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Freyria NJ, Góngora E, Greer CW, Whyte LG. High Arctic seawater and coastal soil microbiome co-occurrence and composition structure and their potential hydrocarbon biodegradation. ISME COMMUNICATIONS 2024; 4:ycae100. [PMID: 39101031 PMCID: PMC11296632 DOI: 10.1093/ismeco/ycae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/18/2024] [Accepted: 07/15/2024] [Indexed: 08/06/2024]
Abstract
The accelerated decline in Arctic sea-ice cover and duration is enabling the opening of Arctic marine passages and improving access to natural resources. The increasing accessibility to navigation and resource exploration and production brings risks of accidental hydrocarbon releases into Arctic waters, posing a major threat to Arctic marine ecosystems where oil may persist for many years, especially in beach sediment. The composition and response of the microbial community to oil contamination on Arctic beaches remain poorly understood. To address this, we analyzed microbial community structure and identified hydrocarbon degradation genes among the Northwest Passage intertidal beach sediments and shoreline seawater from five high Arctic beaches. Our results from 16S/18S rRNA genes, long-read metagenomes, and metagenome-assembled genomes reveal the composition and metabolic capabilities of the hydrocarbon microbial degrader community, as well as tight cross-habitat and cross-kingdom interactions dominated by lineages that are common and often dominant in the polar coastal habitat, but distinct from petroleum hydrocarbon-contaminated sites. In the polar beach sediment habitats, Granulosicoccus sp. and Cyclocasticus sp. were major potential hydrocarbon-degraders, and our metagenomes revealed a small proportion of microalgae and algal viruses possessing key hydrocarbon biodegradative genes. This research demonstrates that Arctic beach sediment and marine microbial communities possess the ability for hydrocarbon natural attenuation. The findings provide new insights into the viral and microalgal communities possessing hydrocarbon degradation genes and might represent an important contribution to the removal of hydrocarbons under harsh environmental conditions in a pristine, cold, and oil-free environment that is threatened by oil spills.
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Affiliation(s)
- Nastasia J Freyria
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Esteban Góngora
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
- Energy, Mining and Environment, Research Centre, National Research Council Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
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2
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Kraemer SA, Ramachandran A, Onana VE, Li WKW, Walsh DA. A multiyear time series (2004-2012) of bacterial and archaeal community dynamics in a changing Arctic Ocean. ISME COMMUNICATIONS 2024; 4:ycad004. [PMID: 38282643 PMCID: PMC10809757 DOI: 10.1093/ismeco/ycad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/16/2023] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
Climate change is profoundly impacting the Arctic, leading to a loss of multiyear sea ice and a warmer, fresher upper Arctic Ocean. The response of microbial communities to these climate-mediated changes is largely unknown. Here, we document the interannual variation in bacterial and archaeal communities across a 9-year time series of the Canada Basin that includes two historic sea ice minima (2007 and 2012). We report an overall loss of bacterial and archaeal community richness and significant shifts in community composition. The magnitude and period of most rapid change differed between the stratified water layers. The most pronounced changes in the upper water layers (surface mixed layer and upper Arctic water) occurred earlier in the time series, while changes in the lower layer (Pacific-origin water) occurred later. Shifts in taxonomic composition across time were subtle, but a decrease in Bacteroidota taxa and increase in Thaumarchaeota and Euryarchaeota taxa were the clearest signatures of change. This time series provides a rare glimpse into the potential influence of climate change on Arctic microbial communities; extension to the present day should contribute to deeper insights into the trajectory of Arctic marine ecosystems in response to warming and freshening.
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Affiliation(s)
- Susanne A Kraemer
- Environment and Climate Change Canada, Montreal, Quebec, H2Y 2E7, Canada
| | - Arthi Ramachandran
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Vera E Onana
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - William K W Li
- Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, B2Y 4A2, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
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3
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Dorrell RG, Kuo A, Füssy Z, Richardson EH, Salamov A, Zarevski N, Freyria NJ, Ibarbalz FM, Jenkins J, Pierella Karlusich JJ, Stecca Steindorff A, Edgar RE, Handley L, Lail K, Lipzen A, Lombard V, McFarlane J, Nef C, Novák Vanclová AM, Peng Y, Plott C, Potvin M, Vieira FRJ, Barry K, de Vargas C, Henrissat B, Pelletier E, Schmutz J, Wincker P, Dacks JB, Bowler C, Grigoriev IV, Lovejoy C. Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae. Life Sci Alliance 2023; 6:6/3/e202201833. [PMID: 36522135 PMCID: PMC9756366 DOI: 10.26508/lsa.202201833] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.
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Affiliation(s)
- Richard G Dorrell
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zoltan Füssy
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Elisabeth H Richardson
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikola Zarevski
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Nastasia J Freyria
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Federico M Ibarbalz
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Juan Jose Pierella Karlusich
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Andrei Stecca Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robyn E Edgar
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Lori Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - John McFarlane
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Charlotte Nef
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Anna Mg Novák Vanclová
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Yi Peng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Marianne Potvin
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colomban de Vargas
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, Roscoff, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eric Pelletier
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Patrick Wincker
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
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4
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Sun P, Liao Y, Wang Y, Yang EJ, Jiao N, Lee Y, Jung J, Cho KH, Moon JK, Xu D. Contrasting Community Composition and Co-Occurrence Relationships of the Active Pico-Sized Haptophytes in the Surface and Subsurface Chlorophyll Maximum Layers of the Arctic Ocean in Summer. Microorganisms 2022; 10:248. [PMID: 35208705 PMCID: PMC8877492 DOI: 10.3390/microorganisms10020248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/10/2022] Open
Abstract
Haptophytes (Hacrobia: Haptophyta), which can perform phototrophic, phagotrophic, or mixotrophic nutritional modes, are critical for element cycling in a variety of aquatic ecosystems. However, their diversity, particularly in the changing Arctic Ocean (AO), remains largely unknown. In the present study, the biodiversity, community composition, and co-occurrence networks of pico-sized haptophytes in the surface water and subsurface chlorophyll maximum (SCM) layer of the AO were explored. Our results found higher alpha diversity estimates in the surface water compared with in the SCM based on high-throughput sequencing of haptophyte specific 18S rRNA. The community composition of the surface water was significantly different from that of the SCM, and water temperature was identified as the primary factor shaping the community compositions. Prymnesiales (mostly Chrysochromulina), uncultured Prymnesiophyceae, and Phaeocystis dominated the surface water communities, whereas Phaeocystis dominated the SCM communities, followed by Chrysochromulina, uncultured Prymnesiophyceae, and the remaining taxa. The communities of the surface water and SCM layer developed relatively independent modules in the metacommunity network. Nodes in the surface water were more closely connected to one another than those in the SCM. Network stability analysis revealed that surface water networks were more stable than SCM networks. These findings suggest that SCM communities are more susceptible to environmental fluctuations than those in surface water and that future global changes (e.g., global warming) may profoundly influence the development, persistence, and service of SCM in the AO.
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Affiliation(s)
- Ping Sun
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Yuyu Liao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Kyoung-Ho Cho
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Jong-Kuk Moon
- Division of Polar Ocean Science, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, Korea; (E.-J.Y.); (Y.L.); (J.J.); (K.-H.C.); (J.-K.M.)
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; (P.S.); (Y.L.); (Y.W.); (N.J.)
- Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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5
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Wietz M, Bienhold C, Metfies K, Torres-Valdés S, von Appen WJ, Salter I, Boetius A. The polar night shift: seasonal dynamics and drivers of Arctic Ocean microbiomes revealed by autonomous sampling. ISME COMMUNICATIONS 2021; 1:76. [PMID: 37938651 PMCID: PMC9723606 DOI: 10.1038/s43705-021-00074-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 06/15/2023]
Abstract
The Arctic Ocean features extreme seasonal differences in daylight, temperature, ice cover, and mixed layer depth. However, the diversity and ecology of microbes across these contrasting environmental conditions remain enigmatic. Here, using autonomous samplers and sensors deployed at two mooring sites, we portray an annual cycle of microbial diversity, nutrient concentrations and physical oceanography in the major hydrographic regimes of the Fram Strait. The ice-free West Spitsbergen Current displayed a marked separation into a productive summer (dominated by diatoms and carbohydrate-degrading bacteria) and regenerative winter state (dominated by heterotrophic Syndiniales, radiolarians, chemoautotrophic bacteria, and archaea). The autumn post-bloom with maximal nutrient depletion featured Coscinodiscophyceae, Rhodobacteraceae (e.g. Amylibacter) and the SAR116 clade. Winter replenishment of nitrate, silicate and phosphate, linked to vertical mixing and a unique microbiome that included Magnetospiraceae and Dadabacteriales, fueled the following phytoplankton bloom. The spring-summer succession of Phaeocystis, Grammonema and Thalassiosira coincided with ephemeral peaks of Aurantivirga, Formosa, Polaribacter and NS lineages, indicating metabolic relationships. In the East Greenland Current, deeper sampling depth, ice cover and polar water masses concurred with weaker seasonality and a stronger heterotrophic signature. The ice-related winter microbiome comprised Bacillaria, Naviculales, Polarella, Chrysophyceae and Flavobacterium ASVs. Low ice cover and advection of Atlantic Water coincided with diminished abundances of chemoautotrophic bacteria while others such as Phaeocystis increased, suggesting that Atlantification alters microbiome structure and eventually the biological carbon pump. These insights promote the understanding of microbial seasonality and polar night ecology in the Arctic Ocean, a region severely affected by climate change.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Sinhué Torres-Valdés
- Marine BioGeoScience, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Ian Salter
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faroe Marine Research Institute, Tórshavn, Faroe Islands
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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