonoma della Sardegna (RAS) (Sardinian Autonomous Region), Regional Law 7th August 2007, no. 7, Promotion of scientific research and technological innovation in Sardinia (Italy).
    Description: Published
    Description: 57-62
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Architectural monumental structures ; Structural Diagnosis ; Digital Color Images ; 3D Terrestrial Laser Scanner ; Acoustic tomography ; Petrographical data ; 3D Modeling ; Cultural Heritage ; Architectural Elements ND Diagnosis
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    The Italian National Seismic Network and the earthquake and tsunami monitoring and surveillance systems (2018)
    Copernicus
    Details
    Publication Date: 2018-03-12
    Description: The Istituto Nazionale di Geofisica e Vulcanologia runs the Italian National Seismic Network (about 400 stations, seismometers, accelerometers and GPS antennas) and other networks at national scale for monitoring earthquakes and tsunami as a part of the National Civil Protection System coordinated by the Italian Department of Civil Protection. This work summarises the acquisition and the distribution of the data and the analysis that are carried out for seismic surveillance and tsunami alert.
    Description: INGV and DPC
    Description: Published
    Description: 31-38
    Description: 1IT. Reti di monitoraggio
    Description: N/A or not JCR
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 22
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    Annual Acoustic Presence of Fin Whale (Balaenoptera physalus) Offshore Eastern Sicily, Central Mediterranean Sea (2016)
    Public Library of Science
    Details
    Publication Date: 2017-04-04
    Description: In recent years, an increasing number of surveys have definitively confirmed the seasonal presence of fin whales (Balaenoptera physalus) in highly productive regions of the Mediterranean Sea. Despite this, very little is yet known about the routes that the species seasonally follows within the Mediterranean basin and, particularly, in the Ionian area. The present study assesses for the first time fin whale acoustic presence offshore Eastern Sicily (Ionian Sea), throughout the processing of about 10 months of continuous acoustic monitoring. The recording of fin whale vocalizations was made possible by the cabled deep-sea multidisciplinary observatory, “NEMO-SN1”, deployed 25 km off the Catania harbor at a depth of about 2,100 meters. NEMO-SN1 is an operational node of the European Multidisciplinary Seafloor and water-column Observatory (EMSO) Research Infrastructure. The observatory was equipped with a low-frequency hydrophone (bandwidth: 0.05 Hz–1 kHz, sampling rate: 2 kHz) which continuously acquired data from July 2012 to May 2013. About 7,200 hours of acoustic data were analyzed by means of spectrogram display. Calls with the typical structure and patterns associated to the Mediterranean fin whale population were identified and monitored in the area for the first time. Furthermore, a background noise analysis within the fin whale communication frequency band (17.9–22.5 Hz) was conducted to investigate possible detection-masking effects. The study confirms the hypothesis that fin whales are present in the Ionian Sea throughout all seasons, with peaks in call detection rate during spring and summer months. The analysis also demonstrates that calls were more frequently detected in low background noise conditions. Further analysis will be performed to understand whether observed levels of noise limit the acoustic detection of the fin whales vocalizations, or whether the animals vocalize less in the presence of high background noise.
    Description: Published
    Description: e0141838
    Description: 3A. Ambiente Marino
    Description: JCR Journal
    Description: open
    Keywords: Whales ; Bioacoustics ; Background noise (acoustics) ; Acoustic signals ; Sperm whales ; Vocalization ; Acoustics ; Data acquisition ; 03. Hydrosphere::03.01. General::03.01.08. Instruments and techniques ; 03. Hydrosphere::03.02. Hydrology::03.02.04. Measurements and monitoring ; 03. Hydrosphere::03.02. Hydrology::03.02.07. Instruments and techniques ; 03. Hydrosphere::03.04. Chemical and biological::03.04.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 23
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    Presence of rapidly degrading permafrost plateaus in southcentral Alaska (2016)
    Copernicus
    In:  EPIC3The Cryosphere Discussions, Copernicus
    Details
    Publication Date: 2016-05-26
    Description: Permafrost presence is determined by a complex interaction of climatic, topographic, and ecological conditions operating over long time scales. In particular, vegetation and organic layer characteristics may act to protect permafrost in regions with a mean annual air temperature (MAAT) above 0 °C. In this study, we document the presence of residual permafrost plateaus on the western Kenai Peninsula lowlands of southcentral Alaska, a region with a MAAT of 1.5 ± 1 °C (1981 to 2010). Continuous ground temperature measurements between 16 September 2012 and 15 September 2015, using calibrated thermistor strings, documented the presence of warm permafrost (−0.04 to −0.08 °C). Field measurements (probing) on several plateau features during the fall of 2015 showed that the depth to the permafrost table averaged 1.48 m but was as shallow as 0.53 m. Late winter surveys (drilling, coring, and GPR) in 2016 showed that the average seasonally frozen ground thickness was 0.45 m, overlying a talik above the permafrost table. Measured permafrost thickness ranged from 0.33 to 〉 6.90 m. Manual interpretation of historic aerial photography acquired in 1950 indicates that residual permafrost plateaus covered 920 ha as mapped across portions of four wetland complexes encompassing 4810 ha. However, between 1950 and ca. 2010, permafrost plateau extent decreased by 60 %, with lateral feature degradation accounting for 85 % of the reduction in area. Permafrost loss on the Kenai Peninsula is likely associated with a warming climate, wildfires that remove the protective forest and organic layer cover, groundwater flow at depth, and lateral heat transfer from wetland surface waters in the summer. Better understanding the resilience and vulnerability of ecosystem-protected permafrost is critical for mapping and predicting future permafrost extent and degradation across all permafrost regions that are currently warming. Further work should focus on reconstructing permafrost history in southcentral Alaska as well as additional contemporary observations of these ecosystem-protected permafrost sites lying south of the regions with relatively stable permafrost.
    Repository Name: EPIC Alfred Wegener Institut
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    ESM-SnowMIP: assessing snow models and quantifying snow-related climate feedbacks (2018)
    Copernicus
    In:  EPIC3Geoscientific Model Development, Copernicus, 11(12), pp. 5027-5049, ISSN: 1991-9603
    Details
    Publication Date: 2018-12-14
    Description: This paper describes ESM-SnowMIP, an international coordinated modelling effort to evaluate current snow schemes, including snow schemes that are included in Earth system models, in a wide variety of settings against local and global observations. The project aims to identify crucial processes and characteristics that need to be improved in snow models in the context of local- and global-scale modelling. A further objective of ESM-SnowMIP is to better quantify snow-related feedbacks in the Earth system. Although it is not part of the sixth phase of the Coupled Model Intercomparison Project (CMIP6), ESM-SnowMIP is tightly linked to the CMIP6-endorsed Land Surface, Snow and Soil Moisture Model Intercomparison (LS3MIP).
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  • 25
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    TurtleCam : a “smart” autonomous underwater vehicle for investigating behaviors and habitats of sea turtles (2018)
    Frontiers Media
    Details
    Publication Date: 2018-05-08
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 90, doi:10.3389/fmars.2018.00090.
    Description: Sea turtles inhabiting coastal environments routinely encounter anthropogenic hazards, including fisheries, vessel traffic, pollution, dredging, and drilling. To support mitigation of potential threats, it is important to understand fine-scale sea turtle behaviors in a variety of habitats. Recent advancements in autonomous underwater vehicles (AUVs) now make it possible to directly observe and study the subsurface behaviors and habitats of marine megafauna, including sea turtles. Here, we describe a “smart” AUV capability developed to study free-swimming marine animals, and demonstrate the utility of this technology in a pilot study investigating the behaviors and habitat of leatherback turtles (Dermochelys coriacea). We used a Remote Environmental Monitoring UnitS (REMUS-100) AUV, designated “TurtleCam,” that was modified to locate, follow and film tagged turtles for up to 8 h while simultaneously collecting environmental data. The TurtleCam system consists of a 100-m depth rated vehicle outfitted with a circular Ultra-Short BaseLine receiver array for omni-directional tracking of a tagged animal via a custom transponder tag that we attached to the turtle with two suction cups. The AUV collects video with six high-definition cameras (five mounted in the vehicle nose and one mounted aft) and we added a camera to the animal-borne transponder tag to record behavior from the turtle's perspective. Since behavior is likely a response to habitat factors, we collected concurrent in situ oceanographic data (bathymetry, temperature, salinity, chlorophyll-a, turbidity, currents) along the turtle's track. We tested the TurtleCam system during 2016 and 2017 in a densely populated coastal region off Cape Cod, Massachusetts, USA, where foraging leatherbacks overlap with fixed fishing gear and concentrated commercial and recreational vessel traffic. Here we present example data from one leatherback turtle to demonstrate the utility of TurtleCam. The concurrent video, localization, depth and environmental data allowed us to characterize leatherback diving behavior, foraging ecology, and habitat use, and to assess how turtle behavior mediates risk to impacts from anthropogenic activities. Our study demonstrates that an AUV can successfully track and image leatherback turtles feeding in a coastal environment, resulting in novel observations of three-dimensional subsurface behaviors and habitat use, with implications for sea turtle management and conservation.
    Description: This research was funded by National Oceanic and Atmospheric Administration Grant #NA16NMF4720074 to the Massachusetts Division of Marine Fisheries under the Species Recovery Grants to States program. Additional funding was provided by Jean Tempel, Hydroid Inc., and over 100 Project WHOI donors.
    Keywords: Autonomous underwater vehicle AUV ; CTD ; Entanglement ; Habitat ; Foraging behavior ; Jellyfish ; Leatherback sea turtle ; Video camera
    Repository Name: Woods Hole Open Access Server
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    High grazing rates on cryptophyte algae in Chesapeake Bay (2018)
    Frontiers Media
    Details
    Publication Date: 2018-07-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 241, doi:10.3389/fmars.2018.00241.
    Description: Cryptophyte algae are globally distributed photosynthetic flagellates found in freshwater, estuarine, and neritic ecosystems. While cryptophytes can be highly abundant and are consumed by a wide variety of protistan predators, few studies have sought to quantify in situ grazing rates on their populations. Here we show that autumnal grazing rates on in situ communities of cryptophyte algae in Chesapeake Bay are high throughout the system, while growth rates, particularly in the lower bay, were low. Analysis of the genetic diversity of cryptophyte populations within dilution experiments suggests that microzooplankton may be selectively grazing the fastest-growing members of the population, which were generally Teleaulax spp. We also demonstrate that potential grazing rates of ciliates and dinoflagellates on fluorescently labeled (FL) Rhodomonas salina, Storeatula major, and Teleaulax amphioxeia can be high (up to 149 prey predator−1 d−1), and that a Gyrodinium sp. and Mesodinium rubrum could be selective grazers. Potential grazing was highest for heterotrophic dinoflagellates, but due to its abundance, M. rubrum also had a high overall impact. This study reveals that cryptophyte algae in Chesapeake Bay can experience extremely high grazing pressure from phagotrophic protists, and that this grazing likely shapes their community diversity.
    Description: The authors thank the National Science Foundation (OCE 1031718 and 1436169) for providing support for this research.
    Keywords: Cryptophytes ; Mixotrophy ; Grazing ; Chesapeake Bay ; Dinoflagellates ; Mesodinium rubrum
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    The amyloid precursor protein of Alzheimer’s disease clusters at the organelle/microtubule interface on organelles that bind microtubules in an ATP dependent manner (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0147808, doi:10.1371/journal.pone.0147808.
    Description: The amyloid precursor protein (APP) is a causal agent in the pathogenesis of Alzheimer’s disease and is a transmembrane protein that associates with membrane-limited organelles. APP has been shown to co-purify through immunoprecipitation with a kinesin light chain suggesting that APP may act as a trailer hitch linking kinesin to its intercellular cargo, however this hypothesis has been challenged. Previously, we identified an mRNA transcript that encodes a squid homolog of human APP770. The human and squid isoforms share 60% sequence identity and 76% sequence similarity within the cytoplasmic domain and share 15 of the final 19 amino acids at the C-terminus establishing this highly conserved domain as a functionally import segment of the APP molecule. Here, we study the distribution of squid APP in extruded axoplasm as well as in a well-characterized reconstituted organelle/microtubule preparation from the squid giant axon in which organelles bind microtubules and move towards the microtubule plus-ends. We find that APP associates with microtubules by confocal microscopy and co-purifies with KI-washed axoplasmic organelles by sucrose density gradient fractionation. By electron microscopy, APP clusters at a single focal point on the surfaces of organelles and localizes to the organelle/microtubule interface. In addition, the association of APP-organelles with microtubules is an ATP dependent process suggesting that the APP-organelles contain a microtubule-based motor protein. Although a direct kinesin/APP association remains controversial, the distribution of APP at the organelle/microtubule interface strongly suggests that APP-organelles have an orientation and that APP like the Alzheimer’s protein tau has a microtubule-based function.
    Description: Research reported in this publication was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20GM103430.
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    Influence of environmental variables on Gambierdiscus spp. (Dinophyceae) growth and distribution (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0153197, doi:10.1371/journal.pone.0153197.
    Description: Benthic dinoflagellates in the genus Gambierdiscus produce the ciguatoxin precursors responsible for the occurrence of ciguatera toxicity. The prevalence of ciguatera toxins in fish has been linked to the presence and distribution of toxin-producing species in coral reef ecosystems, which is largely determined by the presence of suitable benthic habitat and environmental conditions favorable for growth. Here using single factor experiments, we examined the effects of salinity, irradiance, and temperature on growth of 17 strains of Gambierdiscus representing eight species/phylotypes (G. belizeanus, G. caribaeus, G. carolinianus, G. carpenteri, G. pacificus, G. silvae, Gambierdiscus sp. type 4–5), most of which were established from either Marakei Island, Republic of Kiribati, or St. Thomas, United States Virgin Island (USVI). Comparable to prior studies, growth rates fell within the range of 0–0.48 divisions day-1. In the salinity and temperature studies, Gambierdiscus responded in a near Gaussian, non-linear manner typical for such studies, with optimal and suboptimal growth occurring in the range of salinities of 25 and 45 and 21.0 and 32.5°C. In the irradiance experiment, no mortality was observed; however, growth rates at 55μmol photons · m-2 · s-1 were lower than those at 110–400μmol photons · m-2 · s-1. At the extremes of the environmental conditions tested, growth rates were highly variable, evidenced by large coefficients of variability. However, significant differences in intraspecific growth rates were typically found only at optimal or near-optimal growth conditions. Polynomial regression analyses showed that maximum growth occurred at salinity and temperature levels of 30.1–38.5 and 23.8–29.2°C, respectively. Gambierdiscus growth patterns varied among species, and within individual species: G. belizeanus, G. caribaeus, G. carpenteri, and G. pacificus generally exhibited a wider range of tolerance to environmental conditions, which may explain their broad geographic distribution. In contrast, G. silvae and Gambierdiscus sp. types 4–5 all displayed a comparatively narrow range of tolerance to temperature, salinity, and irradiance.
    Description: This study was funded by the National Natural Science Foundation of China (41506137); Guangxi Natural Science Foundation (2015GXNSFCA139003), Centers for Disease Control and Prevention (U01 EH000421); USFDA (F223201000060C); NOAA NOS through the CiguaHAB program (Cooperative Agreement NA11NOS4780060, NA11NOS4780028); the Lana Vento Trust and VI-EPSCoR Program (NSF award # 346483 & 081441); and a System Fund from Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education (2014BGERLXT01). Support was also provided by the Woods Hole Center for Oceans and Human Health through National Science Foundation (NSF) Grant OCE-1314642, National Institute of Environmental Health Sciences (NIEHS) Grant 1-P01-ES021923-014, as well as the China Scholarship Council.
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    Comparative analysis of secretome profiles of manganese(II)-oxidizing Ascomycete fungi (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
    Description: Fungal secretomes contain a wide range of hydrolytic and oxidative enzymes, including cellulases, hemicellulases, pectinases, and lignin-degrading accessory enzymes, that synergistically drive litter decomposition in the environment. While secretome studies of model organisms such as Phanerochaete chrysosporium and Aspergillus species have greatly expanded our knowledge of these enzymes, few have extended secretome characterization to environmental isolates or conducted side-by-side comparisons of diverse species. Thus, the mechanisms of carbon degradation by many ubiquitous soil fungi remain poorly understood. Here we use a combination of LC-MS/MS, genomic, and bioinformatic analyses to characterize and compare the protein composition of the secretomes of four recently isolated, cosmopolitan, Mn(II)-oxidizing Ascomycetes (Alternaria alternata SRC1lrK2f, Stagonospora sp. SRC1lsM3a, Pyrenochaeta sp. DS3sAY3a, and Paraconiothyrium sporulosum AP3s5-JAC2a). We demonstrate that the organisms produce a rich yet functionally similar suite of extracellular enzymes, with species-specific differences in secretome composition arising from unique amino acid sequences rather than overall protein function. Furthermore, we identify not only a wide range of carbohydrate-active enzymes that can directly oxidize recalcitrant carbon, but also an impressive suite of redox-active accessory enzymes that suggests a role for Fenton-based hydroxyl radical formation in indirect, non-specific lignocellulose attack. Our findings highlight the diverse oxidative capacity of these environmental isolates and enhance our understanding of the role of filamentous Ascomycetes in carbon turnover in the environment.
    Description: This work was supported by the National Science Foundation (www.nsf.gov), grant numbers EAR-1249489 and CBET-1336496, both awarded to CMH. Personal support for CAZ was also provided by Harvard University (www.harvard.edu) and by a Ford Foundation (www.fordfoundation.org) Predoctoral Fellowship administered by the National Academies.
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    Potential impacts of offshore wind farms on North Sea stratification (2016)
    Public Library of Science
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0160830, doi:10.1371/journal.pone.0160830 .
    Description: Advances in offshore wind farm (OWF) technology have recently led to their construction in coastal waters that are deep enough to be seasonally stratified. As tidal currents move past the OWF foundation structures they generate a turbulent wake that will contribute to a mixing of the stratified water column. In this study we show that the mixing generated in this way may have a significant impact on the large-scale stratification of the German Bight region of the North Sea. This region is chosen as the focus of this study since the planning of OWFs is particularly widespread. Using a combination of idealised modelling and in situ measurements, we provide order-of-magnitude estimates of two important time scales that are key to understanding the impacts of OWFs: (i) a mixing time scale, describing how long a complete mixing of the stratification takes, and (ii) an advective time scale, quantifying for how long a water parcel is expected to undergo enhanced wind farm mixing. The results are especially sensitive to both the drag coefficient and type of foundation structure, as well as the evolution of the pycnocline under enhanced mixing conditions—both of which are not well known. With these limitations in mind, the results show that OWFs could impact the large-scale stratification, but only when they occupy extensive shelf regions. They are expected to have very little impact on large-scale stratification at the current capacity in the North Sea, but the impact could be significant in future large-scale development scenarios.
    Description: Funding was provided by the Helmholtz Foundation through the Polar Regions and Coasts in the Changing Earth System II (PACES II) program.
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    Predicting interactions between common dolphins and the pole-and-line tuna fishery in the Azores (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 11 (2016): e0164107, doi:10.1371/journal.pone.0164107.
    Description: Common dolphins (Delphinus delphis) are responsible for the large majority of interactions with the pole-and-line tuna fishery in the Azores but the underlying drivers remain poorly understood. In this study we investigate the influence of various environmental and fisheries-related factors in promoting the interaction of common dolphins with this fishery and estimate the resultant catch losses. We analysed 15 years of fishery and cetacean interaction data (1998–2012) collected by observers placed aboard tuna fishing vessels. Dolphins interacted in less than 3% of the fishing events observed during the study period. The probability of dolphin interaction varied significantly between years with no evident trend over time. Generalized additive modeling results suggest that fishing duration, sea surface temperature and prey abundance in the region were the most important factors explaining common dolphin interaction. Dolphin interaction had no impact on the catches of albacore, skipjack and yellowfin tuna but resulted in significantly lower catches of bigeye tuna, with a predicted median annual loss of 13.5% in the number of fish captured. However, impact on bigeye catches varied considerably both by year and fishing area. Our work shows that rates of common dolphin interaction with the pole-and-line tuna fishery in the Azores are low and showed no signs of increase over the study period. Although overall economic impact was low, the interaction may lead to significant losses in some years. These findings emphasize the need for continued monitoring and for further research into the consequences and economic viability of potential mitigation measures.
    Description: This work was funded by Fundação para a Ciência e a Tecnologia (FCT) and DRCT/SRCTE, though FEDER, the Competitiveness Factors Operational (COMPETE), QREN European Social Fund, the Portuguese Ministry for Science and Education, under research projects TRACE (PTDC/MAR/74071/2006), FCT Exploratory Project (IF/00943/2013/CP1199/CT0001), and MAPCET (M2.1.2/F/012/2011). We acknowledge the support of Fundação para a Ciência e Tecnologia (FCT), through the strategic project UID/MAR/04292/2013 granted to MARE. We thank the Azorean Regional Government for funding POPA, the Ship-owners Association and the Association of the Tuna Canning Industries for their support to the program. MJC was supported by a DRCT doctoral grant (M3.1.2/F/008/2009). MAS was supported by POPH, QREN, European Social Fund and Portuguese Ministry for Science and Education, through an FCT Investigator grant (IF/00943/2013).
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    Bacterial biogeography across the Amazon river-ocean continuum (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 882, doi:10.3389/fmicb.2017.00882.
    Description: Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and 〉2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.
    Description: This research is funded by the Gordon and Betty Moore Foundation (GBMF 2293 and 2928), the U.S. National Science Foundation (OCE-0934095, OCE-0424602, DEB-1256724), and the São Paulo Research Foundation (FAPESP 12/51187-0).
    Keywords: Amazon River ; Tropical Atlantic Ocean ; River plume ; Microbial diversity ; Freshwater bacteria ; Marine bacteria ; Diatom-diazotroph assemblage ; Columbia River
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    Seasonal succession and spatial patterns of Synechococcus microdiversity in a salt marsh estuary revealed through 16S rRNA gene oligotyping (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 1496, doi:10.3389/fmicb.2017.01496.
    Description: Synechococcus are ubiquitous and cosmopolitan cyanobacteria that play important roles in global productivity and biogeochemical cycles. This study investigated the fine scale microdiversity, seasonal patterns, and spatial distributions of Synechococcus in estuarine waters of Little Sippewissett salt marsh (LSM) on Cape Cod, MA. The proportion of Synechococcus reads was higher in the summer than winter, and higher in coastal waters than within the estuary. Variations in the V4–V6 region of the bacterial 16S rRNA gene revealed 12 unique Synechococcus oligotypes. Two distinct communities emerged in early and late summer, each comprising a different set of statistically co-occurring Synechococcus oligotypes from different clades. The early summer community included clades I and IV, which correlated with lower temperature and higher dissolved oxygen levels. The late summer community included clades CB5, I, IV, and VI, which correlated with higher temperatures and higher salinity levels. Four rare oligotypes occurred in the late summer community, and their relative abundances more strongly correlated with high salinity than did other co-occurring oligotypes. The analysis revealed that multiple, closely related oligotypes comprised certain abundant clades (e.g., clade 1 in the early summer and clade CB5 in the late summer), but the correlations between these oligotypes varied from pair to pair, suggesting they had slightly different niches despite being closely related at the clade level. Lack of tidal water exchange between sampling stations gave rise to a unique oligotype not abundant at other locations in the estuary, suggesting physical isolation plays a role in generating additional microdiversity within the community. Together, these results contribute to our understanding of the environmental and ecological factors that influence patterns of Synechococcus microbial community composition over space and time in salt marsh estuarine waters.
    Description: This work was supported through a subcontract from the Woods Hole Center for Oceans and Human Health, from the National Institutes of Health and the National Science Foundation (NIH/NIEHS 1 P50 ES012742-01 and NSF/OCE 0430724), a National Research Council Research Associateship Award and L'Oreal USA Fellowship (JH), an Alfred P. Sloan Research Fellowship in Ocean Sciences and the Clare Boothe Luce Program (KM), NASA Astrobiology Institute Cooperative Agreement NNA04CC04A (MS), the Alfred P. Sloan Foundation's ICoMM field project, and the W. M. Keck Foundation.
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    Forecasting the seasonal timing of Maine's lobster fishery (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 337, doi:10.3389/fmars.2017.00337.
    Description: The fishery for American lobster is currently the highest-valued commercial fishery in the United States, worth over US$620 million in dockside value in 2015. During a marine heat wave in 2012, the fishery was disrupted by the early warming of spring ocean temperatures and subsequent influx of lobster landings. This situation resulted in a price collapse, as the supply chain was not prepared for the early and abundant landings of lobsters. Motivated by this series of events, we have developed a forecast of when the Maine (USA) lobster fishery will shift into its high volume summer landings period. The forecast uses a regression approach to relate spring ocean temperatures derived from four NERACOOS buoys along the coast of Maine to the start day of the high landings period of the fishery. Tested against conditions in past years, the forecast is able to predict the start day to within 1 week of the actual start, and the forecast can be issued 3–4 months prior to the onset of the high-landings period, providing valuable lead-time for the fishery and its associated supply chain to prepare for the upcoming season. Forecast results are conveyed in a probabilistic manner and are updated weekly over a 6-week forecasting period so that users can assess the certainty and consistency of the forecast and factor the uncertainty into their use of the information in a given year. By focusing on the timing of events, this type of seasonal forecast provides climate-relevant information to users at time scales that are meaningful for operational decisions. As climate change alters seasonal phenology and reduces the reliability of past experience as a guide for future expectations, this type of forecast can enable fishing industry participants to better adjust to and prepare for operating in the context of climate change.
    Description: This forecast was initiated with support from NSF Coastal SEES (OCE 1325484) and was developed with funds from NASA EPSCoR through Maine Space Grant Consortium (EP-15-03).
    Keywords: Seasonal forecast ; Temperature ; Fishery landings ; Lobster fishery ; Climate variability
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    Characterizing the duration and severity of fishing gear entanglement on a North Atlantic right whale (Eubalaena glacialis) using stable isotopes, steroid and thyroid hormones in baleen (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 168, doi:10.3389/fmars.2018.00168.
    Description: North Atlantic right whales (Eubalaena glacialis) are highly endangered and frequently exposed to a myriad of human activities and stressors in their industrialized habitat. Entanglements in fixed fishing gear represent a particularly pervasive and often drawn-out source of anthropogenic morbidity and mortality to the species. To better understand both the physiological response to entanglement, and to determine fundamental parameters such as acquisition, duration, and severity of entanglement, we measured a suite of biogeochemical markers in the baleen of an adult female that died from a well-documented chronic entanglement in 2005 (whale Eg2301). Steroid hormones (cortisol, corticosterone, estradiol, and progesterone), thyroid hormones (triiodothyronine (T3) and thyroxine (T4)), and stable isotopes (δ13C and δ15N) were all measured in a longitudinally sampled baleen plate. This yielded an 8-year profile of foraging and migration behavior, stress response, and reproduction. Stable isotopes cycled in annual patterns that reflect the animal's north-south migration behavior and seasonally abundant zooplankton diet. A progesterone peak, lasting approximately 23 months, was associated with the single known calving event (in 2002) for this female. Estradiol, cortisol, corticosterone, T3, and T4 were also elevated, although variably so, during the progesterone peak. This whale was initially sighted with a fishing gear entanglement in September 2004, but the hormone panel suggests that the animal first interacted with the gear as early as June 2004. Elevated δ15N, T3, and T4 indicate that Eg2301 potentially experienced increased energy expenditure, significant lipid catabolism, and thermal stress approximately 3 months before the initial sighting with fishing gear. All hormones in the panel (except cortisol) were elevated above baseline by September 2004. This novel study illustrates the value of using baleen to reconstruct recent temporal profiles and as a comparative matrix in which key physiological indicators of individual whales can be used to understand the impacts of anthropogenic activity on threatened whale populations.
    Description: The Woods Hole Oceanographic Institution's Ocean Life Institute and Marine Mammal Center funded this study and NL was supported by a Postdoctoral Fellowship from Baylor University.
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    Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 772, doi:10.3389/fmicb.2018.00772.
    Keywords: Epsilonproteobacteria ; Taxonomy ; Classification ; Genome ; Phylogenomics ; Epsilonbacteraeota ; Epsilonbacterota ; Evolution
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    Integrating archival tag data and a high-resolution oceanographic model to estimate basking shark (Cetorhinus maximus) movements in the western Atlantic (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 25, doi:10.3389/fmars.2018.00025.
    Description: Basking shark (Cetorhinus maximus) populations are considered “vulnerable” globally and “endangered” in the northeast Atlantic by the International Union for the Conservation of Nature (IUCN). Much of our knowledge of this species comes from surface observations in coastal waters, yet recent evidence suggests the majority of their lives may be spent in the deep ocean. Depth preferences of basking sharks have significantly limited movement studies that used pop-up satellite archival transmitting (PSAT) tags as conventional light-based geolocation is impossible for tagged animals that spend significant time below the photic zone. We tagged 57 basking sharks with PSAT tags in the NW Atlantic from 2004 to 2011. Many individuals spent several months at meso- and bathy-pelagic depths where accurate light-level geolocation was impossible during fall, winter and spring. We applied a newly-developed geolocation approach for the PSAT data by comparing three-dimensional depth-temperature profile data recorded by the tags to modeled in situ oceanographic data from the high-resolution HYbrid Coordinate Ocean Model (HYCOM). Observation-based likelihoods were leveraged within a state-space hidden Markov model (HMM). The combined tracks revealed that basking sharks moved from waters around Cape Cod, MA to as far as the SE coast of Brazil (20°S), a total distance of over 17,000 km. Moreover, 59% of tagged individuals with sufficient deployment durations (〉250 days) demonstrated seasonal fidelity to Cape Cod and the Gulf of Maine, with one individual returning to within 60 km of its tagging location 1 year later. Tagged sharks spent most of their time at epipelagic depths during summer months around Cape Cod and in the Gulf of Maine. During winter months, sharks spent extended periods at depths of at least 600 m while moving south to the Sargasso Sea, the Caribbean Sea, or the western tropical Atlantic. Our work demonstrates the utility of applying advances in oceanographic modeling to understanding habitat use of highly migratory, often meso- and bathy-pelagic, ocean megafauna. The large-scale movement patterns of tagged sharks highlight the need for international cooperation when designing and implementing conservation strategies to ensure that the species recovers from the historical effects of over-fishing throughout the North Atlantic Ocean.
    Description: We gratefully acknowledge funding from the US National Science Foundation (OCE 0825148), the National Aeronautics and Space Administration (NNS06AA96G), the Massachusetts Environmental Trust, and the Federal Aid in Sport Fish Restoration Program. CB was funded by the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology, the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution, and the NASA Earth and Space Science Fellowship. Funding for the development of HYCOM has been provided by the National Ocean Partnership Program and the Office of Naval Research.
    Keywords: Movement ecology ; Satellite archival telemetry ; Migration ; Mesopelagic ; Oceanographic modeling ; Site fidelity
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    Identification and removal of contaminant sequences from ribosomal gene databases : lessons from the Census of Deep Life (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 840, doi:10.3389/fmicb.2018.00840.
    Description: Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium, Aquabacterium, Ralstonia, and Acinetobacter. While the top five most frequently observed genera were Pseudomonas, Propionibacterium, Acinetobacter, Ralstonia, and Sphingomonas. The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA extraction and DNA cleanup methods. Thus, controls must be taken at every step of the collection and processing procedure when working with low biomass environments such as, but not limited to, portions of Earth’s deep subsurface. Taken together, we stress that the CoDL dataset is an incredible resource for the broader research community interested in subsurface life, and steps to remove contamination derived sequences must be taken prior to using this dataset.
    Description: We wish to acknowledge the support of the Sloan Foundation and the Deep Carbon Observatory and the Department of Energy, Office of Fossil Energy (Colwell).
    Keywords: 16S rRNA ; Contamination ; Microbial survey ; Census of Deep Life ; Deep subsurface
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    The eruption of submarine rhyolite lavas and domes in the deep ocean – Havre 2012, Kermadec Arc (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Earth Science 6 (2018): 147, doi:10.3389/feart.2018.00147.
    Description: Silicic effusive eruptions in deep submarine environments have not yet been directly observed and very few modern submarine silicic lavas and domes have been described. The eruption of Havre caldera volcano in the Kermadec arc in 2012 provided an outstanding database for research on deep submarine silicic effusive eruptions because it produced 15 rhyolite (70–72 wt.% SiO2) lavas and domes with a total volume of ∼0.21 km3 from 14 separate seafloor vents. Moreover, in 2015, the seafloor products were observed, mapped and sampled in exceptional detail (1-m resolution) using AUV Sentry and ROV Jason2 deployed from R/V Roger Revelle. Vent positions are strongly aligned, defining NW-SE and E-W trends along the southwestern and southern Havre caldera margin, respectively. The alignment of the vents suggests magma ascent along dykes which probably occupy faults related to the caldera margin. Four vents part way up the steeply sloping southwestern caldera wall at 1,200–1,300 m below sea level (bsl) and one on the caldera rim (1,060 m bsl) produced elongate lavas. On the steep caldera wall, the lavas consist of narrow tongues that have triangular cross-section shapes. Two of the narrow-tongue segments are connected to wide lobes on the flat caldera floor at ∼1,500 m bsl. The lavas are characterized by arcuate surface ridges oriented perpendicular to the propagation direction. Eight domes were erupted onto relatively flat sea floor from vents at ∼1,000 m bsl along the southern and southwestern caldera rim. They are characterized by steep margins and gently convex-up upper surfaces. With one exception, the domes have narrow spines and deep clefts above the inferred vent positions. One dome has a relatively smooth upper surface. The lavas and domes all consist of combinations of coherent rhyolite and monomictic rhyolite breccia. Despite eruption from deep-water vents (most 〉900 m bsl), the Havre 2012 rhyolite lavas and domes are very similar to subaerial rhyolite lavas and domes in terms of dimensions, volumes, aspect ratio, textures and morphology. They show that lava morphology was strongly controlled by the pre-existing seafloor topography: domes and wide lobes formed where the rhyolite was emplaced onto flat sea floor, whereas narrow tongues formed where the rhyolite was emplaced on the steep slopes of the caldera wall.
    Description: This research was funded by an Australian Research Council Postdoctoral fellowship to RJC (DP110102196 and DE150101190), and National Science Foundation grants OCE1357443 and OCE1357216. FI was supported by a Tasmanian Government Postgraduate Award.
    Keywords: Lava ; Dome ; Submarine effusive eruption ; Rhyolite ; Havre
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    Light control of G protein signaling pathways by a novel photopigment (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 13 (2018): e0205015, doi:10.1371/journal.pone.0205015.
    Description: Channelopsins and photo-regulated ion channels make it possible to use light to control electrical activity of cells. This powerful approach has lead to a veritable explosion of applications, though it is limited to changing membrane voltage of the target cells. An enormous potential could be tapped if similar opto-genetic techniques could be extended to the control of chemical signaling pathways. Photopigments from invertebrate photoreceptors are an obvious choice—as they do not bleach upon illumination -however, their functional expression has been problematic. We exploited an unusual opsin, pScop2, recently identified in ciliary photoreceptors of scallop. Phylogenetically, it is closer to vertebrate opsins, and offers the advantage of being a bi-stable photopigment. We inserted its coding sequence and a fluorescent protein reporter into plasmid vectors and demonstrated heterologous expression in various mammalian cell lines. HEK 293 cells were selected as a heterologous system for functional analysis, because wild type cells displayed the largest currents in response to the G-protein activator, GTP-γ-S. A line of HEK cells stably transfected with pScop2 was generated; after reconstitution of the photopigment with retinal, light responses were obtained in some cells, albeit of modest amplitude. In native photoreceptors pScop2 couples to Go; HEK cells express poorly this G-protein, but have a prominent Gq/PLC pathway linked to internal Ca mobilization. To enhance pScop2 competence to tap into this pathway, we swapped its third intracellular loop—important to confer specificity of interaction between 7TMDRs and G-proteins—with that of a Gq-linked opsin which we cloned from microvillar photoreceptors present in the same retina. The chimeric construct was evaluated by a Ca fluorescence assay, and was shown to mediate a robust mobilization of internal calcium in response to illumination. The results project pScop2 as a potentially powerful optogenetic tool to control signaling pathways.
    Description: This work was funded by Colciencias grant FP44842-010-2015 and Connecticut Fund for Science.
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    Seasonal succession of free-living bacterial communities in coastal waters of the Western Antarctic Peninsula (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1731, doi: 10.3389/fmicb.2016.01731.
    Description: The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.
    Description: CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR.
    Keywords: 16S rRNA gene ; Ecological succession ; Antarctica ; Bacterial production ; Bacterial community composition ; Polaribacter ; Pelagibacter ubique (SAR11) ; Rhodobacteraceae
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    A few Pseudomonas oligotypes dominate in the meat and dairy processing environment (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 264, doi:10.3389/fmicb.2017.00264.
    Description: The occurrence of bacteria in the food processing environments plays a key role in food contamination and development of spoilage. Species of the genus Pseudomonas are recognized as major food spoilers and the capability to actually determine spoilage can be species- as well as strain-dependent. In order to improve the taxonomic resolution of 16S rRNA gene amplicons, in this study we used oligotyping to investigate the diversity of Pseudomonas populations in meat and dairy processing environments. Sequences of the V1–V3 regions from previous studies were used, including environmental swabs and food samples from both meat and dairy processing plants. We showed that the most frequently found oligotypes belonged to Pseudomonas fragi and P. fluorescens, that the most abundant oligotypes co-occurred, and were shared between the meat and dairy datasets. All the oligotypes occurring in foods were also identified in the environmental samples of the corresponding plants, highlighting the important role of the environment as a source of strains for food contamination. Oligotypes of the same species showed different levels depending on food processing and type of sample, suggesting that different strains of the same species can have different adaptation efficiency, leading to resilient bacterial associations.
    Keywords: Pseudomonas fragi ; Food contamination ; Food processing environment ; Oligotyping ; 16S rRNA gene sequencing
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    Mercury-pollution induction of intracellular lipid accumulation and lysosomal compartment amplification in the benthic foraminifer Ammonia parkinsoniana (2016)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The definitive version was published in PLoS One 11 (2016): e0162401, doi:10.1371/journal.pone.0162401.
    Description: Heavy metals such as mercury (Hg) pose a significant health hazard through bioaccumulation and biomagnification. By penetrating cell membranes, heavy metal ions may lead to pathological conditions. Here we examined the responses of Ammonia parkinsoniana, a benthic foraminiferan, to different concentrations of Hg in the artificial sea water. Confocal images of untreated and treated specimens using fluorescent probes (Nile Red and Acridine Orange) provided an opportunity for visualizing the intracellular lipid accumulation and acidic compartment regulation. With increased Hg over time, we observed an increased number of lipid droplets, which may have acted as a detoxifying organelle where Hg is sequestered and biologically inactivated. Further, Hg seems to promote the proliferation of lysosomes both in terms of number and dimension that, at the highest level of Hg, resulted in cell death. We report, for the first time, the presence of Hg within the foraminiferal cell: at the basal part of pores, in the organic linings of the foramen/septa, and as cytoplasmic accumulations.
    Description: The research for this paper was partially made possible by the financial support from the PRIN 2010-2011 Ministero dell’Istruzione, dell’Università e della Ricerca (MIUR) (protocollo 2010RMTLYR) to RC. JMB acknowledges support from The Investment in Science Fund at WHOI. BG, JRE, AJ, LZ, and EMP were supported in part by the Office of Biological and Environmental Research, US Department of Energy (DOE) as part of the Mercury Science Focus Area at Oak Ridge National Laboratory, which is managed by UT-Battelle LLC for the DOE under contract DE-AC05-00OR22725.
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    Underwater ambient noise in a baleen whale migratory habitat off the Azores (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 109, doi:10.3389/fmars.2017.00109.
    Description: Assessment of underwater noise is of particular interest given the increase in noise-generating human activities and the potential negative effects on marine mammals which depend on sound for many vital processes. The Azores archipelago is an important migratory and feeding habitat for blue (Balaenoptera musculus), fin (Balaenoptera physalus) and sei whales (Balaenoptera borealis) en route to summering grounds in northern Atlantic waters. High levels of low frequency noise in this area could displace whales or interfere with foraging behavior, impacting energy intake during a critical stage of their annual cycle. In this study, bottom-mounted Ecological Acoustic Recorders were deployed at three Azorean seamounts (Condor, Açores, and Gigante) to measure temporal variations in background noise levels and ship noise in the 18–1,000 Hz frequency band, used by baleen whales to emit and receive sounds. Monthly average noise levels ranged from 90.3 dB re 1 μPa (Açores seamount) to 103.1 dB re 1 μPa (Condor seamount) and local ship noise was present up to 13% of the recording time in Condor. At this location, average contribution of local boat noise to background noise levels is almost 10 dB higher than wind contribution, which might temporally affect detection ranges for baleen whale calls and difficult communication at long ranges. Given the low time percentatge with noise levels above 120 dB re 1 μPa found here (3.3% at Condor), we woud expect limited behavioral responses to ships from baleen whales. Sound pressure levels measured in the Azores are lower than those reported for the Mediterranean basin and the Strait of Gibraltar. However, the currently unknown effects of baleen whale vocalization masking and the increasing presence of boats at the monitored sites underline the need for continuous monitoring to understand any long-term impacts on whales.
    Description: Fundação para a Ciência e a Tecnologia (FCT) and Fundo Regional da Ciência e Tecnologia (FRCT), through research projects TRACE (PTDC/MAR/74071/2006), MAPCET (M2.1.2/F/012/2011), and FCT Exploratory project (IF/00943/2013/CP1199/CT0001), supported by funds from FEDER, the Competitiveness Factors Operational (COMPETE), QREN, POPH, European Social Fund, Portuguese Ministry for Science and Education, and Proconvergencia Açores/EU Program. We also acknowledge funds provided by FCT to MARE, through the strategic project UID/MAR/04292/2013, that also supported fees for this open access publication. MR is supported by a DRCT doctoral grant (M3.1.a/F/028/2015), IC was supported by a FCT doctoral grant (SFRH/BD/41192/2007) and MAS is supported by an FCT-Investigator contract (IF/00943/2013).
    Keywords: Underwater noise ; Ship noise ; Baleen whales ; MSFD ; Open ocean environment
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    Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 682, doi:10.3389/fmicb.2017.00682.
    Description: The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
    Description: The study was supported by a Discovery Outstanding Researcher Award (DP120103498) and an Australian Laureate Fellowship (FL150100038) from the Australian Research Council.
    Keywords: Epsilonproteobacteria ; Taxonomy ; Classification ; Genome ; Phylogenomics ; Epsilonbacteraeota ; Evolution
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    High Latitude epipelagic and mesopelagic scattering layers—a reference for future Arctic ecosystem change (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 334, doi:10.3389/fmars.2017.00334.
    Description: Scattering structures, including deep (〉200 m) scattering layers are common in most oceans, but have not previously been properly documented in the Arctic Ocean. In this work, we combine acoustic data for distribution and abundance estimation of zooplankton and fish with biological sampling from the region west and north of Svalbard, to examine high latitude meso- and epipelagic scattering layers and their biological constituents. Our results show that typically, there was strong patchy scattering in the upper part of the epipelagic zone (〈50 m) throughout the area. It was mainly dominated by copepods, krill, and amphipods in addition to 0-group fish that were particularly abundant west of the Spitsbergen Archipelago. Off-shelf there was a distinct deep scattering layer (DSL) between 250 and 600 m containing a range of larger longer lived organisms (mesopelagic fish and macrozooplankton). In eastern Fram Strait, the DSL also included and was in fact dominated by larger fish close to the shelf/slope break that were associated with Warm Atlantic Water moving north toward the Arctic Ocean, but switched to dominance by species having weaker scattering signatures further offshore. The Weighted Mean Depths of the DSL were deeper (WMD 〉 440 m) in the Arctic habitat north of Svalbard compared to those south in the Fram Strait west of Svalbard (WMD ~400 m). The surface integrated backscatter [Nautical Area-Scattering Coefficient, NASC, sA (m2 nmi−2)] was considerably lower in the waters around Svalbard compared to the more southern regions (62–69°N). Also, the integrated DSL nautical area scattering coefficient was a factor of ~6–10 lower around Svalbard compared to the areas in the south-eastern part of the Norwegian Sea ~62°30′N. The documented patterns and structures, particularly the DSL and its constituents, will be key reference points for understanding and quantifying future changes in the pelagic ecosystem at the entrance to the Arctic Ocean.
    Description: The Research Council of Norway is thanked for the financial support through the projects “The Arctic Ocean Ecosystem”—(SI_ARCTIC, RCN 228896), the “Effects of climate change on the Calanus complex”—(ECCO, RCN 200508), “Harvesting marine cold water plankton species—abundance estimation and stock assessment”—(Harvest II, RCN 203871) as well as the Institute of Marine Research, Bergen.
    Keywords: Arctic ; Bioacoustics ; Scattering layers ; Fish ; Micronekton ; Zooplankton ; Svalbard
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    Exploring the ecology of deep-sea hydrothermal vents in a metacommunity framework (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 49, doi:10.3389/fmars.2018.00049.
    Description: Species inhabiting deep-sea hydrothermal vents are strongly influenced by the geological setting, as it provides the chemical-rich fluids supporting the food web, creates the patchwork of seafloor habitat, and generates catastrophic disturbances that can eradicate entire communities. The patches of vent habitat host a network of communities (a metacommunity) connected by dispersal of planktonic larvae. The dynamics of the metacommunity are influenced not only by birth rates, death rates and interactions of populations at the local site, but also by regional influences on dispersal from different sites. The connections to other communities provide a mechanism for dynamics at a local site to affect features of the regional biota. In this paper, we explore the challenges and potential benefits of applying metacommunity theory to vent communities, with a particular focus on effects of disturbance. We synthesize field observations to inform models and identify data gaps that need to be addressed to answer key questions including: (1) what is the influence of the magnitude and rate of disturbance on ecological attributes, such as time to extinction or resilience in a metacommunity; (2) what interactions between local and regional processes control species diversity, and (3) which communities are “hot spots” of key ecological significance. We conclude by assessing our ability to evaluate resilience of vent metacommunities to human disturbance (e.g., deep-sea mining). Although the resilience of a few highly disturbed vent systems in the eastern Pacific has been quantified, these values cannot be generalized to remote locales in the western Pacific or mid Atlantic where disturbance rates are different and information on local controls is missing.
    Description: LM was supported by NSF OCE 1356738 and DEB 1558904. SB was supported by the NSF DEB 1558904 and the Investment in Science Fund at Woods Hole Oceanographic Institution. MB was supported by the Austrian Science Fund grants P20190-B17 and P16774-B03. LL was supported by NSF OCE 1634172 and the JM Kaplan Fund. MN was supported by NSF DEB 1558904. Y-JW was supported by a Korean Institute of Ocean Science and Technology (KIOST) grant PM60210.
    Keywords: Metacommunity ; Metapopulation ; Hydrothermal vent ; Connectivity ; Resilience ; Disturbance ; Species diversity ; Dispersal
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    Coincident mass occurrence of gelatinous zooplankton in northern Norway (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 158, doi:10.3389/fmars.2018.00158.
    Description: In autumn 2015, several sources reported observations of large amounts of gelatinous material in a large north Norwegian fjord system, either caught when trawling for other organisms or fouling fishing gear. The responsible organism was identified as a physonect siphonophore, Nanomia cara, while a ctenophore, Beroe cucumis, and a hydromedusa, Modeeria rotunda, were also registered in high abundances on a couple of occasions. To document the phenomena, we have compiled a variety of data from concurrent fisheries surveys and local fishermen, including physical samples, trawl catch, and acoustic data, photo and video evidence, and environmental data. Because of the gas-filled pneumatophore, characteristic for these types of siphonophores, acoustics provided detailed and unique insight to the horizontal and vertical distribution and potential abundances (~0.2–20 colonies·m−3) of N. cara with the highest concentrations observed in the near bottom region at ~320 m depth in the study area. This suggests that these animals were retained and accumulated in the deep basins of the fjord system possibly blooming here because of favorable environmental conditions and potentially higher prey availability compared to the shallower shelf areas to the north. Few cues as to the origin and onset of the bloom were found, but it may have originated from locally resident siphonophores. The characteristics of the deep-water masses in the fjord basins were different compared to the deep water outside the fjord system, suggesting no recent deep-water import to the fjords. However, water-masses containing siphonophores (not necessarily very abundant), may have been additionally introduced to the fjords at intermediate depths, with the animals subsequently trapped in the deeper fjord basins. The simultaneous observations of abundant siphonophores, hydromedusae, and ctenophores in the Lyngen-Kvænangen fjord system are intriguing, but difficult to provide a unified explanation for, as the organisms differ in their biology and ecology. Nanomia and Beroe spp. are holopelagic, while M. rotunda has a benthic hydroid stage. The species also have different trophic ecologies and dietary preferences. Only by combining information from acoustics, trawling, genetics, and local fishermen, were the identity, abundance, and the vertical and horizontal distribution of the physonect siphonophore, N. cara, established.
    Description: The work was funded by the Ministry of Fisheries and Coastal Affairs through the Institute of Marine Research (IMR), while the Research Council of Norway (RCN) is thanked for the financial support through the project The Arctic Ocean Ecosystem—(SI_ARCTIC, RCN 228896). AH was supported by the Norwegian Taxonony Initiative (NTI 70184233) and ForBio Research School funding (RCN 248799 and NTI 70184215).
    Keywords: Jellyfish bloom ; Genetics ; Acoustics ; Nanomia ; North Norwegian fjords ; Gelatinous zooplankton
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    Microbial community structure and associations during a marine dinoflagellate bloom (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 1201, doi:10.3389/fmicb.2018.01201.
    Description: Interactions between microorganisms and algae during bloom events significantly impacts their physiology, alters ambient chemistry, and shapes ecosystem diversity. The potential role these interactions have in bloom development and decline are also of particular interest given the ecosystem impacts of algal blooms. We hypothesized that microbial community structure and succession is linked to specific bloom stages, and reflects complex interactions among taxa comprising the phycosphere environment. This investigation used pyrosequencing and correlation approaches to assess patterns and associations among bacteria, archaea, and microeukaryotes during a spring bloom of the dinoflagellate Alexandrium catenella. Within the bacterial community, Gammaproteobacteria and Bacteroidetes were predominant during the initial bloom stage, while Alphaproteobacteria, Cyanobacteria, and Actinobacteria were the most abundant taxa present during bloom onset and termination. In the archaea biosphere, methanogenic members were present during the early bloom period while the majority of species identified in the late bloom stage were ammonia-oxidizing archaea and Halobacteriales. Dinoflagellates were the major eukaryotic group present during most stages of the bloom, whereas a mixed assemblage comprising diatoms, green-algae, rotifera, and other microzooplankton were present during bloom termination. Temperature and salinity were key environmental factors associated with changes in bacterial and archaeal community structure, respectively, whereas inorganic nitrogen and inorganic phosphate were associated with eukaryotic variation. The relative contribution of environmental parameters measured during the bloom to variability among samples was 35.3%. Interaction analysis showed that Maxillopoda, Spirotrichea, Dinoflagellata, and Halobacteria were keystone taxa within the positive-correlation network, while Halobacteria, Dictyochophyceae, Mamiellophyceae, and Gammaproteobacteria were the main contributors to the negative-correlation network. The positive and negative relationships were the primary drivers of mutualist and competitive interactions that impacted algal bloom fate, respectively. Functional predictions showed that blooms enhance microbial carbohydrate and energy metabolism, and alter the sulfur cycle. Our results suggest that microbial community structure is strongly linked to bloom progression, although specific drivers of community interactions and responses are not well understood. The importance of considering biotic interactions (e.g., competition, symbiosis, and predation) when investigating the link between microbial ecological behavior and an algal bloom’s trajectory is also highlighted.
    Description: This work was supported by NSFC (41476092, 41741015), S&T Projects of Shenzhen Science and Technology Innovation Committee (JCYJ20150831192329178, JCYJ20170817160708491, and JCYJ20170412171959157), Key Research and Development Plan of Ministry of Science and Technology of China (2017YFC1403600), as well as by the Woods Hole Center for Oceans and Human Health through the National Science Foundation (Grant OCE-1314642), and National Institute of Environmental Health Sciences (Grant 1-P01-ES021923-01).
    Keywords: Microbial community ; Algal bloom ; Dynamic process ; Network interaction ; Ecological function
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    Modeling tissue and blood gas kinetics in coastal and offshore common bottlenose dolphins, Tursiops truncatus (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Physiology 9 (2018): 838, doi: 10.3389/fphys.2018.00838.
    Description: Bottlenose dolphins (Tursiops truncatus) are highly versatile breath-holding predators that have adapted to a wide range of foraging niches from rivers and coastal ecosystems to deep-water oceanic habitats. Considerable research has been done to understand how bottlenose dolphins manage O2 during diving, but little information exists on other gases or how pressure affects gas exchange. Here we used a dynamic multi-compartment gas exchange model to estimate blood and tissue O2, CO2, and N2 from high-resolution dive records of two different common bottlenose dolphin ecotypes inhabiting shallow (Sarasota Bay) and deep (Bermuda) habitats. The objective was to compare potential physiological strategies used by the two populations to manage shallow and deep diving life styles. We informed the model using species-specific parameters for blood hematocrit, resting metabolic rate, and lung compliance. The model suggested that the known O2 stores were sufficient for Sarasota Bay dolphins to remain within the calculated aerobic dive limit (cADL), but insufficient for Bermuda dolphins that regularly exceeded their cADL. By adjusting the model to reflect the body composition of deep diving Bermuda dolphins, with elevated muscle mass, muscle myoglobin concentration and blood volume, the cADL increased beyond the longest dive duration, thus reflecting the necessary physiological and morphological changes to maintain their deep-diving life-style. The results indicate that cardiac output had to remain elevated during surface intervals for both ecotypes, and suggests that cardiac output has to remain elevated during shallow dives in-between deep dives to allow sufficient restoration of O2 stores for Bermuda dolphins. Our integrated modeling approach contradicts predictions from simple models, emphasizing the complex nature of physiological interactions between circulation, lung compression, and gas exchange.
    Description: AF (N00014-17-1-2756), PT (N000141512553) and FHJ (N00014-14-1-0410) were supported by the Office of Naval Research, and FHJ by an AIASCOFUND fellowship from Aarhus Institute of Advanced Studies, Aarhus University, under EU's FP7 program (Agreement No. 609033). PT received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) and their support is gratefully acknowledged.
    Keywords: Diving physiology ; Modeling and simulations ; Gas exchange ; Marine mammals ; Decompression sickness ; Blood gases ; Hypoxia
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    Shipboard design and fabrication of custom 3D-printed soft robotic manipulators for the investigation of delicate deep-sea organisms (2018)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLos One 13 (2018): e0200386, doi:10.1371/journal.pone.0200386.
    Description: Soft robotics is an emerging technology that has shown considerable promise in deep-sea marine biological applications. It is particularly useful in facilitating delicate interactions with fragile marine organisms. This study describes the shipboard design, 3D printing and integration of custom soft robotic manipulators for investigating and interacting with deep-sea organisms. Soft robotics manipulators were tested down to 2224m via a Remotely-Operated Vehicle (ROV) in the Phoenix Islands Protected Area (PIPA) and facilitated the study of a diverse suite of soft-bodied and fragile marine life. Instantaneous feedback from the ROV pilots and biologists allowed for rapid re-design, such as adding “fingernails”, and re-fabrication of soft manipulators at sea. These were then used to successfully grasp fragile deep-sea animals, such as goniasterids and holothurians, which have historically been difficult to collect undamaged via rigid mechanical arms and suction samplers. As scientific expeditions to remote parts of the world are costly and lengthy to plan, on-the-fly soft robot actuator printing offers a real-time solution to better understand and interact with delicate deep-sea environments, soft-bodied, brittle, and otherwise fragile organisms. This also offers a less invasive means of interacting with slow-growing deep marine organisms, some of which can be up to 18,000 years old.
    Description: This work is supported by NOAA OER Grant # NA17OAR0110083 “Exploration of the Seamounts of the Phoenix Islands Protected Area” to RDR, EEC, TMS and DFG and Schmidt Ocean Institute Grant: “What is the Current State of the Deep-Sea Coral Ecosystem in the Phoenix Island Protected Area?” to EEC, RDR, TMS and DFG; NSF Instrument Development for Biological Research Award # 1556164 to RJW and #1556123 to DFG; the National Academies Keck Futures Initiative of the National Academy of Sciences under award #NAKFI DBS21 to RJW and DFG; and NFS Research Fellowship awarded to KPB (#DGE1144152). It is also supported by the Wyss Institute for Biologically Inspired Engineering at Harvard University. We are grateful for the support from the National Geographic Society Innovation Challenge (Grant No.: SP 12-14) to RJW and DFG.
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    Resonance control of acoustic focusing systems through an environmental reference table and impedance spectroscopy (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 13 (2018): e0207532, doi:10.1371/journal.pone.0207532.
    Description: Acoustic standing waves can precisely focus flowing particles or cells into tightly positioned streams for interrogation or downstream separations. The efficiency of an acoustic standing wave device is dependent upon operating at a resonance frequency. Small changes in a system’s temperature and sample salinity can shift the device’s resonance condition, leading to poor focusing. Practical implementation of an acoustic standing wave system requires an automated resonance control system to adjust the standing wave frequency in response to environmental changes. Here we have developed a rigorous approach for quantifying the optimal acoustic focusing frequency at any given environmental condition. We have demonstrated our approach across a wide range of temperature and salinity conditions to provide a robust characterization of how the optimal acoustic focusing resonance frequency shifts across these conditions. To generalize these results, two microfluidic bulk acoustic standing wave systems (a steel capillary and an etched silicon wafer) were examined. Models of these temperature and salinity effects suggest that it is the speed of sound within the liquid sample that dominates the resonance frequency shift. Using these results, a simple reference table can be generated to predict the optimal resonance condition as a function of temperature and salinity. Additionally, we show that there is a local impedance minimum associated with the optimal system resonance. The integration of the environmental results for coarse frequency tuning followed by a local impedance characterization for fine frequency adjustments, yields a highly accurate method of resonance control. Such an approach works across a wide range of environmental conditions, is easy to automate, and could have a significant impact across a wide range of microfluidic acoustic standing wave systems.
    Description: This research was supported by grants from the National Institute of General Medical Sciences of the National Institutes of Health under award number R21GM107805 and the NSF under award number (OCE-1130140 and OCE-1131134) to SWG, RJO, and HMS.
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    The good, the bad, and the tiny : a simple, mechanistic-probabilistic model of virus-nutrient colimitation in microbes (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0143299, doi:10.1371/journal.pone.0143299.
    Description: For phytoplankton and other microbes, nutrient receptors are often the passages through which viruses invade. This presents a bottom-up vs. top-down, co-limitation scenario; how do these would-be-hosts balance minimizing viral susceptibility with maximizing uptake of limiting nutrient(s)? This question has been addressed in the biological literature on evolutionary timescales for populations, but a shorter timescale, mechanistic perspective is lacking, and marine viral literature suggests the strong influence of additional factors, e.g. host size; while the literature on both nutrient uptake and host-virus interactions is expansive, their intersection, of ubiquitous relevance to marine environments, is understudied. I present a simple, mechanistic model from first principles to analyze the effect of this co-limitation scenario on individual growth, which suggests that in environments with high risk of viral invasion or spatial/temporal heterogeneity, an individual host’s growth rate may be optimized with respect to receptor coverage, producing top-down selective pressure on short timescales. The model has general applicability, is suggestive of hypotheses for empirical exploration, and can be extended to theoretical studies of more complex behaviors and systems.
    Description: This work was supported by the Massachusetts Institute of Technology Charles Vest Presidential Fellowship.
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    Species-level variability in extracellular production rates of reactive oxygen species by diatoms (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Chemistry 4 (2016): 5, doi:10.3389/fchem.2016.00005.
    Description: Biological production and decay of the reactive oxygen species (ROS) hydrogen peroxide (H2O2) and superoxide (O−2) likely have significant effects on the cycling of trace metals and carbon in marine systems. In this study, extracellular production rates of H2O2 and O−2 were determined for five species of marine diatoms in the presence and absence of light. Production of both ROS was measured in parallel by suspending cells on filters and measuring the ROS downstream using chemiluminescence probes. In addition, the ability of these organisms to break down O−2 and H2O2 was examined by measuring recovery of O−2 and H2O2 added to the influent medium. O−2 production rates ranged from undetectable to 7.3 × 10−16 mol cell−1 h−1, while H2O2 production rates ranged from undetectable to 3.4 × 10−16 mol cell−1 h−1. Results suggest that extracellular ROS production occurs through a variety of pathways even amongst organisms of the same genus. Thalassiosira spp. produced more O−2 in light than dark, even when the organisms were killed, indicating that O−2 is produced via a passive photochemical process on the cell surface. The ratio of H2O2 to O−2 production rates was consistent with production of H2O2 solely through dismutation of O−2 for T. oceanica, while T. pseudonana made much more H2O2 than O−2. T. weissflogii only produced H2O2 when stressed or killed. P. tricornutum cells did not make cell-associated ROS, but did secrete H2O2-producing substances into the growth medium. In all organisms, recovery rates for killed cultures (94–100% H2O2; 10–80% O−2) were consistently higher than those for live cultures (65–95% H2O2; 10–50% O−2). While recovery rates for killed cultures in H2O2 indicate that nearly all H2O2 was degraded by active cell processes, O−2 decay appeared to occur via a combination of active and passive processes. Overall, this study shows that the rates and pathways for ROS production and decay vary greatly among diatom species, even between those that are closely related, and as a function of light conditions.
    Description: This research was supported by NSF grant OCE-1131734/1246174 to BV and CH.
    Keywords: Reactive oxygen species ; Superoxide ; Hydrogen peroxide ; Diatoms ; Culture
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    New insights into microbial ecology through subtle nucleotide variation (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1318, doi:10.3389/fmicb.2016.01318.
    Description: Characterizing the community structure of naturally occurring microbes through marker gene amplicons has gained widespread acceptance for profiling microbial populations. The 16S ribosomal RNA (rRNA) gene provides a suitable target for most studies since (1) it meets the criteria for robust markers of evolution, e.g., both conserved and rapidly evolving regions that do not undergo horizontal gene transfer, (2) microbial ecologists have identified widely adopted primers and protocols for generating amplicons for sequencing, (3) analyses of both cultivars and environmental DNA have generated well-curated databases for taxonomic profiling, and (4) bioinformaticians and computational biologists have published comprehensive software tools for interpreting the data and generating publication-ready figures. Since the initial descriptions of high-throughput sequencing of 16S rRNA gene amplicons to survey microbial diversity, we have witnessed an explosion of association-based inferences of interactions between microbes and their environment.
    Description: AME was supported by the University of Chicago and the Marine Biological Laboratory collaboration award.
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    Site-specific variation in gene expression from Symbiodinium spp. associated with offshore and inshore Porites astreoides in the lower Florida Keys is lost with bleaching and disease stress (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0173350, doi:10.1371/journal.pone.0173350.
    Description: Scleractinian coral are experiencing unprecedented rates of mortality due to increases in sea surface temperatures in response to global climate change. Some coral species however, survive high temperature events due to a reduced susceptibility to bleaching. We investigated the relationship between bleaching susceptibility and expression of five metabolically related genes of Symbiodinium spp. from the coral Porites astreoides originating from an inshore and offshore reef in the Florida Keys. The acclimatization potential of Symbiodinium spp. to changing temperature regimes was also measured via a two-year reciprocal transplant between the sites. Offshore coral fragments displayed significantly higher expression in Symbiodinium spp. genes PCNA, SCP2, G3PDH, PCP and psaE than their inshore counterparts (p〈0.05), a pattern consistent with increased bleaching susceptibility in offshore corals. Additionally, gene expression patterns in Symbiodinium spp. from site of origin were conserved throughout the two-year reciprocal transplant, indicating acclimatization did not occur within this multi-season time frame. Further, laboratory experiments were used to investigate the influence of acute high temperature (32°C for eight hours) and disease (lipopolysaccharide of Serratia marcescens) on the five metabolically related symbiont genes from the same offshore and inshore P. astreoides fragments. Gene expression did not differ between reef fragments, or as a consequence of acute exposure to heat or heat and disease, contrasting to results found in the field. Gene expression reported here indicates functional variation in populations of Symbiodinium spp. associated with P. astreoides in the Florida Keys, and is likely a result of localized adaptation. However, gene expression patterns observed in the lab imply that functional variation in zooxanthellae observed under conditions of chronic moderate stress is lost under the acute extreme conditions studied here.
    Description: Funding for this research was provided by Coastal Preservation network (KBS, BHS).
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    Characterization of trace metal content in the developing zebrafish embryo (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0179318, doi: 10.1371/journal.pone.0179318.
    Description: Trace metals are essential for health but toxic when present in excess. The maintenance of trace metals at physiologic levels reflects both import and export by cells and absorption and excretion by organs. The mechanism by which this maintenance is achieved in vertebrate organisms is incompletely understood. To explore this, we chose zebrafish as our model organism, as they are amenable to both pharmacologic and genetic manipulation and comprise an ideal system for genetic screens and toxicological studies. To characterize trace metal content in developing zebrafish, we measured levels of three trace elements, copper, zinc, and manganese, from the oocyte stage to 30 days post-fertilization using inductively coupled plasma mass spectrometry. Our results indicate that metal levels are stable until zebrafish can acquire metals from the environment and imply that the early embryo relies on maternal contribution of metals to the oocyte. We also measured metal levels in bodies and yolks of embryos reared in presence and absence of the copper chelator neocuproine. All three metals exhibited different relative abundances between yolks and bodies of embryos. While neocuproine treatment led to an expected phenotype of copper deficiency, total copper levels were unaffected, indicating that measurement of total metal levels does not equate with measurement of biologically active metal levels. Overall, our data not only can be used in the design and execution of genetic, physiologic, and toxicologic studies but also has implications for the understanding of vertebrate metal homeostasis.
    Description: This work was supported by the National Institutes of Health, R00 DK84122.
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    Isolation and characterization of bacteria that degrade phosphonates in marine dissolved organic matter (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 1786, doi:10.3389/fmicb.2017.01786.
    Description: Semi-labile dissolved organic matter (DOM) accumulates in surface waters of the oligotrophic ocean gyres and turns over on seasonal to annual timescales. This reservoir of DOM represents an important source of carbon, energy, and nutrients to marine microbial communities but the identity of the microorganisms and the biochemical pathways underlying the cycling of DOM remain largely uncharacterized. In this study we describe bacteria isolated from the North Pacific Subtropical Gyre (NPSG) near Hawaii that are able to degrade phosphonates associated with high molecular weight dissolved organic matter (HMWDOM), which represents a large fraction of semi-labile DOM. We amended dilution-to-extinction cultures with HMWDOM collected from NPSG surface waters and with purified HMWDOM enriched with polysaccharides bearing alkylphosphonate esters. The HMWDOM-amended cultures were enriched in Roseobacter isolates closely related to Sulfitobacter and close relatives of hydrocarbon-degrading bacteria of the Oceanospirillaceae family, many of which encoded phosphonate degradation pathways. Sulfitobacter cultures encoding C-P lyase were able to catabolize methylphosphonate and 2-hydroxyethylphosphonate, as well as the esters of these phosphonates found in native HMWDOM polysaccharides to acquire phosphorus while producing methane and ethylene, respectively. Conversely, growth of these isolates on HMWDOM polysaccharides as carbon source did not support robust increases in cell yields, suggesting that the constituent carbohydrates in HMWDOM were not readily available to these individual isolates. We postulate that the complete remineralization of HMWDOM polysaccharides requires more complex microbial inter-species interactions. The degradation of phosphonate esters and other common substitutions in marine polysaccharides may be key steps in the turnover of marine DOM.
    Description: Financial support for this work was provided by the National Science Foundation Center for Microbial Oceanography: Research and Education (award #EF0424599 to DK and ED), the National Science Foundation HOT program (OCE-1260164 to M. J. Church and DK), the Gordon and Betty Moore Foundation (grants #492.01 and #3777 to ED, #3298 to DR, and #3794 to DK), and the Simons Foundation (award ID 329108 to DK, DR, and ED). Additional support was provided by the Agouron Institute through a fellowship to OS.
    Keywords: Bacterial degradation ; Dissolved organic matter (DOM) ; Phosphonate metabolism ; C-P lyase ; Methane ; Ethylene ; Oligotrophic conditions
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    Mixotrophic activity and diversity of Antarctic marine protists in austral summer (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 13, doi:10.3389/fmars.2018.00013.
    Description: Identifying putative mixotrophic protist species in the environment is important for understanding their behavior, with the recovery of these species in culture essential for determining the triggers of feeding, grazing rates, and overall impact on bacterial standing stocks. In this project, mixotroph abundances determined using tracer ingestion in water and sea ice samples collected in the Ross Sea, Antarctica during the summer of 2011 were compared with data from the spring (Ross Sea) and fall (Arctic) to examine the impacts of bacterivory/mixotrophy. Mixotrophic nanoplankton (MNAN) were usually less abundant than heterotrophs, but consumed more of the bacterial standing stock per day due to relatively higher ingestion rates (1–7 bacteria mixotroph−1 h−1 vs. 0.1–4 bacteria heterotroph−1 h−1). Yet, even with these high rates observed in the Antarctic summer, mixotrophs appeared to have a smaller contribution to bacterivory than in the Antarctic spring. Additionally, putative mixotroph taxa were identified through incubation experiments accomplished with bromodeoxyuridine-labeled bacteria as food, immunoprecipitation (IP) of labeled DNA, and amplification and high throughput sequencing of the eukaryotic ribosomal V9 region. Putative mixotroph OTUs were identified in the IP samples by taxonomic similarity to known phototroph taxa. OTUs that had increased abundance in IP samples compared to the non-IP samples from both surface and chlorophyll maximum (CM) depths were considered to represent active mixotrophy and include ones taxonomically similar to Dictyocha, Gymnodinium, Pentapharsodinium, and Symbiodinium. These OTUs represent target taxa for isolation and laboratory experiments on triggers for mixotrophy, to be combined with qPCR to estimate their abundance, seasonal distribution and potential impact.
    Description: This work was supported by National Science Foundation Grants OPP-0838955 (RG) and OPP-0838847 (RS).
    Keywords: Protist ; Diversity ; Mixotrophy ; Ross Sea ; Amplicon sequencing
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    Distinct siderophores contribute to iron cycling in the mesopelagic at Station ALOHA (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 61, doi:10.3389/fmars.2018.00061.
    Description: The distribution of dissolved iron (Fe), total organic Fe-binding ligands, and siderophores were measured between the surface and 400 m at Station ALOHA, a long term ecological study site in the North Pacific Subtropical Gyre. Dissolved Fe concentrations were low throughout the water column and strong organic Fe-binding ligands exceeded dissolved Fe at all depths; varying from 0.9 nmol L−1 in the surface to 1.6 nmol L−1 below 150 m. Although Fe does not appear to limit microbial production, we nevertheless found siderophores at nearly all depths, indicating some populations of microbes were responding to Fe stress. Ferrioxamine siderophores were most abundant in the upper water column, with concentrations between 0.1 and 2 pmol L−1, while a suite of amphibactins were found below 200 m with concentrations between 0.8 and 11 pmol L−1. The distinct vertical distribution of ferrioxamines and amphibactins may indicate disparate strategies for acquiring Fe from dust in the upper water column and recycled organic matter in the lower water column. Amphibactins were found to have conditional stability constants (log KcondFeL1,Fe′) ranging from 12.0 to 12.5, while ferrioxamines had much stronger conditional stability constants ranging from 14.0 to 14.4, within the range of observed L1 ligands by voltammetry. We used our data to calculate equilibrium Fe speciation at Station ALOHA to compare the relative concentration of inorganic and siderophore complexed Fe. The results indicate that the concentration of Fe bound to siderophores was up to two orders of magnitude higher than inorganic Fe, suggesting that even if less bioavailable, siderophores were nevertheless a viable pathway for Fe acquisition by microbes at our study site. Finally, we observed rapid production of ferrioxamine E by particle-associated bacteria during incubation of freshly collected sinking organic matter. Fe-limitation may therefore be a factor in regulating carbon metabolism and nutrient regeneration in the mesopelagic.
    Description: This work was funded by the Woods Hole Oceanographic Postdoctoral Fellowship for RaB, the Simons Foundation (Award 329108), and the National Science Foundation (OCE-1356747).
    Keywords: Iron ; Siderophores ; Station ALOHA ; Organic ligands ; Iron limitation
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    The origin and role of organic matrix in coral calcification: insights from comparing coral skeleton and abiogenic aragonite (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 170, doi:10.3389/fmars.2018.00170.
    Description: Understanding the mechanisms of coral calcification is critical for accurately projecting coral reef futures under ocean acidification and warming. Recent suggestions that calcification is primarily controlled by organic molecules and the biological activity of the coral polyp imply that ocean acidification may not affect skeletal accretion. The basis for these suggestions relies heavily on correlating the presence of organic matter with the orientation and disorder of aragonite crystals in the skeleton, carrying the assumption that organic matter observed in the skeleton was produced by the polyp to control calcification. Here we use Raman spectroscopy to test whether there are differences in organic matter content between coral skeleton and abiogenic aragonites precipitated from seawater, both before and after thermal annealing (heating). We measured the background fluxorescence and intensity of C-H bonding signals in the Raman spectra, which are commonly attributed to coral polyp-derived skeletal organic matrix (SOM) and have been used to map its distribution. Surprisingly, we found no differences in either fluorescence or C-H bonding between abiogenic aragonite and coral skeleton. Annealing reduced the molecular disorder in coral skeleton, potentially due to removal of organic matter, but the same effect was also observed in the abiogenic aragonites. The presence of organic molecules in the abiogenic aragonites is further supported by measurements of N content and δ15N. Together, our data suggest that some of what has been interpreted in previous studies as polyp-derived SOM may actually be seawater-sourced organic matter or some other signal not unique to biogenic aragonite. Finally, we create a high-resolution Raman map of a Pocillopora skeleton to demonstrate how patterns of fluorescence and elevated calcifying fluid aragonite saturation state (ΩAr) along centers of calcification are consistent with both biological and physico-chemical controls. Our aim is to advance discussion on biological mediation of calcification and the implications for coral resilience in a high-CO2 world.
    Description: This study was supported by an ARC Laureate Fellowship (FL120100049) awarded to Professor Malcolm McCulloch and the ARC Centre of Excellence for Coral Reef Studies (CE140100020).
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    Electrical synapses enhance and accelerate interneuron recruitment in response to coincident and sequential excitation (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Cellular Neuroscience 12 (2018): 156, doi:10.3389/fncel.2018.00156.
    Description: Electrical synapses are ubiquitous in interneuron networks. They form intercellular pathways, allowing electrical currents to leak between coupled interneurons. I explored the impact of electrical coupling on the integration of excitatory signals and on the coincidence detection abilities of electrically-coupled cerebellar basket cells (BCs). In order to do so, I quantified the influence of electrical coupling on the rate, the probability and the latency at which BCs generate action potentials when stimulated. The long-lasting simultaneous suprathreshold depolarization of a coupled cell evoked an increase in firing rate and a shortening of action potential latency in a reference basket cell, compared to its depolarization alone. Likewise, the action potential probability of coupled cells was strongly increased when they were simultaneously stimulated with trains of short-duration near-threshold current pulses (mimicking the activation of presynaptic granule cells) at 10 Hz, and to a lesser extent at 50 Hz, an effect that was absent in non-coupled cells. Moreover, action potential probability was increased and action potential latency was shortened in response to synaptic stimulations in mice lacking the protein that forms gap junctions between BCs, connexin36, relative to wild-type (WT) controls. These results suggest that electrical synapses between BCs decrease the probability and increase the latency of stimulus-triggered action potentials, both effects being reverted upon simultaneous excitation of coupled cells. Interestingly, varying the delay at which coupled cells are stimulated revealed that the probability and the speed of action potential generation are facilitated maximally when a basket cell is stimulated shortly after a coupled cell. These findings suggest that electrically-coupled interneurons behave as coincidence and sequence detectors that dynamically regulate the latency and the strength of inhibition onto postsynaptic targets depending on the degree of input synchrony in the coupled interneuron network.
    Description: This work was supported by the laboratory of Brain Physiology at Paris Descartes University (UMR8118), the Centre National de la Recherche Scientifique, the Agence Nationale de la Recherche Grant INterneuron NETwork (INNET), the Laboratory of Cellular and Systemic Neurophysiology, Institute for Physiology I at the University of Freiburg, and the Grass foundation.
    Keywords: Gap junction ; Synaptic integration ; Interneurons ; Inhibition ; Coincidence ; Cerebellum
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    Nitrogen limitation of the summer phytoplankton and heterotrophic prokaryote communities in the Chukchi Sea (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 362, doi:10.3389/fmars.2018.00362.
    Description: Major changes to Arctic marine ecosystems have resulted in longer growing seasons with increased phytoplankton production over larger areas. In the Chukchi Sea, the high productivity fuels intense benthic denitrification creating a nitrogen (N) deficit that is transported through the Arctic to the Atlantic Ocean, where it likely fuels N fixation. Given the rapid pace of environmental change and the potentially globally significant N deficit, we conducted experiments aimed at understanding phytoplankton and microbial N utilization in the Chukchi Sea. Ship-board experiments tested the effect of nitrate (NO3-) additions on both phytoplankton and heterotrophic prokaryote abundance, community composition, photophysiology, carbon fixation and NO3- uptake rates. Results support the critical role of NO3- in limiting summer phytoplankton communities to small cells with low production rates. NO3- additions increased particulate concentrations, abundance of large diatoms, and rates of carbon fixation and NO3- uptake by cells 〉1 μm. Increases in the quantum yield and electron turnover rate of photosystem II in +NO3- treatments suggested that phytoplankton in the ambient dissolved N environment were N starved and unable to build new, or repair damaged, reaction centers. While some increases in heterotrophic prokaryote abundance and production were noted with NO3- amendments, phytoplankton competition or grazers likely dampened these responses. Trends toward a warmer more stratified Chukchi Sea will likely enhance summer oligotrophic conditions and further N starve Chukchi Sea phytoplankton communities.
    Description: Fieldwork and analysis for the ICESCAPE program was supported by Ocean Biology and Biogeochemistry Program of the National Aeronautic and Space Administration under Grant No. NNX10AF42G to KA.
    Keywords: Phytoplankton ; Nitrogen ; Chukchi Sea ; Nitrate ; Nutrient limitation
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    AMS radiocarbon dating of large za baobabs (Adansonia za) of Madagascar (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0146977, doi:10.1371/journal.pone.0146977 .
    Description: The article reports the radiocarbon investigation of Anzapalivoro, the largest za baobab (Adansonia za) specimen of Madagascar and of another za, namely the Big cistern baobab. Several wood samples collected from the large inner cavity and from the outer part/exterior of the tree were investigated by AMS (accelerator mass spectrometry) radiocarbon dating. For samples collected from the cavity walls, the age values increase with the distance into the wood up to a point of maximum age, after which the values decrease toward the outer part. This anomaly of age sequences indicates that the inner cavity of Anzapalivoro is a false cavity, practically an empty space between several fused stems disposed in a ring-shaped structure. The radiocarbon date of the oldest sample was 780 ± 30 bp, which corresponds to a calibrated age of around 735 yr. Dating results indicate that Anzapalivoro has a closed ring-shaped structure, which consists of 5 fused stems that close a false cavity. The oldest part of the biggest za baobab has a calculated age of 900 years. We also disclose results of the investigation of a second za baobab, the Big cistern baobab, which was hollowed out for water storage. This specimen, which consists of 4 fused stems, was found to be around 260 years old.
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    A bacterial quorum-sensing precursor induces mortality in the marine coccolithophore, Emiliania huxleyi (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 59, doi:10.3389/fmicb.2016.00059.
    Description: Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. However, deciphering the chemical drivers of these interspecies interactions remains challenging. Here, we report the isolation of 2-heptyl-4-quinolone (HHQ), released by Pseudoalteromonas piscicida, a marine gamma-proteobacteria previously reported to induce phytoplankton mortality through a hitherto unknown algicidal mechanism. HHQ functions as both an antibiotic and a bacterial signaling molecule in cell–cell communication in clinical infection models. Co-culture of the bloom-forming coccolithophore, Emiliania huxleyi with both live P. piscicida and cell-free filtrates caused a significant decrease in algal growth. Investigations of the P. piscicida exometabolome revealed HHQ, at nanomolar concentrations, induced mortality in three strains of E. huxleyi. Mortality of E. huxleyi in response to HHQ occurred slowly, implying static growth rather than a singular loss event (e.g., rapid cell lysis). In contrast, the marine chlorophyte, Dunaliella tertiolecta and diatom, Phaeodactylum tricornutum were unaffected by HHQ exposures. These results suggest that HHQ mediates the type of inter-domain interactions that cause shifts in phytoplankton population dynamics. These chemically mediated interactions, and other like it, ultimately influence large-scale oceanographic processes.
    Description: This research was support through funding from the Gordon and Betty Moore Foundation through Grant GBMF3301 to MJ and TM; NIH grant from the National Institute of Allergy and Infectious Disease (NIAID – 1R21Al119311-01) to TM and KW; the National Science Foundation (OCE – 1313747) and US National Institute of Environmental Health Science (P01-ES021921) through the Oceans and Human Health Program to BM. Additional financial support was provided to TM from the Flatley Discovery Lab.
    Keywords: Infochemicals ; Algicidal compound ; Bacteria–phytoplankton interaction ; HHQ ; Pseudoalteromonas ; Emiliania huxleyi ; IC50 ; Mortality
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    Biochemical mechanisms for geographical adaptations to novel toxin exposures in butterflyfish (2016)
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    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The definitive version was published in PLoS One 11 (2016): e0154208, doi: 10.1371/journal.pone.0154208
    Description: Some species of butterflyfish have had preyed upon corals for millions of years, yet the mechanism of butterflyfish specialized coral feeding strategy remains poorly understood. Certain butterflyfish have the ability to feed on allelochemically rich soft corals, e.g. Sinularia maxima. Cytochrome P450 (CYP) is the predominant enzyme system responsible for the detoxification of dietary allelochemicals. CYP2-like and CYP3A-like content have been associated with butterflyfish that preferentially consumes allelochemically rich soft corals. To investigate the role of butterflyfish CYP2 and CYP3A enzymes in dietary preference, we conducted oral feeding experiments using homogenates of S. maxima and a toxin isolated from the coral in four species of butterflyfish with different feeding strategies. After oral exposure to the S. maxima toxin 5-episinulaptolide (5ESL), which is not normally encountered in the Hawaiian butterflyfish diet, an endemic specialist, Chaetodon multicinctus experienced 100% mortality compared to a generalist, Chaetodon auriga, which had significantly more (3–6 fold higher) CYP3A-like basal content and catalytic activity. The specialist, Chaetodon unimaculatus, which preferentially feed on S. maxima in Guam, but not in Hawaii, had 100% survival, a significant induction of 8–12 fold CYP3A-like content, and an increased ability (2-fold) to metabolize 5ESL over other species. Computer modeling data of CYP3A4 with 5ESL were consistent with microsomal transformation of 5ESL to a C15-16 epoxide from livers of C. unimaculatus. Epoxide formation correlated with CYP3A-like content, catalytic activity, induction, and NADPH-dependent metabolism of 5ESL. These results suggest a potentially important role for the CYP3A family in butterflyfish-coral diet selection through allelochemical detoxification.
    Description: This work received support from the following sources: Resource Allocation Program of the Agricultural Research Station for UCR to DS; Summer funding by Hilda and George Liebig Environmental Sciences Summer Fellowship and travel grant Albert March Environmental Sciences Scholarship from the University of California, Riverside; and the Chemistry and DMPK CORE of COBRE, P20GM104932 from the National Institute of General Medical Sciences (NIGMS), a component of the National Institutes of Health (NIH) supported the chemistry studies.
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    Smartphone-based distributed data collection enables rapid assessment of shorebird habitat suitability (2016)
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    Publication Date: 2022-05-25
    Description: This is an open access article, free of all copyright. The definitive version was published in PLoS ONE 11 (2016): e0164979, doi: 10.1371/journal.pone.0164979.
    Description: Understanding and managing dynamic coastal landscapes for beach-dependent species requires biological and geological data across the range of relevant environments and habitats. It is difficult to acquire such information; data often have limited focus due to resource constraints, are collected by non-specialists, or lack observational uniformity. We developed an open-source smartphone application called iPlover that addresses these difficulties in collecting biogeomorphic information at piping plover (Charadrius melodus) nest sites on coastal beaches. This paper describes iPlover development and evaluates data quality and utility following two years of collection (n = 1799 data points over 1500 km of coast between Maine and North Carolina, USA). We found strong agreement between field user and expert assessments and high model skill when data were used for habitat suitability prediction. Methods used here to develop and deploy a distributed data collection system have broad applicability to interdisciplinary environmental monitoring and modeling.
    Description: This work was supported by the North Atlantic Landscape Conservation Cooperative through the U.S. Department of the Interior Hurricane Sandy recovery program under the Disaster Relief Appropriations Act of 2013, and the U.S. Geological Survey Coastal and Marine Geology Program.
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    Relative importance of chemoautotrophy for primary production in a light exposed marine shallow hydrothermal system (2017)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 702, doi:10.3389/fmicb.2017.00702.
    Description: The unique geochemistry of marine shallow-water hydrothermal systems promotes the establishment of diverse microbial communities with a range of metabolic pathways. In contrast to deep-sea vents, shallow-water vents not only support chemosynthesis, but also phototrophic primary production due to the availability of light. However, comprehensive studies targeting the predominant biogeochemical processes are rare, and consequently a holistic understanding of the functioning of these ecosystems is currently lacking. To this end, we combined stable isotope probing of lipid biomarkers with an analysis of the bacterial communities to investigate if chemoautotrophy, in parallel to photoautotrophy, plays an important role in autotrophic carbon fixation and to identify the key players. The study was carried out at a marine shallow-water hydrothermal system located at 5 m water depth off Dominica Island (Lesser Antilles), characterized by up to 55°C warm hydrothermal fluids that contain high amounts of dissolved Fe2+. Analysis of the bacterial diversity revealed Anaerolineae of the Chloroflexi as the most abundant bacterial class. Furthermore, the presence of key players involved in iron cycling generally known from deep-sea hydrothermal vents (e.g., Zetaproteobacteria and Geothermobacter), supported the importance of iron-driven redox processes in this hydrothermal system. Uptake of 13C-bicarbonate into bacterial fatty acids under light and dark conditions revealed active photo- and chemoautotrophic communities, with chemoautotrophy accounting for up to 65% of the observed autotrophic carbon fixation. Relatively increased 13C-incorporation in the dark allowed the classification of aiC15:0, C15:0, and iC16:0 as potential lipid biomarkers for bacterial chemoautotrophy in this ecosystem. Highest total 13C-incorporation into fatty acids took place at the sediment surface, but chemosynthesis was found to be active down to 8 cm sediment depth. In conclusion, this study highlights the relative importance of chemoautotrophy compared to photoautotrophy in a shallow-water hydrothermal system, emphasizing chemosynthesis as a prominent process for biomass production in marine coastal environments influenced by hydrothermalism.
    Description: SS was supported by NSF grant OCE-1124272. This work was financed through the DFG Emmy Noether Grant BU 2606/1-1 to SB.
    Keywords: Chemoautotrophy ; Marine shallow-water hydrothermal systems ; Lipid biomarker ; Stable isotope probing (SIP) ; Fatty acids ; Dominica (Lesser Antilles) ; Zetaproteobacteria ; Geothermobacter
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    Oxidative formation and removal of complexed Mn(III) by Pseudomonas species (2018)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 560, doi:10.3389/fmicb.2018.00560.
    Description: The observation of significant concentrations of soluble Mn(III) complexes in oxic, suboxic, and some anoxic waters has triggered a re-evaluation of the previous Mn paradigm which focused on the cycling between soluble Mn(II) and insoluble Mn(III,IV) species as operationally defined by filtration. Though Mn(II) oxidation in aquatic environments is primarily bacterially-mediated, little is known about the effect of Mn(III)-binding ligands on Mn(II) oxidation nor on the formation and removal of Mn(III). Pseudomonas putida GB-1 is one of the most extensively investigated of all Mn(II) oxidizing bacteria, encoding genes for three Mn oxidases (McoA, MnxG, and MopA). P. putida GB-1 and associated Mn oxidase mutants were tested alongside environmental isolates Pseudomonas hunanensis GSL-007 and Pseudomonas sp. GSL-010 for their ability to both directly oxidize weakly and strongly bound Mn(III), and to form these complexes through the oxidation of Mn(II). Using Mn(III)-citrate (weak complex) and Mn(III)-DFOB (strong complex), it was observed that P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 and mutants expressing only MnxG and McoA were able to directly oxidize both species at varying levels; however, no oxidation was detected in cultures of a P. putida mutant expressing only MopA. During cultivation in the presence of Mn(II) and citrate or DFOB, P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 formed Mn(III) complexes transiently as an intermediate before forming Mn(III/IV) oxides with the overall rates and extents of Mn(III,IV) oxide formation being greater for Mn(III)-citrate than for Mn(III)-DFOB. These data highlight the role of bacteria in the oxidative portion of the Mn cycle and suggest that the oxidation of strong Mn(III) complexes can occur through enzymatic mechanisms involving multicopper oxidases. The results support the observations from field studies and further emphasize the complexity of the geochemical cycling of manganese.
    Description: This work was funded by grants from the Chemical Oceanography program of the National Science Foundation (OCE-1558738 and OCE-1558692).
    Keywords: Manganese(III) ; Mn(III)-DFOB ; Mn(III)-citrate ; Mn(III)-L ; Pseudomonas ; Bacterial manganese oxidation
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    Resting metabolic rate and lung function in wild offshore common bottlenose dolphins, Tursiops truncatus, near Bermuda (2018)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Physiology 9 (2018): 886, doi:10.3389/fphys.2018.00886.
    Description: Diving mammals have evolved a suite of physiological adaptations to manage respiratory gases during extended breath-hold dives. To test the hypothesis that offshore bottlenose dolphins have evolved physiological adaptations to improve their ability for extended deep dives and as protection for lung barotrauma, we investigated the lung function and respiratory physiology of four wild common bottlenose dolphins (Tursiops truncatus) near the island of Bermuda. We measured blood hematocrit (Hct, %), resting metabolic rate (RMR, l O2 ⋅ min-1), tidal volume (VT, l), respiratory frequency (fR, breaths ⋅ min-1), respiratory flow (l ⋅ min-1), and dynamic lung compliance (CL, l ⋅ cmH2O-1) in air and in water, and compared measurements with published results from coastal, shallow-diving dolphins. We found that offshore dolphins had greater Hct (56 ± 2%) compared to shallow-diving bottlenose dolphins (range: 30–49%), thus resulting in a greater O2 storage capacity and longer aerobic diving duration. Contrary to our hypothesis, the specific CL (sCL, 0.30 ± 0.12 cmH2O-1) was not different between populations. Neither the mass-specific RMR (3.0 ± 1.7 ml O2 ⋅ min-1 ⋅ kg-1) nor VT (23.0 ± 3.7 ml ⋅ kg-1) were different from coastal ecotype bottlenose dolphins, both in the wild and under managed care, suggesting that deep-diving dolphins do not have metabolic or respiratory adaptations that differ from the shallow-diving ecotypes. The lack of respiratory adaptations for deep diving further support the recently developed hypothesis that gas management in cetaceans is not entirely passive but governed by alteration in the ventilation-perfusion matching, which allows for selective gas exchange to protect against diving related problems such as decompression sickness.
    Description: Funding for this project was provided by the Office of Naval Research (ONR YIP Award No. N000141410563, and Dolphin Quest, Inc. FHJ was supported by the Office of Naval Research (Award No. N00014-1410410) and an AIAS-COFUND fellowship from Aarhus Institute of Advanced Studies under the FP7 program of the EU (Agreement No. 609033).
    Keywords: Lung mechanics ; Total lung capacity ; Field metabolic rate ; Energetics ; Minimum air volume ; Diving physiology ; Marine mammals ; Spirometry
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    Neural control of dynamic 3-dimensional skin papillae for cuttlefish camouflage (2018)
    Cell Press
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in iScience 1 (2018): 24-34, doi:10.1016/j.isci.2018.01.001.
    Description: The color and pattern changing abilities of octopus, squid, and cuttlefish via chromatophore neuro-muscular organs are unparalleled. Cuttlefish and octopuses also have a unique muscular hydrostat system in their skin. When this system is expressed, dermal bumps called papillae disrupt body shape and imitate the fine texture of surrounding objects, yet the control system is unknown. Here we report for papillae: (1) the motoneurons and the neurotransmitters that control activation and relaxation, (2) a physiologically fast expression and retraction system, and (3) a complex of smooth and striated muscles that enables long-term expression of papillae through sustained tension in the absence of neural input. The neural circuits controlling acute shape-shifting skin papillae in cuttlefish show homology to the iridescence circuits in squids. The sustained tension in papillary muscles for long-term camouflage utilizes muscle heterogeneity and points toward the existence of a “catch-like” mechanism that would reduce the necessary energy expenditure.
    Description: This work was funded by an AFOSR grant no. FA9550-14-1-0134, Isaac Newton Trust/Wellcome Trust ISSF/University of Cambridge Joint Research Grant (097814/Z/11/Z) to P.T.G-B., and a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (BBSRC, BB/L024667/1) to T.J.W.
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    Evaluation of mixotrophy-associated gene expression in two species of polar marine algae (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 5 (2018): 273, doi:10.3389/fmars.2018.00273.
    Description: Mixotrophic flagellates can comprise significant proportions of plankton biomass in marine ecosystems. Despite the growing recognition of the importance of this ecological strategy, and the identification of major environmental factors controlling phagotrophic behavior (light and nutrients), the physiological and molecular mechanisms underlying mixotrophic behavior are still unclear. In this study, we performed RNA-Seq transcriptomic analysis for two mixotrophic prasinophytes, Micromonas polaris and Pyramimonas tychotreta, under dissolved nutrient regimes that altered their ingestion of bacteria prey. Though the strains examined were polar isolates, both belong to genera with widespread distribution. Our aim was to characterize the transcriptomes of these two non-model phytoflagellates, identify transcripts consistent with phagotrophic activity and assess their differential expression in response to nutrient stress. De novo assembly of the transcriptomes yielded large numbers of novel coding transcripts with no known match within public databases. A summary of the transcripts by Gene Ontology terms showed many expected expression patterns, including genes involved in photosynthetic pathways and enzymes implicated in nutrient uptake pathways. Searches of KEGG databases identified several genes associated with intra-cellular digestive pathways actively transcribed in both prasinophytes. Differential expression analysis showed a larger response in P. tychotreta, where 23,373 genes were up-regulated and 1,752 were down-regulated in the low nutrient treatment when phagotrophy was enhanced. In contrast, in M. polaris, low nutrient treatments resulted in up-regulation of 314 transcripts while down-regulating 371. With respect to phagotrophic-related expression, 37 genes were co-expressed in both P. tychotreta and M. polaris, and although the response was less pronounced in M. polaris, it is consistent with differences in observed ingestion behavior. This study presents the first genomic data for Pyramimonas tychotreta, and also contributes to the limited available data for Micromonas polaris. Furthermore, it provides insight into the presence of genes associated with phagocytosis within the Prasinophyceae and contributes to the understanding of potential target genes required for the construction of a complete model of gene regulation of phagocytic behavior in algae.
    Description: The Owlsnest Super-Computing Cluster at Temple University is funded by a National Science Foundation Grant CNS-09-58854. The CUNY HPCC is operated by the College of Staten Island and funded, in part, by grants from the City of New York, State of New York, CUNY Research Foundation, and National Science Foundation Grants CNS-0958379, CNS-0855217, and ACI 1126113. Support for this work was also supplied by National Science Foundation grants PLR-1341362 (RG), PLR-1603538 (RS), and PLR-1603833 (RG).
    Keywords: Mixotrophy ; Pyramimonas ; Micromonas ; RNA-Seq ; Transcriptomics ; Phagotrophy
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    Strength in numbers : collaborative science for new experimental model systems (2018)
    Public Library of Science
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    Publication Date: 2022-05-25
    Description: The work is made available under the Creative Commons CCO public domain dedication.. The definitive version was published in PLoS Biology 16 (2018): e2006333, doi:10.1371/journal.pbio.2006333.
    Description: Our current understanding of biology is heavily based on a small number of genetically tractable model organisms. Most eukaryotic phyla lack such experimental models, and this limits our ability to explore the molecular mechanisms that ultimately define their biology, ecology, and diversity. In particular, marine protists suffer from a paucity of model organisms despite playing critical roles in global nutrient cycles, food webs, and climate. To address this deficit, an initiative was launched in 2015 to foster the development of ecologically and taxonomically diverse marine protist genetic models. The development of new models faces many barriers, some technical and others institutional, and this often discourages the risky, long-term effort that may be required. To lower these barriers and tackle the complexity of this effort, a highly collaborative community-based approach was taken. Herein, we describe this approach, the advances achieved, and the lessons learned by participants in this novel community-based model for research.
    Description: The research efforts, connections, and collaborations described in this paper and protocols.io (https://www.protocols.io/) were supported by the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative.
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    Using maximum entropy production to describe microbial biogeochemistry over time and space in a meromictic pond (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Environmental Science 6 (2018): 100, doi:10.3389/fenvs.2018.00100.
    Description: Determining how microbial communities organize and function at the ecosystem level is essential to understanding and predicting how they will respond to environmental change. Mathematical models can be used to describe these communities, but properly representing all the biological interactions in extremely diverse natural microbial ecosystems in a mathematical model is challenging. We examine a complementary approach based on the maximum entropy production (MEP) principle, which proposes that systems with many degrees of freedom will likely organize to maximize the rate of free energy dissipation. In this study, we develop an MEP model to describe biogeochemistry observed in Siders Pond, a phosphate limited meromictic system located in Falmouth, MA that exhibits steep chemical gradients due to density-driven stratification that supports anaerobic photosynthesis as well as microbial communities that catalyze redox cycles involving O, N, S, Fe, and Mn. The MEP model uses a metabolic network to represent microbial redox reactions, where biomass allocation and reaction rates are determined by solving an optimization problem that maximizes entropy production over time, and a 1D vertical profile constrained by an advection-dispersion-reaction model. We introduce a new approach for modeling phototrophy and explicitly represent oxygenic photoautotrophs, photoheterotrophs and anoxygenic photoautotrophs. The metabolic network also includes reactions for aerobic organoheterotrophic bacteria, sulfate reducing bacteria, sulfide oxidizing bacteria and aerobic and anaerobic grazers. Model results were compared to observations of biogeochemical constituents collected over a 24 h period at 8 depths at a single 15 m deep station in Siders Pond. Maximizing entropy production over long (3 day) intervals produced results more similar to field observations than short (0.25 day) interval optimizations, which support the importance of temporal strategies for maximizing entropy production over time. Furthermore, we found that entropy production must be maximized locally instead of globally where energy potentials are degraded quickly by abiotic processes, such as light absorption by water. This combination of field observations and modeling results indicate that natural microbial systems can be modeled by using the maximum entropy production principle applied over time and space using many fewer parameters than conventional models.
    Description: Primary funding for this project was from NSF GG grant EAR-1451356 to JV and JH, with additional support from Gordon and Betty Moore Foundation grant GBMF 3297. JV also received support from NSF Grants OCE-1637630 and OCE-1558710 and Simons Foundation grant 549941. The NSF Center for Dark Energy Biosphere Investigations (C-DEBI; OCE-0939564) also supported the participation of JH.
    Keywords: Maximum entropy production ; Microbial biogeochemistry ; Metabolic networks ; Phototrophy ; Community function ; Meromictic
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    Grxcr1 promotes hair bundle development by destabilizing the physical interaction between Harmonin and Sans usher syndrome proteins (2018)
    Cell Press
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cell Reports 25 (2018): 1281–1291, doi:10.1016/j.celrep.2018.10.005.
    Description: Morphogenesis and mechanoelectrical transduction of the hair cell mechanoreceptor depend on the correct assembly of Usher syndrome (USH) proteins into highly organized macromolecular complexes. Defects in these proteins lead to deafness and vestibular areflexia in USH patients. Mutations in a non-USH protein, glutaredoxin domain-containing cysteine-rich 1 (GRXCR1), cause non-syndromic sensorineural deafness. To understand the deglutathionylating enzyme function of GRXCR1 in deafness, we generated two grxcr1 zebrafish mutant alleles. We found that hair bundles are thinner in homozygous grxcr1 mutants, similar to the USH1 mutants ush1c (Harmonin) and ush1ga (Sans). In vitro assays showed that glutathionylation promotes the interaction between Ush1c and Ush1ga and that Grxcr1 regulates mechanoreceptor development by preventing physical interaction between these proteins without affecting the assembly of another USH1 protein complex, the Ush1c- Cadherin23-Myosin7aa tripartite complex. By elucidating the molecular mechanism through which Grxcr1 functions, we also identify a mechanism that dynamically regulates the formation of Usher protein complexes.
    Description: This work was supported by grants from the NIH (DC004186, OD011195, and HD22486).
    Keywords: Grxcr1 ; Usher syndrome ; Hair cell ; Stereocilia ; Glutathionylation ; Harmonin ; Sans
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    Identification of erosional terraces on seamounts : implications for interisland connectivity and subsidence in the Galápagos Archipelago (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Earth Science 6 (2018): 88, doi:10.3389/feart.2018.00088.
    Description: Shallow seamounts at ocean island hotspots and in other settings may record emergence histories in the form of submarine erosional terraces. Exposure histories are valuable for constraining paleo-elevations and sea levels in the absence of more traditional markers, such as drowned coral reefs. However, similar features can also be produced through primary volcanic processes, which complicate the use of terraced seamounts as an indicator of paleo-shorelines. In the western Galápagos Archipelago, we utilize newly collected bathymetry along with seafloor observations from human-occupied submersibles to document the location and depth of erosional terraces on seamounts near the islands of Santiago, Santa Cruz, Floreana, Isabela, and Fernandina. We directly observed erosional features on 22 seamounts with terraces. We use these observations and bathymetric analysis to develop a framework to identify terrace-like morphologic features and classify them as either erosional or volcanic in origin. From this framework we identify 79 erosional terraces on 30 seamounts that are presently found at depths of 30 to 300 m. Although intermittent subaerial connectivity between the islands has been hypothesized, the depths of these erosional terraces in the Santiago region are the first direct evidence of paleo-connectivity in the modern archipelago. Collectively, the terraces have non-randomly distributed depths. We suggest that peaks in the distribution of terrace depths likely represent long durations of exposure (i.e., sea-level still or lowstands). By comparing these peaks to those of subsidence adjusted sea-level curves, we identify the average subsidence rate that best reproduces the observed terrace distributions. These rates are 0.2–0.4 m/ka for this portion of the central Galápagos, since the formation of the seamounts, consistent with previous independent estimates. Using these subsidence rates and evidence for erosional terraces at depths up to 300 m, we conclude that all islands in the central archipelago have been intermittently connected starting between 435 and 900 ka. Individual island pairs have likely been repeatedly subaerially connected for short intervals since that time.
    Description: This project was carried out with financial support from the NSF (OCE-1634685 to SS and OCE-1634952 to VW) and the Dalio Explore Fund.
    Keywords: Erosional terraces ; Paleogeography ; Hotspot ; Ocean island ; Multibeam bathymetry ; Wave erosion
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    Two forms of electrical transmission between neurons (2018)
    Frontiers Media
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Molecular Neuroscience 11 (2018): 427, doi:10.3389/fnmol.2018.00427.
    Description: Electrical signaling is a cardinal feature of the nervous system and endows it with the capability of quickly reacting to changes in the environment. Although synaptic communication between nerve cells is perceived to be mainly chemically mediated, electrical synaptic interactions also occur. Two different strategies are responsible for electrical communication between neurons. One is the consequence of low resistance intercellular pathways, called “gap junctions”, for the spread of electrical currents between the interior of two cells. The second occurs in the absence of cell-to-cell contacts and is a consequence of the extracellular electrical fields generated by the electrical activity of neurons. Here, we place present notions about electrical transmission in a historical perspective and contrast the contributions of the two different forms of electrical communication to brain function.
    Description: This research was supported by National Institutes of Health grants DC03186, DC011099, NS055726, NS085772 and NS0552827 to AP.
    Keywords: Synaptic communication ; Electrical synapse ; Gap junction ; Electric field ; Ephapsis
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    Analysis of lung microbiota in bronchoalveolar lavage, protected brush and sputum samples from subjects with mild-to-moderate cystic fibrosis Lung Disease (2016)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0149998, doi:10.1371/journal.pone.0149998.
    Description: Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irreversible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate CF lung disease, to examine the relationship between the local microbiota and local damage, and to determine the relationships between microbiota in samples taken directly from the lung and the microbiota in spontaneously expectorated sputum. In this initial study, nine stable, adult CF patients with an FEV1〉50% underwent regional sampling of different lobes of the right lung by bronchoalveolar lavage (BAL) and protected brush (PB) sampling of mucus plugs. Sputum samples were obtained from six of the nine subjects immediately prior to the procedure. Microbial community analysis was performed on DNA extracted from these samples and the extent of damage in each lobe was quantified from a recent CT scan. The extent of damage observed in regions of the right lung did not correlate with specific microbial genera, levels of community diversity or composition, or bacterial genome copies per ml of BAL fluid. In all subjects, BAL fluid from different regions of the lung contained similar microbial communities. In eight out of nine subjects, PB samples from different regions of the lung were also similar in microbial community composition, and were similar to microbial communities in BAL fluid from the same lobe. Microbial communities in PB samples were more diverse than those in BAL samples, suggesting enrichment of some taxa in mucus plugs. To our knowledge, this study is the first to examine the microbiota in different regions of the CF lung in clinically stable individuals with mild-to-moderate CF-related lung disease.
    Description: Support from the Cystic Fibrosis Foundation Research Development Program (STANTO07R0) as a pilot grant to DAH and AA. Research reported in this publication was also supported by grants from the National Institutes of Health to DAH (R01 AI091702 to DAH) and the American Asthma Foundation Scholars Award and CFFT-ASHARE15A0 and R01HL122372 to AA and R01 HL074175 (BAS). The Dartmouth Lung Biology Center and CF Translational Research Core was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P30GM106394 and by the CFF RDP (CFRDP STANTO11R0).
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    Abundance and distribution of sperm whales in the Canary Islands : can sperm whales in the archipelago sustain the current level of ship-strike mortalities? (2016)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0150660, doi:10.1371/journal.pone.0150660.
    Description: Sperm whales are present in the Canary Islands year-round, suggesting that the archipelago is an important area for this species in the North Atlantic. However, the area experiences one of the highest reported rates of sperm whale ship-strike in the world. Here we investigate if the number of sperm whales found in the archipelago can sustain the current rate of ship-strike mortality. The results of this study may also have implications for offshore areas where concentrations of sperm whales may coincide with high densities of ship traffic, but where ship-strikes may be undocumented. The absolute abundance of sperm whales in an area of 52933 km2, covering the territorial waters of the Canary Islands, was estimated from 2668 km of acoustic line-transect survey using Distance sampling analysis. Data on sperm whale diving and acoustic behaviour, obtained from bio-logging, were used to calculate g(0) = 0.92, this is less than one because of occasional extended periods when whales do not echolocate. This resulted in an absolute abundance estimate of 224 sperm whales (95% log-normal CI 120–418) within the survey area. The recruitment capability of this number of whales, some 2.5 whales per year, is likely to be exceeded by the current ship-strike mortality rate. Furthermore, we found areas of higher whale density within the archipelago, many coincident with those previously described, suggesting that these are important habitats for females and immature animals inhabiting the archipelago. Some of these areas are crossed by active shipping lanes increasing the risk of ship-strikes. Given the philopatry in female sperm whales, replacement of impacted whales might be limited. Therefore, the application of mitigation measures to reduce the ship-strike mortality rate seems essential for the conservation of sperm whales in the Canary Islands.
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    Individuality, stability, and variability of the plaque microbiome (2016)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 564, doi:10.3389/fmicb.2016.00564.
    Description: Dental plaque is a bacterial biofilm composed of a characteristic set of organisms. Relatively little information from cultivation-independent, high-throughput analyses has been published on the temporal dynamics of the dental plaque microbiome. We used Minimum Entropy Decomposition, an information theory-based approach similar to oligotyping that provides single-nucleotide resolution, to analyze a previously published time series data set and investigate the dynamics of the plaque microbiome at various analytic and taxonomic levels. At both the genus and 97% Operational Taxonomic Unit (OTU) levels of resolution, the range of variation within each individual overlapped that of other individuals in the data set. When analyzed at the oligotype level, however, the overlap largely disappeared, showing that single-nucleotide resolution enables differentiation of individuals from one another without ambiguity. The overwhelming majority of the plaque community in all samples was made up of bacteria from a moderate number of plaque-typical genera, indicating that the overall community framework is shared among individuals. Each of these genera fluctuated in abundance around a stable mean that varied between individuals, with some genera having higher inter-individual variability than others. Thus, at the genus level, differences between individuals lay not in the identity of the major genera but in consistently differing proportions of these genera from mouth to mouth. However, at the oligotype level, we detected oligotype “fingerprints,” a highly individual-specific set of persistently abundant oligotypes fluctuating around a stable mean over time. For example, within the genus Corynebacterium, more than a dozen oligotypes were detectable in each individual, of which a different subset reached high abundance in any given person. This pattern suggests that each mouth contains a subtly different community of organisms. We also compared the Chinese plaque community characterized here to previously characterized Western plaque communities, as represented by analyses of data emerging from the Human Microbiome Project, and found no major differences between Chinese and Western supragingival plaque. In conclusion, we found the plaque microbiome to be highly individualized at the oligotype level and characterized by stability of community membership, with variability in the relative abundance of community members between individuals and over time.
    Description: Our work was supported by National Institutes of Health (NIH) National Institute of Dental and Craniofacial Research Grant DE022586 (to GGB). Additional support was provided by Harvard University's Department of Organismic and Evolutionary Biology graduate program (to DRU).
    Keywords: Human microbiome ; 16S rRNA ; Community dynamics ; Oral microbiota ; Community ecology
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    The Guaymas Basin hiking guide to hydrothermal mounds, chimneys, and microbial mats : complex seafloor expressions of subsurface hydrothermal circulation (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 75, doi:10.3389/fmicb.2016.00075.
    Description: The hydrothermal mats, mounds, and chimneys of the southern Guaymas Basin are the surface expression of complex subsurface hydrothermal circulation patterns. In this overview, we document the most frequently visited features of this hydrothermal area with photographs, temperature measurements, and selected geochemical data; many of these distinct habitats await characterization of their microbial communities and activities. Microprofiler deployments on microbial mats and hydrothermal sediments show their steep geochemical and thermal gradients at millimeter-scale vertical resolution. Mapping these hydrothermal features and sampling locations within the southern Guaymas Basin suggest linkages to underlying shallow sills and heat flow gradients. Recognizing the inherent spatial limitations of much current Guaymas Basin sampling calls for comprehensive surveys of the wider spreading region.
    Description: AT acknowledges a W. Reynolds research leave from UNC, Guaymas-relevant support from the Center for Dark Energy Biosphere Investigations (C-DEBI) at the University of Southern California
    Keywords: Guaymas basin ; Hydrothermal circulation ; Hydrothermal sediment ; Beggiatoa mat ; In situ profiles ; Heatflow ; Porewater chemistry
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    Intracellular isotope localization in Ammonia sp. (Foraminifera) of oxygen-depleted environments : results of nitrate and sulfate labeling experiments (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 163, doi:10.3389/fmicb.2016.00163.
    Description: Some benthic foraminiferal species are reportedly capable of nitrate storage and denitrification, however, little is known about nitrate incorporation and subsequent utilization of nitrate within their cell. In this study, we investigated where and how much 15N or 34S were assimilated into foraminiferal cells or possible endobionts after incubation with isotopically labeled nitrate and sulfate in dysoxic or anoxic conditions. After 2 weeks of incubation, foraminiferal specimens were fixed and prepared for Transmission Electron Microscopy (TEM) and correlative nanometer-scale secondary ion mass spectrometry (NanoSIMS) analyses. TEM observations revealed that there were characteristic ultrastructural features typically near the cell periphery in the youngest two or three chambers of the foraminifera exposed to anoxic conditions. These structures, which are electron dense and ~200–500 nm in diameter and co-occurred with possible endobionts, were labeled with 15N originated from 15N-labeled nitrate under anoxia and were labeled with both 15N and 34S under dysoxia. The labeling with 15N was more apparent in specimens from the dysoxic incubation, suggesting higher foraminiferal activity or increased availability of the label during exposure to oxygen depletion than to anoxia. Our results suggest that the electron dense bodies in Ammonia sp. play a significant role in nitrate incorporation and/or subsequent nitrogen assimilation during exposure to dysoxic to anoxic conditions.
    Description: This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan (Young Scientists B No. 22740340 and Scientific Research C No. 24540504 to HN), an Invitation Fellowship for Research in Japan to JB by Japan Society for the Promotion of Science (JSPS), the Robert W. Morse Chair for Excellence in Oceanography at WHOI to JB, and The Investment in Science Fund at WHOI to JB.
    Keywords: Foraminifer ; Nitrate ; NanoSIMS ; Electron dense body ; Endobionts ; Ultrastructure ; Denitrification
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    Cisplatin resistant spheroids model clinically relevant survival mechanisms in ovarian tumors (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0151089, doi: 10.1371/journal.pone.0151089 .
    Description: The majority of ovarian tumors eventually recur in a drug resistant form. Using cisplatin sensitive and resistant cell lines assembled into 3D spheroids we profiled gene expression and identified candidate mechanisms and biological pathways associated with cisplatin resistance. OVCAR-8 human ovarian carcinoma cells were exposed to sub-lethal concentrations of cisplatin to create a matched cisplatin-resistant cell line, OVCAR-8R. Genome-wide gene expression profiling of sensitive and resistant ovarian cancer spheroids identified 3,331 significantly differentially expressed probesets coding for 3,139 distinct protein-coding genes (Fc 〉2, FDR 〈 0.05) (S2 Table). Despite significant expression changes in some transporters including MDR1, cisplatin resistance was not associated with differences in intracellular cisplatin concentration. Cisplatin resistant cells were significantly enriched for a mesenchymal gene expression signature. OVCAR-8R resistance derived gene sets were significantly more biased to patients with shorter survival. From the most differentially expressed genes, we derived a 17-gene expression signature that identifies ovarian cancer patients with shorter overall survival in three independent datasets. We propose that the use of cisplatin resistant cell lines in 3D spheroid models is a viable approach to gain insight into resistance mechanisms relevant to ovarian tumors in patients. Our data support the emerging concept that ovarian cancers can acquire drug resistance through an epithelial-to-mesenchymal transition.
    Description: This work was funded by the NIH NCRR supplement grant P41 RR001395-27S1 (J.W.H.), NSF DBI-1005378 “REU Site: Biological Discovery in Woods Hole”, faculty startup funds from the Office of Research at Oklahoma State University (W.C.), and the Mary Kay Foundation (A.S.B.).
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    Diversity and distribution of prokaryotes within a shallow-water pockmark field (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 941, doi:10.3389/fmicb.2016.00941.
    Description: Pockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.
    Description: This work was partially supported by a Postdoctoral Fellowship from the Center for Dark Energy Biosphere Investigations [C-DEBI, grant OCE-0939564] awarded to DG, by National Science Foundation grant OCE 11-24141 to CV, and European Science Foundation EuroDeep BIOFUN grant CTM2007-28739-E to EM. This article commits to EU HERMIONE [contract no. 226354] and CoCoNet [contract no. 287844] programs, and the Italian MIUR flag Ritmare within the National Research Program 2011–2013.
    Keywords: Pockmarks ; Cold seeps ; Hydrocarbons ; Prokaryotic diversity ; Bacteria ; Archaea ; Hydrocarbon degradation ; Microbial diversity
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    Multiplexed spectral imaging of 120 different fluorescent labels (2016)
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    Publication Date: 2022-05-26
    Description: This article is distributed under the terms of the Creative Commons public domain dedication. The definitive version was published in PLoS One 11 (2016): e0158495, doi:10.1371/journal.pone.0158495.
    Description: The number of fluorescent labels that can unambiguously be distinguished in a single image when acquired through band pass filters is severely limited by the spectral overlap of available fluorophores. The recent development of spectral microscopy and the application of linear unmixing algorithms to spectrally recorded image data have allowed simultaneous imaging of fluorophores with highly overlapping spectra. However, the number of distinguishable fluorophores is still limited by the unavoidable decrease in signal to noise ratio when fluorescence signals are fractionated over multiple wavelength bins. Here we present a spectral image analysis algorithm to greatly expand the number of distinguishable objects labeled with binary combinations of fluorophores. Our algorithm utilizes a priori knowledge about labeled specimens and imposes a binary label constraint on the unmixing solution. We have applied our labeling and analysis strategy to identify microbes labeled by fluorescence in situ hybridization and here demonstrate the ability to distinguish 120 differently labeled microbes in a single image.
    Description: This work was supported by Grant 2007-3- 13 from the Alfred P. Sloan Foundation (to GGB), National Institutes of Health Grant 1RC1-DE020630 from the National Institute of Dental and Craniofacial Research (NIDCR) (to GGB) and by National Institutes of Health Fellowship 1F31-DE019576 from NIDCR (to AMV).
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    Methanol production by a broad phylogenetic array of marine phytoplankton (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS 11 (2016): e0150820, doi:10.1371/journal.pone.0150820.
    Description: Methanol is a major volatile organic compound on Earth and serves as an important carbon and energy substrate for abundant methylotrophic microbes. Previous geochemical surveys coupled with predictive models suggest that the marine contributions are exceedingly large, rivaling terrestrial sources. Although well studied in terrestrial ecosystems, methanol sources are poorly understood in the marine environment and warrant further investigation. To this end, we adapted a Purge and Trap Gas Chromatography/Mass Spectrometry (P&T-GC/MS) method which allowed reliable measurements of methanol in seawater and marine phytoplankton cultures with a method detection limit of 120 nanomolar. All phytoplankton tested (cyanobacteria: Synechococcus spp. 8102 and 8103, Trichodesmium erythraeum, and Prochlorococcus marinus), and Eukarya (heterokont diatom: Phaeodactylum tricornutum, coccolithophore: Emiliania huxleyi, cryptophyte: Rhodomonas salina, and non-diatom heterokont: Nannochloropsis oculata) produced methanol, ranging from 0.8–13.7 micromolar in culture and methanol per total cellular carbon were measured in the ranges of 0.09–0.3%. Phytoplankton culture time-course measurements displayed a punctuated production pattern with maxima near early stationary phase. Stabile isotope labeled bicarbonate incorporation experiments confirmed that methanol was produced from phytoplankton biomass. Overall, our findings suggest that phytoplankton are a major source of methanol in the upper water column of the world’s oceans.
    Description: This project was solely supported by a grant to TJM from the National Science Foundation (Award# CHE-OCE 1131415).
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    Interspecific hybridization in pilot whales and asymmetric genetic introgression in northern Globicephala melas under the scenario of global warming (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 11 (2016): e0160080, doi: 10.1371/journal.pone.0160080 .
    Description: Pilot whales are two cetacean species (Globicephala melas and G. macrorhynchus) whose distributions are correlated with water temperature and partially overlap in some areas like the North Atlantic Ocean. In the context of global warming, distribution range shifts are expected to occur in species affected by temperature. Consequently, a northward displacement of the tropical pilot whale G. macrorynchus is expected, eventually leading to increased secondary contact areas and opportunities for interspecific hybridization. Here, we describe genetic evidences of recurrent hybridization between pilot whales in northeast Atlantic Ocean. Based on mitochondrial DNA sequences and microsatellite loci, asymmetric introgression of G. macrorhynchus genes into G. melas was observed. For the latter species, a significant correlation was found between historical population growth rate estimates and paleotemperature oscillations. Introgressive hybridization, current temperature increases and lower genetic variation in G. melas suggest that this species could be at risk in its northern range. Under increasing environmental and human-mediated stressors in the North Atlantic Ocean, it seems recommendable to develop a conservation program for G. melas.
    Description: LM had a PCTI Grant from the Asturias Regional Government, referenced BP 10-004. MAS was supported by a 2013 FCT Investigator contract through POPH, QREN European Social Fund and the Portuguese Ministry for Science and Education. This study was also supported by a grant from the Principality of Asturias (reference: GRUPIN-2014-093).
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    Hydrogen limitation and syntrophic growth among natural assemblages of thermophilic methanogens at deep-sea hydrothermal vents (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 1240, doi:10.3389/fmicb.2016.01240.
    Description: Thermophilic methanogens are common autotrophs at hydrothermal vents, but their growth constraints and dependence on H2 syntrophy in situ are poorly understood. Between 2012 and 2015, methanogens and H2-producing heterotrophs were detected by growth at 80∘C and 55∘C at most diffuse (7–40∘C) hydrothermal vent sites at Axial Seamount. Microcosm incubations of diffuse hydrothermal fluids at 80∘C and 55∘C demonstrated that growth of thermophilic and hyperthermophilic methanogens is primarily limited by H2 availability. Amendment of microcosms with NH4+ generally had no effect on CH4 production. However, annual variations in abundance and CH4 production were observed in relation to the eruption cycle of the seamount. Microcosm incubations of hydrothermal fluids at 80∘C and 55∘C supplemented with tryptone and no added H2 showed CH4 production indicating the capacity in situ for methanogenic H2 syntrophy. 16S rRNA genes were found in 80∘C microcosms from H2-producing archaea and H2-consuming methanogens, but not for any bacteria. In 55∘C microcosms, sequences were found from H2-producing bacteria and H2-consuming methanogens and sulfate-reducing bacteria. A co-culture of representative organisms showed that Thermococcus paralvinellae supported the syntrophic growth of Methanocaldococcus bathoardescens at 82∘C and Methanothermococcus sp. strain BW11 at 60∘C. The results demonstrate that modeling of subseafloor methanogenesis should focus primarily on H2 availability and temperature, and that thermophilic H2 syntrophy can support methanogenesis within natural microbial assemblages and may be an important energy source for thermophilic autotrophs in marine geothermal environments.
    Description: This work was funded by the Gordon and Betty Moore Foundation grant GBMF 3297, the NASA Earth and Space Science Fellowship Program grant NNX11AP78H, the National Science Foundation grant OCE-1547004, with funding from NOAA/PMEL, contribution #4493, and JISAO under NOAA Cooperative Agreement NA15OAR4320063, contribution #2706.
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    Functional genomics and phylogenetic evidence suggest genus-wide cobalamin production by the globally distributed marine nitrogen fixer Trichodesmium (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 189, doi:10.3389/fmicb.2018.00189.
    Description: Only select prokaryotes can biosynthesize vitamin B12 (i.e., cobalamins), but these organic co-enzymes are required by all microbial life and can be vanishingly scarce across extensive ocean biomes. Although global ocean genome data suggest cyanobacteria to be a major euphotic source of cobalamins, recent studies have highlighted that 〉95% of cyanobacteria can only produce a cobalamin analog, pseudo-B12, due to the absence of the BluB protein that synthesizes the α ligand 5,6-dimethylbenzimidizole (DMB) required to biosynthesize cobalamins. Pseudo-B12 is substantially less bioavailable to eukaryotic algae, as only certain taxa can intracellularly remodel it to one of the cobalamins. Here we present phylogenetic, metagenomic, transcriptomic, proteomic, and chemical analyses providing multiple lines of evidence that the nitrogen-fixing cyanobacterium Trichodesmium transcribes and translates the biosynthetic, cobalamin-requiring BluB enzyme. Phylogenetic evidence suggests that the Trichodesmium DMB biosynthesis gene, bluB, is of ancient origin, which could have aided in its ecological differentiation from other nitrogen-fixing cyanobacteria. Additionally, orthologue analyses reveal two genes encoding iron-dependent B12 biosynthetic enzymes (cbiX and isiB), suggesting that iron availability may be linked not only to new nitrogen supplies from nitrogen fixation, but also to B12 inputs by Trichodesmium. These analyses suggest that Trichodesmium contains the genus-wide genomic potential for a previously unrecognized role as a source of cobalamins, which may prove to considerably impact marine biogeochemical cycles.
    Description: This work was funded by NSF research grants OCE-1260233, OCE-1260490, OCE-1657757, and OCE-143566.
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    Marine virus-like particles and microbes : a linear interpretation (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 358, doi:10.3389/fmicb.2018.00358.
    Description: Viruses are key players in ocean ecology and biogeochemistry, not only because of their functional roles but also partially due to their sheer abundance (Fuhrman, 1999; Wilhelm and Suttle, 1999). Because viruses cannot replicate without their hosts' machinery, their abundance is inextricably related to that of their (mostly microbial) hosts. The relationship between viral and microbial abundances is thus of great interest.
    Keywords: Marine viruses ; Virus ; Virioplankton ; Viral abundance ; Virus-like particles ; Virus to microbe ratio ; Virus to bacterium ratio ; Virus-microbe relationship
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    Optical dignatures of dissolved organic matter transformation in the global ocean (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 2 (2016): 118, doi:10.3389/fmars.2015.00118.
    Description: Characterization of dissolved organic matter (DOM) in terms of its composition and optical properties, with an eye toward ultimately understanding its deep ocean dynamics, is the currently active frontier in DOM research. We used UV-visible absorption spectroscopy and fluorescence excitation-emission matrix (EEM) spectroscopy to characterize DOM in the open ocean along sections of the U.S. CO2/CLIVAR Repeat Hydrography Project located in all the major ocean basins outside the Arctic. Despite large differences in fluorescence intensity between ocean basins, some variability patterns were similar throughout the global ocean, suggesting similar processes controlling the composition of the DOM. We find that commercially available single channel CDOM sensors are sensitive to the fluorescence of humic materials in the deep ocean and thermocline but not to the UVA-fluorescing and absorbing materials that characterize freshly produced CDOM in surface waters, revealing fundamental diversity in the DOM profile. In surface waters, UVA fluorescence and absorption signatures indicate the presence of freshly produced material and the process of bleaching removal, but in the upper mesopelagic and in the main thermocline these optical signatures are replaced by those of humic materials, with distribution patterns correlated to apparent oxygen utilization (AOU) and other signatures of remineralization. Empirical orthogonal function analysis (EOF) of the EEM data suggests the presence of two (unidentified) processes which convert “fresh” DOM to humic materials: one located in the surface ocean (shallower than 500 m) and one located in the main thermocline. These inferred humification processes represent less than 5% of the overall variability in oceanic humic DOM fluorescence, which appears to be dominated by terrestrial input and solar bleaching of humic materials.
    Description: This research was supported by grants from NASA (grants NAG5-13277 and NNX14AG24G) and NSF (OCE-0241614 and OCE-0648541) to NN and D. A. Siegel.
    Keywords: CDOM ; FDOM ; Humic material ; Oceanic CDOM cycling ; Fluorescence analysis
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    Iron-binding ligands in the Southern California Current System : mechanistic studies (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 27, doi:10.3389/fmars.2016.00027.
    Description: The distributions of dissolved iron and organic iron-binding ligands were examined in water column profiles and deckboard incubation experiments in the southern California Current System (sCCS) along a transition from coastal to semi-oligotrophic waters. Analysis of the iron-binding ligand pool by competitive ligand exchange-adsorptive cathodic stripping voltammetry (CLE-ACSV) using multiple analytical windows (MAWs) revealed three classes of iron-binding ligands present throughout the water column (L1−L3), whose distributions closely matched those of dissolved iron and nitrate. Despite significant biogeochemical gradients, ligand profiles were similar between stations, with surface minima in strong ligands (L1 and L2), and relatively constant concentrations of weaker ligands (L3) down to 500 m. A phytoplankton grow-out incubation, initiated from an iron-limited water mass, showed dynamic temporal cycling of iron-binding ligands. A biological iron model was able to capture the patterns of the strong ligands in the grow-out incubation relatively well with only the microbial community as a biological source. An experiment focused on remineralization of particulate organic matter showed production of both strong and weak iron-binding ligands by the heterotrophic community, supporting a mechanism for in-situ production of both strong and weak iron-binding ligands in the subsurface water column. Photochemical experiments showed a variable influence of sunlight on the degradation of natural iron-binding ligands, providing some evidence to explain differences in surface ligand concentrations between stations. Patterns in ligand distributions between profiles and in the incubation experiments were primarily related to macronutrient concentrations, suggesting microbial remineralization processes might dominate on longer time-scales over short-term changes associated with photochemistry or phytoplankton growth.
    Description: RB, KB, and MC were supported by NSF OCE #10-2667 for the CCE-LTER program. MJ was funded by NSF ANT grant 0948378 and Harbor Branch Oceanographic Institute Foundation.
    Keywords: California Current Ecosystem ; Long term ecological research ; Iron limitation ; Dissolved iron-binding ligands ; Multiple analytical windows ; Electrochemistry
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    Arctic deltaic lake sediments as recorders of fluvial organic matter deposition (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Earth Science 4 (2016): 77, doi:10.3389/feart.2016.00077.
    Description: Arctic deltas are dynamic and vulnerable regions that play a key role in land-ocean interactions and the global carbon cycle. Delta lakes may provide valuable historical records of the quality and quantity of fluvial fluxes, parameters that are challenging to investigate in these remote regions. Here we study lakes from across the Mackenzie Delta, Arctic Canada, that receive fluvial sediments from the Mackenzie River when spring flood water levels rise above natural levees. We compare downcore lake sediments with suspended sediments collected during the spring flood, using bulk (% organic carbon, % total nitrogen, δ13C, Δ14C) and molecular organic geochemistry (lignin, leaf waxes). High-resolution age models (137Cs, 210Pb) of downcore lake sediment records (n = 11) along with lamina counting on high-resolution radiographs show sediment deposition frequencies ranging between annually to every 15 years. Down-core geochemical variability in a representative delta lake sediment core is consistent with historical variability in spring flood hydrology (variability in peak discharge, ice jamming, peak water levels). Comparison with earlier published Mackenzie River depth profiles shows that (i) lake sediments reflect the riverine surface suspended load, and (ii) hydrodynamic sorting patterns related to spring flood characteristics are reflected in the lake sediments. Bulk and molecular geochemistry of suspended particulate matter from the spring flood peak and lake sediments are relatively similar showing a mixture of modern higher-plant derived material, older terrestrial permafrost material, and old rock-derived material. This suggests that deltaic lake sedimentary records hold great promise as recorders of past (century-scale) riverine fluxes and may prove instrumental in shedding light on past behavior of arctic rivers, as well as how they respond to a changing climate.
    Description: Funding was provided by the US National Science Foundation as part of the Arctic Great Rivers Observatory (NSF-0732522 and NSF-1107774), as well as the Netherlands Organization for Scientific Research (Rubicon #825.10.022, and Veni #863.12.004). Additional funding for the lake coring was provided from WHOI through its Ocean and Climate Change Institute.
    Keywords: Lignin ; Biomarkers ; Mackenzie River ; Carbon isotopes ; Lake sediments
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    Prediction of the export and fate of global ocean net primary production : the EXPORTS Science Plan (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 22, doi:10.3389/fmars.2016.00022.
    Description: Ocean ecosystems play a critical role in the Earth's carbon cycle and the quantification of their impacts for both present conditions and for predictions into the future remains one of the greatest challenges in oceanography. The goal of the EXport Processes in the Ocean from Remote Sensing (EXPORTS) Science Plan is to develop a predictive understanding of the export and fate of global ocean net primary production (NPP) and its implications for present and future climates. The achievement of this goal requires a quantification of the mechanisms that control the export of carbon from the euphotic zone as well as its fate in the underlying “twilight zone” where some fraction of exported carbon will be sequestered in the ocean's interior on time scales of months to millennia. Here we present a measurement/synthesis/modeling framework aimed at quantifying the fates of upper ocean NPP and its impacts on the global carbon cycle based upon the EXPORTS Science Plan. The proposed approach will diagnose relationships among the ecological, biogeochemical, and physical oceanographic processes that control carbon cycling across a range of ecosystem and carbon cycling states leading to advances in satellite diagnostic and numerical prognostic models. To collect these data, a combination of ship and robotic field sampling, satellite remote sensing, and numerical modeling is proposed which enables the sampling of the many pathways of NPP export and fates. This coordinated, process-oriented approach has the potential to foster new insights on ocean carbon cycling that maximizes its societal relevance through the achievement of research goals of many international research agencies and will be a key step toward our understanding of the Earth as an integrated system.
    Description: The development of the EXPORTS Science Plan was supported by NASA Ocean Biology and Biogeochemistry program (award NNX13AC35G).
    Keywords: Satellite remote sensing ; Field campain ; Science plan ; Ocean carbon cycling ; Biological pump
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    Differential cellular responses associated with oxidative stress and cell fate decision under nitrate and phosphate limitations in Thalassiosira pseudonana : comparative proteomics (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 12 (2017): e0184849, doi:10.1371/journal.pone.0184849.
    Description: Diatoms are important components of marine ecosystems and contribute greatly to the world's primary production. Despite their important roles in ecosystems, the molecular basis of how diatoms cope with oxidative stress caused by nutrient fluctuations remains largely unknown. Here, an isobaric tags for relative and absolute quantitation (iTRAQ) proteomic method was coupled with a series of physiological and biochemical techniques to explore oxidative stress- and cell fate decision-related cellular and metabolic responses of the diatom Thalassiosira pseudonana to nitrate (N) and inorganic phosphate (P) stresses. A total of 1151 proteins were detected; 122 and 56 were significantly differentially expressed from control under N- and P-limited conditions, respectively. In N-limited cells, responsive proteins were related to reactive oxygen species (ROS) accumulation, oxidative stress responses and cell death, corresponding to a significant decrease in photosynthetic efficiency, marked intracellular ROS accumulation, and caspase-mediated programmed cell death activation. None of these responses were identified in P-limited cells; however, a significant up-regulation of alkaline phosphatase proteins was observed, which could be the major contributor for P-limited cells to cope with ambient P deficiency. These findings demonstrate that fundamentally different metabolic responses and cellular regulations are employed by the diatom in response to different nutrient stresses and to keep the cells viable.
    Description: This study was funded by the National Natural Science Foundation of China (41576138, 41076080, 41576138) to Dr. Jun-Rong Liang; the Woods Hole Center for Oceans and Human Health, National Science Foundation (OCE-1314642) to Dr. DonaldM Anderson; the National Institute of Environmental Health Sciences (1-P01-ES021923- 01) to Dr. DonaldM Anderson; and the ERC Advanced Award Diatomite and ANR project DiaDomOil to Dr. Chris Bowler.
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    Seasonal shifts in bacterial community responses to phytoplankton-derived dissolved organic matter in the Western Antarctic Peninsula (2017)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 8 (2017): 2117, doi:10.3389/fmicb.2017.02117.
    Description: Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August–December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.
    Description: CL was partially funded by the Graduate School and the Department of Ecology and Evolutionary Biology at Brown University and the Brown University-Marine Biological Laboratory Joint Graduate Program. This material is based upon work supported by the National Science Foundation under Grant Nos. ANT-1142114 to LA-Z, OPP-0823101 and PLR-1440435 to HD, and ANT-1141993 to JR. The Gordon and Betty Moore Foundation grant 1711 supported work by DR.
    Keywords: 16S rRNA ; Amplicon sequencing ; Community assembly ; Bacterial succession ; Mesocosms ; Collwelliaceae ; Polaribacter ; Phytoplankton exudates
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    Evidence of diel vertical migration of mesopelagic sound-scattering organisms in the Arctic (2017)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 332, doi:10.3389/fmars.2017.00332.
    Description: While sound scattering layers (SSLs) have been described previously from ice-covered waters in the Arctic, the existence of a viable mesopelagic community that also includes mesopelagic fishes in the Arctic has been questioned. In addition, it has been hypothesized that vertical migration would hardly exist in these areas. We wanted to check if deep scattering layers (DSLs) was found to the west and north of Svalbard (79°30′N−82°10′N) during autumn 2015, and if present; whether organisms in such DSLs undertook vertical migrations. Our null hypothesis was that there would be no evidence of diel vertical migration. Multi-frequency acoustic observations by hull mounted echo sounder (18, 38, and 120 kHz) revealed a DSL at depths ~210–510 m in areas with bottom depths exceeding ~600 m. Investigating eight geographical locations that differed with respect to time periods, light cycle and sea ice conditions, we show that the deeper layer of DSL displayed a clear ascending movement during night time and a descending movement during daytime. The high-light weighted mean depth (WMD) (343–514 m) with respect to backscattered energy was statistically deeper than the low-light WMD (179–437 m) for the locations studied. This behavior of the DSL was found to be consistent both when the sun was continuously above the horizon and after it started to set on 1 September, and both in open water and sea ice covered waters. The WMD showed an increasing trend, while the nautical area backscattering strength from the DSL showed a decreasing trend from south to north among the studied locations. Hydrographic observations revealed that the diel migration was found in the lower part of the north-flowing Atlantic Water, and was disconnected from the surface water masses above the Atlantic Water during day and night. The organisms conducting vertical migrations were studied by vertical and oblique hauls with zooplankton nets and pelagic trawls. These data suggest that these organisms were mainly various mesopelagic fishes, some few larger fishes, large zooplankton like krill and amphipods, and various gelatinous forms.
    Description: The Research Council of Norway is thanked for the financial support through the projects “The Arctic Ocean Ecosystem” — (SI_ARCTIC, RCN 228896), the “Effects of climate change on the Calanus complex”—(ECCO, RCN 200508), “Harvesting marine cold water plankton species—abundance estimation and stock assessment”—(Harvest II, RCN 203871).
    Keywords: Arctic Ocean ; Deep scattering layer ; Diel vertical migration ; Mesopelagic organisms ; Acoustics
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    Positive feedbacks enhance macroalgal resilience on degraded coral reefs (2017)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 11 (2016): e0155049, doi:10.1371/journal.pone.0155049.
    Description: Many reefs have shifted from coral and fish dominated habitats to less productive macroalgal dominated habitats, and current research is investigating means of reversing this phase shift. In the tropical Pacific, overfished reefs with inadequate herbivory can become dominated by the brown alga Sargassum polycystum. This alga suppresses recruitment and survival of corals and fishes, thus limiting the potential for reef recovery. Here we investigate the mechanisms that reinforce S. polycystum dominance and show that in addition to negatively affecting other species, this species acts in a self-reinforcing manner, positively promoting survival and growth of conspecifics. We found that survival and growth of both recruit-sized and mature S. polycystum fronds were higher within Sargassum beds than outside the beds and these results were found in both protected and fished reefs. Much of this benefit resulted from reduced herbivory within the Sargassum beds, but adult fronds also grew ~50% more within the beds even when herbivory did not appear to be occurring, suggesting some physiological advantage despite the intraspecific crowding. Thus via positive feedbacks, S. polycystum enhances its own growth and resistance to herbivores, facilitating its dominance (perhaps also expansion) and thus its resilience on degraded reefs. This may be a key feedback mechanism suppressing the recovery of coral communities in reefs dominated by macroalgal beds.
    Description: Financial support came to MEH from the National Science Foundation (OCE 0929119), the National Institutes of Health (2 U19 TW007401-10), and the Teasley Endowment to the Georgia Institute of Technology.
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    Preservation of three-dimensional spatial structure in the gut microbiome (2017)
    Public Library of Science
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 12 (2017): e0188257, doi:10.1371/journal.pone.0188257.
    Description: Preservation of three-dimensional structure in the gut is necessary in order to analyze the spatial organization of the gut microbiota and gut luminal contents. In this study, we evaluated preparation methods for mouse gut with the goal of preserving micron-scale spatial structure while performing fluorescence imaging assays. Our evaluation of embedding methods showed that commonly used media such as Tissue-Tek Optimal Cutting Temperature (OCT) compound, paraffin, and polyester waxes resulted in redistribution of luminal contents. By contrast, a hydrophilic methacrylate resin, Technovit H8100, preserved three-dimensional organization. Our mouse intestinal preparation protocol optimized using the Technovit H8100 embedding method was compatible with microbial fluorescence in situ hybridization (FISH) and other labeling techniques, including immunostaining and staining with both wheat germ agglutinin (WGA) and 4', 6-diamidino-2-phenylindole (DAPI). Mucus could be visualized whether the sample was fixed with paraformaldehyde (PFA) or with Carnoy’s fixative. The protocol optimized in this study enabled simultaneous visualization of micron-scale spatial patterns formed by microbial cells in the mouse intestines along with biogeographical landmarks such as host-derived mucus and food particles.
    Description: Funding provided by National Science Foundation (www.nsf.gov) grant 1650141 to J.L.M.W. and National Institutes of Health National Institute of Dental and Craniofacial Research (www.nidcr.nih.gov) grant DE022586 to G.G.B.
    Repository Name: Woods Hole Open Access Server
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    Evidence for strain-specific exometabolomic responses of the coccolithophore Emiliania huxleyi to grazing by the dinoflagellate oxyrrhis marina (2017)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 3 (2016): 1, doi:10.3389/fmars.2016.00001.
    Description: The coccolithophore Emiliania huxleyi forms massive blooms and plays a critical role in global elemental cycles, sequestering significant amounts of atmospheric carbon dioxide on geological time scales via production of calcium carbonate coccoliths and emitting dimethyl sulfoniopropionate (DMSP), which has the potential for increasing atmosph-eric albedo. Because grazing in pelagic systems is a major top-down force structuring microbial communities, the influence of grazers on E. huxleyi populations has been of interest to researchers. Roles of DMSP (and related metabolites) in interactions between E. huxleyi and protist grazers have been investigated, however, little is known about the release of other metabolites that may influence, or be influenced by, such grazing interactions. We used high-resolution mass spectrometry in an untargeted approach to survey the suite of low molecular weight compounds released by four different E. huxleyi strains in response to grazing by the dinoflagellate Oxyrrhis marina. Overall, a strikingly small number of metabolites were detected from E. huxleyi and O. marina cells, but these were distinctly informative to construct metabolic footprints. At most, E. huxleyi strains shared 25% of released metabolites. Furthermore, there appeared to be no unified metabolic response in E. huxleyi strains to grazing; rather, these responses were strain specific. Concentrations of several metabolites also positively correlated with grazer activities, including grazing, ingestion, and growth rates; however, no single metabolite responded uniformly across all strains of E. huxleyi tested. Regardless, grazing clearly transformed the constituents of dissolved organic matter produced by these marine microbes. This study addresses several technical challenges, and presents a platform to further study the influence of chemical cues in aquatic systems and demonstrates the impact of strain diversity and grazing on the complexity of dissolved organic matter in marine systems.
    Description: Funding for this work was provided by the Gordon and Betty Moore Foundation, Grant #3301 awarded to A Vardi, BAS. Van Mooy, K Bidle, MJ, and TM. Additional funding for this work was provided by an award from the Flatley Discovery Lab to TM.
    Keywords: Dissolved organic matter ; Environmental metabolomics ; Grazing ; Metabolic footprinting ; Phytoplankton
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