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405 Research products

  • European Marine Science
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Trouche, Blandine;

    Anvi'o databases of the 47 ammonia-oxidizing archaea MAGs from abyssal and hadal surface sediments presented in Trouche et al, 2023 (https://doi.org/10.1038/s43705-023-00341-6). 

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Other ORP type . 2023
    License: CC BY
    Data sources: ZENODO
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Other ORP type . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Wang, Siyuan; Zhang, Futing; Koedooder, Coco; Qafoku, Odeta; +8 Authors

    The uploaded file contains three separate Python scripts aimed at modeling the sinking velocity of natural Trichodesmium colonies loaded with dust particles. Two scripts have been developed to calculate the dust influencing factor (K), and one script is dedicated to calculating the sinking velocity of particle-free Trichodesmium colonies (v0). All Python scripts are available on GitHub (https://github.com/Zhanzhu1110/Trichobuoyancy.git) and can be processed using the "Codespaces" function on GitHub. The file 'K given values' is a specialized script designed to simulate the dust factor (K), assuming seawater and dust densities of 1028 kg/m3 and 2500 kg/m3, respectively, with a colony radius of 1 mm.

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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO
    Model . 2023
    License: CC BY
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Model . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Martínez Moreno, Josué;

    This dataset includes the NEMO 4.0.2 configuration used and analysed in the paper titled "Eddy-driven heterogeneity in sea ice during the ice-growth season". The output data is approximately 4TB for the 3 idealised configuration used in the manuscript, thus we opted to distribute the configuration. Note: The initial conditions for each simulation are compressed into the file `init_cond.zip` The configuration for one of the simulations is compressed in the file `config.zip` In order to reproduce all the runs, it's only required to change the initial conditions in the file namelist_cfg and namelist_ice_cfg. Further information and scripts to reproduce the result of the manuscript can be found at: https://github.com/josuemtzmo/Ice_formation

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    ZENODO
    Model . 2023
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO
      Model . 2023
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Paul Myers;

    Animation of the thickness of Pacific Water throughout the upper 150 m of Baffin Bay, in metres, based upon a passive tracer included with a 1/12 degree NEMO model simulation of the Arctic and North Atlantic (ANHA12-EXH006).

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    Authors: Burkard, Annika;

    This thesis analyzes the flight across the sea in the context of the refugee crisis in 2015/ 2016 in German film and literature. The works chosen are Wolfgang Fischer’s film Styx from 2018, Reinhard Kleist’s graphic novel Der Traum von Olympia (An Olympic Dream) from 2015, and Merle Kröger’s crime novel Havarie (Collision) from 2015. Common motives in the works are the depiction of Europe as a paradise from the refugee’s perspective and the contrast between vacationing and bare survival. However, each author/director based their unique narrative method not only on the medium and genre of delivery but also on choices of narrative perspective. This thesis examines the differences in the narrative methods and gives special attention to the emotional, cognitive, ethical, and political steerings of the recipients. In all works, the steering of the recipients is linked to political topics such as the concepts of agency, solidarity, human rights, and precarity. Furthermore, this thesis examines the depiction of Europe, its responsibilities, and the traces of colonialism as projected in film and literature. At the end of the thesis, I reflect on the representation of the sea, which becomes a political place, a dangerous border region or a resort for vacation in the works.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Orth, Donald J.;

    These supplementary teaching resources align to the open textbook, Fish, Fishing, and Conservation which is a 389-page, peer-reviewed publicly-available, openly-licensed textbook intended for undergraduate students who are exploring majors in Fish & Wildlife. It is also relevant to a general audience or for use in courses which explore social and ethical aspects of fish, fishing and conservation. The open textbook, Fish, Fishing, and Conservation, is freely available at https://doi.org/10.21061/fishandconservation. Supplementary teaching resources include a sample course syllabus, schedule, and a variety of assignments. Individuals who wish to share their materials relevant to teaching in this subject area are encouraged to join and share their openly-licensed resources via the Fish, Fishing, and Conservation instructor group in OER Commons. Are you reviewing or adopting Fish, Fishing, and Conservation for a course? Please help us understand your use by filling out this form. VIVA (Virtual Library of Virginia)

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    VTechWorks
    Other ORP type . 2023
    License: CC BY
    Data sources: VTechWorks
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      VTechWorks
      Other ORP type . 2023
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    Authors: Vigneron, Adrien; Cruaud, Perrine; Lovejoy, Connie; Vincent, Warwick F.;

    Background: Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown. Here, we identifed genes encoding enzymes involved in the hydrocarbon cycle across the salinity gradient of a remote, vertically stratifed, seawater-containing High Arctic lake that is isolated from anthropogenic petroleum sources and natural seeps. Metagenomic analysis revealed diverse hydrocarbon cycling genes and populations, with patterns of variation along gradients of light, salinity, oxygen, and sulfur that are relevant to freshwater, oceanic, hadal, and anoxic deep sea ecosystems. Results Analyzing genes and metagenome-assembled genomes down the water column of Lake A in the Canadian High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia had pathways for alkane and alkene production, providing additional sources of biogenic hydrocarbons. Known oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identifed in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae, and Marinimicrobia. Genes involved in sulfur and nitrogen compound transformations were abundant in hydrocarbon producing and degrading lineages, suggesting strong interconnections with nitrogen and sulfur cycles and a potential for widespread distribution in the ocean. Conclusions Our detailed metagenomic analyses across water column gradients in a remote petroleum-free lake derived from the Arctic Ocean suggest that the current estimation of bacterial hydrocarbon production in the ocean could be substantially underestimated by neglecting non-phototrophic production and by not taking low oxygen zones into account. Our fndings also suggest that biogenic hydrocarbons may sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications for carbon, sulfur, and nitrogen cycles.

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    CorpusUL
    Other ORP type . 2023
    Data sources: CorpusUL
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      CorpusUL
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    Authors: Love, Connor;

    The creation, movement, and consumption of distinct biomolecules by marine organisms has far reaching implications regarding ecosystem material and energy flow and how we manage the marine environment. Lipids are ubiquitous, energy rich biomolecules that are essential for all life and are used for cell membrane structure, energy storage and serve as useful indicators for ecosystem and food web dynamics. In this dissertation, the flow of specific lipid biomolecules through multiple marine environments is measured, explored, and clarified to better understand biogeochemical cycles, marine food webs and ecosystem connectivity. In the first chapter of my dissertation, I measure, quantify, and close the loop of the open ocean microbial hydrocarbon cycle, with implications for priming effects of the ocean microbiome to oil spills. It is estimated that seeps, spills, and other oil pollution introduce ~ 1.3 million tons (1.3 Tg) of hydrocarbons into the ocean each year. Additionally, it is known that globally abundant marine cyanobacteria Prochlorococcus and Synechococcus which account for ~25% of ocean net primary production also produce hydrocarbons from fatty acids. But little is known about the size, turnover and fate of these cyanobacterial hydrocarbons and the implications for the ocean’s microbiome response to future oil spills. From a research expedition in the North Atlantic, I report that cyanobacteria in an oligotrophic gyre mainly produce n-pentadecane which correlates tightly with fluorescence and Prochlorococcus abundance in oligotrophic waters. Using chemical and isotopic tracing I find that pentadecane production and diel dynamics mainly occurs in the lower euphotic zone at the deep chlorophyll maximum. I estimate the global flux of cyanobacteria-produced pentadecane exceeds total oil input in the ocean by 100 to 500-fold, with cyanobacteria producing ~ 130-650 million tons of pentadecane per year. Analysis of sinking particles at the base of the euphotic zone show that nearly all pentadecane (< 0.001 % remaining) is consumed within the euphotic zone, suggesting near complete consumption of these hydrocarbons by hydrocarbon degrading microbes. These findings characterize a wide-spread microbial hydrocarbon cycle that selectively primes the ocean’s microbiome with long-chain alkanes. In the second chapter of my dissertation, I conduct a large-scale feeding experiment on a symbiotic reef-building coral (Stylophora pistillata) in the Red Sea to clarify fatty acid and isotopic biomarker patterns of coral heterotrophy for use in the field. Coral heterotrophy is an often-overlooked facet of coral nutrition that provides essential nutrients that help corals resist and recover from thermally induced bleaching that is degrading reef ecosystems around the world due to rising global ocean temperatures. Yet, methods for measuring coral mixotrophy, the balance between organic matter contributions to the coral host from autotrophic photo endosymbionts and heterotrophy on particles and plankton have typically been too coarse to elucidate source contributions. Through my experiment I show that fatty acids and isotopic biomarkers reliably separate experimental and reef nutritional source groups (heterotrophic or autotrophic). I show that heterotrophic fatty acid biomarkers are reliably recorded into coral host and symbiont tissues, with a divergent metabolic pattern of autotrophic biomarkers as feeding increases due to positive feedback of heterotrophy on the in hospite photo symbiont population. Additionally, I show that nitrogen and essential fatty acids are preferentially recorded into coral tissue while most heterotrophic carbon is respired or exuded as mucous; this shows that the use of bulk carbon isotopes as a feeding proxy for the last ~ 40 years is largely underestimating the contribution of heterotrophy to the trophic ecology of reef building corals. Overall, this finding underscores a connectivity between oceanic phyto- and zooplankton and reef-building coral. In the third chapter of my dissertation, I explore the mixotrophic differences of divergent bleaching responses of Acropora hyacinthus colonies on the forereef of Mo’orea during the 2019 mass bleaching event. During this bleaching event, all colonies of A. hyacinthus on the deep forereef (14 m) bleached and recovered, while colonies on the shallow forereef (5 m) near the reef crest resisted bleaching entirely, despite the same temperature stress. Using fatty acid and isotopic biomarkers I show through several lines of evidence that bleaching resistant colonies near the reef crest were likely consuming more particulate organic matter than deep forereef colonies. This conclusion is supported by isotopic feeding proxies, less isotopic niche overlap of the host and symbiont of resistant colonies, and larger proportions of putative POM fatty acid biomarkers in the host of resistant colonies relative to recovered colonies. This interpretation is in line with observations that benthic communities on the reef crest are a net sink of oceanic POM and that increased reliance on heterotrophy is associated with bleaching resistance. These data show the vital importance of reef environment, coral heterotrophy, and planktonic subsidies in structuring bleaching response of corals in a warming ocean and ultimately show that the reef crest may serve as a potent zone for reseeding coral populations after marine heat waves.

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  • Authors: Anhaus, Philipp; Schiller, Martin; Planat, Noémie; Katlein, Christian; +1 Authors

    The distance between a remotely operated vehicle (ROV) and the sea-ice underside was measured by a single-beam upward-looking acoustic sonar altimeter (Tritech PA500) attached to the ROV during the ARTofMELT2023 expedition in May and June 2023. Sea-ice draft was derived by subtracting the distance to the sea-ice underside from the ROV depth, uncorrected for ROV attitude (pitch, roll). An offset between the depth reference (ROV bumper bars) and the altimeter of 0.105 m is accounted for in the presented data.

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    Authors: Luostarinen, Tiia; Weckström, Kaarina; Ehn, Jens K; Kamula, Michelle; +6 Authors

    Datasets collected during a field campaign in the Belcher Islands Archipelago, Hudson Bay, Canada, during spring and summer 2019 including sea ice, water column, sediment trap and surface sediment samples that were analysed for diatoms, dinoflagellate cysts, highly branched isoprenoid lipids, pigments and geochemistry. The sea ice samples were collected using a Kovacs Mark II core barrel with an internal diameter of 9 cm, and the bottom 5 cm of the sea-ice cores were used for analysis on each sampling day. The water sampling was conducted using a plankton net (Ø 18 cm, 10 µm, 30-m net haul; diatoms) and a 2,5 L Kemmerer water sampler (pooled sample from 2.5-, 5-, 10-, 15-, 20-, 25- and 30-metre depths; highly branched isoprenoid lipids). For sediment trap samples, an automated Gurney Instruments Baker-style, cylindrical sediment trap (aperture 0.032 m2) was deployed at 40-m depth, 30-m above the seafloor and the rotation for the trap was set to 8-day intervals. The surface sediment sample was collected using a Kajak-Brinkhurst gravity corer. The under-ice salinities and temperatures were measured by using with RBR Concerto® and CastAway-CTD® sensors.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Trouche, Blandine;

    Anvi'o databases of the 47 ammonia-oxidizing archaea MAGs from abyssal and hadal surface sediments presented in Trouche et al, 2023 (https://doi.org/10.1038/s43705-023-00341-6). 

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    ZENODO
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    Authors: Wang, Siyuan; Zhang, Futing; Koedooder, Coco; Qafoku, Odeta; +8 Authors

    The uploaded file contains three separate Python scripts aimed at modeling the sinking velocity of natural Trichodesmium colonies loaded with dust particles. Two scripts have been developed to calculate the dust influencing factor (K), and one script is dedicated to calculating the sinking velocity of particle-free Trichodesmium colonies (v0). All Python scripts are available on GitHub (https://github.com/Zhanzhu1110/Trichobuoyancy.git) and can be processed using the "Codespaces" function on GitHub. The file 'K given values' is a specialized script designed to simulate the dust factor (K), assuming seawater and dust densities of 1028 kg/m3 and 2500 kg/m3, respectively, with a colony radius of 1 mm.

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    Authors: Martínez Moreno, Josué;

    This dataset includes the NEMO 4.0.2 configuration used and analysed in the paper titled "Eddy-driven heterogeneity in sea ice during the ice-growth season". The output data is approximately 4TB for the 3 idealised configuration used in the manuscript, thus we opted to distribute the configuration. Note: The initial conditions for each simulation are compressed into the file `init_cond.zip` The configuration for one of the simulations is compressed in the file `config.zip` In order to reproduce all the runs, it's only required to change the initial conditions in the file namelist_cfg and namelist_ice_cfg. Further information and scripts to reproduce the result of the manuscript can be found at: https://github.com/josuemtzmo/Ice_formation

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    Authors: Paul Myers;

    Animation of the thickness of Pacific Water throughout the upper 150 m of Baffin Bay, in metres, based upon a passive tracer included with a 1/12 degree NEMO model simulation of the Arctic and North Atlantic (ANHA12-EXH006).

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    Authors: Burkard, Annika;

    This thesis analyzes the flight across the sea in the context of the refugee crisis in 2015/ 2016 in German film and literature. The works chosen are Wolfgang Fischer’s film Styx from 2018, Reinhard Kleist’s graphic novel Der Traum von Olympia (An Olympic Dream) from 2015, and Merle Kröger’s crime novel Havarie (Collision) from 2015. Common motives in the works are the depiction of Europe as a paradise from the refugee’s perspective and the contrast between vacationing and bare survival. However, each author/director based their unique narrative method not only on the medium and genre of delivery but also on choices of narrative perspective. This thesis examines the differences in the narrative methods and gives special attention to the emotional, cognitive, ethical, and political steerings of the recipients. In all works, the steering of the recipients is linked to political topics such as the concepts of agency, solidarity, human rights, and precarity. Furthermore, this thesis examines the depiction of Europe, its responsibilities, and the traces of colonialism as projected in film and literature. At the end of the thesis, I reflect on the representation of the sea, which becomes a political place, a dangerous border region or a resort for vacation in the works.

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    Authors: Orth, Donald J.;

    These supplementary teaching resources align to the open textbook, Fish, Fishing, and Conservation which is a 389-page, peer-reviewed publicly-available, openly-licensed textbook intended for undergraduate students who are exploring majors in Fish & Wildlife. It is also relevant to a general audience or for use in courses which explore social and ethical aspects of fish, fishing and conservation. The open textbook, Fish, Fishing, and Conservation, is freely available at https://doi.org/10.21061/fishandconservation. Supplementary teaching resources include a sample course syllabus, schedule, and a variety of assignments. Individuals who wish to share their materials relevant to teaching in this subject area are encouraged to join and share their openly-licensed resources via the Fish, Fishing, and Conservation instructor group in OER Commons. Are you reviewing or adopting Fish, Fishing, and Conservation for a course? Please help us understand your use by filling out this form. VIVA (Virtual Library of Virginia)

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    VTechWorks
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    Authors: Vigneron, Adrien; Cruaud, Perrine; Lovejoy, Connie; Vincent, Warwick F.;

    Background: Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown. Here, we identifed genes encoding enzymes involved in the hydrocarbon cycle across the salinity gradient of a remote, vertically stratifed, seawater-containing High Arctic lake that is isolated from anthropogenic petroleum sources and natural seeps. Metagenomic analysis revealed diverse hydrocarbon cycling genes and populations, with patterns of variation along gradients of light, salinity, oxygen, and sulfur that are relevant to freshwater, oceanic, hadal, and anoxic deep sea ecosystems. Results Analyzing genes and metagenome-assembled genomes down the water column of Lake A in the Canadian High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia had pathways for alkane and alkene production, providing additional sources of biogenic hydrocarbons. Known oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identifed in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae, and Marinimicrobia. Genes involved in sulfur and nitrogen compound transformations were abundant in hydrocarbon producing and degrading lineages, suggesting strong interconnections with nitrogen and sulfur cycles and a potential for widespread distribution in the ocean. Conclusions Our detailed metagenomic analyses across water column gradients in a remote petroleum-free lake derived from the Arctic Ocean suggest that the current estimation of bacterial hydrocarbon production in the ocean could be substantially underestimated by neglecting non-phototrophic production and by not taking low oxygen zones into account. Our fndings also suggest that biogenic hydrocarbons may sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications for carbon, sulfur, and nitrogen cycles.

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    CorpusUL
    Other ORP type . 2023
    Data sources: CorpusUL
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