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Cheng X, Wang H, Zeng Z, Li L, Zhao R, Bodelier PLE, Wang Y, Liu X, Su C, Liu S. Niche differentiation of atmospheric methane-oxidizing bacteria and their community assembly in subsurface karst caves. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:886-896. [PMID: 35925016 DOI: 10.1111/1758-2229.13112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/05/2022] [Accepted: 07/17/2022] [Indexed: 06/17/2023]
Abstract
Karst caves are recently proposed as atmospheric methane sinks in terrestrial ecosystems. Despite of the detection of atmospheric methane-oxidizing bacteria (atmMOB) in caves, we still know little about their ecology and potential ability of methane oxidation in this ecosystem. To understand atmMOB ecology and their potential in methane consumption, we collected weathered rocks and sediments from three different caves in southwestern China. We determined the potential methane oxidization rates in the range of 1.25 ± 0.08 to 1.87 ± 0.41 ng CH4 g-1 DW h-1 , which are comparable to those reported in forest and grassland soils. Results showed that alkaline oligotrophic caves harbour high numbers of atmMOB, particularly upland soil cluster (USC), which significantly correlated with temperature, CH4 and CO2 concentrations. The absolute abundance of USCγ was higher than that of USCα. USCγ-OPS (open patch soil) and USCγ-SS (subsurface soil) dominated in most samples, whereas USCα-BFS (boreal forest soil) only predominated in the sediments near cave entrances, indicating niche differentiation of atmMOB in caves. Overwhelming dominance of homogenous selection in community assembly resulted in convergence of atmMOB communities. Collectively, our results demonstrated the niche differentiation of USC in subsurface alkaline caves and their non-negligible methane-oxidizing potential, providing brand-new knowledge about atmMOB ecology in subsurface biosphere.
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Affiliation(s)
- Xiaoyu Cheng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Hongmei Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Zhilin Zeng
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Lu Li
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Rui Zhao
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Yiheng Wang
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Xiaoyan Liu
- State Key Laboratory of Geobiology and Environmental Geology, China University of Geosciences, Wuhan, P. R. China
- School of Environmental Studies, China University of Geosciences, Wuhan, P. R. China
| | - Chuntian Su
- CAGS/Key Laboratory of Karst Dynamics, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, P. R. China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
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Iasakov TR, Kanapatskiy TA, Toshchakov SV, Korzhenkov AA, Ulyanova MO, Pimenov NV. The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation. MARINE ENVIRONMENTAL RESEARCH 2022; 173:105533. [PMID: 34875513 DOI: 10.1016/j.marenvres.2021.105533] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/11/2021] [Accepted: 11/21/2021] [Indexed: 05/20/2023]
Abstract
Pockmarks are important "pumps", which are believed to play a significant role in the global methane cycling and harboring a unique assemblage of very diverse prokaryotes. This study reports the results of massive sequencing of the 16S rRNA gene V4 hypervariable regions for the samples from thirteen pockmark horizons (the Baltic Sea) collected at depths from 0 to 280 cm below seafloor (cmbsf) and the rates of microbially mediated anaerobic oxidation of methane (AOM) and sulfate reduction (SR). Altogether, 76 bacterial and 12 archaeal phyla were identified, 23 of which were candidate divisions. Of the total obtained in the pockmark sequences, 84.3% of them were classified as Bacteria and 12.4% as Archaea; 3.3% of the sequences were assigned to unknown operational taxonomic units (OTUs). Members of the phyla Planctomycetota, Chloroflexota, Desulfobacterota, Caldatribacteriota, Acidobacteriota and Proteobacteria predominated across all horizons, comprising 58.5% of the total prokaryotic community. These phyla showed different types of patterns of relative abundance. Analysis of AOM-SR-mediated prokaryotes abundance and biogeochemical measurements revealed that ANME-2a-2b subcluster was predominant in sulfate-rich upper horizons (including sulfate-methane transition zone (SMTZ)) and together with sulfate-reducing bacterial group SEEP-SRB1 had a primary role in AOM coupled to SR. At deeper sulfate-depleted horizons ANME-2a-2b shifted to ANME-1a and ANME-1b which alone mediated AOM or switch to methanogenic metabolism. Shifting of the ANME subclusters depending on depth reflect a tendency for niche separation in these groups. It was shown that the abundance of Caldatribacteriota and organohalide-respiring Dehalococcoidia (Chloroflexota) exhibited a strong correlation with AOM rates. This is the first detailed study of depth profiles of prokaryotic diversity, patterns of relative abundance, and ANME niche separation in the Baltic Sea pockmark microbiomes sheds light on assembly of prokaryotes in a pockmark.
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Affiliation(s)
- Timur R Iasakov
- Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 69, 450054, Ufa, Russia.
| | - Timur A Kanapatskiy
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Leninsky prospect 33/2, 119071, Moscow, Russia
| | - Stepan V Toshchakov
- Kurchatov Center for Genome Research, NRC "Kurchatov Institute", Ac. Kurchatov square, 1, 123098, Moscow, Russia
| | - Aleksei A Korzhenkov
- Kurchatov Center for Genome Research, NRC "Kurchatov Institute", Ac. Kurchatov square, 1, 123098, Moscow, Russia
| | - Marina O Ulyanova
- Shirshov Institute of Oceanology, Russian Academy of Sciences, 36, Nahimovskiy prospekt, Moscow, 117997, Russia; Immanuel Kant Baltic Federal University, 14, Nevskogo str., Kaliningrad, 236016, Russia
| | - Nikolay V Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Leninsky prospect 33/2, 119071, Moscow, Russia
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van de Kamp J, Hook SE, Williams A, Tanner JE, Bodrossy L. Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep-sea sediments of the Great Australian Bight, Australia. Environ Microbiol 2019; 21:1782-1797. [PMID: 30761716 DOI: 10.1111/1462-2920.14559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/28/2019] [Accepted: 02/07/2019] [Indexed: 11/30/2022]
Abstract
Exploratory drilling for deep-sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional 'ecotypes' related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep-sea ecosystem.
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Affiliation(s)
- Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Sharon E Hook
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Lucas Heights, New South Wales, 2234, Australia
| | - Alan Williams
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Jason E Tanner
- Aquatic Sciences, South Australian Research and Development Institute, West Beach, South Australia, 5024, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
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In situ development of a methanotrophic microbiome in deep-sea sediments. ISME JOURNAL 2018; 13:197-213. [PMID: 30154496 PMCID: PMC6298960 DOI: 10.1038/s41396-018-0263-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/06/2018] [Accepted: 08/04/2018] [Indexed: 01/11/2023]
Abstract
Emission of the greenhouse gas methane from the seabed is globally controlled by marine aerobic and anaerobic methanotrophs gaining energy via methane oxidation. However, the processes involved in the assembly and dynamics of methanotrophic populations in complex natural microbial communities remain unclear. Here we investigated the development of a methanotrophic microbiome following subsurface mud eruptions at Håkon Mosby mud volcano (1250 m water depth). Freshly erupted muds hosted deep-subsurface communities that were dominated by Bathyarchaeota, Atribacteria and Chloroflexi. Methanotrophy was initially limited to a thin surface layer of Methylococcales populations consuming methane aerobically. With increasing distance to the eruptive center, anaerobic methanotrophic archaea, sulfate-reducing Desulfobacterales and thiotrophic Beggiatoaceae developed, and their respective metabolic capabilities dominated the biogeochemical functions of the community. Microbial richness, evenness, and cell numbers of the entire microbial community increased up to tenfold within a few years downstream of the mud flow from the eruptive center. The increasing diversity was accompanied by an up to fourfold increase in sequence abundance of relevant metabolic genes of the anaerobic methanotrophic and thiotrophic guilds. The communities fundamentally changed in their structure and functions as reflected in the metagenome turnover with distance from the eruptive center, and this was reflected in the biogeochemical zonation across the mud volcano caldera. The observed functional succession provides a framework for the response time and recovery of complex methanotrophic communities after disturbances of the deep-sea bed.
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Chronopoulou PM, Shelley F, Pritchard WJ, Maanoja ST, Trimmer M. Origin and fate of methane in the Eastern Tropical North Pacific oxygen minimum zone. THE ISME JOURNAL 2017; 11:1386-1399. [PMID: 28244978 PMCID: PMC5437358 DOI: 10.1038/ismej.2017.6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 12/06/2016] [Accepted: 01/09/2017] [Indexed: 11/23/2022]
Abstract
Oxygen minimum zones (OMZs) contain the largest pools of oceanic methane but its origin and fate are poorly understood. High-resolution (<15 m) water column profiles revealed a 300 m thick layer of elevated methane (20-105 nM) in the anoxic core of the largest OMZ, the Eastern Tropical North Pacific. Sediment core incubations identified a clear benthic methane source where the OMZ meets the continental shelf, between 350 and 650 m, with the flux reflecting the concentration of methane in the overlying anoxic water. Further incubations characterised a methanogenic potential in the presence of both porewater sulphate and nitrate of up to 88 nmol g-1day-1 in the sediment surface layer. In these methane-producing sediments, the majority (85%) of methyl coenzyme M reductase alpha subunit (mcrA) gene sequences clustered with Methanosarcinaceae (⩾96% similarity to Methanococcoides sp.), a family capable of performing non-competitive methanogenesis. Incubations with 13C-CH4 showed potential for both aerobic and anaerobic methane oxidation in the waters within and above the OMZ. Both aerobic and anaerobic methane oxidation is corroborated by the presence of particulate methane monooxygenase (pmoA) gene sequences, related to type I methanotrophs and the lineage of Candidatus Methylomirabilis oxyfera, known to perform nitrite-dependent anaerobic methane oxidation (N-DAMO), respectively.
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Affiliation(s)
| | - Felicity Shelley
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - William J Pritchard
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Susanna T Maanoja
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Mark Trimmer
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Li S, Song L, Gao X, Jin Y, Liu S, Shen Q, Zou J. Microbial Abundances Predict Methane and Nitrous Oxide Fluxes from a Windrow Composting System. Front Microbiol 2017; 8:409. [PMID: 28373862 PMCID: PMC5357657 DOI: 10.3389/fmicb.2017.00409] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/27/2017] [Indexed: 11/22/2022] Open
Abstract
Manure composting is a significant source of atmospheric methane (CH4) and nitrous oxide (N2O) that are two potent greenhouse gases. The CH4 and N2O fluxes are mediated by methanogens and methanotrophs, nitrifying and denitrifying bacteria in composting manure, respectively, while these specific bacterial functional groups may interplay in CH4 and N2O emissions during manure composting. To test the hypothesis that bacterial functional gene abundances regulate greenhouse gas fluxes in windrow composting systems, CH4 and N2O fluxes were simultaneously measured using the chamber method, and molecular techniques were used to quantify the abundances of CH4-related functional genes (mcrA and pmoA genes) and N2O-related functional genes (amoA, narG, nirK, nirS, norB, and nosZ genes). The results indicate that changes in interacting physicochemical parameters in the pile shaped the dynamics of bacterial functional gene abundances. The CH4 and N2O fluxes were correlated with abundances of specific compositional genes in bacterial community. The stepwise regression statistics selected pile temperature, mcrA and NH4+ together as the best predictors for CH4 fluxes, and the model integrating nirK, nosZ with pmoA gene abundances can almost fully explain the dynamics of N2O fluxes over windrow composting. The simulated models were tested against measurements in paddy rice cropping systems, indicating that the models can also be applicable to predicting the response of CH4 and N2O fluxes to elevated atmospheric CO2 concentration and rising temperature. Microbial abundances could be included as indicators in the current carbon and nitrogen biogeochemical models.
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Affiliation(s)
- Shuqing Li
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Lina Song
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Xiang Gao
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Yaguo Jin
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural University Nanjing, China
| | - Shuwei Liu
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
| | - Qirong Shen
- Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University Nanjing, China
| | - Jianwen Zou
- Jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation, College of Resources and Environmental Sciences, Nanjing Agricultural UniversityNanjing, China; Jiangsu Key Laboratory and Engineering Center for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural UniversityNanjing, China
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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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Islam T, Torsvik V, Larsen Ø, Bodrossy L, Øvreås L, Birkeland NK. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps. Front Microbiol 2016; 7:851. [PMID: 27379029 PMCID: PMC4908921 DOI: 10.3389/fmicb.2016.00851] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 05/23/2016] [Indexed: 11/13/2022] Open
Abstract
Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2–7.5 (optimal 5.5–6.0) and at a temperature range of 30–60°C (optimal 51–55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1–94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems.
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Affiliation(s)
- Tajul Islam
- Department of Biology, University of Bergen Bergen, Norway
| | - Vigdis Torsvik
- Department of Biology, University of Bergen Bergen, Norway
| | - Øivind Larsen
- Department of Biology, University of BergenBergen, Norway; Uni Environment, Uni ResearchBergen, Norway
| | | | - Lise Øvreås
- Department of Biology, University of Bergen Bergen, Norway
| | - Nils-Kåre Birkeland
- Department of Biology, University of BergenBergen, Norway; Centre for Geobiology, University of BergenBergen, Norway
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Burns KA, Jones R. Assessment of sediment hydrocarbon contamination from the 2009 Montara oil blow out in the Timor Sea. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 211:214-225. [PMID: 26774768 DOI: 10.1016/j.envpol.2015.10.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
In August 2009, a blowout of the Montara H1 well 260 km off the northwest coast of Australia resulted in the uncontrolled release of about 4.7 M L of light crude oil and gaseous hydrocarbons into the Timor Sea. Over the 74 day period of the spill, the oil remained offshore and did not result in shoreline incidents on the Australia mainland. At various times slicks were sighted over a 90,000 km(2) area, forming a layer of oil which was tracked by airplanes and satellites but the slicks typically remained within 35 km of the well head platform and were treated with 183,000 L of dispersants. The shelf area where the spill occurred is shallow (100-200 m) and includes off shore emergent reefs and cays and submerged banks and shoals. This study describes the increased inputs of oil to the system and assesses the environmental impact. Concentrations of hydrocarbon in the sediment at the time of survey were very low (total aromatic hydrocarbons (PAHs) ranged from 0.04 to 31 ng g(-1)) and were orders of magnitude lower than concentrations at which biological effects would be expected.
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Affiliation(s)
- Kathryn A Burns
- James Cook University, TROPWATER Group, ATSIP Building, Douglas, Qld 4814 Australia.
| | - Ross Jones
- Australian Institute of Marine Sciences, University of WA, Perth, 8001 WA, Australia.
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Ruff SE, Kuhfuss H, Wegener G, Lott C, Ramette A, Wiedling J, Knittel K, Weber M. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy. Front Microbiol 2016; 7:374. [PMID: 27065954 PMCID: PMC4814501 DOI: 10.3389/fmicb.2016.00374] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/08/2016] [Indexed: 11/13/2022] Open
Abstract
The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct microbial habitats due to their unique biogeochemical and physical characteristics. To link AOM phylotypes with seep habitats and to enable future meta-analyses we thus propose that seep environment ontology needs to be further specified.
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Affiliation(s)
- S Emil Ruff
- Department for Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany; HGF MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Hanna Kuhfuss
- Department for Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Gunter Wegener
- HGF MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany; MARUM Center for Marine Environmental Sciences, University of BremenBremen, Germany
| | - Christian Lott
- HYDRA Institute for Marine Sciences, Elba Field Station Campo nell'Elba, Italy
| | - Alban Ramette
- HGF MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Johanna Wiedling
- HYDRA Institute for Marine Sciences, Elba Field StationCampo nell'Elba, Italy; Department of Biogeochemistry, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Katrin Knittel
- Department for Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Miriam Weber
- HYDRA Institute for Marine Sciences, Elba Field StationCampo nell'Elba, Italy; Department of Biogeochemistry, Max Planck Institute for Marine MicrobiologyBremen, Germany
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11
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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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12
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Li M, Jain S, Baker BJ, Taylor C, Dick GJ. Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environ Microbiol 2013; 16:60-71. [PMID: 23826624 DOI: 10.1111/1462-2920.12182] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 05/10/2013] [Accepted: 06/03/2013] [Indexed: 12/30/2022]
Abstract
Particulate membrane-associated hydrocarbon monooxygenases (pHMOs) are critical components of the aerobic degradation pathway for low molecular weight hydrocarbons, including the potent greenhouse gas methane. Here, we analysed pHMO gene diversity in metagenomes and metatranscriptomes of hydrocarbon-rich hydrothermal plumes in the Guaymas Basin (GB) and nearby background waters in the deep Gulf of California. Seven distinct phylogenetic groups of pHMO were present and transcriptionally active in both plume and background waters, including several that are undetectable with currently available polymerase chain reaction (PCR) primers. The seven groups of pHMOs included those related to a putative ethane oxidizing Methylococcaceae-like group, a group of the SAR324 Deltaproteobacteria, three deep-sea clades (Deep sea-1/symbiont-like, Deep sea-2/PS-80 and Deep sea-3/OPU3) within gammaproteobacterial methanotrophs, one clade related to Group Z and one unknown group. Differential abundance of pHMO gene transcripts in plume and background suggests niche differentiation between groups. Corresponding 16S rRNA genes reflected similar phylogenetic and transcriptomic abundance trends. The novelty of transcriptionally active pHMOs we recovered from a hydrocarbon-rich hydrothermal plume suggests there are significant gaps in our knowledge of the diversity and function of these enzymes in the environment.
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Affiliation(s)
- Meng Li
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
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13
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Tavormina PL, Ussler W, Steele JA, Connon SA, Klotz MG, Orphan VJ. Abundance and distribution of diverse membrane-bound monooxygenase (Cu-MMO) genes within the Costa Rica oxygen minimum zone. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:414-423. [PMID: 23754722 DOI: 10.1111/1758-2229.12025] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 12/03/2012] [Indexed: 06/02/2023]
Abstract
Diverse copper-containing membrane-bound monooxygenase-encoding sequences (Cu-MMOs) have recently been described from the marine environment, suggesting widespread potential for oxidation of reduced substrates. Here, we used the well-defined oxygen and methane gradients associated with the Costa Rican oxygen minimum zone (OMZ) to gain insight into the physico-chemical parameters influencing the distribution and abundance of Cu-MMO-encoding marine microorganisms. Two Methylococcales-related Cu-MMO-encoding lineages, termed groups OPU1 and OPU3, demonstrated differences in their relative abundance, with both pmoA and candidate 16S rRNA genes correlating significantly with reduced environmental oxygen concentrations and depth. In contrast, a newly identified Cu-MMO-encoding lineage, Group C, was primarily associated with the oxygenated euphotic zone. An updated phylogenetic analysis including these sequences, a marine pxmABC gene cluster, ethylene-utilizing Cu-MMO-encoding lineages and previously reported planktonic Cu-MMOs (Groups W, X, Z and O) demonstrates the breadth of diversity of Cu-MMO-encoding marine microorganisms. Groups C and X affiliated phylogenetically with ethane- and ethylene-oxidizing Cu-MMOs, Groups W and O affiliated phylogenetically with the recently described Cu-MMO 'pXMO', and Group Z clustered with Cu-MMOs recovered from soils. Collectively, these data demonstrate widespread genetic potential in ocean waters for the oxidation of small, reduced molecules and advance our understanding of the microorganisms involved in methane cycling in the OMZ environment.
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Affiliation(s)
- Patricia L Tavormina
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA.
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14
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Sonoki T, Furukawa T, Jindo K, Suto K, Aoyama M, Sánchez-Monedero MÁ. Influence of biochar addition on methane metabolism during thermophilic phase of composting. J Basic Microbiol 2012; 53:617-21. [DOI: 10.1002/jobm.201200096] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 04/30/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Tomonori Sonoki
- Faculty of Agriculture and Life Science; Hirosaki University; Bunkyo-cho; Hirosaki, Aomori; Japan
| | - Toru Furukawa
- Faculty of Agriculture and Life Science; Hirosaki University; Bunkyo-cho; Hirosaki, Aomori; Japan
| | - Keiji Jindo
- Department of Soil and Water Conservation and Organic Waste Management; Centro de Edafologíay Biología Aplicada del Segura (CEBAS-CSIC); Campus Universitario de Espinardo; Murcia; Spain
| | - Koki Suto
- Faculty of Agriculture and Life Science; Hirosaki University; Bunkyo-cho; Hirosaki, Aomori; Japan
| | - Masakazu Aoyama
- Faculty of Agriculture and Life Science; Hirosaki University; Bunkyo-cho; Hirosaki, Aomori; Japan
| | - Miguel Á. Sánchez-Monedero
- Department of Soil and Water Conservation and Organic Waste Management; Centro de Edafologíay Biología Aplicada del Segura (CEBAS-CSIC); Campus Universitario de Espinardo; Murcia; Spain
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15
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Culture-independent methods for studying environmental microorganisms: methods, application, and perspective. Appl Microbiol Biotechnol 2011; 93:993-1003. [DOI: 10.1007/s00253-011-3800-7] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/23/2011] [Accepted: 11/27/2011] [Indexed: 01/29/2023]
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16
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Kennedy J, O'Leary ND, Kiran GS, Morrissey JP, O'Gara F, Selvin J, Dobson ADW. Functional metagenomic strategies for the discovery of novel enzymes and biosurfactants with biotechnological applications from marine ecosystems. J Appl Microbiol 2011; 111:787-99. [PMID: 21777355 DOI: 10.1111/j.1365-2672.2011.05106.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Marine ecosystems are home to bacteria which are exposed to a wide variety of environmental conditions, such as extremes in temperature, salinity, nutrient availability and pressure. Survival under these conditions must have necessitated the adaptation and the development of unique cellular biochemistry and metabolism by these microbes. Thus, enzymes isolated from these microbes have the potential to possess quite unique physiological and biochemical properties. This review outlines a number of function-based metagenomic approaches which are available to screen metagenomic libraries constructed from marine ecosystems to facilitate the exploitation of some of these potentially novel biocatalysts. Functional screens to isolate novel cellulases, lipases and esterases, proteases, laccases, oxidoreductases and biosurfactants are described, together with approaches which can be employed to help overcome some of the typical problems encountered with functional metagenomic-based screens.
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Affiliation(s)
- J Kennedy
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
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17
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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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Distributions of putative aerobic methanotrophs in diverse pelagic marine environments. ISME JOURNAL 2010; 4:700-10. [PMID: 20147984 DOI: 10.1038/ismej.2009.155] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Aerobic methane oxidization in the pelagic ocean serves an important role in limiting methane release to the atmosphere, yet little is known about the identity and distribution of bacteria that mediate this process. The distribution of putative methane-oxidizing marine groups, OPU1, OPU3 and Group X, was assessed in different ocean provinces using a newly developed fingerprinting method (monooxygenase intergenic spacer analysis (MISA)) in combination with pmoA clone library analysis and quantitative PCR (qPCR). The distribution of these three distinct monooxygenase groups, previously reported from pelagic marine environments, was examined in 39 samples including active methane seeps in the Gulf of Mexico and Santa Monica Bay, submarine canyon heads along the California continental margin, an oligotrophic subtropical gyre and areas proximal to a hydrothermal vent in the North Fiji back-arc basin. OPU1 and OPU3 were widely and similarly distributed within the meso- and bathypelagic zone (110 to approximately 2000 m water depth) and showed a >50-fold greater abundance near methane seeps relative to non-seep sites. In contrast, Group X was predominantly recovered from samples along the California margin, at both seep and non-seep sites. All three phylotypes were below detection in the epipelagic zone to depths of 100 m. Several additional deeply branching monooxygenase sequences were also identified in this study, indicating the presence of uncharacterized groups of microorganisms potentially involved in the cycling of methane or ammonium.
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