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Fu L, Liu Y, Wang M, Lian C, Cao L, Wang W, Sun Y, Wang N, Li C. The diversification and potential function of microbiome in sediment-water interface of methane seeps in South China Sea. Front Microbiol 2024; 15:1287147. [PMID: 38380093 PMCID: PMC10878133 DOI: 10.3389/fmicb.2024.1287147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/11/2024] [Indexed: 02/22/2024] Open
Abstract
The sediment-water interfaces of cold seeps play important roles in nutrient transportation between seafloor and deep-water column. Microorganisms are the key actors of biogeochemical processes in this interface. However, the knowledge of the microbiome in this interface are limited. Here we studied the microbial diversity and potential metabolic functions by 16S rRNA gene amplicon sequencing at sediment-water interface of two active cold seeps in the northern slope of South China Sea, Lingshui and Site F cold seeps. The microbial diversity and potential functions in the two cold seeps are obviously different. The microbial diversity of Lingshui interface areas, is found to be relatively low. Microbes associated with methane consumption are enriched, possibly due to the large and continuous eruptions of methane fluids. Methane consumption is mainly mediated by aerobic oxidation and denitrifying anaerobic methane oxidation (DAMO). The microbial diversity in Site F is higher than Lingshui. Fluids from seepage of Site F are mitigated by methanotrophic bacteria at the cyclical oxic-hypoxic fluctuating interface where intense redox cycling of carbon, sulfur, and nitrogen compounds occurs. The primary modes of microbial methane consumption are aerobic methane oxidation, along with DAMO, sulfate-dependent anaerobic methane oxidation (SAMO). To sum up, anaerobic oxidation of methane (AOM) may be underestimated in cold seep interface microenvironments. Our findings highlight the significance of AOM and interdependence between microorganisms and their environments in the interface microenvironments, providing insights into the biogeochemical processes that govern these unique ecological systems.
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Affiliation(s)
- Lulu Fu
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Yanjun Liu
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Minxiao Wang
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Chao Lian
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Lei Cao
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Weicheng Wang
- State Key Laboratory of Mariculture Breeding, Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Sun
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Nan Wang
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laoshan Laboratory, Qingdao, China
| | - Chaolun Li
- Center of Deep Sea Research and Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laoshan Laboratory, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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2
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Chen Q, Li Z, Chen Y, Liu M, Yang Q, Zhu B, Mu J, Feng L, Chen Z. Effects of electron acceptors and donors on anaerobic biodegradation of PAHs in marine sediments. MARINE POLLUTION BULLETIN 2024; 199:115925. [PMID: 38113802 DOI: 10.1016/j.marpolbul.2023.115925] [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: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 12/21/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are typical organic pollutants accumulated in the environment. PAHs' bioremediation in sediments can be promoted by adding electron acceptor (EA) and electron donor (ED). Bicarbonate and sulfate were chosen as two EAs, and acetate and lactate were selected as two EDs. Six groups of amendments were added into the sediments to access their role in the anaerobic biodegradation of five PAHs, containing phenanthrene, anthracene, fluoranthene, pyrene, and benzo[a]pyrene. The concentrations of PAHs, EAs and EDs, electron transport system activity, and microbial diversity were analyzed during 126-day biodegradation in serum bottles. The HA group (bicarbonate and acetate) achieved the maximum PAH degradation efficiency of 89.67 %, followed by the SL group (sulfate and lactate) with 87.10 %. As the main PAHs degrading bacteria, the abundance of Marinobacter in H group was 8.62 %, and the addition of acetate significantly increased the abundance of Marinobacter in the HA group by 75.65 %.
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Affiliation(s)
- Qingguo Chen
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Zhenzhen Li
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Yu Chen
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Mei Liu
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Qiao Yang
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Baikang Zhu
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Jun Mu
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya 572022, PR China.
| | - Lijuan Feng
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Zhi Chen
- Department of Building, Civil and Environmental Engineering, Faculty of Engineering & Computer Sciences, Concordia University, Montreal, Quebec H3G1M8, Canada
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Zhong S, Feng J, Kong J, Huang Y, Chen X, Zhang S. Differences in Bacterial Co-Occurrence Networks and Ecological Niches at the Surface Sediments and Bottom Seawater in the Haima Cold Seep. Microorganisms 2023; 11:3001. [PMID: 38138145 PMCID: PMC10745737 DOI: 10.3390/microorganisms11123001] [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: 10/18/2023] [Revised: 11/20/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Cold seeps are highly productive chemosynthetic ecosystems in the deep-sea environment. Although microbial communities affected by methane seepage have been extensively studied in sediments and seawater, there is a lack of investigation of prokaryotic communities at the surface sediments and bottom seawater. We revealed the effect of methane seepage on co-occurrence networks and ecological niches of prokaryotic communities at the surface sediments and bottom seawater in the Haima cold seep. The results showed that methane seepage could cause the migration of Mn and Ba from the surface sediments to the overlying seawater, altering the elemental distribution at seepage sites (IS) compared with non-seepage sites (NS). Principal component analysis (PCA) showed that methane seepage led to closer distances of bacterial communities between surface sediments and bottom seawater. Co-occurrence networks indicated that methane seepage led to more complex interconnections at the surface sediments and bottom seawater. In summary, methane seepage caused bacterial communities in the surface sediments and bottom seawater to become more abundant and structurally complex. This study provides a comprehensive comparison of microbial profiles at the surface sediments and bottom seawater of cold seeps in the South China Sea (SCS), illustrating the impact of seepage on bacterial community dynamics.
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Affiliation(s)
- Song Zhong
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China;
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
| | - Jingchun Feng
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China;
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jie Kong
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yongji Huang
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiao Chen
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Si Zhang
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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4
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Wang D, Li J, Su L, Shen W, Feng K, Peng X, Wang Z, Zhao B, Zhang Z, Zhang Z, Yergeau É, Deng Y. Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics. MICROBIOME 2023; 11:276. [PMID: 38102689 PMCID: PMC10722806 DOI: 10.1186/s40168-023-01723-7] [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: 08/15/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND Leakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. However, conventional metagenomic methods largely rely on reference databases and neglect the phylogeny of functional genes. RESULTS In this study, we developed the REMIRGE program to retrieve the full-length functional genes from shotgun metagenomic reads and fully explored the phylogenetic diversity in cold seep sediments. The abundance and diversity of functional genes involved in the methane, sulfur, and nitrogen cycles differed in the non-seep site and five cold seep sites. In one Haima cold seep site, the divergence of functional groups was observed at the centimeter scale of sediment depths, with the surface layer potentially acting as a reservoir of microbial species and functions. Additionally, positive correlations were found between specific gene sequence clusters of relevant genes, indicating coupling occurred within specific functional groups. CONCLUSION REMIRGE revealed divergent phylogenetic diversity of functional groups and functional pathway preferences in a deep-sea cold seep at finer scales, which could not be detected by conventional methods. Our work highlights that phylogenetic information is conducive to more comprehensive functional profiles, and REMIRGE has the potential to uncover more new insights from shotgun metagenomic data. Video Abstract.
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Affiliation(s)
- Danrui Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Wenli Shen
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi Peng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhujun Wang
- College of Tropical Crops, Hainan University, Haikou, 572000, China
| | - Bo Zhao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Étienne Yergeau
- Institut National de La Recherche Scientique, Centre Armand-Frappier Santé Biotechnologie, Laval, H7V 1B7, QC, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
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5
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Zhang T, He W, Liang Q, Zheng F, Xiao X, Zeng Z, Zhou J, Yao W, Chen H, Zhu Y, Zhao J, Zheng Y, Zhang C. Lipidomic diversity and proxy implications of archaea from cold seep sediments of the South China Sea. Front Microbiol 2023; 14:1241958. [PMID: 37954235 PMCID: PMC10635418 DOI: 10.3389/fmicb.2023.1241958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023] Open
Abstract
Cold seeps on the continental margins are characterized by intense microbial activities that consume a large portion of methane by anaerobic methanotrophic archaea (ANME) through anaerobic oxidation of methane (AOM). Although ANMEs are known to contain unique ether lipids that may have an important function in marine carbon cycling, their full lipidomic profiles and functional distribution in particular cold-seep settings are still poorly characterized. Here, we combined the 16S rRNA gene sequencing and lipidomic approaches to analyze archaeal communities and their lipids in cold seep sediments with distinct methane supplies from the South China Sea. The archaeal community was dominated by ANME-1 in the moderate seepage area with strong methane emission. Low seepage area presented higher archaeal diversity covering Lokiarchaeia, Bathyarchaeia, and Thermoplasmata. A total of 55 core lipids (CLs) and intact polar lipids (IPLs) of archaea were identified, which included glycerol dialkyl glycerol tetraethers (GDGTs), hydroxy-GDGTs (OH-GDGTs), archaeol (AR), hydroxyarchaeol (OH-AR), and dihydroxyarchaeol (2OH-AR). Diverse polar headgroups constituted the archaeal IPLs. High concentrations of dissolved inorganic carbon (DIC) with depleted δ13CDIC and high methane index (MI) values based on both CLs (MICL) and IPLs (MIIPL) indicate that ANMEs were active in the moderate seepage area. The ANME-2 and ANME-3 clades were characterized by enhanced glycosidic and phosphoric diether lipids production, indicating their potential role in coupling carbon and phosphurus cycling in cold seep ecosystems. ANME-1, though representing a smaller proportion of total archaea than ANME-2 and ANME-3 in the low seepage area, showed a positive correlation with MIIPL, indicating a different mechanism contributing to the IPL-GDGT pool. This also suggests that MIIPL could be a sensitive index to trace AOM activities performed by ANME-1. Overall, our study expands the understanding of the archaeal lipid composition in the cold seep and improves the application of MI using intact polar lipids that potentially link to extent ANME activities.
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Affiliation(s)
- Tingting Zhang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
- National Engineering Research Center of Gas Hydrate Exploration and Development, Guangzhou, China
- East China Sea Ecological Center, Ministry of Natural Resources, Shanghai, China
| | - Wei He
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Qianyong Liang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
- National Engineering Research Center of Gas Hydrate Exploration and Development, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fengfeng Zheng
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
- National Engineering Research Center of Gas Hydrate Exploration and Development, Guangzhou, China
| | - Zhiyu Zeng
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Jingzhuo Zhou
- Key Laboratory of Coal Processing and Efficient Utilization of Ministry of Education, School of Chemical Engineering and Technology, China University of Mining and Technology, Xuzhou, China
| | - Wenyong Yao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Haodong Chen
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
| | - Jing Zhao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Yan Zheng
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai, China
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6
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Huang Y, Feng JC, Kong J, Sun L, Zhang M, Huang Y, Tang L, Zhang S, Yang Z. Community assemblages and species coexistence of prokaryotes controlled by local environmental heterogeneity in a cold seep water column. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161725. [PMID: 36669671 DOI: 10.1016/j.scitotenv.2023.161725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
The distribution and heterogeneity characteristics of microbial communities in cold seep water columns are significant factors governing the efficiency of methane filtering and carbon turnover. However, this process is poorly understood. The diversity of vertically stratified microbial communities and the factors controlling the community assemblage process in the water column above the Haima cold seep were investigated in this study. The prokaryotic community diversities varied distinctly with vertical changes in hydrochemistry. Cyanobacteria dominated the light-transmitting layers and Proteobacteria dominated the deeper layers. With respect to microbial community assemblages and co-occurrence networks, stochastic processes were particularly important in shaping prokaryotic communities. In the shallow (≥85 m) and mesopelagic water columns (600-800 m), microbial community characteristics were affected by deterministic processes, reduced network connectivity, and modularity. Microbial community diversities and assemblage processes along a vertical profile were influenced by the vertical variations in pH, temperature, DIC, and nutrients. Stochastic processes may have facilitated the formation of complex co-occurrence networks. Briefly, the distribution of local environmental heterogeneity along the vertical dimension could drive unique microbial community assemblage and species coexistence patterns. This study provides new perspectives on how microorganisms adapt to the environment and build communities, and how species coexist in shared habitats.
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Affiliation(s)
- Yongji Huang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Jing-Chun Feng
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China.
| | - Jie Kong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Liwei Sun
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Mingrui Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Yanyan Huang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Li Tang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Si Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
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7
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Liu R, Shan Y, Xi S, Zhang X, Sun C. A deep-sea sulfate-reducing bacterium generates zero-valent sulfur via metabolizing thiosulfate. MLIFE 2022; 1:257-271. [PMID: 38818226 PMCID: PMC10989961 DOI: 10.1002/mlf2.12038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 06/01/2024]
Abstract
Zero-valent sulfur (ZVS) is a crucial intermediate in the sulfur geobiochemical circulation and is widespread in deep-sea cold seeps. Sulfur-oxidizing bacteria are thought to be the major contributors to the formation of ZVS. However, ZVS production mediated by sulfate-reducing bacteria (SRB) has rarely been reported. In this study, we isolated and cultured a typical SRB designated Oceanidesulfovibrio marinus CS1 from deep-sea cold seep sediment in the South China Sea. We show that O. marinus CS1 forms ZVS in the medium supplemented with thiosulfate. Proteomic and protein activity assays revealed that thiosulfate reductase (PhsA) and the sulfide:quinone oxidoreductase (SQR) played key roles in driving ZVS formation in O. marinus CS1. During this process, thiosulfate firstly was reduced by PhsA to form sulfide, then sulfide was oxidized by SQR to produce ZVS. The expressions of PhsA and SQR were significantly upregulated when O. marinus CS1 was cultured in a deep-sea cold seep, strongly indicating that strain CS1 might form ZVS in the deep-sea environment. Notably, homologs of phsA and sqr were widely identified from microbes living in sediments of deep-sea cold seep in the South China Sea by the metagenomic analysis. We thus propose that SRB containing phsA and sqr genes potentially contribute to the formation of ZVS in deep-sea cold seep environments.
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Affiliation(s)
- Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine BiologyCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
| | - Yeqi Shan
- CAS and Shandong Province Key Laboratory of Experimental Marine BiologyCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
| | - Shichuan Xi
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
- CAS Key Laboratory of Marine Geology and EnvironmentCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Xin Zhang
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
- CAS Key Laboratory of Marine Geology and EnvironmentCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine BiologyCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
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8
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Cold Seeps on the Passive Northern U.S. Atlantic Margin Host Globally Representative Members of the Seep Microbiome with Locally Dominant Strains of Archaea. Appl Environ Microbiol 2022; 88:e0046822. [PMID: 35607968 DOI: 10.1128/aem.00468-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Marine cold seeps are natural sites of methane emission and harbor distinct microbial communities capable of oxidizing methane. The majority of known cold seeps are on tectonically active continental margins, but recent discoveries have revealed abundant seeps on passive margins as well, including on the U.S. Atlantic Margin (USAM). We sampled in and around four USAM seeps and combined pore water geochemistry measurements with amplicon sequencing of 16S rRNA and mcrA (DNA and RNA) to investigate the microbial communities present, their assembly processes, and how they compare to communities at previously studied sites. We found that the USAM seeps contained communities consistent with the canonical seep microbiome at the class and order levels but differed markedly at the sequence variant level, especially within the anaerobic methanotrophic (ANME) archaea. The ANME populations were highly uneven, with just a few dominant mcrA sequence variants at each seep. Interestingly, the USAM seeps did not form a distinct phylogenetic cluster when compared with other previously described seeps around the world. Consistent with this, we found only a very weak (though statistically significant) distance-decay trend in seep community similarity across a global data set. Ecological assembly indices suggest that the USAM seep communities were assembled primarily deterministically, in contrast to the surrounding nonseep sediments, where stochastic processes dominated. Together, our results suggest that the primary driver of seep microbial community composition is local geochemistry-specifically methane, sulfide, nitrate, acetate, and ammonium concentrations-rather than the geologic context, the composition of nearby seeps, or random events of dispersal. IMPORTANCE Cold seeps are now known to be widespread features of passive continental margins, including the northern U.S. Atlantic Margin (USAM). Methane seepage is expected to intensify at these relatively shallow seeps as bottom waters warm and underlying methane hydrates dissociate. While methanotrophic microbial communities might reduce or prevent methane release, microbial communities on passive margins have rarely been characterized. In this study, we investigated the Bacteria and Archaea at four cold seeps on the northern USAM and found that despite being colocated on the same continental slope, the communities significantly differ by site at the sequence variant level, particularly methane-cycling community members. Differentiation by site was not observed in similarly spaced background sediments, raising interesting questions about the dispersal pathways of cold seep microorganisms. Understanding the genetic makeup of these discrete seafloor ecosystems and how their microbial communities develop will be increasingly important as the climate changes.
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Zhang X, Liu S, Jiang Z, Wu Y, Huang X. Gradient of microbial communities around seagrass roots was mediated by sediment grain size. Ecosphere 2022. [DOI: 10.1002/ecs2.3942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province Sanya Institute of Oceanology, SCSIO Sanya China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
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Iasakov TR, Kanapatskiy TA, Toshchakov SV, Korzhenkov AA, Ulyanova MO, Pimenov NV. The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation. MARINE ENVIRONMENTAL RESEARCH 2022; 173:105533. [PMID: 34875513 DOI: 10.1016/j.marenvres.2021.105533] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/11/2021] [Accepted: 11/21/2021] [Indexed: 05/20/2023]
Abstract
Pockmarks are important "pumps", which are believed to play a significant role in the global methane cycling and harboring a unique assemblage of very diverse prokaryotes. This study reports the results of massive sequencing of the 16S rRNA gene V4 hypervariable regions for the samples from thirteen pockmark horizons (the Baltic Sea) collected at depths from 0 to 280 cm below seafloor (cmbsf) and the rates of microbially mediated anaerobic oxidation of methane (AOM) and sulfate reduction (SR). Altogether, 76 bacterial and 12 archaeal phyla were identified, 23 of which were candidate divisions. Of the total obtained in the pockmark sequences, 84.3% of them were classified as Bacteria and 12.4% as Archaea; 3.3% of the sequences were assigned to unknown operational taxonomic units (OTUs). Members of the phyla Planctomycetota, Chloroflexota, Desulfobacterota, Caldatribacteriota, Acidobacteriota and Proteobacteria predominated across all horizons, comprising 58.5% of the total prokaryotic community. These phyla showed different types of patterns of relative abundance. Analysis of AOM-SR-mediated prokaryotes abundance and biogeochemical measurements revealed that ANME-2a-2b subcluster was predominant in sulfate-rich upper horizons (including sulfate-methane transition zone (SMTZ)) and together with sulfate-reducing bacterial group SEEP-SRB1 had a primary role in AOM coupled to SR. At deeper sulfate-depleted horizons ANME-2a-2b shifted to ANME-1a and ANME-1b which alone mediated AOM or switch to methanogenic metabolism. Shifting of the ANME subclusters depending on depth reflect a tendency for niche separation in these groups. It was shown that the abundance of Caldatribacteriota and organohalide-respiring Dehalococcoidia (Chloroflexota) exhibited a strong correlation with AOM rates. This is the first detailed study of depth profiles of prokaryotic diversity, patterns of relative abundance, and ANME niche separation in the Baltic Sea pockmark microbiomes sheds light on assembly of prokaryotes in a pockmark.
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Affiliation(s)
- Timur R Iasakov
- Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 69, 450054, Ufa, Russia.
| | - Timur A Kanapatskiy
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Leninsky prospect 33/2, 119071, Moscow, Russia
| | - Stepan V Toshchakov
- Kurchatov Center for Genome Research, NRC "Kurchatov Institute", Ac. Kurchatov square, 1, 123098, Moscow, Russia
| | - Aleksei A Korzhenkov
- Kurchatov Center for Genome Research, NRC "Kurchatov Institute", Ac. Kurchatov square, 1, 123098, Moscow, Russia
| | - Marina O Ulyanova
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36, Nahimovskiy prospekt, Moscow, 117997, Russia; Immanuel Kant Baltic Federal University, 14, Nevskogo str., Kaliningrad, 236016, Russia
| | - Nikolay V Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Leninsky prospect 33/2, 119071, Moscow, Russia
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Li WL, Dong X, Lu R, Zhou YL, Zheng PF, Feng D, Wang Y. Microbial ecology of sulfur cycling near the sulfate-methane transition of deep-sea cold seep sediments. Environ Microbiol 2021; 23:6844-6858. [PMID: 34622529 DOI: 10.1111/1462-2920.15796] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 11/27/2022]
Abstract
Microbial sulfate reduction is largely associated with anaerobic methane oxidation and alkane degradation in sulfate-methane transition zone (SMTZ) of deep-sea cold seeps. How the sulfur cycling is mediated by microbes near SMTZ has not been fully understood. In this study, we detected a shallow SMTZ in three of eight sediment cores sampled from two cold seep areas in the South China Sea. One hundred ten genomes representing sulfur-oxidizing bacteria (SOB) and sulfur-reducing bacteria (SRB) strains were identified from three SMTZ-bearing cores. In the layers above SMTZ, SOB were mostly constituted by Campylobacterota, Gammaproteobacteria and Alphaproteobacteria that probably depended on nitrogen oxides and/or oxygen for oxidation of sulfide and thiosulfate in near-surface sediment layers. In the layers below the SMTZ, the deltaproteobacterial SRB genomes and metatranscriptomes revealed CO2 fixation by Wood-Ljungdahl pathway, sulfate reduction and nitrogen fixation for syntrophic or fermentative lifestyle. A total of 68% of the metagenome assembled genomes were not adjacent to known species in a phylogenomic tree, indicating a high diversity of bacteria involved in sulfur cycling. With the large number of genomes for SOB and SRB, our study uncovers the microbial populations that potentially mediate sulfur metabolism and associated carbon and nitrogen cycles, which sheds light on complex biogeochemical processes in deep-sea environments.
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Affiliation(s)
- Wen-Li Li
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Rui Lu
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Li Zhou
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng-Fei Zheng
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
| | - Dong Feng
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Yong Wang
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
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Jing H, Wang R, Jiang Q, Zhang Y, Peng X. Anaerobic methane oxidation coupled to denitrification is an important potential methane sink in deep-sea cold seeps. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 748:142459. [PMID: 33113688 DOI: 10.1016/j.scitotenv.2020.142459] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/13/2020] [Accepted: 09/13/2020] [Indexed: 06/11/2023]
Abstract
Microbes play a crucial role in mediating the methane flux in deep-sea cold seep ecosystems, where only methane-related microbes have been well studied, while the whole microbial community and their ecological functions were still largely unknown. Here, we utilized metagenomic data to investigate how the structure and metabolism of microbial community shift in the reduced sediment habitats along the spatial scales. Microbial communities in cold seeps and troughs formed two distinct clades likely driven by environmental factors, such as total sulfur, total phosphate and NO3-, rather than geographical proximity. The predominance of Methanosarcinales reflected a high potential for methane production. In addition to the already well-reported ANME-1/SRB consortia, prevalence of bacterial Methylomirabilis and archaeal Methanoperedens as important performers in the n-damo process with respective of nitrite and nitrate as respective electron acceptor was observed in deep-sea hydrate-bearing regions as well. Aerobic methane oxidization was conducted mainly by type I methanotrophs at Site F (Formosa Ridge), but also via the n-damo process by Methanoperedens and Methylomirabilis in the Haima seep and Xisha Trough, respectively. Based on the high abundance of those denitrifying-dependent methane oxidizers and their related functional genes, we concluded that the previously overlooked n-damo process might be a major methane sink in cold seeps or in gas hydrate-bearing sediments if nitrate is available in the anoxic zones. The signature of isotopic labeling would be essential to confirm the contribution of different anaerobic methane oxidizing pathways in deep-sea cold seep ecosystems.
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Affiliation(s)
- Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Southern Marine Science and Engineering Guangdong Laboratory, ZhuHai, China.
| | - Ruonan Wang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Qiuyun Jiang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Yue Zhang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Xiaotong Peng
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
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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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Sun QL, Zhang J, Wang MX, Cao L, Du ZF, Sun YY, Liu SQ, Li CL, Sun L. High-Throughput Sequencing Reveals a Potentially Novel Sulfurovum Species Dominating the Microbial Communities of the Seawater-Sediment Interface of a Deep-Sea Cold Seep in South China Sea. Microorganisms 2020; 8:microorganisms8050687. [PMID: 32397229 PMCID: PMC7284658 DOI: 10.3390/microorganisms8050687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022] Open
Abstract
In the Formosa cold seep of the South China Sea (SCS), large amounts of methane and sulfide hydrogen are released from the subseafloor. In this study, we systematically investigated the microbial communities in the seawater–sediment interface of Formosa cold seep using high-throughput sequencing techniques including amplicon sequencing based on next-generation sequencing and Pacbio amplicon sequencing platforms, and metagenomics. We found that Sulfurovum dominated the microbial communities in the sediment–seawater interface, including the seawater close to the seepage, the surface sediments, and the gills of the dominant animal inhabitant (Shinkaia crosnieri). A nearly complete 16S rRNA gene sequence of the dominant operational taxonomic units (OTUs) was obtained from the Pacbio sequencing platforms and classified as OTU-L1, which belonged to Sulfurovum. This OTU was potentially novel as it shared relatively low similarity percentages (<97%) of the gene sequence with its close phylogenetic species. Further, a draft genome of Sulfurovum was assembled using the binning technique based on metagenomic data. Genome analysis suggested that Sulfurovum sp. in this region may fix carbon by the reductive tricarboxylic acid (rTCA) pathway, obtain energy by oxidizing reduced sulfur through sulfur oxidizing (Sox) pathway, and utilize nitrate as electron acceptors. These results demonstrated that Sulfurovum probably plays an important role in the carbon, sulfur, and nitrogen cycles of the Formosa cold seep of the SCS. This study improves our understanding of the diversity, distribution, and function of sulfur-oxidizing bacteria in deep-sea cold seep.
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Affiliation(s)
- Qing-Lei Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Q.-L.S.); (J.Z.); (Y.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jian Zhang
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Q.-L.S.); (J.Z.); (Y.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.-X.W.); (L.C.); (Z.-F.D.)
| | - Min-Xiao Wang
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.-X.W.); (L.C.); (Z.-F.D.)
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lei Cao
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.-X.W.); (L.C.); (Z.-F.D.)
| | - Zeng-Feng Du
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.-X.W.); (L.C.); (Z.-F.D.)
- Key Lab of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuan-Yuan Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Q.-L.S.); (J.Z.); (Y.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Shi-Qi Liu
- Faculty of Science, University of Amsterdam, 1098XH Amsterdam, The Netherlands;
| | - Chao-Lun Li
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.-X.W.); (L.C.); (Z.-F.D.)
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (C.-L.L.); (L.S.); Tel.: +86-532-8289-8599 (C.-L.L.); +86-532-8289-8829 (L.S.)
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Q.-L.S.); (J.Z.); (Y.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Correspondence: (C.-L.L.); (L.S.); Tel.: +86-532-8289-8599 (C.-L.L.); +86-532-8289-8829 (L.S.)
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New Microbial Lineages Capable of Carbon Fixation and Nutrient Cycling in Deep-Sea Sediments of the Northern South China Sea. Appl Environ Microbiol 2019; 85:AEM.00523-19. [PMID: 31126943 DOI: 10.1128/aem.00523-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/15/2019] [Indexed: 12/18/2022] Open
Abstract
Metagenomics of marine sediments has uncovered a broad diversity of new uncultured taxa and provided insights into their metabolic capabilities. Here, we detected microbial lineages from a sediment core near the Jiulong methane reef of the northern South China Sea (at 1,100-m depth). Assembly and binning of the metagenomes resulted in 11 genomes (>85% complete) that represented nine distinct phyla, including candidate phyla TA06 and LCP-89, Lokiarchaeota, Heimdallarchaeota, and a newly described globally distributed phylum (B38). The genome of LCP-89 has pathways for nitrate, selenate, and sulfate reduction, suggesting that they may be involved in mediating these important processes. B38 are able to participate in the cycling of hydrogen and selenocompounds. Many of these uncultured microbes may also be capable of autotrophic CO2 fixation, as exemplified by identification of the Wood-Ljungdahl (W-L) pathway. Genes encoding carbohydrate degradation, W-L pathway, Rnf-dependent energy conservation, and Ni/Fe hydrogenases were detected in the transcriptomes of these novel members. Characterization of these new lineages provides insight to the undescribed branches in the tree of life.IMPORTANCE Sedimentary microorganisms in the South China Sea (SCS) remain largely unknown due to the complexity of sediment communities impacted by continent rifting and extension. Distinct geochemical environments may breed special microbial communities including microbes that are still enigmatic. Functional inference of their metabolisms and transcriptional activity provides insight in the ecological roles and substrate-based interactivity of these uncultured Archaea and Bacteria These microorganisms play different roles in utilizing inorganic carbon and scavenging diverse organic compounds involved in the deep-sea carbon cycle. The genomes recovered here contributed undescribed species to the tree of life and laid the foundation for future study on these novel phyla persisting in marginal sediments of the SCS.
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