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  • Nature Publishing Group
  • 2015-2019  (32)
  • 2016  (32)
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  • 2015-2019  (32)
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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.
    Type: Article , PeerReviewed
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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).
    Type: Article , PeerReviewed
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  • 3
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    Lipid remodelling is a widespread strategy in marine heterotrophic bacteria upon phosphorus deficiency (2016)
    Nature Publishing Group
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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).
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Punctuated shutdown of Atlantic Meridional Overturning Circulation during Greenland Stadial 1 (2016)
    Nature Publishing Group
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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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  • 5
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    Full circumpolar migration ensures evolutionary unity in the Emperor penguin (2016)
    Nature Publishing Group
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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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  • 6
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    Coral reef soundscapes may not be detectable far from the reef (2016)
    Nature Publishing Group
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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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  • 7
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    Bacterial diversity and community composition from seasurface to subseafloor (2016)
    Nature Publishing Group
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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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  • 8
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    Prevalence of influenza A virus in live-captured North Atlantic gray seals : a possible wild reservoir (2016)
    Nature Publishing Group
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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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  • 9
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    The size-distribution of Earth’s lakes (2016)
    Nature Publishing Group
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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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  • 10
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    Mitigation of coral reef warming across the central Pacific by the Equatorial Undercurrent : a past and future divide (2016)
    Nature Publishing Group
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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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