1
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Liu J, Li DW, He X, Liu R, Cheng H, Su C, Chen M, Wang Y, Zhao Z, Xu H, Cheng Z, Wang Z, Pedentchouk N, Lea-Smith DJ, Todd JD, Liu X, Zhao M, Zhang XH. A unique subseafloor microbiosphere in the Mariana Trench driven by episodic sedimentation. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:168-181. [PMID: 38433963 PMCID: PMC10902237 DOI: 10.1007/s42995-023-00212-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/23/2023] [Indexed: 03/05/2024]
Abstract
Hadal trenches are characterized by enhanced and infrequent high-rate episodic sedimentation events that likely introduce not only labile organic carbon and key nutrients but also new microbes that significantly alter the subseafloor microbiosphere. Currently, the role of high-rate episodic sedimentation in controlling the composition of the hadal subseafloor microbiosphere is unknown. Here, analyses of carbon isotope composition in a ~ 750 cm long sediment core from the Challenger Deep revealed noncontinuous deposition, with anomalous 14C ages likely caused by seismically driven mass transport and the funneling effect of trench geomorphology. Microbial community composition and diverse enzyme activities in the upper ~ 27 cm differed from those at lower depths, probably due to sudden sediment deposition and differences in redox condition and organic matter availability. At lower depths, microbial population numbers, and composition remained relatively constant, except at some discrete depths with altered enzyme activity and microbial phyla abundance, possibly due to additional sudden sedimentation events of different magnitude. Evidence is provided of a unique role for high-rate episodic sedimentation events in controlling the subsurface microbiosphere in Earth's deepest ocean floor and highlight the need to perform thorough analysis over a large depth range to characterize hadal benthic populations. Such depositional processes are likely crucial in shaping deep-water geochemical environments and thereby the deep subseafloor biosphere. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00212-y.
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Affiliation(s)
- Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Da-Wei Li
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237 China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Xinxin He
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Ronghua Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Haojin Cheng
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Chenglong Su
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Mengna Chen
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Yonghong Wang
- Key Lab of Submarine Geosciences and Prospecting Techniques, Ministry of Education/College of Marine Geosciences, Ocean University of China, Qingdao, 266100 China
| | - Zhongsheng Zhao
- Key Laboratory of Physical Oceanography, Ministry of Education/Research Vessel Centre, Ocean University of China, Qingdao, 266100 China
| | - Hanyue Xu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Zhangyu Cheng
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Zicheng Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Nikolai Pedentchouk
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | - David J. Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | - Xiaoshou Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Meixun Zhao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237 China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100 China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237 China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
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2
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Hutchinson TF, Kessler AJ, Wong WW, Hall P, Leung PM, Jirapanjawat T, Greening C, Glud RN, Cook PLM. Microorganisms oxidize glucose through distinct pathways in permeable and cohesive sediments. THE ISME JOURNAL 2024; 18:wrae001. [PMID: 38365261 PMCID: PMC10939381 DOI: 10.1093/ismejo/wrae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 02/18/2024]
Abstract
In marine sediments, microbial degradation of organic matter under anoxic conditions is generally thought to proceed through fermentation to volatile fatty acids, which are then oxidized to CO2 coupled to the reduction of terminal electron acceptors (e.g. nitrate, iron, manganese, and sulfate). It has been suggested that, in environments with a highly variable oxygen regime, fermentation mediated by facultative anaerobic bacteria (uncoupled to external terminal electron acceptors) becomes the dominant process. Here, we present the first direct evidence for this fermentation using a novel differentially labeled glucose isotopologue assay that distinguishes between CO2 produced from respiration and fermentation. Using this approach, we measured the relative contribution of respiration and fermentation of glucose in a range of permeable (sandy) and cohesive (muddy) sediments, as well as four bacterial isolates. Under anoxia, microbial communities adapted to high-energy sandy or bioturbated sites mediate fermentation via the Embden-Meyerhof-Parnas pathway, in a manner uncoupled from anaerobic respiration. Prolonged anoxic incubation suggests that this uncoupling lasts up to 160 h. In contrast, microbial communities in anoxic muddy sediments (smaller median grain size) generally completely oxidized 13C glucose to 13CO2, consistent with the classical redox cascade model. We also unexpectedly observed that fermentation occurred under oxic conditions in permeable sediments. These observations were further confirmed using pure cultures of four bacteria isolated from permeable sediments. Our results suggest that microbial communities adapted to variable oxygen regimes metabolize glucose (and likely other organic molecules) through fermentation uncoupled to respiration during transient anoxic conditions.
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Affiliation(s)
- Tess F Hutchinson
- Water Studies, School of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Adam J Kessler
- School of Earth, Atmosphere & Environment, Monash University, Clayton, VIC 3800, Australia
| | - Wei Wen Wong
- Water Studies, School of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Puspitaningsih Hall
- Water Studies, School of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Thanavit Jirapanjawat
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ronnie N Glud
- University of Southern Denmark, HADAL, Nordcee and DIAS, Odense M 5230, Denmark
- Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Perran L M Cook
- Water Studies, School of Chemistry, Monash University, Clayton, VIC 3800, Australia
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3
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Broman E, Olsson M, Maciute A, Donald D, Humborg C, Norkko A, Jilbert T, Bonaglia S, Nascimento FJA. Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments. THE ISME JOURNAL 2024; 18:wrae013. [PMID: 38366020 PMCID: PMC10942774 DOI: 10.1093/ismejo/wrae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/18/2024]
Abstract
Coastal ecosystems dominate oceanic methane (CH4) emissions. However, there is limited knowledge about how biotic interactions between infauna and aerobic methanotrophs (i.e. CH4 oxidizing bacteria) drive the spatial-temporal dynamics of these emissions. Here, we investigated the role of meio- and macrofauna in mediating CH4 sediment-water fluxes and aerobic methanotrophic activity that can oxidize significant portions of CH4. We show that macrofauna increases CH4 fluxes by enhancing vertical solute transport through bioturbation, but this effect is somewhat offset by high meiofauna abundance. The increase in CH4 flux reduces CH4 pore-water availability, resulting in lower abundance and activity of aerobic methanotrophs, an effect that counterbalances the potential stimulation of these bacteria by higher oxygen flux to the sediment via bioturbation. These findings indicate that a larger than previously thought portion of CH4 emissions from coastal ecosystems is due to faunal activity and multiple complex interactions with methanotrophs.
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Affiliation(s)
- Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm 10691, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm 10691, Sweden
| | - Markus Olsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm 10691, Sweden
| | - Adele Maciute
- Department of Marine Sciences, University of Gothenburg, Gothenburg 41390, Sweden
| | - Daniel Donald
- Tvärminne Zoological Station, Faculty of Biological of Environmental Sciences, University of Helsinki, Helsinki 10900, Finland
| | - Christoph Humborg
- Baltic Sea Centre, Stockholm University, Stockholm 10691, Sweden
- Tvärminne Zoological Station, Faculty of Biological of Environmental Sciences, University of Helsinki, Helsinki 10900, Finland
| | - Alf Norkko
- Baltic Sea Centre, Stockholm University, Stockholm 10691, Sweden
- Tvärminne Zoological Station, Faculty of Biological of Environmental Sciences, University of Helsinki, Helsinki 10900, Finland
| | - Tom Jilbert
- Tvärminne Zoological Station, Faculty of Biological of Environmental Sciences, University of Helsinki, Helsinki 10900, Finland
- Environmental Geochemistry Group, Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki 00014, Finland
| | - Stefano Bonaglia
- Department of Marine Sciences, University of Gothenburg, Gothenburg 41390, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm 10691, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm 10691, Sweden
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4
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Ni X, Song J, Lu D, Tong H, Zhou H, Liu Y, Zhan J, Yi X. Effect of bioturbation of the mitten crab on distribution of tire wear particles and their combined effect on sediment ecosystem. CHEMOSPHERE 2024; 346:140603. [PMID: 37918532 DOI: 10.1016/j.chemosphere.2023.140603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
Abstract
Tire wear particles (TWPs) are a major source of environmental microplastic pollution which gradually settle and accumulate in sediments after entering the aquatic environment, which can affect the behaviors of benthic organisms. Bioturbation of benthic species could affect the fate, impacts and potential risks of TWPs by altering the properties and structure of sediments. Therefore, in this study, the effect of TWPs on the burrowing activity of Chinese mitten crab (Eriocheir sinensis) was investigated. In addition, the effects of crab bioturbation on the distribution of TWPs and their additives were studied. The combined effects of TWPs and crab bioturbation on the microbial communities in the sediments were also explored. The results of this study showed that both TWPs and the leachate significantly inhibited the burrowing activity of crabs. TWPs in the surface layer of sediments were re-distributed by crab bioturbation and enriched mainly in the sediments near the burrow walls. Meanwhile, the heavy metals (i.e., Zn, Ca, Mg, Ba and Al) used as additives during the tire production in the burrow walls significantly increased as the accumulation of TWPs near burrow walls. In this study, TWP exposure decreased the bacterial diversity and abundance, as well as the functional genes related to carbon and nitrogen cycling process, but crab bioturbation increased them in the sediments of burrow walls by constructing a unique habitat. However, after TWPs entering into burrows, they were significantly decreased in the sediments near the burrow walls like the effects of TWPs, suggesting the negative effects of TWPs could play a dominant role in this combined system. Overall, this study is important for evaluating the distribution and effects of TWP pollution in the sediment ecosystem under biological factors such as bioturbation.
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Affiliation(s)
- Xiaoming Ni
- School of Ocean Science and Technology, Dalian University of Technology, Panjin Campus, Panjin City, Liaoning, China
| | - Jinbo Song
- School of Ocean Science and Technology, Dalian University of Technology, Panjin Campus, Panjin City, Liaoning, China
| | - Dongliang Lu
- Guangxi Key Laboratory of Marine Environmental Change and Disaster in Beibu Gulf, Qinzhou, Guangxi, China
| | - Huiyan Tong
- School of Ocean Science and Technology, Dalian University of Technology, Panjin Campus, Panjin City, Liaoning, China
| | - Hao Zhou
- School of Ocean Science and Technology, Dalian University of Technology, Panjin Campus, Panjin City, Liaoning, China
| | - Yang Liu
- School of Ocean Science and Technology, Dalian University of Technology, Panjin Campus, Panjin City, Liaoning, China
| | - Jingjing Zhan
- School of Ocean Science and Technology, Dalian University of Technology, Panjin Campus, Panjin City, Liaoning, China
| | - Xianliang Yi
- School of Ocean Science and Technology, Dalian University of Technology, Panjin Campus, Panjin City, Liaoning, China.
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5
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Jaussi M, Jørgensen BB, Kjeldsen KU, Lomstein BA, Pearce C, Seidenkantz MS, Røy H. Cell-specific rates of sulfate reduction and fermentation in the sub-seafloor biosphere. Front Microbiol 2023; 14:1198664. [PMID: 37555068 PMCID: PMC10405931 DOI: 10.3389/fmicb.2023.1198664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023] Open
Abstract
Microorganisms in subsurface sediments live from recalcitrant organic matter deposited thousands or millions of years ago. Their catabolic activities are low, but the deep biosphere is of global importance due to its volume. The stability of deeply buried sediments provides a natural laboratory where prokaryotic communities that live in steady state with their environments can be studied over long time scales. We tested if a balance is established between the flow of energy, the microbial community size, and the basal power requirement needed to maintain cells in sediments buried meters below the sea floor. We measured rates of carbon oxidation by sulfate reduction and counted the microbial cells throughout ten carefully selected sediment cores with ages from years to millions of years. The rates of carbon oxidation were converted to power (J s-1 i.e., Watt) using the Gibbs free energy of the anaerobic oxidation of complex organic carbon. We separated energy dissipation by fermentation from sulfate reduction. Similarly, we separated the community into sulfate reducers and non-sulfate reducers based on the dsrB gene, so that sulfate reduction could be related to sulfate reducers. We found that the per-cell sulfate reduction rate was stable near 10-2 fmol C cell-1 day-1 right below the zone of bioturbation and did not decrease with increasing depth and sediment age. The corresponding power dissipation rate was 10-17 W sulfate-reducing cell-1. The cell-specific power dissipation of sulfate reducers in old sediments was similar to the slowest growing anaerobic cultures. The energy from mineralization of organic matter that was not dissipated by sulfate reduction was distributed evenly to all cells that did not possess the dsrB gene, i.e., cells operationally defined as fermenting. In contrast to sulfate reducers, the fermenting cells had decreasing catabolism as the sediment aged. A vast difference in power requirement between fermenters and sulfate reducers caused the microbial community in old sediments to consist of a minute fraction of sulfate reducers and a vast majority of fermenters.
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Affiliation(s)
- Marion Jaussi
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | | | | | - Christof Pearce
- Department of Geoscience, Aarhus University, Aarhus, Denmark
| | | | - Hans Røy
- Department of Biology, Aarhus University, Aarhus, Denmark
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6
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Lever MA, Alperin MJ, Hinrichs KU, Teske A. Zonation of the active methane-cycling community in deep subsurface sediments of the Peru trench. Front Microbiol 2023; 14:1192029. [PMID: 37250063 PMCID: PMC10213550 DOI: 10.3389/fmicb.2023.1192029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
The production and anaerobic oxidation of methane (AOM) by microorganisms is widespread in organic-rich deep subseafloor sediments. Yet, the organisms that carry out these processes remain largely unknown. Here we identify members of the methane-cycling microbial community in deep subsurface, hydrate-containing sediments of the Peru Trench by targeting functional genes of the alpha subunit of methyl coenzyme M reductase (mcrA). The mcrA profile reveals a distinct community zonation that partially matches the zonation of methane oxidizing and -producing activity inferred from sulfate and methane concentrations and carbon-isotopic compositions of methane and dissolved inorganic carbon (DIC). McrA appears absent from sulfate-rich sediments that are devoid of methane, but mcrA sequences belonging to putatively methane-oxidizing ANME-1a-b occur from the zone of methane oxidation to several meters into the methanogenesis zone. A sister group of ANME-1a-b, referred to as ANME-1d, and members of putatively aceticlastic Methanothrix (formerly Methanosaeta) occur throughout the remaining methanogenesis zone. Analyses of 16S rRNA and mcrA-mRNA indicate that the methane-cycling community is alive throughout (rRNA to 230 mbsf) and active in at least parts of the sediment column (mRNA at 44 mbsf). Carbon-isotopic depletions of methane relative to DIC (-80 to -86‰) suggest mostly methane production by CO2 reduction and thus seem at odds with the widespread detection of ANME-1 and Methanothrix. We explain this apparent contradiction based on recent insights into the metabolisms of both ANME-1 and Methanothricaceae, which indicate the potential for methanogenetic growth by CO2 reduction in both groups.
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Affiliation(s)
- Mark A. Lever
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, United States
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Marc J. Alperin
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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7
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Niu M, Deng L, Su L, Ruff SE, Yang N, Luo M, Qi Q, Li J, Wang F. Methane supply drives prokaryotic community assembly and networks at cold seeps of the South China Sea. Mol Ecol 2023; 32:660-679. [PMID: 36408814 DOI: 10.1111/mec.16786] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 10/10/2022] [Accepted: 11/01/2022] [Indexed: 11/22/2022]
Abstract
Marine cold seeps are unique chemosynthetic habitats fuelled by deeply sourced hydrocarbon-rich fluids discharged at the seafloor. Through oxidizing methane and other hydrocarbons, microorganisms inhabiting cold seeps supply subsurface-derived energy to higher trophic levels, sustaining highly productive oases of life in the deep sea. Despite the central role of microbiota in mediating biogeochemical cycles, the factors that govern the assembly and network of prokaryotic communities in cold seeps remain poorly understood. Here we analysed the geochemical and microbiological profiles of 11 different sediment cores from two spatially distant cold seeps of the South China Sea. We show that prokaryotic communities belonging to the same methane-supply regimes (high-methane-supply, low-methane-supply and non-seep control sediments) had a highly similar community structure, regardless of geographical location, seep-associated biota (mussel, clam, microbial mat) and sediment depth. Methane supply appeared to drive the niche partitioning of anaerobic methanotrophic archaea (ANME) at the regional scale, with ANME-1 accounting for >60% sequence abundance of ANME in the high-methane-supply sediments, while ANME-2 dominated (>90%) the low-methane-supply sediments. Increasing methane supply enhanced the contribution of environmental selection but lessened the contributions of dispersal limitation and drift to overall community assembly. High methane supply, moreover, promoted a more tightly connected, less stable prokaryotic network dominated by positive correlations. Together, these results provide a potentially new framework for understanding the niches and network interplay of prokaryotic communities across different methane seepage regimes in cold-seep sediments.
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Affiliation(s)
- Mingyang Niu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Longhui Deng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - S Emil Ruff
- Ecosystems Center and Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Na Yang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Min Luo
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Qi Qi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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8
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Pettersen R, Ormaasen I, Angell IL, Keeley NB, Lindseth A, Snipen L, Rudi K. Bimodal distribution of seafloor microbiota diversity and function are associated with marine aquaculture. Mar Genomics 2022; 66:100991. [PMID: 36116403 DOI: 10.1016/j.margen.2022.100991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 12/01/2022]
Abstract
The aim of the current work was to investigate the impact of marine aquaculture on seafloor biogeochemistry and diversity from pristine environments in the northern part of Norway. Our analytical approach included analyses of 182 samples from 16 aquaculture sites using 16S and 18S rRNA, shotgun analyses, visual examination of macro-organisms, in addition to chemical measurements. We observed a clear bimodal distribution of the prokaryote composition and richness, determined by analyses of 16S rRNA gene operational taxonomic units (OTUs). The high OTU richness cluster was associated with non-perturbed environments and farness from the aquaculture sites, while the low OTU richness cluster was associated with perturbed environments and proximity to the aquaculture sites. Similar patterns were also observed for eukaryotes using 18S rRNA gene analyses and visual examination, but without a bimodal distribution of OTU richness. Shotgun sequencing showed the archaeum Nitrosopumilus as dominant for the high OTU richness cluster, and the epsilon protobacterium Sulfurovum as dominant for the low OTU richness cluster. Metabolic reconstruction of Nitrosopumilus indicates nitrification as the main metabolic pathway. Sulfurovum, on the other hand, was associated with sulfur oxidation and denitrification. Changes in nitrogen and sulfur metabolism is proposed as a potential explanation for the difference between the high and low OTU richness clusters. In conclusion, these findings suggest that pollution from elevated loads of organic waste drives the microbiota towards a complete alteration of respiratory routes and species composition, in addition to a collapse in prokaryote OTU richness.
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Affiliation(s)
| | - I Ormaasen
- Norwegian University of Life Sciences, Ås, Norway
| | - I L Angell
- Norwegian University of Life Sciences, Ås, Norway
| | - N B Keeley
- Institute of Marine Research, Tromsø, Norway
| | | | - L Snipen
- Norwegian University of Life Sciences, Ås, Norway
| | - K Rudi
- Norwegian University of Life Sciences, Ås, Norway.
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9
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Deng L, Meile C, Fiskal A, Bölsterli D, Han X, Gajendra N, Dubois N, Bernasconi SM, Lever MA. Deposit-feeding worms control subsurface ecosystem functioning in intertidal sediment with strong physical forcing. PNAS NEXUS 2022; 1:pgac146. [PMID: 36714871 PMCID: PMC9802194 DOI: 10.1093/pnasnexus/pgac146] [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: 02/21/2022] [Accepted: 07/25/2022] [Indexed: 06/18/2023]
Abstract
Intertidal sands are global hotspots of terrestrial and marine carbon cycling with strong hydrodynamic forcing by waves and tides and high macrofaunal activity. Yet, the relative importance of hydrodynamics and macrofauna in controlling these ecosystems remains unclear. Here, we compare geochemical gradients and bacterial, archaeal, and eukaryotic gene sequences in intertidal sands dominated by subsurface deposit-feeding worms (Abarenicola pacifica) to adjacent worm-free areas. We show that hydrodynamic forcing controls organismal assemblages in surface sediments, while in deeper layers selective feeding by worms on fine, algae-rich particles strongly decreases the abundance and richness of all three domains. In these deeper layers, bacterial and eukaryotic network connectivity decreases, while percentages of clades involved in degradation of refractory organic matter, oxidative nitrogen, and sulfur cycling increase. Our findings reveal macrofaunal activity as the key driver of biological community structure and functioning, that in turn influence carbon cycling in intertidal sands below the mainly physically controlled surface layer.
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Affiliation(s)
| | - Christof Meile
- Department of Marine Sciences, University of Georgia, 325 Sanford Drive, Athens, GA 30602, USA
| | | | - Damian Bölsterli
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | | | - Niroshan Gajendra
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Nathalie Dubois
- Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
- Department of Earth Sciences, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Sonneggstrasse 5, 8092 Zürich, Switzerland
| | - Stefano M Bernasconi
- Department of Earth Sciences, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Sonneggstrasse 5, 8092 Zürich, Switzerland
| | - Mark A Lever
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
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10
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Han X, Tolu J, Deng L, Fiskal A, Schubert CJ, Winkel LHE, Lever MA. Long-term preservation of biomolecules in lake sediments: potential importance of physical shielding by recalcitrant cell walls. PNAS NEXUS 2022; 1:pgac076. [PMID: 36741427 PMCID: PMC9896894 DOI: 10.1093/pnasnexus/pgac076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023]
Abstract
Even though lake sediments are globally important organic carbon (OC) sinks, the controls on long-term OC storage in these sediments are unclear. Using a multiproxy approach, we investigate changes in diatom, green algae, and vascular plant biomolecules in sedimentary records from the past centuries across five temperate lakes with different trophic histories. Despite past increases in the input and burial of OC in sediments of eutrophic lakes, biomolecule quantities in sediments of all lakes are primarily controlled by postburial microbial degradation over the time scales studied. We, moreover, observe major differences in biomolecule degradation patterns across diatoms, green algae, and vascular plants. Degradation rates of labile diatom DNA exceed those of chemically more resistant diatom lipids, suggesting that chemical reactivity mainly controls diatom biomolecule degradation rates in the lakes studied. By contrast, degradation rates of green algal and vascular plant DNA are significantly lower than those of diatom DNA, and in a similar range as corresponding, much less reactive lipid biomarkers and structural macromolecules, including lignin. We propose that physical shielding by degradation-resistant cell wall components, such as algaenan in green algae and lignin in vascular plants, contributes to the long-term preservation of labile biomolecules in both groups and significantly influences the long-term burial of OC in lake sediments.
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Affiliation(s)
| | - Julie Tolu
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland,Department of Water Resources and Drinking Water, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Longhui Deng
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | | | - Carsten Johnny Schubert
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland,Department of Surface Waters - Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Lenny H E Winkel
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland,Department of Water Resources and Drinking Water, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
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11
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Møller TE, Le Moine Bauer S, Hannisdal B, Zhao R, Baumberger T, Roerdink DL, Dupuis A, Thorseth IH, Pedersen RB, Jørgensen SL. Mapping Microbial Abundance and Prevalence to Changing Oxygen Concentration in Deep-Sea Sediments Using Machine Learning and Differential Abundance. Front Microbiol 2022; 13:804575. [PMID: 35663876 PMCID: PMC9158483 DOI: 10.3389/fmicb.2022.804575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/09/2022] [Indexed: 12/28/2022] Open
Abstract
Oxygen constitutes one of the strongest factors explaining microbial taxonomic variability in deep-sea sediments. However, deep-sea microbiome studies often lack the spatial resolution to study the oxygen gradient and transition zone beyond the oxic-anoxic dichotomy, thus leaving important questions regarding the microbial response to changing conditions unanswered. Here, we use machine learning and differential abundance analysis on 184 samples from 11 sediment cores retrieved along the Arctic Mid-Ocean Ridge to study how changing oxygen concentrations (1) are predicted by the relative abundance of higher taxa and (2) influence the distribution of individual Operational Taxonomic Units. We find that some of the most abundant classes of microorganisms can be used to classify samples according to oxygen concentration. At the level of Operational Taxonomic Units, however, representatives of common classes are not differentially abundant from high-oxic to low-oxic conditions. This weakened response to changing oxygen concentration suggests that the abundance and prevalence of highly abundant OTUs may be better explained by other variables than oxygen. Our results suggest that a relatively homogeneous microbiome is recruited to the benthos, and that the microbiome then becomes more heterogeneous as oxygen drops below 25 μM. Our analytical approach takes into account the oft-ignored compositional nature of relative abundance data, and provides a framework for extracting biologically meaningful associations from datasets spanning multiple sedimentary cores.
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Affiliation(s)
- Tor Einar Møller
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Sven Le Moine Bauer
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Bjarte Hannisdal
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
| | - Rui Zhao
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tamara Baumberger
- Cooperative Institute for Marine Ecosystem and Resources Studies, Oregon State University, Newport, OR, United States
| | - Desiree L Roerdink
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | | | - Ingunn H Thorseth
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Rolf Birger Pedersen
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Steffen Leth Jørgensen
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
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12
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Amiraux R, Patricia B, Christopher B, Jean-François R. Use of Stress Signals of Their Attached Bacteria to Monitor Sympagic Algae Preservation in Canadian Arctic Sediments. Microorganisms 2021; 9:microorganisms9122626. [PMID: 34946228 PMCID: PMC8704379 DOI: 10.3390/microorganisms9122626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/12/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022] Open
Abstract
Based on the strong aggregation of sympagic (ice-associated) algae and the high mortality or inactivity of bacteria attached to them, it was previously hypothesized that sympagic algae should be significant contributors to the export of carbon to Arctic sediments. In the present work, the lipid content of 30 sediment samples collected in the Canadian Arctic was investigated to test this hypothesis. The detection of high proportions of trans vaccenic fatty acid (resulting from cis-trans isomerase (CTI) activity of bacteria under hypersaline conditions) and 10S-hydroxyhexadec-8(trans)-enoic acid (resulting from 10S-DOX bacterial detoxification activity in the presence of deleterious free palmitoleic acid) confirmed: (i) the strong contribution of sympagic material to some Arctic sediments, and (ii) the impaired physiological status of its associated bacterial communities. Unlike terrestrial material, sympagic algae that had escaped zooplanktonic grazing appeared relatively preserved from biotic degradation in Arctic sediments. The expected reduction in sea ice cover resulting from global warming should cause a shift in the relative contributions of ice-associated vs. pelagic algae to the seafloor, and thus to a strong modification of the carbon cycle.
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Affiliation(s)
- Rémi Amiraux
- CNRS/INSU/IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Aix-Marseille University, Université de Toulon, 13288 Marseille, France; (R.A.); (B.P.); (B.C.)
- UMR 6539 Laboratoire des Sciences de l’Environnement Marin, (CNRS, UBO, IRD, Ifremer) Institut, Universitaire Européen de la Mer (IUEM), 29280 Plouzané, France
- Takuvik Joint International Laboratory, Département de Biologie, Laval University (Canada)—CNRS, Université Laval, Québec, QC G1V 0A6, Canada
| | - Bonin Patricia
- CNRS/INSU/IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Aix-Marseille University, Université de Toulon, 13288 Marseille, France; (R.A.); (B.P.); (B.C.)
| | - Burot Christopher
- CNRS/INSU/IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Aix-Marseille University, Université de Toulon, 13288 Marseille, France; (R.A.); (B.P.); (B.C.)
| | - Rontani Jean-François
- CNRS/INSU/IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Aix-Marseille University, Université de Toulon, 13288 Marseille, France; (R.A.); (B.P.); (B.C.)
- Correspondence:
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13
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Cariou M, Francois CM, Voisin J, Pigneret M, Hervant F, Volatier L, Mermillod-Blondin F. Effects of bioturbation by tubificid worms on biogeochemical processes, bacterial community structure and diversity in heterotrophic wetland sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148842. [PMID: 34328914 DOI: 10.1016/j.scitotenv.2021.148842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/09/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Bioturbation activity of tubificid worms has been recognized as a key process influencing organic matter processing and nutrient cycling in benthic aquatic ecosystems. This activity is expected to modify benthic microbial communities by affecting the physical and chemical environment in sediments. Nevertheless, quantifications of bacterial community changes associated with bioturbation in freshwater ecosystems are still lacking. The present study aimed at evaluating the impact of tubificid worms on bacterial community structure using NGS approach (16S metabarcoding) and long (6 months) laboratory experiments on four heterotrophic wetland sediments. Worm bioturbation activity significantly stimulated biogeochemical processes at the water-sediment interface but only had a marginally significant effect on bacterial community structures. Yet, bacterial diversity was consistently reduced in presence of worms. Such decrease could be associated with the stimulation of organic matter mineralization by worms, leading to a reduction of the diversity of trophic niches available for bacterial species. The slight changes in bacterial community structures induced by bioturbation did not appear to control biogeochemical processes. Thus, the stimulation of biogeochemical processes by worm bioturbation was more associated with a stimulation of the initial bacterial community than with a drastic change in bacterial communities induced by worms.
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Affiliation(s)
- Marie Cariou
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Clémentine M Francois
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Jérémy Voisin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Mathilde Pigneret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Frédéric Hervant
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Laurence Volatier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Florian Mermillod-Blondin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France.
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14
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Interactions between temperature and energy supply drive microbial communities in hydrothermal sediment. Commun Biol 2021; 4:1006. [PMID: 34433861 PMCID: PMC8387401 DOI: 10.1038/s42003-021-02507-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/30/2021] [Indexed: 11/23/2022] Open
Abstract
Temperature and bioavailable energy control the distribution of life on Earth, and interact with each other due to the dependency of biological energy requirements on temperature. Here we analyze how temperature-energy interactions structure sediment microbial communities in two hydrothermally active areas of Guaymas Basin. Sites from one area experience advective input of thermogenically produced electron donors by seepage from deeper layers, whereas sites from the other area are diffusion-dominated and electron donor-depleted. In both locations, Archaea dominate at temperatures >45 °C and Bacteria at temperatures <10 °C. Yet, at the phylum level and below, there are clear differences. Hot seep sites have high proportions of typical hydrothermal vent and hot spring taxa. By contrast, high-temperature sites without seepage harbor mainly novel taxa belonging to phyla that are widespread in cold subseafloor sediment. Our results suggest that in hydrothermal sediments temperature determines domain-level dominance, whereas temperature-energy interactions structure microbial communities at the phylum-level and below. Lagostina et al. show that relative abundances of Bacteria and Archaea in sediments of Guaymas Basin, Gulf of California, are controlled by temperature, while energy flux explains microbial community structure at the phylum-level and below. Hot diffusion-dominated and energy-depleted sediments are dominated by taxa with relatives in cold subseafloor sediments, while hot sediments with high energy supply from fluid seepage are dominated by taxa also found at hydrothermal vents and in hot springs.
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15
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Ashford OS, Guan S, Capone D, Rigney K, Rowley K, Cordes EE, Cortés J, Rouse GW, Mendoza GF, Sweetman AK, Levin LA. Relationships between biodiversity and ecosystem functioning proxies strengthen when approaching chemosynthetic deep-sea methane seeps. Proc Biol Sci 2021; 288:20210950. [PMID: 34403635 PMCID: PMC8370799 DOI: 10.1098/rspb.2021.0950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As biodiversity loss accelerates globally, understanding environmental influence over biodiversity-ecosystem functioning (BEF) relationships becomes crucial for ecosystem management. Theory suggests that resource supply affects the shape of BEF relationships, but this awaits detailed investigation in marine ecosystems. Here, we use deep-sea chemosynthetic methane seeps and surrounding sediments as natural laboratories in which to contrast relationships between BEF proxies along with a gradient of trophic resource availability (higher resource methane seep, to lower resource photosynthetically fuelled deep-sea habitats). We determined sediment fauna taxonomic and functional trait biodiversity, and quantified bioturbation potential (BPc), calcification degree, standing stock and density as ecosystem functioning proxies. Relationships were strongly unimodal in chemosynthetic seep habitats, but were undetectable in transitional 'chemotone' habitats and photosynthetically dependent deep-sea habitats. In seep habitats, ecosystem functioning proxies peaked below maximum biodiversity, perhaps suggesting that a small number of specialized species are important in shaping this relationship. This suggests that absolute biodiversity is not a good metric of ecosystem 'value' at methane seeps, and that these deep-sea environments may require special management to maintain ecosystem functioning under human disturbance. We promote further investigation of BEF relationships in non-traditional resource environments and emphasize that deep-sea conservation should consider 'functioning hotspots' alongside biodiversity hotspots.
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Affiliation(s)
- Oliver S Ashford
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA 92007, USA
| | - Shuzhe Guan
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA 92007, USA
| | - Dante Capone
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA 92007, USA.,University of California, Santa Cruz, CA 95064, USA
| | - Katherine Rigney
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA 92007, USA.,Carleton College, Northfield, MN 55057, USA
| | - Katelynn Rowley
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA 92007, USA
| | - Erik E Cordes
- Department of Biology, Temple University, Temple, PA 19122, USA
| | - Jorge Cortés
- CIMAR, Universidad de Costa Rica, San José, Costa Rica
| | - Greg W Rouse
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA 92007, USA
| | - Guillermo F Mendoza
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA 92007, USA
| | - Andrew K Sweetman
- The Lyell Centre for Earth and Marine Science and Technology, Heriot-Watt University, Edinburgh, UK
| | - Lisa A Levin
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA 92007, USA.,Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, University of California San Diego, San Diego, CA 92093, USA
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16
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Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites. Proc Natl Acad Sci U S A 2021; 118:2006857118. [PMID: 34161255 PMCID: PMC8237665 DOI: 10.1073/pnas.2006857118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Methane is a strong greenhouse gas that plays a key role in Earth’s climate. At methane seeps, large amounts of methane move upward through the seafloor, where microbial communities consume much of it. A full accounting of methane’s sources and sinks has evaded researchers—in part, perhaps, because key habitats including carbonate rock mounds have been largely neglected. We sampled seven methane seeps representing four geological settings and found that all sites had rock-hosted microbes capable of consuming methane; in lab-based incubations, some did so at the highest rates reported to date. We demonstrate several factors that help determine a sample’s methane-consuming potential and propose that carbonate rocks at methane seeps may represent a methane sink of far-reaching importance. At marine methane seeps, vast quantities of methane move through the shallow subseafloor, where it is largely consumed by microbial communities. This process plays an important role in global methane dynamics, but we have yet to identify all of the methane sinks in the deep sea. Here, we conducted a continental-scale survey of seven geologically diverse seafloor seeps and found that carbonate rocks from all sites host methane-oxidizing microbial communities with substantial methanotrophic potential. In laboratory-based mesocosm incubations, chimney-like carbonates from the newly described Point Dume seep off the coast of Southern California exhibited the highest rates of anaerobic methane oxidation measured to date. After a thorough analysis of physicochemical, electrical, and biological factors, we attribute this substantial metabolic activity largely to higher cell density, mineral composition, kinetic parameters including an elevated Vmax, and the presence of specific microbial lineages. Our data also suggest that other features, such as electrical conductance, rock particle size, and microbial community alpha diversity, may influence a sample’s methanotrophic potential, but these factors did not demonstrate clear patterns with respect to methane oxidation rates. Based on the apparent pervasiveness within seep carbonates of microbial communities capable of performing anaerobic oxidation of methane, as well as the frequent occurrence of carbonates at seeps, we suggest that rock-hosted methanotrophy may be an important contributor to marine methane consumption.
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17
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Han C, Xu Z, Liu X. Characteristics of macrofaunal assemblages and their relationships with environmental factors in a semi-enclosed bay. MARINE POLLUTION BULLETIN 2021; 167:112348. [PMID: 33865043 DOI: 10.1016/j.marpolbul.2021.112348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/27/2021] [Accepted: 04/04/2021] [Indexed: 06/12/2023]
Abstract
Characteristics of macrofaunal assemblages and their relationships with environmental factors in a semi-enclosed bay were studied seasonally in China. A total of 251 species were identified, including polychaetes (104 species), crustaceans (73 species), mollusks (51 species), and other phyla (23 species). Mean values of macrofaunal abundance were 1210, 2483, 3209, 3600 ind./m2 while those of biomass were 56.88, 176.15, 136.28, 265.55 g/m2, respectively. Ranges of species richness index, evenness index, Shannon-Wiener index were 1.54-8.16, 0.17-0.90, 0.69-4.78, respectively. The diversity indices were affected by bottom water salinity and pH. BIOENV analysis showed that water depth, phaeophorbide, and silt-clay proportion had important impacts on macrofaunal assemblages while abundance and biomass were affected by bottom water temperature, salinity, and water depth. Compared with historical data, macrofaunal species number, abundance and biomass showed a slight increasing trend, which may be due to the water quality improvement of this bay.
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Affiliation(s)
- Chen Han
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Zhaodong Xu
- North China Sea Environmental Monitoring Center, State Oceanic Administration, Qingdao 266033, China
| | - Xiaoshou Liu
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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18
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Frühe L, Dully V, Forster D, Keeley NB, Laroche O, Pochon X, Robinson S, Wilding TA, Stoeck T. Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms. Front Microbiol 2021; 12:637811. [PMID: 33995296 PMCID: PMC8116884 DOI: 10.3389/fmicb.2021.637811] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3-V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.
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Affiliation(s)
- Larissa Frühe
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Verena Dully
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Dominik Forster
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Nigel B Keeley
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Research, Bergen, Norway
| | - Olivier Laroche
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Shawn Robinson
- St. Andrews Biological Station, Department of Fisheries and Oceans, St. Andrews, NB, Canada
| | | | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
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19
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Wallenius AJ, Dalcin Martins P, Slomp CP, Jetten MSM. Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments. Front Microbiol 2021; 12:631621. [PMID: 33679659 PMCID: PMC7935538 DOI: 10.3389/fmicb.2021.631621] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/29/2021] [Indexed: 12/05/2022] Open
Abstract
Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.
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Affiliation(s)
- Anna J. Wallenius
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Paula Dalcin Martins
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Caroline P. Slomp
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
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20
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Stevenson MA, Faust JC, Andrade LL, Freitas FS, Gray ND, Tait K, Hendry KR, Hilton RG, Henley SF, Tessin A, Leary P, Papadaki S, Ford A, März C, Abbott GD. Transformation of organic matter in a Barents Sea sediment profile: coupled geochemical and microbiological processes. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20200223. [PMID: 32862813 PMCID: PMC7481670 DOI: 10.1098/rsta.2020.0223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Process-based, mechanistic investigations of organic matter transformation and diagenesis directly beneath the sediment-water interface (SWI) in Arctic continental shelves are vital as these regions are at greatest risk of future change. This is in part due to disruptions in benthic-pelagic coupling associated with ocean current change and sea ice retreat. Here, we focus on a high-resolution, multi-disciplinary set of measurements that illustrate how microbial processes involved in the degradation of organic matter are directly coupled with inorganic and organic geochemical sediment properties (measured and modelled) as well as the extent/depth of bioturbation. We find direct links between aerobic processes, reactive organic carbon and highest abundances of bacteria and archaea in the uppermost layer (0-4.5 cm depth) followed by dominance of microbes involved in nitrate/nitrite and iron/manganese reduction across the oxic-anoxic redox boundary (approx. 4.5-10.5 cm depth). Sulfate reducers dominate in the deeper (approx. 10.5-33 cm) anoxic sediments which is consistent with the modelled reactive transport framework. Importantly, organic matter reactivity as tracked by organic geochemical parameters (n-alkanes, n-alkanoic acids, n-alkanols and sterols) changes most dramatically at and directly below the SWI together with sedimentology and biological activity but remained relatively unchanged across deeper changes in sedimentology. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.
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Affiliation(s)
- Mark A. Stevenson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- e-mail:
| | - Johan C. Faust
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Luiza L. Andrade
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Felipe S. Freitas
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
| | - Neil D. Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Karen Tait
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
| | | | - Robert G. Hilton
- Department of Geography, Science Laboratories, Durham University, South Road, Durham DH1 3LE, UK
| | - Sian F. Henley
- School of GeoSciences, University of Edinburgh, James Hutton Road, Edinburgh EH9 3FE, UK
| | - Allyson Tessin
- Department of Geology, Kent State University, Kent, OH 44240, USA
| | - Peter Leary
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Sonia Papadaki
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
| | - Ailbe Ford
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Christian März
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Geoffrey D. Abbott
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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