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  • Nature Publishing Group  (363,432)
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  • 1
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    Quorum sensing signal–response systems in Gram-negative bacteria (2016)
    Nature Publishing Group
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    Publication Date: 2024-04-12
    Description: Bacteria use quorum sensing to orchestrate gene expression programmes that underlie collective behaviours. Quorum sensing relies on the production, release, detection and group-level response to extracellular signalling molecules, which are called autoinducers. Recent work has discovered new autoinducers in Gram-negative bacteria, shown how these molecules are recognized by cognate receptors, revealed new regulatory components that are embedded in canonical signalling circuits and identified novel regulatory network designs. In this Review we examine how, together, these features of quorum sensing signal–response systems combine to control collective behaviours in Gram-negative bacteria and we discuss the implications for host–microbial associations and antibacterial therapy.
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  • 2
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    Advancing microbial sciences by individual-based modelling (2016)
    Nature Publishing Group
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    Publication Date: 2023-12-21
    Description: Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage–CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE).
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  • 3
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    A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity (2015)
    Nature Publishing Group
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    Publication Date: 2023-11-29
    Description: Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is a key enzyme of the Calvin cycle, which is responsible for most of Earth's primary production. Although research on RubisCO genes and enzymes in plants, cyanobacteria and bacteria has been ongoing for years, still little is understood about its regulation and activation in bacteria. Even more so, hardly any information exists about the function of metagenomic RubisCOs and the role of the enzymes encoded on the flanking DNA owing to the lack of available function-based screens for seeking active RubisCOs from the environment. Here we present the first solely activity-based approach for identifying RubisCO active fosmid clones from a metagenomic library. We constructed a metagenomic library from hydrothermal vent fluids and screened 1056 fosmid clones. Twelve clones exhibited RubisCO activity and the metagenomic fragments resembled genes from Thiomicrospira crunogena. One of these clones was further analyzed. It contained a 35.2 kb metagenomic insert carrying the RubisCO gene cluster and flanking DNA regions. Knockouts of twelve genes and two intergenic regions on this metagenomic fragment demonstrated that the RubisCO activity was significantly impaired and was attributed to deletions in genes encoding putative transcriptional regulators and those believed to be vital for RubisCO activation. Our new technique revealed a novel link between a poorly characterized gene and RubisCO activity. This screen opens the door to directly investigating RubisCO genes and respective enzymes from environmental samples.
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  • 4
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    Adaptive evolution of a key phytoplankton species to ocean acidification (2012)
    Nature Publishing Group
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    Publication Date: 2023-11-08
    Description: Ocean acidification, the drop in seawater pH associated with the ongoing enrichment of marine waters with carbon dioxide from fossil fuel burning, may seriously impair marine calcifying organisms. Our present understanding of the sensitivity of marine life to ocean acidification is based primarily on short-term experiments, in which organisms are exposed to increased concentrations of CO2. However, phytoplankton species with short generation times, in particular, may be able to respond to environmental alterations through adaptive evolution. Here, we examine the ability of the world’s single most important calcifying organism, the coccolithophore Emiliania huxleyi, to evolve in response to ocean acidification in two 500-generation selection experiments. Specifically, we exposed E. huxleyi populations founded by single or multiple clones to increased concentrations of CO2. Around 500 asexual generations later we assessed their fitness. Compared with populations kept at ambient CO2 partial pressure, those selected at increased partial pressure exhibited higher growth rates, in both the single- and multiclone experiment, when tested under ocean acidification conditions. Calcification was partly restored: rates were lower under increased CO2 conditions in all cultures, but were up to 50% higher in adapted compared with non-adapted cultures. We suggest that contemporary evolution could help to maintain the functionality of microbial processes at the base of marine food webs in the face of global change.
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  • 5
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    Interannual atmospheric variability forced by the deep equatorial Atlantic Ocean (2011)
    Nature Publishing Group
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    Publication Date: 2023-11-08
    Description: Climate variability in the tropical Atlantic Ocean is determined by large-scale ocean–atmosphere interactions, which particularly affect deep atmospheric convection over the ocean and surrounding continents1. Apart from influences from the Pacific El Niño/Southern Oscillation2 and the North Atlantic Oscillation3, the tropical Atlantic variability is thought to be dominated by two distinct ocean–atmosphere coupled modes of variability that are characterized by meridional4, 5 and zonal6, 7 sea-surface-temperature gradients and are mainly active on decadal and interannual timescales, respectively8, 9. Here we report evidence that the intrinsic ocean dynamics of the deep equatorial Atlantic can also affect sea surface temperature, wind and rainfall in the tropical Atlantic region and constitutes a 4.5-yr climate cycle. Specifically, vertically alternating deep zonal jets of short vertical wavelength with a period of about 4.5 yr and amplitudes of more than 10 cm s−1 are observed, in the deep Atlantic, to propagate their energy upwards, towards the surface10, 11. They are linked, at the sea surface, to equatorial zonal current anomalies and eastern Atlantic temperature anomalies that have amplitudes of about 6 cm s−1 and 0.4 °C, respectively, and are associated with distinct wind and rainfall patterns. Although deep jets are also observed in the Pacific12 and Indian13 oceans, only the Atlantic deep jets seem to oscillate on interannual timescales. Our knowledge of the persistence and regularity of these jets is limited by the availability of high-quality data. Despite this caveat, the oscillatory behaviour can still be used to improve predictions of sea surface temperature in the tropical Atlantic. Deep-jet generation and upward energy transmission through the Equatorial Undercurrent warrant further theoretical study.
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  • 6
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    Bending-related faulting and mantle serpentinization at the Middle America Trench (2003)
    Nature Publishing Group
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    Publication Date: 2023-09-26
    Description: The dehydration of subducting oceanic crust and upper mantle has been inferred both to promote the partial melting leading to arc magmatism and to induce intraslab intermediate-depth earthquakes, at depths of 50–300 km. Yet there is still no consensus about how slab hydration occurs or where and how much chemically bound water is stored within the crust and mantle of the incoming plate. Here we document that bending-related faulting of the incoming plate at the Middle America trench creates a pervasive tectonic fabric that cuts across the crust, penetrating deep into the mantle. Faulting is active across the entire ocean trench slope, promoting hydration of the cold crust and upper mantle surrounding these deep active faults. The along-strike length and depth of penetration of these faults are also similar to the dimensions of the rupture area of intermediate-depth earthquakes.
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  • 7
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    Massive nitrous oxide emissions from the tropical South Pacific Ocean (2015)
    Nature Publishing Group
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    Publication Date: 2023-09-19
    Description: Nitrous oxide is a potent greenhouse gas and a key compound in stratospheric ozone depletion. In the ocean, nitrous oxide is produced at intermediate depths through nitrification and denitrification, in particular at low oxygen concentrations. Although a third of natural emissions of nitrous oxide to the atmosphere originate from the ocean, considerable uncertainties in the distribution and magnitude of the emissions still exist. Here we present high-resolution surface measurements and vertical profiles of nitrous oxide that include the highest reported nitrous oxide concentrations in marine surface waters, suggesting that there is a hotspot of nitrous oxide emissions in high-productivity upwelling ecosystems along the Peruvian coast. We estimate that off Peru, the extremely high nitrous oxide supersaturations we observed drive a massive efflux of 0.2–0.9 Tg of nitrogen emitted as nitrous oxide per year, equivalent to 5–22% of previous estimates of global marine nitrous oxide emissions. Nutrient and gene abundance data suggest that coupled nitrification–denitrification in the upper oxygen minimum zone and transport of resulting nitrous oxide to the surface by upwelling lead to the high nitrous oxide concentrations. Our estimate of nitrous oxide emissions from the Peruvian coast surpasses values from similar, highly productive areas.
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  • 8
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    An environmental bacterial taxon with a large and distinct metabolic repertoire (2014)
    Nature Publishing Group
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    Publication Date: 2023-02-14
    Description: Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such ‘talented’ producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Here we report the single-cell- and metagenomics-based discovery of such producers. Two phylotypes of the candidate genus ‘Entotheonella’ with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei. Almost all bioactive polyketides and peptides known from this animal were attributed to a single phylotype. ‘Entotheonella’ spp. are widely distributed in sponges and belong to an environmental taxon proposed here as candidate phylum ‘Tectomicrobia’. The pronounced bioactivities and chemical uniqueness of ‘Entotheonella’ compounds provide significant opportunities for ecological studies and drug discovery.
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  • 9
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    Coralline algal Barium as indicator for 20th century northwestern North Atlantic surface ocean freshwater variability (2013)
    Nature Publishing Group
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    Publication Date: 2023-01-31
    Description: During the past decades climate and freshwater dynamics in the northwestern North Atlantic have undergone major changes. Large-scale freshening episodes, related to polar freshwater pulses, have had a strong influence on ocean variability in this climatically important region. However, little is known about variability before 1950, mainly due to the lack of long-term high-resolution marine proxy archives. Here we present the first multidecadal-length records of annually resolved Ba/Ca variations from Northwest Atlantic coralline algae. We observe positive relationships between algal Ba/Ca ratios from two Newfoundland sites and salinity observations back to 1950. Both records capture episodical multi-year freshening events during the 20th century. Variability in algal Ba/Ca is sensitive to freshwater-induced changes in upper ocean stratification, which affect the transport of cold, Ba-enriched deep waters onto the shelf (highly stratified equals less Ba/Ca). Algal Ba/Ca ratios therefore may serve as a new resource for reconstructing past surface ocean freshwater changes.
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  • 10
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    Persistent summer expansion of the Atlantic Warm Pool during glacial abrupt cold events (2008)
    Nature Publishing Group
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    Publication Date: 2023-01-31
    Description: Palaeoclimate records and numerical model simulations indicate that changes in tropical and subtropical sea surface temperatures and in the annual average position of the intertropical convergence zone are linked to high-latitude climate changes on millennial to glacial–interglacial timescales. It has recently been suggested that cooling in the high latitudes associated with abrupt climate-change events is evident primarily during the northern hemisphere winter, implying increased seasonality at these times8. However, it is unclear whether such a seasonal bias also exists for the low latitudes. Here we analyse the Mg/Ca ratios of surface-dwelling foraminifera to reconstruct sea surface temperatures in the northeastern Gulf of Mexico for the past 300,000 years. We suggest that sea surface temperatures are controlled by the migration of the northern boundary of the Atlantic Warm Pool, and hence the position of the intertropical convergence zone during boreal summer, and are relatively insensitive to winter conditions. Our results suggest that summer Atlantic Warm Pool expansion is primarily affected by glacial–interglacial variability and low-latitude summer insolation. Because a clear signature of rapid climate-change events, such as the Younger Dryas cold event, is lacking in our record, we conclude that high-latitude events seem to influence only the winter Caribbean climate conditions, consistent with the hypothesis of extreme northern-hemisphere seasonality during abrupt cooling events.
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  • 11
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    Multidrug efflux pumps: structure, function and regulation (2018)
    Nature Publishing Group
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    Publication Date: 2022-12-22
    Description: Infections arising from multidrug-resistant pathogenic bacteria are spreading rapidly throughout the world and threaten to become untreatable. The origins of resistance are numerous and complex, but one underlying factor is the capacity of bacteria to rapidly export drugs through the intrinsic activity of efflux pumps. In this Review, we describe recent advances that have increased our understanding of the structures and molecular mechanisms of multidrug efflux pumps in bacteria. Clinical and laboratory data indicate that efflux pumps function not only in the drug extrusion process but also in virulence and the adaptive responses that contribute to antimicrobial resistance during infection. The emerging picture of the structure, function and regulation of efflux pumps suggests opportunities for countering their activities.
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  • 12
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    The impact of faulting complexity and type on earthquake rupture dynamics (2022)
    Nature Publishing Group
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    Publication Date: 2022-10-31
    Description: The statistical properties of seismicity are known to be affected by several factors such as the rheological parameters of rocks. We analysed the earthquake double-couple as a function of the faulting type. Here we show that it impacts the moment tensors of earthquakes: thrust- faulting events are characterized by higher double-couple components with respect to strike- slip- and normal-faulting earthquakes. Our results are coherent with the stress dependence of the scaling exponent of the Gutenberg-Richter law, which is anticorrelated to the double- couple. We suggest that the structural and tectonic control of seismicity may have its origin in the complexity of the seismogenic source marked by the width of the cataclastic damage zone and by the slip of different fault planes during the same seismic event; the sharper and concentrated the slip as along faults, the higher the double-couple. This phenomenon may introduce bias in magnitude estimation, with possible impact on seismic forecasting.
    Description: Published
    Description: 258
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: double couple ; damage zone ; different fault type ; seismicity ; tectonics ; fault type ; seismicity ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
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    Complementary effects of species and genetic diversity on productivity and stability of sown grasslands (2015)
    Nature Publishing Group
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    Publication Date: 2022-09-21
    Description: Plant species diversity regulates the productivity1–3 and stability2,4 of natural ecosystems, along with their resilience to disturbance5,6. The influence of species diversity on the productivity of agronomic systems is less clear7–10. Plant genetic diversity is also suspected to influence ecosystem function3,11–14, although empirical evidence is scarce. Given the large range of genotypes that can be generated per species through artificial selection, genetic diversity is a potentially important leverage of productivity in cultivated systems. Here we assess the effect of species and genetic diversity on the production and sustainable supply of livestock fodder in sown grasslands, comprising single and multispecies assemblages characterized by different levels of genetic diversity, exposed to drought and non-drought conditions. Multispecies assemblages proved more productive than monocultures when subject to drought, regardless of the number of genotypes per species present. Conversely, the temporal stability of production increased only with the number of genotypes present under both drought and non-drought conditions, and was unaffected by the number of species. We conclude that taxonomic and genetic diversity can play complementary roles when it comes to optimizing livestock fodder production in managed grasslands, and suggest that both levels of diversity should be considered in plant breeding programmes designed to boost the productivity and resilience of managed grasslands in the face of increasing environmental hazards.
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  • 14
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    Continuous flow of Upper Labrador Sea Water around Cape Hatteras (2018)
    Nature Publishing Group
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    Publication Date: 2022-08-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 8 (2018): 4494, doi:10.1038/s41598-018-22758-z.
    Description: Six velocity sections straddling Cape Hatteras show a deep counterflow rounding the Cape wedged beneath the poleward flowing Gulf Stream and the continental slope. This counterflow is likely the upper part of the equatorward-flowing Deep Western Boundary Current (DWBC). Hydrographic data suggest that the equatorward flow sampled by the shipboard 38 kHz ADCP comprises the Upper Labrador Sea Water (ULSW) layer and top of the Classical Labrador Sea Water (CLSW) layer. Continuous DWBC flow around the Cape implied by the closely-spaced velocity sections here is also corroborated by the trajectory of an Argo float. These findings contrast with previous studies based on floats and tracers in which the lightest DWBC constituents did not follow the boundary to cross under the Gulf Stream at Cape Hatteras but were diverted into the interior as the DWBC encountered the Gulf Stream in the crossover region. Additionally, our six quasi-synoptic velocity sections confirm that the Gulf Stream intensified markedly at that time as it approached the separation point and flowed into deeper waters. Downstream increases were observed not only in the poleward transport across the sections but also in the current’s maximum speed.
    Description: This research was supported by NSF through OCE-1558521 and OCE-1332667 and by a grant from North Carolina to the Renewable Ocean Energy Program.
    Repository Name: Woods Hole Open Access Server
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  • 15
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    Small sinking particles control anammox rates in the Peruvian oxygen minimum zone (2021)
    Nature Publishing Group
    In:  EPIC3Nature Communications, Nature Publishing Group, 12(1), pp. 1-12
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    Publication Date: 2022-08-15
    Description: Anaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April–June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128–512 µm), even though anammox bacteria were not directly associated with particles. This suggests that the relationship between anammox rates and particles is related to the ammonium released from particles by remineralization. To investigate this, ammonium release from particles was modelled and theoretical encounters of free-living anammox bacteria with ammonium in the particle boundary layer were calculated. These results indicated that small sinking particles could be responsible for ~75% of ammonium release in anoxic waters and that free-living anammox bacteria frequently encounter ammonium in the vicinity of smaller particles. This indicates a so far underestimated role of abundant, slow-sinking small particles in controlling oceanic nutrient budgets, and furthermore implies that observations of the volume of small particles could be used to estimate N-loss across large areas.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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    Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species (2022)
    Nature Publishing Group
    In:  EPIC3Nature, Nature Publishing Group, 601(7892), pp. 257-262
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    Publication Date: 2022-08-11
    Description: The methanogenic degradation of oil hydrocarbons can proceed through syntrophic partnerships of hydrocarbon-degrading bacteria and methanogenic archaea1,2,3. However, recent culture-independent studies have suggested that the archaeon ‘Candidatus Methanoliparum’ alone can combine the degradation of long-chain alkanes with methanogenesis4,5. Here we cultured Ca. Methanoliparum from a subsurface oil reservoir. Molecular analyses revealed that Ca. Methanoliparum contains and overexpresses genes encoding alkyl-coenzyme M reductases and methyl-coenzyme M reductases, the marker genes for archaeal multicarbon alkane and methane metabolism. Incubation experiments with different substrates and mass spectrometric detection of coenzyme-M-bound intermediates confirm that Ca. Methanoliparum thrives not only on a variety of long-chain alkanes, but also on n-alkylcyclohexanes and n-alkylbenzenes with long n-alkyl (C≥13) moieties. By contrast, short-chain alkanes (such as ethane to octane) or aromatics with short alkyl chains (C≤12) were not consumed. The wide distribution of Ca. Methanoliparum4,5,6 in oil-rich environments indicates that this alkylotrophic methanogen may have a crucial role in the transformation of hydrocarbons into methane.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    Return to rapid ice loss in Greenland and record loss in 2019 detected by the GRACE-FO satellites (2020)
    Nature Publishing Group
    In:  EPIC3Communications Earth & Environment, Nature Publishing Group, 1(1), pp. 1-8
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    Publication Date: 2022-06-20
    Description: Between 2003-2016, the Greenland ice sheet (GrIS) was one of the largest contributors to sea level rise, as it lost about 255 Gt of ice per year. This mass loss slowed in 2017 and 2018 to about 100 Gt yr−1. Here we examine further changes in rate of GrIS mass loss, by analyzing data from the GRACE-FO (Gravity Recovery and Climate Experiment – Follow On) satellite mission, launched in May 2018. Using simulations with regional climate models we show that the mass losses observed in 2017 and 2018 by the GRACE and GRACE-FO missions are lower than in any other two year period between 2003 and 2019, the combined period of the two missions. We find that this reduced ice loss results from two anomalous cold summers in western Greenland, compounded by snow-rich autumn and winter conditions in the east. For 2019, GRACE-FO reveals a return to high melt rates leading to a mass loss of 223 ± 12 Gt month−1 during the month of July alone, and a record annual mass loss of 532 ± 58 Gt yr−1.
    Repository Name: EPIC Alfred Wegener Institut
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  • 18
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    Arctic glaciers record wavier circumpolar winds (2022)
    Nature Publishing Group
    In:  EPIC3Nature Climate Change, Nature Publishing Group, 12(3), pp. 249-255
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    Publication Date: 2022-06-20
    Repository Name: EPIC Alfred Wegener Institut
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  • 19
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    Contributions of GRACE to understanding climate change (2019)
    Nature Publishing Group
    In:  EPIC3Nature Climate Change, Nature Publishing Group, 9(5), pp. 358-369
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    Publication Date: 2022-06-20
    Description: Time-resolved satellite gravimetry has revolutionized understanding of mass transport in the Earth system. Since 2002, the Gravity Recovery and Climate Experiment (GRACE) has enabled monitoring of the terrestrial water cycle, ice sheet and glacier mass balance, sea level change and ocean bottom pressure variations, as well as understanding responses to changes in the global climate system. Initially a pioneering experiment of geodesy, the time-variable observations have matured into reliable mass transport products, allowing assessment and forecast of a number of important climate trends, and improvements in service applications such as the United States Drought Monitor. With the successful launch of the GRACE Follow-On mission, a multi-decadal record of mass variability in the Earth system is within reach.
    Repository Name: EPIC Alfred Wegener Institut
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  • 20
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    Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita (2008)
    Nature Publishing Group
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    Publication Date: 2022-05-26
    Description: © 2008 Nature Publishing Group. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike license. The definitive version was published in Nature Biotechnology 26 (2008): 909-915, doi:10.1038/nbt.1482.
    Description: Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall–degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.
    Description: SCRI laboratory (V.C.B. and J.T.J.) received funding from the Scottish Government. This work benefited from links funded via COST Action 872. G.V.M. and V.L. are supported by ARC, CNRS, EMBO, MENRT and Region Rhone-Alpes. G.V.M., M.R.-R. and V.L. are also funded by the EU Cascade Network of Excellence and the integrated project Crescendo. M.-C.C. is supported by MENRT.
    Repository Name: Woods Hole Open Access Server
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  • 21
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    Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga (2013)
    Nature Publishing Group
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature 500 (2013): 453–457, doi:10.1038/nature12326.
    Description: Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years1. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing2. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873)3, and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex.
    Description: This work was supported by Genoscope-CES (where most of the sequencing was performed), by US National Science Foundation grants MCB-0821956 and MCB-1121334 to I.A., by German Research Foundation grant HA 5163/2-1 to O.H., by grant 11.G34.31.0008 fromthe Ministry of Education and Science of the Russian Federation to A.S.K., by grant NSF CAREER number 0644282 to M.K., by US National Science Foundation grant MCB-0923676 to D.B.M.W., by FRFC grant 2.4.655.09.F from the Belgian Fonds National de la Recherche Scientifique (FNRS) and a start-up grant from the University of Namur to K.V.D.; J.F.F. and K.V.D. thank also J.-P. Descy (University of Namur) for funding support.
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  • 22
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    Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis (2014)
    Nature Publishing Group
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 5 (2014): 4342, doi:10.1038/ncomms5342.
    Description: Three-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain.
    Description: This work was mainly supported by Howard Hughes Medical Institute. H.P. is currently supported by the Allen Institute for Brain Science. R.W.T. and A.M. were supported by a grant MH071739 (MERIT).
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    Eruption of a deep-sea mud volcano triggers rapid sediment movement (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 5 (2014): 5385, doi:10.1038/ncomms6385.
    Description: Submarine mud volcanoes are important sources of methane to the water column. However, the temporal variability of their mud and methane emissions is unknown. Methane emissions were previously proposed to result from a dynamic equilibrium between upward migration and consumption at the seabed by methane-consuming microbes. Here we show non-steady-state situations of vigorous mud movement that are revealed through variations in fluid flow, seabed temperature and seafloor bathymetry. Time series data for pressure, temperature, pH and seafloor photography were collected over 431 days using a benthic observatory at the active Håkon Mosby Mud Volcano. We documented 25 pulses of hot subsurface fluids, accompanied by eruptions that changed the landscape of the mud volcano. Four major events triggered rapid sediment uplift of more than a metre in height, substantial lateral flow of muds at average velocities of 0.4 m per day, and significant emissions of methane and CO2 from the seafloor.
    Description: Participation of the Sentry AUV and TETHYS team from WHOI was funded by the Arctic Research Initiative of WHOI’s Ocean and Climate Change Institute and the NASA ASTEP grant NNX09AB76G. Additional funds were made available by the AWI, the Max Planck Society and the DFG METEOR/MERIAN programme, as well as the Leibniz programme to A.B.
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    Intensification of the meridional temperature gradient in the Great Barrier Reef following the Last Glacial Maximum (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 5 (2014): 4102, doi:10.1038/ncomms5102.
    Description: Tropical south-western Pacific temperatures are of vital importance to the Great Barrier Reef (GBR), but the role of sea surface temperatures (SSTs) in the growth of the GBR since the Last Glacial Maximum remains largely unknown. Here we present records of Sr/Ca and δ18O for Last Glacial Maximum and deglacial corals that show a considerably steeper meridional SST gradient than the present day in the central GBR. We find a 1–2 °C larger temperature decrease between 17° and 20°S about 20,000 to 13,000 years ago. The result is best explained by the northward expansion of cooler subtropical waters due to a weakening of the South Pacific gyre and East Australian Current. Our findings indicate that the GBR experienced substantial meridional temperature change during the last deglaciation, and serve to explain anomalous deglacial drying of northeastern Australia. Overall, the GBR developed through significant SST change and may be more resilient than previously thought.
    Description: Funding was provided by Deutsche Forschungsgemeinschaft (FE 615/4-1), Australian Research Council (Discovery grant DP1094001), Australia and New Zealand IODP Consortium, Australian Institute of Nuclear Science and Engineering, Natural Environmental Research Council (NE/H014136/1, NE/H014268/1), the Cooperative Research Program of the Center for Advanced Marine Core Research (10B039, 11A013, 11B041), Ministry of Earth Sciences, Govt. of India (with partial support from DST & ISRO-GBP) and Japan Society for the Promotion of Science (JSPS NEXT-GR031).
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    Life-cycle modification in open oceans accounts for genome variability in a cosmopolitan phytoplankton (2015)
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    Publication Date: 2022-05-26
    Description: © International Society for Microbial Ecology, 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 1365–1377, doi:10.1038/ismej.2014.221.
    Description: Emiliania huxleyi is the most abundant calcifying plankton in modern oceans with substantial intraspecific genome variability and a biphasic life cycle involving sexual alternation between calcified 2N and flagellated 1N cells. We show that high genome content variability in Emiliania relates to erosion of 1N-specific genes and loss of the ability to form flagellated cells. Analysis of 185 E. huxleyi strains isolated from world oceans suggests that loss of flagella occurred independently in lineages inhabiting oligotrophic open oceans over short evolutionary timescales. This environmentally linked physiogenomic change suggests life cycling is not advantageous in very large/diluted populations experiencing low biotic pressure and low ecological variability. Gene loss did not appear to reflect pressure for genome streamlining in oligotrophic oceans as previously observed in picoplankton. Life-cycle modifications might be common in plankton and cause major functional variability to be hidden from traditional taxonomic or molecular markers.
    Description: This research was supported by a Marie Curie International Incoming Fellowship FUNSEXDEPHYND to PvD within the 7th European Community Framework Programme, FONDECYT Projects 1110575 (to PvD) and 312004 (to DM-F), the French Agence Nationale de la Recherche/Investissements d’Avenir Grants POSEIDON and OCEANOMICS (Grant No. ANR-11-BTBR-0008 to CdV and IP), the European ERA-net program BiodivERsA under the BioMarks project (to EMB), funding from NASA and NSF (Grants NNX11AF55G and EF-0424599 to DMG and SD), the Genoscope 2007-2008 sequencing initiative and the PACES research program of the Alfred Wegener Helmholtz Institute Helmhotz Centre for Polar and Marine Research.
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    Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency (2016)
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    Publication Date: 2022-05-26
    Description: © The International Society for Microbial Ecology, 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 10 (2016): 968–978, doi:10.1038/ismej.2015.172.
    Description: Upon phosphorus (P) deficiency, marine phytoplankton reduce their requirements for P by replacing membrane phospholipids with alternative non-phosphorus lipids. It was very recently demonstrated that a SAR11 isolate also shares this capability when phosphate starved in culture. Yet, the extent to which this process occurs in other marine heterotrophic bacteria and in the natural environment is unknown. Here, we demonstrate that the substitution of membrane phospholipids for a variety of non-phosphorus lipids is a conserved response to P deficiency among phylogenetically diverse marine heterotrophic bacteria, including members of the Alphaproteobacteria and Flavobacteria. By deletion mutagenesis and complementation in the model marine bacterium Phaeobacter sp. MED193 and heterologous expression in recombinant Escherichia coli, we confirm the roles of a phospholipase C (PlcP) and a glycosyltransferase in lipid remodelling. Analyses of the Global Ocean Sampling and Tara Oceans metagenome data sets demonstrate that PlcP is particularly abundant in areas characterized by low phosphate concentrations. Furthermore, we show that lipid remodelling occurs seasonally and responds to changing nutrient conditions in natural microbial communities from the Mediterranean Sea. Together, our results point to the key role of lipid substitution as an adaptive strategy enabling heterotrophic bacteria to thrive in the vast P-depleted areas of the ocean.
    Description: This work was partially supported by grants STORM (CTM2009-09352/MAR), MALASPINA (CSD2008-00077), HOTMIX (CTM2011-30010/MAR), DOREMI (CTM2012-34294) and EcoBGM (CTM2013-48292-C3-3-R) funded by the Spanish Government, GAČR project GA13-11281S and MESOAQUA (228224) funded by the European Union Seventh Framework Program (FP7/2007-2013) and by the Natural Environment Research Council (NERC), UK (NE/M002233/1).
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    Punctuated shutdown of Atlantic Meridional Overturning Circulation during Greenland Stadial 1 (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 6 (2016): 25902, doi:10.1038/srep25902.
    Description: The Greenland Stadial 1 (GS-1; ~12.9 to 11.65 kyr cal BP) was a period of North Atlantic cooling, thought to have been initiated by North America fresh water runoff that caused a sustained reduction of North Atlantic Meridional Overturning Circulation (AMOC), resulting in an antiphase temperature response between the hemispheres (the ‘bipolar seesaw’). Here we exploit sub-fossil New Zealand kauri trees to report the first securely dated, decadally-resolved atmospheric radiocarbon (14C) record spanning GS-1. By precisely aligning Southern and Northern Hemisphere tree-ring 14C records with marine 14C sequences we document two relatively short periods of AMOC collapse during the stadial, at ~12,920-12,640 cal BP and 12,050-11,900 cal BP. In addition, our data show that the interhemispheric atmospheric 14C offset was close to zero prior to GS-1, before reaching ‘near-modern’ values at ~12,660 cal BP, consistent with synchronous recovery of overturning in both hemispheres and increased Southern Ocean ventilation. Hence, sustained North Atlantic cooling across GS-1 was not driven by a prolonged AMOC reduction but probably due to an equatorward migration of the Polar Front, reducing the advection of southwesterly air masses to high latitudes. Our findings suggest opposing hemispheric temperature trends were driven by atmospheric teleconnections, rather than AMOC changes.
    Description: This work was part funded by the Foundation for Research, Science and Technology (FRST)—now Ministry for Business, Innovation & Employment (MBIE)-PROP-20224-SFK-UOA), a Royal Society of New Zealand grant, the Australian Research Council (FL100100195 and DP0664898) and the Natural Environment Research Council (NE/H009922/1, NE/I007660/1, NER/A/S/2001/01037 and NE/H007865/1).
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    Full circumpolar migration ensures evolutionary unity in the Emperor penguin (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 7 (2016): 11842, doi:10.1038/ncomms11842.
    Description: Defining reliable demographic models is essential to understand the threats of ongoing environmental change. Yet, in the most remote and threatened areas, models are often based on the survey of a single population, assuming stationarity and independence in population responses. This is the case for the Emperor penguin Aptenodytes forsteri, a flagship Antarctic species that may be at high risk continent-wide before 2100. Here, using genome-wide data from the whole Antarctic continent, we reveal that this top-predator is organized as one single global population with a shared demography since the late Quaternary. We refute the view of the local population as a relevant demographic unit, and highlight that (i) robust extinction risk estimations are only possible by including dispersal rates and (ii) colony-scaled population size is rather indicative of local stochastic events, whereas the species’ response to global environmental change is likely to follow a shared evolutionary trajectory.
    Description: This study was undertaken within the framework of the Programme 137 of the Institut Polaire Français Paul-Emile Victor (IPEV), with additional support from the French National Research Agency (ANR) ‘PICASO’ grant (ANR-2010-BLAN-1728-01, PI: Y.L.M.), from Marie Curie Intra European Fellowships (FP7-PEOPLE-IEF-2008, European Commission; project no. 235962 to CLB and FP7-PEOPLE-IEF-2010, European Commission; project no. 252252 to E.T.), from the Centre Scientifique de Monaco through budget allocated to the Laboratoire International Associé 647 ‘BioSensib’ (CSM/CNRS-University of Strasbourg), from the Centre National de la Recherche Scientifique (Programme Zone Atelier de Recherches sur l’Environnement Antarctique et Subantarctique) and from the British Antarctic Survey Ecosystems Programme, NERC (P.N.T.). Logistic and field costs of research were supported by IPEV (C.L.B.), the British Antarctic Survey Ecosystems Programme, NERC (P.N.T.), AWI (D.P.Z.), US NSF grant number NSF 0229638 (P.J.P.).
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    Coral reef soundscapes may not be detectable far from the reef (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 6 (2016): 31862, doi:10.1038/srep31862.
    Description: Biological sounds produced on coral reefs may provide settlement cues to marine larvae. Sound fields are composed of pressure and particle motion, which is the back and forth movement of acoustic particles. Particle motion (i.e., not pressure) is the relevant acoustic stimulus for many, if not most, marine animals. However, there have been no field measurements of reef particle motion. To address this deficiency, both pressure and particle motion were recorded at a range of distances from one Hawaiian coral reef at dawn and mid-morning on three separate days. Sound pressure attenuated with distance from the reef at dawn. Similar trends were apparent for particle velocity but with considerable variability. In general, average sound levels were low and perhaps too faint to be used as an orientation cue except very close to the reef. However, individual transient sounds that exceeded the mean values, sometimes by up to an order of magnitude, might be detectable far from the reef, depending on the hearing abilities of the larva. If sound is not being used as a long-range cue, it might still be useful for habitat selection or other biological activities within a reef.
    Description: This work was funded by the Woods Hole Oceanographic Institution Ocean Ventures Fund, the PADI Foundation, the Woods Hole Oceanographic Institution Access To The Sea program, and the National Science Foundation grant OCE-1536782.
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    A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters (2012)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 6 (2012): 1901-1915, doi:10.1038/ismej.2012.31.
    Description: Antarctic surface oceans are well-studied during summer when irradiance levels are high, sea ice is melting and primary productivity is at a maximum. Coincident with this timing, the bacterioplankton respond with significant increases in secondary productivity. Little is known about bacterioplankton in winter when darkness and sea-ice cover inhibit photoautotrophic primary production. We report here an environmental genomic and small subunit ribosomal RNA (SSU rRNA) analysis of winter and summer Antarctic Peninsula coastal seawater bacterioplankton. Intense inter-seasonal differences were reflected through shifts in community composition and functional capacities encoded in winter and summer environmental genomes with significantly higher phylogenetic and functional diversity in winter. In general, inferred metabolisms of summer bacterioplankton were characterized by chemoheterotrophy, photoheterotrophy and aerobic anoxygenic photosynthesis while the winter community included the capacity for bacterial and archaeal chemolithoautotrophy. Chemolithoautotrophic pathways were dominant in winter and were similar to those recently reported in global ‘dark ocean’ mesopelagic waters. If chemolithoautotrophy is widespread in the Southern Ocean in winter, this process may be a previously unaccounted carbon sink and may help account for the unexplained anomalies in surface inorganic nitrogen content.
    Description: CSR was supported by an NSF Postdoctoral Fellowship in Biological Informatics (DBI-0532893). The research was supported by National Science Foundation awards: ANT 0632389 (to AEM and JJG), and ANT 0632278 and 0217282 (to HWD), all from the Antarctic Organisms and Ecosystems Program.
    Keywords: Antarctic bacterioplankton ; Metagenomics ; Chemolithoautotrophy
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    The NF2 tumor suppressor regulates microtubule-based vesicle trafficking via a novel Rac, MLK and p38SAPK pathway (2013)
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    Publication Date: 2022-05-26
    Description: © Macmillan Publishers, 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Oncogene 32 (2013): 1135–1143, doi:10.1038/onc.2012.135.
    Description: Neurofibromatosis type 2 patients develop schwannomas, meningiomas and ependymomas resulting from mutations in the tumor suppressor gene, NF2, encoding a membrane-cytoskeleton adapter protein called merlin. Merlin regulates contact inhibition of growth and controls the availability of growth factor receptors at the cell surface. We tested if microtubule-based vesicular trafficking might be a mechanism by which merlin acts. We found that schwannoma cells, containing merlin mutations and constitutive activation of the Rho/Rac family of GTPases, had decreased intracellular vesicular trafficking relative to normal human Schwann cells. In Nf2−/− mouse Schwann (SC4) cells, re-expression of merlin as well as inhibition of Rac or its effector kinases, MLK and p38SAPK, each increased the velocity of Rab6 positive exocytic vesicles. Conversely, an activated Rac mutant decreased Rab6 vesicle velocity. Vesicle motility assays in isolated squid axoplasm further demonstrated that both mutant merlin and active Rac specifically reduce anterograde microtubule-based transport of vesicles dependent upon the activity of p38SAPK kinase. Taken together, our data suggest loss of merlin results in the Rac-dependent decrease of anterograde trafficking of exocytic vesicles, representing a possible mechanism controlling the concentration of growth factor receptors at the cell surface.
    Description: This work was supported by NIH R01 CA118032 (to NR), and MBL research fellowships (to NR and GM), NIH R01 NS23868 (to STB).
    Keywords: Merlin ; NF2 ; Rac ; Trafficking ; Exocytosis
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    Counting whales in a challenging, changing environment (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 4170, doi:10.1038/srep04170.
    Description: Estimating abundance of Antarctic minke whales is central to the International Whaling Commission's conservation and management work and understanding impacts of climate change on polar marine ecosystems. Detecting abundance trends is problematic, in part because minke whales are frequently sighted within Antarctic sea ice where navigational safety concerns prevent ships from surveying. Using icebreaker-supported helicopters, we conducted aerial surveys across a gradient of ice conditions to estimate minke whale density in the Weddell Sea. The surveys revealed substantial numbers of whales inside the sea ice. The Antarctic summer sea ice is undergoing rapid regional change in annual extent, distribution, and length of ice-covered season. These trends, along with substantial interannual variability in ice conditions, affect the proportion of whales available to be counted by traditional shipboard surveys. The strong association between whales and the dynamic, changing sea ice requires reexamination of the power to detect trends in whale abundance or predict ecosystem responses to climate change.
    Description: This work received funding from the following institutions: Alfred Wegener Institute for Polar and Marine Research (AWI); Dutch Ministry of Agriculture, Nature and Food Quality (EL & I); German Federal Ministry of Food, Agriculture and Consumer Protection (BMELV); German Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU); the Institute for Marine Resources and Ecosystem Studies (Wageningen IMARES); Johann Heinrich von Thu¨nen Institute (Federal Research Institute for Rural Areas, Forestry and Fisheries); the Netherlands Polar Programme (NPP) of the Netherlands Organisation for Scientific Research (NOW); Research and Technology Centre Westcoast (FTZ) of the University Kiel. RW was funded by a Marie Curie International Incoming Fellowship within the 7th European Community Framework Programme (proposal Nu 253407 (call reference: FP7- PEOPLE-2009-IIF).
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    MIxS-BE : a MIxS extension defining a minimum information standard for sequence data from the built environment (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 8 (2014): 1-3, doi:10.1038/ismej.2013.176.
    Description: The need for metadata standards for microbe sampling in the built environment.
    Description: We would like to thank the Alfred P Sloan Foundation grant FP047325-01-PR for support for this project.
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    A reversal of fortunes : climate change ‘winners’ and ‘losers’ in Antarctic Peninsula penguins (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 5024, doi:10.1038/srep05024.
    Description: Climate change is a major threat to global biodiversity. Antarctic ecosystems are no exception. Investigating past species responses to climatic events can distinguish natural from anthropogenic impacts. Climate change produces ‘winners’, species that benefit from these events and ‘losers’, species that decline or become extinct. Using molecular techniques, we assess the demographic history and population structure of Pygoscelis penguins in the Scotia Arc related to climate warming after the Last Glacial Maximum (LGM). All three pygoscelid penguins responded positively to post-LGM warming by expanding from glacial refugia, with those breeding at higher latitudes expanding most. Northern (Pygoscelis papua papua) and Southern (Pygoscelis papua ellsworthii) gentoo sub-species likely diverged during the LGM. Comparing historical responses with the literature on current trends, we see Southern gentoo penguins are responding to current warming as they did during post-LGM warming, expanding their range southwards. Conversely, Adélie and chinstrap penguins are experiencing a ‘reversal of fortunes’ as they are now declining in the Antarctic Peninsula, the opposite of their response to post-LGM warming. This suggests current climate warming has decoupled historic population responses in the Antarctic Peninsula, favoring generalist gentoo penguins as climate change ‘winners’, while Adélie and chinstrap penguins have become climate change ‘losers’.
    Description: We thank the Zoological Society of London, Quark Expeditions, Exodus Travels ltd., Oceanites, the Holly Hill Charitable Trust, the Charities Advisory Trust and an U.S. National Science Foundation (NSF) Office of Polar Programs grant (ANT-0739575) for funding.
    Keywords: Climate-change ecology ; Molecular ecology ; Molecular evolution ; Population genetics
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    Horizontal eddy energy flux in the world oceans diagnosed from altimetry data (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 5316, doi:10.1038/srep05316.
    Description: During the propagation of coherent mesoscale eddies, they directly or indirectly induce many effects and interactions at different scales, implying eddies are actually serving as a kind of energy carrier or energy source for these eddy-related dynamic processes. To quantify this dynamically significant energy flow, the multi-year averaged horizontal eddy energy fluxes (EEFs) were estimated by using satellite altimetry data and a two-layer model based on hydrographic climatology. There is a strong net westward transport of eddy energy estimated at the mean value of ~13.3 GW north of 5°N and ~14.6 GW at the band 5°S ~ 44°S in the Southern Hemisphere. However, poleward of 44°S east-propagating eddies carry their energy eastward with an averaged net flux of ~3.2 GW. If confirmed, it would signify that geostrophic eddies not only contain the most of oceanic kinetic energy (KE), but also carry and spread a significant amount of energy with them.
    Description: This study is supported by Grants XDA11010202, 2011CB403505, 2013CB430303; Projects 41306016, U1033002, 40976021 of NNSFC and LTOZZ1304.
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    Oceanography : oxygen and climate dynamics (2014)
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    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Climate Change 4 (2014): 862-863, doi:10.1038/nclimate2386.
    Description: Low oxygen levels in tropical oceans shape marine ecosystems and biogeochemistry with climate change expected to expand these regions. Now, a study indicates that regional dynamics control tropical oxygen trends, bucking projected global reductions in ocean oxygen.
    Description: 2015-03-25
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    Satellite remote sensing data can be used to model marine microbial metabolite turnover (2015)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 166–179, doi:10.1038/ismej.2014.107.
    Description: Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km2) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes’ predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value 〈10−6) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ~3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology.
    Description: This work was supported by the US Department of Energy under Contract DE-AC02-06CH11357 and by the Howard Hughes Medical Institute.
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    Bacterial diversity and community composition from seasurface to subseafloor (2016)
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    Publication Date: 2022-05-26
    Description: © The International Society for Microbial Ecology, 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 10 (2016): 979–989, doi:10.1038/ismej.2015.175.
    Description: We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (greater than or equal to1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.
    Description: This study was funded by the Biological Oceanography Program of the US National Science Foundation (grant OCE-0752336) and by the NSF-funded Center for Dark Energy Biosphere Investigations (grant NSF-OCE-0939564).
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    Prevalence of influenza A virus in live-captured North Atlantic gray seals : a possible wild reservoir (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Emerging Microbes and Infections 5 (2016): e81, doi:10.1038/emi.2016.77.
    Description: Influenza A virus (IAV) has been associated with multiple unusual mortality events (UMEs) in North Atlantic pinnipeds, frequently attributed to spillover of virus from wild-bird reservoirs. To determine if endemic infection persists outside of UMEs, we undertook a multiyear investigation of IAV in healthy, live-captured Northwest Atlantic gray seals (Halichoerus grypus). From 2013 to 2015, we sampled 345 pups and 57 adults from Cape Cod, MA, USA and Nova Scotia, Canada consistently detecting IAV infection across all groups. There was an overall viral prevalence of 9.0% (95% confidence interval (CI): 6.4%–12.5%) in weaned pups and 5.3% (CI: 1.2%–14.6%) in adults, with seroprevalences of 19.3% (CI: 15.0%–24.5%) and 50% (CI: 33.7%–66.4%), respectively. Positive sera showed a broad reactivity to diverse influenza subtypes. IAV status did not correlate with measures of animal health nor impact animal movement or foraging. This study demonstrated that Northwest Atlantic gray seals are both permissive to and tolerant of diverse IAV, possibly representing an endemically infected wild reservoir population.
    Description: This work was supported in part by National Institute of Allergy and Infectious Diseases (NIAID), the Centers of Excellence for Influenza Research and Surveillance (CEIRS) HHSN272201400008C, MIT Sea Grant Project 2013-DOH-45-LEV, National Science and Engineering Research Council of Canada (NSERC), NMFS #17670-01, NMFS #10080-95 and FWS #53514-13003.
    Keywords: Gray seal ; Halichoerus grypus ; Influenza ; Pinniped ; Reservoir ; Telemetry
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    The size-distribution of Earth’s lakes (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 6 (2016): 29633, doi:10.1038/srep29633.
    Description: Globally, there are millions of small lakes, but a small number of large lakes. Most key ecosystem patterns and processes scale with lake size, thus this asymmetry between area and abundance is a fundamental constraint on broad-scale patterns in lake ecology. Nonetheless, descriptions of lake size-distributions are scarce and empirical distributions are rarely evaluated relative to theoretical predictions. Here we develop expectations for Earth’s lake area-distribution based on percolation theory and evaluate these expectations with data from a global lake census. Lake surface areas ≥8.5 km2 are power-law distributed with a tail exponent (τ = 1.97) and fractal dimension (d = 1.38), similar to theoretical expectations (τ = 2.05; d = 4/3). Lakes 〈8.5 km2 are not power-law distributed. An independently developed regional lake census exhibits a similar transition and consistency with theoretical predictions. Small lakes deviate from the power-law distribution because smaller lakes are more susceptible to dynamical change and topographic behavior at sub-kilometer scales is not self-similar. Our results provide a robust characterization and theoretical explanation for the lake size-abundance relationship, and form a fundamental basis for understanding and predicting patterns in lake ecology at broad scales.
    Description: This paper is based on research supported by the National Science Foundation (OCE-1315201), the Swedish Research Council Formas, and the Carl Tryggers Foundation for Scientific Research.
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    A single genus in the gut microbiome reflects host preference and specificity (2015)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 90–100, doi:10.1038/ismej.2014.97.
    Description: Delineating differences in gut microbiomes of human and animal hosts contributes towards understanding human health and enables new strategies for detecting reservoirs of waterborne human pathogens. We focused upon Blautia, a single microbial genus that is important for nutrient assimilation as preliminary work suggested host-related patterns within members of this genus. In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping. Our analysis revealed 13 host-specific oligotypes that occurred exclusively in fecal samples of humans (three oligotypes), swine (six oligotypes), cows (one oligotype), deer (one oligotype), or chickens (two oligotypes). We identified an additional 171 oligotypes that exhibited differential abundance patterns among all the host species. Blautia oligotypes in the human population obtained from sewage and fecal samples displayed remarkable continuity. Oligotypes from only 10 Brazilian human fecal samples collected from individuals in a rural village encompassed 97% of all Blautia oligotypes found in a Brazilian sewage sample from a city of three million people. Further, 75% of the oligotypes in Brazilian human fecal samples matched those in US sewage samples, implying that a universal set of Blautia strains may be shared among culturally and geographically distinct human populations. Such strains can serve as universal markers to assess human fecal contamination in environmental samples. Our results indicate that host-specificity and host-preference patterns of organisms within this genus are driven by host physiology more than dietary habits.
    Description: This study was funded by the NIH grant R01AI091829-01A1 to SLM.
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    Mitigation of coral reef warming across the central Pacific by the Equatorial Undercurrent : a past and future divide (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 6 (2016): 21213, doi:10.1038/srep21213.
    Description: Global climate models (GCMs) predict enhanced warming and nutrient decline across the central tropical Pacific as trade winds weaken with global warming. Concurrent changes in circulation, however, have potential to mitigate these effects for equatorial islands. The implications for densely populated island nations, whose livelihoods depend on ecosystem services, are significant. A unique suite of in situ measurements coupled with state-of-the-art GCM simulations enables us to quantify the mitigation potential of the projected circulation change for three coral reef ecosystems under two future scenarios. Estimated historical trends indicate that over 100% of the large-scale warming to date has been offset locally by changes in circulation, while future simulations predict a warming mitigation effect of only 5–10% depending on the island. The pace and extent to which GCM projections overwhelm historical trends will play a key role in defining the fate of marine ecosystems and island communities across the tropical Pacific.
    Description: Support provided by NSF OCE-1031971 (ALC and KBK). KBK also acknowledges support from NSF OCE-1233282, the DoD Strategic Environmental Research and Development Program (SERDP), the WHOI Ocean and Climate Change Institute Moltz Fellowship, and the Alfred P. Sloan Foundation. Funding for the Pacific Reef Assessment and Monitoring Program, was provided by NOAA’s Coral Reef Conservation Program.
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    A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 6 (2016): 22541, doi:10.1038/srep22541.
    Description: The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25°C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere. An Author Correction to this article was published on 16 April 2020
    Description: This work was supported by NSF OCE1062006 to JAH, NSF OCE1061934 to PRG, and NSF OCE1061827 to BTG. The Center for Dark Energy Biosphere Investigations (C-DEBI) (OCE-0939564), a National Science Foundation-funded Science and Technology Centers of Excellence also supported the participation of CGW, THL, JPC, JAH, BT, and CHH, as well as JLM and UJ through C-DEBI Postdoctoral Fellowships.
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    CO2 and fire influence tropical ecosystem stability in response to climate change (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 6 (2016): 29587, doi:10.1038/srep29587.
    Description: Interactions between climate, fire and CO2 are believed to play a crucial role in controlling the distributions of tropical woodlands and savannas, but our understanding of these processes is limited by the paucity of data from undisturbed tropical ecosystems. Here we use a 28,000-year integrated record of vegetation, climate and fire from West Africa to examine the role of these interactions on tropical ecosystem stability. We find that increased aridity between 28–15 kyr B.P. led to the widespread expansion of tropical grasslands, but that frequent fires and low CO2 played a crucial role in stabilizing these ecosystems, even as humidity changed. This resulted in an unstable ecosystem state, which transitioned abruptly from grassland to woodlands as gradual changes in CO2 and fire shifted the balance in favor of woody plants. Since then, high atmospheric CO2 has stabilized tropical forests by promoting woody plant growth, despite increased aridity. Our results indicate that the interactions between climate, CO2 and fire can make tropical ecosystems more resilient to change, but that these systems are dynamically unstable and potentially susceptible to abrupt shifts between woodland and grassland dominated states in the future.
    Description: This work was supported by NSF grants EAR0601998, EAR0602355, AGS0402010, ATM0401908, ATM0214525, ATM0096232 and AGS1243125 and a Chevron Centennial Fellowship at the University of Texas at Austin awarded to T.M.S.
    Keywords: Climate-change ecology ; Palaeoclimate
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    Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 6 (2016): 21871, doi:10.1038/srep21871.
    Description: Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the microbial metabolism is considered difficult to control. Microbial community succession and the related gene expression were analysed during ripening of a traditional Italian cheese, identifying parameters that could be modified to accelerate ripening. Afterwards, we modulated ripening conditions and observed consistent changes in microbial community structure and function. We provide concrete evidence of the essential contribution of non-starter lactic acid bacteria in ripening-related activities. An increase in the ripening temperature promoted the expression of genes related to proteolysis, lipolysis and amino acid/lipid catabolism and significantly increases the cheese maturation rate. Moreover, temperature-promoted microbial metabolisms were consistent with the metabolomic profiles of proteins and volatile organic compounds in the cheese. The results clearly indicate how processing-driven microbiome responses can be modulated in order to optimize production efficiency and product quality.
    Description: F.D.F. was supported by a grant from Regione Campania within the program “POR CAMPANIA FSE 2007/2013” - project CARINA (Safety sustainability and competitiveness of the agro-food production in Campania) – CUP B25B09000080007.
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    Toward a consistent modeling framework to assess multi-sectoral climate impacts (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 9 (2018): 660, doi:10.1038/s41467-018-02984-9.
    Description: Efforts to estimate the physical and economic impacts of future climate change face substantial challenges. To enrich the currently popular approaches to impact analysis—which involve evaluation of a damage function or multi-model comparisons based on a limited number of standardized scenarios—we propose integrating a geospatially resolved physical representation of impacts into a coupled human-Earth system modeling framework. Large internationally coordinated exercises cannot easily respond to new policy targets and the implementation of standard scenarios across models, institutions and research communities can yield inconsistent estimates. Here, we argue for a shift toward the use of a self-consistent integrated modeling framework to assess climate impacts, and discuss ways the integrated assessment modeling community can move in this direction. We then demonstrate the capabilities of such a modeling framework by conducting a multi-sectoral assessment of climate impacts under a range of consistent and integrated economic and climate scenarios that are responsive to new policies and business expectations.
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    Multi-modal survey of Adélie penguin mega-colonies reveals the Danger Islands as a seabird hotspot (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 8 (2018): 3926, doi:10.1038/s41598-018-22313-w.
    Description: Despite concerted international effort to track and interpret shifts in the abundance and distribution of Adélie penguins, large populations continue to be identified. Here we report on a major hotspot of Adélie penguin abundance identified in the Danger Islands off the northern tip of the Antarctic Peninsula (AP). We present the first complete census of Pygoscelis spp. penguins in the Danger Islands, estimated from a multi-modal survey consisting of direct ground counts and computer-automated counts of unmanned aerial vehicle (UAV) imagery. Our survey reveals that the Danger Islands host 751,527 pairs of Adélie penguins, more than the rest of AP region combined, and include the third and fourth largest Adélie penguin colonies in the world. Our results validate the use of Landsat medium-resolution satellite imagery for the detection of new or unknown penguin colonies and highlight the utility of combining satellite imagery with ground and UAV surveys. The Danger Islands appear to have avoided recent declines documented on the Western AP and, because they are large and likely to remain an important hotspot for avian abundance under projected climate change, deserve special consideration in the negotiation and design of Marine Protected Areas in the region.
    Description: We gratefully acknowledge the financial support of the Dalio Foundation, Inc. through the Dalio Explore Fund, which provided all the financing for the Danger Island Expedition. We would like to thank additional support for analysis from the National Science Foundation (NSF PLR&GSS 1255058 - H.J.L. and P.M.; NSF PLR 1443585 – M.J.P.) and the National Aeronautical and Space Administration (NNX14AC32G; H.J.L. and M.S.). Geospatial support for the analysis of high resolution satellite imagery provided by the Polar Geospatial Center under NSF PLR awards 1043681 & 1559691.
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    ALS-linked FUS exerts a gain of toxic function involving aberrant p38 MAPK activation (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 115, doi:10.1038/s41598-017-00091-1.
    Description: Mutations in Fused in Sarcoma/Translocated in Liposarcoma (FUS) cause familial forms of amyotrophic lateral sclerosis (ALS), a neurodegenerative disease characterized by progressive axonal degeneration mainly affecting motor neurons. Evidence from transgenic mouse models suggests mutant forms of FUS exert an unknown gain-of-toxic function in motor neurons, but mechanisms underlying this effect remain unknown. Towards this end, we studied the effect of wild type FUS (FUS WT) and three ALS-linked variants (G230C, R521G and R495X) on fast axonal transport (FAT), a cellular process critical for appropriate maintenance of axonal connectivity. All ALS-FUS variants impaired anterograde and retrograde FAT in squid axoplasm, whereas FUS WT had no effect. Misfolding of mutant FUS is implicated in this process, as the molecular chaperone Hsp110 mitigated these toxic effects. Interestingly, mutant FUS-induced impairment of FAT in squid axoplasm and of axonal outgrowth in mammalian primary motor neurons involved aberrant activation of the p38 MAPK pathway, as also reported for ALS-linked forms of Cu, Zn superoxide dismutase (SOD1). Accordingly, increased levels of active p38 MAPK were detected in post-mortem human ALS-FUS brain tissues. These data provide evidence for a novel gain-of-toxic function for ALS-linked FUS involving p38 MAPK activation.
    Description: We are grateful for funding from NIH/NINDS (R01 NS078145, R01 NS090352, and R21 NS091860 to D.A.B., R01 NS066942A and R21 NS096642 to G.M., R01NS023868 and R01NS041170 to S.T.B.), the ALS Therapy Alliance/CVS Pharmacy (to D.A.B. and G.M.) and the ALS Association (to C.F. and J.M.).
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    Meridional heat transport variability induced by mesoscale processes in the subpolar North Atlantic (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 9 (2018): 1124, doi:10.1038/s41467-018-03134-x.
    Description: The ocean’s role in global climate change largely depends on its heat transport. Therefore, understanding the oceanic meridional heat transport (MHT) variability is a fundamental issue. Prevailing observational and modeling evidence suggests that MHT variability is primarily determined by the large-scale ocean circulation. Here, using new in situ observations in the eastern subpolar North Atlantic Ocean and an eddy-resolving numerical model, we show that energetic mesoscale eddies with horizontal scales of about 10–100 km profoundly modulate MHT variability on time scales from intra-seasonal to interannual. Our results reveal that the velocity changes due to mesoscale processes produce substantial variability for the MHT regionally (within sub-basins) and the subpolar North Atlantic as a whole. The findings have important implications for understanding the mechanisms for poleward heat transport variability in the subpolar North Atlantic Ocean, a key region for heat and carbon sequestration, ice–ocean interaction, and biological productivity.
    Description: J.Z. was financially supported by the Postdoctoral Scholar Program at WHOI, with funding provided by the Ocean and Climate Change Institute. This work was also supported by the US National Science Foundation (OCE-1258823 and OCE-1634886), as well as by China’s national key research and development projects (2016YFA0601803), the National Natural Science Foundation of China (41521091 and U1606402), the Qingdao National Laboratory for Marine Science and Technology (2015ASKJ01), and the Fundamental Research Funds for the Central Universities (201424001 and 201362048).
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    Seismic hazards implications of uplifted Pleistocene coral terraces in the Gulf of Aqaba (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 38, doi:10.1038/s41598-017-00074-2.
    Description: The Gulf of Aqaba transform plate boundary is a source of destructive teleseismic earthquakes. Seismicity is concentrated in the central sub-basin and decreases to both the north and south. Although principally a strike-slip plate boundary, the faulted margins of the Gulf display largely dip-slip extensional movement and accompanying footwall uplift. We have constrained rates of this uplift by measurements of elevated Pleistocene coral terraces. In particular the terrace that formed during the last interglacial (~125 ka) is found discontinuously along the length of the Gulf at elevations of 3 to 26 m. Global sea level was ~7 m higher than today at 125 ka indicating net maximum tectonic uplift of ~19 m with an average rate of ~0.015 cm/yr. Uplift has been greatest adjacent to the central sub-basin and like the seismicity decreases to the north and south. We suggest that the present pattern of a seismically active central region linked to more aseismic areas in the north and south has therefore persisted for at least the past 125 kyr. Consequently the potential for future destructive earthquakes in the central Gulf is greater than in the sub-basins to the north and south.
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    Mutations underlying Episodic Ataxia type-1 antagonize Kv1.1 RNA editing (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 41095, doi:10.1038/srep41095.
    Description: Adenosine-to-inosine RNA editing in transcripts encoding the voltage-gated potassium channel Kv1.1 converts an isoleucine to valine codon for amino acid 400, speeding channel recovery from inactivation. Numerous Kv1.1 mutations have been associated with the human disorder Episodic Ataxia Type-1 (EA1), characterized by stress-induced ataxia, myokymia, and increased prevalence of seizures. Three EA1 mutations, V404I, I407M, and V408A, are located within the RNA duplex structure required for RNA editing. Each mutation decreased RNA editing both in vitro and using an in vivo mouse model bearing the V408A allele. Editing of transcripts encoding mutant channels affects numerous biophysical properties including channel opening, closing, and inactivation. Thus EA1 symptoms could be influenced not only by the direct effects of the mutations on channel properties, but also by their influence on RNA editing. These studies provide the first evidence that mutations associated with human genetic disorders can affect cis-regulatory elements to alter RNA editing.
    Description: This work was supported by the Vanderbilt Molecular Endocrinology Training Program (T32DK007563; E.A.F.K.), a Ruth L. Kirschstein National Research Service Award (F31NS087911; E.A.F.K), a Vanderbilt Dissertation Enhancement Grant (E.A.F.K.), and the Vanderbilt Joel G. Hardman Chair in Pharmacology (R.B.E). Additional support for J.J.C.R. included NINDS (R0111223855, R01NS64259) and the Cystic Fibrosis Foundation Therapeutics (Rosent14XXO). Infrastructural support for J.J.C.R. was provided by NIGMS (P20GM103642), NIMH (G12-MD007600), and NSF (DBI 0115825, DBI 1337284).
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    Topographic enhancement of vertical turbulent mixing in the Southern Ocean (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 14197, doi:10.1038/ncomms14197.
    Description: It is an open question whether turbulent mixing across density surfaces is sufficiently large to play a dominant role in closing the deep branch of the ocean meridional overturning circulation. The diapycnal and isopycnal mixing experiment in the Southern Ocean found the turbulent diffusivity inferred from the vertical spreading of a tracer to be an order of magnitude larger than that inferred from the microstructure profiles at the mean tracer depth of 1,500 m in the Drake Passage. Using a high-resolution ocean model, it is shown that the fast vertical spreading of tracer occurs when it comes in contact with mixing hotspots over rough topography. The sparsity of such hotspots is made up for by enhanced tracer residence time in their vicinity due to diffusion toward weak bottom flows. The increased tracer residence time may explain the large vertical fluxes of heat and salt required to close the abyssal circulation.
    Description: Financial support for A.M. and R.F. under the US National Science Foundation grant OCE-1233832 is gratefully acknowledged. A.M. also acknowledges support from an NSERC PDF award.
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    Organic carbon budget for the eastern boundary of the North Atlantic subtropical gyre : major role of DOC in mesopelagic respiration (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 10129, doi:10.1038/s41598-017-10974-y.
    Description: Transports of suspended particulate (POCsusp) and dissolved (DOC) organic carbon are inferred from a box-model covering the eastern boundary of the North Atlantic subtropical gyre. Corresponding net respiration rates (R) are obtained from a net organic carbon budget that is based on the transport estimates, and includes both vertical and lateral fluxes. The overall R in the mesopelagic layer (100–1500 m) is 1.6 ± 0.4 mmol C m−2 d−1. DOC accounts for up to 53% of R as a result of drawdown of organic carbon within Eastern North Atlantic Central Water (ENACW) that is entrained into sinking Mediterranean Overflow Water (MOW) that leads to formation of Mediterranean water (MW) at intermediate depths (~900 m). DOC represents 90% of the respired non-sinking organic carbon. When converted into oxygen units, the computed net respiration rate represents less than half the oxygen utilization rates (OUR) reported for the mesopelagic waters of the subtropical North Atlantic. Mesoscale processes in the area, not quantified with our approach, could account in part for the OUR differences observed between our carbon budget and other published studies from the North Atlantic, although seasonal or interannual variability could also be responsible for the difference in the estimates.
    Description: This research was supported by projects ORCA (CTM2005-04701-CO2-01), Malaspina (CSD2008-00077), HOTMIX (CTM2011-30010-C02) and FLUXES (CTM2015-69392-C3), financed by the Spanish “Plan Nacional de I + D”. YSF was supported by a Spanish fellowship from the Agencia Canaria de Investigación, Innovación y Sociedad de la Información (ACIISI). EM has been partially supported by the Copernicus Marine Environment Monitoring Service (CMEMS) MedSUB project, and a post-doctoral grant from the Conselleria d’Educació, Cultura i Universitats del Govern de les Illes Balears (Mallorca, Spain) and the European Social Fund.
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    Restoring tides to reduce methane emissions in impounded wetlands : a new and potent Blue Carbon climate change intervention (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 11914, doi::10.1038/s41598-017-12138-4.
    Description: Coastal wetlands are sites of rapid carbon (C) sequestration and contain large soil C stocks. Thus, there is increasing interest in those ecosystems as sites for anthropogenic greenhouse gas emission offset projects (sometimes referred to as “Blue Carbon”), through preservation of existing C stocks or creation of new wetlands to increase future sequestration. Here we show that in the globallywidespread occurrence of diked, impounded, drained and tidally-restricted salt marshes, substantial methane (CH4) and CO2 emission reductions can be achieved through restoration of disconnected saline tidal flows. Modeled climatic forcing indicates that tidal restoration to reduce emissions has a much greater impact per unit area than wetland creation or conservation to enhance sequestration. Given that GHG emissions in tidally-restricted, degraded wetlands are caused by human activity, they are anthropogenic emissions, and reducing them will have an effect on climate that is equivalent to reduced emission of an equal quantity of fossil fuel GHG. Thus, as a landuse-based climate change intervention, reducing CH4 emissions is an entirely distinct concept from biological C sequestration projects to enhance C storage in forest or wetland biomass or soil, and will not suffer from the non-permanence risk that stored C will be returned to the atmosphere.
    Description: Research supported by the USGS Coastal & Marine Geology Program, USGS Land Carbon Program, and NOAA Science Collaborative grant #NA09NOS4190153.
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    Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1452, doi:10.1038/s41467-017-01250-8.
    Description: Light-sheet fluorescence microscopy (LSFM) enables high-speed, high-resolution, and gentle imaging of live specimens over extended periods. Here we describe a technique that improves the spatiotemporal resolution and collection efficiency of LSFM without modifying the underlying microscope. By imaging samples on reflective coverslips, we enable simultaneous collection of four complementary views in 250 ms, doubling speed and improving information content relative to symmetric dual-view LSFM. We also report a modified deconvolution algorithm that removes associated epifluorescence contamination and fuses all views for resolution recovery. Furthermore, we enhance spatial resolution (to 〈300 nm in all three dimensions) by applying our method to single-view LSFM, permitting simultaneous acquisition of two high-resolution views otherwise difficult to obtain due to steric constraints at high numerical aperture. We demonstrate the broad applicability of our method in a variety of samples, studying mitochondrial, membrane, Golgi, and microtubule dynamics in cells and calcium activity in nematode embryos.
    Description: This work was supported by the Intramural Research Program of the National Institute of Biomedical Imaging and Bioengineering at the National Institutes of Health. P.L. and H.S. acknowledge summer support from the Marine Biological Laboratory at Woods Hole, through the Whitman- and Fellows- program. P.L. acknowledges support from NIH National Institute of Biomedical Imaging and Bioengineering (NIBIB) of the National Institutes of Health (NIH) under grant number R01EB017293. C.S. acknowledges funding from the National Institute of General Medical Sciences of NIH under Award Number R25GM109439 (Project Title: University of Chicago Initiative for Maximizing Student Development [IMSD]) and NIBIB under grant number T32 EB002103. Partial funding for the computation in this work was provided by NIH grant numbers S10 RRO21039 and P30 CA14599. A.U. and I.R.-S. were supported by the NSF grant number 1607645.
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    Rapid global ocean-atmosphere response to Southern Ocean freshening during the last glacial (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 520, doi:10.1038/s41467-017-00577-6.
    Description: Contrasting Greenland and Antarctic temperatures during the last glacial period (115,000 to 11,650 years ago) are thought to have been driven by imbalances in the rates of formation of North Atlantic and Antarctic Deep Water (the ‘bipolar seesaw’). Here we exploit a bidecadally resolved 14C data set obtained from New Zealand kauri (Agathis australis) to undertake high-precision alignment of key climate data sets spanning iceberg-rafted debris event Heinrich 3 and Greenland Interstadial (GI) 5.1 in the North Atlantic (~30,400 to 28,400 years ago). We observe no divergence between the kauri and Atlantic marine sediment 14C data sets, implying limited changes in deep water formation. However, a Southern Ocean (Atlantic-sector) iceberg rafted debris event appears to have occurred synchronously with GI-5.1 warming and decreased precipitation over the western equatorial Pacific and Atlantic. An ensemble of transient meltwater simulations shows that Antarctic-sourced salinity anomalies can generate climate changes that are propagated globally via an atmospheric Rossby wave train.
    Description: This work was funded by the Australian Research Council (FL100100195, DP170104665 and SR140300001) and the Natural Environment Research Council (NE/H009922/1 and NE/H007865/1).
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    Bisphenol A in eggs causes development-specific liver molecular reprogramming in two generations of rainbow trout (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 14131, doi:10.1038/s41598-017-13301-7.
    Description: Bisphenol A (BPA) is widely used in the manufacture of plastics and epoxy resins and is prevalent in the aquatic environment. BPA disrupts endocrine pathways in fish, but the long-term developmental implications are unknown. We demonstrate that BPA deposition in the eggs of rainbow trout (Oncorhynchus mykiss), an ecologically and economically important species of fish, reprograms liver metabolism in the offspring and alters the developmental growth trajectory in two generations. Specifically, BPA reduces growth during early development, followed by a catch-up growth post-juveniles. More importantly, we observed a developmental shift in the liver transcriptome, including an increased propensity for protein breakdown during early life stages to lipid and cholesterol synthesis post- juveniles. The liver molecular responses corresponded with the transient growth phenotypes observed in the F1 generation, and this was also evident in the F2 generation. Altogether, maternal and/or ancestral embryonic exposure to BPA affects liver metabolism leading to development-distinct effects on growth, underscoring the need for novel risk assessment strategies for this chemical in the aquatic environment. This is particularly applicable to migratory species, such as salmon, where distinct temporal changes in growth and physiology during development are critical for their spawning success.
    Description: This study was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and Strategic Project Grants to MMV. Drs. Neel Aluru and Oana Birceanu received a NSERC post-doctoral fellowship and Canada Graduate Scholarship.
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    Pelagic barite precipitation at micromolar ambient sulfate (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1342, doi:10.1038/s41467-017-01229-5.
    Description: Geochemical analyses of sedimentary barites (barium sulfates) in the geological record have yielded fundamental insights into the chemistry of the Archean environment and evolutionary origin of microbial metabolisms. However, the question of how barites were able to precipitate from a contemporary ocean that contained only trace amounts of sulfate remains controversial. Here we report dissolved and particulate multi-element and barium-isotopic data from Lake Superior that evidence pelagic barite precipitation at micromolar ambient sulfate. These pelagic barites likely precipitate within particle-associated microenvironments supplied with additional barium and sulfate ions derived from heterotrophic remineralization of organic matter. If active during the Archean, pelagic precipitation and subsequent sedimentation may account for the genesis of enigmatic barite deposits. Indeed, barium-isotopic analyses of barites from the Paleoarchean Dresser Formation are consistent with a pelagic mechanism of precipitation, which altogether offers a new paradigm for interpreting the temporal occurrence of barites in the geological record.
    Description: This research was made possible with support from the National Science Foundation Division of Ocean Sciences (OCE-PRF 1421196, OCE-1430015, and OCE-1443577), The Andrew W. Mellon Foundation Endowed Fund for Innovative Research, and the Agouron Institute Geobiology Postdoctoral Fellowship Program.
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    Highly conserved molecular pathways, including Wnt signaling, promote functional recovery from spinal cord injury in lampreys (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 8 (2018): 742, doi:10.1038/s41598-017-18757-1.
    Description: In mammals, spinal cord injury (SCI) leads to dramatic losses in neurons and synaptic connections, and consequently function. Unlike mammals, lampreys are vertebrates that undergo spontaneous regeneration and achieve functional recovery after SCI. Therefore our goal was to determine the complete transcriptional responses that occur after SCI in lampreys and to identify deeply conserved pathways that promote regeneration. We performed RNA-Seq on lamprey spinal cord and brain throughout the course of functional recovery. We describe complex transcriptional responses in the injured spinal cord, and somewhat surprisingly, also in the brain. Transcriptional responses to SCI in lampreys included transcription factor networks that promote peripheral nerve regeneration in mammals such as Atf3 and Jun. Furthermore, a number of highly conserved axon guidance, extracellular matrix, and proliferation genes were also differentially expressed after SCI in lampreys. Strikingly, ~3% of differentially expressed transcripts belonged to the Wnt pathways. These included members of the Wnt and Frizzled gene families, and genes involved in downstream signaling. Pharmacological inhibition of Wnt signaling inhibited functional recovery, confirming a critical role for this pathway. These data indicate that molecular signals present in mammals are also involved in regeneration in lampreys, supporting translational relevance of the model.
    Description: We gratefully acknowledge support from the National Institutes of Health (R03NS078519 to OB; R01GM104123 to JJS; R01NS078165 to JRM), The Feinstein Institute for Medical Research and The Marine Biological Laboratory, including the Charles Evans Foundation Research Award, the Albert and Ellen Grass Foundation Faculty Research Award, and The Eugene and Millicent Bell Fellowship Fund in Tissue Engineering.
    Keywords: Computational biology and bioinformatics ; Gene expression ; Spinal cord injury
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    High resolution time series reveals cohesive but short-lived communities in coastal plankton (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 9 (2018): 266, doi:10.1038/s41467-017-02571-4.
    Description: Because microbial plankton in the ocean comprise diverse bacteria, algae, and protists that are subject to environmental forcing on multiple spatial and temporal scales, a fundamental open question is to what extent these organisms form ecologically cohesive communities. Here we show that although all taxa undergo large, near daily fluctuations in abundance, microbial plankton are organized into clearly defined communities whose turnover is rapid and sharp. We analyze a time series of 93 consecutive days of coastal plankton using a technique that allows inference of communities as modular units of interacting taxa by determining positive and negative correlations at different temporal frequencies. This approach shows both coordinated population expansions that demarcate community boundaries and high frequency of positive and negative associations among populations within communities. Our analysis thus highlights that the environmental variability of the coastal ocean is mirrored in sharp transitions of defined but ephemeral communities of organisms.
    Description: This work was supported by grants from the U.S. National Science Foundation (OCE-1441943) to M.F.P. and the U.S. Department of Energy (DE-SC0008743) to M.F.P. and E.J.A. A.M.M.-P. was partially supported by the Ramon Areces foundation through a postdoctoral fellowship. D.J.M. was supported by the U.S. National Science Foundation (OCE-1314642) and National Institute of Environmental Health Sciences (1P01ES021923-01) through the Woods Hole Center for Oceans and Human Health.
    Keywords: Marine biology ; Microbial ecology
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    Tectonically-triggered sediment and carbon export to the Hadal zone (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 9 (2018): 121, doi:10.1038/s41467-017-02504-1.
    Description: Sediments in deep ocean trenches may contain crucial information on past earthquake history and constitute important sites of carbon burial. Here we present 14C data on bulk organic carbon (OC) and its thermal decomposition fractions produced by ramped pyrolysis/oxidation for a core retrieved from the 〉7.5 km-deep Japan Trench. High-resolution 14C measurements, coupled with distinctive thermogram characteristics of OC, reveal hemipelagic sedimentation interrupted by episodic deposition of pre-aged OC in the trench. Low δ13C values and diverse 14C ages of thermal fractions imply that the latter material originates from the adjacent margin, and the co-occurrence of pre-aged OC with intervals corresponding to known earthquake events implies tectonically triggered, gravity-flow-driven supply. We show that 14C ages of thermal fractions can yield valuable chronological constraints on sedimentary sequences. Our findings shed new light on links between tectonically driven sedimentological processes and marine carbon cycling, with implications for carbon dynamics in hadal environments.
    Description: This study is supported by Doc.Mobility Fellowship (P1EZP2_159064) (R.B.) from the Swiss National Science Foundation (SNSF). This work is also supported by SNF “CAPS-LOCK” project 200021_140850 (T.I.E.), by SNSF grant (133481) (M.S.), and Austrian Science Foundation (P 29678-N28) (M.S.).
    Keywords: Carbon cycle ; Sedimentology
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    Methane- and dissolved organic carbon-fueled microbial loop supports a tropical subterranean estuary ecosystem (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1835, doi:10.1038/s41467-017-01776-x.
    Description: Subterranean estuaries extend inland into density-stratified coastal carbonate aquifers containing a surprising diversity of endemic animals (mostly crustaceans) within a highly oligotrophic habitat. How complex ecosystems (termed anchialine) thrive in this globally distributed, cryptic environment is poorly understood. Here, we demonstrate that a microbial loop shuttles methane and dissolved organic carbon (DOC) to higher trophic levels of the anchialine food web in the Yucatan Peninsula (Mexico). Methane and DOC production and consumption within the coastal groundwater correspond with a microbial community capable of methanotrophy, heterotrophy, and chemoautotrophy, based on characterization by 16S rRNA gene amplicon sequencing and respiratory quinone composition. Fatty acid and bulk stable carbon isotope values of cave-adapted shrimp suggest that carbon from methanotrophic bacteria comprises 21% of their diet, on average. These findings reveal a heretofore unrecognized subterranean methane sink and contribute to our understanding of the carbon cycle and ecosystem function of karst subterranean estuaries.
    Description: Funding for T.M.I. and D.B. was provided by TAMU-CONACYT (project no: 2015-049). D.B. was supported by Research-in-Residence program (NSF award #1137336, Inter-University Training in Continental-scale Ecology), Cave Research Foundation Graduate Student Grant, Cave Conservancy Foundation PhD Fellowship, Ralph W. Stone Fellowship (National Speleological Society), Grants-in-Aid of Graduate Student Research Award (Texas Sea Grant College Program), and Boost Fellowship (Texas A&M University at Galveston). Additional financial support was provided by NSF DEB-1257424 (M.B.L. and M.C.L.), the Postdoctoral Program at Woods Hole Oceanographic Institution and U.S. Geological Survey (K.W.B.).
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    Microvillar and ciliary defects in zebrafish lacking an actin-binding bioactive peptide amidating enzyme (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 8 (2018): 4547, doi:10.1038/s41598-018-22732-9.
    Description: The assembly of membranous extensions such as microvilli and cilia in polarized cells is a tightly regulated, yet poorly understood, process. Peptidylglycine α-amidating monooxygenase (PAM), a membrane enzyme essential for the synthesis of amidated bioactive peptides, was recently identified in motile and non-motile (primary) cilia and has an essential role in ciliogenesis in Chlamydomonas, Schmidtea and mouse. In mammalian cells, changes in PAM levels alter secretion and organization of the actin cytoskeleton. Here we show that lack of Pam in zebrafish recapitulates the lethal edematous phenotype observed in Pam−/− mice and reveals additional defects. The pam−/− zebrafish embryos display an initial striking loss of microvilli and subsequently impaired ciliogenesis in the pronephros. In multiciliated mouse tracheal epithelial cells, vesicular PAM staining colocalizes with apical actin, below the microvilli. In PAM-deficient Chlamydomonas, the actin cytoskeleton is dramatically reorganized, and expression of an actin paralogue is upregulated. Biochemical assays reveal that the cytosolic PAM C-terminal domain interacts directly with filamentous actin but does not alter the rate of actin polymerization or disassembly. Our results point to a critical role for PAM in organizing the actin cytoskeleton during development, which could in turn impact both microvillus formation and ciliogenesis.
    Description: This study was supported by grants DK032949 (to BAE and REM), DK044464 (to JDG) and GM051293 (to SMK) from the National Institutes of Health.
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    Mass coral mortality under local amplification of 2°C ocean warming (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 44586, doi:10.1038/srep44586.
    Description: A 2°C increase in global temperature above pre-industrial levels is considered a reasonable target for avoiding the most devastating impacts of anthropogenic climate change. In June 2015, sea surface temperature (SST) of the South China Sea (SCS) increased by 2 °C in response to the developing Pacific El Niño. On its own, this moderate, short-lived warming was unlikely to cause widespread damage to coral reefs in the region, and the coral reef “Bleaching Alert” alarm was not raised. However, on Dongsha Atoll, in the northern SCS, unusually weak winds created low-flow conditions that amplified the 2°C basin-scale anomaly. Water temperatures on the reef flat, normally indistinguishable from open-ocean SST, exceeded 6°C above normal summertime levels. Mass coral bleaching quickly ensued, killing 40% of the resident coral community in an event unprecedented in at least the past 40 years. Our findings highlight the risks of 2°C ocean warming to coral reef ecosystems when global and local processes align to drive intense heating, with devastating consequences.
    Description: This research was funded by the National Science Foundation (OCE-1031971 and OCE-1605365 to A.L.C), the Sustainability Science Research Program of the Academia Sinica (G.T.F.W. and A.L.C), a Woods Hole Oceanographic Institution Coastal Ocean Institute award to T.M.D., and a National Science Foundation Graduate Research Fellowship awarded to T.M.D.
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    A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 12 (2018): 1-16, doi:10.1038/ismej.2017.187.
    Description: The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.
    Description: This work was supported by NSF OCE1062006 to JAH and NSF OCE1061827 to BTG. The Gordon and Betty Moore Foundation sponsored most of the observatory components at North Pond through grant GBMF1609. The Center for Dark Energy Biosphere Investigations (C-DEBI) (OCE-0939564), a National Science Foundation-funded Science and Technology Centers of Excellence also supported the participation of CGW, JAH and BJT.
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    Author Correction : Spiraling pathways of global deep waters to the surface of the Southern Ocean (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 9 (2018): 209, doi:10.1038/s41467-017-02105-y.
    Description: Correction to: Nature Communications 8:172 https://doi.org/10.1038/s41467-017-00197-0; Article published online: 2 August 2017
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    Multi-scale magnetic mapping of serpentinite carbonation (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1870, doi:10.1038/s41467-017-01610-4.
    Description: Peridotite carbonation represents a critical step within the long-term carbon cycle by sequestering volatile CO2 in solid carbonate. This has been proposed as one potential pathway to mitigate the effects of greenhouse gas release. Most of our current understanding of reaction mechanisms is based on hand specimen and laboratory-scale analyses. Linking laboratory-scale observations to field scale processes remains challenging. Here we present the first geophysical characterization of serpentinite carbonation across scales ranging from km to sub-mm by combining aeromagnetic observations, outcrop- and thin section-scale magnetic mapping. At all scales, magnetic anomalies coherently change across reaction fronts separating assemblages indicative of incipient, intermittent, and final reaction progress. The abundance of magnetic minerals correlates with reaction progress, causing amplitude and wavelength variations in associated magnetic anomalies. This correlation represents a foundation for characterizing the extent and degree of in situ ultramafic rock carbonation in space and time.
    Description: This project was supported by the Woods Hole Oceanographic Institution Independent Study Award (Tivey and Tominaga) and by NASA Astrobiology Institute NNA15BB02A (Tominaga). M.T. and A.B. are grateful to B. Jamtveit and H. Austrheim (University of Oslo) for their support during the 2011 and 2013 field campaigns. B.W. and E.A.L. thank the National Science Foundation grant DMS-1521765 and Thomas F. Peterson, Jr for generous support.
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    Implications of improved representations of plant respiration in a changing climate (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 1602, doi:10.1038/s41467-017-01774-z.
    Description: Land-atmosphere exchanges influence atmospheric CO2. Emphasis has been on describing photosynthetic CO2 uptake, but less on respiration losses. New global datasets describe upper canopy dark respiration (Rd) and temperature dependencies. This allows characterisation of baseline Rd, instantaneous temperature responses and longer-term thermal acclimation effects. Here we show the global implications of these parameterisations with a global gridded land model. This model aggregates Rd to whole-plant respiration Rp, driven with meteorological forcings spanning uncertainty across climate change models. For pre-industrial estimates, new baseline Rd increases Rp and especially in the tropics. Compared to new baseline, revised instantaneous response decreases Rp for mid-latitudes, while acclimation lowers this for the tropics with increases elsewhere. Under global warming, new Rd estimates amplify modelled respiration increases, although partially lowered by acclimation. Future measurements will refine how Rd aggregates to whole-plant respiration. Our analysis suggests Rp could be around 30% higher than existing estimates.
    Description: C.H. acknowledges the NERC CEH National Capability fund. The support of the Australian Research Council to O.K.A. and P.M. (DP130101252, CE140100008, FT0991448, FT110100457) is acknowledged, as are awards DE-FG02-07ER64456 from the US Department of Energy, Office of Science, Office of Biological and Environmental Research and DEB-1234162 from the U.S. National Science Foundation (NSF) Long-Term Ecological Research Program (to P.B.R.); and National Science Foundation International Polar Year Grant (to K.L.G.). L.M.M. acknowledges the support of the Natural Environment Research Council (NERC) South American Biomass Burning Analysis (SAMBBA) project grant code NE/J010057/1.
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    Publisher Correction : Pelagic barite precipitation at micromolar ambient sulfate (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 9 (2018): 305, doi:10.1038/s41467-017-02701-y.
    Description: Correction to: Nature Communications https://doi.org/10.1038/s41467-017-01229-5, Article published online 07 November 2017
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    Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration (2017)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 2047, doi:10.1038/s41467-017-01848-y.
    Description: Integrin αβ heterodimer cell surface receptors mediate adhesive interactions that provide traction for cell migration. Here, we test whether the integrin, when engaged to an extracellular ligand and the cytoskeleton, adopts a specific orientation dictated by the direction of actin flow on the surface of migrating cells. We insert GFP into the rigid, ligand-binding head of the integrin, model with Rosetta the orientation of GFP and its transition dipole relative to the integrin head, and measure orientation with fluorescence polarization microscopy. Cytoskeleton and ligand-bound integrins orient in the same direction as retrograde actin flow with their cytoskeleton-binding β-subunits tilted by applied force. The measurements demonstrate that intracellular forces can orient cell surface integrins and support a molecular model of integrin activation by cytoskeletal force. Our results place atomic, Å-scale structures of cell surface receptors in the context of functional and cellular, μm-scale measurements.
    Description: Supported by the Lillie Research award from Marine Biological Laboratory and the University of Chicago (C.M.W., T.A.S., S.M., T.T.), NIH 5R13GM085967 grant to the Physiology Course at Marine Biological Laboratory, HHMI Summer Institute at Marine Biological Laboratory (S.M.), NIH CA31798 (T.A.S., P.N., T.I.M.), NIH GM100160 (T.T., S.M.), NIH GM092802 (D.B., N.K.), NIH GM114274 (R.O., S.M.) National Center for Biological Sciences-Tata Institute of Fundamental Research (S.M., J.M.K.), J.C. Bose Fellowship and HFSP Grant RGP0027/2012 (S.M.), NHLBI Division of Intramural Research (C.M.W., V.S.), Swedish Research Council VR 524-2011-891 Fellowship (P.N.), Swedish Society for Medical Research SSMF Fellowship (P.N.), Crafoord Foundation (P.N.).
    Keywords: Actin ; Integrin signalling ; Integrins ; Molecular imaging ; Polarization microscopy
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    Recurrent patterns of microdiversity in a temperate coastal marine environment (2018)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 12 (2018): 237–252, doi:10.1038/ismej.2017.165.
    Description: Temperate coastal marine environments are replete with complex biotic and abiotic interactions that are amplified during spring and summer phytoplankton blooms. During these events, heterotrophic bacterioplankton respond to successional releases of dissolved organic matter as algal cells are lysed. Annual seasonal shifts in the community composition of free-living bacterioplankton follow broadly predictable patterns, but whether similar communities respond each year to bloom disturbance events remains unknown owing to a lack of data sets, employing high-frequency sampling over multiple years. We capture the fine-scale microdiversity of these events with weekly sampling using a high-resolution method to discriminate 16S ribosomal RNA gene amplicons that are 〉99% identical. Furthermore, we used 2 complete years of data to facilitate identification of recurrent sub-networks of co-varying microbes. We demonstrate that despite inter-annual variation in phytoplankton blooms and despite the dynamism of a coastal–oceanic transition zone, patterns of microdiversity are recurrent during both bloom and non-bloom conditions. Sub-networks of co-occurring microbes identified reveal that correlation structures between community members appear quite stable in a seasonally driven response to oligotrophic and eutrophic conditions.
    Description: PLB is supported by the European Research Council Advanced Investigator grant ABYSS 294757 to Antje Boetius. AF-G is supported by the European Union’s Horizon 2020 research and innovation program (Blue Growth: Unlocking the potential of Seas and Oceans) under grant agreement no. (634486) (project acronym INMARE). This study was funded by the Max Planck Society. Further support by the Department of Energy Joint Genome Institute (CSP COGITO) and DFG (FOR2406) is acknowledged by HT (TE 813/2-1) and RA (Am 73/9-1).
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    Extreme diving behaviour in devil rays links surface waters and the deep ocean (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 5 (2014): 4274, doi:10.1038/ncomms5274.
    Description: Ecological connections between surface waters and the deep ocean remain poorly studied despite the high biomass of fishes and squids residing at depths beyond the euphotic zone. These animals likely support pelagic food webs containing a suite of predators that include commercially important fishes and marine mammals. Here we deploy pop-up satellite archival transmitting tags on 15 Chilean devil rays (Mobula tarapacana) in the central North Atlantic Ocean, which provide movement patterns of individuals for up to 9 months. Devil rays were considered surface dwellers but our data reveal individuals descending at speeds up to 6.0 m s−1 to depths of almost 2,000 m and water temperatures 〈4 °C. The shape of the dive profiles suggests that the rays are foraging at these depths in deep scattering layers. Our results provide evidence of an important link between predators in the surface ocean and forage species occupying pelagic habitats below the euphotic zone in ocean ecosystems.
    Description: This research was partially supported by the Portuguese Foundation for Science and Technology/Ministry of Education and Science (FCT/MCTES-MEC) through individual support to P.A. (Cieˆncia 2008/POPH/QREN) and J.F. (SFRH/BPD/66532/2009) and the LARSyS Strategic Project (PEst/OE/EEI/LA00009/2011). This study was support by the US National Science Foundation (OCE 0825148 to S.R.T. and G.B.S.), The Harrison Foundation, Rodney and Elizabeth Berens, the King Abdullah University of Science and Technology (baseline research funds to M.L.B.) and the Woods Hole Oceanographic Institution.
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    Antarctic-wide array of high-resolution ice core records reveals pervasive lead pollution began in 1889 and persists today (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 5848, doi:10.1038/srep05848.
    Description: Interior Antarctica is among the most remote places on Earth and was thought to be beyond the reach of human impacts when Amundsen and Scott raced to the South Pole in 1911. Here we show detailed measurements from an extensive array of 16 ice cores quantifying substantial toxic heavy metal lead pollution at South Pole and throughout Antarctica by 1889 – beating polar explorers by more than 22 years. Unlike the Arctic where lead pollution peaked in the 1970s, lead pollution in Antarctica was as high in the early 20th century as at any time since industrialization. The similar timing and magnitude of changes in lead deposition across Antarctica, as well as the characteristic isotopic signature of Broken Hill lead found throughout the continent, suggest that this single emission source in southern Australia was responsible for the introduction of lead pollution into Antarctica at the end of the 19th century and remains a significant source today. An estimated 660 t of industrial lead have been deposited over Antarctica during the past 130 years as a result of mid-latitude industrial emissions, with regional-to-global scale circulation likely modulating aerosol concentrations. Despite abatement efforts, significant lead pollution in Antarctica persists into the 21st century.
    Description: This work primarily was supported by the U.S. National Science Foundation Division of Polar Programs (research grants 9903744, 0538427, 0538416, 0968391, 1142166, 0632031; instrument grants 0216552, 0421412).
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    How unique was Hurricane Sandy? Sedimentary reconstructions of extreme flooding from New York Harbor (2014)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 4 (2014): 7366, doi:10.1038/srep07366.
    Description: The magnitude of flooding in New York City by Hurricane Sandy is commonly believed to be extremely rare, with estimated return periods near or greater than 1000 years. However, the brevity of tide gauge records result in significant uncertainties when estimating the uniqueness of such an event. Here we compare resultant deposition by Hurricane Sandy to earlier storm-induced flood layers in order to extend records of flooding to the city beyond the instrumental dataset. Inversely modeled storm conditions from grain size trends show that a more compact yet more intense hurricane in 1821 CE probably resulted in a similar storm tide and a significantly larger storm surge. Our results indicate the occurrence of additional flood events like Hurricane Sandy in recent centuries, and highlight the inadequacies of the instrumental record in estimating current flood risk by such extreme events.
    Description: Funding for this work was provided by the Hudson River Foundation Expedited Grant #004/12E, the Hudson River Foundation Graduate Fellowship 02–13, the National Science Foundation (RAPID grant #1313859 and instrument and facility support via grant IF-0949313), and the Dalio Explore Fund.
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    Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 6 (2016): 27357, doi:10.1038/srep27357.
    Description: Organisms that have evolved alternative modes of reproduction, complementary to the sexual mode, are found across metazoans. The chordate Botryllus schlosseri is an emerging model for asexual development studies. Botryllus can rebuild its entire body from a portion of adult epithelia in a continuous and stereotyped process called blastogenesis. Anatomy and ontogenies of blastogenesis are well described, however molecular signatures triggering this developmental process are entirely unknown. We isolated tissues at the site of blastogenesis onset and from the same epithelia where this process is never triggered. We linearly amplified an ultra-low amount of mRNA (〈10ng) and generated three transcriptome datasets. To provide a conservative landscape of transcripts differentially expressed between blastogenic vs. non-blastogenic epithelia we compared three different mapping and analysis strategies with a de novo assembled transcriptome and partially assembled genome as references, additionally a self-mapping strategy on the dataset. A subset of differentially expressed genes were analyzed and validated by in situ hybridization. The comparison of different analyses allowed us to isolate stringent sets of target genes, including transcripts with potential involvement in the onset of a non-embryonic developmental pathway. The results provide a good entry point to approach regenerative event in a basal chordate.
    Description: This work was supported by AFM Telethon grant (#16611), IRG Marie Curie grant (#276974), ANR (ANR-14-CE02-0019-01) and IDEX Super (INDIBIO). L.R. was supported by an UPMC-EMREGENCE grant and by a FRM grant (#FDT20140931163). A.C. was supported by a FRM grant (ING 20140129231).
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    Mechanisms of increased Trichodesmium fitness under iron and phosphorus co-limitation in the present and future ocean (2016)
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 7 (2016): 12081, doi:10.1038/ncomms12081.
    Description: Nitrogen fixation by cyanobacteria supplies critical bioavailable nitrogen to marine ecosystems worldwide; however, field and lab data have demonstrated it to be limited by iron, phosphorus and/or CO2. To address unknown future interactions among these factors, we grew the nitrogen-fixing cyanobacterium Trichodesmium for 1 year under Fe/P co-limitation following 7 years of both low and high CO2 selection. Fe/P co-limited cell lines demonstrated a complex cellular response including increased growth rates, broad proteome restructuring and cell size reductions relative to steady-state growth limited by either Fe or P alone. Fe/P co-limitation increased abundance of a protein containing a conserved domain previously implicated in cell size regulation, suggesting a similar role in Trichodesmium. Increased CO2 further induced nutrient-limited proteome shifts in widespread core metabolisms. Our results thus suggest that N2-fixing microbes may be significantly impacted by interactions between elevated CO2 and nutrient limitation, with broad implications for global biogeochemical cycles in the future ocean.
    Description: Grant support was provided by U.S. National Science Foundation OCE 1260490 to D.A.H., E.A.W. and F.-X.F., and OCE OA 1220484 and G.B. Moore Foundation 3782 and 3934 to M.A.S.
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    Ancestry of motor innervation to pectoral fin and forelimb (2010)
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    Publication Date: 2022-05-25
    Description: © Macmillan Publishers Limited, 2010. This article is distributed under the terms of the Creative Commons Attribution-NonCommercial-No Derivative Works 3.0 Unported License. The definitive version was published in Nature Communications 1 (2010): 49, doi:10.1038/ncomms1045.
    Description: Motor innervation to the tetrapod forelimb and fish pectoral fin is assumed to share a conserved spinal cord origin, despite major structural and functional innovations of the appendage during the vertebrate water-to-land transition. In this paper, we present anatomical and embryological evidence showing that pectoral motoneurons also originate in the hindbrain among ray-finned fish. New and previous data for lobe-finned fish, a group that includes tetrapods, and more basal cartilaginous fish showed pectoral innervation that was consistent with a hindbrain-spinal origin of motoneurons. Together, these findings support a hindbrain–spinal phenotype as the ancestral vertebrate condition that originated as a postural adaptation for pectoral control of head orientation. A phylogenetic analysis indicated that Hox gene modules were shared in fish and tetrapod pectoral systems. We propose that evolutionary shifts in Hox gene expression along the body axis provided a transcriptional mechanism allowing eventual decoupling of pectoral motoneurons from the hindbrain much like their target appendage gained independence from the head.
    Description: Th is work was supported by the National Institutes of Health and National Science Foundation.
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    The dynamic relationships between the three events that release individual Na+ ions from the Na+/K+-ATPase (2012)
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    Publication Date: 2022-05-25
    Description: © Macmillan Publishers Limited, 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 3 (2012): 669, doi:10.1038/ncomms1673.
    Description: Na+/K+ pumps move net charge through the cell membrane by mediating unequal exchange of intracellular Na+ and extracellular K+. Most charge moves during transitions that release Na+ to the cell exterior. When pumps are constrained to bind and release only Na+, a membrane voltage-step redistributes pumps among conformations with zero, one, two or three bound Na+, thereby transiently generating current. By applying rapid voltage steps to squid giant axons, we previously identified three components in such transient currents, with distinct relaxation speeds: fast (which nearly parallels the voltage-jump time course), medium speed (τm=0.2–0.5 ms) and slow (τs=1–10 ms). Here we show that these three components are tightly correlated, both in their magnitudes and in the time courses of their changes. The correlations reveal the dynamics of the conformational rearrangements that release three Na+ to the exterior (or sequester them into their binding sites) one at a time, in an obligatorily sequential manner.
    Description: This research was directly supported by the Intramural Research Program of the National Institutes of Health (NIH), NINDS, grants NIH HL36783 to D.C.G., and NIH U54GM087519 and R01GM030376 to F.B.
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    Early anthropogenic transformation of the Danube-Black Sea system (2012)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 2 (2012): 582, doi:10.1038/srep00582.
    Description: Over the last century humans have altered the export of fluvial materials leading to significant changes in morphology, chemistry, and biology of the coastal ocean. Here we present sedimentary, paleoenvironmental and paleogenetic evidence to show that the Black Sea, a nearly enclosed marine basin, was affected by land use long before the changes of the Industrial Era. Although watershed hydroclimate was spatially and temporally variable over the last ~3000 years, surface salinity dropped systematically in the Black Sea. Sediment loads delivered by Danube River, the main tributary of the Black Sea, significantly increased as land use intensified in the last two millennia, which led to a rapid expansion of its delta. Lastly, proliferation of diatoms and dinoflagellates over the last five to six centuries, when intensive deforestation occurred in Eastern Europe, points to an anthropogenic pulse of river-borne nutrients that radically transformed the food web structure in the Black Sea.
    Description: This study was supported by grants OISE 0637108, EAR 0952146, OCE 0602423 and OCE 0825020 from the National Science Foundation and grants from the Woods Hole Oceanographic Institution.
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    First biological measurements of deep-sea corals from the Red Sea (2013)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 3 (2013): 2802, doi:10.1038/srep02802.
    Description: It is usually assumed that metabolic constraints restrict deep-sea corals to cold-water habitats, with ‘deep-sea’ and ‘cold-water’ corals often used as synonymous. Here we report on the first measurements of biological characters of deep-sea corals from the central Red Sea, where they occur at temperatures exceeding 20°C in highly oligotrophic and oxygen-limited waters. Low respiration rates, low calcification rates, and minimized tissue cover indicate that a reduced metabolism is one of the key adaptations to prevailing environmental conditions. We investigated four sites and encountered six species of which at least two appear to be undescribed. One species is previously reported from the Red Sea but occurs in deep cold waters outside the Red Sea raising interesting questions about presumed environmental constraints for other deep-sea corals. Our findings suggest that the present understanding of deep-sea coral persistence and resilience needs to be revisited.
    Keywords: Ecosystem ecology ; Biodiversity ; Genetics ; Metabolism
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    Acidification reduced growth rate but not swimming speed of larval sea urchins (2015)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 5 (2015): 9764, doi:10.1038/srep09764.
    Description: Swimming behaviors of planktonic larvae impact dispersal and population dynamics of many benthic marine invertebrates. This key ecological function is modulated by larval development dynamics, biomechanics of the resulting morphology, and behavioral choices. Studies on ocean acidification effects on larval stages have yet to address this important interaction between development and swimming under environmentally-relevant flow conditions. Our video motion analysis revealed that pH covering present and future natural variability (pH 8.0, 7.6 and 7.2) did not affect age-specific swimming of larval green urchin Strongylocentrotus droebachiensis in still water nor in shear, despite acidified individuals being significantly smaller in size (reduced growth rate). This maintenance of speed and stability in shear was accompanied by an overall change in size-corrected shape, implying changes in swimming biomechanics. Our observations highlight strong evolutionary pressure to maintain swimming in a varying environment and the plasticity in larval responses to environmental change.
    Description: K.C. was supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution (WHOI), with funding provided by the Coastal Ocean Institute, the Croucher Foundation, and the Royal Swedish Academy of Sciences. S.D. was financially supported by the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg (http://www.cemeb.science.gu.se/) and a Linnaeus grant from the Swedish Research Councils VR and Formas. Additional funding was provided from the European Seventh Framework Programme under grant agreement 265847.
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    Irreversibly increased nitrogen fixation in Trichodesmium experimentally adapted to elevated carbon dioxide (2015)
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    Publication Date: 2022-05-25
    Description: This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 6 (2015): 8155, doi:10.1038/ncomms9155.
    Description: Nitrogen fixation rates of the globally distributed, biogeochemically important marine cyanobacterium Trichodesmium increase under high carbon dioxide (CO2) levels in short-term studies due to physiological plasticity. However, its long-term adaptive responses to ongoing anthropogenic CO2 increases are unknown. Here we show that experimental evolution under extended selection at projected future elevated CO2 levels results in irreversible, large increases in nitrogen fixation and growth rates, even after being moved back to lower present day CO2 levels for hundreds of generations. This represents an unprecedented microbial evolutionary response, as reproductive fitness increases acquired in the selection environment are maintained after returning to the ancestral environment. Constitutive rate increases are accompanied by irreversible shifts in diel nitrogen fixation patterns, and increased activity of a potentially regulatory DNA methyltransferase enzyme. High CO2-selected cell lines also exhibit increased phosphorus-limited growth rates, suggesting a potential advantage for this keystone organism in a more nutrient-limited, acidified future ocean.
    Description: Grant support was provided by U.S. National Science Foundation OCE 1260490 and OCE 1143760 to D.A.H., E.A.W., and F.-X.F, and OCE 1260233, OCE OA 1220484, and G.B. Moore Foundation 3782 and 3934 to M.A.S.© The Author(s), [year].
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    Jurassic zircons from the Southwest Indian Ridge (2016)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 6 (2016): 26260, doi:10.1038/srep26260.
    Description: The existence of ancient rocks in present mid-ocean ridges have long been observed but received less attention. Here we report the discovery of zircons with both reasonably young ages of about 5 Ma and abnormally old ages of approximate 180 Ma from two evolved gabbroic rocks that were dredged from the Southwest Indian Ridge (SWIR) in the Gallieni fracture zone. U–Pb and Lu–Hf isotope analyses of zircons were made using ion probe and conventional laser abrasion directly in petrographic thin sections. Young zircons and their host oxide gabbro have positive Hf isotope compositions (εHf = +15.7–+12.4), suggesting a highly depleted mantle beneath the SWIR. The spread εHf values (from−2.3 to−4.5) of abnormally old zircons, together with the unradiogenic Nd-Hf isotope of the host quartz diorite, appears to suggest an ancient juvenile magmatism along the rifting margin of the southern Gondwana prior to the opening of the Indian Ocean. A convincing explanation for the origin of the unusually old zircons is yet to surface, however, an update of the theory of plate tectonics would be expected with continuing discovery of ancient rocks in the mid-oceanic ridges and abyssal ocean basins.
    Description: This work was supported by the National Natural Science Foundation of China (41573046) to H.C. and the Chinese National Key Basic Research Program (2012CB417300) to H.Z.
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    Paleochannel and beach-bar palimpsest topography as initial substrate for coralligenous buildups offshore Venice, Italy (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 1321, doi:10.1038/s41598-017-01483-z.
    Description: We provide a model for the genesis of Holocene coralligenous buildups occurring in the northwestern Adriatic Sea offshore Venice at 17–24 m depth. High-resolution geophysical surveys and underwater SCUBA diving reconnaissance revealed meandering shaped morphologies underneath bio-concretionned rocky buildups. These morphologies are inferred to have been inherited from Pleistocene fluvial systems reactivated as tidal channels during the post- Last Glacial Maximum transgression, when the study area was a lagoon protected by a sandy barrier. The lithification of the sandy fossil channel-levee systems is estimated to have occurred at ca. 7 cal. ka BP, likely due to the interaction between marine and less saline fluids related to onshore freshwater discharge at sea through a sealed water-table. The carbonate-cemented sandy layers served as nucleus for subsequent coralligenous buildups growth.
    Description: Funded by the Italian Ministry of Education, University and Research within the National Research Program 2011–2013.
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    El Niño increases the risk of lower Mississippi River flooding (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 1772, doi:10.1038/s41598-017-01919-6.
    Description: Mississippi River floods rank among the costliest climate-related disasters in the world. Improving flood predictability, preparedness, and response at seasonal to decadal time-scales requires an understanding of the climatic controls that govern flood occurrence. Linking flood occurrence to persistent modes of climate variability like the El Niño-Southern Oscillation (ENSO) has proven challenging, due in part to the limited number of high-magnitude floods available for study in the instrumental record. To augment the relatively short instrumental record, we use output from the Community Earth System Model (CESM) Last Millennium Ensemble (LME) to investigate the dynamical controls on discharge extremes of the lower Mississippi River. We show that through its regional influence on surface water storage, the warm phase of ENSO preconditions the lower Mississippi River to be vulnerable to flooding. In the 6–12 months preceding a flood, El Niño generates a positive precipitation anomaly over the lower Mississippi basin that gradually builds up soil moisture and reduces the basin’s infiltration capacity, thereby elevating the risk of a major flood during subsequent rainstorms. Our study demonstrates how natural climate variability mediates the formation of extreme floods on one of the world’s principal commercial waterways, adding significant predictive ability to near- and long-term forecasts of flood risk.
    Description: This work was funded through the Postdoctoral Scholar Program of the Woods Hole Oceanographic Institution and the Voss Environmental Postdoctoral Fellows Program at Brown University.
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    Evidence for fungal and chemodenitrification based N2O flux from nitrogen impacted coastal sediments (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 15595, doi:10.1038/ncomms15595.
    Description: Although increasing atmospheric nitrous oxide (N2O) has been linked to nitrogen loading, predicting emissions remains difficult, in part due to challenges in disentangling diverse N2O production pathways. As coastal ecosystems are especially impacted by elevated nitrogen, we investigated controls on N2O production mechanisms in intertidal sediments using novel isotopic approaches and microsensors in flow-through incubations. Here we show that during incubations with elevated nitrate, increased N2O fluxes are not mediated by direct bacterial activity, but instead are largely catalysed by fungal denitrification and/or abiotic reactions (e.g., chemodenitrification). Results of these incubations shed new light on nitrogen cycling complexity and possible factors underlying variability of N2O fluxes, driven in part by fungal respiration and/or iron redox cycling. As both processes exhibit N2O yields typically far greater than direct bacterial production, these results emphasize their possibly substantial, yet widely overlooked, role in N2O fluxes, especially in redox-dynamic sediments of coastal ecosystems.
    Description: D.D.B. acknowledges support from the Max Planck Institute for Marine Microbiology. This work was supported by the National Science Foundation grants to W.Z. and S.D.W. (OCE-1260373) and to S.D.W. (EAR-1252161).
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    Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in The ISME Journal 11 (2017): 186–200, doi:10.1038/ismej.2016.95.
    Description: Reef-building corals are well regarded not only for their obligate association with endosymbiotic algae, but also with prokaryotic symbionts, the specificity of which remains elusive. To identify the central microbial symbionts of corals, their specificity across species and conservation over geographic regions, we sequenced partial SSU ribosomal RNA genes of Bacteria and Archaea from the common corals Stylophora pistillata and Pocillopora verrucosa across 28 reefs within seven major geographical regions. We demonstrate that both corals harbor Endozoicomonas bacteria as their prevalent symbiont. Importantly, catalyzed reporter deposition–fluorescence in situ hybridization (CARD–FISH) with Endozoicomonas-specific probes confirmed their residence as large aggregations deep within coral tissues. Using fine-scale genotyping techniques and single-cell genomics, we demonstrate that P. verrucosa harbors the same Endozoicomonas, whereas S. pistillata associates with geographically distinct genotypes. This specificity may be shaped by the different reproductive strategies of the hosts, potentially uncovering a pattern of symbiont selection that is linked to life history. Spawning corals such as P. verrucosa acquire prokaryotes from the environment. In contrast, brooding corals such as S. pistillata release symbiont-packed planula larvae, which may explain a strong regional signature in their microbiome. Our work contributes to the factors underlying microbiome specificity and adds detail to coral holobiont functioning.
    Description: This research was supported by a KAUST-WHOI Post-doctoral Partnership Award to MN and a KAUST-WHOI Special Academic Partnership Funding Reserve Award to CRV and AA. Research in this study was further supported by baseline research funds to CRV by KAUST and NSF award OCE-1233612 to AA. RR was supported by the ct-PIRE Project, Robert Lemelson Fellowship, Graduate Research Award (UCLA), Women Divers Hall of Fame—Sister Fund Conservation Award and a Betty and E. P. Franklin Grant in Tropical Biology and Conservation.
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    Assessing the dynamics of organic aerosols over the North Atlantic Ocean (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 45476, doi:10.1038/srep45476.
    Description: The influence of aerosols on climate is highly dependent on the particle size distribution, concentration, and composition. In particular, the latter influences their ability to act as cloud condensation nuclei, whereby they impact cloud coverage and precipitation. Here, we simultaneously measured the concentration of aerosols from sea spray over the North Atlantic on board the exhaust-free solar-powered vessel “PlanetSolar”, and the sea surface physico-chemical parameters. We identified organic-bearing particles based on individual particle fluorescence spectra. Organic-bearing aerosols display specific spatio-temporal distributions as compared to total aerosols. We propose an empirical parameterization of the organic-bearing particle concentration, with a dependence on water salinity and sea-surface temperature only. We also show that a very rich mixture of organic aerosols is emitted from the sea surface. Such data will certainly contribute to providing further insight into the influence of aerosols on cloud formation, and be used as input for the improved modeling of aerosols and their role in global climate processes.
    Description: We gratefully acknowledge the financial support by the H. Dudley Wright and the Henri Moser Foundations, the Rector’s Office and the Institute for Environmental Sciences at the University of Geneva, as well as a generous anonymous donator.
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    Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 772, doi:10.1038/s41467-017-00759-2.
    Description: In sunlit waters, photochemical alteration of dissolved organic carbon (DOC) impacts the microbial respiration of DOC to CO2. This coupled photochemical and biological degradation of DOC is especially critical for carbon budgets in the Arctic, where thawing permafrost soils increase opportunities for DOC oxidation to CO2 in surface waters, thereby reinforcing global warming. Here we show how and why sunlight exposure impacts microbial respiration of DOC draining permafrost soils. Sunlight significantly increases or decreases microbial respiration of DOC depending on whether photo-alteration produces or removes molecules that native microbial communities used prior to light exposure. Using high-resolution chemical and microbial approaches, we show that rates of DOC processing by microbes are likely governed by a combination of the abundance and lability of DOC exported from land to water and produced by photochemical processes, and the capacity and timescale that microbial communities have to adapt to metabolize photo-altered DOC.
    Description: Funding for this work was provided by NSF grants OPP 1023270, 1022876, CAREER 1351745, DEB 1147378, 1347042, 0639790, 1147336, 1026843, PLR 1504006, DOE-JGI-CSP 1782, and the Camille and Henry Dreyfus Foundation Postdoctoral Program in Environmental Chemistry.
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    Defining a critical period for inhibitory circuits within the somatosensory cortex (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 7271, doi:10.1038/s41598-017-07400-8.
    Description: Although experience-dependent changes in brain inhibitory circuits are thought to play a key role during the “critical period” of brain development, the nature and timing of these changes are poorly understood. We examined the role of sensory experience in sculpting an inhibitory circuit in the primary somatosensory cortex (S1) of mice by using optogenetics to map the connections between parvalbumin (PV) expressing interneurons and layer 2/3 pyramidal cells. Unilateral whisker deprivation decreased the strength and spatial range of inhibitory input provided to pyramidal neurons by PV interneurons in layers 2/3, 4 and 5. By varying the time when sensory input was removed, we determined that the critical period closes around postnatal day 14. This yields the first precise time course of critical period plasticity for an inhibitory circuit.
    Description: This work was supported by a fellowship from NUS to SQL, A*STAR intramural funding for the Integrative Neuroscience Programme, Singapore Institute for Clinical Sciences for JCGS, and a Competitive Research Programme (CRP) grant from the National Research Foundation of Singapore (NRF Grant Number 2008 NRF-CRP 002-082).
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    Climate oscillations reflected within the microbiome of Arabian Sea sediments (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 6040, doi:10.1038/s41598-017-05590-9.
    Description: Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.
    Description: his work was primarily supported by NSF MGG Grant #1357017 to MJLC, VG, and LG, and the KAUST-WHOI Special Academic Partnership Program OCRF-SP-WHOI-2013 (grants 7000000463 to XI and 7000000464 to MJLC). Additional financial support was provided via a C-DEBI grant #OCE-0939564 to WDO.
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    Pan-Antarctic analysis aggregating spatial estimates of Adélie penguin abundance reveals robust dynamics despite stochastic noise (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 8 (2017): 832, doi:10.1038/s41467-017-00890-0.
    Description: Colonially-breeding seabirds have long served as indicator species for the health of the oceans on which they depend. Abundance and breeding data are repeatedly collected at fixed study sites in the hopes that changes in abundance and productivity may be useful for adaptive management of marine resources, but their suitability for this purpose is often unknown. To address this, we fit a Bayesian population dynamics model that includes process and observation error to all known Adélie penguin abundance data (1982–2015) in the Antarctic, covering 〉95% of their population globally. We find that process error exceeds observation error in this system, and that continent-wide “year effects” strongly influence population growth rates. Our findings have important implications for the use of Adélie penguins in Southern Ocean feedback management, and suggest that aggregating abundance across space provides the fastest reliable signal of true population change for species whose dynamics are driven by stochastic processes.
    Description: H.J.L., C.C.-C., G.H., C.Y., and K.T.S. gratefully acknowledge funding provided by US National Aeronautics and Space Administration Award No. NNX14AC32G and U.S. National Science Foundation Office of Polar Programs Award No. NSF/OPP-1255058. S.J., L.L., M.M.H., Y.L., and R.J. gratefully acknowledge funding provided by US National Aeronautics and Space Administration Award No. NNX14AH74G. H.J.L., C.Y., S.J., Y.L., and R.J. gratefully acknowledge funding provided by U.S. National Science Foundation Office of Polar Programs Award No. NSF/PLR-1341548. S.J. gratefully acknowledges support from the Dalio Explore Fund.
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    Long-term passive acoustic recordings track the changing distribution of North Atlantic right whales (Eubalaena glacialis) from 2004 to 2014 (2017)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 13460, doi:10.1038/s41598-017-13359-3.
    Description: Given new distribution patterns of the endangered North Atlantic right whale (NARW; Eubalaena glacialis) population in recent years, an improved understanding of spatio-temporal movements are imperative for the conservation of this species. While so far visual data have provided most information on NARW movements, passive acoustic monitoring (PAM) was used in this study in order to better capture year-round NARW presence. This project used PAM data from 2004 to 2014 collected by 19 organizations throughout the western North Atlantic Ocean. Overall, data from 324 recorders (35,600 days) were processed and analyzed using a classification and detection system. Results highlight almost year-round habitat use of the western North Atlantic Ocean, with a decrease in detections in waters off Cape Hatteras, North Carolina in summer and fall. Data collected post 2010 showed an increased NARW presence in the mid-Atlantic region and a simultaneous decrease in the northern Gulf of Maine. In addition, NARWs were widely distributed across most regions throughout winter months. This study demonstrates that a large-scale analysis of PAM data provides significant value to understanding and tracking shifts in large whale movements over long time scales.
    Description: This research was funded and supported by many organizations, specified by projects as follows: Data recordings from region 1 were provided by K. Stafford and this research effort was funded by the National Science Foundation #NSF-ARC 0532611. Region 2 data were provided by D. K. Mellinger and S. Nieukirk, funded by National Oceanic and Atmospheric Agency (NOAA) and the Office of Naval Research (ONR) #N00014–03–1–0099, NOAA #NA06OAR4600100, US Navy #N00244-08-1-0029, N00244-09-1-0079, and N00244-10-1-0047.
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    Ocean convection linked to the recent ice edge retreat along east Greenland (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 9 (2018): 1287, doi:10.1038/s41467-018-03468-6.
    Description: Warm subtropical-origin Atlantic water flows northward across the Greenland-Scotland Ridge into the Nordic Seas, where it relinquishes heat to the atmosphere and gradually transforms into dense Atlantic-origin water. Returning southward along east Greenland, this water mass is situated beneath a layer of cold, fresh surface water and sea ice. Here we show, using measurements from autonomous ocean gliders, that the Atlantic-origin water was re-ventilated while transiting the western Iceland Sea during winter. This re-ventilation is a recent phenomenon made possible by the retreat of the ice edge toward Greenland. The fresh surface layer that characterises this region in summer is diverted onto the Greenland shelf by enhanced onshore Ekman transport induced by stronger northerly winds in fall and winter. Severe heat loss from the ocean offshore of the ice edge subsequently triggers convection, which further transforms the Atlantic-origin water. This re-ventilation is a counterintuitive occurrence in a warming climate, and highlights the difficulties inherent in predicting the behaviour of the complex coupled climate system.
    Description: Support for this work was provided by the Norwegian Research Council under Grant agreement no. 231647 (L.H. and K.V.), the Bergen Research Foundation under Grant BFS2016REK01 (K.V.), and the Centre for Climate Dynamics at the Bjerknes Centre through the FRESHWATER project (K.V.). Additional funding was provided by the Swiss National Science Foundation grants P2EZP2162267 and P300P2174307 (L.P.), the National Science Foundation grant OCE-1558742 (M.A.S.), the Norway Fulbright Foundation (K.V.), the Canada Fulbright Foundation (G.W.K.M.), and the Natural Sciences and Engineering Research Council of Canada (G.W.K.M.).
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    Tidal and diel orchestration of behaviour and gene expression in an intertidal mollusc (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 8 (2018): 4917, doi:10.1038/s41598-018-23167-y.
    Description: Intertidal inhabitants are exposed to the 24-hour solar day, and the 12.4 hour rising and falling of the tides. One or both of these cycles govern intertidal organisms’ behaviour and physiology, yet little is known about the molecular clockworks of tidal rhythmicity. Here, we show that the limpet Cellana rota exhibits robust tidally rhythmic behaviour and gene expression. We assembled a de-novo transcriptome, identifying novel tidal, along with known circadian clock genes. Surprisingly, most of the putative circadian clock genes, lack a typical rhythmicity. We identified numerous tidally rhythmic genes and pathways commonly associated with the circadian clock. We show that not only is the behaviour of an intertidal organism in tune with the tides, but so too are many of its genes and pathways. These findings highlight the plasticity of biological timekeeping in nature, strengthening the growing notion that the role of ‘canonical’ circadian clock genes may be more fluid than previously thought, as exhibited in an organism which has evolved in an environment where tidal oscillations are the dominant driving force.
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    Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 8 (2018): 8128, doi:10.1038/s41598-018-26484-4.
    Description: The kakapo is a critically endangered, herbivorous parrot endemic to New Zealand. The kakapo hindgut hosts a dense microbial community of low taxonomic diversity, typically dominated by Escherichia fergusonii, and has proven to be a remarkably stable ecosystem, displaying little variation in core membership over years of study. To elucidate mechanisms underlying this robustness, we performed 16S rRNA gene-based co-occurrence network analysis to identify potential interactions between E. fergusonii and the wider bacterial community. Genomic and metagenomic sequencing were employed to facilitate interpretation of potential interactions observed in the network. E. fergusonii maintained very few correlations with other members of the microbiota, and isolates possessed genes for the generation of energy from a wide range of carbohydrate sources, including plant fibres such as cellulose. We surmise that this dominant microorganism is abundant not due to ecological interaction with other members of the microbiota, but its ability to metabolise a wide range of nutrients in the gut. This research represents the first concerted effort to understand the functional roles of the kakapo microbiota, and leverages metagenomic data to contextualise co-occurrence patterns. By combining these two techniques we provide a means for studying the diversity-stability hypothesis in the context of bacterial ecosystems.
    Description: This work was supported by funding from the Department of Conservation (DOC) as well as a University of Auckland Faculty Research Development Fund grant (9841 3626187) to MWT, and a University of Auckland Doctoral Scholarship to DWW.
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    Mesoscale eddies influence the movements of mature female white sharks in the Gulf Stream and Sargasso Sea (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 8 (2018): 7363, doi:10.1038/s41598-018-25565-8.
    Description: Satellite-tracking of mature white sharks (Carcharodon carcharias) has revealed open-ocean movements spanning months and covering tens of thousands of kilometers. But how are the energetic demands of these active apex predators met as they leave coastal areas with relatively high prey abundance to swim across the open ocean through waters often characterized as biological deserts? Here we investigate mesoscale oceanographic variability encountered by two white sharks as they moved through the Gulf Stream region and Sargasso Sea in the North Atlantic Ocean. In the vicinity of the Gulf Stream, the two mature female white sharks exhibited extensive use of the interiors of clockwise-rotating anticyclonic eddies, characterized by positive (warm) temperature anomalies. One tagged white shark was also equipped with an archival tag that indicated this individual made frequent dives to nearly 1,000 m in anticyclones, where it was presumably foraging on mesopelagic prey. We propose that warm temperature anomalies in anticyclones make prey more accessible and energetically profitable to adult white sharks in the Gulf Stream region by reducing the physiological costs of thermoregulation in cold water. The results presented here provide valuable new insight into open ocean habitat use by mature, female white sharks that may be applicable to other large pelagic predators.
    Description: This work was supported by the WHOI Ocean Life Institute and awards from NASA and NSF.
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    Author correction : Meridional heat transport variability induced by mesoscale processes in the subpolar North Atlantic (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 9 (2018): 2398, doi:10.1038/s41467-018-04809-1.
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    Keystone Arctic paleoceanographic proxy association with putative methanotrophic bacteria (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 8 (2018): 10610, doi:10.1038/s41598-018-28871-3.
    Description: Foraminifera in sediments exposed to gas-hydrate dissociation are not expected to have cellular adaptations that facilitate inhabitation of chemosynthesis-based ecosystems because, to date, there are no known endemic seep foraminifera. To establish if foraminifera inhabit sediments impacted by gas-hydrate dissociation, we examined the cellular ultrastructure of Melonis barleeanus (Williamson, 1858) from the Vestnesa gas hydrate province (Arctic Ocean, west of Svalbard at ~79 °N; ~1200-m depth; n = 4). From sediments with gas hydrate indicators, living M. barleeanus had unusual pore plugs composed of a thick, fibrous meshwork; mitochondria were concentrated at the cell periphery, under pore plugs. While there was no evidence of endosymbioses with prokaryotes, most M. barleeanus specimens were associated with what appear to be Type I methanotrophic bacteria. One foraminifer had a particularly large bolus of these microbes concentrated near its aperture. This is the first documented instance of bona fide living M. barleeanus in gas-hydrate sediments and first documentation of a foraminifer living in close association with putative methanotrophs. Our observations have implications to paleoclimate records utilizing this foundational foraminiferal species.
    Description: JMB was funded by a WHOI Independent Study Award (Mellon Grant), with partial support from NSF grant OCE-1634469. GP and CAGE 15-2 cruise were supported by the Research Council of Norway through CAGE Center for Excellence in Arctic Gas Hydrate Environment and Climate project 223259 and NORCRUST (project number 255150).
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    The solute carrier SLC9C1 is a Na+/H+-exchanger gated by an S4-type voltage-sensor and cyclic-nucleotide binding (2018)
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    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 9 (2018): 2809, doi:10.1038/s41467-018-05253-x.
    Description: Voltage-sensing (VSD) and cyclic nucleotide-binding domains (CNBD) gate ion channels for rapid electrical signaling. By contrast, solute carriers (SLCs) that passively redistribute substrates are gated by their substrates themselves. Here, we study the orphan sperm-specific solute carriers SLC9C1 that feature a unique tripartite structure: an exchanger domain, a VSD, and a CNBD. Voltage-clamp fluorimetry shows that SLC9C1 is a genuine Na+/H+ exchanger gated by voltage. The cellular messenger cAMP shifts the voltage range of activation. Mutations in the transport domain, the VSD, or the CNBD strongly affect Na+/H+ exchange, voltage gating, or cAMP sensitivity, respectively. Our results establish SLC9C1 as a phylogenetic chimaera that combines the ion-exchange mechanism of solute carriers with the gating mechanism of ion channels. Classic SLCs slowly readjust changes in the intra- and extracellular milieu, whereas voltage gating endows the Na+/H+ exchanger with the ability to produce a rapid pH response that enables downstream signaling events.
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