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  • Springer Nature  (263,838)
  • Molecular Diversity Preservation International (MDPI)
  • 2020-2023  (36)
  • 2015-2019  (249,936)
  • 1945-1949  (14,934)
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  • 1
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    South Atlantic paleobathymetry since early Creteceous (2017)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 7(11819)
    Details
    Publication Date: 2017-09-24
    Description: We present early Cretaceous to present paleobathymetric reconstructions and quantitative uncertainty estimates for the South Atlantic, offering a strong basis for studies of paleocirculation, paleoclimate and paleobiogeography. Circulation in an initially salty and anoxic ocean, restricted by the topography of the Falkland Plateau, Rio Grande Ridge and Walvis Rise, favoured deposition of thick evaporites in shallow water of the Brazilian-Angolan margins. This ceased as sea oor spreading propagated northwards, opening an equatorial gateway to shallow and intermediate circulation. This gateway, together with subsiding volcano-tectonic barriers would have played a key role in Late Cretaceous climate changes. Later deepening and widening of the South Atlantic, together with gateway opening at Drake Passage would lead, by mid-Miocene (∼15 Ma) to the establishment of modern-style thermohaline circulation.
    Repository Name: EPIC Alfred Wegener Institut
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  • 2
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    Evidence of long-term NAO influence on East-Central Europe winter precipitation from a guano-derived δ15N record (2017)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 7(1), ISSN: 2045-2322
    Details
    Publication Date: 2017-11-06
    Description: Currently there is a scarcity of paleo-records related to the North Atlantic Oscillation (NAO), particularly in East-Central Europe (ECE). Here we report δ15N analysis of guano from a cave in NW Romania with the intent of reconstructing past variation in ECE hydroclimate and examine NAO impacts on winter precipitation. We argue that the δ15N values of guano indicate that the nitrogen cycle is hydrologically controlled and the δ15N values likely reflect winter precipitation related to nitrogen mineralization prior to the growing season. Drier conditions indicated by δ15N values at AD 1848–1852 and AD 1880–1930 correspond to the positive phase of the NAO. The increased frequency of negative phases of the NAO between AD 1940–1975 is contemporaneous with higher δ15N values (wetter conditions). A 4‰ decrease in δ15N values at the end of the 1970’s corresponds to a strong reduction in precipitation associated with a shift from negative to positive phase of the NAO. Using the relationship between NAO index and δ15N values in guano for the instrumental period, we reconstructed NAO-like phases back to AD 1650. Our results advocate that δ15N values of guano offer a proxy of the NAO conditions in the more distant past, helping assess its predictability.
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
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    Along-shelf connectivity and circumpolar gene flow in Antarctic silverfish (Pleuragramma antarctica) (2018)
    Springer Nature
    In:  EPIC3Scientific reports, Springer Nature, 8(17856), pp. 1-16
    Details
    Publication Date: 2019-10-04
    Description: The Antarctic silverfish (Pleuragramma antarctica) is a critically important forage species with a circumpolar distribution and is unique among other notothenioid species for its wholly pelagic life cycle. Previous studies have provided mixed evidence of population structure over regional and circumpolar scales. The aim of the present study was to test the recent population hypothesis for Antarctic silverfish, which emphasizes the interplay between life history and hydrography in shaping connectivity. A total of 1067 individuals were collected over 25 years from different locations on a circumpolar scale. Samples were genotyped at fifteen microsatellites to assess population differentiation and genetic structuring using clustering methods, F-statistics, and hierarchical analysis of variance. A lack of differentiation was found between locations connected by the Antarctic Slope Front Current (ASF), indicative of high levels of gene flow. However, gene flow was significantly reduced at the South Orkney Islands and the western Antarctic Peninsula where the ASF is absent. This pattern of gene flow emphasized the relevance of large-scale circulation as a mechanism for circumpolar connectivity. Chaotic genetic patchiness characterized population structure over time, with varying patterns of differentiation observed between years, accompanied by heterogeneous standard length distributions. The present study supports a more nuanced version of the genetic panmixia hypothesis that reflects physical-biological interactions over the life history.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
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    Arctic megaslide at presumed rest (2016)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 6(38529), ISSN: 2045-2322
    Details
    Publication Date: 2016-12-16
    Description: Slope failure like in the Hinlopen/Yermak Megaslide is one of the major geohazards in a changing Arctic environment. We analysed hydroacoustic and 2D high-resolution seismic data from the apparently intact continental slope immediately north of the Hinlopen/Yermak Megaslide for signs of past and future instabilities. Our new bathymetry and seismic data show clear evidence for incipient slope instability. Minor slide deposits and an internally-deformed sedimentary layer near the base of the gas hydrate stability zone imply an incomplete failure event, most probably about 30000 years ago, contemporaneous to or shortly after the Hinlopen/Yermak Megaslide. An active gas reservoir at the base of the gas hydrate stability zone demonstrate that over-pressured fluids might have played a key role in the initiation of slope failure at the studied slope, but more importantly also for the giant HYM slope failure. To date, it is not clear, if the studied slope is fully preconditioned to fail completely in future or if it might be slowly deforming and creeping at present. We detected widespread methane seepage on the adjacent shallow shelf areas not sealed by gas hydrates.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
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    Production of fluorescent dissolved organic matter in Arctic Ocean sediments (2016)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, (39213), pp. 1-10
    Details
    Publication Date: 2017-07-05
    Description: Little is known about the production of fluorescent dissolved organic matter (FDOM) in the anoxic oceanic sediments. In this study, sediment pore waters were sampled from four different sites in the Chukchi-East Siberian Seas area to examine the bulk dissolved organic carbon (DOC) and their optical properties. The production of FDOM, coupled with the increase of nutrients, was observed above the sulfate-methane-transition-zone (SMTZ). The presence of FDOM was concurrent with sulfate reduction and increased alkalinity (R2 〉 0.96, p 〈 0.0001), suggesting a link to organic matter degradation. This inference was supported by the positive correlation (R2 〉 0.95, p 〈 0.0001) between the net production of FDOM and the modeled degradation rates of particulate organic carbon sulfate reduction. The production of FDOM was more pronounced in a shallow shelf site S1 with a total net production ranging from 17.9 to 62.3 RU for different FDOM components above the SMTZ depth of ca. 4.1 mbsf, which presumably underwent more accumulation of particulate organic matter than the other three deeper sites. The sediments were generally found to be the sources of CDOM and FDOM to the overlying water column, unearthing a channel of generally bio-refractory and pre-aged DOM to the oceans.
    Repository Name: EPIC Alfred Wegener Institut
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  • 6
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    Reconciling glacial Antarctic water stable isotopes with ice sheet topography and the isotopic paleothermometer (2018)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 9(3537), ISSN: 2041-1723
    Details
    Publication Date: 2018-09-17
    Description: Stable water isotope records from Antarctica are key for our understanding of Quaternary climate variations. However, the exact quantitative interpretation of these important climate proxy records in terms of surface temperature, ice sheet height and other climatic changes is still a matter of debate. Here we report results obtained with an atmospheric general circulation model equipped with water isotopes, run at a high-spatial horizontal resolution of one-by-one degree. Comparing different glacial maximum ice sheet reconstructions, a best model data match is achieved for the PMIP3 reconstruction. Reduced West Antarctic elevation changes between 400 and 800 m lead to further improved agreement with ice core data. Our modern and glacial climate simulations support the validity of the isotopic paleothermometer approach based on the use of present-day observations and reveal that a glacial ocean state as displayed in the GLAMAP reconstruction is suitable for capturing the observed glacial isotope changes in Antarctic ice cores.
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
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    The winter pack-ice zone provides a sheltered but food-poor habitat for larval Antarctic krill (2017)
    Springer Nature
    In:  EPIC3Nature Ecology & Evolution, Springer Nature, 1, pp. 1853-1861, ISSN: 2397-334X
    Details
    Publication Date: 2018-01-03
    Description: A dominant Antarctic ecological paradigm suggests that winter sea ice is generally the main feeding ground for krill larvae. Observations from our winter cruise to the southwest Atlantic sector of the Southern Ocean contradict this view and present the first evidence that the pack-ice zone is a food-poor habitat for larval development. In contrast, the more open marginal ice zone provides a more favourable food environment for high larval krill growth rates. We found that complex under-ice habitats are, however, vital for larval krill when water column productivity is limited by light, by providing structures that offer protec- tion from predators and to collect organic material released from the ice. The larvae feed on this sparse ice-associated food during the day. After sunset, they migrate into the water below the ice (upper 20 m) and drift away from the ice areas where they have previously fed. Model analyses indicate that this behaviour increases both food uptake in a patchy food environment and the likelihood of overwinter transport to areas where feeding conditions are more favourable in spring.
    Repository Name: EPIC Alfred Wegener Institut
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  • 8
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    Submarine slope failures due to pipe structure formation (2018)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 9(1), pp. 715, ISSN: 2041-1723
    Details
    Publication Date: 2018-03-04
    Description: There is a strong spatial correlation between submarine slope failures and the occurrence of gas hydrates. This has been attributed to the dynamic nature of gas hydrate systems and the potential reduction of slope stability due to bottom water warming or sea level drop. However, 30 years of research into this process found no solid supporting evidence. Here we present new reflection seismic data from the Arctic Ocean and numerical modelling results supporting a different link between hydrates and slope stability. Hydrates reduce sediment permeability and cause build-up of overpressure at the base of the gas hydrate stability zone. Resulting hydro-fracturing forms pipe structures as pathways for overpressured fluids to migrate upward. Where these pipe structures reach shallow permeable beds, this overpressure transfers laterally and destabilises the slope. This process reconciles the spatial correlation of submarine landslides and gas hydrate, and it is independent of environmental change and water depth.
    Repository Name: EPIC Alfred Wegener Institut
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  • 9
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    Tundra landform and vegetation productivity trend maps for the Arctic Coastal Plain of northern Alaska (2018)
    Springer Nature
    In:  EPIC3Scientific Data, Springer Nature, 5, pp. 180058, ISSN: 2052-4463
    Details
    Publication Date: 2018-04-15
    Description: Arctic tundra landscapes are composed of a complex mosaic of patterned ground features, varying in soil moisture, vegetation composition, and surface hydrology over small spatial scales (10–100 m). The importance of microtopography and associated geomorphic landforms in influencing ecosystem structure and function is well founded, however, spatial data products describing local to regional scale distribution of patterned ground or polygonal tundra geomorphology are largely unavailable. Thus, our understanding of local impacts on regional scale processes (e.g., carbon dynamics) may be limited. We produced two key spatiotemporal datasets spanning the Arctic Coastal Plain of northern Alaska (~60,000 km2) to evaluate climate-geomorphological controls on arctic tundra productivity change, using (1) a novel 30m classification of polygonal tundra geomorphology and (2) decadal-trends in surface greenness using the Landsat archive (1999–2014). These datasets can be easily integrated and adapted in an array of local to regional applications such as (1) upscaling plot-level measurements (e.g., carbon/energy fluxes), (2) mapping of soils, vegetation, or permafrost, and/or (3) initializing ecosystem biogeochemistry, hydrology, and/or habitat modeling.
    Repository Name: EPIC Alfred Wegener Institut
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  • 10
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    Predictability of Arctic sea ice on weather time scales (2018)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 8(6514), pp. 1-7, ISSN: 2045-2322
    Details
    Publication Date: 2018-04-30
    Description: The field of Arctic sea ice prediction on “weather time scales” is still in its infancy with little existing understanding of the limits of predictability. This is especially true for sea ice deformation along so-called Linear Kinematic Features (LKFs) including leads that are relevant for marine operations. Here the potential predictability of the sea ice pack in the wintertime Arctic up to ten days ahead is determined, exploiting the fact that sea ice-ocean models start to show skill at representing sea ice deformation at high spatial resolutions. Results are based on ensemble simulations with a high-resolution sea ice-ocean model driven by atmospheric ensemble forecasts. The predictability of LKFs as measured by different metrics drops quickly, with predictability being almost completely lost after 4–8 days. In contrast, quantities such as sea ice concentration or the location of the ice edge retain high levels of predictability throughout the full 10-day forecast period. It is argued that the rapid error growth for LKFs is mainly due to the chaotic behaviour of the atmosphere associated with the low predictability of near surface wind divergence and vorticity; initial condition uncertainty for ice thickness is found to be of minor importance as long as LKFs are initialized at the right locations.
    Repository Name: EPIC Alfred Wegener Institut
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  • 11
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    Functional characterization of the circadian clock in the Antarctic krill, Euphausia superba (2017)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 7(17742), ISSN: 2045-2322
    Details
    Publication Date: 2018-01-08
    Description: Antarctic krill (Euphausia superba) is a key species in Southern Ocean ecosystem where it plays a central role in the Antarctic food web. Available information supports the existence of an endogenous timing system in krill enabling it to synchronize metabolism and behavior with an environment characterized by extreme seasonal changes in terms of day length, food availability, and surface ice extent. A screening of our transcriptome database “KrillDB” allowed us to identify the putative orthologues of 20 circadian clock components. Mapping of conserved domains and phylogenetic analyses strongly supported annotations of the identi ed sequences. Luciferase assays and co-immunoprecipitation experiments allowed us to de ne the role of the main clock components. Our ndings provide an overall picture of the molecular mechanisms underlying the functioning of the endogenous circadian clock in the Antarctic krill and shed light on their evolution throughout crustaceans speciation. Interestingly, the core clock machinery shows both mammalian and insect features that presumably contribute to an evolutionary strategy to cope with polar environment’s challenges. Moreover, despite the extreme variability characterizing the Antarctic seasonal day length, the conserved light mediated degradation of the photoreceptor EsCRY1 suggests a persisting pivotal role of light as a Zeitgeber.
    Repository Name: EPIC Alfred Wegener Institut
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  • 12
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    Reduced arctic tundra productivity linked with landform and climate change interactions (2018)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 8(1), pp. 2345, ISSN: 2045-2322
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    Publication Date: 2018-04-15
    Description: Arctic tundra ecosystems have experienced unprecedented change associated with climate warming over recent decades. Across the Pan-Arctic, vegetation productivity and surface greenness have trended positively over the period of satellite observation. However, since 2011 these trends have slowed considerably, showing signs of browning in many regions. It is unclear what factors are driving this change and which regions/landforms will be most sensitive to future browning. Here we provide evidence linking decadal patterns in arctic greening and browning with regional climate change and local permafrost-driven landscape heterogeneity. We analyzed the spatial variability of decadal-scale trends in surface greenness across the Arctic Coastal Plain of northern Alaska (~60,000 km²) using the Landsat archive (1999–2014), in combination with novel 30 m classifications of polygonal tundra and regional watersheds, finding landscape heterogeneity and regional climate change to be the most important factors controlling historical greenness trends. Browning was linked to increased temperature and precipitation, with the exception of young landforms (developed following lake drainage), which will likely continue to green. Spatiotemporal model forecasting suggests carbon uptake potential to be reduced in response to warmer and/or wetter climatic conditions, potentially increasing the net loss of carbon to the atmosphere, at a greater degree than previously expected.
    Repository Name: EPIC Alfred Wegener Institut
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  • 13
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    Competition-induced starvation drives large-scale population cycles in Antarctic krill (2017)
    Springer Nature
    In:  EPIC3Nature Ecology & Evolution, Springer Nature, 1(0177)
    Details
    Publication Date: 2017-11-29
    Description: Antarctic krill (Euphausia superba)—one of the most abundant animal species on Earth—exhibits a five to six year population cycle, with oscillations in biomass exceeding one order of magnitude. Previous studies have postulated that the krill cycle is induced by periodic climatological factors, but these postulated drivers neither show consistent agreement, nor are they supported by quantitative models. Here, using data analysis complemented with modelling of krill ontogeny and population dynamics, we identify intraspecific competition for food as the main driver of the krill cycle, while external climatological factors possibly modulate its phase and synchronization over large scales. Our model indicates that the cycle amplitude increases with reduction of krill loss rates. Thus, a decline of apex predators is likely to increase the oscillation amplitude, potentially destabilizing the marine food web, with drastic consequences for the entire Antarctic ecosystem.
    Repository Name: EPIC Alfred Wegener Institut
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  • 14
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    An innovative methodology for the non-destructive diagnosis of architectural elements of ancient historical buildings (2018)
    Springer Nature
    In:  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
    Details
    Publication Date: 2019-03-26
    Description: In the following we present a new non-invasive methodology aimed at the diagnosis of stone building materials used in historical buildings and architectural elements. This methodology consists of the integrated sequential application of in situ proximal sensing methodologies such as the 3D Terrestrial Laser Scanner for the 3D modelling of investigated objects together with laboratory and in situ non-invasive multi-techniques acoustic data, preceded by an accurate petrographical study of the investigated stone materials by optical and scanning electron microscopy. The increasing necessity to integrate different types of techniques in the safeguard of the Cultural Heritage is the result of the following two interdependent factors: 1) The diagnostic process on the building stone materials of monuments is increasingly focused on difficult targets in critical situations. In these cases, the diagnosis using only one type of non-invasive technique may not be sufficient to investigate the conservation status of the stone materials of the superficial and inner parts of the studied structures 2) Recent technological and scientific developments in the field of non-invasive diagnostic techniques for different types of materials favors and supports the acquisition, processing and interpretation of huge multidisciplinary datasets.
    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: 4334
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Non-invasive methodology ; Stone building materials ; Diagnosis ; 3D Terrestrial Laser Scanner ; Non-invasive multi-techniques acoustic data ; Microscopy ; Methodology for the non-destructive diagnosis of architectural elements ; Cultural Heritage
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
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    Enhanced North Pacific deep-ocean stratification by stronger intermediate water formation during Heinrich Stadial 1 (2019)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 10(656), ISSN: 2041-1723
    Details
    Publication Date: 2021-02-16
    Description: The deglacial history of CO2 release from the deep North Pacific remains unresolved. This is due to conflicting indications about subarctic Pacific ventilation changes based on various marine proxies, especially for Heinrich Stadial 1 (HS-1) when a rapid atmospheric CO2 rise occurs. Here, we use a complex Earth System Model to investigate the deglacial North Pacific overturning and its control on ocean stratification. Our results show an enhanced intermediate-to-deep ocean stratification coeval with intensified North Pacific Intermediate Water (NPIW) formation during HS-1, compared to the Last Glacial Maximum. The stronger NPIW formation causes lower salinities and higher temperatures at intermediate depths. By lowering NPIW densities, this enlarges vertical density gradient and thus enhances intermediate-to-deep ocean stratification during HS-1. Physically, this process prevents the North Pacific deep waters from a better communication with the upper oceans, thus prolongs the existing isolation of glacial Pacific abyssal carbons during HS-1.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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    Studying the cardiovascular system of a marine crustacean with magnetic resonance imaging at 9.4 T (2019)
    Springer Nature
    In:  EPIC3Magnetic Resonance Materials in Physics, Biology and Medicine, Springer Nature, ISSN: 1352-8661
    Details
    Publication Date: 2019-05-27
    Description: An approach is presented for high-field MRI studies of the cardiovascular system (CVS) of a marine crustacean, the edible crab Cancer pagurus, submerged in highly conductive seawater. Structure and function of the CVS were investigated at 9.4 T. Cardiac motion was studied using self-gated CINE MRI. Imaging protocols and radio-frequency coil arrangements were tested for anatomical imaging. Haemolymph flow was quantified using phase-contrast angiography. Signal-to-noise-ratios and flow velocities in afferent and efferent branchial veins were compared with Student’s t test (n = 5). Seawater induced signal losses were dependent on imaging protocols and RF coil setup. Internal cardiac structures could be visualized with high spatial resolution within 8 min using a gradient-echo technique. Variations in haemolymph flow in different vessels could be determined over time. Maximum flow was similar within individual vessels and corresponded to literature values from Doppler measurements. Heart contractions were more pronounced in lateral and dorso-ventral directions than in the anterior–posterior direction. Choosing adequate imaging protocols in combination with a specific RF coil arrangement allows to monitor various parts of the crustacean CVS with exceptionally high spatial resolution despite the adverse effects of seawater at 9.4 T.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    Magma plumbing system and seismicity of an active mid-ocean ridge volcano (2017)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 7(42949), pp. 1-9
    Details
    Publication Date: 2017-03-23
    Description: At mid-ocean ridges volcanism generally decreases with spreading rate but surprisingly massive volcanic centres occur at the slowest spreading ridges. These volcanoes can host unexpectedly strong earthquakes and vigorous, explosive submarine eruptions. Our understanding of the geodynamic processes forming these volcanic centres is still incomplete due to a lack of geophysical data and the difficulty to capture their rare phases of magmatic activity. We present a local earthquake tomographic image of the magma plumbing system beneath the Segment 8 volcano at the ultraslow-spreading Southwest Indian Ridge. The tomography shows a confined domain of partial melt under the volcano. We infer that from there melt is horizontally transported to a neighbouring ridge segment at 35 km distance where microearthquake swarms and intrusion tremor occur that suggest ongoing magmatic activity. Teleseismic earthquakes around the Segment 8 volcano, prior to our study, indicate that the current magmatic spreading episode may already have lasted over a decade and hence its temporal extent greatly exceeds the frequent short-lived spreading episodes at faster opening mid-ocean ridges.
    Repository Name: EPIC Alfred Wegener Institut
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  • 18
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    Evidence for a palaeo-subglacial lake on the Antarctic continental shelf (2017)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 8, pp. 15591, ISSN: 2041-1723
    Details
    Publication Date: 2018-08-10
    Description: Subglacial lakes are widespread beneath the Antarctic Ice Sheet but their control on ice-sheet dynamics and their ability to harbour life remain poorly characterized. Here we present evidence for a palaeo-subglacial lake on the Antarctic continental shelf. A distinct sediment facies recovered from a bedrock basin in Pine Island Bay indicates deposition within a low-energy lake environment. Diffusive-advection modelling demonstrates that low chloride concentrations in the pore water of the corresponding sediments can only be explained by initial deposition of this facies in a freshwater setting. These observations indicate that an active subglacial meltwater network, similar to that observed beneath the extant ice sheet, was also active during the last glacial period. It also provides a new framework for refining the exploration of these unique environments.
    Repository Name: EPIC Alfred Wegener Institut
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  • 19
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    West Antarctic Ice Sheet retreat driven by Holocene warm water incursions (2017)
    Springer Nature
    In:  EPIC3Nature, Springer Nature, 547(7661), pp. 43-48, ISSN: 0028-0836
    Details
    Publication Date: 2018-08-10
    Description: Glaciological and oceanographic observations coupled with numerical models show that warm Circumpolar Deep Water (CDW) incursions onto the West Antarctic continental shelf cause melting of the undersides of floating ice shelves. Because these ice shelves buttress glaciers feeding into them, their ocean-induced thinning is driving Antarctic ice-sheet retreat today. Here we present a multi-proxy data based reconstruction of variability in CDW inflow to the Amundsen Sea sector, the most vulnerable part of the West Antarctic Ice Sheet, during the Holocene epoch (from 11.7 thousand years ago to the present). The chemical compositions of foraminifer shells and benthic foraminifer assemblages in marine sediments indicate that enhanced CDW upwelling, controlled by the latitudinal position of the Southern Hemisphere westerly winds, forced deglaciation of this sector from at least 10,400 years ago until 7,500 years ago—when an ice-shelf collapse may have caused rapid ice-sheet thinning further upstream—and since the 1940s. These results increase confidence in the predictive capability of current ice-sheet models.
    Repository Name: EPIC Alfred Wegener Institut
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  • 20
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    Erratum to: Distribution, density and abundance of Antarctic ice seals off Queen Maud Land and the eastern Weddell Sea (2017)
    Springer Nature
    In:  EPIC3Polar Biology, Springer Nature, 40(5), pp. 1167-1168, ISSN: 0722-4060
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    Publication Date: 2017-10-20
    Repository Name: EPIC Alfred Wegener Institut
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  • 21
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    Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ferrer-González, F. X., Widner, B., Holderman, N. R., Glushka, J., Edison, A. S., Kujawinski, E. B., & Moran, M. A. Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy. ISME Journal, (2020), doi:10.1038/s41396-020-00811-y.
    Description: The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-d-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.
    Description: This work was supported by grants from the Gordon and Betty Moore Foundation (5503) and the National Science Foundation (IOS-1656311) to MAM, ASE, and EBK, and by the Simons Foundation grant 542391 to MAM within the Principles of Microbial Ecosystems (PriME) Collaborative.
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    Paleozoic diversification of terrestrial chitin-degrading bacterial lineages (2019)
    Springer Nature
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gruen, D. S., Wolfe, J. M., & Fournier, G. P.. Paleozoic diversification of terrestrial chitin-degrading bacterial lineages. BMC Evolutionary Biology, 19, (2019): 34, doi:10.1186/s12862-019-1357-8.
    Description: Background Establishing the divergence times of groups of organisms is a major goal of evolutionary biology. This is especially challenging for microbial lineages due to the near-absence of preserved physical evidence (diagnostic body fossils or geochemical biomarkers). Horizontal gene transfer (HGT) can serve as a temporal scaffold between microbial groups and other fossil-calibrated clades, potentially improving these estimates. Specifically, HGT to or from organisms with fossil-calibrated age estimates can propagate these constraints to additional groups that lack fossils. While HGT is common between lineages, only a small subset of HGT events are potentially informative for dating microbial groups. Results Constrained by published fossil-calibrated studies of fungal evolution, molecular clock analyses show that multiple clades of Bacteria likely acquired chitinase homologs via HGT during the very late Neoproterozoic into the early Paleozoic. These results also show that, following these HGT events, recipient terrestrial bacterial clades likely diversified ~ 300–500 million years ago, consistent with established timescales of arthropod and plant terrestrialization. Conclusions We conclude that these age estimates are broadly consistent with the dispersal of chitinase genes throughout the microbial world in direct response to the evolution and ecological expansion of detrital-chitin producing groups. The convergence of multiple lines of evidence demonstrates the utility of HGT-based dating methods in microbial evolution. The pattern of inheritance of chitinase genes in multiple terrestrial bacterial lineages via HGT processes suggests that these genes, and possibly other genes encoding substrate-specific enzymes, can serve as a “standard candle” for dating microbial lineages across the Tree of Life.
    Description: This work was supported by a National Science Foundation (NSF) Graduate Research Fellowship Program Award to DSG., and Simons Collaboration on the Origins of Life Award #339603 and NSF Integrated Earth Systems Program Award #1615426 to GPF. The funding agencies for this study had no role in study design, data collection, data analysis and interpretation, or in writing the manuscript.
    Keywords: Horizontal gene transfer ; Chitinase ; Chitin ; Bacteria ; Fungi ; Arthropods
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    Superplume mantle tracked isotopically the length of Africa from the Indian Ocean to the Red Sea (2019)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 10(5493), ISSN: 2041-1723
    Details
    Publication Date: 2019-12-02
    Description: Seismological findings show a complex scenario of plume upwellings from a deep thermo-chemical anomaly (superplume) beneath the East African Rift System (EARS). It is unclear if these geophysical observations represent a true picture of the superplume and its influence on magmatism along the EARS. Thus, it is essential to find a geochemical tracer to establish where upwellings are connected to the deep-seated thermo-chemical anomaly. Here we identify a unique non-volatile superplume isotopic signature (‘C’) in the youngest (after 10 Ma) phase of widespread EARS rift-related magmatism where it extends into the Indian Ocean and the Red Sea. This is the first sound evidence that the superplume influences the EARS far from the low seismic velocities in the magma-rich northern half. Our finding shows for the first time that superplume mantle exists beneath the rift the length of Africa from the Red Sea to the Indian Ocean offshore southern Mozambique
    Repository Name: EPIC Alfred Wegener Institut
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    Antarctic marine animal forests: three-dimensional communities in Southern Ocean ecosystems (2017)
    Springer Nature
    In:  EPIC3Marine Animal Forests - The Ecology of Benthic Biodiversity Hotspots, Marine Animal Forests - The Ecology of Benthic Biodiversity Hotspots, Cham, Switzerland, Springer Nature, 29 p., pp. 315-344, ISBN: 978-3-319-21011-7
    Details
    Publication Date: 2019-11-19
    Repository Name: EPIC Alfred Wegener Institut
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    Exploring Employee Perceptions towards Smart Working during the COVID-19 Pandemic: a Comparative Analysis of Two Italian Public Research Organizations (2021)
    Springer Nature
    Details
    Publication Date: 2022-03-16
    Description: Of all the socio-economic changes caused by the Covid-19 pandemic, the disruption to workforce organizations will probably leave the largest indelible mark. The way work will be organized in the future will be closely linked to the experience of work-ing under the same institution’s response to the pandemic. This paper aims to fill the gap in knowledge about smart working (SW) in public organizations, with a focus on the experience of the employees of two Italian research organizations, CNR and INGV. Analysing primary data, it explored and assessed how SW had been experi-enced following the implementation of governmental measures aimed at limiting the spread of COVID-19
    Description: Published
    Description: 815–833
    Description: 2TM. Divulgazione Scientifica
    Description: JCR Journal
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    Combining audio and visual displays to highlight temporal and spatial seismic patterns (2021)
    Springer Nature
    Details
    Publication Date: 2022-03-16
    Description: Data visualization, and to a lesser extent data sonification, are classic tools to the scientific community. However, these two approaches are very rarely combined, although they are highly complementary: our visual system is good at recognizing spatial patterns, whereas our auditory system is better tuned for temporal patterns. In this article, data representation methods are proposed that combine visualization, sonification, and spatial audio techniques, in order to optimize the user’s perception of spatial and temporal patterns in a single display, to increase the feeling of immersion, and to take advantage of multimodal integration mechanisms. Three seismic data sets are used to illustrate the methods, covering different physical phenomena, time scales, spatial distributions, and spatio-temporal dynamics. The methods are adapted to the specificities of each data set, and to the amount of information that the designer wants to display. This leads to further developments, namely the use of audification with two time scales, the switch from pure audification to time-modulated noise, and the switch from pure audification to sonic icons. First user feedback from live demonstrations indicates that the methods presented in this article seem to enhance the perception of spatio-temporal patterns, which is a key parameter to the understanding of seismically active systems, and a step towards apprehending the processes that drive this activity.
    Description: Published
    Description: 125–142
    Description: 7T. Variazioni delle caratteristiche crostali e "precursori"
    Description: JCR Journal
    Keywords: 04.06. Seismology
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    Sediment characteristics of a thermokarst lagoon in the northeastern Siberian Arctic (Ivashkina Lagoon, Bykovsky Peninsula) (2018)
    Springer Nature
    In:  EPIC3Arktos, Springer Nature, 4(13), ISSN: ISSN: 2364-9461
    Details
    Publication Date: 2022-03-25
    Description: Lagoon development in ice-rich permafrost environments such as the Alaskan Beaufort Sea coastline and the Yedoma coastlines of northern Siberia represents a key mechanism of marine inundation of permafrost along the Arctic coastal plains. Here we show lithological, geochronological, and geochemical data from a core drilled in 1999 in Ivashkina Lagoon on the Bykovsky Peninsula in northeastern Siberia. This study extends previous studies of the Ivashkina Lagoon, and provides a first dated geochronological context for sedimentation and lithological characteristics. In addition, we report ground temperature measurements from different borehole sites in and around the lagoon to support our analysis of the thermokarst lagoon environment. Furthermore, a change detection study was carried out using historical aerial photography and modern satellite imagery for the 1982 to 2016 period. Several stages of landscape dynamics were reconstructed, starting with an initial Yedoma Ice Complex that covered the area during the late Pleistocene and which was locally thawed by thermokarst lake development during the Late Glacial with subsequent lacustrine sedimentation. A final stage completed the landscape dynamics during the last few hundreds of years. This stage was characterized by lake drainage and lagoon development, including strong reworking of surface sediments. By extrapolating the organic carbon data from Ivashkina Lagoon to the lagoons of the Bykovsky Peninsula, we estimate that lagoons contain 1.68 ± 0.04 Mt of organic carbon in their upper 6 m.
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    Deep water inflow slowed offshore expansion of the West Antarctic Ice Sheet at the Eocene-Oligocene transition (2022)
    Springer Nature
    In:  EPIC3Nature Communications Earth & Environment, Springer Nature, 3(1)
    Details
    Publication Date: 2022-02-21
    Description: The stability of the West Antarctic Ice Sheet is threatened by the incursion of warm Circumpolar Deepwater which flows southwards via cross-shelf troughs towards the coast there melting ice shelves. However, the onset of this oceanic forcing on the development and evolution of the West Antarctic Ice Sheet remains poorly understood. Here, we use single- and multichannel seismic reflection profiles to investigate the architecture of a sediment body on the shelf of the Amundsen Sea Embayment. We estimate the formation age of this sediment body to be around the Eocene-Oligocene Transition and find that it possesses the geometry and depositional pattern of a plastered sediment drift. We suggest this indicates a southward inflow of deep water which probably supplied heat and, thus, prevented West Antarctic Ice Sheet advance beyond the coast at this time. We conclude that the West Antarctic Ice Sheet has likely experienced a strong oceanic influence on its dynamics since its initial formation.
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    Short-term clustering modeling of seismicity in Eastern Aegean Sea (Greece): a retrospective forecast test of the 2017 Mw = 6.4 Lesvos, 2017 Mw = 6.6 Kos and 2020 Mw = 7.0 Samos earthquake sequences (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-03
    Description: Short-term earthquake clustering properties in the Eastern Aegean Sea (Greece) area investigated through the application of an epidemic type stochastic model (Epidemic Type Earthquake Sequence; ETES). The computations are performed in an earthquake catalog covering the period 2008 to 2020 and including 2332 events with a completeness threshold of Mc = 3.1 and separated into two subcatalogs. The first subcatalog is employed for the learning period, which is between 2008/01/01 and 2016/12/31 (N = 1197 earthquakes), and used for the model’s parameters estimation. The second subcatalog from 2017/01/01 to 2020/11/10 (1135 earthquakes), in which the sequences of 2017 Mw = 6.4 Lesvos, 2017 Mw = 6.6 Kos and 2020 Mw = 7.0 Samos main shocks are included, and used for a retrospective forecast testing based on the constructed model. The estimated model parameters imply a swarm like behavior, indicating the ability of earthquakes of small to moderate magnitude above Mc to produce their own offsprings, along with the stronger earthquakes. The retrospective evaluation of the model is examined in the three aftershock sequences, where lack of foreshocks resulted in low predictability of the mainshocks, with estimated daily probabilities around 10– 5. Immediately after the mainshocks occurrence the model adjusts with notable resemblance between the expected and observed aftershock rates, particularly for earthquakes with M ≥ 3.5.
    Description: Published
    Description: 1085–1099
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
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    Simulation of non-stationary stochastic ground motions based on recent Italian earthquakes (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-29
    Description: This work presents an up-to-date model for the simulation of non-stationary ground motions, including several novelties compared to the original study of Sabetta and Pugliese (Bull Seism Soc Am 86:337–352, 1996). The selection of the input motion in the framework of earthquake engineering has become progressively more important with the growing use of nonlinear dynamic analyses. Regardless of the increasing availability of large strong motion databases, ground motion records are not always available for a given earthquake scenario and site condition, requiring the adoption of simulated time series. Among the different techniques for the generation of ground motion records, we focused on the methods based on stochastic simulations, considering the time- frequency decomposition of the seismic ground motion. We updated the non-stationary stochastic model initially developed in Sabetta and Pugliese (Bull Seism Soc Am 86:337–352, 1996) and later modified by Pousse et al. (Bull Seism Soc Am 96:2103–2117, 2006) and Laurendeau et al. (Nonstationary stochastic simulation of strong ground-motion time histories: application to the Japanese database. 15 WCEE Lisbon, 2012). The model is based on the S-transform that implicitly considers both the amplitude and frequency modulation. The four model parameters required for the simulation are: Arias intensity, significant duration, central frequency, and frequency bandwidth. They were obtained from an empirical ground motion model calibrated using the accelerometric records included in the updated Italian strong-motion database ITACA. The simulated accelerograms show a good match with the ground motion model prediction of several amplitude and frequency measures, such as Arias intensity, peak acceleration, peak velocity, Fourier spectra, and response spectra.
    Description: Published
    Description: 3287–3315
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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    Insights on the Italian Seismic Network from location uncertainties (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-01
    Description: Probabilistic earthquake locations provide confidence intervals for the hypocentre solutions such as errors encountered in the position, the origin time, and in magnitude. If the relationship of the parameters relative to the local arrangement of the seismic network is considered, such as the node distance, the number of stations, the seismic gap, and the quality of phase readings), the uncertainties can then provide insights on the location capability of the network. In this paper, we collect the earthquake data recorded from the Italian Seismic Network for a time span of 5 years. The data pertain to three different catalogues according to the progressive refinement phases of the location procedure: automatic location, revised location, and published location. By means of spatial analysis,we assess the distribution of the location-related and network-related estimators across the study area. These estimators are subsequently combined to assess the existence of spatial correlations at a local scale. The results indicate that the Italian network is generally able to provide robust locations at the national scale and for smaller earthquakes, and the elongated shape of Italy (and of its network) does not cause systematic bias in the locations. However, we highlight the existence of subregions in which the performance of the network is weaker. At present, a unique 2D, 3-layer velocity model is used for the earthquake location procedure, and this could represent the main limitation for the improvement of the locations. Therefore, the assessment of locally optimized velocity models is the priority for the homogenization and the improvement of the Italian Seismic Network performance.
    Description: Published
    Description: 1061–1076
    Description: 1IT. Reti di monitoraggio e sorveglianza
    Description: JCR Journal
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    New trenching results along the İznik segment of the central strand of the North Anatolian Fault (Turkey): an integration with preexisting data (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-06
    Description: This paper provides a new contribution to the construction of the complex and fragmentary mosaic of the Late Holocene earthquakes history of the İznik segment of the central strand of the North Anatolian Fault (CNAF) in Turkey. The CNAF clearly displays lower dextral slip rates with respect to the northern strand however, surface rupturing and large damaging earthquakes (M 〉 7) occurred in the past, leaving clear signatures in the built and natural environments. The association of these historical events to specific earthquake sources (e.g., Gemlik, İznik, or Geyve fault segments) is still a matter of debate. We excavated two trenches across the İznik fault trace near Mustafali, a village about 10 km WSW of İznik where the morphological fault scarp was visible although modified by agricultural activities. Radiocarbon and TL dating on samples collected from the trenches show that the displaced deposits are very recent and span the past 2 millennia at most. Evidence for four surface faulting events was found in the Mustafali trenches. The integration of these results with historical data and previous paleoseismological data yields an updated Late Holocene history of surface-rupturing earthquakes along the İznik Fault in 1855, 740 (715), 362, and 121 CE. Evidence for the large M7 + historical earthquake dated 1419 CE generally attributed to this fault, was not found at any trench site along the İznik fault nor in the subaqueous record. This unfit between paleoseismological, stratigraphic, and historical data highlights one more time the urge for extensive paleoseismological trenching and offshore campaigns because of the high potential to solve the uncertainties on the seismogenic history (age, earthquake location, extent of the rupture and size) of this portion of NAFZ and especially on the attribution of historical earthquakes to the causative fault.
    Description: Published
    Description: 115–128
    Description: 2T. Deformazione crostale attiva
    Description: N/A or not JCR
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    Checking the site categorization criteria and amplification factors of the 2021 draft of Eurocode 8 Part 1–1 (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-29
    Description: In this paper the site categorization criteria and the corresponding site amplification factors proposed in the 2021 draft of Part 1 of Eurocode 8 (2021-draft, CEN/TC250/SC8 Working Draft N1017) are first introduced and compared with the current version of Eurocode 8, as well as with site amplification factors from recent empirical ground motion prediction equations. Afterwards, these values are checked by two approaches. First, a wide dataset of strong motion records is built, where recording stations are classified according to 2021-draft, and the spectral amplifications are empirically estimated computing the site-to-site residuals from regional and global ground motion models for reference rock conditions. Second, a comprehensive parametric numerical study of one-dimensional (1D) site amplification is carried out, based on randomly generated shear-wave velocity profiles, classified according to the new criteria. A reasonably good agreement is found by both approaches. The most relevant discrepancies occur for the shallow soft soil conditions (soil category E) that, owing to the complex interaction of shear wave velocity, soil deposit thickness and frequency range of the excitation, show the largest scatter both in terms of records and of 1D numerical simulations. Furthermore, 1D numerical simulations for soft soil conditions tend to provide lower site amplification factors than 2021-draft, as well as lower than the corresponding site-to-site residuals from records, because of higher impact of non-linear (NL) site effects in the simulations. A site-specific study on NL effects at three KiK-net stations with a significantly large amount of high-intensity recorded ground motions gives support to the 2021-draft NL reduction factors, although the very limited number of recording stations allowing such analysis prevents deriving more general implications. In the presence of such controversial arguments, it is reasonable that a standard should adopt a prudent solution, with a limited reduction of the site amplification factors to account for NL soil response, while leaving the possibility to carry out site-specific estimations of such factors when sufficient information is available to model the ground strain dependency of local soil properties.
    Description: Published
    Description: 4199–4234
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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    Exceedance of design actions in epicentral areas: insights from the ShakeMap envelopes for the 2016–2017 central Italy sequence (2021)
    Springer Nature
    Details
    Publication Date: 2021-11-29
    Description: ShakeMap is the tool to evaluate the ground motion effect of earthquakes in vast areas. It is useful to delimit the zones where the shaking is expected to have been most significant, for civil defense rapid response. From the earthquake engineering point of view, it can be used to infer the seismic actions on the built environment to calibrate vulnerability models or to define the reconstruction policies based on observed damage vs shaking. In the case of long-lasting seismic sequences, it can be useful to develop ShakeMap envelopes, that is, maps of the largest ground intensity among those from the ShakeMap of (selected) events of a seismic sequence, to delimit areas where the effects of the whole sequence have been of structural engineering relevance. This study introduces ShakeMap envelopes and discusses them for the central Italy 2016–2017 seismic sequence. The specific goals of the study are: (i) to compare the envelopes and the ShakeMap of the main events of the sequence to make the case for sequence-based maps; (ii) to quantify the exceedance of design seismic actions based on the envelopes; (iii) to make envelopes available for further studies and the reconstruction planning; (iv) to gather insights on the (repeated) exceedance of design seismic actions at some sites. Results, which include considerations of uncertainty in ShakeMap, show that the sequence caused exceedance of design hazard in thousands of square kilometers. The most relevant effects of the sequence are, as expected, due to the mainshock, yet seismic actions larger than those enforced by the code for structural design are found also around the epicenters of the smaller magnitude events. At some locations, the succession of ground-shaking that has excited structures, provides insights on structural damage accumulation that has likely taken place; something that is not accounted for explicitly in modern seismic design. The envelopes developed are available as supplemental material.
    Description: Published
    Description: 5391–5414
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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    Automatic inspection and analysis of digital waveform images by means of convolutional neural networks (2021)
    Springer Nature
    Details
    Publication Date: 2021-12-13
    Description: Analyzing seismic data to get information about earthquakes has always been a major task for seismologists and, more in general, for geophysicists. Recently, thanks to the technological development of observation systems, more and more data are available to perform such tasks. However, this data “grow up” makes “human possibility” of data processing more complex in terms of required efforts and time demanding. That is why new technological approaches such as artificial intelligence are becoming very popular and more and more exploited. In this paper, we explore the possibility of interpreting seismic waveform segments by means of pre-trained deep learning. More specifically, we apply convolutional networks to seismological waveforms recorded at local or regional distances without any pre-elaboration or filtering. We show that such an approach can be very successful in determining if an earthquake is “included” in the seismic wave image and in estimating the distance between the earthquake epicenter and the recording station.
    Description: Published
    Description: 1347–1359
    Description: 1T. Struttura della Terra
    Description: 3T. Fisica dei terremoti e Sorgente Sismica
    Description: JCR Journal
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    Midlatitude climatology of the ionospheric equivalent slab thickness over two solar cycles (2021)
    Springer Nature
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    Publication Date: 2021-10-25
    Description: Themain climatological features of the ionospheric equivalent slab thickness (τ ) for the Northern hemispheremidlatitudes are analyzed. F2-layer peak electron density values recorded at three midlatitude ionospheric stations (Chilton 51.5° N, 0.6° W, U.K.; Roquetes 40.8° N, 0.5° E, Spain;Wallops Island 37.9° N, 75.5°W, USA) and vertical total electron content values from colocated ground-based Global Navigation Satellite System receivers are used to calculate a dataset of τ values for the last two solar cycles, considering only magnetically quiet periods. Results are presented both as grids of binned medians and as boxplots as a function of local time and month of the year, for different solar activity levels. Corresponding trends are first compared to those output by the midlatitude empirical model developed by Fox et al. (Radio Sci 26:429–438, 1991) and then discussed in the light of what is known so far. From this investigation, the strong need to implement an improved empirical model of τ has emerged. Both Space Weather and Space Geodesy applications might benefit from such model. Therefore, both the dataset and the methodology described in the paper represent a first fundamental step aimed at implementing an empirical climatological model of the ionospheric equivalent slab thickness. The study highlighted also that at midlatitudes τ shows the following main patterns: daytime values considerably smaller than nighttime ones (except in summer); well-defined maxima at solar terminator hours; a greater dispersion during nighttime and solar terminator hours; no clear and evident solar activity dependence.
    Description: Published
    Description: 124
    Description: 2A. Fisica dell'alta atmosfera
    Description: JCR Journal
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    Fracturing and healing of basaltic magmas during explosive volcanic eruptions (2021)
    Springer Nature
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    Publication Date: 2021-11-26
    Description: The eruption of basaltic magmas dominates explosive volcanism on Earth and other planets within the Solar System. The mechanism through which continuous magma fragments into volcanic particles is central in governing eruption dynamics and the ensuing hazards. However, the mechanism of fragmentation of basaltic magmas is still disputed, with both viscous and brittle mechanisms having been proposed. Here we carry out textural analysis of the products of ten eruptions from seven volcanoes by scanning electron microscopy. We find broken crystals surrounded by intact glass that testify to the brittle fragmentation of basaltic magmas during explosive activity worldwide. We then replicated the natural textures of broken crystals in laboratory experiments where variably crystallized basaltic melt was fragmented by rapid deformation. The experiments reveal that crystals are broken by the propagation of a network of fractures through magma, and that afterwards the fractures heal by viscous flow of the melt. Fracturing and healing affect gas mobility, stress distribution, and bubble and crystal size distributions in magma. Our results challenge the idea that the grain size distribution of basaltic eruption products reflects the density of fractures that initially fragmented the magma and ultimately indicate that brittle fracturing and viscous healing of magma may underlie basaltic explosive eruptions globally.
    Description: Published
    Description: 248–254
    Description: 4V. Processi pre-eruttivi
    Description: 5V. Processi eruttivi e post-eruttivi
    Description: JCR Journal
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    Catching the Main Ethiopian Rift evolving towards plate divergence (2022)
    Springer Nature
    Details
    Publication Date: 2022-02-11
    Description: Magmatism accompanies rifting along divergent plate boundaries, although its role before continental breakup remains poorly understood. For example, the magma-assisted Northern Main Ethiopian Rift (NMER) lacks current volcanism and clear tectono-magmatic relationships with its contiguous rift portions. Here we define its magmatic behaviour, identifying the most recent eruptive fissures (EF) whose aphyric basalts have a higher Ti content than those of older monogenetic scoria cones (MSC), which are porphyritic and plagioclase-dominated. Despite these differences, calculations highlight a similar parental melt for EF and MSC products, suggesting only a different evolutionary history after melt generation. While MSC magmas underwent a further step of storage at intermediate crustal levels, EF magmas rose directly from the base of the crust without contamination, even below older polygenetic volcanoes, suggesting rapid propagation of transcrustal dikes across solidified magma chambers. Whether this recent condition in the NMER is stable or transient, it indicates a transition from central polygenetic to linear fissure volcanism, indicative of increased tensile conditions and volcanism directly fed from the base of the crust, suggesting transition towards mature rifting.
    Description: Published
    Description: 21821
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
    Keywords: 04.08. Volcanology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Neapolitan volcanoes (2021)
    Springer Nature
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    Publication Date: 2021-12-24
    Description: This book serves as a guide to discovering the most interesting volcano sites in Italy. Accompanied by some extraordinary contemporary images of active Neapolitan volcanoes, it explains the main volcanic processes that have been shaping the landscape of the Campania region and influencing human settlements in this area since Greek and Roman times and that have prompted leading international scientists to visit and study this natural volcanology laboratory. While volcanology is the central topic, the book also addresses other aspects related to the area’s volcanism and is divided into three sections: 1) Neapolitan volcanic activity and processes (with a general introduction to volcanology and its development around Naples together with descriptions of the landscape and the main sites worth visiting); 2) Volcanoes and their interactions with local human settlements since the Bronze Age, recent population growth and the transformation of the territory; 3) The risks posed by Neapolitan Volcanoes, their recent activity and the problem of forecasting any future eruption.
    Description: Published
    Description: 2TM. Divulgazione Scientifica
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Northern Hemisphere drought risk in a warming climate (2021)
    Springer Nature
    In:  EPIC3npj Climate and Atmospheric Science, Springer Nature, 4(1), ISSN: 2397-3722
    Details
    Publication Date: 2022-02-15
    Repository Name: EPIC Alfred Wegener Institut
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    Environmental stability and phenotypic plasticity benefit the cold-water coral Desmophyllum dianthus in an acidified fjord (2022)
    Springer Nature
    In:  EPIC3Communications Biology, Springer Nature, 5(683)
    Details
    Publication Date: 2022-07-13
    Description: The stratified Chilean Comau Fjord sustains a dense population of the cold-water coral (CWC) Desmophyllum dianthus in aragonite supersaturated shallow and aragonite under- saturated deep water. This provides a rare opportunity to evaluate CWC fitness trade-offs in response to physico-chemical drivers and their variability. Here, we combined year-long reciprocal transplantation experiments along natural oceanographic gradients with an in situ assessment of CWC fitness. Following transplantation, corals acclimated fast to the novel environment with no discernible difference between native and novel (i.e. cross-transplanted) corals, demonstrating high phenotypic plasticity. Surprisingly, corals exposed to lowest ara- gonite saturation (Ωarag 〈 1) and temperature (T 〈 12.0 °C), but stable environmental condi- tions, at the deep station grew fastest and expressed the fittest phenotype. We found an inverse relationship between CWC fitness and environmental variability and propose to consider the high frequency fluctuations of abiotic and biotic factors to better predict the future of CWCs in a changing ocean.
    Repository Name: EPIC Alfred Wegener Institut
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    Mid-Pliocene El Niño/Southern Oscillation suppressed by Pacific intertropical convergence zone shift (2022)
    Springer Nature
    In:  EPIC3Nature Geoscience, Springer Nature, ISSN: 1752-0908
    Details
    Publication Date: 2022-08-16
    Description: The El Niño/Southern Oscillation (ENSO), the dominant driver of year-to-year climate variability in the equatorial Pacific Ocean, impacts climate pattern across the globe. However, the response of the ENSO system to past and potential future temperature increases is not fully understood. Here we investigate ENSO variability in the warmer climate of the mid-Pliocene (~3.0–3.3 Ma), when surface temperatures were ~2–3 °C above modern values, in a large ensemble of climate models—the Pliocene Model Intercomparison Project. We show that the ensemble consistently suggests a weakening of ENSO variability, with a mean reduction of 25% (±16%). We further show that shifts in the equatorial Pacific mean state cannot fully explain these changes. Instead, ENSO was suppressed by a series of off-equatorial processes triggered by a northward displacement of the Pacific intertropical convergence zone: weakened convective feedback and intensified Southern Hemisphere circulation, which inhibit various processes that initiate ENSO. The connection between the climatological intertropical convergence zone position and ENSO we find in the past is expected to operate in our warming world with important ramifications for ENSO variability.
    Repository Name: EPIC Alfred Wegener Institut
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    Stable aerobic and anaerobic coexistence in anoxic marine zones (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zakem, E. J., Mahadevan, A., Lauderdale, J. M., & Follows, M. J. Stable aerobic and anaerobic coexistence in anoxic marine zones. ISME Journal, 14, (2019): 288–301, doi: 10.1038/s41396-019-0523-8.
    Description: Mechanistic description of the transition from aerobic to anaerobic metabolism is necessary for diagnostic and predictive modeling of fixed nitrogen loss in anoxic marine zones (AMZs). In a metabolic model where diverse oxygen- and nitrogen-cycling microbial metabolisms are described by underlying redox chemical reactions, we predict a transition from strictly aerobic to predominantly anaerobic regimes as the outcome of ecological interactions along an oxygen gradient, obviating the need for prescribed critical oxygen concentrations. Competing aerobic and anaerobic metabolisms can coexist in anoxic conditions whether these metabolisms represent obligate or facultative populations. In the coexistence regime, relative rates of aerobic and anaerobic activity are determined by the ratio of oxygen to electron donor supply. The model simulates key characteristics of AMZs, such as the accumulation of nitrite and the sustainability of anammox at higher oxygen concentrations than denitrification, and articulates how microbial biomass concentrations relate to associated water column transformation rates as a function of redox stoichiometry and energetics. Incorporating the metabolic model into an idealized two-dimensional ocean circulation results in a simulated AMZ, in which a secondary chlorophyll maximum emerges from oxygen-limited grazing, and where vertical mixing and dispersal in the oxycline also contribute to metabolic co-occurrence. The modeling approach is mechanistic yet computationally economical and suitable for global change applications.
    Description: We are grateful for the thorough and thoughtful comments of two anonymous reviewers. We also thank Andrew Babbin for helpful comments. EJZ was supported by the Simons Foundation (Postdoctoral Fellowship in Marine Microbial Ecology). AM was supported by the Office of Naval Research (ONR #N000-14-15-1-2555). JML was supported by U.S. National Science Foundation (NSF #OCE-1259388). MJF was supported by the Gordon and Betty Moore Foundation (GBMF #3778) and the Simons Foundation: the Simons Collaboration on Ocean Processes and Ecology (SCOPE #329108) and the Simons Collaboration on Computational Biogeochemical Modeling of Marine Ecosystems (CBIOMES #549931).
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    Comparative proteomics of related symbiotic mussel species reveals high variability of host-symbiont interactions (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ponnudurai, R., Heiden, S. E., Sayavedra, L., Hinzke, T., Kleiner, M., Hentschker, C., Felbeck, H., Sievert, S. M., Schlüter, R., Becher, D., Schweder, T., & Markert, S. Comparative proteomics of related symbiotic mussel species reveals high variability of host-symbiont interactions. ISME Journal, 14, (2019): 649–656, doi: 10.1038/s41396-019-0517-6.
    Description: Deep-sea Bathymodiolus mussels and their chemoautotrophic symbionts are well-studied representatives of mutualistic host–microbe associations. However, how host–symbiont interactions vary on the molecular level between related host and symbiont species remains unclear. Therefore, we compared the host and symbiont metaproteomes of Pacific B. thermophilus, hosting a thiotrophic symbiont, and Atlantic B. azoricus, containing two symbionts, a thiotroph and a methanotroph. We identified common strategies of metabolic support between hosts and symbionts, such as the oxidation of sulfide by the host, which provides a thiosulfate reservoir for the thiotrophic symbionts, and a cycling mechanism that could supply the host with symbiont-derived amino acids. However, expression levels of these processes differed substantially between both symbioses. Backed up by genomic comparisons, our results furthermore revealed an exceptionally large repertoire of attachment-related proteins in the B. thermophilus symbiont. These findings imply that host–microbe interactions can be quite variable, even between closely related systems.
    Description: Thanks to captain, crew, and pilots of the research vessels Atlantis (ROV Jason cruise AT26–10 in 2014) and Meteor (cruise M82–3 in 2010). We thank Jana Matulla, Sebastian Grund, and Annette Meuche for excellent technical assistance during sample preparation, MS measurements in the Orbitrap Classic, and TEM imaging preparation, respectively. We appreciate Nikolaus Leisch’s help with TEM image interpretation, Inna Sokolova’s advice on bivalve physiology, and Marie Zühlke’s support during manuscript revision. RP was supported by the EU-funded Marie Curie Initial Training Network ‘Symbiomics’ (project no. 264774) and by a fellowship of the Institute of Marine Biotechnology e.V. TH was supported by the German Research Foundation DFG (grant MA 6346/2–1 to SM). The Atlantis cruise was funded by a grant of the US National Science Foundation’s Dimensions of Biodiversity program to SMS (OCE-1136727).
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    Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Miller, C. A., Holm, H. C., Horstmann, L., George, J. C., Fredricks, H. F., Van Mooy, B. A. S., & Apprill, A. Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion. ISME Journal, 14, (2019): 688-701, doi: 10.1038/s41396-019-0549-y.
    Description: Whale digestion plays an integral role in many ocean ecosystems. By digesting enormous quantities of lipid-rich prey, whales support their energy intensive lifestyle, but also excrete nutrients important to ocean biogeochemical cycles. Nevertheless, whale digestion is poorly understood. Gastrointestinal microorganisms play a significant role in vertebrate digestion, but few studies have examined them in whales. To investigate digestion of lipids, and the potential contribution of microbes to lipid digestion in whales, we characterized lipid composition (lipidomes) and bacterial communities (microbiotas) in 126 digesta samples collected throughout the gastrointestinal tracts of 38 bowhead whales (Balaena mysticetus) harvested by Alaskan Eskimos. Lipidomes and microbiotas were strongly correlated throughout the gastrointestinal tract. Lipidomes and microbiotas were most variable in the small intestine and most similar in the large intestine, where microbiota richness was greatest. Our results suggest digestion of wax esters, the primary lipids in B. mysticetus prey representing more than 80% of total dietary lipids, occurred in the mid- to distal small intestine and was correlated with specific microorganisms. Because wax esters are difficult to digest by other marine vertebrates and constitute a large reservoir of carbon in the ocean, our results further elucidate the essential roles that whales and their gastrointestinal microbiotas play in the biogeochemical cycling of carbon and nutrients in high-latitude seas.
    Description: Devonshire Foundation (to CAM), Marine Mammal Center, Woods Hole Oceanographic Institution (WHOI; to CAM), WHOI Ocean Life Institute (to AA and CAM), Dalio Foundation’s Dalio Ocean Initiative (now ‘OceanX’) (to AA), National Science Foundation (OCE-1756254 and OPP-1543328 to BASVM). Samples were collected under Department of Commerce National Oceanic and Atmospheric Administration National Marine Fisheries Service permit numbers 17350-00, 17350-01, and 17350-02 to North Slope Borough Department of Wildlife Management.
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    Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gazitua, M. C., Vik, D. R., Roux, S., Gregory, A. C., Bolduc, B., Widner, B., Mulholland, M. R., Hallam, S. J., Ulloa, O., & Sullivan, M. B. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. Isme Journal, (2020), doi:10.1038/s41396-020-00825-6.
    Description: Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.
    Description: We thank Sullivan Lab members and Heather Maughan for comments on the paper, Bess Ward for her contribution in the N-cycle context of our story, Kurt Hanselmann for his assistance in the calculations of the Gibbs-free energies, and the scientific party and crew of the R/V Atlantis (grant OCE-1356056 to MRM) for the sampling opportunity and support at sea. This work was funded in part by awards from the Agouron Institute to OU and MBS, a Gordon and Betty Moore Foundation Investigator Award (#3790) and NSF Biological Oceanography Awards (#1536989 and #1829831) to MBS, and the Millennium Science Initiative (grant ICN12_019-IMO) to OU. The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.
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    Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Babbin, A. R., Tamasi, T., Dumit, D., Weber, L., Rodríguez, M. V. I., Schwartz, S. L., Armenteros, M., Wankel, S. D., & Apprill, A. Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals. ISME Journal, (2020), doi:10.1038/s41396-020-00845-2.
    Description: Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use 15N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N2O) production among five iconic species of reef-building corals (Acropora palmata, Diploria labyrinthiformis, Orbicella faveolata, Porites astreoides, and Porites porites) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N2O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis, at rates of ~1 nmol cm−2 d−1. In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N2O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.
    Description: Research was conducted in the Gardens of the Queen, Cuba in accordance with the requirements of the Republic of Cuba, conducted under permit NV2370 and NV2568 issued by the Ministerio de Relaciones Exteriores. We gratefully acknowledge funding for this research by MIT Sea Grant award #2018-DOH-49-LEV, Simons Foundation award #622065, and MIT ESI seed funding to ARB, the MIT Montrym, Ferry, and mTerra Seed Grant Funds, and the generous contributions by Dr Bruce L. Heflinger.
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    Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Trembath-Reichert, E., Tully, B. J., & Huber, J. A. Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community. Isme Journal, (2020), doi:10.1038/s41396-020-00843-4.
    Description: The oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.
    Description: The Gordon and Betty Moore Foundation sponsored most of the observatory components at North Pond through grant GBMF1609. This work was supported by NSF OCE-1062006, OCE-1745589 and OCE-1635208 to J.A.H. E.T.R. was supported by a NASA Postdoctoral Fellowship with the NASA Astrobiology Institute and a L’Oréal USA For Women in Science Fellowship. The Center for Dark Energy Biosphere Investigations (C-DEBI OCE-0939564) also supported the participation of J.A.H. and B.T. This is C-DEBI contribution number 548.
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    Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coskun, O. K., Vuillemin, A., Schubotz, F., Klein, F., Sichel, S. E., Eisenreich, W., & Orsi, W. D. Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks. Isme Journal. (2021), https://doi.org/10.1038/s41396-021-01066-x.
    Description: Thermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.
    Description: This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 364653263—TRR 235 to WDO and WE, and under Germany’s Excellence Strategy—EXC 2077-390741603. The work was also supported by the Dalio Explore Fund and LMU Mentoring Program. Open Access funding enabled and organized by Projekt DEAL.
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    Quantifying population-specific growth in benthic bacterial communities under low oxygen using H218O (2019)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal (2019), doi:10.1038/s41396-019-0373-4.
    Description: The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of “microbial dark matter”, validating hypotheses put forth by earlier metagenomic studies.
    Description: This work was supported by a grant OR 417/1-1 from the Deutsche Forschungsgemeinschaft, and a Junior Researcher Fund grant from LMU Munich to WDO. This work was performed in part, through the Master’s Program in Geobiology and Paleontology (MGAP) at LMU Munich.
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    Sea ice surface temperatures from helicopter-borne thermal infrared imaging during the MOSAiC expedition (2022)
    Springer Nature
    In:  EPIC3Scientific Data, Springer Nature, 9(1), ISSN: 2052-4463
    Details
    Publication Date: 2022-06-27
    Description: The sea ice surface temperature is important to understand the Arctic winter heat budget. We conducted 35 helicopter flights with an infrared camera in winter 2019/2020 during the Multidisciplinary Drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition. The flights were performed from a local, 5 to 10 km scale up to a regional, 20 to 40 km scale. The infrared camera recorded thermal infrared brightness temperatures, which we converted to surface temperatures. More than 150000 images from all flights can be investigated individually. As an advanced data product, we created surface temperature maps for every flight with a 1 m resolution. We corrected image gradients, applied an ice drift correction, georeferenced all pixels, and corrected the surface temperature by its natural temporal drift, which results in time-fixed surface temperature maps for a consistent analysis of one flight. The temporal and spatial variability of sea ice characteristics is an important contribution to an increased understanding of the Arctic heat budget and, in particular, for the validation of satellite products.
    Repository Name: EPIC Alfred Wegener Institut
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    Ocean Colour Remote Sensing in the Laptev Sea (2018)
    Springer Nature
    In:  EPIC3Springer Nature, 15 p., ISBN: 978-3-319-94067-0
    Details
    Publication Date: 2022-06-16
    Description: The Laptev and Eastern Siberian shelves are the world’s broadest shallow shelf systems. Large Siberian rivers and coastal erosion of up to meters per summer deliver large volumes of terrestrial matter into the Arctic shelf seas. In this chapter we investigate the applicability of Ocean Colour Remote Sensing during the ice-free summer season in the Siberian Laptev Sea region. We show that the early summer river peak discharge may be traced using remote sensing in years characterized by early sea-ice retreat. In the summer time after the peak discharge, the spreading of the main Lena River plume east and north-east of the Lena River Delta into the shelf system becomes hardly traceable using optical remote sensing methods. Measurements of suspended particulate matter (SPM) and coloured dissolved organic matter (cDOM) are of the same magnitude in the coastal waters of Buor Khaya Bay as in the Lena River. Match-up analyses of in situ chlorophyll-a (Chl-a) show that standard Medium Resolution Imaging Spectrometer (MERIS) and Moderate Resolution Imaging Spectroradiometer (MODIS) satellite-derived Chl-a is not a valid remote sensing product for the coastal waters and the inner shelf region of the Laptev Sea. All MERIS and MODIS-derived Chl-a products are overestimated by at least a factor of ten, probably due to absorption by the extraordinarily high amount of non-algal particles and cDOM in these coastal and inner-shelf waters. Instead, Ocean Colour remote sensing provides information on wide-spread resuspension over shallows and lateral advection visible in satellite-derived turbidity. Satellite Sea Surface Temperature (SST) data clearly show hydrodynamics and delineate the outflow of the Lena River for hundreds of kilometres out into the shelf seas.
    Repository Name: EPIC Alfred Wegener Institut
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    Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean (2022)
    Springer Nature
    Details
    Publication Date: 2022-06-14
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Luo, E., Leu, A. O., Eppley, J. M., Karl, D. M., & DeLong, E. F. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. ISME Journal, 16, : 1627–1635, https://doi.org/10.1038/s41396-022-01202-1.
    Description: Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.
    Description: This project is funded by grants from the Simons Foundation (#329108 to EFD and DMK, #721223 to EFD, and #721252 to DMK) and the Gordon and Betty Moore Foundation (GBMF3777 to EFD and GBMF3794 to DMK). Partial support for EL was provided by the Natural Sciences and Engineering Research Council of Canada (PGSD3-487490-2016).
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    Intracellular nitrate storage by diatoms can be an important nitrogen pool in freshwater and marine ecosystems (2022)
    Springer Nature
    In:  EPIC3Communications Earth & Environment, Springer Nature, 3(1), ISSN: 2662-4435
    Details
    Publication Date: 2022-07-06
    Description: Identifying and quantifying nitrogen pools is essential for understanding the nitrogen cycle in aquatic ecosystems. The ubiquitous diatoms represent an overlooked nitrate pool as they can accumulate nitrate intracellularly and utilize it for nitrogen assimilation, dissipation of excess photosynthetic energy, and Dissimilatory Nitrate Reduction to Ammonium (DNRA). Here, we document the global co-occurrence of diatoms and intracellular nitrate in phototrophic microbial communities in freshwater (n = 69), coastal (n = 44), and open marine (n = 4) habitats. Diatom abundance and total intracellular nitrate contents in water columns, sediments, microbial mats, and epilithic biofilms were highly significantly correlated. In contrast, diatom community composition had only a marginal influence on total intracellular nitrate contents. Nitrate concentrations inside diatom cells exceeded ambient nitrate concentrations ∼100–4000-fold. The collective intracellular nitrate pool of the diatom community accounted for 〈1% of total nitrate in pelagic habitats and 65–95% in benthic habitats. Accordingly, nitrate-storing diatoms are emerging as significant contributors to benthic nitrogen cycling, in particular through Dissimilatory Nitrate Reduction to Ammonium activity under anoxic conditions.
    Repository Name: EPIC Alfred Wegener Institut
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    Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Breusing, C., Mitchell, J., Delaney, J., Sylva, S. P., Seewald, J. S., Girguis, P. R., & Beinart, R. A. Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails. Isme Journal, (2020), doi:10.1038/s41396-020-0707-2.
    Description: Symbioses between invertebrate animals and chemosynthetic bacteria form the basis of hydrothermal vent ecosystems worldwide. In the Lau Basin, deep-sea vent snails of the genus Alviniconcha associate with either Gammaproteobacteria (A. kojimai, A. strummeri) or Campylobacteria (A. boucheti) that use sulfide and/or hydrogen as energy sources. While the A. boucheti host–symbiont combination (holobiont) dominates at vents with higher concentrations of sulfide and hydrogen, the A. kojimai and A. strummeri holobionts are more abundant at sites with lower concentrations of these reductants. We posit that adaptive differences in symbiont physiology and gene regulation might influence the observed niche partitioning between host taxa. To test this hypothesis, we used high-pressure respirometers to measure symbiont metabolic rates and examine changes in gene expression among holobionts exposed to in situ concentrations of hydrogen (H2: ~25 µM) or hydrogen sulfide (H2S: ~120 µM). The campylobacterial symbiont exhibited the lowest rate of H2S oxidation but the highest rate of H2 oxidation, with fewer transcriptional changes and less carbon fixation relative to the gammaproteobacterial symbionts under each experimental condition. These data reveal potential physiological adaptations among symbiont types, which may account for the observed net differences in metabolic activity and contribute to the observed niche segregation among holobionts.
    Description: We thank the Schmidt Ocean Institute, the crew of the R/V Falkor and the pilots of the ROV ROPOS for facilitating the sample collections and shipboard experiments, and the Broad Institute Microbial ‘Omics Core for preparing and sequencing the transcriptomic libraries. This material is based in part upon work supported by the National Science Foundation under Grant Numbers NSF OCE-1536653 (to PRG), OCE-1536331 (to RAB and JSS), OCE-1819530 and OCE-1736932 (to RAB).
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    Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa (2019)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Trembath-Reichert, E., Butterfield, D. A., & Huber, J. A. Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa. Isme Journal, 13(9), (2019): 2264-2279, doi: 10.1038/s41396-019-0431-y.
    Description: There are many unknowns regarding the distribution, activity, community composition, and metabolic repertoire of microbial communities in the subseafloor of deep-sea hydrothermal vents. Here we provide the first characterization of subseafloor microbial communities from venting fluids along the central Mariana back-arc basin (15.5–18°N), where the slow-spreading rate, depth, and variable geochemistry along the back-arc distinguish it from other spreading centers. Results indicated that diverse Epsilonbacteraeota were abundant across all sites, with a population of high temperature Aquificae restricted to the northern segment. This suggests that differences in subseafloor populations along the back-arc are associated with local geologic setting and resultant geochemistry. Metatranscriptomics coupled to stable isotope probing revealed bacterial carbon fixation linked to hydrogen oxidation, denitrification, and sulfide or thiosulfate oxidation at all sites, regardless of community composition. NanoSIMS (nanoscale secondary ion mass spectrometry) incubations at 80 °C show only a small portion of the microbial community took up bicarbonate, but those autotrophs had the highest overall rates of activity detected across all experiments. By comparison, acetate was more universally utilized to sustain growth, but within a smaller range of activity. Together, results indicate that microbial communities in venting fluids from the Mariana back-arc contain active subseafloor communities reflective of their local conditions with metabolisms commonly shared across geologically disparate spreading centers throughout the ocean.
    Description: This work was funded by the NOAA Ocean Exploration and Research (OER) Program, the NSF Center for Dark Energy Biosphere Investigations (C-DEBI) (OCE-0939564), and NOAA/PMEL and JISAO under NOAA Cooperative Agreement NA15OAR4320063. ETR was supported by a NASA Postdoctoral Fellowship with the NASA Astrobiology Institute and a L’Oréal USA For Women in Science Fellowship. The data collected in this study includes work supported by the Schmidt Ocean Institute during cruise FK161129 aboard R/V Falkor. We thank the captains and crews of the R/V Falkor and ROV SuBastian. Critical support in cruise planning and sampling at sea was carried out by Andra Bobbitt, Bill Chadwick, Bob Embley, Ben Larson, and Kevin Roe. Caroline Fortunato, Connor Skennerton, Rika Anderson, Karthik Anantharaman, Jaclyn Saunders, Hank Yu, Lewis Ward, Elaina Graham, and Ben Tully aided bioinformatics pipeline development and Victoria Orphan and Yunbin Guan aided with NanoSIMS analysis. This is C-DEBI Contribution 470, JISAO Contribution 2018-0173, and PMEL Contribution 4867.
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    Ocean acidification responses in paralarval squid swimming behavior using a novel 3D tracking system (2019)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Springer Nature for personal use, not for redistribution. The definitive version was published in Zakroff, C., Mooney, T.A. & Wirth, C. Ocean acidification responses in paralarval squid swimming behavior using a novel 3D tracking system. Hydrobiologia, 808(1),(2018):83-106, doi:10.1007/s10750-017-3342-9.
    Description: Chronic embryonic exposure to ocean acidification (OA) has been shown to degrade the aragonitic statolith of paralarval squid, Doryteuthis pealeii, a key structure for their swimming behavior. This study examined if day-of-hatching paralarval D. pealeii from eggs reared under chronic OA demonstrated measurable impairments to swimming activity and control. This required the development of a novel, cost-effective, and robust method for 3D motion tracking and analysis. Squid eggs were reared in pCO2 levels in a dose-dependent manner ranging from 400 - 2200 ppm. Initial 2D experiments showed paralarvae in higher acidification environments spent more time at depth. In 3D experiments, velocity, particularly positive and negative vertical velocities, significantly decreased from 400 to 1000 ppm pCO2, but showed non-significant decreases at higher concentrations. Activity and horizontal velocity decreased linearly with increasing pCO2, indicating a subtle impact to paralarval energetics. Patterns may have been obscured by notable individual variability in the paralarvae. Responses were also seen to vary between trials on cohort or potentially annual scales. Overall, paralarval swimming appeared resilient to OA, with effects being slight. The newly developed 3D tracking system provides a powerful and accessible method for future studies to explore similar questions in the larvae of aquatic taxa.
    Description: We thank D. Remsen, the MBL Marine Resources Center staff, and MBL Gemma crew for their support in acquiring squid. R. Galat and the facilities staff of the WHOI ESL provided system support. D. McCorkle, KYK Chan, and M. White provided valuable insight on the OA system. E. Moberg, A. Beet, and A. Solow assisted in the development and coding of the 3D model system. We also thank E. Bonk, K. Hoering, M. Lee, D. Weiler, and A. Schlunk for their assistance and input with the experiments. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 1122374. This project is funded by NSF Grant No. 1220034.
    Keywords: Hypercapnia ; Cephalopod ; Larvae ; Movement analysis ; Stress physiology
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    Parkinson's disease protein DJ-1 regulates ATP synthase protein components to increase neuronal process outgrowth (2019)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chen, R.; Park, H. A.; Mnatsakanyan, N.; Niu, Y.; Licznerski, P.; Wu, J.; Miranda, P.; Graham, M.; Tang, J.; Boon, A. J. W.; Cossu, G.; Mandemakers, W.; Bonifati, V.; Smith, P. J. S.; Alavian, K. N.; Jonas, E. A. Parkinson's disease protein DJ-1 regulates ATP synthase protein components to increase neuronal process outgrowth. Cell Death & Disease, 10(6), (2019):469, doi:10.1038/s41419-019-1679-x.
    Description: Familial Parkinson’s disease (PD) protein DJ-1 mutations are linked to early onset PD. We have found that DJ-1 binds directly to the F1FO ATP synthase β subunit. DJ-1’s interaction with the β subunit decreased mitochondrial uncoupling and enhanced ATP production efficiency while in contrast mutations in DJ-1 or DJ-1 knockout increased mitochondrial uncoupling, and depolarized neuronal mitochondria. In mesencephalic DJ-1 KO cultures, there was a progressive loss of neuronal process extension. This was ameliorated by a pharmacological reagent, dexpramipexole, that binds to ATP synthase, closing a mitochondrial inner membrane leak and enhancing ATP synthase efficiency. ATP synthase c-subunit can form an uncoupling channel; we measured, therefore, ATP synthase F1 (β subunit) and c-subunit protein levels. We found that ATP synthase β subunit protein level in the DJ-1 KO neurons was approximately half that found in their wild-type counterparts, comprising a severe defect in ATP synthase stoichiometry and unmasking c-subunit. We suggest that DJ-1 enhances dopaminergic cell metabolism and growth by its regulation of ATP synthase protein components.
    Description: The research was supported by NIH (NS081746) to E.A.J., W.M. and V.B. are supported by the Stichting Parkinson Fonds (The Netherlands).
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    Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments (2021)
    Springer Nature
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Castro, S. P., Borton, M. A., Regan, K., de Angelis, I. H., Wrighton, K. C., Teske, A. P., Strous, M., & Ruff, S. E. Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments. Isme Journal. (2021), https://doi.org/10.1038/s41396-021-01026-5.
    Description: Hydrothermal sediments contain large numbers of uncultured heterotrophic microbial lineages. Here, we amended Guaymas Basin sediments with proteins, polysaccharides, nucleic acids or lipids under different redox conditions and cultivated heterotrophic thermophiles with the genomic potential for macromolecule degradation. We reconstructed 20 metagenome-assembled genomes (MAGs) of uncultured lineages affiliating with known archaeal and bacterial phyla, including endospore-forming Bacilli and candidate phylum Marinisomatota. One Marinisomatota MAG had 35 different glycoside hydrolases often in multiple copies, seven extracellular CAZymes, six polysaccharide lyases, and multiple sugar transporters. This population has the potential to degrade a broad spectrum of polysaccharides including chitin, cellulose, pectin, alginate, chondroitin, and carrageenan. We also describe thermophiles affiliating with the genera Thermosyntropha, Thermovirga, and Kosmotoga with the capability to make a living on nucleic acids, lipids, or multiple macromolecule classes, respectively. Several populations seemed to lack extracellular enzyme machinery and thus likely scavenged oligo- or monomers (e.g., MAGs affiliating with Archaeoglobus) or metabolic products like hydrogen (e.g., MAGs affiliating with Thermodesulfobacterium or Desulforudaceae). The growth of methanogens or the production of methane was not observed in any condition, indicating that the tested macromolecules are not degraded into substrates for methanogenesis in hydrothermal sediments. We provide new insights into the niches, and genomes of microorganisms that actively degrade abundant necromass macromolecules under oxic, sulfate-reducing, and fermentative thermophilic conditions. These findings improve our understanding of the carbon flow across trophic levels and indicate how primary produced biomass sustains complex and productive ecosystems.
    Description: We are grateful to the captain and crew of the R/V Atlantis AT37-06 as well as the crew of the human occupied vehicle Alvin for their tireless support. Sampling at Guaymas Basin was supported by NSF (OCE-1357238).
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    Using spatial variability in the rate of change of chlorophyll a to improve water quality management in a subtropical oligotrophic estuary (2019)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Millette, N. C., Kelble, C., Linhoss, A., Ashby, S., & Visser, L. Using spatial variability in the rate of change of chlorophyll a to improve water quality management in a subtropical oligotrophic estuary. Estuaries and Coasts, 42(7), (2019): 1792-1803, doi:10.1007/s12237-019-00610-5.
    Description: Anthropogenic eutrophication threatens numerous aquatic ecosystems across the globe. Proactive management that prevents a system from becoming eutrophied is more effective and cheaper than restoring a eutrophic system, but detecting early warning signs and problematic nutrient sources in a relatively healthy system can be difficult. The goal of this study was to investigate if rates of change in chlorophyll a and nutrient concentrations at individual stations can be used to identify specific areas that need to be targeted for management. Biscayne Bay is a coastal embayment in southeast Florida with primarily adequate water quality that has experienced rapid human population growth over the last century. Water quality data collected at 48 stations throughout Biscayne Bay over a 20-year period (1995–2014) were examined to identify any water quality trends associated with eutrophication. Chlorophyll a and phosphate concentrations have increased throughout Biscayne Bay, which is a primary indicator of eutrophication. Moreover, chlorophyll a concentrations throughout the northern area, where circulation is restricted, and in nearshore areas of central Biscayne Bay are increasing at a higher rate compared to the rest of the Bay. This suggests increases in chlorophyll a are due to local nutrient sources from the watershed. These areas are also where recent seagrass die-offs have occurred, suggesting an urgent need for management intervention. This is in contrast with the state of Florida listing of Biscayne Bay as a medium priority impaired body of water.
    Description: Data provided by the SERC-FIU/SFWMD Water Quality Monitoring Network is supported by SFWMD/SERC Cooperative Agreement #4600000352 as well as EPA Agreement #X7-96410603-3. This research was also funded by a NOAA/Atlantic Oceanographic and Meteorological Laboratory grant to the Northern Gulf Institute (award number NA160AR4320199).
    Keywords: Chlorophyll a ; Eutrophication ; Oligotrophic ; Ecological indicators
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    Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline (2020)
    Springer Nature
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mara, P., Vik, D., Pachiadaki, M. G., Suter, E. A., Poulos, B., Taylor, G. T., Sullivan, M. B., & Edgcomb, V. P. Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline. ISME Journal, (2020), doi:10.1038/s41396-020-00739-3.
    Description: Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key microbial pathways. Here we identify 748 viral populations that cluster into 94 genera along a vertical geochemical gradient in the Cariaco Basin, a permanently stratified and euxinic ocean basin. The viral communities in this ODWC appear to be relatively novel as 80 of these viral genera contained no reference viral sequences, likely due to the isolation and unique features of this system. We identify viral elements that encode AMGs implicated in distinctive processes, such as sulfur cycling, acetate fermentation, signal transduction, [Fe–S] formation, and N-glycosylation. These AMG-encoding viruses include two putative Mu-like viruses, and viral-like regions that may constitute degraded prophages that have been modified by transposable elements. Our results provide an insight into the ecological and biogeochemical impact of viruses oxygen-depleted and euxinic habitats.
    Description: This work was supported by the National Science Foundation grant OCE-1336082 to VPE, OCE-1335436 to GTT, OCE-1536989, a Moore Foundation Award (#3790) to MBS, and WHOI subaward A101259 to MP. The sequencing conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231.
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    Sediment dynamics of a divergent bay-marsh complex (2020)
    Springer Nature
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    Publication Date: 2022-05-26
    Description: Author Posting. © Springer Nature , 2020. This article is posted here by permission of Springer Nature for personal use, not for redistribution. The definitive version was published in Nowacki, D. J., & Ganju, N. K. Sediment dynamics of a divergent bay-marsh complex. Estuaries and Coasts, (2020), doi:10.1007/s12237-020-00855-5.
    Description: Bay–marsh systems, composed of an embayment surrounded by fringing marsh incised by tidal channels, are widely distributed coastal environments. External sediment availability, marsh-edge erosion, and sea-level rise acting on such bay–marsh complexes may drive diverse sediment-flux regimes. These factors reinforce the ephemeral and dynamic nature of fringing marshes: material released by marsh-edge erosion becomes part of a bay–marsh exchange that fuels the geomorphic evolution of the coupled system. The dynamics of this sediment exchange determine the balance among seaward export, deposition on the embayment seabed, flux into tidal channels, and import to the marsh platform. In this work, we investigate the sediment dynamics of a transgressive bay–marsh complex and link them to larger-scale considerations of its geomorphic trajectory. Grand Bay, Alabama/Mississippi, is a shallow microtidal embayment surrounded by salt marshes with lateral erosion rates of up to 5 m year−1. We collected 6 months of oceanographic data at four moorings within Grand Bay and its tidal channels to assess hydrographic conditions and net sediment-flux patterns and augmented the observations with numerical modeling. The observations imply a divergent sedimentary system in which a majority of the suspended sediment is exported seaward, while a smaller fraction is imported landward via tidal channels, assisting in vertical marsh-plain accumulation, maintenance of channel and intertidal-flat morphologies, and landward transgression. These results describe a dynamic system that is responsive to episodic atmospheric forcing in the absence of a strong tidal signal and the presence of severe lateral marsh loss.
    Description: We thank the staff of the Grand Bay NERR for their role in facilitating fieldwork within Grand Bay. Jonathan Pitchford, also of the Grand Bay NERR, provided the SET data. Giulio Mariotti and an anonymous reviewer are acknowledged for their helpful comments.
    Keywords: Salt marsh ; Geomorphic trajectory ; Sediment flux
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    Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions (2021)
    Springer Nature
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bayer, B., Saito, M. A., McIlvin, M. R., Lucker, S., Moran, D. M., Lankiewicz, T. S., Dupont, C. L., & Santoro, A. E. (2020). Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions. Isme Journal, doi:10.1038/s41396-020-00828-3.
    Description: The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved pCO2, and requires exogenous vitamin B12. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O2 concentrations. The abundance of a potentially more efficient CO2-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb3-type terminal oxidase increased under O2 limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O2-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O2 conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.
    Description: We thank John B. Waterbury and Frederica Valois for providing the culture of Nitrospira marina Nb-295T and for continued advice about cultivation. The N. marina genome was sequenced as part of US Department of Energy Joint Genome Institute Community Sequencing Project 1337 to CLD, AES, and MAS in collaboration with the user community. We thank Claus Pelikan for bioinformatic assistance. This research was supported by a Simons Foundation Early Career Investigator in Marine Microbiology and Evolution Award (345889) and US National Science Foundation (NSF) award OCE-1924512 to AES. Proteomics analysis was supported by NSF awards OCE-1924554 and OCE-1850719, and NIH award R01GM135709 to MAS. BB was supported by the Austrian Science Fund (FWF) Project Number: J4426-B (“The influence of nitrifiers on the oceanic carbon cycle”), SL by the Netherlands Organization for Scientific Research (NWO) grant 016.Vidi.189.050, and CLD by NSF award OCE-125999.
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    Marine litter: Sea change for plastic pollution (2017)
    Springer Nature
    In:  EPIC3Nature, Springer Nature, 544(7650), pp. 297-297, ISSN: 0028-0836
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    Publication Date: 2023-06-21
    Repository Name: EPIC Alfred Wegener Institut
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    Energy threshold changes in volcanic activity at Mt. Etna (Italy) inferred from volcanic tremor (2022)
    Springer Nature
    Details
    Publication Date: 2022-10-28
    Description: From the 2010s on, pattern classification has proven an effective method for flagging alerts of volcano unrest before eruptive activity at Mt. Etna, Italy. The analysis has been applied online to volcanic tremor data, and has supported the surveillance activity of the volcano that provides timely information to Civil Protection and other authorities. However, after declaring an alert, no one knows how long the volcano unrest will last and if a climactic eruptive activity will actually begin. These are critical aspects when considering the effects of a prolonged state of alert. An example of longstanding unrest is related to the Christmas Eve eruption in 2018, which was heralded by several months of almost continuous Strombolian activity. Here, we discuss the usage of thresholds to detect conditions leading to paroxysmal activity, and the challenges associated with defining such thresholds, leveraging a dataset of 52 episodes of lava fountains occurring in 2021. We were able to identify conservative settings regarding the thresholds, allowing for an early warning of impending paroxysm in almost all cases (circa 85% for the first 4 months in 2021, and over 90% for the whole year). The chosen thresholds also proved useful to predict that a paroxysmal activity was about to end. Such information provides reliable numbers for volcanologists for their assessments, based on visual information, which may not be available in bad weather or cloudy conditions.
    Description: Project IMPACT (A multidisciplinary Insight on the kinematics and dynamics of Magmatic Processes at Mt. Etna Aimed at identifying preCursor phenomena and developing early warning sysTems). IMPACT belongs to the Progetti Dipartimentali INGV [DIP7], https://progetti.ingv.it/index.php/it/progetti-dipartimentali/vulcani/impact#informazioni-sul-progetto.
    Description: Published
    Description: 17895
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: Volcanic tremor ; Volcano monitoring ; Pattern recognition ; Self Organizing maps ; Fuzzy clustering ; Mt. Etna ; 04.06. Seismology ; 04.08. Volcanology ; 05.01. Computational geophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Evidence for late glacial oceanic carbon redistribution and discharge from the Pacific Southern Ocean (2022)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 13, 12 p., ISSN: 2041-1723
    Details
    Publication Date: 2022-11-14
    Description: Southern Ocean deep-water circulation plays an important role in the global carbon cycle. On geological time-scales, upwelling along the Chilean continental margin likely contributed to the deglacial atmospheric carbon dioxide rise, but little quantitative evidence exists of carbon storage. Here, we use a new X-ray Micro-Computer-Tomography method to assess foraminiferal test dissolution as proxy for paleo-carbonate ion concentrations [CO3^2−]. Our subantarctic Southeast Pacific sediment core depth transect shows significant deep-water [CO3^2−] variations during the Last Glacial Maximum and Deglaciation (10 – 22 ka BP). We provide evidence for an increase in [CO3^2−] during the early deglacial period (15-19 ka BP), followed by a ca. 40 µmol kg^-1 reduction in Lower Circumpolar Deepwater (CDW). This decreased Pacific to Atlantic export of low-carbon CDW contributed to significantly lowered carbon storage within the Southern Ocean, highlighting the importance of a dynamic Pacific–Southern Ocean deep-water reconfiguration for shaping late-glacial oceanic carbon storage, and subsequent deglacial oceanic-atmospheric CO2 transfer.
    Repository Name: EPIC Alfred Wegener Institut
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    Living on Cold Substrata: New Insights and Approaches in the Study of Microphytobenthos Ecophysiology and Ecology in Kongsfjorden (2019)
    Springer Nature
    In:  EPIC3Advances in Polar Ecology 2, The Ecosystem of Kongsfjorden, Svalbard, Switzerland, Springer Nature, 2, pp. 303-330, ISSN: 2468-5712
    Details
    Publication Date: 2023-06-21
    Description: Organisms in shallow waters at high latitudes are under pressure due to climate change. These areas are typically inhabited by microphytobenthos (MPB) communities, composed mainly of diatoms. Only sparse information is available on the ecophysiology and acclimation processes within MPBs from Arctic regions. The physico-chemical environment and the ecology and ecophysiology of benthic diatoms in Kongsfjorden (Svalbard, Norway) are addressed in this review. MPB biofilms cover extensive areas of sediment. They show high rates of primary production, stabilise sediment surfaces against erosion under hydrodynamic forces,and affect the exchange of oxygen and nutrients across the sediment-water interface. Additionally, this phototrophic community represents a key component in the functioning of the Kongsfjorden trophic web, particularly as a major food source for benthic suspension- or deposit-feeders. MPB in Kongsfjorden is confronted with pronounced seasonal variations in solar radiation, low temperatures, and hyposaline (meltwater) conditions in summer, as well as long periods of ice and snow cover in winter. From the few data available, it seems that these organisms can easily cope with these environmental extremes. The underlying physiological mechanisms that allow growth and photosynthesis to continue under widely varying abiotic parameters, along with vertical migration and heterotrophy, and biochemical features such as a pronounced fatty-acid metabolism and silicate incorporation are discussed. Existing gaps in our knowledge of benthic diatoms in Kongsfjorden, such as the chemical ecology of biotic interactions, need to be filled. In addition, since many of the underlying molecular acclimation mechanisms are poorly understood, modern approaches based on transcriptomics, proteomics, and/or metabolomics, in conjunction with cell biological and biochemical techniques, are urgently needed. Climate change models for the Arctic predict other multifactorial stressors, such as an increase in precipitation and permafrost thawing, with consequences for the shallow-water regions. Both precipitation and permafrost thawing are likely to increase nutrient-enriched, turbid freshwater runoff and may locally counteract the expected increase in coastal radiation availability. So far, complex interactions among factors, as well as the full genetic diversity and physiological plasticity of Arctic benthic diatoms, have only rarely been considered. The limited existing information is described and discussed in this review.
    Repository Name: EPIC Alfred Wegener Institut
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    Southern Ocean biogenic blooms freezing-in Oligocene colder climates (2022)
    Springer Nature
    In:  EPIC3Nature Communications, Springer Nature, 13(1), pp. 1-10, ISSN: 2041-1723
    Details
    Publication Date: 2022-11-24
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Crossing a key atmospheric CO〈jats:sub〉2〈/jats:sub〉 threshold triggered a fundamental global climate reorganisation ~34 million years ago (Ma) establishing permanent Antarctic ice sheets. Curiously, a more dramatic CO〈jats:sub〉2〈/jats:sub〉 decline (~800–400 ppm by the Early Oligocene(~27 Ma)), postdates initial ice sheet expansion but the mechanisms driving this later, rapid drop in atmospheric carbon during the early Oligocene remains elusive and controversial. Here we use marine seismic reflection and borehole data to reveal an unprecedented accumulation of early Oligocene strata (up to 2.2 km thick over 1500 × 500 km) with a major biogenic component in the Australian Southern Ocean. High-resolution ocean simulations demonstrate that a tectonically-driven, one-off reorganisation of ocean currents, caused a unique period where current instability coincided with high nutrient input from the Antarctic continent. This unrepeated and short-lived environment favoured extreme bioproductivity and enhanced sediment burial. The size and rapid accumulation of this sediment package potentially holds ~1.067 × 10〈jats:sup〉15〈/jats:sup〉 kg of the ‘missing carbon’ sequestered during the decline from an Eocene high CO〈jats:sub〉2〈/jats:sub〉-world to a mid-Oligocene medium CO〈jats:sub〉2〈/jats:sub〉-world, highlighting the exceptional role of the Southern Ocean in modulating long-term climate.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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    Phytoplankton responses to temperature increases are constrained by abiotic conditions and community composition (2016)
    Springer Nature
    In:  EPIC3Oecologia, Springer Nature, 182(3), pp. 815-827, ISSN: 0029-8549
    Details
    Publication Date: 2023-09-22
    Description: Effects of temperature changes on phytoplankton communities seem to be highly context-specific, but few studies have analyzed whether this context specificity depends on differences in the abiotic conditions or in species composition between studies. We present an experiment that allows disentangling the contribution of abiotic and biotic differences in shaping the response to two aspects of temperature change: permanent increase of mean temperature versus pulse disturbance in form of a heat wave. We used natural communities from six different sites of a floodplain system as well as artificially mixed communities from laboratory cultures and grew both, artificial and natural communities, in water from the six different floodplain lakes (sites). All 12 contexts (2 communities × 6 sites) were first exposed to three different temperature levels (12, 18, 24 °C, respectively) and afterward to temperature pulses (4 °C increase for 7 h day(-1)). Temperature-dependent changes in biomass and community composition depended on the initial composition of phytoplankton communities. Abiotic conditions had a major effect on biomass of phytoplankton communities exposed to different temperature conditions, however, the effect of biotic and abiotic conditions together was even more pronounced. Additionally, phytoplankton community responses to pulse temperature effects depended on the warming history. By disentangling abiotic and biotic effects, our study shows that temperature-dependent effects on phytoplankton communities depend on both, biotic and abiotic constraints.
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    The body-size structure of macrobenthos changes predictably along gradients of hydrodynamic stress and organic enrichment (2015)
    Springer Nature
    In:  EPIC3Marine Biology, Springer Nature, 162(3), pp. 675-685, ISSN: 0025-3162
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    Publication Date: 2023-09-22
    Repository Name: EPIC Alfred Wegener Institut
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    Far-ranging generalist top predators enhance the stability of meta-foodwebs (2019)
    Springer Nature
    In:  EPIC3Scientific Reports, Springer Nature, 9(1), pp. 12268-12268, ISSN: 2045-2322
    Details
    Publication Date: 2023-09-25
    Description: Identifying stabilizing factors in foodwebs is a long standing challenge with wide implications for community ecology and conservation. Here, we investigate the stability of spatially resolved meta-foodwebs with far-ranging super-predators for whom the whole meta-foodwebs appears to be a single habitat. By using a combination of generalized modeling with a master stability function approach, we are able to efficiently explore the asymptotic stability of large classes of realistic many-patch meta-foodwebs. We show that meta-foodwebs with far-ranging top predators are more stable than those with localized top predators. Moreover, adding far-ranging generalist top predators to a system can have a net stabilizing effect. These results highlight the importance of top predator conservation.
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    Correction to: Sedimentary and geochemical characteristics of two small permafrost-dominated Arctic river deltas in northern Alaska (2018)
    Springer Nature
    In:  EPIC3arktos, Springer Nature, 4(1), pp. 1-1, ISSN: 2364-9453
    Details
    Publication Date: 2024-04-11
    Description: Arctic river deltas are highly dynamic environments in the northern circumpolar permafrost region that are affected by fluvial, coastal, and permafrost-thaw processes. They are characterized by thick sediment deposits containing large but poorly constrained amounts of frozen organic carbon and nitrogen. This study presents new data on soil organic carbon and nitrogen storage as well as accumulation rates from the Ikpikpuk and Fish Creek river deltas, two small, permafrost-dominated Arctic river deltas on the Arctic Coastal Plain of northern Alaska. A soil organic carbon storage of 42.4 ± 1.6 and 37.9 ± 3.5 kg C m− 2 and soil nitrogen storage of 2.1 ± 0.1 and 2.0 ± 0.2 kg N m− 2 was found for the first 2 m of soil for the Ikpikpuk and Fish Creek river delta, respectively. While the upper meter of soil contains 3.57 Tg C, substantial amounts of carbon (3.09 Tg C or 46%) are also stored within the second meter of soil (100–200 cm) in the two deltas. An increasing and inhomogeneous distribution of C with depth is indicative of the dominance of deltaic depositional rather than soil forming processes for soil organic carbon storage. Largely, mid- to late Holocene radiocarbon dates in our cores suggest different carbon accumulation rates for the two deltas for the last 2000 years. Rates up to 28 g C m− 2 year− 1 for the Ikpikpuk river delta are about twice as high as for the Fish Creek river delta. With this study, we highlight the importance of including these highly dynamic permafrost environments in future permafrost carbon estimations.
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    Gene editing fixes cystic fibrosis gene in mice before birth (2019)
    Springer Nature
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    Publication Date: 2019-05-08
    Print ISSN: 1078-8956
    Electronic ISSN: 1546-170X
    Topics: Biology , Medicine
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    Protein kinase N controls a lysosomal lipid switch to facilitate nutrient signalling via mTORC1 (2019)
    Springer Nature
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    Publication Date: 2019-08-26
    Print ISSN: 1465-7392
    Electronic ISSN: 1476-4679
    Topics: Biology , Medicine
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    EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research (2017)
    Springer Nature
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    Publication Date: 2017-02-28
    Print ISSN: 1548-7091
    Electronic ISSN: 1548-7105
    Topics: Biology , Medicine
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    Biology and evolution of poorly differentiated neuroendocrine tumors (2017)
    Springer Nature
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    Publication Date: 2017-06-01
    Print ISSN: 1078-8956
    Electronic ISSN: 1546-170X
    Topics: Biology , Medicine
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    Analyzing bacterial extracellular vesicles in human body fluids by orthogonal biophysical separation and biochemical characterization (2019)
    Springer Nature
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    Publication Date: 2019-11-27
    Print ISSN: 1754-2189
    Electronic ISSN: 1750-2799
    Topics: Natural Sciences in General
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    A new era for solar (2017)
    Springer Nature
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    Publication Date: 2017-01-01
    Print ISSN: 1749-4885
    Electronic ISSN: 1749-4893
    Topics: Physics
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    CRISPR off-targets: a reassessment (2018)
    Springer Nature
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    Publication Date: 2018-03-30
    Print ISSN: 1548-7091
    Electronic ISSN: 1548-7105
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    Turning point: Industry immigrant (2017)
    Springer Nature
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    Publication Date: 2017-11-02
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Adaptation of muscle activation after patellar loading demonstrates neural control of joint variables (2019)
    Springer Nature
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    Publication Date: 2019-12-01
    Description: We evaluated whether the central nervous system (CNS) chooses muscle activations not only to achieve behavioral goals but also to minimize stresses and strains within joints. We analyzed the coordination between quadriceps muscles during locomotion in rats before and after imposing a lateral force on the patella. Vastus lateralis (VL) and vastus medialis (VM) in the rat produce identical knee torques but opposing mediolateral patellar forces. If the CNS regulates internal joint stresses, we predicted that after imposing a lateral patellar load by attaching a spring between the patella and lateral femur, the CNS would reduce the ratio between VL and VM activation to minimize net mediolateral patellar forces. Our results confirmed this prediction, showing that VL activation was reduced after attaching the spring whereas VM and rectus femoris (RF) activations were not significantly changed. This adaptation was reversed after the spring was detached. These changes were not observed immediately after attaching the spring but only developed after 3–5 days, suggesting that they reflected gradual processes rather than immediate compensatory reflexes. Overall, these results support the hypothesis that the CNS chooses muscle activations to regulate internal joint variables.
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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    Context is everything: aneuploidy in cancer (2019)
    Springer Nature
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    Publication Date: 2019-09-23
    Print ISSN: 1471-0056
    Electronic ISSN: 1471-0064
    Topics: Biology , Medicine
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    Modelling Cryptosporidium infection in human small intestinal and lung organoids (2018)
    Springer Nature
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    Publication Date: 2018-06-25
    Electronic ISSN: 2058-5276
    Topics: Biology
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    Spotlight on Food Science in Japan (2017)
    Springer Nature
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    Publication Date: 2017-03-30
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Therapeutic cancer vaccine survives biotech bust (2015)
    Springer Nature
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    Publication Date: 2015-02-26
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Chronic oral exposure to field-realistic pesticide combinations via pollen and nectar: effects on feeding and thermal performance in a solitary bee (2019)
    Springer Nature
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    Publication Date: 2019-09-24
    Description: Pesticide use is one of the main causes of pollinator declines in agricultural ecosystems. Traditionally, most laboratory studies on bee ecotoxicology test acute exposure to single compounds. However, under field conditions, bees are often chronically exposed to a variety of chemicals, with potential synergistic effects. We studied the effects of field-realistic concentrations of three pesticides measured in pollen and nectar of commercial melon fields on the solitary bee Osmia bicornis L. We orally exposed females of this species throughout their life span to 8 treatments combining two neonicotinoid insecticides (acetamiprid, imidacloprid) and a triazole fungicide (myclobutanil) via pollen and sugar syrup. We measured pollen and syrup consumption, longevity, ovary maturation and thermogenesis. Although bees consumed larger amounts of syrup than pollen, pesticide intake via syrup and pollen were similar. At the tested concentrations, no synergistic effects emerged, and we found no effects on longevity and ovary maturation. However, all treatments containing imidacloprid resulted in suppressed syrup consumption and drastic decreases in thoracic temperature and bee activity. Our results have important implications for pesticide regulation. If we had measured only lethal effects we would have wrongly concluded that the pesticide combinations containing imidacloprid were safe to O. bicornis. The incorporation of tests specifically intended to detect sublethal effects in bee risk assessment schemes should be an urgent priority. In this way, the effects of pesticide exposure on the dynamics of bee populations in agroecosystems will be better assessed.
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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    Inactivation of Ppp1r15a minimises weight gain and insulin resistance during caloric excess in female mice (2019)
    Springer Nature
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    Publication Date: 2019-02-27
    Description: Phosphorylation of the translation initiation factor eIF2α within the mediobasal hypothalamus is known to suppress food intake, but the role of the eIF2α phosphatases in regulating body weight is poorly understood. Mice deficient in active PPP1R15A, a stress-inducible eIF2α phosphatase, are healthy and more resistant to endoplasmic reticulum stress than wild type controls. We report that when female Ppp1r15a mutant mice are fed a high fat diet they gain less weight than wild type littermates owing to reduced food intake. This results in healthy leaner Ppp1r15a mutant animals with reduced hepatic steatosis and improved insulin sensitivity, albeit with a possible modest defect in insulin secretion. By contrast, no weight differences are observed between wild type and Ppp1r15a deficient mice fed a standard diet. We conclude that female mice lacking the C-terminal PP1-binding domain of PPP1R15A show reduced dietary intake and preserved glucose tolerance. Our data indicate that this results in reduced weight gain and protection from diet-induced obesity.
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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    Loss of mRNA surveillance pathways results in widespread protein aggregation (2018)
    Springer Nature
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    Publication Date: 2018-03-01
    Description: Eukaryotic cells contain translation-associated mRNA surveillance pathways which prevent the production of potentially toxic proteins from aberrant mRNA translation events. We found that loss of mRNA surveillance pathways in mutants deficient in nonsense-mediated decay (NMD), no-go decay (NGD) and nonstop decay (NSD) results in increased protein aggregation. We have isolated and identified the proteins that aggregate and our bioinformatic analyses indicates that increased aggregation of aggregation-prone proteins is a general occurrence in mRNA surveillance mutants, rather than being attributable to specific pathways. The proteins that aggregate in mRNA surveillance mutants tend to be more highly expressed, more abundant and more stable proteins compared with the wider proteome. There is also a strong correlation with the proteins that aggregate in response to nascent protein misfolding and an enrichment for proteins that are substrates of ribosome-associated Hsp70 chaperones, consistent with susceptibility for aggregation primarily occurring during translation/folding. We also identified a significant overlap between the aggregated proteins in mRNA surveillance mutants and ageing yeast cells suggesting that translation-dependent protein aggregation may be a feature of the loss of proteostasis that occurs in aged cell populations.
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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    ICP4-induced miR-101 attenuates HSV-1 replication (2016)
    Springer Nature
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    Publication Date: 2016-03-17
    Description: Hepes simplex Virus type 1 (HSV-1) is an enveloped DNA virus that can cause lytic and latent infection. miRNAs post-transcriptionally regulate gene expression and our previous work has indicated that HSV-1 infection induces miR-101 expression in HeLa cells. The present study demonstrates that HSV-1-induced miR-101 is mainly derived from its precursor hsa-mir-101-2 and the HSV-1 immediate early gene ICP4 (infected-cell polypeptide 4) directly binds to the hsa-mir-101-2 promoter to activate its expression. RNA-binding protein G-rich sequence factor 1 (GRSF1) was identified as a new target of miR-101; GRSF1 binds to HSV-1 p40 mRNA and enhances its expression, facilitating viral proliferation. Together, ICP4 induces miR-101 expression, which downregulates GRSF1 expression and attenuates the replication of HSV-1. This allows host cells to maintain a permissive environment for viral replication by preventing lytic cell death. These findings indicate that HSV-1 early gene expression modulates host miRNAs to regulate molecular defense mechanisms. This study provides novel insight into host-virus interactions in HSV-1 infection and may contribute to the development of antiviral therapeutics.
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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    Emissions mitigation opportunities for savanna countries from early dry season fire management (2018)
    Springer Nature
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    Publication Date: 2018-06-08
    Description: Savanna fires produce significant emissions globally, but if managed effectively could provide an important mitigation opportunity, particularly in African least developed countries. Here we show global opportunities for emissions reductions through early dry season burning for 37 countries including: 29 countries in Africa (69.1 MtCO2-e yr−1), six countries in South America (13.3 MtCO2-e yr−1), and Australia and Papua New Guinea (6.9 MtCO2-e yr−1). Emissions reduction estimates are based on the successful approach developed in Australia to reduce emissions from savanna fires using global-scale, remotely sensed estimates of monthly emissions. Importantly, 20 least developed countries in Africa account for 74% of the mitigation potential (60.2 MtCO2-e yr−1). More than 1.02 million km2 of savanna dominated protected areas within these countries could be used as pilot sites to test and advance a regional approach to mitigation efforts for savanna fires in Africa. Potential versus actual abatement opportunities are discussed.
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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    Intensifying the response of distributed optical fibre sensors using 2D and 3D image restoration (2016)
    Springer Nature
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    Publication Date: 2016-03-01
    Description: Distributed optical fibre sensors possess the unique capability of measuring the spatial and temporal map of environmental quantities that can be of great interest for several field applications. Although existing methods for performance enhancement have enabled important progresses in the field, they do not take full advantage of all information present in the measured data, still giving room for substantial improvement over the state-of-the-art. Here we propose and experimentally demonstrate an approach for performance enhancement that exploits the high level of similitude and redundancy contained on the multidimensional information measured by distributed fibre sensors. Exploiting conventional image and video processing, an unprecedented boost in signal-to-noise ratio and measurement contrast is experimentally demonstrated. The method can be applied to any white-noise-limited distributed fibre sensor and can remarkably provide a 100-fold improvement in the sensor performance with no hardware modification.
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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    Brainstem and spinal cord MRI identifies altered sensorimotor pathways post-stroke (2019)
    Springer Nature
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    Publication Date: 2019-08-06
    Description: Damage to the corticospinal tract is widely studied following unilateral subcortical stroke, whereas less is known about changes to other sensorimotor pathways. This may be due to the fact that many studies investigated morphological changes in the brain, where the majority of descending and ascending brain pathways are overlapping, and did not investigate the brainstem where they separate. Moreover, these pathways continue passing through separate regions in the spinal cord. Here, using a high-resolution structural MRI of both the brainstem and the cervical spinal cord, we were able to identify a number of microstructurally altered pathways, in addition to the corticospinal tract, post stroke. Moreover, decreases in ipsi-lesional corticospinal tract integrity and increases in contra-lesional medial reticulospinal tract integrity were correlated with motor impairment severity in individuals with stroke.
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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    CRISPR knockout screening identifies combinatorial drug targets in pancreatic cancer and models cellular drug response (2018)
    Springer Nature
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    Publication Date: 2018-10-15
    Description: Predicting the response and identifying additional targets that will improve the efficacy of chemotherapy is a major goal in cancer research. Through large-scale in vivo and in vitro CRISPR knockout screens in pancreatic ductal adenocarcinoma cells, we identified genes whose genetic deletion or pharmacologic inhibition synergistically increase the cytotoxicity of MEK signaling inhibitors. Furthermore, we show that CRISPR viability scores combined with basal gene expression levels could model global cellular responses to the drug treatment. We develop drug response evaluation by in vivo CRISPR screening (DREBIC) method and validated its efficacy using large-scale experimental data from independent experiments. Comparative analyses demonstrate that DREBIC predicts drug response in cancer cells from a wide range of tissues with high accuracy and identifies therapeutic vulnerabilities of cancer-causing mutations to MEK inhibitors in various cancer types.
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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    Age-dependent carry-over effects in a long-distance migratory bird (2019)
    Springer Nature
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    Publication Date: 2019-08-19
    Description: Migratory birds usually respond to climate change by modifying breeding and/or wintering areas, as well as by reproducing earlier. In addition, changes in winter habitat use or breeding phenology could have important carry-over effects on subsequent breeding success. Here, we studied age- and sex-dependent carry-over effects from wintering to the breeding stage of a small aerial insectivorous long-distance migratory bird, the barn swallows (Hirundo rustica) breeding in Denmark during 1984–2013. First, we used stable isotope analyses combined with ringing recoveries to identify wintering areas. Second, we found that environmental conditions as inferred by Normalized Difference Vegetation Index (NDVI) have improved at the wintering grounds. Third, we used confirmatory path analysis to quantify the indirect effect of winter conditions on subsequent breeding success. Males delayed onset of breeding and raised fewer fledglings in the first brood when ecological conditions during the previous winter improved. This response was age dependent, since yearlings did not respond to this environmental cue but the response was increasingly stronger as males aged. Females showed a similar response to winter conditions, although not statistically significant. These results highlight the importance of studying carry-over effects within the context of climate change, especially in relation to age of individuals.
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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    Adaptable surfactant-mediated method for the preparation of anisotropic metal chalcogenide nanomaterials (2018)
    Springer Nature
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    Publication Date: 2018-02-12
    Description: The hot injection synthesis of nanomaterials is a highly diverse and fundamental field of chemical research, which has shown much success in the bottom up approach to nanomaterial design. Here we report a synthetic strategy for the production of anisotropic metal chalcogenide nanomaterials of different compositions and shapes, using an optimised hot injection approach. Its unique advantage compared to other hot injection routes is that it employs one chemical to act as many agents: high boiling point, viscous solvent, reducing agent, and surface coordinating ligand. It has been employed to produce a range of nanomaterials, such as CuS, Bi2S3, Cu2-xSe, FeSe2, and Bi4Se3, among others, with various structures including nanoplates and nanosheets. Overall, this article will highlight the excellent versatility of the method, which can be tuned to produce many different materials and shapes. In addition, due to the nature of the synthesis, 2D nanomaterial products are produced as monolayers without the need for exfoliation; a significant achievement towards future development of these materials.
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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    A simple and robust real-time qPCR method for the detection of PIK3CA mutations (2018)
    Springer Nature
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    Publication Date: 2018-03-09
    Description: PIK3CA mutations are seemingly the most common driver mutations in breast cancer with H1047R and E545K being the most common of these, accounting together for around 60% of all PIK3CA mutations and have promising therapeutic implications. Given the low sensitivity and the high cost of current genotyping methods we sought to develop fast, simple and inexpensive assays for PIK3CA H1047R and E545K mutation screening in clinical material. The methods we describe are based on a real-time PCR including a mutation specific primer combined with a non-productive oligonucleotide which inhibits wild-type amplification and a parallel internal control reaction. We demonstrate consistent detection of PIK3CA H1047R mutant DNA in genomic DNA extracted from frozen breast cancer biopsies, FFPE material or cancer cell lines with a detection sensitivity of approximately 5% mutant allele fraction and validate these results using both Sanger sequencing and deep next generation sequencing methods. The detection sensitivity for PIK3CA E545K mutation was approximately 10%. We propose these methods as simple, fast and inexpensive diagnostic tools to determine PIK3CA mutation status.
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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    Novel Hybrid Evolutionary Algorithms for Spatial Prediction of Floods (2018)
    Springer Nature
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    Publication Date: 2018-10-18
    Description: Adaptive neuro-fuzzy inference system (ANFIS) includes two novel GIS-based ensemble artificial intelligence approaches called imperialistic competitive algorithm (ICA) and firefly algorithm (FA). This combination could result in ANFIS-ICA and ANFIS-FA models, which were applied to flood spatial modelling and its mapping in the Haraz watershed in Northern Province of Mazandaran, Iran. Ten influential factors including slope angle, elevation, stream power index (SPI), curvature, topographic wetness index (TWI), lithology, rainfall, land use, stream density, and the distance to river were selected for flood modelling. The validity of the models was assessed using statistical error-indices (RMSE and MSE), statistical tests (Friedman and Wilcoxon signed-rank tests), and the area under the curve (AUC) of success. The prediction accuracy of the models was compared to some new state-of-the-art sophisticated machine learning techniques that had previously been successfully tested in the study area. The results confirmed the goodness of fit and appropriate prediction accuracy of the two ensemble models. However, the ANFIS-ICA model (AUC = 0.947) had a better performance in comparison to the Bagging-LMT (AUC = 0.940), BLR (AUC = 0.936), LMT (AUC = 0.934), ANFIS-FA (AUC = 0.917), LR (AUC = 0.885) and RF (AUC = 0.806) models. Therefore, the ANFIS-ICA model can be introduced as a promising method for the sustainable management of flood-prone areas.
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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    High diversity stabilizes the thermal resilience of pollinator communities in intensively managed grasslands (2015)
    Springer Nature
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    Publication Date: 2015-08-12
    Description: Article How variation in species responses to climate may influence the resilience of ecological communities to environmental change is not fully understood. Here, the authors characterize the thermal niches of insect pollinator communities and show that resilience increases along a gradient of land-use intensity. Nature Communications doi: 10.1038/ncomms8989 Authors: Sara Kühsel, Nico Blüthgen
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 99
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    Oestrogen sulfotransferase ablation sensitizes mice to sepsis (2015)
    Springer Nature
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    Publication Date: 2015-08-12
    Description: Article Sepsis, a systemic inflammatory response to bacterial infection, can lead to organ failure and death. Here, Chai et al. investigate the mechanisms behind the septic response and identify the role of oestrogen sulfotransferase in this process in mice. Nature Communications doi: 10.1038/ncomms8979 Authors: Xiaojuan Chai, Yan Guo, Mengxi Jiang, Bingfang Hu, Zhigang Li, Jie Fan, Meihong Deng, Timothy R. Billiar, Heidi R. Kucera, Nilesh W. Gaikwad, Meishu Xu, Peipei Lu, Jiong Yan, Haiyan Fu, Youhua Liu, Lushan Yu, Min Huang, Su Zeng, Wen Xie
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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    DNA/RNA heteroduplex oligonucleotide for highly efficient gene silencing (2015)
    Springer Nature
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    Publication Date: 2015-08-12
    Description: Article Antisense oligonucleotides (ASOs) can repress the expression of specific genes. Here, the authors show that a DNA/RNA heteroduplex oligonucleotide (HDO) with a structure different from ASOs is more potent in suppressing target gene expression, and causes a less adverse effect in mouse liver. Nature Communications doi: 10.1038/ncomms8969 Authors: Kazutaka Nishina, Wenying Piao, Kie Yoshida-Tanaka, Yumiko Sujino, Tomoko Nishina, Tsuyoshi Yamamoto, Keiko Nitta, Kotaro Yoshioka, Hiroya Kuwahara, Hidenori Yasuhara, Takeshi Baba, Fumiko Ono, Kanjiro Miyata, Koichi Miyake, Punit P. Seth, Audrey Low, Masayuki Yoshida, C. Frank Bennett, Kazunori Kataoka, Hidehiro Mizusawa, Satoshi Obika, Takanori Yokota
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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