251
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Deng Y, Liu Y, Dumont M, Conrad R. Salinity Affects the Composition of the Aerobic Methanotroph Community in Alkaline Lake Sediments from the Tibetan Plateau. MICROBIAL ECOLOGY 2017; 73:101-110. [PMID: 27878346 DOI: 10.1007/s00248-016-0879-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Lakes are widely distributed on the Tibetan Plateau, which plays an important role in natural methane emission. Aerobic methanotrophs in lake sediments reduce the amount of methane released into the atmosphere. However, no study to date has analyzed the methanotroph community composition and their driving factors in sediments of these high-altitude lakes (>4000 m). To provide new insights on this aspect, the abundance and composition in the sediments of six high-altitude alkaline lakes (including both freshwater and saline lakes) on the Tibetan Plateau were studied. The quantitative PCR, terminal restriction fragment length polymorphism, and 454-pyrosequencing methods were used to target the pmoA genes. The pmoA gene copies ranged 104-106 per gram fresh sediment. Type I methanotrophs predominated in Tibetan lake sediments, with Methylobacter and uncultivated type Ib methanotrophs being dominant in freshwater lakes and Methylomicrobium in saline lakes. Combining the pmoA-pyrosequencing data from Tibetan lakes with other published pmoA-sequencing data from lake sediments of other regions, a significant salinity and alkalinity effect (P = 0.001) was detected, especially salinity, which explained ∼25% of methanotroph community variability. The main effect was Methylomicrobium being dominant (up to 100%) in saline lakes only. In freshwater lakes, however, methanotroph composition was relatively diverse, including Methylobacter, Methylocystis, and uncultured type Ib clusters. This study provides the first methanotroph data for high-altitude lake sediments (>4000 m) and shows that salinity is a driving factor for the community composition of aerobic methanotrophs.
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Affiliation(s)
- Yongcui Deng
- College of Geographic Sciences, Nanjing Normal University, 1 Wenyuan Road, 210023, Nanjing, China
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, 1 Wenyuan Road, 210023, Nanjing, China
| | - Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100085, Beijing, China.
| | - Marc Dumont
- Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043, Marburg, Germany
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252
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Lanthanide-dependent cross-feeding of methane-derived carbon is linked by microbial community interactions. Proc Natl Acad Sci U S A 2016; 114:358-363. [PMID: 28028242 DOI: 10.1073/pnas.1619871114] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The utilization of methane, a potent greenhouse gas, is an important component of local and global carbon cycles that is characterized by tight linkages between methane-utilizing (methanotrophic) and nonmethanotrophic bacteria. It has been suggested that the methanotroph sustains these nonmethanotrophs by cross-feeding, because subsequent products of the methane oxidation pathway, such as methanol, represent alternative carbon sources. We established cocultures in a microcosm model system to determine the mechanism and substrate that underlay the observed cross-feeding in the environment. Lanthanum, a rare earth element, was applied because of its increasing importance in methylotrophy. We used co-occurring strains isolated from Lake Washington sediment that are involved in methane utilization: a methanotroph and two nonmethanotrophic methylotrophs. Gene-expression profiles and mutant analyses suggest that methanol is the dominant carbon and energy source the methanotroph provides to support growth of the nonmethanotrophs. However, in the presence of the nonmethanotroph, gene expression of the dominant methanol dehydrogenase (MDH) shifts from the lanthanide-dependent MDH (XoxF)-type, to the calcium-dependent MDH (MxaF)-type. Correspondingly, methanol is released into the medium only when the methanotroph expresses the MxaF-type MDH. These results suggest a cross-feeding mechanism in which the nonmethanotrophic partner induces a change in expression of methanotroph MDHs, resulting in release of methanol for its growth. This partner-induced change in gene expression that benefits the partner is a paradigm for microbial interactions that cannot be observed in studies of pure cultures, underscoring the importance of synthetic microbial community approaches to understand environmental microbiomes.
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253
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Methylacidiphilum fumariolicum SolV, a thermoacidophilic 'Knallgas' methanotroph with both an oxygen-sensitive and -insensitive hydrogenase. ISME JOURNAL 2016; 11:945-958. [PMID: 27935590 PMCID: PMC5364354 DOI: 10.1038/ismej.2016.171] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/26/2016] [Accepted: 10/19/2016] [Indexed: 11/09/2022]
Abstract
Methanotrophs play a key role in balancing the atmospheric methane concentration. Recently, the microbial methanotrophic diversity was extended by the discovery of thermoacidophilic methanotrophs belonging to the Verrucomicrobia phylum in geothermal areas. Here we show that a representative of this new group, Methylacidiphilum fumariolicum SolV, is able to grow as a real 'Knallgas' bacterium on hydrogen/carbon dioxide, without addition of methane. The full genome of strain SolV revealed the presence of two hydrogen uptake hydrogenases genes, encoding an oxygen-sensitive (hup-type) and an oxygen-insensitive enzyme (hhy-type). The hhy-type hydrogenase was constitutively expressed and active and supported growth on hydrogen alone up to a growth rate of 0.03 h-1, at O2 concentrations below 1.5%. The oxygen-sensitive hup-type hydrogenase was expressed when oxygen was reduced to below 0.2%. This resulted in an increase of the growth rate to a maximum of 0.047 h-1, that is 60% of the rate on methane. The results indicate that under natural conditions where both hydrogen and methane might be limiting strain SolV may operate primarily as a methanotrophic 'Knallgas' bacterium. These findings argue for a revision of the role of hydrogen in methanotrophic ecosystems, especially in soil and related to consumption of atmospheric methane.
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254
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Liu Y, Liu X, Cheng K, Li L, Zhang X, Zheng J, Zheng J, Pan G. Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO 2 and Temperature in a Paddy Field. Front Microbiol 2016; 7:1895. [PMID: 27933055 PMCID: PMC5121223 DOI: 10.3389/fmicb.2016.01895] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/11/2016] [Indexed: 11/13/2022] Open
Abstract
Although climate change is predicted to affect methane (CH4) emissions in paddy soil, the dynamics of methanogens and methanotrophs in paddy fields under climate change have not yet been fully investigated. To address this issue, a multifactor climate change experiment was conducted in a Chinese paddy field using the following experimental treatments: (1) enrichment of atmospheric CO2 concentrations (500 ppm, CE), (2) canopy air warming (2°C above the ambient, WA), (3) combined CO2 enrichment and warming (CW), and (4) ambient conditions (CK). We analyzed the abundance of methanogens and methanotrophs, community structures, CH4 production and oxidation potentials, in situ CH4 emissions using real-time PCR, T-RFLP, and clone library techniques, as well as biochemical assays. Compared to the control under CE and CW treatments, CH4 production potential, methanogenic gene abundance and soil microbial biomass carbon significantly increased; the methanogenic community, however, remained stable. The canopy air warming treatment only had an effect on CH4 oxidation potential at the ripening stage. Phylogenic analysis indicated that methanogens in the rhizosphere were dominated by Methanosarcina, Methanocellales, Methanobacteriales, and Methanomicrobiales, while methanotrophic sequences were classified as Methylococcus, Methylocaldum, Methylomonas, Methylosarcina (Type I) and Methylocystis (Type II). However, the relative abundance of Methylococcus (Type I) decreased under CE and CW treatments and the relative abundance of Methylocystis (Type II) increased. The in situ CH4 fluxes indicated similar seasonal patterns between treatments; both CE and CW increased CH4 emissions. In conclusion results suggest that methanogens and methanotrophs respond differently to elevated atmospheric CO2 concentrations and warming, thus adding insights into the effects of simulated global climate change on CH4 emissions in paddy fields.
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Affiliation(s)
- Yuan Liu
- Department of Bioengineering, College of Life Science, Huaibei Normal University Huaibei, China
| | - Xiaoyu Liu
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Kun Cheng
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Lianqing Li
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Xuhui Zhang
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Jufeng Zheng
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Jinwei Zheng
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University Nanjing, China
| | - Genxing Pan
- Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural UniversityNanjing, China; Zhejiang Provincial Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration, School of Environmental and Resource Sciences, Zhejiang A & F University, Lin'anHangzhou, China
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255
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Ho A, Angel R, Veraart AJ, Daebeler A, Jia Z, Kim SY, Kerckhof FM, Boon N, Bodelier PLE. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System. Front Microbiol 2016; 7:1285. [PMID: 27602021 PMCID: PMC4993757 DOI: 10.3389/fmicb.2016.01285] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/04/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.
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Affiliation(s)
- Adrian Ho
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna Vienna, Austria
| | - Annelies J Veraart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Anne Daebeler
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna Vienna, Austria
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences Nanjing, China
| | - Sang Yoon Kim
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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256
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Fradet DT, Tavormina PL, Orphan VJ. Members of the methanotrophic genus Methylomarinum inhabit inland mud pots. PeerJ 2016; 4:e2116. [PMID: 27478692 PMCID: PMC4950536 DOI: 10.7717/peerj.2116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/18/2016] [Indexed: 11/24/2022] Open
Abstract
Proteobacteria capable of converting the greenhouse gas methane to biomass, energy, and carbon dioxide represent a small but important sink in global methane inventories. Currently, 23 genera of methane oxidizing (methanotrophic) proteobacteria have been described, although many are represented by only a single validly described species. Here we describe a new methanotrophic isolate that shares phenotypic characteristics and phylogenetic relatedness with the marine methanotroph Methylomarinum vadi. However, the new isolate derives from a terrestrial saline mud pot at the northern terminus of the Eastern Pacific Rise (EPR). This new cultivar expands our knowledge of the ecology of Methylomarinum, ultimately towards a fuller understanding of the role of this genus in global methane cycling.
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Affiliation(s)
- Danielle T Fradet
- Flintridge Sacred Heart Academy , La Canada Flintridge, CA , United States
| | - Patricia L Tavormina
- Geological and Planetary Sciences, California Institute of Technology , Pasadena, CA , United States
| | - Victoria J Orphan
- Geological and Planetary Sciences, California Institute of Technology , Pasadena, CA , United States
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257
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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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258
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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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259
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Bornemann M, Bussmann I, Tichy L, Deutzmann J, Schink B, Pester M. Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance. FEMS Microbiol Ecol 2016; 92:fiw123. [PMID: 27267930 DOI: 10.1093/femsec/fiw123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 11/14/2022] Open
Abstract
Methane emissions from freshwater environments contribute substantially to global warming but are under strong control of aerobic methane-oxidizing bacteria. Recently discovered methane seeps (pockmarks) in freshwater lake sediments have the potential to bypass this control by their strong outgassing activity. Whether this is counteracted by pelagic methanotrophs is not well understood yet. We used a (3)H-CH4-radiotracer technique and pmoA-based molecular approaches to assess the activity, abundance and community structure of pelagic methanotrophs above active pockmarks in deep oligotrophic Lake Constance. Above profundal pockmarks, methane oxidation rates (up to 458 nmol CH4 l(-1) d(-1)) exceeded those of the surrounding water column by two orders of magnitude and coincided with maximum methanotroph abundances of 0.6% of the microbial community. Phylogenetic analysis indicated a dominance of members of the Methylococcaceae in the water column of both, pockmark and reference sites, with most of the retrieved sequences being associated with a water-column specific clade. Communities at pockmark and reference locations also differed in parts, which was likely caused by entrainment of sediment-hosted methanotrophs at pockmark sites. Our results show that the release of seep-derived methane to the atmosphere is counteracted by a distinct methanotrophic community with a pronounced activity throughout bottom waters.
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Affiliation(s)
- Maren Bornemann
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Ingeborg Bussmann
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Meeresstation Helgoland, Kurpromenade 201, D-27498 Helgoland, Germany
| | - Lucas Tichy
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Jörg Deutzmann
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany Department of Civil and Environmental Engineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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260
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Osudar R, Liebner S, Alawi M, Yang S, Bussmann I, Wagner D. Methane turnover and methanotrophic communities in arctic aquatic ecosystems of the Lena Delta, Northeast Siberia. FEMS Microbiol Ecol 2016; 92:fiw116. [PMID: 27230921 DOI: 10.1093/femsec/fiw116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 01/01/2023] Open
Abstract
Large amounts of organic carbon are stored in Arctic permafrost environments, and microbial activity can potentially mineralize this carbon into methane, a potent greenhouse gas. In this study, we assessed the methane budget, the bacterial methane oxidation (MOX) and the underlying environmental controls of arctic lake systems, which represent substantial sources of methane. Five lake systems located on Samoylov Island (Lena Delta, Siberia) and the connected river sites were analyzed using radiotracers to estimate the MOX rates, and molecular biology methods to characterize the abundance and the community composition of methane-oxidizing bacteria (MOB). In contrast to the river, the lake systems had high variation in the methane concentrations, the abundance and composition of the MOB communities, and consequently, the MOX rates. The highest methane concentrations and the highest MOX rates were detected in the lake outlets and in a lake complex in a flood plain area. Though, in all aquatic systems, we detected both, Type I and II MOB, in lake systems, we observed a higher diversity including MOB, typical of the soil environments. The inoculation of soil MOB into the aquatic systems, resulting from permafrost thawing, might be an additional factor controlling the MOB community composition and potentially methanotrophic capacity.
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Affiliation(s)
- Roman Osudar
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Research Unit Potsdam, Telegrafenberg, 14473 Potsdam, Germany GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Sizhong Yang
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Ingeborg Bussmann
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Biological Station Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
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261
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Imhoff JF. New Dimensions in Microbial Ecology-Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment. Microorganisms 2016; 4:microorganisms4020019. [PMID: 27681913 PMCID: PMC5029485 DOI: 10.3390/microorganisms4020019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/20/2016] [Accepted: 05/20/2016] [Indexed: 12/11/2022] Open
Abstract
During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5'phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria.
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Affiliation(s)
- Johannes F Imhoff
- GEOMAR Helmholtz-Zentrum für Ozeanforschung, Düsternbrooker Weg 20, D-24105 Kiel, Germany.
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262
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Danilova OV, Suzina NE, Van De Kamp J, Svenning MM, Bodrossy L, Dedysh SN. A new cell morphotype among methane oxidizers: a spiral-shaped obligately microaerophilic methanotroph from northern low-oxygen environments. ISME JOURNAL 2016; 10:2734-2743. [PMID: 27058508 DOI: 10.1038/ismej.2016.48] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/05/2016] [Accepted: 02/25/2016] [Indexed: 12/29/2022]
Abstract
Although representatives with spiral-shaped cells are described for many functional groups of bacteria, this cell morphotype has never been observed among methanotrophs. Here, we show that spiral-shaped methanotrophic bacteria do exist in nature but elude isolation by conventional approaches due to the preference for growth under micro-oxic conditions. The helical cell shape may enable rapid motility of these bacteria in water-saturated, heterogeneous environments with high microbial biofilm content, therefore offering an advantage of fast cell positioning under desired high methane/low oxygen conditions. The pmoA genes encoding a subunit of particulate methane monooxygenase from these methanotrophs form a new genus-level lineage within the family Methylococcaceae, type Ib methanotrophs. Application of a pmoA-based microarray detected these bacteria in a variety of high-latitude freshwater environments including wetlands and lake sediments. As revealed by the environmental pmoA distribution analysis, type Ib methanotrophs tend to live very near the methane source, where oxygen is scarce. The former perception of type Ib methanotrophs as being typical for thermal habitats appears to be incorrect because only a minor proportion of pmoA sequences from these bacteria originated from environments with elevated temperatures.
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Affiliation(s)
- Olga V Danilova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Natalia E Suzina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | | | - Mette M Svenning
- UiT The Arctic University of Norway, Department of Arctic and Marine Biology, Tromsø, Norway
| | | | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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Ho A, van den Brink E, Reim A, Krause SMB, Bodelier PLE. Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure. Front Microbiol 2016; 6:1493. [PMID: 26779148 PMCID: PMC4700171 DOI: 10.3389/fmicb.2015.01493] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/11/2015] [Indexed: 11/18/2022] Open
Abstract
Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a ‘tipping point’ where activity no longer recovered if disturbance persists and increase in frequency.
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Affiliation(s)
- Adrian Ho
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Erik van den Brink
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Andreas Reim
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Sascha M B Krause
- Department of Chemical Engineering, University of Washington, Seattle WA, USA
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
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