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Zhu QZ, Yin X, Taubner H, Wendt J, Friedrich MW, Elvert M, Hinrichs KU, Middelburg JJ. Secondary production and priming reshape the organic matter composition in marine sediments. SCIENCE ADVANCES 2024; 10:eadm8096. [PMID: 38758798 PMCID: PMC11100564 DOI: 10.1126/sciadv.adm8096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/11/2024] [Indexed: 05/19/2024]
Abstract
Organic matter (OM) transformations in marine sediments play a crucial role in the global carbon cycle. However, secondary production and priming have been ignored in marine biogeochemistry. By incubating shelf sediments with various 13C-labeled algal substrates for 400 days, we show that ~65% of the lipids and ~20% of the proteins were mineralized by numerically minor heterotrophic bacteria as revealed by RNA stable isotope probing. Up to 11% of carbon from the algal lipids was transformed into the biomass of secondary producers as indicated by 13C incorporation in amino acids. This biomass turned over throughout the experiment, corresponding to dynamic microbial shifts. Algal lipid addition accelerated indigenous OM degradation by 2.5 to 6 times. This priming was driven by diverse heterotrophic bacteria and sulfur- and iron-cycling bacteria and, in turn, resulted in extra secondary production, which exceeded that stimulated by added substrates. These interactions between degradation, secondary production, and priming govern the eventual fate of OM in marine sediments.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Xiuran Yin
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Heidi Taubner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jenny Wendt
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W. Friedrich
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jack J. Middelburg
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
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2
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Yin X, Zhou G, Cai M, Richter-Heitmann T, Zhu QZ, Maeke M, Kulkarni AC, Nimzyk R, Elvert M, Friedrich MW. Physiological versatility of ANME-1 and Bathyarchaeotoa-8 archaea evidenced by inverse stable isotope labeling. MICROBIOME 2024; 12:68. [PMID: 38570877 PMCID: PMC10988981 DOI: 10.1186/s40168-024-01779-z] [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: 08/27/2023] [Accepted: 02/15/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND The trophic strategy is one key principle to categorize microbial lifestyles, by broadly classifying microorganisms based on the combination of their preferred carbon sources, electron sources, and electron sinks. Recently, a novel trophic strategy, i.e., chemoorganoautotrophy-the utilization of organic carbon as energy source but inorganic carbon as sole carbon source-has been specifically proposed for anaerobic methane oxidizing archaea (ANME-1) and Bathyarchaeota subgroup 8 (Bathy-8). RESULTS To further explore chemoorganoautotrophy, we employed stable isotope probing (SIP) of nucleic acids (rRNA or DNA) using unlabeled organic carbon and 13C-labeled dissolved inorganic carbon (DIC), i.e., inverse stable isotope labeling, in combination with metagenomics. We found that ANME-1 archaea actively incorporated 13C-DIC into RNA in the presence of methane and lepidocrocite when sulfate was absent, but assimilated organic carbon when cellulose was added to incubations without methane additions. Bathy-8 archaea assimilated 13C-DIC when lignin was amended; however, their DNA was derived from both inorganic and organic carbon sources rather than from inorganic carbon alone. Based on SIP results and supported by metagenomics, carbon transfer between catabolic and anabolic branches of metabolism is possible in these archaeal groups, indicating their anabolic versatility. CONCLUSION We provide evidence for the incorporation of the mixed organic and inorganic carbon by ANME-1 and Bathy-8 archaea in the environment. Video Abstract.
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Affiliation(s)
- Xiuran Yin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Renmin Ave. No.58, Haikou, 570228, China.
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany.
| | - Guowei Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Renmin Ave. No.58, Haikou, 570228, China
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
| | - Mingwei Cai
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
| | - Qing-Zeng Zhu
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
| | - Mara Maeke
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
| | - Ajinkya C Kulkarni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
| | - Rolf Nimzyk
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
| | - Marcus Elvert
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
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3
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Xie M, Zhang X, Li S, Maulani N, Cai F, Zheng Y, Cai C, Virdis B, Yuan Z, Hu S. Humic substances as electron acceptor for anaerobic oxidation of methane (AOM) and electron shuttle in Mn (IV)-dependent AOM. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169576. [PMID: 38145665 DOI: 10.1016/j.scitotenv.2023.169576] [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: 09/05/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 12/27/2023]
Abstract
Anaerobic methanotrophic archaea (ANME) belonging to the family Methanoperedenaceae are crucial for the global carbon cycle and different biogeochemical processes, owing to their metabolic versatility to couple anaerobic oxidation of methane (AOM) with different electron acceptors. A universal feature of Methanoperedenaceae is the abundant genes encoded in their genomes associated with extracellular electron transfer (EET) pathways. Candidatus. 'Methanoperedens manganicus', an archaeon belonging to the family Methanoperedenaceae, was recently enriched in a bioreactor performing AOM coupled with Mn (IV) reduction. Using this EET-capable ANME, we tested the hypothesis in this study that ANME can catalyse the humic-dependent AOM for growth. A two-year incubation showed that AOM activity can be sustained by Ca. 'M. manganicus' consortium in a bioreactor fed only with humic acids and methane. An isotopic mass balance batch test confirmed that the observed AOM was coupled to the reduction of humic acids. The increase of relative abundance of Ca. 'M. manganicus', and the total archaea population in the microbial community suggested that Ca. 'M. manganicus' can grow on methane and humic acids. The observation of humic-dependent AOM led to a subsequent hypothesis that humic acids could be used as the electron shuttle to mediate the EET in dissimilatory Mn (IV) reduction by Ca. 'M. manganicus'. We tested this hypothesis by adding humic acids to a Ca. 'M. manganicus' dominated-culture, which showed that the AOM rate was doubled by the addition of humic acids. X-ray photoelectron spectroscopy (XPS) showed that quinone moieties were consumed when humic acids worked as electron acceptors while remaining stable when functioning as a shuttle for electron transfer. The results of our study suggest that humic acids may serve as electron shuttles to allow ANME to access more electron acceptors through long-range EET.
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Affiliation(s)
- Mengying Xie
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Xueqin Zhang
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia.
| | - Shiqing Li
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Nova Maulani
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Fangrui Cai
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Chen Cai
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zhiguo Yuan
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
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Huang L, Parsons CT, Slowinski S, Van Cappellen P. Co-precipitation of iron and silicon: Reaction kinetics, elemental ratios and the influence of phosphorus. CHEMOSPHERE 2024; 349:140930. [PMID: 38101480 DOI: 10.1016/j.chemosphere.2023.140930] [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: 09/04/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
A sufficient supply of dissolved silicon (DSi) relative to dissolved phosphorus (DP) may decrease the likelihood of harmful algal blooms in eutrophic waters. Oxidative precipitation of Fe(II) at oxic-anoxic interfaces may contribute to the immobilization of DSi, thereby exerting control over the DSi availability in the overlying water. Nevertheless, the efficacy of DSi immobilization in this context remains to be precisely determined. To investigate the behavior of DSi during Fe(II) oxidation, anoxic solutions containing mixtures of aqueous Fe(II), DSi, and dissolved phosphorus (DP) were exposed to dissolved oxygen (DO) in the batch system. The experimental data, combined with kinetic reaction modeling, indicate that DSi removal during Fe(II) oxidation occurs via two pathways. At the beginning of the experiments, the oxidation of Fe(II)-DSi complexes induces the fast removal of DSi. Upon complete oxidation of Fe(II), further DSi removal is due to adsorption to surface sites of the Fe(III) oxyhydroxides. The presence of DP effectively competes with DSi via both of these pathways during the initial and later stages of the experiments, with as a result more limited removal of DSi during Fe(II) oxidation. Overall, we conclude that at near neutral pH the oxidation of Fe(II) has considerable capacity to immobilize DSi, where the rapid homogeneous oxidation of Fe(II)-DSi results in greater DSi removal compared to surface adsorption. Elevated DP concentration, however, effectively outcompetes DSi in co-precipitation interactions, potentially contributing to enhanced DSi availability within aquatic systems.
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Affiliation(s)
- Lu Huang
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, No. 18 Ruihe Road, Guangzhou, 510530, China; Ecohydrology Research Group, Department of Earth and Environmental Sciences and The Water Institute, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| | - Chris T Parsons
- Ecohydrology Research Group, Department of Earth and Environmental Sciences and The Water Institute, University of Waterloo, Waterloo, ON, N2L 3G1, Canada; Watershed Hydrology and Ecology Research Division, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington, Ontario, L7S 1A1, Canada
| | - Stephanie Slowinski
- Ecohydrology Research Group, Department of Earth and Environmental Sciences and The Water Institute, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Philippe Van Cappellen
- Ecohydrology Research Group, Department of Earth and Environmental Sciences and The Water Institute, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
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Yin X, Zhou G, Wang H, Han D, Maeke M, Richter-Heitmann T, Wunder LC, Aromokeye DA, Zhu QZ, Nimzyk R, Elvert M, Friedrich MW. Unexpected carbon utilization activity of sulfate-reducing microorganisms in temperate and permanently cold marine sediments. THE ISME JOURNAL 2024; 18:wrad014. [PMID: 38365251 PMCID: PMC10811731 DOI: 10.1093/ismejo/wrad014] [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: 11/10/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 02/18/2024]
Abstract
Significant amounts of organic carbon in marine sediments are degraded, coupled with sulfate reduction. However, the actual carbon and energy sources used in situ have not been assigned to each group of diverse sulfate-reducing microorganisms (SRM) owing to the microbial and environmental complexity in sediments. Here, we probed microbial activity in temperate and permanently cold marine sediments by using potential SRM substrates, organic fermentation products at very low concentrations (15-30 μM), with RNA-based stable isotope probing. Unexpectedly, SRM were involved only to a minor degree in organic fermentation product mineralization, whereas metal-reducing microbes were dominant. Contrastingly, distinct SRM strongly assimilated 13C-DIC (dissolved inorganic carbon) with H2 as the electron donor. Our study suggests that canonical SRM prefer autotrophic lifestyle, with hydrogen as the electron donor, while metal-reducing microorganisms are involved in heterotrophic organic matter turnover, and thus regulate carbon fluxes in an unexpected way in marine sediments.
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Affiliation(s)
- Xiuran Yin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - Guowei Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- School of Resources and Environmental Engineering, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China
| | - Haihua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- College of Urban and Environmental Sciences, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
| | - Dukki Han
- Department of Marine Bioscience, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung-si 25457, Republic of Korea
| | - Mara Maeke
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - Tim Richter-Heitmann
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Lea C Wunder
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - David A Aromokeye
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Qing-Zeng Zhu
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
| | - Rolf Nimzyk
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Marcus Elvert
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Strasse 2-4, Bremen D-28359, Germany
| | - Michael W Friedrich
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
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Fenibo EO, Selvarajan R, Wang H, Wang Y, Abia ALK. Untapped talents: insight into the ecological significance of methanotrophs and its prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166145. [PMID: 37579801 DOI: 10.1016/j.scitotenv.2023.166145] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/06/2023] [Accepted: 08/06/2023] [Indexed: 08/16/2023]
Abstract
The deep ocean is a rich reservoir of unique organisms with great potential for bioprospecting, ecosystem services, and the discovery of novel materials. These organisms thrive in harsh environments characterized by high hydrostatic pressure, low temperature, and limited nutrients. Hydrothermal vents and cold seeps, prominent features of the deep ocean, provide a habitat for microorganisms involved in the production and filtration of methane, a potent greenhouse gas. Methanotrophs, comprising archaea and bacteria, play a crucial role in these processes. This review examines the intricate relationship between the roles, responses, and niche specialization of methanotrophs in the deep ocean ecosystem. Our findings reveal that different types of methanotrophs dominate specific zones depending on prevailing conditions. Type I methanotrophs thrive in oxygen-rich zones, while Type II methanotrophs display adaptability to diverse conditions. Verrumicrobiota and NC10 flourish in hypoxic and extreme environments. In addition to their essential role in methane regulation, methanotrophs contribute to various ecosystem functions. They participate in the degradation of foreign compounds and play a crucial role in cycling biogeochemical elements like metals, sulfur, and nitrogen. Methanotrophs also serve as a significant energy source for the oceanic food chain and drive chemosynthesis in the deep ocean. Moreover, their presence offers promising prospects for biotechnological applications, including the production of valuable compounds such as polyhydroxyalkanoates, methanobactin, exopolysaccharides, ecotines, methanol, putrescine, and biofuels. In conclusion, this review highlights the multifaceted roles of methanotrophs in the deep ocean ecosystem, underscoring their ecological significance and their potential for advancements in biotechnology. A comprehensive understanding of their niche specialization and responses will contribute to harnessing their full potential in various domains.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Huiqi Wang
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China
| | - Yue Wang
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China
| | - Akebe Luther King Abia
- Environmental Research Foundation, Westville 3630, South Africa; Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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Köster M, Staubwasser M, Meixner A, Kasemann SA, Manners HR, Morono Y, Inagaki F, Heuer VB, Kasten S, Henkel S. Uniquely low stable iron isotopic signatures in deep marine sediments caused by Rayleigh distillation. Sci Rep 2023; 13:10281. [PMID: 37355766 DOI: 10.1038/s41598-023-37254-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/19/2023] [Indexed: 06/26/2023] Open
Abstract
Dissimilatory iron reduction (DIR) is suggested to be one of the earliest forms of microbial respiration. It plays an important role in the biogeochemical cycling of iron in modern and ancient sediments. Since microbial iron cycling is typically accompanied by iron isotope fractionation, stable iron isotopes are used as tracer for biological activity. Here we present iron isotope data for dissolved and sequentially extracted sedimentary iron pools from deep and hot subseafloor sediments retrieved in the Nankai Trough off Japan. Dissolved iron (Fe(II)aq) is isotopically light throughout the ferruginous sediment interval but some samples have exceptionally light isotope values. Such light values have never been reported in natural marine environments and cannot be solely attributed to DIR. We show that the light isotope values are best explained by a Rayleigh distillation model where Fe(II)aq is continuously removed from the pore water by adsorption onto iron (oxyhydr)oxide surfaces. While the microbially mediated Fe(II)aq release has ceased due to an increase in temperature beyond the threshold of mesophilic microorganisms, the abiotic adsorptive Fe(II)aq removal continued, leading to uniquely light isotope values. These findings have important implications for the interpretation of dissolved iron isotope data especially in deep subseafloor sediments.
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Affiliation(s)
- Male Köster
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- Faculty of Geosciences, University of Bremen, Bremen, Germany.
| | | | - Anette Meixner
- Faculty of Geosciences, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Simone A Kasemann
- Faculty of Geosciences, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Hayley R Manners
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Plymouth, UK
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Sciences and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Fumio Inagaki
- Institute for Marine-Earth Exploration and Engineering (MarE3), JAMSTEC, Yokohama, Japan
- Department of Earth Sciences, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Verena B Heuer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Sabine Kasten
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Susann Henkel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
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8
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Baloza M, Henkel S, Kasten S, Holtappels M, Molari M. The Impact of Sea Ice Cover on Microbial Communities in Antarctic Shelf Sediments. Microorganisms 2023; 11:1572. [PMID: 37375074 DOI: 10.3390/microorganisms11061572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/30/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The area around the Antarctic Peninsula (AP) is facing rapid climatic and environmental changes, with so far unknown impacts on the benthic microbial communities of the continental shelves. In this study, we investigated the impact of contrasting sea ice cover on microbial community compositions in surface sediments from five stations along the eastern shelf of the AP using 16S ribosomal RNA (rRNA) gene sequencing. Redox conditions in sediments with long ice-free periods are characterized by a prevailing ferruginous zone, whereas a comparatively broad upper oxic zone is present at the heavily ice-covered station. Low ice cover stations were highly dominated by microbial communities of Desulfobacterota (mostly Sva1033, Desulfobacteria, and Desulfobulbia), Myxococcota, and Sva0485, whereas Gammaproteobacteria, Alphaproteobacteria, Bacteroidota, and NB1-j prevail at the heavy ice cover station. In the ferruginous zone, Sva1033 was the dominant member of Desulfuromonadales for all stations and, along with eleven other taxa, showed significant positive correlations with dissolved Fe concentrations, suggesting a significant role in iron reduction or an ecological relationship with iron reducers. Our results indicate that sea ice cover and its effect on organic carbon fluxes are the major drivers for changes in benthic microbial communities, favoring potential iron reducers at stations with increased organic matter fluxes.
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Affiliation(s)
- Marwa Baloza
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Faculty 2 Biology/Chemistry, University of Bremen, Leobener Str., 28359 Bremen, Germany
| | - Susann Henkel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Sabine Kasten
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Str., 28359 Bremen, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Moritz Holtappels
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Massimiliano Molari
- HGF-MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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Zhang X, Zhang C, Liu Y, Zhang R, Li M. Non-negligible roles of archaea in coastal carbon biogeochemical cycling. Trends Microbiol 2022; 31:586-600. [PMID: 36567186 DOI: 10.1016/j.tim.2022.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 12/25/2022]
Abstract
Coastal zones are among the world's most productive ecosystems. They store vast amounts of organic carbon, as 'blue carbon' reservoirs, and impact global climate change. Archaeal communities are integral components of coastal microbiomes but their ecological roles are often overlooked. However, archaeal diversity, metabolism, evolution, and interactions, revealed by recent studies using rapidly developing cutting-edge technologies, place archaea as important players in coastal carbon biogeochemical cycling. We here summarize the latest advances in the understanding of archaeal carbon cycling processes in coastal ecosystems, specifically, archaeal involvement in CO2 fixation, organic biopolymer transformation, and methane metabolism. We also showcase the potential to use of archaeal communities to increase carbon sequestration and reduce methane production, with implications for mitigating climate change.
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Affiliation(s)
- Xinxu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Cuijing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Rui Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China.
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10
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Liang L, Vigderovich H, Sivan O, Hou J, Niu M, Yorshansky O, Zhang T, Bosco-Santos A, Wang F. Iron (oxyhydr)oxides shift the methanogenic community in deep sea methanic sediment - insights from long-term high-pressure incubations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157590. [PMID: 35901888 DOI: 10.1016/j.scitotenv.2022.157590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/03/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Intermittent increases of dissolved ferrous iron concentrations have been observed in deep marine methanic sediments which is different from the traditional diagenetic electron acceptor cascade, where iron reduction precedes methanogenesis. Here we aimed to gain insight into the mechanism of iron reduction and the associated microbial processes in deep sea methanic sediment by setting up long-term high-pressure incubation experiments supplemented with ferrihydrite and methane. Continuous iron reduction was observed during the entire incubation period. Intriguingly, ferrihydrite addition shifted the archaeal community from the dominance of hydrogenotrophic methanogens (Methanogenium) to methylotrophic methanogens (Methanococcoides). The enriched samples were then amended with 13C-labeled methane and different iron (oxyhydr)oxides in batch slurries to test the mechanism of iron reduction. Intensive iron reduction was observed, the highest rates with ferrihydrite, followed by hematite and then magnetite, however, no anaerobic oxidation of methane (AOM) was observed in any treatment. Further tests on the enriched slurry showed that the addition of molybdate decreased iron reduction, suggesting a link between iron reduction with sulfur cycling. This was accompanied by the enrichment of microbes capable of dissimilatory sulfate reduction and sulfur/thiosulfate oxidation, which indicates the presence of a cryptic sulfur cycle in the incubation system with the addition of iron (oxyhydr)oxides. Our work suggests that under low sulfate conditions, the presence of iron (oxyhydr)oxides would trigger a cascade of microbial reactions, and iron reduction could link with the microbial sulfur cycle, changing the kinetics of the methanogenesis process in methanic sediment.
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Affiliation(s)
- Lewen Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hanni Vigderovich
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Orit Sivan
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingyang Niu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Omer Yorshansky
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Taoliang Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Alice Bosco-Santos
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; Institute of Earth Surface Dynamics, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China.
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11
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Yin X, Zhou G, Cai M, Zhu QZ, Richter-Heitmann T, Aromokeye DA, Liu Y, Nimzyk R, Zheng Q, Tang X, Elvert M, Li M, Friedrich MW. Catabolic protein degradation in marine sediments confined to distinct archaea. THE ISME JOURNAL 2022; 16:1617-1626. [PMID: 35220398 PMCID: PMC9123169 DOI: 10.1038/s41396-022-01210-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/03/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022]
Abstract
Metagenomic analysis has facilitated prediction of a variety of carbon utilization potentials by uncultivated archaea including degradation of protein, which is a wide-spread carbon polymer in marine sediments. However, the activity of detrital catabolic protein degradation is mostly unknown for the vast majority of archaea. Here, we show actively executed protein catabolism in three archaeal phyla (uncultivated Thermoplasmata, SG8-5; Bathyarchaeota subgroup 15; Lokiarchaeota subgroup 2c) by RNA- and lipid-stable isotope probing in incubations with different marine sediments. However, highly abundant potential protein degraders Thermoprofundales (MBG-D) and Lokiarchaeota subgroup 3 were not incorporating 13C-label from protein during incubations. Nonetheless, we found that the pathway for protein utilization was present in metagenome associated genomes (MAGs) of active and inactive archaea. This finding was supported by screening extracellular peptidases in 180 archaeal MAGs, which appeared to be widespread but not correlated to organisms actively executing this process in our incubations. Thus, our results have important implications: (i) multiple low-abundant archaeal groups are actually catabolic protein degraders; (ii) the functional role of widespread extracellular peptidases is not an optimal tool to identify protein catabolism, and (iii) catabolic degradation of sedimentary protein is not a common feature of the abundant archaeal community in temperate and permanently cold marine sediments.
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Affiliation(s)
- Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany. .,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany. .,Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Guowei Zhou
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany. .,School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China.
| | - Mingwei Cai
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.,Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Qing-Zeng Zhu
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - David A Aromokeye
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Rolf Nimzyk
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Qingfei Zheng
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.,School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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12
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Chen Y, Xu C, Wu N, Sun Z, Liu C, Zhen Y, Xin Y, Zhang X, Geng W, Cao H, Zhai B, Li J, Qin S, Zhou Y. Diversity of Anaerobic Methane Oxidizers in the Cold Seep Sediments of the Okinawa Trough. Front Microbiol 2022; 13:819187. [PMID: 35495656 PMCID: PMC9048799 DOI: 10.3389/fmicb.2022.819187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Active cold seeps in the Okinawa Trough (OT) have been widely identified, but the sediment microbial communities associated with these sites are still poorly understood. Here, we investigated the distribution and biomass of the microbial communities, particularly those associated with the anaerobic oxidation of methane (AOM), in sediments from an active cold seep in the mid-Okinawa Trough. Methane-oxidizing archaea, including ANME-1a, ANME-1b, ANME-2a/b, ANME-2c, and ANME-3, were detected in the OT cold seep sediments. Vertical stratification of anaerobic methanotrophic archaea (ANME) communities was observed in the following order: ANME-3, ANME-1a, and ANME-1b. In addition, the abundance of methyl coenzyme M reductase A (mcrA) genes corresponded to high levels of dissolved iron, suggesting that methane-metabolizing archaea might participate in iron reduction coupled to methane oxidation (Fe-AOM) in the OT cold seep. Furthermore, the relative abundance of ANME-1a was strongly related to the concentration of dissolved iron, indicating that ANME-1a is a key microbial player for Fe-AOM in the OT cold seep sediments. Co-occurrence analysis revealed that methane-metabolizing microbial communities were mainly associated with heterotrophic microorganisms, such as JS1, Bathy-1, and Bathy-15.
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Affiliation(s)
- Ye Chen
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Cuiling Xu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Nengyou Wu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- *Correspondence: Nengyou Wu,
| | - Zhilei Sun
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Zhilei Sun,
| | - Changling Liu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu Zhen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Youzhi Xin
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xilin Zhang
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wei Geng
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hong Cao
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bin Zhai
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jing Li
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shuangshuang Qin
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Yucheng Zhou
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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13
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Wunder LC, Aromokeye DA, Yin X, Richter-Heitmann T, Willis-Poratti G, Schnakenberg A, Otersen C, Dohrmann I, Römer M, Bohrmann G, Kasten S, Friedrich MW. Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments. THE ISME JOURNAL 2021; 15:3587-3604. [PMID: 34155335 PMCID: PMC8630232 DOI: 10.1038/s41396-021-01014-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 11/30/2022]
Abstract
Permanently cold marine sediments are heavily influenced by increased input of iron as a result of accelerated glacial melt, weathering, and erosion. The impact of such environmental changes on microbial communities in coastal sediments is poorly understood. We investigated geochemical parameters that shape microbial community compositions in anoxic surface sediments of four geochemically differing sites (Annenkov Trough, Church Trough, Cumberland Bay, Drygalski Trough) around South Georgia, Southern Ocean. Sulfate reduction prevails in Church Trough and iron reduction at the other sites, correlating with differing local microbial communities. Within the order Desulfuromonadales, the family Sva1033, not previously recognized for being capable of dissimilatory iron reduction, was detected at rather high relative abundances (up to 5%) while other members of Desulfuromonadales were less abundant (<0.6%). We propose that Sva1033 is capable of performing dissimilatory iron reduction in sediment incubations based on RNA stable isotope probing. Sulfate reducers, who maintain a high relative abundance of up to 30% of bacterial 16S rRNA genes at the iron reduction sites, were also active during iron reduction in the incubations. Thus, concurrent sulfate reduction is possibly masked by cryptic sulfur cycling, i.e., reoxidation or precipitation of produced sulfide at a small or undetectable pool size. Our results show the importance of iron and sulfate reduction, indicated by ferrous iron and sulfide, as processes that shape microbial communities and provide evidence for one of Sva1033's metabolic capabilities in permanently cold marine sediments.
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Affiliation(s)
- Lea C Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - David A Aromokeye
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Graciana Willis-Poratti
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Instituto Antártico Argentino, Buenos Aires, Argentina
- Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Annika Schnakenberg
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carolin Otersen
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ingrid Dohrmann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Miriam Römer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Gerhard Bohrmann
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Sabine Kasten
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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14
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Zhang X, Yuan Z, Hu S. Anaerobic oxidation of methane mediated by microbial extracellular respiration. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:790-804. [PMID: 34523810 DOI: 10.1111/1758-2229.13008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic oxidation of methane (AOM) can be microbially mediated by the reduction of different terminal electron acceptors. AOM coupled to reduction of sulfate, manganese/iron oxides, humic substances, selenate, arsenic and other artificial extracellular electron acceptors are recognized as processes associated with microbial extracellular respiration. In these processes, methane-oxidizing archaea transfer electrons to external electron acceptors or to interdependent microbial species, which are mechanistically dependent on versatile extracellular electron transfer (EET) pathways. This review compiles recent progress in the research of electromicrobiology of AOM based on the catalogue of different electron acceptors. Naturally distributed and artificially constructed EET-mediated AOM is summarized, with the discussion of their environmental importance and application potentials. The diversity of responsible microorganisms involved in EET-mediated AOM is discussed with both methane-oxidizing archaea and their putative bacterial partners. More importantly, the review highlights progress and deficiencies in our understanding of EET pathways in EET-mediated AOM, raising open research questions for future research.
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Affiliation(s)
- Xueqin Zhang
- Advanced Water Management Centre, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Shihu Hu
- Advanced Water Management Centre, The University of Queensland, Brisbane, Qld, 4072, Australia
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15
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Merkel AY, Chernyh NA, Pimenov NV, Bonch-Osmolovskaya EA, Slobodkin AI. Diversity and Metabolic Potential of the Terrestrial Mud Volcano Microbial Community with a High Abundance of Archaea Mediating the Anaerobic Oxidation of Methane. Life (Basel) 2021; 11:life11090953. [PMID: 34575103 PMCID: PMC8470020 DOI: 10.3390/life11090953] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 12/26/2022] Open
Abstract
Terrestrial mud volcanoes (TMVs) are important natural sources of methane emission. The microorganisms inhabiting these environments remain largely unknown. We studied the phylogenetic composition and metabolic potential of the prokaryotic communities of TMVs located in the Taman Peninsula, Russia, using a metagenomic approach. One of the examined sites harbored a unique community with a high abundance of anaerobic methane-oxidizing archaea belonging to ANME-3 group (39% of all 16S rRNA gene reads). The high number of ANME-3 archaea was confirmed by qPCR, while the process of anaerobic methane oxidation was demonstrated by radioisotopic experiments. We recovered metagenome-assembled genomes (MAGs) of archaeal and bacterial community members and analyzed their metabolic capabilities. The ANME-3 MAG contained a complete set of genes for methanogenesis as well as of ribosomal RNA and did not encode proteins involved in dissimilatory nitrate or sulfate reduction. The presence of multiheme c-type cytochromes suggests that ANME-3 can couple methane oxidation with the reduction of metal oxides or with the interspecies electron transfer to a bacterial partner. The bacterial members of the community were mainly represented by autotrophic, nitrate-reducing, sulfur-oxidizing bacteria, as well as by fermentative microorganisms. This study extends the current knowledge of the phylogenetic and metabolic diversity of prokaryotes in TMVs and provides a first insight into the genomic features of ANME-3 archaea.
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16
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Schnakenberg A, Aromokeye DA, Kulkarni A, Maier L, Wunder LC, Richter-Heitmann T, Pape T, Ristova PP, Bühring SI, Dohrmann I, Bohrmann G, Kasten S, Friedrich MW. Electron Acceptor Availability Shapes Anaerobically Methane Oxidizing Archaea (ANME) Communities in South Georgia Sediments. Front Microbiol 2021; 12:617280. [PMID: 33935987 PMCID: PMC8081031 DOI: 10.3389/fmicb.2021.617280] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/11/2021] [Indexed: 11/24/2022] Open
Abstract
Anaerobic methane oxidizing archaea (ANME) mediate anaerobic oxidation of methane (AOM) in marine sediments and are therefore important for controlling atmospheric methane concentrations in the water column and ultimately the atmosphere. Numerous previous studies have revealed that AOM is coupled to the reduction of different electron acceptors such as sulfate, nitrate/nitrite or Fe(III)/Mn(IV). However, the influence of electron acceptor availability on the in situ ANME community composition in sediments remains largely unknown. Here, we investigated the electron acceptor availability and compared the microbial in situ communities of three methane-rich locations offshore the sub-Antarctic island South Georgia, by Illumina sequencing and qPCR of mcrA genes. The methanic zone (MZ) sediments of Royal Trough and Church Trough comprised high sulfide concentrations of up to 4 and 19 mM, respectively. In contrast, those of the Cumberland Bay fjord accounted for relatively high concentrations of dissolved iron (up to 186 μM). Whereas the ANME community in the sulfidic sites Church Trough and Royal Trough mainly comprised members of the ANME-1 clade, the order-level clade “ANME-1-related” (Lever and Teske, 2015) was most abundant in the iron-rich site in Cumberland Bay fjord, indicating that the availability of electron acceptors has a strong selective effect on the ANME community. This study shows that potential electron acceptors for methane oxidation may serve as environmental filters to select for the ANME community composition and adds to a better understanding of the global importance of AOM.
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Affiliation(s)
- Annika Schnakenberg
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,International Max Planck Research School of Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - David A Aromokeye
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Ajinkya Kulkarni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,International Max Planck Research School of Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Lisa Maier
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Lea C Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,International Max Planck Research School of Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Thomas Pape
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Petra Pop Ristova
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Solveig I Bühring
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Ingrid Dohrmann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Gerhard Bohrmann
- Faculty of Geosciences, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Sabine Kasten
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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17
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Aromokeye DA, Oni OE, Tebben J, Yin X, Richter-Heitmann T, Wendt J, Nimzyk R, Littmann S, Tienken D, Kulkarni AC, Henkel S, Hinrichs KU, Elvert M, Harder T, Kasten S, Friedrich MW. Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures. THE ISME JOURNAL 2021; 15:965-980. [PMID: 33154547 PMCID: PMC8115662 DOI: 10.1038/s41396-020-00824-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/09/2020] [Accepted: 10/22/2020] [Indexed: 01/29/2023]
Abstract
Elevated dissolved iron concentrations in the methanic zone are typical geochemical signatures of rapidly accumulating marine sediments. These sediments are often characterized by co-burial of iron oxides with recalcitrant aromatic organic matter of terrigenous origin. Thus far, iron oxides are predicted to either impede organic matter degradation, aiding its preservation, or identified to enhance organic carbon oxidation via direct electron transfer. Here, we investigated the effect of various iron oxide phases with differing crystallinity (magnetite, hematite, and lepidocrocite) during microbial degradation of the aromatic model compound benzoate in methanic sediments. In slurry incubations with magnetite or hematite, concurrent iron reduction, and methanogenesis were stimulated during accelerated benzoate degradation with methanogenesis as the dominant electron sink. In contrast, with lepidocrocite, benzoate degradation, and methanogenesis were inhibited. These observations were reproducible in sediment-free enrichments, even after five successive transfers. Genes involved in the complete degradation of benzoate were identified in multiple metagenome assembled genomes. Four previously unknown benzoate degraders of the genera Thermincola (Peptococcaceae, Firmicutes), Dethiobacter (Syntrophomonadaceae, Firmicutes), Deltaproteobacteria bacteria SG8_13 (Desulfosarcinaceae, Deltaproteobacteria), and Melioribacter (Melioribacteraceae, Chlorobi) were identified from the marine sediment-derived enrichments. Scanning electron microscopy (SEM) and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) images showed the ability of microorganisms to colonize and concurrently reduce magnetite likely stimulated by the observed methanogenic benzoate degradation. These findings explain the possible contribution of organoclastic reduction of iron oxides to the elevated dissolved Fe2+ pool typically observed in methanic zones of rapidly accumulating coastal and continental margin sediments.
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Affiliation(s)
- David A. Aromokeye
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Oluwatobi E. Oni
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Jan Tebben
- grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Xiuran Yin
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Tim Richter-Heitmann
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Jenny Wendt
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Rolf Nimzyk
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Sten Littmann
- grid.419529.20000 0004 0491 3210Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Daniela Tienken
- grid.419529.20000 0004 0491 3210Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ajinkya C. Kulkarni
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Susann Henkel
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Kai-Uwe Hinrichs
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Tilmann Harder
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Sabine Kasten
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W. Friedrich
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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18
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Dang CC, Xie GJ, Liu BF, Xing DF, Ding J, Ren NQ. Heavy metal reduction coupled to methane oxidation:Mechanisms, recent advances and future perspectives. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124076. [PMID: 33268204 DOI: 10.1016/j.jhazmat.2020.124076] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/08/2020] [Accepted: 09/21/2020] [Indexed: 06/12/2023]
Abstract
Methane emission has contributed greatly to the global warming and climate change, and the pollution of heavy metals is an important concern due to their toxicity and environmental persistence. Recently, multiple heavy metals have been demonstrated to be electron acceptors for methane oxidation, which offers a potential for simultaneous methane emission mitigation and heavy metal detoxification. This review provides a comprehensive discussion of heavy metals reduction coupled to methane oxidation, and identifies knowledge gaps and opportunities for future research. The functional microorganisms and possible mechanisms are detailed in groups under aerobic, hypoxic and anaerobic conditions. The potential application and major environmental significances for global methane mitigation, the elements cycle and heavy metals detoxification are also discussed. The future research opportunities are also discussed to provide insights for further research and efficient practical application.
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Affiliation(s)
- Cheng-Cheng Dang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - De-Feng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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19
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Yin X, Cai M, Liu Y, Zhou G, Richter-Heitmann T, Aromokeye DA, Kulkarni AC, Nimzyk R, Cullhed H, Zhou Z, Pan J, Yang Y, Gu JD, Elvert M, Li M, Friedrich MW. Subgroup level differences of physiological activities in marine Lokiarchaeota. THE ISME JOURNAL 2021; 15:848-861. [PMID: 33149207 PMCID: PMC8027215 DOI: 10.1038/s41396-020-00818-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 11/12/2022]
Abstract
Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus 'Prometheoarchaeum syntrophicum'. Here, we tracked the activity of Lokiarchaeota in incubations with Helgoland mud area sediments (North Sea) by stable isotope probing (SIP) with organic polymers, 13C-labelled inorganic carbon, fermentation intermediates and proteins. Within the active archaea, we detected members of the Lokiarchaeota class Loki-3, which appeared to mixotrophically participate in the degradation of lignin and humic acids while assimilating CO2, or heterotrophically used lactate. In contrast, members of the Lokiarchaeota class Loki-2 utilized protein and inorganic carbon, and degraded bacterial biomass formed in incubations. Metagenomic analysis revealed pathways for lactate degradation, and involvement in aromatic compound degradation in Loki-3, while the less globally distributed Loki-2 instead rely on protein degradation. We conclude that Lokiarchaeotal subgroups vary in their metabolic capabilities despite overlaps in their genomic equipment, and suggest that these subgroups occupy different ecologic niches in marine sediments.
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Affiliation(s)
- Xiuran Yin
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Mingwei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Guowei Zhou
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | | | - David A Aromokeye
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Ajinkya C Kulkarni
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Rolf Nimzyk
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Henrik Cullhed
- International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Zhichao Zhou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Marcus Elvert
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
| | - Michael W Friedrich
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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20
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Chen H, Xiao T, Ning Z, Li Q, Xiao E, Liu Y, Xiao Q, Lan X, Ma L, Lu F. In-situ remediation of acid mine drainage from abandoned coal mine by filed pilot-scale passive treatment system: Performance and response of microbial communities to low pH and elevated Fe. BIORESOURCE TECHNOLOGY 2020; 317:123985. [PMID: 32805482 DOI: 10.1016/j.biortech.2020.123985] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
A field pilot-scale passive treatment system was developed for in-situ bioremediation of acid mine drainage (AMD). The microbial community and its variation were analyzed. The data proved that 93.7% of total soluble Fe and 99% of soluble Fe(II) could be removed by the system. Principal coordinates analysis (PCoA) showed that a low pH and an elevated Fe concentration within the system created a unique microbial community that was dominated by acidophilic iron-oxidizing bacteria and iron-reducing bacteria. Canonical correlation analysis (CCA) indicated that the pH, iron content and total sulfur jointly determined the composition of the microbial communities. Species of Ferrovum, Delftia, Acinetobacter, Metallibacterium, Acidibacter and Acidiphilium were highly enriched, which promoted the removal of iron. Furthermore, the results revealed important data for the biogeochemical coupling of microbial communities and environmental parameters. These findings are beneficial for further application of in-situ field bioreactors to remediate AMD.
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Affiliation(s)
- Haiyan Chen
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tangfu Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China.
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Qian Li
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Enzong Xiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Yizhang Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Qingxiang Xiao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; School of Tourism Management, Guizhou University of Commerce, Guiyang 550014, China
| | - Xiaolong Lan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; School of Chemistry and Environmental Engineering, Hanshan Normal University, Chaozhou 521041, China
| | - Liang Ma
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanghai Lu
- School of Materials and Metallurgical Engineering, Guizhou Institute of Technology, Guiyang 550003, China
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21
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Li H, Yang Q, Zhou H. Niche Differentiation of Sulfate- and Iron-Dependent Anaerobic Methane Oxidation and Methylotrophic Methanogenesis in Deep Sea Methane Seeps. Front Microbiol 2020; 11:1409. [PMID: 32733397 PMCID: PMC7360803 DOI: 10.3389/fmicb.2020.01409] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/29/2020] [Indexed: 11/18/2022] Open
Abstract
Methane seeps are widespread seafloor ecosystems shaped by complex physicochemical-biological interactions over geological timescales, and seep microbiomes play a vital role in global biogeochemical cycling of key elements on Earth. However, the mechanisms underlying the coexistence of methane-cycling microbial communities remain largely elusive. Here, high-resolution sediment incubation experiments revealed a cryptic methane cycle in the South China Sea (SCS) methane seep ecosystem, showing the coexistence of sulfate (SO4 2-)- or iron (Fe)-dependent anaerobic oxidation of methane (AOM) and methylotrophic methanogenesis. This previously unrecognized methane cycling is not discernible from geochemical profiles due to high net methane consumption. High-throughput sequencing and Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) results suggested that anaerobic methane-oxidizing archaea (ANME)-2 and -3 coupled to sulfate-reducing bacteria (SRB) carried out SO4 2--AOM, and alternative ANME-2 and -3 solely or coupled to iron-reducing bacteria (IRB) might participate in Fe-AOM in sulfate-depleted environments. This finding suggested that ANME could alter AOM metabolic pathways according to geochemical changes. Furthermore, the majority of methylotrophic methanogens belonged to Methanimicrococcus, and hydrogenotrophic and acetoclastic methanogens were likely inhibited by sulfate or iron respiration. Fe-AOM and methylotrophic methanogenesis are overlooked potential sources and sinks of methane in methane seep ecosystems, thus influencing methane budgets and even the global carbon budget in the ocean.
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Affiliation(s)
| | - Qunhui Yang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Huaiyang Zhou
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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22
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Wang W, Tao J, Liu H, Li P, Chen S, Wang P, Zhang C. Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River Estuary. AMB Express 2020; 10:16. [PMID: 31970539 PMCID: PMC6975606 DOI: 10.1186/s13568-020-0950-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 01/06/2020] [Indexed: 01/27/2023] Open
Abstract
Microbial community structure and metabolic activities have profound impacts on biogeochemical processes in marine sediments. Functional bacteria such as nitrate- and sulfate-reducing bacteria respond to redox gradients by coupling specific reactions amenable to relevant energy metabolisms. However, similar functional patterns have not been observed for sedimentary archaea (except for anaerobic methanotrophs and methanogens). We coupled taxonomic composition with comprehensive geochemical species to investigate the participation of distinct bacteria and archaea in sedimentary geochemical cycles in a sediment core (300 cm) from Pearl River Estuary (PRE). Geochemical properties (NO3−, dissolved Mn and Fe, SO42+, NH4+; dissolved inorganic carbon (DIC), δ13CDIC, dissolved organic carbon (DOC), total organic carbon (TOC), δ13CTOC, and fluorescent dissolved organic matter (FDOM)) exhibited strong depth variability of different trends. Bacterial 16S rRNA- and dsrB gene abundance decreased sharply with depth while archaeal and bathyarchaeotal 16S rRNA gene copies were relatively constant. This resulted in an increase in relative abundance of archaea from surface (11.6%) to bottom (42.8%). Network analysis showed that bacterial groups of Desulfobacterales, Syntrophobacterales and Gammaproteobacteria were significantly (P < 0.0001) associated with SO42− and dissolved Mn while archaeal groups of Bathyarchaeota, Group C3 and Marine Benthic Group D (MBGD) showed close positive correlations (P < 0.0001) with NH4+, δ13CTOC values and humic-like FDOM. Our study suggested that these bacterial groups dominated in redox processes relevant to sulfate or metal oxides, while the archaeal groups are more like to degrade recalcitrant organic compounds in anaerobic sediments.
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23
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Aromokeye DA, Kulkarni AC, Elvert M, Wegener G, Henkel S, Coffinet S, Eickhorst T, Oni OE, Richter-Heitmann T, Schnakenberg A, Taubner H, Wunder L, Yin X, Zhu Q, Hinrichs KU, Kasten S, Friedrich MW. Rates and Microbial Players of Iron-Driven Anaerobic Oxidation of Methane in Methanic Marine Sediments. Front Microbiol 2020; 10:3041. [PMID: 32010098 PMCID: PMC6979488 DOI: 10.3389/fmicb.2019.03041] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/17/2019] [Indexed: 11/15/2022] Open
Abstract
The flux of methane, a potent greenhouse gas, from the seabed is largely controlled by anaerobic oxidation of methane (AOM) coupled to sulfate reduction (S-AOM) in the sulfate methane transition (SMT). S-AOM is estimated to oxidize 90% of the methane produced in marine sediments and is mediated by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria. An additional methane sink, i.e., iron oxide coupled AOM (Fe-AOM), has been suggested to be active in the methanic zone of marine sediments. Geochemical signatures below the SMT such as high dissolved iron, low to undetectable sulfate and high methane concentrations, together with the presence of iron oxides are taken as prerequisites for this process. So far, Fe-AOM has neither been proven in marine sediments nor have the governing key microorganisms been identified. Here, using a multidisciplinary approach, we show that Fe-AOM occurs in iron oxide-rich methanic sediments of the Helgoland Mud Area (North Sea). When sulfate reduction was inhibited, different iron oxides facilitated AOM in long-term sediment slurry incubations but manganese oxide did not. Especially magnetite triggered substantial Fe-AOM activity and caused an enrichment of ANME-2a archaea. Methane oxidation rates of 0.095 ± 0.03 nmol cm-3 d-1 attributable to Fe-AOM were obtained in short-term radiotracer experiments. The decoupling of AOM from sulfate reduction in the methanic zone further corroborated that AOM was iron oxide-driven below the SMT. Thus, our findings prove that Fe-AOM occurs in methanic marine sediments containing mineral-bound ferric iron and is a previously overlooked but likely important component in the global methane budget. This process has the potential to sustain microbial life in the deep biosphere.
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Affiliation(s)
- David A. Aromokeye
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Ajinkya C. Kulkarni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- International Max Planck Research School of Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marcus Elvert
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Gunter Wegener
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Susann Henkel
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Sarah Coffinet
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Thilo Eickhorst
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Oluwatobi E. Oni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Annika Schnakenberg
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- International Max Planck Research School of Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Heidi Taubner
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Lea Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Qingzeng Zhu
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Sabine Kasten
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM – Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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24
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Yin X, Wu W, Maeke M, Richter-Heitmann T, Kulkarni AC, Oni OE, Wendt J, Elvert M, Friedrich MW. CO 2 conversion to methane and biomass in obligate methylotrophic methanogens in marine sediments. ISME JOURNAL 2019; 13:2107-2119. [PMID: 31040382 PMCID: PMC6775961 DOI: 10.1038/s41396-019-0425-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/04/2019] [Accepted: 04/13/2019] [Indexed: 11/24/2022]
Abstract
Methyl substrates are important compounds for methanogenesis in marine sediments but diversity and carbon utilization by methylotrophic methanogenic archaea have not been clarified. Here, we demonstrate that RNA-stable isotope probing (SIP) requires 13C-labeled bicarbonate as co-substrate for identification of methylotrophic methanogens in sediment samples of the Helgoland mud area, North Sea. Using lipid-SIP, we found that methylotrophic methanogens incorporate 60–86% of dissolved inorganic carbon (DIC) into lipids, and thus considerably more than what can be predicted from known metabolic pathways (~40% contribution). In slurry experiments amended with the marine methylotroph Methanococcoides methylutens, up to 12% of methane was produced from CO2, indicating that CO2-dependent methanogenesis is an alternative methanogenic pathway and suggesting that obligate methylotrophic methanogens grow in fact mixotrophically on methyl compounds and DIC. Although methane formation from methanol is the primary pathway of methanogenesis, the observed high DIC incorporation into lipids is likely linked to CO2-dependent methanogenesis, which was triggered when methane production rates were low. Since methylotrophic methanogenesis rates are much lower in marine sediments than under optimal conditions in pure culture, CO2 conversion to methane is an important but previously overlooked methanogenic process in sediments for methylotrophic methanogens.
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Affiliation(s)
- Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Weichao Wu
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,Department of Geosciences, University of Bremen, Bremen, Germany.,Department of Biogeochemistry of Agroecosystems, University of Goettingen, Goettingen, Germany
| | - Mara Maeke
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ajinkya C Kulkarni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Oluwatobi E Oni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM - Center for Marine Environmental Sciences, Bremen, Germany
| | - Jenny Wendt
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,Department of Geosciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, Bremen, Germany.,Department of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany. .,MARUM - Center for Marine Environmental Sciences, Bremen, Germany.
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25
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Yan Z, Hao Z, Wu H, Jiang H, Yang M, Wang C. Co-occurrence patterns of the microbial community in polycyclic aromatic hydrocarbon-contaminated riverine sediments. JOURNAL OF HAZARDOUS MATERIALS 2019; 367:99-108. [PMID: 30594728 DOI: 10.1016/j.jhazmat.2018.12.071] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/16/2018] [Accepted: 12/19/2018] [Indexed: 06/09/2023]
Abstract
Understanding environmental and spatial gradient influences on sediment microbial communities, especially the communities of highly contaminated subsurface sediments, has received great attention with respect to natural attenuation and bioremediation. Here, we investigated the spatial variation and the co-occurrence patterns of microbial communities in polycyclic aromatic hydrocarbon (PAH)-contaminated riverine sediments by using spatial-series 16S rRNA gene data. The results showed that species from the surface and subsurface sediment samples tended to show greater co-occurrence patterns and facilitative interactions in the sediment microbial community as environmental severity increased. Microorganisms in the heavier PAH-contaminated sediment have stronger relationships and are more centrally clustered within the network compared to microorganisms in the lower PAH-contaminated sediment. The core communities harbored the keystone species (Dechloromonas, Crenothrix, Desulfuromonadales, Xanthomonadales, Anaerolineaceae and Dehalococcoidales), which responded to changes in the environmental and spatial gradients. The sediment PAH concentrations, ferrous iron and vertical distance were identified as the main drivers in determining the bacterial community assembly. The keystone species were linked to PAHs biodegradation coupled with iron cycling in sediments and could orchestrate core communities to perform ecosystem processes. Overall, these findings provide new insight into microbial community assembly and contribute to harnessing their functions in ecosystems for bioremediation.
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Affiliation(s)
- Zaisheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zheng Hao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, China
| | - Huifang Wu
- College of Urban Construction, Nanjing University of Technology, Nanjing, 211816, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Mingzhong Yang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; College of Urban Construction, Nanjing University of Technology, Nanjing, 211816, China
| | - Changhui Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
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26
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Banos S, Lentendu G, Kopf A, Wubet T, Glöckner FO, Reich M. A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms. BMC Microbiol 2018; 18:190. [PMID: 30458701 PMCID: PMC6247509 DOI: 10.1186/s12866-018-1331-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several fungi-specific primers target the 18S rRNA gene sequence, one of the prominent markers for fungal classification. The design of most primers goes back to the last decades. Since then, the number of sequences in public databases increased leading to the discovery of new fungal groups and changes in fungal taxonomy. However, no reevaluation of primers was carried out and relevant information on most primers is missing. With this study, we aimed to develop an 18S rRNA gene sequence primer toolkit allowing an easy selection of the best primer pair appropriate for different sequencing platforms, research aims (biodiversity assessment versus isolate classification) and target groups. RESULTS We performed an intensive literature research, reshuffled existing primers into new pairs, designed new Illumina-primers, and annealing blocking oligonucleotides. A final number of 439 primer pairs were subjected to in silico PCRs. Best primer pairs were selected and experimentally tested. The most promising primer pair with a small amplicon size, nu-SSU-1333-5'/nu-SSU-1647-3' (FF390/FR-1), was successful in describing fungal communities by Illumina sequencing. Results were confirmed by a simultaneous metagenomics and eukaryote-specific primer approach. Co-amplification occurred in all sample types but was effectively reduced by blocking oligonucleotides. CONCLUSIONS The compiled data revealed the presence of an enormous diversity of fungal 18S rRNA gene primer pairs in terms of fungal coverage, phylum spectrum and co-amplification. Therefore, the primer pair has to be carefully selected to fulfill the requirements of the individual research projects. The presented primer toolkit offers comprehensive lists of 164 primers, 439 primer combinations, 4 blocking oligonucleotides, and top primer pairs holding all relevant information including primer's characteristics and performance to facilitate primer pair selection.
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Affiliation(s)
- Stefanos Banos
- Molecular Ecology, Institute of Ecology, FB02, University of Bremen, Leobener Str. 2, 28359, Bremen, Germany
| | - Guillaume Lentendu
- Department of Soil Ecology, Helmholtz Centre for Environmental Research GmbH - UFZ, Halle-Saale, Germany.,Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Anna Kopf
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental Research GmbH - UFZ, Halle-Saale, Germany.,Present address: Department of Community Ecology, Helmholtz Centre for Environmental Research GmbH - UFZ, Halle-Saale, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Frank Oliver Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany
| | - Marlis Reich
- Molecular Ecology, Institute of Ecology, FB02, University of Bremen, Leobener Str. 2, 28359, Bremen, Germany.
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27
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Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland. GEOSCIENCES 2018. [DOI: 10.3390/geosciences8110399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Crystalline bedrock has been chosen for deep geologic long-term storage of used nuclear fuel in Finland. The risks generated by the deep subsurface microbial communities in these disposal sites need to be well characterised in advance to ensure safety. Deep subsurface microbial communities in a steady state are unlikely to contribute to known risk factors, such as corrosion or gas production. However, the construction of the geological final-disposal facility, bedrock disturbances, and hydraulic gradients cause changes that affect the microbial steady-state. To study the induced metabolism of deep microbial communities in changing environmental conditions, the activating effect of different electron donors and acceptors were measured with redox sensing fluorescent dyes (5-Cyano-2,3-ditolyl tetrazolium chloride, CTC and RedoxSensor™ Green, RSG). Fluids originating from two different fracture zones of the Finnish disposal site in Olkiluoto were studied. These fracture fluids were very dissimilar both chemically and in terms of bacterial and archaeal diversity. However, the microbial communities of both fracture fluids were activated, especially with acetate, which indicates the important role of acetate as a preferred electron donor for Olkiluoto deep subsurface communities.
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28
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Aromokeye DA, Richter-Heitmann T, Oni OE, Kulkarni A, Yin X, Kasten S, Friedrich MW. Temperature Controls Crystalline Iron Oxide Utilization by Microbial Communities in Methanic Ferruginous Marine Sediment Incubations. Front Microbiol 2018; 9:2574. [PMID: 30425692 PMCID: PMC6218420 DOI: 10.3389/fmicb.2018.02574] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/09/2018] [Indexed: 11/13/2022] Open
Abstract
Microorganisms can use crystalline iron minerals for iron reduction linked to organic matter degradation or as conduits for direct interspecies electron transfer (mDIET) to syntrophic partners, e.g., methanogens. The environmental conditions that lead either to reduction or conduit use are so far unknown. We investigated microbial community shifts and interactions with crystalline iron minerals (hematite and magnetite) in methanic ferruginous marine sediment incubations during organic matter (glucose) degradation at varying temperatures. Iron reduction rates increased with decreasing temperature from 30°C to 4°C. Both hematite and magnetite facilitated iron reduction at 4°C, demonstrating that microorganisms in the methanic zone of marine sediments can reduce crystalline iron oxides under psychrophilic conditions. Methanogenesis occurred, however, at higher rates with increasing temperature. At 30°C, both hematite and magnetite accelerated methanogenesis onset and maximum process rates. At lower temperatures (10°C and 4°C), hematite could still facilitate methanogenesis but magnetite served more as an electron acceptor for iron reduction than as a conduit. Different temperatures selected for different key microorganisms: at 30°C, members of genus Orenia, Halobacteroidaceae, at 10°C, Photobacterium and the order Clostridiales, and at 4°C Photobacterium and Psychromonas were enriched. Members of the order Desulfuromonadales harboring known dissimilatory iron reducers were also enriched at all temperatures. Our results show that crystalline iron oxides predominant in some natural environments can facilitate electron transfer between microbial communities at psychrophilic temperatures. Furthermore, temperature has a critical role in determining the pathway of crystalline iron oxide utilization in marine sediment shifting from conduction at 30°C to predominantly iron reduction at lower temperatures.
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Affiliation(s)
- David A Aromokeye
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,International Max Planck Research School for Marine Microbiology, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Oluwatobi E Oni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Ajinkya Kulkarni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,International Max Planck Research School for Marine Microbiology, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,International Max Planck Research School for Marine Microbiology, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Sabine Kasten
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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29
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Wang Y, Li P, Jiang Z, Liu H, Wei D, Wang H, Wang Y. Diversity and abundance of arsenic methylating microorganisms in high arsenic groundwater from Hetao Plain of Inner Mongolia, China. ECOTOXICOLOGY (LONDON, ENGLAND) 2018; 27:1047-1057. [PMID: 29951795 DOI: 10.1007/s10646-018-1958-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Abstract
Arsenic methylation is regarded as an effective way of arsenic detoxification. Current knowledge about arsenic biomethylation in high arsenic groundwater remains limited. In the present study, 16 high arsenic groundwater samples from deep wells of the Hetao Plain were investigated using clone library and quantitative polymerase chain reaction (qPCR) analyses of arsM genes as well as geochemical analysis. The concentrations of methylated arsenic (including monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA)) varied from 2.40 to 16.85 μg/L. Both bacterial and archaeal arsenic methylating populations were detected in the high arsenic aquifer. They were dominated by Proteobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Methanomicrobia and a large unidentified group. The abundances of predominant populations were correlated positively to either total organic carbon or total arsenic and arsenite concentrations. The arsM gene abundances in high arsenic groundwater ranged from below detection to 5.71 × 106 copies/L and accounted for 0-3.32‰ of total bacterial and archaeal 16S rRNA genes. The arsM gene copies in high arsenic groundwater showed closely positive correlations with methylated arsenic concentrations. The overall results implied that arsenic methylating microorganisms were abundant and diverse in high arsenic groundwater. This was the first study of arsenic methylating microbial communities in high arsenic groundwater aquifers and might provide useful information for arsenic bioremediation in groundwater systems.
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Affiliation(s)
- Yanhong Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Ping Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.
| | - Zhou Jiang
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Han Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Dazhun Wei
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Helin Wang
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Yanxin Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.
- School of Environmental Studies, China University of Geosciences, Wuhan, China.
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30
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Ren G, Ma A, Zhang Y, Deng Y, Zheng G, Zhuang X, Zhuang G, Fortin D. Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes. Environ Microbiol 2018; 20:2370-2385. [DOI: 10.1111/1462-2920.14128] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/02/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Ge Ren
- Research Center for Eco‐Environmental Sciences, Chinese Academy of SciencesBeijing 100085 China
- University of Chinese Academy of SciencesBeijing 100049 China
| | - Anzhou Ma
- Research Center for Eco‐Environmental Sciences, Chinese Academy of SciencesBeijing 100085 China
- University of Chinese Academy of SciencesBeijing 100049 China
- University of California, Los Angeles (UCLA)Los Angeles CA 90095 USA
| | - Yanfen Zhang
- Research Center for Eco‐Environmental Sciences, Chinese Academy of SciencesBeijing 100085 China
- University of Chinese Academy of SciencesBeijing 100049 China
| | - Ye Deng
- Research Center for Eco‐Environmental Sciences, Chinese Academy of SciencesBeijing 100085 China
| | - Guodong Zheng
- Institute of Geology and Geophysics, Chinese Academy of SciencesBeijing 100029 China
| | - Xuliang Zhuang
- Research Center for Eco‐Environmental Sciences, Chinese Academy of SciencesBeijing 100085 China
- University of Chinese Academy of SciencesBeijing 100049 China
| | - Guoqiang Zhuang
- Research Center for Eco‐Environmental Sciences, Chinese Academy of SciencesBeijing 100085 China
- University of Chinese Academy of SciencesBeijing 100049 China
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31
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Winkel M, Mitzscherling J, Overduin PP, Horn F, Winterfeld M, Rijkers R, Grigoriev MN, Knoblauch C, Mangelsdorf K, Wagner D, Liebner S. Anaerobic methanotrophic communities thrive in deep submarine permafrost. Sci Rep 2018; 8:1291. [PMID: 29358665 PMCID: PMC5778128 DOI: 10.1038/s41598-018-19505-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/22/2017] [Indexed: 11/09/2022] Open
Abstract
Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in anaerobic oxidation of methane (AOM) we found a large diversity of archaea mainly belonging to Bathyarchaeota, Thaumarchaeota, and Euryarchaeota. Methane concentrations and δ13C-methane signatures distinguish horizons of potential AOM coupled either to sulfate reduction in a sulfate-methane transition zone (SMTZ) or to the reduction of other electron acceptors, such as iron, manganese or nitrate. Analysis of functional marker genes (mcrA) and fluorescence in situ hybridization (FISH) corroborate potential activity of AOM communities in submarine permafrost sediments at low temperatures. Modeled potential AOM consumes 72-100% of submarine permafrost methane and up to 1.2 Tg of carbon per year for the total expected area of submarine permafrost. This is comparable with AOM habitats such as cold seeps. We thus propose that AOM is active where submarine permafrost thaws, which should be included in global methane budgets.
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Affiliation(s)
- Matthias Winkel
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany.
| | - Julia Mitzscherling
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Pier P Overduin
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Periglacial Research, 14473, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Maria Winterfeld
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Marine Geochemistry, 27570, Bremerhaven, Germany
| | - Ruud Rijkers
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | | | | | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic Geochemistry, 14473, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473, Potsdam, Germany
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32
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He Z, Zhang Q, Feng Y, Luo H, Pan X, Gadd GM. Microbiological and environmental significance of metal-dependent anaerobic oxidation of methane. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 610-611:759-768. [PMID: 28830047 DOI: 10.1016/j.scitotenv.2017.08.140] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/22/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic oxidation of methane (AOM) can be coupled to the reduction of sulfate, nitrate and nitrite, which effectively reduces methane emission into the atmosphere. Recently, metal-dependent AOM (metal-AOM, AOM coupled to metal reduction) was demonstrated to occur in both environmental samples and enrichment cultures. Anaerobic methanotrophs are capable of respiration using Fe(III) or Mn(IV), whether they are in the form of soluble metal species or insoluble minerals. Given the wide distribution of Fe(III)/Mn(IV)-bearing minerals in aquatic methane-rich environments, metal-AOM is considered to be globally important, although it has generally been overlooked in previous studies. In this article, we discuss the discovery of this process, the microorganisms and mechanisms involved, environmental significance and factors influencing metal-AOM. Since metal-AOM is poorly studied to date, some discussion is included on the present understanding of sulfate- and nitrate-AOM and traditional metal reduction processes using organic substrates or hydrogen as electron donors. Metal-AOM is a relatively new research field, and therefore more studies are needed to fully characterize the process. This review summarizes current studies and discusses the many unanswered questions, which should be useful for future research in this field.
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Affiliation(s)
- Zhanfei He
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Qingying Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yudong Feng
- College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Hongwei Luo
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China
| | - Xiangliang Pan
- College of Environment, Zhejiang University of Technology, Hangzhou, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, Zhejiang University of Technology, Hangzhou, China.
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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33
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Xia X, Guo W, Liu H. Basin Scale Variation on the Composition and Diversity of Archaea in the Pacific Ocean. Front Microbiol 2017; 8:2057. [PMID: 29109713 PMCID: PMC5660102 DOI: 10.3389/fmicb.2017.02057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/06/2017] [Indexed: 01/09/2023] Open
Abstract
The Archaea are a widely distributed group of prokaryotes that inhabit and thrive in many different environments. In the sea, they play key roles in various global biogeochemical processes. Here, in order to investigate the vertical profiles of archaeal community across a large geographic distance, the compositions of archaeal communities in seven seawater columns in the Pacific Ocean were investigated using high throughput 454 pyrosequencing of the 16S rRNA gene. The surface archaeal communities showed lower diversity and greater variability than those in the deeper layers. Two of the major archaeal phyla that displayed different depth preferences were Thaumarchaeota and Euryarchaeota. The majority of Thaumarchaeota belonged to Marine Group I (MGI), which had high relative abundance in deep water. In contrast, Euryarchaeota, which mainly consisted of Marine Group II (MGII) and III (MGIII), were dominant in the surface layer. Compared with MGI and MGII, MGIII were less abundant in seawater and generally absent from the surface water of the subarctic Pacific. In addition, niche separation in the MGI, MGII, and MGIII subgroups was also observed. For example, MGI.C and MGII.A (the major subgroups of MGI and MGII, respectively) displayed a strong negative correlation with each other. The highest level of archaeal diversity was found in the core of an oxygen minimum zone (OMZ) located off Costa Rica, which resulted from the co-occurrence of both anaerobic and aerobic archaea. For example, methanotrophic archaea ANME-2, methanogenic archaea and several sediment origin archaea, such as Marine Benthic Group A (MBGA) and Bathyarchaeota, were all detected at relatively high abundance in the OMZ. Together, our findings indicate that vertical heterogeneities along water columns and latitudinal differentiation in the surface waters are ubiquitous features of archaeal communities in the Pacific Ocean, and the OMZ off Costa Rica is an archaeal biodiversity hot-spot.
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Affiliation(s)
| | | | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong
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34
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Bhattarai S, Cassarini C, Gonzalez-Gil G, Egger M, Slomp CP, Zhang Y, Esposito G, Lens PNL. Anaerobic Methane-Oxidizing Microbial Community in a Coastal Marine Sediment: Anaerobic Methanotrophy Dominated by ANME-3. MICROBIAL ECOLOGY 2017; 74:608-622. [PMID: 28389729 DOI: 10.1007/s00248-017-0978-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 03/28/2017] [Indexed: 06/07/2023]
Abstract
The microbial community inhabiting the shallow sulfate-methane transition zone in coastal sediments from marine Lake Grevelingen (The Netherlands) was characterized, and the ability of the microorganisms to carry out anaerobic oxidation of methane coupled to sulfate reduction was assessed in activity tests. In vitro activity tests of the sediment with methane and sulfate demonstrated sulfide production coupled to the simultaneous consumption of sulfate and methane at approximately equimolar ratios over a period of 150 days. The maximum sulfate reduction rate was 5 μmol sulfate per gram dry weight per day during the incubation period. Diverse archaeal and bacterial clades were retrieved from the sediment with the majority of them clustered with Euryarchaeota, Thaumarcheota, Bacteroidetes, and Proteobacteria. The 16S rRNA gene sequence analysis showed that the sediment from marine Lake Grevelingen contained anaerobic methanotrophic Archaea (ANME) and methanogens as archaeal clades with a role in the methane cycling. ANME at the studied site mainly belong to the ANME-3 clade. This study provides one of the few reports for the presence of ANME-3 in a shallow coastal sediment. Sulfate-reducing bacteria from Desulfobulbus clades were found among the sulfate reducers, however, with very low relative abundance. Desulfobulbus has previously been commonly found associated with ANME, whereas in our study, ANME-3 and Desulfobulbus were not observed simultaneously in clusters, suggesting the possibility of independent AOM by ANME-3.
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Affiliation(s)
- Susma Bhattarai
- UNESCO-IHE, Westvest-7, P.O. Box 3015, Delft, 2601, DA, The Netherlands.
| | - Chiara Cassarini
- UNESCO-IHE, Westvest-7, P.O. Box 3015, Delft, 2601, DA, The Netherlands
| | | | - Matthias Egger
- Department of Earth Sciences - Geochemistry, Faculty of Geosciences, Utrecht University, P.O. Box 80021, 3508 TA, Utrecht, The Netherlands
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000, Aarhus, Denmark
| | - Caroline P Slomp
- Department of Earth Sciences - Geochemistry, Faculty of Geosciences, Utrecht University, P.O. Box 80021, 3508 TA, Utrecht, The Netherlands
| | - Yu Zhang
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Dongchuan Rd. 800, Shanghai, 200240, People's Republic of China
| | - Giovanni Esposito
- Department of Civil and Mechanical Engineering, University of Cassino and Southern Lazio, via Di Biasio 43, 03043, Cassino, FR, Italy
| | - Piet N L Lens
- UNESCO-IHE, Westvest-7, P.O. Box 3015, Delft, 2601, DA, The Netherlands
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35
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Hoshino T, Toki T, Ijiri A, Morono Y, Machiyama H, Ashi J, Okamura K, Inagaki F. Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes. Front Microbiol 2017; 8:1135. [PMID: 28676800 PMCID: PMC5476839 DOI: 10.3389/fmicb.2017.01135] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/06/2017] [Indexed: 11/23/2022] Open
Abstract
Submarine mud volcanoes (SMVs) are formed by muddy sediments and breccias extruded to the seafloor from a source in the deep subseafloor and are characterized by the discharge of methane and other hydrocarbon gasses and deep-sourced fluids into the overlying seawater. Although SMVs act as a natural pipeline connecting the Earth’s surface and subsurface biospheres, the dispersal of deep-biosphere microorganisms and their ecological roles remain largely unknown. In this study, we investigated the microbial communities in sediment and overlying seawater at two SMVs located on the Ryukyu Trench off Tanegashima Island, southern Japan. The microbial communities in mud volcano sediments were generally distinct from those in the overlying seawaters and in the well-stratified Pacific margin sediments collected at the Peru Margin, the Juan de Fuca Ridge flank off Oregon, and offshore of Shimokita Peninsula, northeastern Japan. Nevertheless, in-depth analysis of different taxonomic groups at the sub-species level revealed that the taxon affiliated with Atribacteria, heterotrophic anaerobic bacteria that typically occur in organic-rich anoxic subseafloor sediments, were commonly found not only in SMV sediments but also in the overlying seawater. We designed a new oligonucleotide probe for detecting Atribacteria using the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). CARD-FISH, digital PCR and sequencing analysis of 16S rRNA genes consistently showed that Atribacteria are abundant in the methane plumes of the two SMVs (0.58 and 1.5 × 104 cells/mL, respectively) but not in surrounding waters, suggesting that microbial cells in subseafloor sediments are dispersed as “deep-biosphere seeds” into the ocean. These findings may have important implications for the microbial transmigration between the deep subseafloor biosphere and the hydrosphere.
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Affiliation(s)
- Tatsuhiko Hoshino
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan
| | - Tomohiro Toki
- Faculty of Science, University of the RyukyusNishihara, Japan
| | - Akira Ijiri
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan
| | - Hideaki Machiyama
- Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan
| | - Juichiro Ashi
- Atmosphere and Ocean Research Institute, The University of TokyoTokyo, Japan
| | - Kei Okamura
- Department of Marine Resource Science, Faculty of Agriculture and Marine Science, Kochi UniversityNankoku, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan.,Research and Development Center for Submarine Resources, Japan Agency for Marine-Earth Science TechnologyNankoku, Japan.,Research and Development Center for Ocean Drilling Science, Japan Agency for Marine-Earth Science TechnologyYokohama, Japan
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36
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Weber HS, Habicht KS, Thamdrup B. Anaerobic Methanotrophic Archaea of the ANME-2d Cluster Are Active in a Low-sulfate, Iron-rich Freshwater Sediment. Front Microbiol 2017; 8:619. [PMID: 28446901 PMCID: PMC5389135 DOI: 10.3389/fmicb.2017.00619] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/27/2017] [Indexed: 12/04/2022] Open
Abstract
ANaerobic MEthanotrophic (ANME) archaea remove the greenhouse gas methane from anoxic environments and diminish its flux to the atmosphere. High methane removal efficiencies are well documented in marine environments, whereas anaerobic oxidation of methane (AOM) was only recently indicated as an important methane sink in freshwater systems. Freshwater AOM-mediating microorganisms lack taxonomic identification and only little is known about metabolic adaptions to prevailing biogeochemical conditions. One of the first study sites providing information about AOM activity in freshwater sediment is Lake Ørn, a low-sulfate, iron-rich Danish lake. With the aim to identify freshwater AOM-mediating archaea, we incubated AOM-active anoxic, nitrate-free freshwater sediment from Lake Ørn with 13C-labeled methane (13CCH4) and 13C-labeled bicarbonate (13CDIC) and followed the assimilation of 13C into RNA by stable isotope probing. While AOM was active, 13CCH4 and probably also 13CDIC were incorporated into uncultured archaea of the Methanosarcinales-related cluster ANME-2d, whereas other known ANME lineages were not detected. This finding strongly suggests that ANME-2d archaea perform AOM coupled to sulfate and/or iron reduction and may have the capability of mixed assimilation of CH4 and DIC. ANME-2d archaea may thus play an important role in controlling methane emissions from nitrate-depleted and low-sulfate freshwater systems.
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Affiliation(s)
- Hannah S Weber
- Nordic Center for Earth Evolution and Department of Biology, University of Southern DenmarkOdense, Denmark
| | - Kirsten S Habicht
- Nordic Center for Earth Evolution and Department of Biology, University of Southern DenmarkOdense, Denmark
| | - Bo Thamdrup
- Nordic Center for Earth Evolution and Department of Biology, University of Southern DenmarkOdense, Denmark
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Reverse Methanogenesis and Respiration in Methanotrophic Archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2017; 2017:1654237. [PMID: 28154498 PMCID: PMC5244752 DOI: 10.1155/2017/1654237] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/11/2016] [Accepted: 10/31/2016] [Indexed: 12/21/2022]
Abstract
Anaerobic oxidation of methane (AOM) is catalyzed by anaerobic methane-oxidizing archaea (ANME) via a reverse and modified methanogenesis pathway. Methanogens can also reverse the methanogenesis pathway to oxidize methane, but only during net methane production (i.e., “trace methane oxidation”). In turn, ANME can produce methane, but only during net methane oxidation (i.e., enzymatic back flux). Net AOM is exergonic when coupled to an external electron acceptor such as sulfate (ANME-1, ANME-2abc, and ANME-3), nitrate (ANME-2d), or metal (oxides). In this review, the reversibility of the methanogenesis pathway and essential differences between ANME and methanogens are described by combining published information with domain based (meta)genome comparison of archaeal methanotrophs and selected archaea. These differences include abundances and special structure of methyl coenzyme M reductase and of multiheme cytochromes and the presence of menaquinones or methanophenazines. ANME-2a and ANME-2d can use electron acceptors other than sulfate or nitrate for AOM, respectively. Environmental studies suggest that ANME-2d are also involved in sulfate-dependent AOM. ANME-1 seem to use a different mechanism for disposal of electrons and possibly are less versatile in electron acceptors use than ANME-2. Future research will shed light on the molecular basis of reversal of the methanogenic pathway and electron transfer in different ANME types.
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38
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Dörries M, Wöhlbrand L, Kube M, Reinhardt R, Rabus R. Genome and catabolic subproteomes of the marine, nutritionally versatile, sulfate-reducing bacterium Desulfococcus multivorans DSM 2059. BMC Genomics 2016; 17:918. [PMID: 27846794 PMCID: PMC5109826 DOI: 10.1186/s12864-016-3236-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sulfate-reducing bacteria (SRB) are key players of the carbon- and sulfur-cycles in the sediments of the world's oceans. Habitat relevant SRBs are often members of the Desulfosarcina-Desulfococcus clade belonging to the deltaproteobacterial family of Desulfobacteraceae. Despite this environmental recognition, their molecular (genome-based) physiology and their potential to contribute to organic carbon mineralization as well as to adapt to changing environmental conditions have been scarcely investigated. A metabolically versatile representative of this family is Desulfococcus multivorans that is able to completely oxidize (to CO2) a variety of organic acids, including fatty acids up to C14, as well as aromatic compounds. RESULTS In this study the complete 4.46 Mbp and manually annotated genome of metabolically versatile Desulfococcus multivorans DSM 2059 is presented with particular emphasis on a proteomics-driven metabolic reconstruction. Proteomic profiling covered 17 substrate adaptation conditions (6 aromatic and 11 aliphatic compounds) and comprised 2D DIGE, shotgun proteomics and analysis of the membrane protein-enriched fractions. This comprehensive proteogenomic dataset allowed for reconstructing a metabolic network of degradation pathways and energy metabolism that consists of 170 proteins (154 detected; ~91 % coverage). Peripheral degradation routes feed via central benzoyl-CoA, (modified) β-oxidation or methylmalonyl-CoA pathways into the Wood-Ljungdahl pathway for complete oxidation of acetyl-CoA to CO2. Dissimilatory sulfate reduction is fueled by a complex electron transfer network composed of cytoplasmic components (e.g., electron transfer flavoproteins) and diverse membrane redox complexes (Dsr, Qmo, Hmc, Tmc, Qrc, Nuo and Rnf). Overall, a high degree of substrate-specific formation of catabolic enzymes was observed, while most complexes involved in electron transfer appeared to be constitutively formed. CONCLUSIONS A highly dynamic genome structure in combination with substrate-specifically formed catabolic subproteomes and a constitutive subproteome for energy metabolism and electron transfer appears to be a common trait of Desulfobacteraceae members.
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Affiliation(s)
- Marvin Dörries
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Michael Kube
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, Waldsieversdorf, Germany
| | | | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Sun W, Xiao E, Krumins V, Dong Y, Xiao T, Ning Z, Chen H, Xiao Q. Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage. Appl Microbiol Biotechnol 2016; 100:8523-35. [PMID: 27277134 DOI: 10.1007/s00253-016-7653-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 05/23/2016] [Accepted: 05/26/2016] [Indexed: 01/09/2023]
Abstract
A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities, suggesting that the microbial communities are shaped by three major environmental parameters (i.e., Fe, pH, and TOC). These findings were beneficial to a better understanding of natural attenuation of AMD.
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Affiliation(s)
- Weimin Sun
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA.,Guangdong Institute of Eco-environment and Soil Sciences, Guangzhou, 510650, China
| | - Enzong Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Valdis Krumins
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Yiran Dong
- Department of Geology, University of Illinois-Urbana Champaign, Urbana, IL, 61801, USA
| | - Tangfu Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China. .,Innovation Center and Key Laboratory of Waters Safety & Protection in the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| | - Zengping Ning
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China
| | - Haiyan Chen
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingxiang Xiao
- State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences, 99 Lincheng Road West, Guiyang, 550081, Guizhou Province, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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40
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Zhao MY, Zheng YF, Zhao YY. Seeking a geochemical identifier for authigenic carbonate. Nat Commun 2016; 7:10885. [PMID: 26947562 PMCID: PMC4786675 DOI: 10.1038/ncomms10885] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 01/29/2016] [Indexed: 11/29/2022] Open
Abstract
Authigenic carbonate was recently invoked as a third major global carbon sink in addition to primary marine carbonate and organic carbon. Distinguishing the two carbonate sinks is fundamental to our understanding of Earth's carbon cycle and its role in regulating the evolution of atmospheric oxygen. Here, using microscale geochemical measurements of carbonates in Early Triassic strata, we show that the growth of authigenic carbonate follows a different trajectory from primary marine carbonate in a cross-plot of uranium concentration and carbon isotope composition. Thus, a combination of the two geochemical variables is able to distinguish between the two carbonate sinks. The temporal distribution of authigenic carbonates in the Early Triassic strata suggests that the increase in the extent of carbonate authigenesis acted as a negative feedback to the elevated atmospheric CO2 concentration. Distinguishing between authigenic carbonate and primary marine carbonate is fundamental to our understanding of Earth's carbon, oxygen and calcium cycles. Here, the authors show that a combination of uranium concentration and carbon isotope composition is able to distinguish between the two carbonate sinks.
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Affiliation(s)
- Ming-Yu Zhao
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yong-Fei Zheng
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yan-Yan Zhao
- CAS Key Laboratory of Crust-Mantle Materials and Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
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41
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Oni OE, Schmidt F, Miyatake T, Kasten S, Witt M, Hinrichs KU, Friedrich MW. Microbial Communities and Organic Matter Composition in Surface and Subsurface Sediments of the Helgoland Mud Area, North Sea. Front Microbiol 2015; 6:1290. [PMID: 26635758 PMCID: PMC4658423 DOI: 10.3389/fmicb.2015.01290] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/04/2015] [Indexed: 01/05/2023] Open
Abstract
The role of microorganisms in the cycling of sedimentary organic carbon is a crucial one. To better understand relationships between molecular composition of a potentially bioavailable fraction of organic matter and microbial populations, bacterial and archaeal communities were characterized using pyrosequencing-based 16S rRNA gene analysis in surface (top 30 cm) and subsurface/deeper sediments (30-530 cm) of the Helgoland mud area, North Sea. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) was used to characterize a potentially bioavailable organic matter fraction (hot-water extractable organic matter, WE-OM). Algal polymer-associated microbial populations such as members of the Gammaproteobacteria, Bacteroidetes, and Verrucomicrobia were dominant in surface sediments while members of the Chloroflexi (Dehalococcoidales and candidate order GIF9) and Miscellaneous Crenarchaeota Groups (MCG), both of which are linked to degradation of more recalcitrant, aromatic compounds and detrital proteins, were dominant in subsurface sediments. Microbial populations dominant in subsurface sediments (Chloroflexi, members of MCG, and Thermoplasmata) showed strong correlations to total organic carbon (TOC) content. Changes of WE-OM with sediment depth reveal molecular transformations from oxygen-rich [high oxygen to carbon (O/C), low hydrogen to carbon (H/C) ratios] aromatic compounds and highly unsaturated compounds toward compounds with lower O/C and higher H/C ratios. The observed molecular changes were most pronounced in organic compounds containing only CHO atoms. Our data thus, highlights classes of sedimentary organic compounds that may serve as microbial energy sources in methanic marine subsurface environments.
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Affiliation(s)
- Oluwatobi E Oni
- Department of Microbial Ecophysiology, University of Bremen Bremen, Germany ; MARUM-Center for Marine Environmental Sciences, University of Bremen Bremen, Germany ; International Max-Planck Research School for Marine Microbiology Bremen, Germany
| | - Frauke Schmidt
- MARUM-Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| | - Tetsuro Miyatake
- Department of Microbial Ecophysiology, University of Bremen Bremen, Germany
| | - Sabine Kasten
- MARUM-Center for Marine Environmental Sciences, University of Bremen Bremen, Germany ; Department of Marine Geochemistry, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven, Germany
| | | | - Kai-Uwe Hinrichs
- MARUM-Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
| | - Michael W Friedrich
- Department of Microbial Ecophysiology, University of Bremen Bremen, Germany ; MARUM-Center for Marine Environmental Sciences, University of Bremen Bremen, Germany
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