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Islam T, Larsen Ø, Birkeland NK. A Novel Cold-adapted Methylovulum species, with a High C16:1ω5c Content, Isolated from an Arctic Thermal Spring in Spitsbergen. Microbes Environ 2020; 35:ME20044. [PMID: 32536671 PMCID: PMC7511782 DOI: 10.1264/jsme2.me20044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/25/2020] [Indexed: 11/12/2022] Open
Abstract
A novel cold-adapted methane-oxidizing bacterium, termed TFB, was isolated from the thermoglacial Arctic karst spring, Trollosen, located in the South Spitsbergen National Park (Norway). The source water is cold and extremely low in phosphate and nitrate. The isolate belongs to the Methylovulum genus of gammaproteobacterial methanotrophs, with the closest phylogenetic affiliation with Methylovulum miyakonense and Methylovulum psychrotolerans (96.2 and 96.1% 16S rRNA gene sequence similarities, respectively). TFB is a strict aerobe that only grows in the presence of methane or methanol. It fixes atmospheric nitrogen and contains Type I intracellular membranes. The growth temperature range was 2-22°C, with an optimum at 13-18°C. The functional genes pmoA, mxaF, and nifH were identified by PCR, whereas mmoX and cbbL were not. C16:1ω5c was identified as the major fatty acid constituent, at an amount (>49%) not previously found in any methanotrophs, and is likely to play a major role in cold adaptation. Strain TFB may be regarded as a new psychrotolerant or psychrophilic species within the genus Methylovulum. The recovery of this cold-adapted bacterium from a neutral Arctic thermal spring increases our knowledge of the diversity and adaptation of extremophilic gammaproteobacterial methanotrophs in the candidate family "Methylomonadaceae".
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Affiliation(s)
- Tajul Islam
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Bergen Katedralskole, Kong Oscars gate 36, 5017 Bergen, Norway
| | - Øivind Larsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- NORCE Norwegian Research Centre AS, Bergen, Norway
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Guerrero-Cruz S, Stultiens K, van Kessel MAHJ, Versantvoort W, Jetten MSM, Op den Camp HJM, Kartal B. Key Physiology of a Nitrite-Dependent Methane-Oxidizing Enrichment Culture. Appl Environ Microbiol 2019; 85:e00124-19. [PMID: 30770408 PMCID: PMC6450021 DOI: 10.1128/aem.00124-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/11/2019] [Indexed: 11/20/2022] Open
Abstract
Nitrite-dependent methane-oxidizing bacteria couple the reduction of nitrite to the oxidation of methane via a unique oxygen-producing pathway. This process is carried out by members of the genus Methylomirabilis that belong to the NC10 phylum. Contrary to other known anaerobic methane oxidizers, they do not employ the reverse methanogenesis pathway for methane activation but instead a canonical particulate methane monooxygenase similar to those used by aerobic methanotrophs. Methylomirabilis-like bacteria are detected in many natural and manmade ecosystems, but their physiology is not well understood. Here, using continuous cultivation techniques, batch activity assays, and state-of-the-art membrane-inlet mass spectrometry, we determined growth rate, doubling time, and methane and nitrite affinities of the nitrite-dependent methane-oxidizing bacterium "Candidatus Methylomirabilis lanthanidiphila." Our results provide insight into understanding the interactions of these microorganisms with methanotrophs and other nitrite-reducing microorganisms, such as anaerobic ammonium-oxidizing bacteria. Furthermore, our data can be used in modeling studies as well as wastewater treatment plant design.IMPORTANCE Methane is an important greenhouse gas with a radiative forcing 28 times that of carbon dioxide over a 100-year time scale. The emission of methane to the atmosphere is controlled by aerobic and anaerobic methanotrophs, which are microorganisms that are able to oxidize methane to conserve energy. While aerobic methanotrophs have been studied for over a century, knowledge on the physiological characteristics of anaerobic methanotrophs is scarce. Here, we describe kinetic properties of "Candidatus Methylomirabilis lanthanidiphila," a nitrite-dependent methane-oxidizing microorganism, which is ecologically important and can be applied in wastewater treatment.
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Affiliation(s)
- Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Karin Stultiens
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | | | - Wouter Versantvoort
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | | | - Boran Kartal
- Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
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3
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Deng Y, Gui Q, Dumont M, Han C, Deng H, Yun J, Zhong W. Methylococcaceae are the dominant active aerobic methanotrophs in a Chinese tidal marsh. Environ Sci Pollut Res Int 2019; 26:636-646. [PMID: 30411293 DOI: 10.1007/s11356-018-3560-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Although coastal marshes are net carbon sinks, they are net methane sources. Aerobic methanotrophs in coastal marsh soils are important methane consumers, but their activity and populations are poorly characterized. DNA stable-isotope probing followed by sequencing was used to determine how active methanotrophic populations differed in the main habitats of a Chinese coastal marsh. These habitats included mudflat, native plant-dominated, and alien plant-dominated habitats. Methylococcaceae was the most active methanotroph family across four habitats. Abundant methylotroph sequences, including methanotrophs and non-methane-oxidizing methylotrophs (Methylotenera and Methylophaga), constituted 50-70% of the 16S rRNA genes detected in the labeled native plant-dominated and mudflat soils. Methylotrophs were less abundant (~ 20%) in labeled alien plant-dominated soil, suggesting less methane assimilation into the target community or a different extent of carbon cross-feeding. Canonical correspondence analysis indicated a significant correlation between the active bacterial communities and soil properties (salinity, organic carbon, total nitrogen, pH, and available phosphorus). Importantly, these results highlight how changing vegetation or soil features in coastal marshes may change their resident active methanotrophic populations, which will further influence methane cycling.
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Affiliation(s)
- Yongcui Deng
- School of Geography Science, Nanjing Normal University, Nanjing, China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing, China
| | - Qian Gui
- School of Geography Science, Nanjing Normal University, Nanjing, China
| | - Marc Dumont
- Biological Sciences, University of Southampton, Southampton, UK
| | - Cheng Han
- School of Geography Science, Nanjing Normal University, Nanjing, China
| | - Huan Deng
- School of Geography Science, Nanjing Normal University, Nanjing, China
| | - Juanli Yun
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenhui Zhong
- School of Geography Science, Nanjing Normal University, Nanjing, China.
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China.
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing, China.
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Crevecoeur S, Vincent WF, Comte J, Matveev A, Lovejoy C. Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds. PLoS One 2017; 12:e0188223. [PMID: 29182670 PMCID: PMC5705078 DOI: 10.1371/journal.pone.0188223] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/02/2017] [Indexed: 11/27/2022] Open
Abstract
Lakes and ponds derived from thawing permafrost are strong emitters of carbon dioxide and methane to the atmosphere, but little is known about the methane oxidation processes in these waters. Here we investigated the distribution and potential activity of aerobic methanotrophic bacteria in thaw ponds in two types of eroding permafrost landscapes in subarctic Québec: peatlands and mineral soils. We hypothesized that methanotrophic community composition and potential activity differ regionally as a function of the landscape type and permafrost degradation stage, and locally as a function of depth-dependent oxygen conditions. Our analysis of pmoA transcripts by Illumina amplicon sequencing and quantitative PCR showed that the communities were composed of diverse and potentially active lineages. Type I methanotrophs, particularly Methylobacter, dominated all communities, however there was a clear taxonomic separation between the two landscape types, consistent with environmental control of community structure. In contrast, methanotrophic potential activity, measured by pmoA transcript concentrations, did not vary with landscape type, but correlated with conductivity, phosphorus and total suspended solids. Methanotrophic potential activity was also detected in low-oxygen bottom waters, where it was inversely correlated with methane concentrations, suggesting methane depletion by methanotrophs. Methanotrophs were present and potentially active throughout the water column regardless of oxygen concentration, and may therefore be resilient to future mixing and oxygenation regimes in the warming subarctic.
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Affiliation(s)
- Sophie Crevecoeur
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Warwick F. Vincent
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
| | - Jérôme Comte
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Alex Matveev
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
| | - Connie Lovejoy
- Département de Biologie, Centre d’études nordiques (CEN) and Takuvik Joint International Laboratory, Université Laval, Québec, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
- Québec-Océan, Université Laval, Québec, Québec, Canada
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Osborne KA, Gray ND, Sherry A, Leary P, Mejeha O, Bischoff J, Rush D, Sidgwick FR, Birgel D, Kalyuzhnaya MG, Talbot HM. Methanotroph-derived bacteriohopanepolyol signatures as a function of temperature related growth, survival, cell death and preservation in the geological record. Environ Microbiol Rep 2017; 9:492-500. [PMID: 28772060 DOI: 10.1111/1758-2229.12570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
Interpretation of bacteriohopanepolyol (BHP) biomarkers tracing microbiological processes in modern and ancient sediments relies on understanding environmental controls of production and preservation. BHPs from methanotrophs (35-aminoBHPs) were studied in methane-amended aerobic river-sediment incubations at different temperatures. It was found that: (i) With increasing temperature (4°C-40°C) a 10-fold increase in aminopentol (associated with Crenothrix and Methylobacter spp. growth) occurred with only marginal increases in aminotriol and aminotetrol; (ii) A further increase in temperature (50°C) saw selection for the thermophile Methylocaldum and mixtures of aminopentol and C-3 methylated aminopentol, again, with no increase in aminotriol and aminotetrol. (iii) At 30°C, more aminopentol and an aminopentol isomer and unsaturated aminopentol were produced after methanotroph growth and the onset of substrate starvation/oxygen depletion. (iv) At 50°C, aminopentol and C-3 methylated aminopentol, only accumulated during growth but were clearly resistant to remineralization despite cell death. These results have profound implications for the interpretation of aminoBHP distributions and abundances in modern and past environments. For instance, a temperature regulation of aminopentol production but not aminotetrol or aminotriol is consistent with and, corroborative of, observed aminopentol sensitivity to climate warming recorded in a stratigraphic sequence deposited during the Paleocene-Eocene thermal maximum (PETM).
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Affiliation(s)
- Kate A Osborne
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Neil D Gray
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Angela Sherry
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Peter Leary
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Obioma Mejeha
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Juliane Bischoff
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Darci Rush
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Department of Microbiology & Biogeochemistry, The Royal Netherlands Institute for Sea Research (NIOZ), Den Hag, Texel, The Netherlands
| | - Frances R Sidgwick
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Newcastle University Protein and Proteome Analysis (NUPPA), Devonshire Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Daniel Birgel
- Institute for Geology, Universität Hamburg, Bundesstraße 55, Hamburg 20146, Germany
| | | | - Helen M Talbot
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Liu H, Wu X, Li Z, Wang Q, Liu D, Liu G. Responses of soil methanogens, methanotrophs, and methane fluxes to land-use conversion and fertilization in a hilly red soil region of southern China. Environ Sci Pollut Res Int 2017; 24:8731-8743. [PMID: 28213705 DOI: 10.1007/s11356-017-8628-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
Changes in land-uses and fertilization are important factors regulating methane (CH4) emissions from paddy soils. However, the responses of soil CH4 emissions to these factors and the underlying mechanisms remain unclear. The objective of this study was to explore the effects of land-use conversion from paddies to orchards and fertilization on soil CH4 fluxes, and the abundance and community compositions of methanogens and methanotrophs. Soil CH4 fluxes were quantified by static chamber and gas chromatography technology. Abundance and community structures of methanogens and methanotrophs (based on mcrA and pmoA genes, respectively) were determined by quantitative real-time PCR (qPCR), and terminal restriction fragment length polymorphism (TRFLP), cloning and sequence analysis, respectively. Results showed that land-use conversion from paddies to orchards dramatically decreased soil CH4 fluxes, whereas fertilization did not distinctly affect soil CH4 fluxes. Furthermore, abundance of methanogens and methanotrophs were decreased after converting paddies to orchards. Fertilization decreased the abundance of these microorganisms, but the values were not statistically significant. Moreover, land-use conversion had fatal effects on some members of the methanogenic archaea (Methanoregula and Methanosaeta), increased type II methanotrophs (Methylocystis and Methylosinus), and decreased type I methanotrophs (Methylobacter and Methylococcus). However, fertilization could only significantly affect type I methanotrophs in the orchard plots. In addition, CH4 fluxes from paddy soils were positively correlated with soil dissolved organic carbon contents and methanogens abundance, whereas CH4 fluxes in orchard plots were negatively related to methanotroph abundance. Therefore, our results suggested that land-use conversion from paddies to orchards could change the abundance and community compositions of methanogens and methanotrophs, and ultimately alter the soil CH4 fluxes. Overall, our study shed insight on the underlying mechanisms of how land-use conversion from paddies to orchards decreased CH4 emissions.
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Affiliation(s)
- Huifeng Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Xing Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Joint Center for Global Change Studies, Beijing, 100875, China.
| | - Zongshan Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Joint Center for Global Change Studies, Beijing, 100875, China
| | - Qing Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Dan Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Guohua Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- Joint Center for Global Change Studies, Beijing, 100875, China.
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7
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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. Microb Ecol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Vekeman B, Speth D, Wille J, Cremers G, De Vos P, Op den Camp HJM, Heylen K. Genome Characteristics of Two Novel Type I Methanotrophs Enriched from North Sea Sediments Containing Exclusively a Lanthanide-Dependent XoxF5-Type Methanol Dehydrogenase. Microb Ecol 2016; 72:503-509. [PMID: 27457652 DOI: 10.1007/s00248-016-0808-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Microbial methane oxidizers play a crucial role in the oxidation of methane in marine ecosystems, as such preventing the escape of excessive methane to the atmosphere. Despite the important role of methanotrophs in marine ecosystems, only a limited number of isolates are described, with only four genomes available. Here, we report on two genomes of gammaproteobacterial methanotroph cultures, affiliated with the deep-sea cluster 2, obtained from North Sea sediment. Initial enrichments using methane as sole source of carbon and energy and mimicking the in situ conditions followed by serial subcultivations and multiple extinction culturing events over a period of 3 years resulted in a highly enriched culture. The draft genomes of the methane oxidizer in both cultures showed the presence of genes typically found in type I methanotrophs, including genes encoding particulate methane monooxygenase (pmoCAB), genes for tetrahydromethanopterin (H4MPT)- and tetrahydrofolate (H4F)-dependent C1-transfer pathways, and genes of the ribulose monophosphate (RuMP) pathway. The most distinctive feature, when compared to other available gammaproteobacterial genomes, is the absence of a calcium-dependent methanol dehydrogenase. Both genomes reported here only have a xoxF gene encoding a lanthanide-dependent XoxF5-type methanol dehydrogenase. Thus, these genomes offer novel insight in the genomic landscape of uncultured diversity of marine methanotrophs.
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Affiliation(s)
- Bram Vekeman
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, 9000, Ghent, Belgium.
| | - Daan Speth
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jasper Wille
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Geert Cremers
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Paul De Vos
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Kim Heylen
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, 9000, Ghent, Belgium
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Rahalkar MC, Pandit PS, Dhakephalkar PK, Pore S, Arora P, Kapse N. Genome Characteristics of a Novel Type I Methanotroph (Sn10-6) Isolated from a Flooded Indian Rice Field. Microb Ecol 2016; 71:519-523. [PMID: 26547566 DOI: 10.1007/s00248-015-0699-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/27/2015] [Indexed: 06/05/2023]
Abstract
Flooded rice fields are important sources of atmospheric methane. Aerobic methanotrophs living in the vicinity of rice roots oxidize methane and act as environmental filters. Here, we present genome characteristics of a gammaproteobacterial methanotroph, isolate Sn10-6, which was isolated from a rice rhizosphere of a flooded field in India. Sn10-6 has been identified as a member of a putative novel genus and species within the family Methylococcaceae (Type I methanotrophs). The draft genome of Sn10-6 showed pathways for the following: methane oxidation, formaldehyde assimilation (RuMP), nitrogen fixation, conversion of nitrite to nitrous oxide, and other interesting genes including the ones responsible for survival in the rhizosphere environment. The majority of genes found in this genome were most similar to Methylovulum miyakonese which is a forest isolate. This draft genome provided insight into the physiology, ecology, and phylogeny of this gammaproteobacterial methanotroph.
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Affiliation(s)
- Monali C Rahalkar
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India.
| | - Pranitha S Pandit
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India
| | | | - Soham Pore
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India
| | - Preeti Arora
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India
| | - Neelam Kapse
- MACS Agharkar Research Institute, G.G. Agarkar Road, Pune, 411004, Maharashtra, India
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10
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Detree C, Chabenat A, Lallier FH, Satoh N, Shoguchi E, Tanguy A, Mary J. Multiple I-Type Lysozymes in the Hydrothermal Vent Mussel Bathymodiolus azoricus and Their Role in Symbiotic Plasticity. PLoS One 2016; 11:e0148988. [PMID: 26882089 PMCID: PMC4755537 DOI: 10.1371/journal.pone.0148988] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 01/26/2016] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was first to identify lysozymes paralogs in the deep sea mussel Bathymodiolus azoricus then to measure their relative expression or activity in different tissue or conditions. B. azoricus is a bivalve that lives close to hydrothermal chimney in the Mid-Atlantic Ridge (MAR). They harbour in specialized gill cells two types of endosymbiont (gram-bacteria): sulphide oxidizing bacteria (SOX) and methanotrophic bacteria (MOX). This association is thought to be ruled by specific mechanism or actors of regulation to deal with the presence of symbiont but these mechanisms are still poorly understood. Here, we focused on the implication of lysozyme, a bactericidal enzyme, in this endosymbiosis. The relative expression of Ba-lysozymes paralogs and the global anti-microbial activity, were measured in natural population (Lucky Strike--1700 m, Mid-Atlantic Ridge), and in in situ experimental conditions. B. azoricus individuals were moved away from the hydrothermal fluid to induce a loss of symbiont. Then after 6 days some mussels were brought back to the mussel bed to induce a re-acquisition of symbiotic bacteria. Results show the presence of 6 paralogs in B. azoricus. In absence of symbionts, 3 paralogs are up-regulated while others are not differentially expressed. Moreover the global activity of lysozyme is increasing with the loss of symbiont. All together these results suggest that lysozyme may play a crucial role in symbiont regulation.
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Affiliation(s)
- Camille Detree
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Apolline Chabenat
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29680 Roscoff, France
| | - François H. Lallier
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology, Onna, Japan
| | - Arnaud Tanguy
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Jean Mary
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 7144, Adaptation et Diversité en Milieu Marin, Equipe ABICE, Station Biologique de Roscoff, 29680 Roscoff, France
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11
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Sherry A, Osborne KA, Sidgwick FR, Gray ND, Talbot HM. A temperate river estuary is a sink for methanotrophs adapted to extremes of pH, temperature and salinity. Environ Microbiol Rep 2016; 8:122-31. [PMID: 26617278 PMCID: PMC4959530 DOI: 10.1111/1758-2229.12359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 11/19/2015] [Indexed: 05/08/2023]
Abstract
River Tyne (UK) estuarine sediments harbour a genetically and functionally diverse community of methane-oxidizing bacteria (methanotrophs), the composition and activity of which were directly influenced by imposed environmental conditions (pH, salinity, temperature) that extended far beyond those found in situ. In aerobic sediment slurries methane oxidation rates were monitored together with the diversity of a functional gene marker for methanotrophs (pmoA). Under near in situ conditions (4-30°C, pH 6-8, 1-15 g l(-1) NaCl), communities were enriched by sequences affiliated with Methylobacter and Methylomonas spp. and specifically a Methylobacter psychrophilus-related species at 4-21°C. More extreme conditions, namely high temperatures ≥ 40°C, high ≥ 9 and low ≤ 5 pH, and high salinities ≥ 35 g l(-1) selected for putative thermophiles (Methylocaldum), acidophiles (Methylosoma) and haloalkaliphiles (Methylomicrobium). The presence of these extreme methanotrophs (unlikely to be part of the active community in situ) indicates passive dispersal from surrounding environments into the estuary.
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Affiliation(s)
- Angela Sherry
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kate A Osborne
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Frances R Sidgwick
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Neil D Gray
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Helen M Talbot
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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12
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Danilova OV, Belova SE, Kulichevskaya IS, Dedysh SN. [Decline of Activity and Shifts in the Methanotrophic Community Structure of an Ombrotrophic Peat Bog after Wildfire]. Mikrobiologiia 2015; 84:546-552. [PMID: 27169243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This study examined potential disturbances of methanotrophic communities playing a key role in reducing methane emissions from the peat bog Tasin Borskoye, Vladimir oblast, Russia as a result of the 2007 wildfire. The potential activity of the methane-oxidizing filter in the burned peatland site and the abundance of indigenous methanotrophic bacteria were significantly reduced in comparison to the undisturbed site. Molecular analysis of methanotrophic community structure by means of PCR amplification and cloning of the pmoAgene encoding particulate methane monooxygenase revealed the replacement of typical peat-inhabiting, acidophilic type II methanotrophic bacteria with type I methanotrophs, which are less active in acidic environments. In summary, both the structure and the activity of the methane-oxidizing filter in burned peatland sites underwent significant changes, which were clearly pronounced even after 7 years of the natural ecosystem recovery. These results point to the long-term character of the disturbances caused by wildfire in peatlands.
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13
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Zhu G, Zhou L, Wang Y, Wang S, Guo J, Long XE, Sun X, Jiang B, Hou Q, Jetten MSM, Yin C. Biogeographical distribution of denitrifying anaerobic methane oxidizing bacteria in Chinese wetland ecosystems. Environ Microbiol Rep 2015; 7:128-38. [PMID: 25223900 DOI: 10.1111/1758-2229.12214] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 08/31/2014] [Accepted: 09/04/2014] [Indexed: 05/26/2023]
Abstract
The discovery of denitrifying anaerobic methane oxidation with nitrite as electron acceptor mediated by 'Candidatus Methylomirabilis oxyfera' connected the biogeochemical carbon and nitrogen cycle in a new way. However, it is important to have a comprehensive understanding about the distribution of M. oxyfera-like bacteria in the terrestrial realm, especially the wetland ecosystems that are known as the largest natural source of atmospheric methane. Here, our molecular evidence demonstrated that a wide geographical distribution of M. oxyfera-like bacteria at oxic/anoxic interfaces of various wetlands (n = 91) over the Chinese territory. Intriguingly, the M. oxyfera-like bacteria were detected in some extreme environments, indicating that M. oxyfera-like bacteria occupied a wide range of habitats. Quantitative polymerase chain reaction estimated that the abundance of M. oxyfera-like bacteria ranged from 2.2 × 10(3) to 2.3 × 10(7) copies g(-1) dry soil, and up to around 0.62% of the total number of bacteria. Moreover, the M. oxyfera-like bacteria showed high biodiversity in wetland ecosystems based on the analysis of 462 pmoA and 287 16S rRNA gene sequences. The current study revealed the widespread distribution and biogeography of M. oxyfera-like bacteria in the terrestrial system.
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Affiliation(s)
- Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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14
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Cai Y, Jia Z. [Research progress of atmospheric methane oxidizers in soil]. Wei Sheng Wu Xue Bao 2014; 54:841-853. [PMID: 25345015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Microbial oxidation in soil is the only biological sink for atmospheric methane (about 1.8 ppmv). Two groups of atmospheric methane oxidizing bacteria are existed in aerobic soils: obligate and alternative atmospheric methane oxidizing bacteria. The former, such as upland soil cluster alpha (USCalpha) and upland soil cluster gamma (USCgamma), are widely distributed in a variety of aerobic upland soils, and their particulate methane monooxygenase (pMMO) have very high affinity for methane in low concentration. Bacteria in this group are probably genuine oligotrophs. However, so far, there is still no cultivated strain of this group. The latter (Methylocystis/Methylosinus) belongs to traditional methane-oxidizing bacteria, and are widely distributed in soil environments with periodic high methane emission. Most strains of these two genera are known to possess two pMMO isozymes with low and high affinity to methane respectively, and these strains can keep atmospheric methane oxidizing activity for relative long periods ( > 3 months) relying on the high affinity pMMO (pMMO2). However, the growth and reproduction of bacteria in this group are still dependent on endogenous high-concentration methane which is periodically produced within the soils. We reviewed the research progress of these two groups of atmospheric methane-oxidizing bacteria, their possible living strategies, and the effects of several key environmental factors (e. g. soil temperature and moisture, soil pH, vegetation, land use, nitrogen input) on their community composition and methane oxidizing activity. Several important research directions of atmospheric methane oxidizing bacteria have also been proposed.
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15
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Pan Y, Abell GCJ, Bodelier PLE, Meima-Franke M, Sessitsch A, Bodrossy L. Remarkable recovery and colonization behaviour of methane oxidizing bacteria in soil after disturbance is controlled by methane source only. Microb Ecol 2014; 68:259-270. [PMID: 24658413 DOI: 10.1007/s00248-014-0402-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
Little is understood about the relationship between microbial assemblage history, the composition and function of specific functional guilds and the ecosystem functions they provide. To learn more about this relationship we used methane oxidizing bacteria (MOB) as model organisms and performed soil microcosm experiments comprised of identical soil substrates, hosting distinct overall microbial diversities(i.e., full, reduced and zero total microbial and MOB diversities). After inoculation with undisturbed soil, the recovery of MOB activity, MOB diversity and total bacterial diversity were followed over 3 months by methane oxidation potential measurements and analyses targeting pmoA and 16S rRNA genes. Measurement of methane oxidation potential demonstrated different recovery rates across the different treatments. Despite different starting microbial diversities, the recovery and succession of the MOB communities followed a similar pattern across the different treatment microcosms. In this study we found that edaphic parameters were the dominant factor shaping microbial communities over time and that the starting microbial community played only a minor role in shaping MOB microbial community.
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16
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Sow SLS, Khoo G, Chong LK, Smith TJ, Harrison PL, Ong HKA. Molecular diversity of the methanotrophic bacteria communities associated with disused tin-mining ponds in Kampar, Perak, Malaysia. World J Microbiol Biotechnol 2014; 30:2645-53. [PMID: 24929362 DOI: 10.1007/s11274-014-1687-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/07/2014] [Indexed: 11/25/2022]
Abstract
In a previous study, notable differences of several physicochemical properties, as well as the community structure of ammonia oxidizing bacteria as judged by 16S rRNA gene analysis, were observed among several disused tin-mining ponds located in the town of Kampar, Malaysia. These variations were associated with the presence of aquatic vegetation as well as past secondary activities that occurred at the ponds. Here, methane oxidizing bacteria (MOB), which are direct participants in the nutrient cycles of aquatic environments and biological indicators of environmental variations, have been characterised via analysis of pmoA functional genes in the same environments. The MOB communities associated with disused tin-mining ponds that were exposed to varying secondary activities were examined in comparison to those in ponds that were left to nature. Comparing the sequence and phylogenetic analysis of the pmoA clone libraries at the different ponds (idle, lotus-cultivated and post-aquaculture), we found pmoA genes indicating the presence of type I and type II MOB at all study sites, but type Ib sequences affiliated with the Methylococcus/Methylocaldum lineage were most ubiquitous (46.7 % of clones). Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture was observed to harbor the highest richness of MOB. However, varying secondary activity or sample type did not show a strong variation in community patterns as compared to the ammonia oxidizers in our previous study.
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Affiliation(s)
- S L S Sow
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar, 31900, Perak, Malaysia
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17
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Deutzmann JS, Hoppert M, Schink B. Characterization and phylogeny of a novel methanotroph, Methyloglobulus morosus gen. nov., spec. nov. Syst Appl Microbiol 2014; 37:165-9. [PMID: 24685906 DOI: 10.1016/j.syapm.2014.02.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 02/24/2014] [Accepted: 02/28/2014] [Indexed: 11/18/2022]
Abstract
A novel methanotrophic gammaproteobacterium, strain KoM1, was isolated from the profundal sediment of Lake Constance after initial enrichment in opposing gradients of methane and oxygen. Strain KoM1 grows on methane or methanol as its sole source of carbon and energy. It is a Gram-negative methanotroph, often expressing red pigmentation. Cells are short rods and occur sometimes in pairs or short chains. Strain KoM1 grows preferably at reduced oxygen concentrations (pO2=0.05-0.1bar). It can fix nitrogen, and grows at neutral pH and at temperatures between 4 and 30°C. Phylogenetically, the closest relatives are Methylovulum miyakonense and Methylosoma difficile showing 91% 16S rRNA gene sequence identity. The only respiratory quinone is ubiquinone Q8; the main polar lipids are phosphatidyl ethanolamine and phosphatidyl glycerol. The major cellular fatty acids are summed feature 3 (presumably C16:1ω7c) and C16:1ω5c, and the G+C content of the DNA is 47.7mol%. Strain KoM1 is described as the type strain of a novel species within a new genus, Methyloglobulus morosus gen. nov., sp. nov.
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Affiliation(s)
- J S Deutzmann
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - M Hoppert
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - B Schink
- Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.
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18
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Belova SÉ, Oshkin II, Glagolev MV, Lapshina ED, Maksiutov SS, Dedysh SN. [Methanotrophic bacteria in cold seeps of the floodplains of northern rivers]. Mikrobiologiia 2013; 82:732-740. [PMID: 25509412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Small mud volcanoes (cold seeps), which are common in the floodplains of northern rivers, are a potentially important, although poorly studied sources of atmospheric methane. Field research on the cold seeps of the Mukhrina River (Khanty-Mansiysk Autonomous okrug, Russia) revealed methane fluxes from these structures to be orders of magnitude higher than from equivalent areas of the mid-taiga bogs. Microbial communities developing around the seeps were formed under conditions of high methane concentrations, low temperatures (3-5 degrees C), and near-neutral pH. Molecular identification of methane-oxidizing bacteria from this community by analysis of the pmoA gene encoding particulate methane monooxygenase revealed both type I and type II methanotrophs (classes Gammaproteobacteria and Alphaproteobacteria, respectively), with predomination of type I methanotrophs. Among the latter, microorganisms related to Methylobacterpsychrophilus and Methylobacter tundripaludum, Crenothrix polyspora (a stagnant water dweller), and a number of methanotrophs belonging to unknown taxa were detected. Growth characteristics of two isolates were determined. Methylobactersp. CMS7 exhibited active growth at 4-10 degrees C, while Methylocystis sp. SB12 grew better at 20 degrees C. Experimental results confirmed the major role ofmethanotrophic gammaproteobacteria in controlling the methane emission from cold river seeps.
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19
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Ho A, Kerckhof FM, Luke C, Reim A, Krause S, Boon N, Bodelier PLE. Conceptualizing functional traits and ecological characteristics of methane-oxidizing bacteria as life strategies. Environ Microbiol Rep 2013; 5:335-45. [PMID: 23754714 DOI: 10.1111/j.1758-2229.2012.00370.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/06/2012] [Accepted: 07/15/2012] [Indexed: 05/11/2023]
Abstract
Methane-oxidizing bacteria (MOB) possess the ability to use methane for energy generation and growth, thereby, providing a key ecosystem service that is highly relevant to the regulation of the global climate. MOB subgroups have different responses to key environmental controls, reflecting on their functional traits. Their unique features (C1-metabolism, unique lipids and congruence between the 16S rRNA and pmoA gene phylogeny) have facilitated numerous environmental studies, which in combination with the availability of cultured representatives, yield the most comprehensive ecological picture of any known microbial functional guild. Here, we focus on the broad MOB subgroups (type I and type II MOB), and aim to conceptualize MOB functional traits and observational characteristics derived primarily from these environmental studies to be interpreted as microbial life strategies. We focus on the functional traits, and the conditions under which these traits will render different MOB subgroups a selective advantage. We hypothesize that type I and type II MOB generally have distinct life strategies, enabling them to predominate under different conditions and maintain functionality. The ecological characteristics implicated in their adopted life strategies are discussed, and incorporated into the Competitor-Stress tolerator-Ruderal functional classification framework as put forward for plant communities. In this context, type I MOB can broadly be classified as competitor-ruderal while type II MOB fit more within the stress tolerator categories. Finally, we provide an outlook on MOB applications by exemplifying two approaches where their inferred life strategies could be exploited thereby, putting MOB into the context of microbial resource management.
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Affiliation(s)
- Adrian Ho
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of Bioscience Engineering, Coupure Links 653, B-9000 Ghent, Belgium
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20
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Chauhan A, Pathak A, Ogram A. Composition of methane-oxidizing bacterial communities as a function of nutrient loading in the Florida everglades. Microb Ecol 2012; 64:750-759. [PMID: 22544346 DOI: 10.1007/s00248-012-0058-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 04/11/2012] [Indexed: 05/31/2023]
Abstract
Agricultural runoff of phosphorus (P) in the northern Florida Everglades has resulted in several ecosystem level changes, including shifts in the microbial ecology of carbon cycling, with significantly higher methane being produced in the nutrient-enriched soils. Little is, however, known of the structure and activities of methane-oxidizing bacteria (MOB) in these environments. To address this, 0 to 10 cm plant-associated soil cores were collected from nutrient-impacted (F1), transition (F4), and unimpacted (U3) areas, sectioned in 2-cm increments, and methane oxidation rates were measured. F1 soils consumed approximately two-fold higher methane than U3 soils; additionally, most probable numbers of methanotrophs were 4-log higher in F1 than U3 soils. Metabolically active MOB containing pmoA sequences were characterized by stable-isotope probing using 10 % (v/v) (13)CH(4). pmoA sequences, encoding the alpha subunit of methane monooxygenase and related to type I methanotrophs, were identified from both impacted and unimpacted soils. Additionally, impacted soils also harbored type II methanotrophs, which have been shown to exhibit preferences for high methane concentrations. Additionally, across all soils, novel pmoA-type sequences were also detected, indicating presence of MOB specific to the Everglades. Multivariate statistical analyses confirmed that eutrophic soils consisted of metabolically distinct MOB community that is likely driven by nutrient enrichment. This study enhances our understanding on the biological fate of methane being produced in productive wetland soils of the Florida Everglades and how nutrient-enrichment affects the composition of methanotroph bacterial communities.
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Affiliation(s)
- Ashvini Chauhan
- School of the Environment, Florida A&M University, Tallahassee, FL 32307, USA.
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21
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Guan J, Zhang Y, Shi RJ, Li H, Han SQ, Xu H. [Effects of elevated CO2 on forest soil CH4 consumption in Changbai Mountains]. Ying Yong Sheng Tai Xue Bao 2012; 23:328-334. [PMID: 22586954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Elevated atmospheric CO2 concentration may affect the oxidation rate of methane (CH4 ) in forest soil. In this study, the effects of a 6-year exposure to elevated CO2 concentration (500 micromol x mol(-1)) on the soil microbial process of CH4 oxidation under Quercus mongolica seedlings were investigated with open top chamber (OTC), and specific 16S rRNA and pmoA gene fragment primers were adopted to analyze the diversity and abundance of soil methanotrophs. Comparing with that under ambient CO2 and open-air, the soil methane consumption under elevated atmospheric CO2 during growth season was reduced by 4% and 22%, respectively. The specific 16S rRNA PCR-DGGE analysis showed that under elevated CO2, the community structure of methane-oxidizing bacteria (MOB) changed, and the diversity index decreased. Elevated CO2 concentration had no distinct effects on the abundance of Type I MOB, but decreased the amount of Type II MOB significantly. The pmoA gene copy number under elevated CO2 concentration decreased by 15% and 46%, respectively, as compared with that under ambient CO2 and open-air. Our results suggested that elevated atmospheric CO2 decreased the abundance and activity of soil methanotrophs, and the main cause could be the increase of soil moisture content.
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Affiliation(s)
- Jian Guan
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
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Dvorianchikova EN, Kizilova AK, Men'ko EV, Kravchenko IK, Gal'chenko VF. [Molecular detection of methanotrophic bacteria in hot springs from the vicinity of the Uzon volcano, Kamchatka]. Mikrobiologiia 2011; 80:860-862. [PMID: 22393772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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Reshetnikov AS, Khmelenina VN, Mustakhimov II, Kalyuzhnaya M, Lidstrom M, Trotsenko YA. Diversity and phylogeny of the ectoine biosynthesis genes in aerobic, moderately halophilic methylotrophic bacteria. Extremophiles 2011; 15:653-63. [PMID: 21971967 DOI: 10.1007/s00792-011-0396-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 08/26/2011] [Indexed: 11/30/2022]
Abstract
The genes of ectoine biosynthesis pathway were identified in six species of aerobic, slightly halophilic bacteria utilizing methane, methanol or methylamine. Two types of ectoine gene cluster organization were revealed in the methylotrophs. The gene cluster ectABC coding for diaminobutyric acid (DABA) acetyltransferase (EctA), DABA aminotransferase (EctB) and ectoine synthase (EctC) was found in methanotrophs Methylobacter marinus 7C and Methylomicrobium kenyense AMO1(T). In methanotroph Methylomicrobium alcaliphilum ML1, methanol-utilizers Methylophaga thalassica 33146(T) , Methylophaga alcalica M8 and methylamine-utilizer Methylarcula marina h1(T), the genes forming the ectABC-ask operon are preceded by ectR, encoding a putative transcriptional regulatory protein EctR. Phylogenetic relationships of the Ect proteins do not correlate with phylogenetic affiliation of the strains, thus implying that the ability of methylotrophs to produce ectoine is most likely the result of a horizontal transfer event.
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Affiliation(s)
- Alexander S Reshetnikov
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region
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Lüke C, Frenzel P. Potential of pmoA amplicon pyrosequencing for methanotroph diversity studies. Appl Environ Microbiol 2011; 77:6305-9. [PMID: 21764977 PMCID: PMC3165393 DOI: 10.1128/aem.05355-11] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 06/30/2011] [Indexed: 11/20/2022] Open
Abstract
We analyzed the potential of pmoA amplicon pyrosequencing compared to that of Sanger sequencing with paddy soils as a model environment. We defined operational taxonomic unit (OTU) cutoff values of 7% and 18%, reflecting methanotrophic species and major phylogenetic pmoA lineages, respectively. Major lineages were already well covered by clone libraries; nevertheless, pyrosequencing provided a higher level of diversity at the species level.
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Affiliation(s)
- Claudia Lüke
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043 Marburg, Germany.
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25
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Romanovskaia VA, Rokitko PV. [Analysis of phylogenetic criteria for estimation of the rank of taxa in methane-oxidizing bacteria]. Mikrobiol Z 2011; 73:3-12. [PMID: 21598653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
To determine a possibility of application of phylogenetic criteria for estimating the taxa rank, the intra- and interspecies, as well as intergeneric relatedness of methanotrophs on the basis of 16S rRNA gene sequences was estimated. We used sequences of 16S rRNA genes of the studied isolates of obligate methanotrophs which have been deposited in UCM (Ukrainian Collection of Microorganisms), and of type strains of other obligate methanotrophs species (from GenBank database). It is shown, that the levels of interspecies and intergeneric relatedness in different families of methanotrophs are not identical, and therefore they can be used for differentiation of taxa only within one family. The carried out analysis has shown, that it is necessary to reconsider taxonomic position: (1) of two phenotypically similar species of Methylomonas (M. aurantiaca and M. fodinarum), similarity of 16S rRNA genes which is 99.4%, similarity of their total DNA--up to 80% that rather testifies to strain differences, than to species differences; (2) of species Methylomicrobium agile and M album which are phylogenetically more related to genus Methylobacter (97% of affinity), than Methylomicrobium (94% of affinity); (3) of genera of the family Beijerinckiaceae (Methylocella and Methylocapsa), and also genera of the family Methylocystaceae (Methylosinus and Methylocystis), whereas high level of relatedness (97% and more) of these bacteria with other methanotrophic genera (within one family) practically corresponds to a range of relatedness of species (within some genera) in the family Methylococcaceae. When determining phylogenetic criteria which can characterize the ranks of taxa, it was revealed, that the levels of interspecies relatedness of methanotrophic genera of the families Methylocystaceae and Beijerinckiaceae (97.8-99.1% and 97.8%, accordingly) considerably exceed the level of genera formation in the family Methylococcaceae (94.0-98.2%) and, moreover, approach the value of intraspecies relatedness of the family Methylococcaceae (97.5-99.3%). Coefficients of intraspecies relatedness of methanotrophs of the families Methylocystaceae and Beijerinckiaceae are sometimes equal to interspecies relatedness. Hence, taxa of various rank can have the identical level of genes divergence. Thus, methanotrophic taxons of the families Methylocystaceae and Beijerinckiaceae have not demonstrated precise phylogenetic criteria which could correspond both to the species rank, or the genus rank. At the same time, the criteria, being adequate to the rank of certain taxa, are revealed in methanotrophs of the family Methylococcaceae. The level of genotypic relatedness of strains of the same species is in the range of 97.5-99.3%, species of the same genus--94-98%, the highest levels of relatedness between genera of this family are 90-96%.
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Yang QB, Fan FL, Wang WX, Liang YC, Li ZJ, Cui XA, Wei D. [Effects of different long-term fertilizations on community properties and functions of methanotrophs in dark brown soil]. Huan Jing Ke Xue 2010; 31:2756-2762. [PMID: 21250462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The microbial mechanisms of how different long-term fertilizations change methane oxidation of Chinese upland arable soil is unclear so far. In the present study, we attempted to investigate the "soil properties-community properties of methanotrophs-methane oxidation" relation of dark brown soil in Northeastern China under different long-term fertilization regimes. Community structure and abundance were monitored with PCR-DGGE and real time PCR, respectively. Methane oxidizing rate and soil properties were measured as well. The results show that combined use of mineral fertilizer and compost (MNP) reduce soil methane oxidation by 61.2%, whereas either mineral fertilizer (NP) or compost (M) shows no effect. Comparing with no fertilizer (CK), M and MNP increase the Shannon index of methanotrophs by 91.9% and 102.5%, respectively, whereas NP has no effect. Similarly, M ( M or MNP) significantly increases pmoA gene abundance by up to 12.7 folds compared with no M addition (CK or NP). Methane oxidizing rates are significantly correlated with community structure and specific activity of methanotrophs, with correlation coefficients of 0.363 and 0.684, respectively. However, methane oxidizing rates do not correlate with abundance and diversity of methanotrophs. In addition, community structures and specific activity of methanotrophs are significantly correlated with soil pH and content of total nitrogen and organic matter. Our results suggest that long-term different fertilizations may change soil properties (such as pH and content of total nitrogen and organic matter) and thereafter the community structure and specific activity of soil methanotrophs, by which long-term different fertilizations influence soil methane oxidizing rate. The opposite change of methane oxidation to methanotrophs diversity and abundance in MNP suggests that only parts of the methanotrophs are active, which needs further research.
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Affiliation(s)
- Qian-Bao Yang
- Institute of Resources and Environment, Gansu Agricultural University, Lanzhou 730070, China.
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Yun J, Ma A, Li Y, Zhuang G, Wang Y, Zhang H. Diversity of methanotrophs in Zoige wetland soils under both anaerobic and aerobic conditions. J Environ Sci (China) 2010; 22:1232-1238. [PMID: 21179963 DOI: 10.1016/s1001-0742(09)60243-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Zoige wetland is one of the most important methane emission centers in China. The oxidation of methane in the wetland affects global warming, soil ecology and atmospheric chemistry. Despite their global significance, microorganisms that consume methane in Zoige wetland remain poorly characterized. In this study, we investigated methanotrophs diversity in soil samples from both anaerobic site and aerobic site in Zoige wetland using pmoA gene as a molecular marker. The cloning library was constructed according to the pmoA sequences detected. Four clusters of methanotrophs were detected. The phylogenetic tree showed that all four clusters detected were affiliated to type I methanotrophs. Two novel clusters (cluster 1, cluster 2) were found to relate to none of the recognized genera of methanotrophs. These clusters have no cultured representatives and reveal an ecological adaptation of particular uncultured methanotrophs in Zoige wetland. Two clusters were belonging to Methylobacter and Methylococcus separately. Denaturing gradient gel electrophoresis gel bands pattern retrieved from these two samples revealed that the community compositions of anaerobic soil and aerobic soil were different from each other while anaerobic soil showed a higher metanotrophs diversity. Real-time PCR assays of the two samples demonstrated that aerobic soil sample in Zoige wetland was 1.5 times as much copy numbers as anaerobic soil. These data illustrated that methanotrophs are a group of microorganisms influence the methane consumption in Zoige wetland.
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Affiliation(s)
- Juanli Yun
- Graduate University of Chinese Academy of Sciences, Beijing 100049, China.
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Ait-Benichou S, Jugnia LB, Greer CW, Cabral AR. Methanotrophs and methanotrophic activity in engineered landfill biocovers. Waste Manag 2009; 29:2509-2517. [PMID: 19477627 DOI: 10.1016/j.wasman.2009.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 05/01/2009] [Accepted: 05/05/2009] [Indexed: 05/27/2023]
Abstract
The dynamics and changes in the potential activity and community structure of methanotrophs in landfill covers, as a function of time and depth were investigated. A passive methane oxidation biocover (PMOB-1) was constructed in St-Nicéphore MSW Landfill (Quebec, Canada). The most probable number (MPN) method was used for methanotroph counts, methanotrophic diversity was assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting of the pmoA gene and the potential CH(4) oxidation rate was determined using soil microcosms. Results of the PMOB-1 were compared with those obtained for the existing landfill cover (silty clay) or a reference soil (RS). During the monitoring period, changes in the number of methanotrophic bacteria in the PMOB-1 exhibited different developmental phases and significant variations with depth. In comparison, no observable changes over time occurred in the number of methanotrophs in the RS. The maximum counts measured in the uppermost layer was 1.5x10(9) cells g dw(-1) for the PMOB-1 and 1.6x10(8) cells g dw(-1) for the RS. No distinct difference was observed in the methanotroph diversity in the PMOB-1 or RS. As expected, the potential methane oxidation rate was higher in the PMOB-1 than in the RS. The maximum potential rates were 441.1 and 76.0 microg CH(4) h(-1) g dw(-1) in the PMOB and RS, respectively. From these results, the PMOB was found to be a good technology to enhance methane oxidation, as its performance was clearly better than the starting soil that was present in the landfill site.
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Affiliation(s)
- S Ait-Benichou
- Faculty of Engineering, Civil Engineering Department, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke, Québec, Canada J1K 2R1
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29
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Trotsenko IA, Medvedkova KA, Khmelenina VN, Eshinimaev BT. [Thermophilic and thermotolerant aerobic methanotrophs]. Mikrobiologiia 2009; 78:435-450. [PMID: 19827708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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30
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Romanovskaia VA, Rokitko PV, Shilin SO, Chernaia NA. [Specification of species status of some colleciton strains of methanotrophs]. Mikrobiol Z 2009; 71:3-7. [PMID: 19663320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sequence-analysis of genes 16S rRNA has demonstrated the high-level relationship (99%) of the strains Methylobacter ucrainicus UCM B-3159, and Methylobacter marinus A45(T). The strain UCM B-3159 has lower coefficients of similarity (97.4-96.4%) for other species of that genus. These strains are similar as to their phenotypical properties and form one branch on the dendrogram which demonstrates species relations of Methylococcaceae family, that permitted reclassifying M. ucrainicus as M. marinus. Phylogenetic analysis has confirmed the belonging of strains UCM B-3002 and UCM B-3494 to Methylococcus capsulatus species. Those strains were earlier related to this species on the basis of phenotype features.
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31
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Liebner S, Rublack K, Stuehrmann T, Wagner D. Diversity of aerobic methanotrophic bacteria in a permafrost active layer soil of the Lena Delta, Siberia. Microb Ecol 2009; 57:25-35. [PMID: 18592300 DOI: 10.1007/s00248-008-9411-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 05/20/2008] [Indexed: 05/26/2023]
Abstract
With this study, we present first data on the diversity of aerobic methanotrophic bacteria (MOB) in an Arctic permafrost active layer soil of the Lena Delta, Siberia. Applying denaturing gradient gel electrophoresis and cloning of 16S ribosomal ribonucleic acid (rRNA) and pmoA gene fragments of active layer samples, we found a general restriction of the methanotrophic diversity to sequences closely related to the genera Methylobacter and Methylosarcina, both type I MOB. In contrast, we revealed a distinct species-level diversity. Based on phylogenetic analysis of the 16S rRNA gene, two new clusters of MOB specific for the permafrost active layer soil of this study were found. In total, 8 out of 13 operational taxonomic units detected belong to these clusters. Members of these clusters were closely related to Methylobacter psychrophilus and Methylobacter tundripaludum, both isolated from Arctic environments. A dominance of MOB closely related to M. psychrophilus and M. tundripaludum was confirmed by an additional pmoA gene analysis. We used diversity indices such as the Shannon diversity index or the Chao1 richness estimator in order to compare the MOB community near the surface and near the permafrost table. We determined a similar diversity of the MOB community in both depths and suggest that it is not influenced by the extreme physical and geochemical gradients in the active layer.
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Affiliation(s)
- Susanne Liebner
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Telegrafenberg A43, 14473, Potsdam, Germany.
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Nakamura T, Hoaki T, Hanada S, Maruyama A, Kamagata Y, Fuse H. Soluble and particulate methane monooxygenase gene clusters in the marine methanotroph Methylomicrobium sp. strain NI. FEMS Microbiol Lett 2008; 277:157-64. [PMID: 18031335 DOI: 10.1111/j.1574-6968.2007.00953.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Soluble methane monooxygenase (sMMO) and particulate methane monooxygenase (pMMO) gene clusters in the marine methanotroph Methylomicrobium sp. strain NI were completely sequenced and analysed. Degenerated primers were newly designed and used to amplify the gene fragments containing intergenic mmoX-Y and mmoD-C regions and a partial pmoC region. Phylogenetic analysis of amino acid sequences deduced from mmoX and pmoA, as well as of 16S rRNA gene sequences, indicated that this strain was most closely related to the halotolerant methanotroph Methylomicrobium buryatense. There were putative sigma(54)- and sigma(70)-dependent promoter sequences upstream of the sMMO and pMMO genes, respectively, and mmoG, which is known to be related to the expression and assembly of sMMO, existed downstream of the sMMO genes. These findings suggest that the major components and regulation of MMOs in this marine methanotroph are quite similar to those in freshwater methane oxidizers, despite the difference in their habitats.
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Cébron A, Bodrossy L, Chen Y, Singer AC, Thompson IP, Prosser JI, Murrell JC. Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing. FEMS Microbiol Ecol 2007; 62:12-23. [PMID: 17714486 DOI: 10.1111/j.1574-6941.2007.00368.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
A considerable amount of methane produced during decomposition of landfill waste can be oxidized in landfill cover soil by methane-oxidizing bacteria (methanotrophs) thus reducing greenhouse gas emissions to the atmosphere. The identity of active methanotrophs in Roscommon landfill cover soil, a slightly acidic peat soil, was assessed by DNA-stable isotope probing (SIP). Landfill cover soil slurries were incubated with (13)C-labelled methane and under either nutrient-rich nitrate mineral salt medium or water. The identity of active methanotrophs was revealed by analysis of (13)C-labelled DNA fractions. The diversity of functional genes (pmoA and mmoX) and 16S rRNA genes was analyzed using clone libraries, microarrays and denaturing gradient gel electrophoresis. 16S rRNA gene analysis revealed that the cover soil was mainly dominated by Type II methanotrophs closely related to the genera Methylocella and Methylocapsa and to Methylocystis species. These results were supported by analysis of mmoX genes in (13)C-DNA. Analysis of pmoA gene diversity indicated that a significant proportion of active bacteria were also closely related to the Type I methanotrophs, Methylobacter and Methylomonas species. Environmental conditions in the slightly acidic peat soil from Roscommon landfill cover allow establishment of both Type I and Type II methanotrophs.
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MESH Headings
- Bacterial Proteins/genetics
- Biodiversity
- Carbon Isotopes/metabolism
- Cloning, Molecular
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Isotope Labeling/methods
- Methane/metabolism
- Methylococcaceae/classification
- Methylococcaceae/genetics
- Molecular Sequence Data
- Oligonucleotide Array Sequence Analysis
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology
- Soil Microbiology
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Affiliation(s)
- Aurélie Cébron
- Department of Biological Sciences, University of Warwick, Coventry, UK
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34
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Abstract
Temperature change affects methane consumption in soil. However, there is no information on possible temperature control of methanotrophic bacterial populations. Therefore, we studied CH(4) consumption and populations of methanotrophs in an upland forest soil and a rice field soil incubated at different temperatures between 5 and 45 degrees C for up to 40 days. Potential methane consumption was measured at 4% CH(4). The temporal progress of CH(4) consumption indicated growth of methanotrophs. Both soils showed maximum CH(4) consumption at 25-35 degrees C, but no activity at >40 degrees C. In forest soil CH(4) was also consumed at 5 degrees C, but in rice soil only at 15 degrees C. Methanotroph populations were assessed by terminal restriction fragment length polymorphism (T-RFLP) targeting particulate methane monooxygenase (pmoA) genes. Eight T-RFs with relative abundance >1% were retrieved from both forest and rice soil. The individual T-RFs were tentatively assigned to different methanotrophic populations (e.g. Methylococcus/Methylocaldum, Methylomicrobium, Methylobacter, Methylocystis/Methylosinus) according to published sequence data. Two T-RFs were assigned to ammonium monooxygenase (amoA) gene sequences. Statistical tests showed that temperature affected the relative abundance of most T-RFs. Furthermore, the relative abundance of individual T-RFs differed between the two soils, and also exhibited different temperature dependence. We conclude that temperature can be an important factor regulating the community composition of methanotrophs in soil.
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Affiliation(s)
- Santosh R Mohanty
- Department of Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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35
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Rahalkar M, Bussmann I, Schink B. Methylosoma difficile gen. nov., sp. nov., a novel methanotroph enriched by gradient cultivation from littoral sediment of Lake Constance. Int J Syst Evol Microbiol 2007; 57:1073-1080. [PMID: 17473262 DOI: 10.1099/ijs.0.64574-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel methanotroph, strain LC 2(T), was isolated from the littoral sediment of Lake Constance by enrichment in opposing gradients of methane and oxygen, followed by traditional isolation methods. Strain LC 2(T) grows on methane or methanol as its sole carbon and energy source. It is a Gram-negative, non-motile, pale-pink-coloured methanotroph showing typical intracytoplasmic membranes arranged in stacks. Cells are coccoid, elliptical or rod-shaped and occur often in pairs. Strain LC 2(T) grows at low oxygen concentrations and in counter-gradients of methane and oxygen. It can grow on medium free of bound nitrogen, possesses the nifH gene and fixes atmospheric nitrogen at low oxygen pressure. It grows at neutral pH and at temperatures between 10 and 30 degrees C. Phylogenetically, it is most closely related to the genus Methylobacter, with the type strains of Methylobacter tundripaludum and Methylobacter psychrophilus showing 94 and 93.4 % 16S rRNA gene sequence similarity, respectively. Furthermore, the pmoA gene sequence of strain LC 2(T) is most closely related to pmoA gene sequences of Methylobacter strains (92 % similar to Methylobacter sp. LW 12 by deduced amino acid sequence identity). The DNA G+C content is 49.9 mol% and the major cellular fatty acid is 16 : 1omega7c (60 %). Strain LC 2(T) (=JCM 14076(T)=DSM 18750(T)) is described as the type strain of a novel species within a new genus, Methylosoma difficile gen. nov., sp. nov.
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MESH Headings
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Composition
- Carbon/metabolism
- Cytoplasm/ultrastructure
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fresh Water/microbiology
- Genes, rRNA
- Geologic Sediments/microbiology
- Germany
- Hydrogen-Ion Concentration
- Membranes/ultrastructure
- Methane/metabolism
- Methanol/metabolism
- Methylococcaceae/classification
- Methylococcaceae/cytology
- Methylococcaceae/isolation & purification
- Methylococcaceae/physiology
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Movement
- Nitrogenase/metabolism
- Oxidoreductases/genetics
- Phylogeny
- Pigments, Biological/biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/metabolism
- Temperature
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Affiliation(s)
- Monali Rahalkar
- LS Mikrobielle Ökologie, Fachbereich Biologie, Universität Konstanz, Fach M 654, 78457 Konstanz, Germany
| | - Ingeborg Bussmann
- LS Mikrobielle Ökologie, Fachbereich Biologie, Universität Konstanz, Fach M 654, 78457 Konstanz, Germany
| | - Bernhard Schink
- LS Mikrobielle Ökologie, Fachbereich Biologie, Universität Konstanz, Fach M 654, 78457 Konstanz, Germany
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Singh BK, Tate KR, Kolipaka G, Hedley CB, Macdonald CA, Millard P, Murrell JC. Effect of afforestation and reforestation of pastures on the activity and population dynamics of methanotrophic bacteria. Appl Environ Microbiol 2007; 73:5153-61. [PMID: 17574997 PMCID: PMC1950977 DOI: 10.1128/aem.00620-07] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the effect of afforestation and reforestation of pastures on methane oxidation and the methanotrophic communities in soils from three different New Zealand sites. Methane oxidation was measured in soils from two pine (Pinus radiata) forests and one shrubland (mainly Kunzea ericoides var. ericoides) and three adjacent permanent pastures. The methane oxidation rate was consistently higher in the pine forest or shrubland soils than in the adjacent pasture soils. A combination of phospholipid fatty acid (PLFA) and stable isotope probing (SIP) analyses of these soils revealed that different methanotrophic communities were active in soils under the different vegetations. The C18 PLFAs (signature of type II methanotrophs) predominated under pine and shrublands, and C16 PLFAs (type I methanotrophs) predominated under pastures. Analysis of the methanotrophs by molecular methods revealed further differences in methanotrophic community structure under the different vegetation types. Cloning and sequencing and terminal-restriction fragment length polymorphism analysis of the particulate methane oxygenase gene (pmoA) from different samples confirmed the PLFA-SIP results that methanotrophic bacteria related to type II methanotrophs were dominant in pine forest and shrubland, and type I methanotrophs (related to Methylococcus capsulatus) were dominant in all pasture soils. We report that afforestation and reforestation of pastures caused changes in methane oxidation by altering the community structure of methanotrophic bacteria in these soils.
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Affiliation(s)
- Brajesh K Singh
- Macaulay Institute, Environmental Sciences, Aberdeen AB15 8QH, United Kingdom.
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37
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Rahalkar M, Schink B. Comparison of aerobic methanotrophic communities in littoral and profundal sediments of Lake Constance by a molecular approach. Appl Environ Microbiol 2007; 73:4389-94. [PMID: 17483263 PMCID: PMC1932771 DOI: 10.1128/aem.02602-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of pmoA and 16S rRNA gene clone libraries of methanotrophic bacteria in Lake Constance revealed an overall dominance of type I methanotrophs in both littoral and profundal sediments. The sediments exhibited minor differences in their methanotrophic community structures. Type X methanotrophs made up a significant part of the clone libraries only in the profundal sediment and were also found only there as a prominent peak by T-RFLP analyses.
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Affiliation(s)
- Monali Rahalkar
- LS Mikrobielle Okologie, Fachbereich Biologie, Universität Konstanz, Fach M 654, Konstanz, Germany
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38
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Vigliotta G, Nutricati E, Carata E, Tredici SM, De Stefano M, Pontieri P, Massardo DR, Prati MV, De Bellis L, Alifano P. Clonothrix fusca Roze 1896, a filamentous, sheathed, methanotrophic gamma-proteobacterium. Appl Environ Microbiol 2007; 73:3556-65. [PMID: 17416684 PMCID: PMC1932688 DOI: 10.1128/aem.02678-06] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Crenothrix polyspora Cohn 1870 and Clonothrix fusca Roze 1896 are two filamentous, sheathed microorganisms exhibiting complex morphological differentiation, whose phylogeny and physiology have been obscure for a long time due to the inability to cultivate them. Very recently, DNA sequencing data from uncultured C. polyspora-enriched material have suggested that Crenothrix is a methane-oxidizing gamma-proteobacterium (39). In contrast, the possible ecological function of C. fusca, originally considered a developmental stage of C. polyspora, is unknown. In this study, temporal succession of two filamentous, sheathed microorganisms resembling Cohn's Crenothrix and Roze's Clonothrix was observed by analyzing the microbial community of an artesian well by optical microscopy. Combined culture-based and culture-independent approaches enabled us to assign C. fusca to a novel subgroup of methane-oxidizing gamma-proteobacteria distinct from that of C. polyspora. This assignment was supported by (i) methane uptake and assimilation experiments, (ii) ultrastructural data showing the presence in C. fusca cytoplasm of an elaborate membrane system resembling that of methanotrophic gamma-proteobacteria, and (iii) sequencing data demonstrating the presence in its genome of a methanol dehydrogenase alpha subunit-encoding gene (mxaF) and a conventional particulate methane mono-oxygenase alpha subunit-encoding gene (pmoA) that is different from the unusual pmoA (u-pmoA) of C. polyspora.
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Affiliation(s)
- Giovanni Vigliotta
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università degli Studi di Lecce, Via Monteroni, 73100 Lecce, Italy
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39
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Lösekann T, Knittel K, Nadalig T, Fuchs B, Niemann H, Boetius A, Amann R. Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea. Appl Environ Microbiol 2007; 73:3348-62. [PMID: 17369343 PMCID: PMC1907091 DOI: 10.1128/aem.00016-07] [Citation(s) in RCA: 301] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Submarine mud volcanoes are formed by expulsions of mud, fluids, and gases from deeply buried subsurface sources. They are highly reduced benthic habitats and often associated with intensive methane seepage. In this study, the microbial diversity and community structure in methane-rich sediments of the Haakon Mosby Mud Volcano (HMMV) were investigated by comparative sequence analysis of 16S rRNA genes and fluorescence in situ hybridization. In the active volcano center, which has a diameter of about 500 m, the main methane-consuming process was bacterial aerobic oxidation. In this zone, aerobic methanotrophs belonging to three bacterial clades closely affiliated with Methylobacter and Methylophaga species accounted for 56%+/-8% of total cells. In sediments below Beggiatoa mats encircling the center of the HMMV, methanotrophic archaea of the ANME-3 clade dominated the zone of anaerobic methane oxidation. ANME-3 archaea form cell aggregates mostly associated with sulfate-reducing bacteria of the Desulfobulbus (DBB) branch. These ANME-3/DBB aggregates were highly abundant and accounted for up to 94%+/-2% of total microbial biomass at 2 to 3 cm below the surface. ANME-3/DBB aggregates could be further enriched by flow cytometry to identify their phylogenetic relationships. At the outer rim of the mud volcano, the seafloor was colonized by tubeworms (Siboglinidae, formerly known as Pogonophora). Here, both aerobic and anaerobic methane oxidizers were found, however, in lower abundances. The level of microbial diversity at this site was higher than that at the central and Beggiatoa species-covered part of the HMMV. Analysis of methyl-coenzyme M-reductase alpha subunit (mcrA) genes showed a strong dominance of a novel lineage, mcrA group f, which could be assigned to ANME-3 archaea. Our results further support the hypothesis of Niemann et al. (54), that high methane availability and different fluid flow regimens at the HMMV provide distinct niches for aerobic and anaerobic methanotrophs.
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MESH Headings
- Aerobiosis
- Anaerobiosis
- Archaea/classification
- Archaea/genetics
- Archaea/isolation & purification
- Archaea/metabolism
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- Base Sequence
- Beggiatoa/classification
- Beggiatoa/genetics
- Beggiatoa/isolation & purification
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Deltaproteobacteria/classification
- Deltaproteobacteria/genetics
- Deltaproteobacteria/isolation & purification
- Geologic Sediments/microbiology
- In Situ Hybridization, Fluorescence
- Methane/metabolism
- Methylococcaceae/classification
- Methylococcaceae/genetics
- Methylococcaceae/isolation & purification
- Microscopy, Fluorescence
- Molecular Sequence Data
- Oxidation-Reduction
- Oxidoreductases/genetics
- Phylogeny
- Piscirickettsiaceae/classification
- Piscirickettsiaceae/genetics
- Piscirickettsiaceae/isolation & purification
- Protein Subunits/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
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Affiliation(s)
- Tina Lösekann
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
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40
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Stoecker K, Bendinger B, Schöning B, Nielsen PH, Nielsen JL, Baranyi C, Toenshoff ER, Daims H, Wagner M. Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc Natl Acad Sci U S A 2006; 103:2363-7. [PMID: 16452171 PMCID: PMC1413686 DOI: 10.1073/pnas.0506361103] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
135 years ago Ferdinand Cohn, the founder of bacteriology, microscopically observed a conspicuous filamentous bacterium with a complex life cycle and described it as Crenothrix polyspora. This uncultured bacterium is infamous for mass developments in drinking water systems, but its phylogeny and physiology remained unknown. We show that C. polyspora is a gammaproteobacterium closely related to methanotrophs and capable of oxidizing methane. We discovered that C. polyspora encodes a phylogenetically very unusual particulate methane monooxygenase whose expression is strongly increased in the presence of methane. Our findings demonstrate a previously unrecognized complexity of the evolutionary history and cell biology of methane-oxidizing bacteria.
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Affiliation(s)
- Kilian Stoecker
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Bernd Bendinger
- Deutsche Vereinigung des Gas- und Wasserfaches-Forschungsstelle, Technische Universität Hamburg, D-21073 Hamburg, Germany; and
| | - Björn Schöning
- Deutsche Vereinigung des Gas- und Wasserfaches-Forschungsstelle, Technische Universität Hamburg, D-21073 Hamburg, Germany; and
| | - Per H. Nielsen
- Department of Life Sciences, Aalborg University, DK-9000 Aalborg, Denmark
| | - Jeppe L. Nielsen
- Department of Life Sciences, Aalborg University, DK-9000 Aalborg, Denmark
| | - Christian Baranyi
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Elena R. Toenshoff
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Holger Daims
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Michael Wagner
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
- To whom correspondence should be addressed at:
Department for Mikrobielle Ökologie, Universität Wien, Althanstrasse 14, A-1090 Wien, Austria. E-mail:
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41
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Wartiainen I, Hestnes AG, McDonald IR, Svenning MM. Methylobacter tundripaludum sp. nov., a methane-oxidizing bacterium from Arctic wetland soil on the Svalbard islands, Norway (78 N). Int J Syst Evol Microbiol 2006; 56:109-13. [PMID: 16403874 DOI: 10.1099/ijs.0.63728-0] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, rod-shaped, non-motile, non-spore forming bacterium (SV96T) was isolated from wetland soil near Ny-Alesund, Svalbard. On the basis of 16S rRNA gene sequence similarity, strain SV96T was shown to belong to the Gammaproteobacteria, related to Methylobacter psychrophilus Z-0021T (99.1 %), Methylobacter luteus ATCC 49878T (97.3 %), Methylobacter marinus A45T (97.0 %) and Methylobacter whittenburyi ATCC 51738T (95.8 %); the closest related species within the genus Methylomicrobium with a validly published name was Methylomicrobium album ATCC 33003T (95.0 %). Chemotaxonomic data (including the major fatty acids: 16 : 1omega8, 16 : 1omega7 and 16 : 1omega5t) supported the affiliation of strain SV96T to the genus Methylobacter. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain SV96T from the four Methylobacter species mentioned above. Strain SV96T therefore represents a novel species, for which the name Methylobacter tundripaludum sp. nov. is proposed (type strain SV96T = DSM 17260T = ATCC BAA-1195T).
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Affiliation(s)
- Ingvild Wartiainen
- Department of Biology, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
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42
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Abstract
The abundance and activity of methane-oxidizing bacteria (MOB) in the water column were investigated in three lakes with different contents of nutrients and humic substances. The abundance of MOB was determined by analysis of group-specific phospholipid fatty acids from type I and type II MOB, and in situ activity was measured with a 14CH4 transformation method. The fatty acid analyses indicated that type I MOB most similar to species of Methylomonas, Methylomicrobium, and Methylosarcina made a substantial contribution (up to 41%) to the total bacterial biomass, whereas fatty acids from type II MOB generally had very low concentrations. The MOB biomass and oxidation activity were positively correlated and were highest in the hypo- and metalimnion during summer stratification, whereas under ice during winter, maxima occurred close to the sediments. The methanotroph biomass-specific oxidation rate (V) ranged from 0.001 to 2.77 mg CH4-C mg(-1) C day(-1) and was positively correlated with methane concentration, suggesting that methane supply largely determined the activity and biomass distribution of MOB. Our results demonstrate that type I MOB often are a large component of pelagic bacterial communities in temperate lakes. They represent a potentially important pathway for reentry of carbon and energy into pelagic food webs that would otherwise be lost as evasion of CH4.
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Affiliation(s)
- Ingvar Sundh
- Department of Microbiology, Swedish University of Agricultural Sciences, PO Box 7025, SE-750 07 Uppsala, Sweden.
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Lin JL, Joye SB, Scholten JCM, Schäfer H, McDonald IR, Murrell JC. Analysis of methane monooxygenase genes in mono lake suggests that increased methane oxidation activity may correlate with a change in methanotroph community structure. Appl Environ Microbiol 2005; 71:6458-62. [PMID: 16204580 PMCID: PMC1265977 DOI: 10.1128/aem.71.10.6458-6462.2005] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mono Lake is an alkaline hypersaline lake that supports high methane oxidation rates. Retrieved pmoA sequences showed a broad diversity of aerobic methane oxidizers including the type I methanotrophs Methylobacter (the dominant genus), Methylomicrobium, and Methylothermus, and the type II methanotroph Methylocystis. Stratification of Mono Lake resulted in variation of aerobic methane oxidation rates with depth. Methanotroph diversity as determined by analysis of pmoA using new denaturing gradient gel electrophoresis primers suggested that variations in methane oxidation activity may correlate with changes in methanotroph community composition.
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Affiliation(s)
- Ju-Ling Lin
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, England
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44
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Tsubota J, Eshinimaev BT, Khmelenina VN, Trotsenko YA. Methylothermus thermalis gen. nov., sp. nov., a novel moderately thermophilic obligate methanotroph from a hot spring in Japan. Int J Syst Evol Microbiol 2005; 55:1877-1884. [PMID: 16166682 DOI: 10.1099/ijs.0.63691-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel moderately thermophilic methanotroph, strain MYHT(T), was isolated from a hot spring in Japan. The isolate grew on methane or methanol at 37-67 degrees C, and optimally at 57-59 degrees C. It was found to be a Gram-negative aerobe, with colourless colonies of non-motile coccoid cells, possessing type I intracytoplasmic membranes and regularly arranged surface layers of linear (p2) symmetry. Strain MYHT(T) expressed only the particulate methane monooxygenase and employed the ribulose monophosphate pathway for formaldehyde assimilation. It is a neutrophilic and halotolerant organism capable of growth at pH 6.5-7.5 (optimum pH 6.8) and in up to 3% NaCl (optimum 0.5-1% NaCl). Phylogenetic analysis based on 16S rRNA gene sequence analysis indicated that strain MYHT(T) is most closely related to the thermophilic undescribed methanotroph 'Methylothermus' HB (91% identity) and the novel halophilic methanotroph Methylohalobius crimeensis 10Ki(T) (90% identity). Comparative sequence analysis of particulate methane monooxygenase (pmoA) genes also confirmed the clustering of strain MYHT(T) with 'Methylothermus' HB and Methylohalobius crimeensis 10Ki(T) (98 and 92% derived amino acid sequence identity, respectively). The DNA G+C content was 62.5 mol%. The major cellular fatty acids were C(16:0) (37.2%) and C(18:1)omega9c (35.2%) and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The major ubiquinone was Q-8. On the basis of comparative phenotypic and genotypic characteristics, a new genus and species, Methylothermus thermalis gen. nov., sp. nov., is proposed, with MYHT(T) as the type strain (=VKM B-2345(T)=IPOD FERM P-19714(T)).
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Affiliation(s)
- Jun Tsubota
- Energy and Technology Laboratories, Osaka Gas Co., Ltd, 6-19-9 Torishima Konohana-ku, Osaka 554-0051, Japan
| | - Bulat Ts Eshinimaev
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Valentina N Khmelenina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Yuri A Trotsenko
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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45
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Kalyuzhnaya MG, Stolyar SM, Auman AJ, Lara JC, Lidstrom ME, Chistoserdova L. Methylosarcina lacus sp. nov., a methanotroph from Lake Washington, Seattle, USA, and emended description of the genus Methylosarcina. Int J Syst Evol Microbiol 2005; 55:2345-2350. [PMID: 16280494 DOI: 10.1099/ijs.0.63405-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately methanotrophic bacterial strain, LW14T, isolated from the sediment of Lake Washington, Seattle, USA, is described taxonomically. The isolate is an aerobic, Gram-negative, non-motile bacterium capable of growth on methane, and possesses type I intracytoplasmic membranes (i.e. it is a type I methanotroph). The strain possesses particulate methane monooxygenase (MMO) and has no soluble MMO. Formaldehyde is assimilated via the ribulose monophosphate cycle. The isolate grows within a pH range of 4–8, with the optimum between pH 5·5 and 6·5. The cellular fatty acid profile is dominated by C16 :
ω18c, C16 : 1
ω7c and C16 : 1
ω5t fatty acids. The DNA G+C content is 53·3±0·4 mol%. On the basis of sequence analysis of the 16S rRNA gene, isolate LW14T is related most closely to representatives of the genus Methylosarcina. However, DNA–DNA hybridization analysis reveals only a distant relationship between isolate LW14T and the previously described Methylosarcina species. On the basis of its phenotypic and genotypic characteristics, LW14T represents a novel species of the genus Methylosarcina, for which the name Methylosarcina lacus sp. nov. is proposed, with LW14T (=ATCC BAA-1047T=JCM 13284T) as the type strain.
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Affiliation(s)
- Marina G Kalyuzhnaya
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Sergey M Stolyar
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Ann J Auman
- Department of Biology, Pacific Lutheran University, Tacoma, WA 98447, USA
| | - Jimmie C Lara
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Mary E Lidstrom
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
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46
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Knief C, Vanitchung S, Harvey NW, Conrad R, Dunfield PF, Chidthaisong A. Diversity of methanotrophic bacteria in tropical upland soils under different land uses. Appl Environ Microbiol 2005; 71:3826-31. [PMID: 16000794 PMCID: PMC1169035 DOI: 10.1128/aem.71.7.3826-3831.2005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three upland soils from Thailand, a natural forest, a 16-year-old reforested site, and an agricultural field, were studied with regard to methane uptake and the community composition of methanotrophic bacteria (MB). The methane uptake rates were similar to rates described previously for forest and farmland soils of the temperate zone. The rates were lower at the agricultural site than at the native forest and reforested sites. The sites also differed in the MB community composition, which was characterized by denaturing gradient gel electrophoresis (DGGE) of pmoA gene fragments (coding for a subunit of particulate methane monooxygenase) that were PCR amplified from total soil DNA extracts. Cluster analysis based on the DGGE banding patterns indicated that the MB communities at the forested and reforested sites were similar to each other but different from that at the farmland site. Sequence analysis of excised DGGE bands indicated that Methylobacter spp. and Methylocystis spp. were present. Sequences of the "forest soil cluster" or "upland soil cluster alpha," which is postulated to represent organisms involved in atmospheric methane consumption in diverse soils, were detected only in samples from the native forest and reforested sites. Additional sequences that may represent uncultivated groups of MB in the Gammaproteobacteria were also detected.
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Affiliation(s)
- Claudia Knief
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse, 35043 Marburg, Germany
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47
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Heyer J, Berger U, Hardt M, Dunfield PF. Methylohalobius crimeensis gen. nov., sp. nov., a moderately halophilic, methanotrophic bacterium isolated from hypersaline lakes of Crimea. Int J Syst Evol Microbiol 2005; 55:1817-1826. [PMID: 16166672 DOI: 10.1099/ijs.0.63213-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel genus and species are proposed for two strains of methanotrophic bacteria isolated from hypersaline lakes in the Crimean Peninsula of Ukraine. Strains 10KiT and 4Kr are moderate halophiles that grow optimally at 1–1·5 M (5·8–8·7 %, w/v) NaCl and tolerate NaCl concentrations from 0·2 M up to 2·5 M (1·2–15 %). This optimum and upper limit are the highest for any methanotrophic bacterium known to date. The strains are Gram-negative, aerobic, non-pigmented, motile, coccoid to spindle-shaped bacteria that grow on methane or methanol only and utilize the ribulose monophosphate pathway for carbon assimilation. They are neutrophilic (growth occurs only in the range pH 6·5–7·5) and mesophilic (optimum growth occurs at 30 °C). On the basis of 16S rRNA gene sequence phylogeny, strains 10KiT and 4Kr represent a type I methanotroph within the ‘Gammaproteobacteria’. However, the 16S rRNA gene sequence displays <91·5 % identity to any public-domain sequence. The most closely related methanotrophic bacterium is the thermophilic strain HB. The DNA G+C content is 58·7 mol%. The major phospholipid fatty acids are 18 : 1ω7 (52–61 %), 16 : 0 (22–23 %) and 16 : 1ω7 (14–20 %). The dominance of 18 : 1 over 16 : 0 and 16 : 1 fatty acids is unique among known type I methanotrophs. The data suggest that strains 10KiT and 4Kr should be considered as belonging to a novel genus and species of type I methanotrophic bacteria, for which the name Methylohalobius crimeensis gen. nov., sp. nov. is proposed. Strain 10KiT (=DSM 16011T=ATCC BAA-967T) is the type strain.
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Affiliation(s)
- Jürgen Heyer
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
| | - Ursula Berger
- Research Centre Karlsruhe, Institute for Meteorology and Climate Research, Atmospheric Environmental Research, D-82467 Garmisch-Partenkirchen, Germany
| | - Martin Hardt
- Zentrale Biotechnische Betriebseinheit, Justus-Liebig-Universität, D-35392 Giessen, Germany
| | - Peter F Dunfield
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
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48
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Erwin DP, Erickson IK, Delwiche ME, Colwell FS, Strap JL, Crawford RL. Diversity of oxygenase genes from methane- and ammonia-oxidizing bacteria in the Eastern Snake River Plain aquifer. Appl Environ Microbiol 2005; 71:2016-25. [PMID: 15812034 PMCID: PMC1082543 DOI: 10.1128/aem.71.4.2016-2025.2005] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PCR amplification, restriction fragment length polymorphism, and phylogenetic analysis of oxygenase genes were used for the characterization of in situ methane- and ammonia-oxidizing bacteria from free-living and attached communities in the Eastern Snake River Plain aquifer. The following three methane monooxygenase (MMO) PCR primer sets were used: A189-A682, which amplifies an internal region of both the pmoA gene of the MMO particulate form and the amoA gene of ammonia monooxygenase; A189-mb661, which specifically targets the pmoA gene; and mmoXA-mmoXB, which amplifies the mmoX gene of the MMO soluble form (sMMO). Whole-genome amplification (WGA) was used to amplify metagenomic DNA from each community to assess its applicability for generating unbiased metagenomic template DNA. The majority of sequences in each archive were related to oxygenases of type II-like methanotrophs of the genus Methylocystis. A small subset of type I sequences found only in free-living communities possessed oxygenase genes that grouped nearest to Methylobacter and Methylomonas spp. Sequences similar to that of the amoA gene associated with ammonia-oxidizing bacteria (AOB) most closely matched a sequence from the uncultured bacterium BS870 but showed no substantial alignment to known cultured AOB. Based on these functional gene analyses, bacteria related to the type II methanotroph Methylocystis sp. were found to dominate both free-living and attached communities. Metagenomic DNA amplified by WGA showed characteristics similar to those of unamplified samples. Overall, numerous sMMO-like gene sequences that have been previously associated with high rates of trichloroethylene cometabolism were observed in both free-living and attached communities in this basaltic aquifer.
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Affiliation(s)
- Daniel P Erwin
- Environmental Biotechnology Institute, Idaho National Engineering and Environmental Laboratory, Idaho, USA
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49
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Horz HP, Rich V, Avrahami S, Bohannan BJM. Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global change. Appl Environ Microbiol 2005; 71:2642-52. [PMID: 15870356 PMCID: PMC1087552 DOI: 10.1128/aem.71.5.2642-2652.2005] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern California, using comparative sequence analysis of the pmoA gene. In addition to identifying type II methanotrophs commonly found in soils, we discovered three novel pmoA lineages for which no cultivated members have been previously reported. These novel pmoA clades clustered together either with clone sequences related to "RA 14" or "WB5FH-A," which both represent clusters of environmentally retrieved sequences of putative atmospheric methane oxidizers. Conservation of amino acid residues and rates of nonsynonymous versus synonymous nucleotide substitution in these novel lineages suggests that the pmoA genes in these clades code for functionally active methane monooxygenases. The novel clades responded to simulated global changes differently than the type II methanotrophs. We observed that the relative abundance of type II methanotrophs declined in response to increased precipitation and increased atmospheric temperature, with a significant antagonistic interaction between these factors such that the effect of both together was less than that expected from their individual effects. Two of the novel clades were not observed to respond significantly to these environmental changes, while one of the novel clades had an opposite response, increasing in relative abundance in response to increased precipitation and atmospheric temperature, with a significant antagonistic interaction between these factors.
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Affiliation(s)
- Hans-Peter Horz
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
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50
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Pester M, Friedrich MW, Schink B, Brune A. pmoA-based analysis of methanotrophs in a littoral lake sediment reveals a diverse and stable community in a dynamic environment. Appl Environ Microbiol 2004; 70:3138-42. [PMID: 15128578 PMCID: PMC404456 DOI: 10.1128/aem.70.5.3138-3142.2004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diversity and community structure of aerobic methane-oxidizing bacteria in the littoral sediment of Lake Constance was investigated by cloning analysis and terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the pmoA gene. Phylogenetic analysis revealed a high diversity of type I and type II methanotrophs in the oxygenated uppermost centimeter of the sediment. T-RFLP profiles indicated a high similarity between the active methanotrophic community in the oxic layer and the inactive community in an anoxic sediment layer at a 10-cm depth. There were also no major changes in community structure between littoral sediment cores sampled in summer and winter. By contrast, the fingerprint patterns showed substantial differences between the methanotrophic communities of littoral and profundal sediments.
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Affiliation(s)
- Michael Pester
- Department of Biology, University of Konstanz, 78457 Konstanz. Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
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