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Zou D, Zhang C, Liu Y, Li M. Biogeographical distribution and community assembly of Myxococcota in mangrove sediments. ENVIRONMENTAL MICROBIOME 2024; 19:47. [PMID: 39003484 PMCID: PMC11245791 DOI: 10.1186/s40793-024-00593-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND Myxococcota, characterized by their distinct social lifestyles, are widely distributed micro-predators in global sediments. They can feed on a wide range of bacterial, archaeal, and fungal prey. Myxococcota are capable of producing diverse secondary metabolites, playing key roles in microbial food webs, and regulating the microbial community structures in different ecosystems. However, Myxococcota are rarely pure cultured due to the challenging and stringent culturing conditions. Their natural distribution, niche differentiation, and predator-prey relationships in a specific habitat are poorly understood. RESULTS In this study, we conducted a comprehensive analysis of the 16S rRNA gene sequence data from public databases and our collection. We compared the abundance, diversity, and distribution patterns of Myxococcota in various habitats, with a specific focus on mangroves. We found that Myxococcota accounted for 1.45% of the total prokaryotes in global sediments based on the abundance of 16S rRNA genes. Myxococcota are abundant and diverse in mangrove sediments. They tend to be more generalistic in mangroves than in other habitats due to their wide niche breadth. Besides, the deterministic processes (variable selection) influenced the assembly of mangrove Myxococcota communities significantly more than stochastic processes. Further, we determined that environmental factors explained a greater amount of total community variation in mangrove Myxococcota than geographical variables (latitude and sediment depth). In the end, through the analysis of microbial co-occurrence networks, Myxococcota emerges as a key component and functions as a connector in the mangrove microbial community. CONCLUSIONS Our study enhances comprehension of mangrove Myxococcota's biogeography, assembly patterns, driving factors, and co-occurrence relationships, as well as highlights their unique niche and ecological importance in mangrove sediments.
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Affiliation(s)
- Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Institute for Advanced Study, Shenzhen Key Laboratory of Marine Microbiome Engineering, Shenzhen University, Shenzhen, 518060, China
- Synthetic Biology Research Center, Shenzhen University, Shenzhen, 518060, China
| | - Cuijing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Institute for Advanced Study, Shenzhen Key Laboratory of Marine Microbiome Engineering, Shenzhen University, Shenzhen, 518060, China
- Synthetic Biology Research Center, Shenzhen University, Shenzhen, 518060, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Institute for Advanced Study, Shenzhen Key Laboratory of Marine Microbiome Engineering, Shenzhen University, Shenzhen, 518060, China.
- Synthetic Biology Research Center, Shenzhen University, Shenzhen, 518060, China.
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Institute for Advanced Study, Shenzhen Key Laboratory of Marine Microbiome Engineering, Shenzhen University, Shenzhen, 518060, China.
- Synthetic Biology Research Center, Shenzhen University, Shenzhen, 518060, China.
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Xu L, Wang Y, Xuan L, Mei H, He C, Yang J, Wang W. New attempts on acidic anaerobic digestion of poly (butylene adipate-co-terephthalate) wastewater in upflow anaerobic sludge blanket reactor. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132586. [PMID: 37748315 DOI: 10.1016/j.jhazmat.2023.132586] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/16/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023]
Abstract
Poly (butylene adipate-co-terephthalate) (PBAT) wastewater is a highly concentrated, acidic, and toxic wastewater generated from biodegradable plastics production. Large amounts of alkali would be consumed when treating PBAT wastewater by anaerobic digestion due to the low pH value. This study employed acidic anaerobic digestion to treat PBAT wastewater and compared to neutral anaerobic digestion. The results indicated that the COD removal rates in the acidic upflow anaerobic sludge blanket (UASB) reactor were 65.5% and 59.9%, respectively at influent pH 6.0 and 5.0 with the COD concentration of around 11,000 mg L-1, and the methane conversion efficiency were 172.5 and 183.8 mLCH4/gCODr (gCODr: COD removed amount), respectively. Correspondingly, the average COD removal and methane conversion efficiency in the neutral UASB reactor were 63.2% and 188.0 mLCH4/gCODr, respectively. The treatment efficiency of acidic and neutral UASB reactors for PBAT wastewater was similar. The hydrogenotrophic methanogenic activity was further enhanced in the acidic UASB reactor compared to the neutral one. The increase of alkalinity in the acidic UASB reactor (2.4 mmol L-1) was higher than the neutral (2.0 mmol L-1). A higher level of syntrophic acetate oxidation bacteria and hydrogenotrophic methanogen was enriched in the acidic UASB reactor, ensuring efficient treatment and saving costs.
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Affiliation(s)
- Luyao Xu
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei 230009, China
| | - Yan Wang
- Anhui Provincial Key Laboratory of Industrial Wastewater and Environmental Treatment, East China Engineering Science and Technology Co., Ltd., Hefei 230022, China
| | - Liang Xuan
- Anhui Provincial Key Laboratory of Industrial Wastewater and Environmental Treatment, East China Engineering Science and Technology Co., Ltd., Hefei 230022, China
| | - Hong Mei
- Anhui Provincial Key Laboratory of Industrial Wastewater and Environmental Treatment, East China Engineering Science and Technology Co., Ltd., Hefei 230022, China
| | - Chunhua He
- Department of Municipal Engineering, School of Environment and Energy Engineering, Anhui JianZhu University, Hefei 230009, China
| | - Jing Yang
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei 230009, China
| | - Wei Wang
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei 230009, China.
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3
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Lyu Y, Zhang J, Chen Y, Li Q, Ke Z, Zhang S, Li J. Distinct diversity patterns and assembly mechanisms of prokaryotic microbial sub-community in the water column of deep-sea cold seeps. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119240. [PMID: 37837767 DOI: 10.1016/j.jenvman.2023.119240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/05/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023]
Abstract
Methane leakage from deep-sea cold seeps has a major impact on marine ecosystems. Microbes sequester methane in the water column of cold seeps and can be divided into abundant and rare groups. Both abundant and rare groups play an important role in cold seep ecosystems, and the environmental heterogeneity in cold seeps may enhance conversion between taxa with different abundances. Yet, the environmental stratification and assembly mechanisms of these microbial sub-communities remain unclear. We investigated the diversities and assembly mechanisms in microbial sub-communities with distinct abundance in the deep-sea cold seep water column, from 400 m to 1400 m. We found that bacterial β-diversity, as measured by Sørensen dissimilarities, exhibited a significant species turnover pattern that was influenced by several environmental factors including depth, temperature, SiO32-, and salinity. In contrast, archaeal β-diversity showed a relatively high percentage of nestedness pattern, which was driven by the levels of soluble reactive phosphate and SiO32-. During the abundance dependency test, abundant taxa of both bacteria and archaea showed a significant species turnover, while the rare taxa possessed a higher percentage of nestedness. Stochastic processes were prominent in shaping the prokaryotic community, but deterministic processes were more pronounced for the abundant taxa than rare ones. Furthermore, the metagenomics results revealed that the abundances of methane oxidation, sulfur oxidation, and nitrogen fixation-related genes and related microbial groups were significantly higher in the bottom water. Our results implied that the carbon, sulfur, and nitrogen cycles were potentially strongly coupled in the bottom water. Overall, the results obtained in this study highlight taxonomic and abundance-dependent microbial community diversity patterns and assembly mechanisms in the water column of cold seeps, which will help understand the impacts of fluid seepage from the sea floor on the microbial community in the water column and further provide guidance for the management of cold seep ecosystem under future environmental pressures.
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Affiliation(s)
- Yuanjiao Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Zhixin Ke
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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Engelen B, Nguyen T, Heyerhoff B, Kalenborn S, Sydow K, Tabai H, Peterson RN, Wegener G, Teske A. Microbial Communities of Hydrothermal Guaymas Basin Surficial Sediment Profiled at 2 Millimeter-Scale Resolution. Front Microbiol 2021; 12:710881. [PMID: 34335545 PMCID: PMC8322767 DOI: 10.3389/fmicb.2021.710881] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/22/2021] [Indexed: 01/10/2023] Open
Abstract
The surficial hydrothermal sediments of Guaymas Basin harbor complex microbial communities where oxidative and reductive nitrogen, sulfur, and carbon-cycling populations and processes overlap and coexist. Here, we resolve microbial community profiles in hydrothermal sediment cores of Guaymas Basin on a scale of 2 millimeters, using Denaturing Gradient Gel Electrophoresis (DGGE) to visualize the rapid downcore changes among dominant bacteria and archaea. DGGE analysis of bacterial 16S rRNA gene amplicons identified free-living and syntrophic deltaproteobacterial sulfate-reducing bacteria, fermentative Cytophagales, members of the Chloroflexi (Thermoflexia), Aminicenantes, and uncultured sediment clades. The DGGE pattern indicates a gradually changing downcore community structure where small changes on a 2-millimeter scale accumulate to significantly changing populations within the top 4 cm sediment layer. Functional gene DGGE analyses identified anaerobic methane-oxidizing archaea (ANME) based on methyl-coenzyme M reductase genes, and members of the Betaproteobacteria and Thaumarchaeota based on bacterial and archaeal ammonia monooxygenase genes, respectively. The co-existence and overlapping habitat range of aerobic, nitrifying, sulfate-reducing and fermentative bacteria and archaea, including thermophiles, in the surficial sediments is consistent with dynamic redox and thermal gradients that sustain highly complex microbial communities in the hydrothermal sediments of Guaymas Basin.
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Affiliation(s)
- Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Tien Nguyen
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Saskia Kalenborn
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Katharina Sydow
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Houssem Tabai
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Richard N Peterson
- Department of Coastal and Marine Systems Science, Coastal Carolina University, Conway, SC, United States
| | - Gunter Wegener
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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5
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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: 24] [Impact Index Per Article: 6.0] [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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6
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Hu YY, Wu J, Li HZ, Poncin S, Wang KJ, Zuo JE. Novel insight into high solid anaerobic digestion of swine manure after thermal treatment: Kinetics and microbial community properties. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 235:169-177. [PMID: 30682669 DOI: 10.1016/j.jenvman.2019.01.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/24/2018] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
Compared to traditional anaerobic digestion (AD), high solid anaerobic digestion (HSAD) had the advantages of small digester, low heating energy and less digestate. However, the methane production was poor. In our previous study, thermal treatment (70 ± 1 °C, 3 days) without any dilution could satisfactorily enhance the methane production rate of HSAD by up to 39.5%. However, effects of solid content on HSAD after thermal treatment were not yet studied. In this study, HSAD was conducted at 11.7-17.6% solid content, and the control experiment was conducted at low solid content (4.4% solid content). Results showed that HSAD's methane production rate was the highest at 11.7% solid content (158 mL CH4/g VS), and could reach up to 89.2% of that at 4.4% solid content. The utilization of organics was revealed by kinetics analysis that the readily biodegradable organics could be utilized at increasing solid content with decreasing hydrolysis rate. Furthermore, it was notable that methylotrophic methanogens predominated in HSAD with the abundance of 82.6%. This was quite unique from the general belief that AD system was usually dominated by acetoclastic or hydrogenotrophic methanogenic pathways. In this study, the microbial community structure of HSAD after thermal treatment was firstly studied, its unique specific methanogenic pathways was firstly revealed.
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Affiliation(s)
- Yu-Ying Hu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China; School of Civil Engineering and Architecture, East China Jiao Tong University, Nanchang, 330013, China
| | - Jing Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Huai-Zhi Li
- Laboratory of Reactions and Process Engineering, Université de Lorraine, CNRS, 1, rue Grandville, BP 20451, 54001, Nancy Cedex, France
| | - Souhila Poncin
- Laboratory of Reactions and Process Engineering, Université de Lorraine, CNRS, 1, rue Grandville, BP 20451, 54001, Nancy Cedex, France
| | - Kai-Jun Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jian-E Zuo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
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Contrasting Pathways for Anaerobic Methane Oxidation in Gulf of Mexico Cold Seep Sediments. mSystems 2019; 4:mSystems00091-18. [PMID: 30834326 PMCID: PMC6392090 DOI: 10.1128/msystems.00091-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/04/2019] [Indexed: 12/15/2022] Open
Abstract
Cold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction by Deltaproteobacteria by electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction. Gulf of Mexico sediments harbor numerous hydrocarbon seeps associated with high sedimentation rates and thermal maturation of organic matter. These ecosystems host abundant and diverse microbial communities that directly or indirectly metabolize components of the emitted fluid. To investigate microbial function and activities in these ecosystems, metabolic potential (metagenomic) and gene expression (metatranscriptomic) analyses of two cold seep areas of the Gulf of Mexico were carried out. Seeps emitting biogenic methane harbored microbial communities dominated by archaeal anaerobic methane oxidizers of phylogenetic group 1 (ANME-1), whereas seeps producing fluids containing a complex mixture of thermogenic hydrocarbons were dominated by ANME-2 lineages. Metatranscriptome measurements in both communities indicated high levels of expression of genes for methane metabolism despite their distinct microbial communities and hydrocarbon composition. In contrast, the transcription level of sulfur cycle genes was quite different. In the thermogenic seep community, high levels of transcripts indicative of syntrophic anaerobic oxidation of methane (AOM) coupled to sulfate reduction were detected. This syntrophic partnership between the dominant ANME-2 and sulfate reducers potentially involves direct electron transfer through multiheme cytochromes. In the biogenic methane seep, genes from an ANME-1 lineage that are potentially involved in polysulfide reduction were highly expressed, suggesting a novel bacterium-independent anaerobic methane oxidation pathway coupled to polysulfide reduction. The observed divergence in AOM activities provides a new model for bacterium-independent AOM and emphasizes the variation that exists in AOM pathways between different ANME lineages. IMPORTANCE Cold seep sediments are complex and widespread marine ecosystems emitting large amounts of methane, a potent greenhouse gas, and other hydrocarbons. Within these sediments, microbial communities play crucial roles in production and degradation of hydrocarbons, modulating oil and gas emissions to seawater. Despite this ecological importance, our understanding of microbial functions and methane oxidation pathways in cold seep ecosystems is poor. Based on gene expression profiling of environmental seep sediment samples, the present work showed that (i) the composition of the emitted fluids shapes the microbial community in general and the anaerobic methanotroph community specifically and (ii) AOM by ANME-2 in this seep may be coupled to sulfate reduction by Deltaproteobacteria by electron transfer through multiheme cytochromes, whereas AOM by ANME-1 lineages in this seep may involve a different, bacterium-independent pathway, coupling methane oxidation to elemental sulfur/polysulfide reduction.
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Labrado AL, Brunner B, Bernasconi SM, Peckmann J. Formation of Large Native Sulfur Deposits Does Not Require Molecular Oxygen. Front Microbiol 2019; 10:24. [PMID: 30740094 PMCID: PMC6355691 DOI: 10.3389/fmicb.2019.00024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/09/2019] [Indexed: 01/05/2023] Open
Abstract
Large native (i.e., elemental) sulfur deposits can be part of caprock assemblages found on top of or in lateral position to salt diapirs and as stratabound mineralization in gypsum and anhydrite lithologies. Native sulfur is formed when hydrocarbons come in contact with sulfate minerals in presence of liquid water. The prevailing model for native sulfur formation in such settings is that sulfide produced by sulfate-reducing bacteria is oxidized to zero-valent sulfur in presence of molecular oxygen (O2). Although possible, such a scenario is problematic because: (1) exposure to oxygen would drastically decrease growth of microbial sulfate-reducing organisms, thereby slowing down sulfide production; (2) on geologic timescales, excess supply with oxygen would convert sulfide into sulfate rather than native sulfur; and (3) to produce large native sulfur deposits, enormous amounts of oxygenated water would need to be brought in close proximity to environments in which ample hydrocarbon supply sustains sulfate reduction. However, sulfur stable isotope data from native sulfur deposits emplaced at a stage after the formation of the host rocks indicate that the sulfur was formed in a setting with little solute exchange with the ambient environment and little supply of dissolved oxygen. We deduce that there must be a process for the formation of native sulfur in absence of an external oxidant for sulfide. We hypothesize that in systems with little solute exchange, sulfate-reducing organisms, possibly in cooperation with other anaerobic microbial partners, drive the formation of native sulfur deposits. In order to cope with sulfide stress, microbes may shift from harmful sulfide production to non-hazardous native sulfur production. We propose four possible mechanisms as a means to form native sulfur: (1) a modified sulfate reduction process that produces sulfur compounds with an intermediate oxidation state, (2) coupling of sulfide oxidation to methanogenesis that utilizes methylated compounds, acetate or carbon dioxide, (3) ammonium oxidation coupled to sulfate reduction, and (4) sulfur comproportionation of sulfate and sulfide. We show these reactions are thermodynamically favorable and especially useful in environments with multiple stressors, such as salt and dissolved sulfide, and provide evidence that microbial species functioning in such environments produce native sulfur. Integrating these insights, we argue that microbes may form large native sulfur deposits in absence of light and external oxidants such as O2, nitrate, and metal oxides. The existence of such a process would not only explain enigmatic occurrences of native sulfur in the geologic record, but also provide an explanation for cryptic sulfur and carbon cycling beneath the seabed.
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Affiliation(s)
- Amanda L. Labrado
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | - Benjamin Brunner
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | | | - Jörn Peckmann
- Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
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9
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Yin DM, Westerholm M, Qiao W, Bi SJ, Wandera SM, Fan R, Jiang MM, Dong RJ. An explanation of the methanogenic pathway for methane production in anaerobic digestion of nitrogen-rich materials under mesophilic and thermophilic conditions. BIORESOURCE TECHNOLOGY 2018; 264:42-50. [PMID: 29783130 DOI: 10.1016/j.biortech.2018.05.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
The impact of temperature on the anaerobic digestion of chicken manure was investigated by studying the process performance and pathway for continuously-fed digesters under mesophilic and thermophilic conditions. The mesophilic digester obtained a 15% higher methane yield compared with the thermophilic digester. Mesophilic and thermophilic digester had free ammonia of 31 and 145 mg/L, respectively. The stable carbon isotope analysis indicated that 41% and 50% of acetate was converted to methane through the syntrophic acetate oxidation and hydrogenotrophic methanogenesis (SAO-HM) pathway under mesophilic and thermophilic conditions, respectively. The genus Pseudomonas represented 10% and 16% under mesophilic and thermophilic conditions, respectively. A high abundance of the methanogens genus Methanoculleus (94% of total methanogens) in mesophilic and the genus Methanothermobacter (96%) in thermophilic digesters indicated they were the main hydrogenotrophic partners in SAO. The present study therefore illustrated that methanogenic pathway shifting, induced by free ammonia, closely correlated to the process performance.
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Affiliation(s)
- Dong-Min Yin
- College of Engineering, China Agricultural University, Beijing 100083, China; R&D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development and Reform Committee (BGFeuls), Beijing 100083, China
| | - Maria Westerholm
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, Box 7025, SE-750 07 Uppsala, Sweden
| | - Wei Qiao
- College of Engineering, China Agricultural University, Beijing 100083, China; R&D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development and Reform Committee (BGFeuls), Beijing 100083, China.
| | - Shao-Jie Bi
- College of Engineering, China Agricultural University, Beijing 100083, China; R&D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development and Reform Committee (BGFeuls), Beijing 100083, China
| | - Simon M Wandera
- College of Engineering, China Agricultural University, Beijing 100083, China; R&D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development and Reform Committee (BGFeuls), Beijing 100083, China
| | - Run Fan
- College of Engineering, China Agricultural University, Beijing 100083, China; R&D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development and Reform Committee (BGFeuls), Beijing 100083, China
| | - Meng-Meng Jiang
- College of Engineering, China Agricultural University, Beijing 100083, China; R&D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development and Reform Committee (BGFeuls), Beijing 100083, China
| | - Ren-Jie Dong
- College of Engineering, China Agricultural University, Beijing 100083, China; R&D Center for Efficient Production and Comprehensive Utilization of Biobased Gaseous Fuels, Energy Authority, National Development and Reform Committee (BGFeuls), Beijing 100083, China
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10
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Lomakina AV, Mamaeva EV, Pogodaeva TV, Kalmychkov GV, Khal’zov IA, Zemskaya TI. Anaerobic Methane Oxidation in Enrichment Cultures from Deep Sediments of a Mud Volcano Peschanka (South Baikal). Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718030049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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11
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Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico. Sci Rep 2017; 7:16015. [PMID: 29167487 PMCID: PMC5700182 DOI: 10.1038/s41598-017-16375-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/10/2017] [Indexed: 11/18/2022] Open
Abstract
Oil and gas percolate profusely through the sediments of the Gulf of Mexico, leading to numerous seeps at the seafloor, where complex microbial, and sometimes animal communities flourish. Sediments from three areas (two cold seeps with contrasting hydrocarbon composition and a site outside any area of active seepage) of the Gulf of Mexico were investigated and compared. Consistent with the existence of a seep microbiome, a distinct microbial community was observed in seep areas compared to sediment from outside areas of active seepage. The microbial community from sediments without any influence from hydrocarbon seepage was characterized by Planctomycetes and the metabolic potential was consistent with detrital marine snow degradation. By contrast, in seep samples with methane as the principal hydrocarbon, methane oxidation by abundant members of ANME-1 was likely the predominant process. Seep samples characterized by fluids containing both methane and complex hydrocarbons, were characterized by abundant Chloroflexi (Anaerolinaceae) and deltaproteobacterial lineages and exhibited potential for complex hydrocarbon degradation. These different metabolic capacities suggested that microorganisms in cold seeps can potentially rely on other processes beyond methane oxidation and that the hydrocarbon composition of the seep fluids may be a critical factor structuring the seafloor microbial community composition and function.
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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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Vigneron A, Bishop A, Alsop EB, Hull K, Rhodes I, Hendricks R, Head IM, Tsesmetzis N. Microbial and Isotopic Evidence for Methane Cycling in Hydrocarbon-Containing Groundwater from the Pennsylvania Region. Front Microbiol 2017; 8:593. [PMID: 28424678 PMCID: PMC5380731 DOI: 10.3389/fmicb.2017.00593] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 03/22/2017] [Indexed: 11/13/2022] Open
Abstract
The Pennsylvania region hosts numerous oil and gas reservoirs and the presence of hydrocarbons in groundwater has been locally observed. However, these methane-containing freshwater ecosystems remain poorly explored despite their potential importance in the carbon cycle. Methane isotope analysis and analysis of low molecular weight hydrocarbon gases from 18 water wells indicated that active methane cycling may be occurring in methane-containing groundwater from the Pennsylvania region. Consistent with this observation, multigenic qPCR and gene sequencing (16S rRNA genes, mcrA, and pmoA genes) indicated abundant populations of methanogens, ANME-2d (average of 1.54 × 104mcrA gene per milliliter of water) and bacteria associated with methane oxidation (NC10, aerobic methanotrophs, methylotrophs; average of 2.52 × 103pmoA gene per milliliter of water). Methane cycling therefore likely represents an important process in these hydrocarbon-containing aquifers. The microbial taxa and functional genes identified and geochemical data suggested that (i) methane present is at least in part due to methanogens identified in situ; (ii) Potential for aerobic and anaerobic methane oxidation is important in groundwater with the presence of lineages associated with both anaerobic an aerobic methanotrophy; (iii) the dominant methane oxidation process (aerobic or anaerobic) can vary according to prevailing conditions (oxic or anoxic) in the aquifers; (iv) the methane cycle is closely associated with the nitrogen cycle in groundwater methane seeps with methane and/or methanol oxidation coupled to denitrification or nitrate and nitrite reduction.
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Affiliation(s)
- Adrien Vigneron
- School of Civil Engineering and Geosciences, Newcastle UniversityNewcastle upon Tyne, UK.,Biodomain, Shell International Exploration and Production Inc.Houston, TX, USA
| | - Andrew Bishop
- Biodomain, Shell International Exploration and Production Inc.Houston, TX, USA
| | - Eric B Alsop
- Biodomain, Shell International Exploration and Production Inc.Houston, TX, USA.,DOE Joint Genome InstituteWalnut Creek, CA, USA
| | - Kellie Hull
- Biodomain, Shell International Exploration and Production Inc.Houston, TX, USA
| | | | | | - Ian M Head
- School of Civil Engineering and Geosciences, Newcastle UniversityNewcastle upon Tyne, UK
| | - Nicolas Tsesmetzis
- Biodomain, Shell International Exploration and Production Inc.Houston, TX, USA
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Yang C, Che Y, Qi Y, Liang P, Song C. High-Throughput Sequencing of Viable Microbial Communities in Raw Pork Subjected to a Fast Cooling Process. J Food Sci 2016; 82:145-153. [PMID: 27871121 DOI: 10.1111/1750-3841.13566] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/08/2016] [Accepted: 10/24/2016] [Indexed: 11/29/2022]
Abstract
This study aimed to investigate the effect of the fast cooling process on the microbiological community in chilled fresh pork during storage. We established a culture-independent method to study viable microbes in raw pork. Tray-packaged fresh pork and chilled fresh pork were completely spoiled after 18 and 49 d in aseptic bags at 4 °C, respectively. 16S/18S ribosomal RNAs were reverse transcribed to cDNA to characterize the activity of viable bacteria/fungi in the 2 types of pork. Both cDNA and total DNA were analyzed by high-throughput sequencing, which revealed that viable Bacteroides sp. were the most active genus in rotten pork, although viable Myroides sp. and Pseudomonas sp. were also active. Moreover, viable fungi were only detected in chilled fresh pork. The sequencing results revealed that the fast cooling process could suppress the growth of microbes present initially in the raw meat to extend its shelf life. Our results also suggested that fungi associated with pork spoilage could not grow well in aseptic tray-packaged conditions.
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Affiliation(s)
- Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai Univ, 94 Weijin Road, Tianjin, 300071, China
| | - You Che
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai Univ, 94 Weijin Road, Tianjin, 300071, China
| | - Yan Qi
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai Univ, 94 Weijin Road, Tianjin, 300071, China
| | - Peixin Liang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai Univ, 94 Weijin Road, Tianjin, 300071, China
| | - Cunjiang Song
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Nankai Univ, 94 Weijin Road, Tianjin, 300071, China
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Landreau M, Duthoit F, Roussel E, Schönherr S, Georges M, Godfroy A, Le Blay G. Cultivation of an immobilized (hyper)thermophilic marine microbial community in a bioreactor. FEMS Microbiol Lett 2016; 363:fnw194. [PMID: 27528693 DOI: 10.1093/femsle/fnw194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2016] [Indexed: 01/23/2023] Open
Abstract
Cultivation in a bioreactor of immobilized deep-sea hydrothermal microbial community was tested in order to assess the stability and reactivity of this new system. A community composed of eight hydrothermal strains was entrapped in a polymer matrix that was used to inoculate a continuous culture in a gas-lift bioreactor. The continuous culture was performed for 41 days at successively 60°C, 55°C, 60°C, 85°C and 60°C, at pH 6.5, in anaerobic condition and constant dilution rate. Oxic stress and pH variations were tested at the beginning of the incubation. Despite these detrimental conditions, three strains including two strict anaerobes were maintained in the bioreactor. High cell concentrations (3 × 10(8) cells mL(-1)) and high ATP contents were measured in both liquid fractions and beads. Cloning-sequencing and qPCR revealed that Bacillus sp. dominated at the early stage, and was later replaced by Thermotoga maritima and Thermococcus sp. Acetate, formate and propionate concentrations varied simultaneously in the liquid fractions. These results demonstrate that these immobilized cells were reactive to culture conditions. They were protected inside the beads during the stress period and released in the liquid fraction when conditions were more favorable. This confirms the advantage of immobilization that highlights the resilience capacity of certain hydrothermal microorganisms after a stress period.
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Affiliation(s)
- M Landreau
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Technopôle Brest-Iroise, Place Nicolas Copernic, F-29280 Plouzané, France CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France
| | - F Duthoit
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Technopôle Brest-Iroise, Place Nicolas Copernic, F-29280 Plouzané, France CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France
| | - E Roussel
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Technopôle Brest-Iroise, Place Nicolas Copernic, F-29280 Plouzané, France CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France
| | - S Schönherr
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Technopôle Brest-Iroise, Place Nicolas Copernic, F-29280 Plouzané, France CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France
| | - Myriam Georges
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Technopôle Brest-Iroise, Place Nicolas Copernic, F-29280 Plouzané, France CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France
| | - A Godfroy
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Technopôle Brest-Iroise, Place Nicolas Copernic, F-29280 Plouzané, France CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France
| | - G Le Blay
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM)-UMR 6197, Technopôle Brest-Iroise, Place Nicolas Copernic, F-29280 Plouzané, France CNRS, IUEM-UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France
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Krukenberg V, Harding K, Richter M, Glöckner FO, Gruber-Vodicka HR, Adam B, Berg JS, Knittel K, Tegetmeyer HE, Boetius A, Wegener G. CandidatusDesulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane. Environ Microbiol 2016; 18:3073-91. [DOI: 10.1111/1462-2920.13283] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 01/20/2023]
Affiliation(s)
| | - Katie Harding
- Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Michael Richter
- Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology; Bremen Germany
- Jacobs University Bremen gGmbH; Bremen Germany
| | | | - Birgit Adam
- Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Jasmine S. Berg
- Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Katrin Knittel
- Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Halina E. Tegetmeyer
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research; Bremerhaven Germany
- Center for Biotechnology, Bielefeld University; Bielefeld Germany
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology; Bremen Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research; Bremerhaven Germany
- MARUM, Center for Marine Environmental Sciences, University Bremen; Bremen Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology; Bremen Germany
- MARUM, Center for Marine Environmental Sciences, University Bremen; Bremen Germany
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17
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Dowell F, Cardman Z, Dasarathy S, Kellermann MY, Lipp JS, Ruff SE, Biddle JF, McKay LJ, MacGregor BJ, Lloyd KG, Albert DB, Mendlovitz H, Hinrichs KU, Teske A. Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin. Front Microbiol 2016; 7:17. [PMID: 26858698 PMCID: PMC4731509 DOI: 10.3389/fmicb.2016.00017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 01/11/2016] [Indexed: 12/15/2022] Open
Abstract
The hydrothermal sediments of Guaymas Basin, an active spreading center in the Gulf of California (Mexico), are rich in porewater methane, short-chain alkanes, sulfate and sulfide, and provide a model system to explore habitat preferences of microorganisms, including sulfate-dependent, methane- and short chain alkane-oxidizing microbial communities. In this study, hot sediments (above 60°C) covered with sulfur-oxidizing microbial mats surrounding a hydrothermal mound (termed “Mat Mound”) were characterized by porewater geochemistry of methane, C2–C6 short-chain alkanes, sulfate, sulfide, sulfate reduction rate measurements, in situ temperature gradients, bacterial and archaeal 16S rRNA gene clone libraries and V6 tag pyrosequencing. The most abundantly detected groups in the Mat mound sediments include anaerobic methane-oxidizing archaea of the ANME-1 lineage and its sister clade ANME-1Guaymas, the uncultured bacterial groups SEEP-SRB2 within the Deltaproteobacteria and the separately branching HotSeep-1 Group; these uncultured bacteria are candidates for sulfate-reducing alkane oxidation and for sulfate-reducing syntrophy with ANME archaea. The archaeal dataset indicates distinct habitat preferences for ANME-1, ANME-1-Guaymas, and ANME-2 archaea in Guaymas Basin hydrothermal sediments. The bacterial groups SEEP-SRB2 and HotSeep-1 co-occur with ANME-1 and ANME-1Guaymas in hydrothermally active sediments underneath microbial mats in Guaymas Basin. We propose the working hypothesis that this mixed bacterial and archaeal community catalyzes the oxidation of both methane and short-chain alkanes, and constitutes a microbial community signature that is characteristic for hydrothermal and/or cold seep sediments containing both substrates.
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Affiliation(s)
- Frederick Dowell
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Zena Cardman
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Srishti Dasarathy
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Matthias Y Kellermann
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of BremenBremen, Germany; Department of Earth Science and Marine Science Institute, University of California at Santa BarbaraSanta Barbara, CA, USA
| | - Julius S Lipp
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen Bremen, Germany
| | - S Emil Ruff
- HGF-MPG Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware Lewes, DE, USA
| | - Luke J McKay
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Barbara J MacGregor
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Karen G Lloyd
- Department of Microbiology, The University of Tennessee Knoxville, TN, USA
| | - Daniel B Albert
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Howard Mendlovitz
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen Bremen, Germany
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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Growth of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a high-pressure membrane capsule bioreactor. Appl Environ Microbiol 2016; 81:1286-96. [PMID: 25501484 DOI: 10.1128/aem.03255-14] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Communities of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB) grow slowly, which limits the ability to perform physiological studies. High methane partial pressure was previously successfully applied to stimulate growth, but it is not clear how different ANME subtypes and associated SRB are affected by it. Here, we report on the growth of ANME-SRB in a membrane capsule bioreactor inoculated with Eckernförde Bay sediment that combines high-pressure incubation (10.1 MPa methane) and thorough mixing (100 rpm) with complete cell retention by a 0.2-m-pore-size membrane. The results were compared to previously obtained data from an ambient-pressure (0.101 MPa methane) bioreactor inoculated with the same sediment. The rates of oxidation of labeled methane were not higher at 10.1 MPa, likely because measurements were done at ambient pressure. The subtype ANME-2a/b was abundant in both reactors, but subtype ANME-2c was enriched only at 10.1 MPa. SRB at 10.1 MPa mainly belonged to the SEEP-SRB2 and Eel-1 groups and the Desulfuromonadales and not to the typically found SEEP-SRB1 group. The increase of ANME-2a/b occurred in parallel with the increase of SEEP-SRB2, which was previously found to be associated only with ANME-2c. Our results imply that the syntrophic association is flexible and that methane pressure and sulfide concentration influence the growth of different ANME-SRB consortia. We also studied the effect of elevated methane pressure on methane production and oxidation by a mixture of methanogenic and sulfate-reducing sludge. Here, methane oxidation rates decreased and were not coupled to sulfide production, indicating trace methane oxidation during net methanogenesis and not anaerobic methane oxidation, even at a high methane partial pressure.
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Anaerobic oxidation of methane associated with sulfate reduction in a natural freshwater gas source. ISME JOURNAL 2015; 10:1400-12. [PMID: 26636551 PMCID: PMC5029187 DOI: 10.1038/ismej.2015.213] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/29/2015] [Accepted: 10/06/2015] [Indexed: 12/18/2022]
Abstract
The occurrence of anaerobic oxidation of methane (AOM) and trace methane oxidation (TMO) was investigated in a freshwater natural gas source. Sediment samples were taken and analyzed for potential electron acceptors coupled to AOM. Long-term incubations with 13C-labeled CH4 (13CH4) and different electron acceptors showed that both AOM and TMO occurred. In most conditions, 13C-labeled CO2 (13CO2) simultaneously increased with methane formation, which is typical for TMO. In the presence of nitrate, neither methane formation nor methane oxidation occurred. Net AOM was measured only with sulfate as electron acceptor. Here, sulfide production occurred simultaneously with 13CO2 production and no methanogenesis occurred, excluding TMO as a possible source for 13CO2 production from 13CH4. Archaeal 16S rRNA gene analysis showed the highest presence of ANME-2a/b (ANaerobic MEthane oxidizing archaea) and AAA (AOM Associated Archaea) sequences in the incubations with methane and sulfate as compared with only methane addition. Higher abundance of ANME-2a/b in incubations with methane and sulfate as compared with only sulfate addition was shown by qPCR analysis. Bacterial 16S rRNA gene analysis showed the presence of sulfate-reducing bacteria belonging to SEEP-SRB1. This is the first report that explicitly shows that AOM is associated with sulfate reduction in an enrichment culture of ANME-2a/b and AAA methanotrophs and SEEP-SRB1 sulfate reducers from a low-saline environment.
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Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses. ISME JOURNAL 2015; 10:678-92. [PMID: 26394007 PMCID: PMC4817681 DOI: 10.1038/ismej.2015.145] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 05/29/2015] [Accepted: 07/05/2015] [Indexed: 01/15/2023]
Abstract
To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteobacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5′-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no 15NH4+ assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active ‘free-living' population, and are not dependent on methane or ANME activity. We investigated the possibility of N2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic Deltaproteobacteria. However, nifH expression was methane-dependent. 15N2 incorporation was not observed in single DSS cells, but was detected in single DSB cells. Interestingly, 15N2 incorporation in single DSB cells was methane-dependent, raising the possibility that DSB cells acquired reduced 15N products from diazotrophic ANME while spatially coupled, and then subsequently dissociated. With this combined data set we address several outstanding questions in methane seep microbial ecosystems and highlight the benefit of measuring microbial activity in the context of spatial associations.
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Cao H, Zhang W, Wang Y, Qian PY. Microbial community changes along the active seepage site of one cold seep in the Red Sea. Front Microbiol 2015; 6:739. [PMID: 26284035 PMCID: PMC4523032 DOI: 10.3389/fmicb.2015.00739] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/06/2015] [Indexed: 01/11/2023] Open
Abstract
The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.
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Affiliation(s)
- Huiluo Cao
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
| | - Weipeng Zhang
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
| | - Yong Wang
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong ; Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences Sanya, China
| | - Pei-Yuan Qian
- Division of Life Sciences, The Hong Kong University of Science and Technology Clear Water Bay, Hong Kong
| |
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22
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Influence of DNA extraction method, 16S rRNA targeted hypervariable regions, and sample origin on microbial diversity detected by 454 pyrosequencing in marine chemosynthetic ecosystems. Appl Environ Microbiol 2015; 80:4626-39. [PMID: 24837380 DOI: 10.1128/aem.00592-14] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Next-generation sequencing (NGS) opens up exciting possibilities for improving our knowledge of environmental microbial diversity, allowing rapid and cost-effective identification of both cultivated and uncultivated microorganisms. However, library preparation, sequencing, and analysis of the results can provide inaccurate representations of the studied community compositions. Therefore, all these steps need to be taken into account carefully. Here we evaluated the effects of DNA extraction methods, targeted 16S rRNA hypervariable regions, and sample origins on the diverse microbes detected by 454 pyrosequencing in marine cold seep and hydrothermal vent sediments. To assign the reads with enough taxonomic precision, we built a database with about 2,500 sequences from Archaea and Bacteria from deep-sea marine sediments, affiliated according to reference publications in the field. Thanks to statistical and diversity analyses as well as inference of operational taxonomic unit (OTU) networks, we show that (i) while DNA extraction methods do not seem to affect the results for some samples, they can lead to dramatic changes for others; and (ii) the choice of amplification and sequencing primers also considerably affects the microbial community detected in the samples. Thereby, very different proportions of pyrosequencing reads were obtained for some microbial lineages, such as the archaeal ANME-1, ANME-2c, and MBG-D and deltaproteobacterial subgroups. This work clearly indicates that the results from sequencing-based analyses, such as pyrosequencing, should be interpreted very carefully. Therefore, the combination of NGS with complementary approaches, such as fluorescence in situ hybridization (FISH)/catalyzed reporter deposition (CARD)-FISH or quantitative PCR (Q-PCR), would be desirable to gain a more comprehensive picture of environmental microbial communities.
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23
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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24
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 rlike (select (case when (5853=5853) then 0x31302e313132382f61656d2e30303134372d3135 else 0x28 end))-- yhjw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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25
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and (select (case when (4843=4843) then null else ctxsys.drithsx.sn(1,4843) end) from dual) is null] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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26
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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27
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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28
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and (select (case when (4809=6114) then null else ctxsys.drithsx.sn(1,4809) end) from dual) is null-- zlmh] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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29
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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30
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and extractvalue(5836,concat(0x5c,0x7162707671,(select (elt(5836=5836,1))),0x717a6b7171))-- jijh] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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31
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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32
|
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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33
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 order by 1-- wjpz] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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34
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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35
|
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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36
|
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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37
|
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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38
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 or extractvalue(9645,concat(0x5c,0x7162707671,(select (elt(9645=9645,1))),0x717a6b7171))-- tzdx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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39
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 order by 1#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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40
|
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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41
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and 9969=9969-- bqjm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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42
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and 5417=7636-- tabb] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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43
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 order by 1-- ntbd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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44
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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|
45
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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46
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 rlike (select (case when (7991=6814) then 0x31302e313132382f61656d2e30303134372d3135 else 0x28 end))-- awkz] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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|
47
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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|
48
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Evidence of Active Methanogen Communities in Shallow Sediments of the Sonora Margin Cold Seeps. Appl Environ Microbiol 2015. [DOI: 10.1128/aem.00147-15 and (select (case when (8714=1632) then null else ctxsys.drithsx.sn(1,8714) end) from dual) is null] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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|
49
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Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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|
50
|
Abstract
ABSTRACT
In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic
Archaea
were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic
Methanococcoides
burtonii
relatives and several new autotrophic
Methanogenium
lineages, confirming the cooccurrence of
Methanosarcinales
and
Methanomicrobiales
methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps.
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|