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Zhu P, Yang S, Wu Y, Ru Y, Yu X, Wang L, Guo W. Shifts in Soil Microbial Community Composition, Function, and Co-occurrence Network of Phragmites australis in the Yellow River Delta. Front Microbiol 2022; 13:858125. [PMID: 35928147 PMCID: PMC9344067 DOI: 10.3389/fmicb.2022.858125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022] Open
Abstract
Soil microorganisms play vital roles in regulating biogeochemical processes. The composition and function of soil microbial community have been well studied, but little is known about the responses of bacterial and fungal communities to different habitats of the same plant, especially the inter-kingdom co-occurrence pattern including bacteria and fungi. Herein, we used high-throughput sequencing to investigate the bacterial and fungal communities of five Phragmites australis habitats in the Yellow River Delta and constructed their inter-kingdom interaction network by network analysis. The results showed that richness did not differ significantly among habitats for either the bacterial or fungal communities. The distribution of soil bacterial community was significantly affected by soil physicochemical properties, whereas that of the fungal community was not. The main functions of the bacterial and fungal communities were to participate in the degradation of organic matter and element cycling, both of which were significantly affected by soil physicochemical properties. Network analysis revealed that bacteria and fungi participated in the formation of networks through positive interactions; the role of intra-kingdom interactions were more important than inter-kingdom interactions. In addition, rare species acted as keystones played a critical role in maintaining the network structure, while NO3−−N likely played an important role in maintaining the network topological properties. Our findings provided insights into the inter-kingdom microbial co-occurrence network and response of the soil microbial community composition and function to different P. australis habitats in coastal wetlands, which will deepen our insights into microbial community assembly in coastal wetlands.
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Affiliation(s)
- Pengcheng Zhu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Shuren Yang
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Yuxin Wu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Yuning Ru
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Xiaona Yu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Lushan Wang,
| | - Weihua Guo
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, School of Life Sciences, Ministry of Natural Resources, Shandong University, Qingdao, China
- *Correspondence: Weihua Guo, whguo@
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2
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La W, Han X, Liu CQ, Ding H, Liu M, Sun F, Li S, Lang Y. Sulfate concentrations affect sulfate reduction pathways and methane consumption in coastal wetlands. WATER RESEARCH 2022; 217:118441. [PMID: 35430469 DOI: 10.1016/j.watres.2022.118441] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/24/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Coastal wetlands are an important source of methane emissions, and understanding the mechanisms that control methane emissions from coastal wetlands is of great significance to global warming. Anaerobic oxidation of methane driven by sulfate is an important process to prevent methane emissions from coastal wetlands. The effects of environmental changes on this process and the function of the sulfate-methane transition zone (SMTZ) are poorly understood. In this study, spatiotemporal variations in pore-water geochemistry (concentrations of SO42-, CH4 and DIC as well as δ13C-DIC and δ13C-CH4) in the Beidagang wetland, Tianjin, China, were investigated to unravel factors controlling the role of anaerobic oxidation of methane in coastal wetlands. Results show that the geochemical profile of pore-water is characterized by significant spatial and temporal variability, which may be related to changes in sulfate concentration, temperature and dissolved oxygen. The carbon isotope fractionation factors (εC) during methane oxidation range from 8.9‰ to 12.5‰, indicating that the sulfate-driven anaerobic oxidation of methane (S-AOM) dominates the methane oxidation in the Beidagang coastal wetland in both winter and summer, in both high and low salinity wetlands, and in both open water and littoral areas. However, sulfate concentration has a strong influence on the sulfate reduction pathways and methane consumption. The consumption of methane and sulfate by S-AOM is more significant in coastal wetlands with high sulfate concentrations, with S-AOM consuming nearly all of the upward-diffusing methane (96%) and downward-diffusing sulfate (96%). In addition, the dissolved inorganic carbon (DIC) produced in the pore-water mainly comes from methanogenesis, accounting for more than 80% of the total DIC pool, but in the areas with high sulfate concentrations in water column, the contribution of S-AOM to the DIC pool is greater, although only a small fraction of the total DIC pool (9%). The depth and width of the SMTZ show a clear spatial and temporal pattern, with active methanogenesis activity and upward high methane flux shoaling the SMTZ and increasing the risk of high methane emissions from coastal wetlands with low sulfate concentrations. Our findings highlight the importance of sulfate-driven anaerobic oxidation of methane in coastal wetlands and the effect of sulfate concentration on it. It contributes to our understanding of the mechanism of methane production and emissions from the coastal wetland system, particularly in light of the increased demand for coastal wetland restoration under global warming.
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Affiliation(s)
- Wei La
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Xiaokun Han
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China; Critical Zone Observatory of Bohai Coastal Region, Tianjin University, Tianjin 300072, China
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China; Critical Zone Observatory of Bohai Coastal Region, Tianjin University, Tianjin 300072, China
| | - Hu Ding
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China; Critical Zone Observatory of Bohai Coastal Region, Tianjin University, Tianjin 300072, China
| | - Mingxuan Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Fusheng Sun
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China; Critical Zone Observatory of Bohai Coastal Region, Tianjin University, Tianjin 300072, China
| | - Siliang Li
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China; Critical Zone Observatory of Bohai Coastal Region, Tianjin University, Tianjin 300072, China
| | - Yunchao Lang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China; Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China; Critical Zone Observatory of Bohai Coastal Region, Tianjin University, Tianjin 300072, China.
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3
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Yang Y, Chen J, Pratscher J, Xie S. DNA-SIP reveals an overlooked methanotroph, Crenothrix sp., involved in methane consumption in shallow lake sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152742. [PMID: 34974014 DOI: 10.1016/j.scitotenv.2021.152742] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Methanotrophs are the main consumers of methane produced in lake sediments. In shallow lakes suffering from eutrophication, methanogenesis is accelerated by the excess organic carbon input, and thus methanotrophs play a key role in regulating this methane flux as well as carbon cycling. Here, we applied nucleic acid stable isotope probing (SIP) to investigate the active methanotrophic microbial community in sediments of several shallow lakes affected by eutrophication. Our results showed that an active methanotrophic community dominated by gamma-proteobacterial methanotrophs, as well as abundant beta-proteobacterial methanol-utilizers, was involved in methane-derived carbon assimilation. Crenothrix, a filamentous methanotroph, was found to be a key methane consumer in all studied lakes. The ecological role of Crenothrix in lacustrine ecosystems is so far poorly understood, with only limited information on its existence in the water column of stratified lakes. Our results provide a novel ecological insight into this group by revealing a wide distribution of Crenothrix in lake sediments. The active methane assimilation by Crenothrix also suggested that it might represent a so far overlooked but crucial biological sink of methane in shallow lakes.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; The Lyell Centre, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Research Avenue South, Edinburgh EH14 4AP, UK
| | - Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jennifer Pratscher
- The Lyell Centre, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Research Avenue South, Edinburgh EH14 4AP, UK
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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Xie H, Hong Y, Liu H, Jiao L, Wu J, Wang L. Spatio-temporal shifts in community structure and activity of nirS-type denitrifiers in the sediment cores of Pearl River Estuary. PLoS One 2020; 15:e0231271. [PMID: 32315323 PMCID: PMC7173864 DOI: 10.1371/journal.pone.0231271] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/19/2020] [Indexed: 12/04/2022] Open
Abstract
Denitrification, an important process in microbial mediated nitrogen cycle, plays important roles in nitrogen loss in estuarine sediments. However, the function of denitrifiers in the estuarine subsurface sediments remained poorly understood. In this study, we analyzed the potential activity, abundance and community structure of nirS-type denitrifiers using 15N-labeled incubation quantitative-PCR and high throughput sequencing techniques in sediment cores from Pearl River Estuary (PRE). Results showed that subsurface sediments had nearly same level denitrification potential activity compare to surface sediments, although the abundance of nirS gene decreased sharply from surface to bottom in sediment cores. Meanwhile, nirS gene abundance exhibit significant temporal variations, which is consistent with denitrification potential activity. Moreover, the community structure and diversity of nirS-type denitrifiers in sediment cores exhibited remarkable temporal shift pattern. For spatial variation, no significant difference was observed of denitrifiers community structure in each sediment core from the surface to the subsurface, while there were significant different diversity characteristic among different cores. Redundancy analysis (RDA) showed that multiple environmental factors including salinity, pH, oxidation-reduction potential, nutrient content and organic substances synergistically shaped the diversity and distribution of nirS-type denitrifers in PRE sediments. Our results showed that nirS-type denitrifers played important roles in the nitrogen removal in subsurface sediments of PRE.
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Affiliation(s)
- Haitao Xie
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou, China
- The School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Yiguo Hong
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou, China
- * E-mail: (YH); (HL)
| | - Huamin Liu
- The School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- * E-mail: (YH); (HL)
| | - Lijing Jiao
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou, China
| | - Jiapeng Wu
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou, China
| | - Lixin Wang
- The School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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5
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Taubert M, Grob C, Howat AM, Burns OJ, Pratscher J, Jehmlich N, von Bergen M, Richnow HH, Chen Y, Murrell JC. Methylamine as a nitrogen source for microorganisms from a coastal marine environment. Environ Microbiol 2017; 19:2246-2257. [PMID: 28244196 DOI: 10.1111/1462-2920.13709] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/13/2017] [Accepted: 02/19/2017] [Indexed: 11/27/2022]
Abstract
Nitrogen is a key limiting resource for biomass production in the marine environment. Methylated amines, released from the degradation of osmolytes, could provide a nitrogen source for marine microbes. Thus far, studies in aquatic habitats on the utilization of methylamine, the simplest methylated amine, have mainly focussed on the fate of the carbon from this compound. Various groups of methylotrophs, microorganisms that can grow on one-carbon compounds, use methylamine as a carbon source. Non-methylotrophic microorganisms may also utilize methylamine as a nitrogen source, but little is known about their diversity, especially in the marine environment. In this proof-of-concept study, stable isotope probing (SIP) was used to identify microorganisms from a coastal environment that assimilate nitrogen from methylamine. SIP experiments using 15 N methylamine combined with metagenomics and metaproteomics facilitated identification of active methylamine-utilizing Alpha- and Gammaproteobacteria. The draft genomes of two methylamine utilizers were obtained and their metabolism with respect to methylamine was examined. Both bacteria identified in these SIP experiments used the γ-glutamyl-methylamide pathway, found in both methylotrophs and non-methylotrophs, to metabolize methylamine. The utilization of 15 N methylamine also led to the release of 15 N ammonium that was used as nitrogen source by other microorganisms not directly using methylamine.
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Affiliation(s)
- Martin Taubert
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Dornburger Str. 159, Jena, 07743, Germany.,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Carolina Grob
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Alexandra M Howat
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Oliver J Burns
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Jennifer Pratscher
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Brüderstraße 32, Leipzig, 04103, Germany.,Department of Chemistry and Bioscience, University of Aalborg, Fredrik Bajers Vej 7H, Aalborg East, 9220, Denmark
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, 04318, Germany
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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Rush D, Osborne KA, Birgel D, Kappler A, Hirayama H, Peckmann J, Poulton SW, Nickel JC, Mangelsdorf K, Kalyuzhnaya M, Sidgwick FR, Talbot HM. The Bacteriohopanepolyol Inventory of Novel Aerobic Methane Oxidising Bacteria Reveals New Biomarker Signatures of Aerobic Methanotrophy in Marine Systems. PLoS One 2016; 11:e0165635. [PMID: 27824887 PMCID: PMC5100885 DOI: 10.1371/journal.pone.0165635] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 10/15/2016] [Indexed: 12/24/2022] Open
Abstract
Aerobic methane oxidation (AMO) is one of the primary biologic pathways regulating the amount of methane (CH4) released into the environment. AMO acts as a sink of CH4, converting it into carbon dioxide before it reaches the atmosphere. It is of interest for (paleo)climate and carbon cycling studies to identify lipid biomarkers that can be used to trace AMO events, especially at times when the role of methane in the carbon cycle was more pronounced than today. AMO bacteria are known to synthesise bacteriohopanepolyol (BHP) lipids. Preliminary evidence pointed towards 35-aminobacteriohopane-30,31,32,33,34-pentol (aminopentol) being a characteristic biomarker for Type I methanotrophs. Here, the BHP compositions were examined for species of the recently described novel Type I methanotroph bacterial genera Methylomarinum and Methylomarinovum, as well as for a novel species of a Type I Methylomicrobium. Aminopentol was the most abundant BHP only in Methylomarinovum caldicuralii, while Methylomicrobium did not produce aminopentol at all. In addition to the expected regular aminotriol and aminotetrol BHPs, novel structures tentatively identified as methylcarbamate lipids related to C-35 amino-BHPs (MC-BHPs) were found to be synthesised in significant amounts by some AMO cultures. Subsequently, sediments and authigenic carbonates from methane-influenced marine environments were analysed. Most samples also did not contain significant amounts of aminopentol, indicating that aminopentol is not a useful biomarker for marine aerobic methanotophic bacteria. However, the BHP composition of the marine samples do point toward the novel MC-BHPs components being potential new biomarkers for AMO.
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Affiliation(s)
- Darci Rush
- School of Civil Engineering & Geosciences, Newcastle University, Drummond Building, Newcastle upon Tyne, NE1 7RU, Newcastle-upon-Tyne, United Kingdom
- * E-mail:
| | - Kate A. Osborne
- School of Civil Engineering & Geosciences, Newcastle University, Drummond Building, Newcastle upon Tyne, NE1 7RU, Newcastle-upon-Tyne, United Kingdom
| | - Daniel Birgel
- Institute of Geology, University of Hamburg, Hamburg, Germany
| | - Andreas Kappler
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
- Center for Geomicrobiology, Department of Bioscience, Ny Munkegade 116, 8000, Aarhus C, Denmark
| | - Hisako Hirayama
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Jörn Peckmann
- Institute of Geology, University of Hamburg, Hamburg, Germany
- Department of Geodynamics and Sedimentology, University of Vienna, 1090, Vienna, Austria
| | - Simon W. Poulton
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Julia C. Nickel
- GFZ German Research Centre for Geosciences, Telegrafenberg, D-14473, Potsdam, Germany
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Telegrafenberg, D-14473, Potsdam, Germany
| | - Marina Kalyuzhnaya
- Faculty of Biology, San Diego State University, 5500 Campanile Drive, San Diego, 92182, United States of America
| | - Frances R. Sidgwick
- School of Civil Engineering & Geosciences, Newcastle University, Drummond Building, Newcastle upon Tyne, NE1 7RU, Newcastle-upon-Tyne, United Kingdom
| | - Helen M. Talbot
- School of Civil Engineering & Geosciences, Newcastle University, Drummond Building, Newcastle upon Tyne, NE1 7RU, Newcastle-upon-Tyne, United Kingdom
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7
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Deng Y, Cui X, Dumont MG. Identification of active aerobic methanotrophs in plateau wetlands using DNA stable isotope probing. FEMS Microbiol Lett 2016; 363:fnw168. [PMID: 27369086 DOI: 10.1093/femsle/fnw168] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2016] [Indexed: 01/21/2023] Open
Abstract
Sedge-dominated wetlands on the Qinghai-Tibetan Plateau are methane emission centers. Methanotrophs at these sites play a role in reducing methane emissions, but relatively little is known about the composition of active methanotrophs in these wetlands. Here, we used DNA stable isotope probing to identify the key active aerobic methanotrophs in three sedge-dominated wetlands on the plateau. We found that Methylocystis species were active in two peatlands, Hongyuan and Dangxiong. Methylobacter species were found to be active only in Dangxiong peat. Hongyuan peat had the highest methane oxidation rate, and cross-feeding of carbon from methanotrophs to methylotrophic Hyphomicrobium species was observed. Owing to a low methane oxidation rate during the incubation, the labeling of methanotrophs in Maduo wetland samples was not detected. Our results indicate that there are large differences in the activity of methanotrophs in the wetlands of this region.
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Affiliation(s)
- Yongcui Deng
- School of Geography Science Nanjing Normal University, Nanjing 210023, China Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Xiaoyong Cui
- College of Life Sciences University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Marc G Dumont
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
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Meena KK, Kumar M, Mishra S, Ojha SK, Wakchaure GC, Sarkar B. Phylogenetic study of methanol oxidizers from chilika-lake sediments using genomic and metagenomic approaches. Indian J Microbiol 2015; 55:151-62. [PMID: 25805901 DOI: 10.1007/s12088-015-0510-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/03/2015] [Indexed: 01/13/2023] Open
Abstract
Group-wise diversity of sediment methylotrophs of Chilika lake (Lat. 19°28'-19°54'N; Long. 85°06'-85°35'E) Odisha, India at various identified sites was studied. Both the culturable and unculturable (metagenome) methylotrophs were investigated in the lake sediments employing both mxaF and 16S rRNA genes as markers. ARDRA profiling, 16S rRNA gene sequencing, PAGE profiling of HaeIII, EcoRI restricted mxaF gene and the mxaF gene sequences using culture-dependent approach revealed the relatedness of α-proteobacteria and Methylobacterium, Hyphomicrobium and Ancyclobacter sp. The total viable counts of the culturable aerobic methylotrophs were relatively higher in sediments near the sea mouth (S3; Panaspada), also demonstrated relatively high salinity (0.1 M NaCl) tolerance. Metagenomic DNA from the sediments, amplified using GC clamp mxaF primers and resolved through DGGE, revealed the diversity within the unculturable methylotrophic bacterium Methylobacterium organophilum, Ancyclobacter aquaticus, Burkholderiales and Hyphomicrobium sp. Culture-independent analyses revealed that up to 90 % of the methylotrophs were unculturable. The study enhances the general understandings of the metagenomic methylotrophs from such a special ecological niche.
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Affiliation(s)
- Kamlesh K Meena
- National Bureau of Agriculturally Important Microorganisms, Mau Nath Bhanjan, 275 101 UP India ; National Institute of Abiotic Stress Management, Malegaon, Baramati, Pune, Maharashtra India
| | - Manish Kumar
- National Bureau of Agriculturally Important Microorganisms, Mau Nath Bhanjan, 275 101 UP India
| | - Snehasish Mishra
- School of Biotechnology, KIIT University, Campus-11, Bhubaneswar, 751024 Odisha India
| | - Sanjay Kumar Ojha
- School of Biotechnology, KIIT University, Campus-11, Bhubaneswar, 751024 Odisha India
| | - Goraksha C Wakchaure
- National Institute of Abiotic Stress Management, Baramati, Pune, 413115 Maharashtra India
| | - Biplab Sarkar
- National Institute of Abiotic Stress Management, Baramati, Pune, 413115 Maharashtra India
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9
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Abdallah RZ, Adel M, Ouf A, Sayed A, Ghazy MA, Alam I, Essack M, Lafi FF, Bajic VB, El-Dorry H, Siam R. Aerobic methanotrophic communities at the Red Sea brine-seawater interface. Front Microbiol 2014; 5:487. [PMID: 25295031 PMCID: PMC4172156 DOI: 10.3389/fmicb.2014.00487] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/28/2014] [Indexed: 01/16/2023] Open
Abstract
The central rift of the Red Sea contains 25 brine pools with different physicochemical conditions, dictating the diversity and abundance of the microbial community. Three of these pools, the Atlantis II, Kebrit and Discovery Deeps, are uniquely characterized by a high concentration of hydrocarbons. The brine-seawater interface, described as an anoxic-oxic (brine-seawater) boundary, is characterized by a high methane concentration, thus favoring aerobic methane oxidation. The current study analyzed the aerobic free–living methane-oxidizing bacterial communities that potentially contribute to methane oxidation at the brine-seawater interfaces of the three aforementioned brine pools, using metagenomic pyrosequencing, 16S rRNA pyrotags and pmoA library constructs. The sequencing of 16S rRNA pyrotags revealed that these interfaces are characterized by high microbial community diversity. Signatures of aerobic methane-oxidizing bacteria were detected in the Atlantis II Interface (ATII-I) and the Kebrit Deep Upper (KB-U) and Lower (KB-L) brine-seawater interfaces. Through phylogenetic analysis of pmoA, we further demonstrated that the ATII-I aerobic methanotroph community is highly diverse. We propose four ATII-I pmoA clusters. Most importantly, cluster 2 groups with marine methane seep methanotrophs, and cluster 4 represent a unique lineage of an uncultured bacterium with divergent alkane monooxygenases. Moreover, non-metric multidimensional scaling (NMDS) based on the ordination of putative enzymes involved in methane metabolism showed that the Kebrit interface layers were distinct from the ATII-I and DD-I brine-seawater interfaces.
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Affiliation(s)
- Rehab Z Abdallah
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt
| | - Mustafa Adel
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Amged Ouf
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Ahmed Sayed
- Department of Biology, American University in Cairo Cairo, Egypt
| | - Mohamed A Ghazy
- Department of Biology, American University in Cairo Cairo, Egypt
| | - Intikhab Alam
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Feras F Lafi
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Vladimir B Bajic
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Hamza El-Dorry
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Rania Siam
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt ; YJ-Science and Technology Research Center, American University in Cairo Cairo, Egypt
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Putkinen A, Larmola T, Tuomivirta T, Siljanen HMP, Bodrossy L, Tuittila ES, Fritze H. Peatland succession induces a shift in the community composition of Sphagnum-associated active methanotrophs. FEMS Microbiol Ecol 2014; 88:596-611. [PMID: 24701995 DOI: 10.1111/1574-6941.12327] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 01/01/2023] Open
Abstract
Sphagnum-associated methanotrophs (SAM) are an important sink for the methane (CH4) formed in boreal peatlands. We aimed to reveal how peatland succession, which entails a directional change in several environmental variables, affects SAM and their activity. Based on the pmoA microarray results, SAM community structure changes when a peatland develops from a minerotrophic fen to an ombrotrophic bog. Methanotroph subtypes Ia, Ib, and II showed slightly contrasting patterns during succession, suggesting differences in their ecological niche adaptation. Although the direct DNA-based analysis revealed a high diversity of type Ib and II methanotrophs throughout the studied peatland chronosequence, stable isotope probing (SIP) of the pmoA gene indicated they were active mainly during the later stages of succession. In contrast, type Ia methanotrophs showed active CH4 consumption in all analyzed samples. SIP-derived (13)C-labeled 16S rRNA gene clone libraries revealed a high diversity of SAM in every succession stage including some putative Methylocella/Methyloferula methanotrophs that are not detectable with the pmoA-based approach. In addition, a high diversity of 16S rRNA gene sequences likely representing cross-labeled nonmethanotrophs was discovered, including a significant proportion of Verrucomicrobia-related sequences. These results help to predict the effects of changing environmental conditions on SAM communities and activity.
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Affiliation(s)
- Anuliina Putkinen
- Southern Finland Regional Unit, Finnish Forest Research Institute, Vantaa, Finland
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11
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Abell GCJ, Stralis-Pavese N, Pan Y, Bodrossy L. Analysis of methanotroph community structure using a pmoA-based microarray. Methods Mol Biol 2014; 1096:111-122. [PMID: 24515364 DOI: 10.1007/978-1-62703-712-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The analysis of methanotroph community composition is relevant to studies of methane oxidation in a number of environments where methane is a significant carbon source. The development and application of a microarray targeting the particulate methane monooxygenase gene (pmoA) have allowed a high-throughput, semiquantitative analysis of the major methanotroph groups in a number of different environments. Here we describe the use of a pmoA-based short oligo array for the analysis of methanotroph populations in sediment samples. The method is suitable for analysis of any type of environmental sample from which DNA can be extracted.
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Affiliation(s)
- Guy C J Abell
- CSIRO Marine and Atmospheric Research and Wealth from Ocean Flagship, Hobart, TAS, Australia
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12
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Kurt Z, Shin K, Spain JC. Biodegradation of chlorobenzene and nitrobenzene at interfaces between sediment and water. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:11829-35. [PMID: 23035795 DOI: 10.1021/es302897j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plumes of contaminated groundwater often pass through an oxic/anoxic interface when they discharge into surface water bodies. We tested the hypothesis that contaminants recalcitrant under anaerobic conditions but degradable under aerobic conditions can be biodegraded at the interface resulting in the protection of the overlying water. Flow-through columns containing sediment and water were used to evaluate degradation of synthetic organic compounds at the thin organic layer at the sediment/water interface. Sediment samples collected from several sites contaminated with nitrobenzene (NB) or chlorobenzene (CB) were tested for their biodegradation capacities in the columns. The biodegradation capacities of sediment in the columns were 2-4.2 g CB·m(-2)·d(-1) and 6.5 g NB·m(2)·d(-1). Bacteria able to carry out rapid and complete biodegradation of CB or NB were detected in the sediments prior to the experiments, which suggested the presence of an active microbial community at the contaminated sites. The results revealed robust biodegradation of toxic compounds migrating across the sediment/water interface and indicate that the biodegradation capacities were sufficient to eliminate transport of the contaminants to the overlying water in the field.
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Affiliation(s)
- Zohre Kurt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0512, USA
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13
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Chen Y. Comparative genomics of methylated amine utilization by marine Roseobacter clade bacteria and development of functional gene markers (tmm, gmaS). Environ Microbiol 2012; 14:2308-22. [DOI: 10.1111/j.1462-2920.2012.02765.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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14
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Bissett A, Abell GCJ, Bodrossy L, Richardson AE, Thrall PH. Methanotrophic communities in Australian woodland soils of varying salinity. FEMS Microbiol Ecol 2012; 80:685-95. [PMID: 22375901 DOI: 10.1111/j.1574-6941.2012.01341.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 02/17/2012] [Accepted: 02/17/2012] [Indexed: 11/29/2022] Open
Abstract
Despite their large areas and potential importance as methane sinks, the role of methane-oxidizing bacteria (MOB) in native woodland soils is poorly understood. These environments are increasingly being altered by anthropogenic disturbances, which potentially alter ecosystem service provision. Dryland salinity is one such disturbance and is becoming increasingly prevalent in Australian soils. We used microarrays and analysis of soil physicochemical variables to investigate the methane-oxidizing communities of several Australian natural woodland soils affected to varying degrees by dryland salinity. Soils varied in terms of salinity, gravitational water content, NO(3)-N, SO(4)-S and Mg, all of which explained to a significant degree MOB community composition. Analysis of the relative abundance and diversity of the MOB communities also revealed significant differences between soils of different salinities. Type II and type Ib methanotrophs dominated the soils and differences in methanotroph communities existed between salinity groups. The low salinity soils possessed less diverse MOB communities, including most conspicuously, the low numbers or absence of type II Methylocystis phylotypes. The differences in MOB communities suggest niche separation of MOB across varying salinities, as has been observed in the closely related ammonia-oxidizing bacteria, and that anthropogenic disturbance, such as dryland salinity, has the potential to alter MOB community and therefore the methane uptake rates in soils in which disturbance occurs.
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15
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Irvine IC, Vivanco L, Bentley PN, Martiny JBH. The effect of nitrogen enrichment on c(1)-cycling microorganisms and methane flux in salt marsh sediments. Front Microbiol 2012; 3:90. [PMID: 22470369 PMCID: PMC3307020 DOI: 10.3389/fmicb.2012.00090] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 02/23/2012] [Indexed: 11/13/2022] Open
Abstract
Methane (CH4) flux from ecosystems is driven by C1-cycling microorganisms – the methanogens and the methylotrophs. Little is understood about what regulates these communities, complicating predictions about how global change drivers such as nitrogen enrichment will affect methane cycling. Using a nitrogen addition gradient experiment in three Southern California salt marshes, we show that sediment CH4 flux increased linearly with increasing nitrogen addition (1.23 μg CH4 m−2 day−1 for each g N m−2 year−1 applied) after 7 months of fertilization. To test the reason behind this increased CH4 flux, we conducted a microcosm experiment altering both nitrogen and carbon availability under aerobic and anaerobic conditions. Methanogenesis appeared to be both nitrogen and carbon (acetate) limited. N and C each increased methanogenesis by 18%, and together by 44%. In contrast, methanotrophy was stimulated by carbon (methane) addition (830%), but was unchanged by nitrogen addition. Sequence analysis of the sediment methylotroph community with the methanol dehydrogenase gene (mxaF) revealed three distinct clades that fall outside of known lineages. However, in agreement with the microcosm results, methylotroph abundance (assayed by qPCR) and composition (assayed by terminal restriction fragment length polymorphism analysis) did not vary across the experimental nitrogen gradient in the field. Together, these results suggest that nitrogen enrichment to salt marsh sediments increases methane flux by stimulating the methanogen community.
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Affiliation(s)
- Irina C Irvine
- Department of Ecology and Evolutionary Biology, University of California Irvine Irvine, CA, USA
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Kessler JD, Valentine DL, Redmond MC, Du M. Response to Comment on "A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico". Science 2011. [DOI: 10.1126/science.1203428] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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17
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Analysis of methanotroph community composition using a pmoA-based microbial diagnostic microarray. Nat Protoc 2011; 6:609-24. [PMID: 21527919 DOI: 10.1038/nprot.2010.191] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Microbial diagnostic microarrays (MDMs) are highly parallel hybridization platforms containing multiple sets of immobilized oligonucleotide probes used for parallel detection and identification of many different microorganisms in environmental and clinical samples. Each probe is approximately specific to a given group of organisms. Here we describe the protocol used to develop and validate an MDM method for the semiquantification of a range of functional genes--in this case, particulate methane monooxygenase (pmoA)--and we give an example of its application to the study of the community structure of methanotrophs and functionally related bacteria in the environment. The development and validation of an MDM, following this protocol, takes ∼6 months. The pmoA MDM described in detail comprises 199 probes and addresses ∼50 different species-level clades. An experiment comprising 24 samples can be completed, from DNA extraction to data acquisition, within 3 d (12-13 h bench work).
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Abstract
Our knowledge of physical, chemical, geological and biological processes affecting methane in the ocean and in underlying sediments is expanding at a rapid pace. On first inspection, marine methane biogeochemistry appears simple: Methane distribution in sediment is set by the deposition pattern of organic material, and the balance of sources and sinks keeps its concentration low in most waters. However, recent research reveals that methane is affected by complex biogeochemical processes whose interactions are understood only at a superficial level. Such processes span the deep-subsurface, near subsurface, and ocean waters, and relate primarily to the production, consumption, and transport of methane. The purpose of this synthesis is to examine select processes within the framework of methane biogeochemistry, to formulate hypotheses on how they might operate and interact with one another, and to consider their controls.
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Affiliation(s)
- David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, California 93106, USA.
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Identification of novel methane-, ethane-, and propane-oxidizing bacteria at marine hydrocarbon seeps by stable isotope probing. Appl Environ Microbiol 2010; 76:6412-22. [PMID: 20675448 DOI: 10.1128/aem.00271-10] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine hydrocarbon seeps supply oil and gas to microorganisms in sediments and overlying water. We used stable isotope probing (SIP) to identify aerobic bacteria oxidizing gaseous hydrocarbons in surface sediment from the Coal Oil Point seep field located offshore of Santa Barbara, California. After incubating sediment with (13)C-labeled methane, ethane, or propane, we confirmed the incorporation of (13)C into fatty acids and DNA. Terminal restriction fragment length polymorphism (T-RFLP) analysis and sequencing of the 16S rRNA and particulate methane monooxygenase (pmoA) genes in (13)C-DNA revealed groups of microbes not previously thought to contribute to methane, ethane, or propane oxidation. First, (13)C methane was primarily assimilated by Gammaproteobacteria species from the family Methylococcaceae, Gammaproteobacteria related to Methylophaga, and Betaproteobacteria from the family Methylophilaceae. Species of the latter two genera have not been previously shown to oxidize methane and may have been cross-feeding on methanol, but species of both genera were heavily labeled after just 3 days. pmoA sequences were affiliated with species of Methylococcaceae, but most were not closely related to cultured methanotrophs. Second, (13)C ethane was consumed by members of a novel group of Methylococcaceae. Growth with ethane as the major carbon source has not previously been observed in members of the Methylococcaceae; a highly divergent pmoA-like gene detected in the (13)C-labeled DNA may encode an ethane monooxygenase. Third, (13)C propane was consumed by members of a group of unclassified Gammaproteobacteria species not previously linked to propane oxidation. This study identifies several bacterial lineages as participants in the oxidation of gaseous hydrocarbons in marine seeps and supports the idea of an alternate function for some pmoA-like genes.
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Antony CP, Kumaresan D, Ferrando L, Boden R, Moussard H, Scavino AF, Shouche YS, Murrell JC. Active methylotrophs in the sediments of Lonar Lake, a saline and alkaline ecosystem formed by meteor impact. ISME JOURNAL 2010; 4:1470-80. [DOI: 10.1038/ismej.2010.70] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
This special issue highlights several recent discoveries in the microbial methane cycle, including the diversity and activity of methanotrophic bacteria in special habitats, distribution and contribution of the newly discovered Verrucomicrobia, metabolism of methane and related one-carbon compounds such as methanol and methylamine in freshwater and marine environments, methanol and methane-dependent nitrate reduction, the relationships of methane cycle microorganisms with plants and animals, and the environmental factors that regulate microbial processes of the methane cycle. These articles also highlight the plethora of new organisms and metabolism relating to the methane cycle that have been discovered in recent years and outline the many questions in the methane cycle that still need to be addressed. It is clear that despite a tremendous amount of research on the biology of the methane cycle, the microbes involved in catalysing methane production and consumption harbour many secrets that need to be disclosed in order for us to fully understand how the biogeochemical methane cycle is regulated in the environment, and for us to make future predictions about the global sources and sinks of methane and how anthropogenic changes impact on the cycling of this important greenhouse gas.
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Affiliation(s)
- J Colin Murrell
- Department of Microbiology, Warwick University, Warwick, UK. Department of Microbiology, IWWR Radboud University, Nijmegen, The Netherlands. Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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