1
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Ahmadi F, Lackner M. Recent findings in methanotrophs: genetics, molecular ecology, and biopotential. Appl Microbiol Biotechnol 2024; 108:60. [PMID: 38183483 DOI: 10.1007/s00253-023-12978-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/08/2023] [Accepted: 10/01/2023] [Indexed: 01/08/2024]
Abstract
The potential consequences for mankind could be disastrous due to global warming, which arises from an increase in the average temperature on Earth. The elevation in temperature primarily stems from the escalation in the concentration of greenhouse gases (GHG) such as CO2, CH4, and N2O within the atmosphere. Among these gases, methane (CH4) is particularly significant in driving alterations to the worldwide climate. Methanotrophic bacteria possess the distinctive ability to employ methane as both as source of carbon and energy. These bacteria show great potential as exceptional biocatalysts in advancing C1 bioconversion technology. The present review describes recent findings in methanotrophs including aerobic and anaerobic methanotroph bacteria, phenotypic characteristics, biotechnological potential, their physiology, ecology, and native multi-carbon utilizing pathways, and their molecular biology. The existing understanding of methanogenesis and methanotrophy in soil, as well as anaerobic methane oxidation and methanotrophy in temperate and extreme environments, is also covered in this discussion. New types of methanogens and communities of methanotrophic bacteria have been identified from various ecosystems and thoroughly examined for a range of biotechnological uses. Grasping the processes of methanogenesis and methanotrophy holds significant importance in the development of innovative agricultural techniques and industrial procedures that contribute to a more favorable equilibrium of GHG. This current review centers on the diversity of emerging methanogen and methanotroph species and their effects on the environment. By amalgamating advanced genetic analysis with ecological insights, this study pioneers a holistic approach to unraveling the biopotential of methanotrophs, offering unprecedented avenues for biotechnological applications. KEY POINTS: • The physiology of methanotrophic bacteria is fundamentally determined. • Native multi-carbon utilizing pathways in methanotrophic bacteria are summarized. • The genes responsible for encoding methane monooxygenase are discussed.
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Affiliation(s)
- Fatemeh Ahmadi
- School of Agriculture and Environment, University of Western Australia, Crawley, 6009, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, 7001, Australia
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2
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Yao X, Wang J, Hu B. How methanotrophs respond to pH: A review of ecophysiology. Front Microbiol 2023; 13:1034164. [PMID: 36687570 PMCID: PMC9853399 DOI: 10.3389/fmicb.2022.1034164] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/09/2022] [Indexed: 01/08/2023] Open
Abstract
Varying pH globally affects terrestrial microbial communities and biochemical cycles. Methanotrophs effectively mitigate methane fluxes in terrestrial habitats. Many methanotrophs grow optimally at neutral pH. However, recent discoveries show that methanotrophs grow in strongly acidic and alkaline environments. Here, we summarize the existing knowledge on the ecophysiology of methanotrophs under different pH conditions. The distribution pattern of diverse subgroups is described with respect to their relationship with pH. In addition, their responses to pH stress, consisting of structure-function traits and substrate affinity traits, are reviewed. Furthermore, we propose a putative energy trade-off model aiming at shedding light on the adaptation mechanisms of methanotrophs from a novel perspective. Finally, we take an outlook on methanotrophs' ecophysiology affected by pH, which would offer new insights into the methane cycle and global climate change.
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Affiliation(s)
- Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China,Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China,*Correspondence: Baolan Hu ✉
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3
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Bussmann I, Horn F, Hoppert M, Klings KW, Saborowski A, Warnstedt J, Liebner S. Methylomonas albis sp. nov. and Methylomonas fluvii sp. nov.: Two cold-adapted methanotrophs from the river Elbe and emended description of the species Methylovulum psychrotolerans. Syst Appl Microbiol 2021; 44:126248. [PMID: 34624710 DOI: 10.1016/j.syapm.2021.126248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/16/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
Three strains of methanotrophic bacteria (EbAT, EbBT and Eb1) were isolated from the River Elbe, Germany. These Gram-negative, rod-shaped or coccoid cells contain intracytoplasmic membranes perpendicular to the cell surface. Colonies and liquid cultures appeared bright-pink. The major cellular fatty acids were 12:0 and 14:0, in addition in Eb1 the FA 16:1ω5t was also dominant. Methane and methanol were utilized as sole carbon sources by EbBT and Eb1, while EbAT could not use methanol. All strains oxidize methane using the particulate methane monooxygenase. Both strains contain an additional soluble methane monooxygenase. The strains grew optimally at 15-25 °C and at pH 6 and 8. Based on 16S rRNA gene analysis recovered from the full genome, the phylogenetic position of EbAT is robustly outside any species clade with its closest relatives being Methylomonas sp. MK1 (98.24%) and Methylomonas sp. 11b (98.11%). Its closest type strain is Methylomonas methanica NCIMB11130 (97.91%). The 16S rRNA genes of EbBT are highly similar to Methylomonas methanica strains with Methylomonas methanica R-45371 as the closest relative (99.87% sequence identity). However, average nucleotide identity (ANI) and digital DNA-DNA-hybridization (dDDH) values reveal it as distinct species. The DNA G + C contents were 51.07 mol% and 51.5 mol% for EbAT and EbBT, and 50.7 mol% for Eb1, respectively. Strains EbAT and EbBT are representing two novel species within the genus Methylomonas. For strain EbAT we propose the name Methylomonas albis sp. nov (LMG 29958, JCM 32282) and for EbBT, we propose the name Methylomonas fluvii sp. nov (LMG 29959, JCM 32283). Eco-physiological descriptions for both strains are provided. Strain Eb1 (LMG 30323, JCM 32281) is a member of the species Methylovulum psychrotolerans. This genus is so far only represented by two isolates but Eb1 is the first isolate from a temperate environment; so, an emended description of the species is given.
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Affiliation(s)
- Ingeborg Bussmann
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Marine Station Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Michael Hoppert
- University of Göttingen, Institute of Microbiology and Genetics, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Karl-Walter Klings
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Marine Station Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Anke Saborowski
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Julia Warnstedt
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Marine Station Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; University of Potsdam, Institute of Biochemistry and Biology, 14469 Potsdam, Germany
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4
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Dong Y, Sanford RA, Connor L, Chee-Sanford J, Wimmer BT, Iranmanesh A, Shi L, Krapac IG, Locke RA, Shao H. Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL. WATER RESEARCH 2021; 202:117431. [PMID: 34320445 DOI: 10.1016/j.watres.2021.117431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Despite the clear ecological significance of the microbiomes inhabiting groundwater and connected ecosystems, our current understanding of their habitats, functionality, and the ecological processes controlling their assembly have been limited. In this study, an efficient pipeline combining geochemistry, high-throughput FluidigmTM functional gene amplification and sequencing was developed to analyze the suspended and attached microbial communities inhabiting five groundwater monitoring wells in the Illinois Basin, USA. The dominant taxa in the suspended and the attached microbial communities exhibited significantly different spatial and temporal changes in both alpha- and beta-diversity. Further analyses of representative functional genes affiliated with N2 fixation (nifH), methane oxidation (pmoA), and sulfate reduction (dsrB, and aprA), suggested functional redundancy within the shallow aquifer microbiomes. While more diversified functional gene taxa were observed for the suspended microbial communities than the attached ones except for pmoA, different levels of changes over time and space were observed between these functional genes. Notably, deterministic and stochastic ecological processes shaped the assembly of microbial communities and functional gene reservoirs differently. While homogenous selection was the prevailing process controlling assembly of microbial communities, the neutral processes (e.g., dispersal limitation, drift and others) were more important for the functional genes. The results suggest complex and changing shallow aquifer microbiomes, whose functionality and assembly vary even between the spatially proximate habitats and fractions. This research underscored the importance to include all the interface components for a more holistic understanding of the biogeochemical processes in aquifer ecosystems, which is also instructive for practical applications.
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Affiliation(s)
- Yiran Dong
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Robert A Sanford
- Department of Geology, University of Illinois Urbana-Champaign, USA
| | | | | | | | | | - Liang Shi
- School of Environmental Studies, China University of Geosciences, Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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5
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Yun J, Crombie AT, Ul Haque MF, Cai Y, Zheng X, Wang J, Jia Z, Murrell JC, Wang Y, Du W. Revealing the community and metabolic potential of active methanotrophs by targeted metagenomics in the Zoige wetland of the Tibetan Plateau. Environ Microbiol 2021; 23:6520-6535. [PMID: 34390603 DOI: 10.1111/1462-2920.15697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 01/21/2023]
Abstract
The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy-making decisions and policies to counteract global warming in this unique ecosystem. Here we applied DNA stable isotope probing using 13 C-labelled methane to label the genomes of active methanotrophs, examine the methane oxidation potential and recover metagenome-assembled genomes (MAGs) of active methanotrophs. We found that gammaproteobacteria of type I methanotrophs are responsible for methane oxidation in the wetland. We recovered two phylogenetically novel methanotroph MAGs distantly related to extant Methylobacter and Methylovulum. They belong to type I methanotrophs of gammaproteobacteria, contain both mxaF and xoxF types of methanol dehydrogenase coding genes, and participate in methane oxidation via H4 MPT and RuMP pathways. Overall, the community structure of active methanotrophs and their methanotrophic pathways revealed by DNA-SIP metagenomics and retrieved methanotroph MAGs highlight the importance of methanotrophs in suppressing methane emission in the wetland under the scenario of global warming.
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Affiliation(s)
- Juanli Yun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Andrew T Crombie
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, 210008, China
| | - Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, 210008, China
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 10049, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 10049, China
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6
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Kumar M, Yadav AN, Saxena R, Rai PK, Paul D, Tomar RS. Novel methanotrophic and methanogenic bacterial communities from diverse ecosystems and their impact on environment. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Saidi-Mehrabad A, Kits DK, Kim JJ, Tamas I, Schumann P, Khadka R, Strilets T, Smirnova AV, Rijpstra WIC, Sinninghe Damsté JS, Dunfield PF. Methylicorpusculum oleiharenae gen. nov., sp. nov., an aerobic methanotroph isolated from an oil sands tailings pond. Int J Syst Evol Microbiol 2020; 70:2499-2508. [DOI: 10.1099/ijsem.0.004064] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic methane oxidizing bacterium, designated XLMV4T, was isolated from the oxic surface layer of an oil sands tailings pond in Alberta, Canada. Strain XLMV4T is capable of growth on methane and methanol as energy sources. NH4Cl and sodium nitrate are nitrogen sources. Cells are Gram-negative, beige to yellow-pigmented, motile (via a single polar flagellum), short rods 2.0–3.3 µm in length and 1.0–1.6 µm in width. A thick capsule is produced. Surface glycoprotein or cup shape proteins typical of the genera Methylococcus, Methylothermus and
Methylomicrobium
were not observed. Major isoprenoid quinones are Q-8 and Q-7 at an approximate molar ratio of 71 : 22. Major polar lipids are phosphoglycerol and ornithine lipids. Major fatty acids are C16 : 1 ω8+C16 : 1 ω7 (34 %), C16 : 1 ω5 (16 %), and C18 : 1 ω7 (11 %). Optimum growth is observed at pH 8.0 and 25 °C. The DNA G+C content based on a draft genome sequence is 46.7 mol%. Phylogenetic analysis of 16S rRNA genes and a larger set of conserved genes place strain XLMV4T within the class
Gammaproteobacteria
and family
Methylococcaceae
, most closely related to members of the genera
Methylomicrobium
and
Methylobacter
(95.0–97.1 % 16S rRNA gene sequence identity). In silico genomic predictions of DNA–DNA hybridization values of strain XLMV4T to the nearest phylogenetic neighbours were all below 26 %. On the basis of the data presented, strain XLMV4T is considered to represent a new genus and species for which the name Methylicorpusculum oleiharenae is proposed. Strain XLMV4T (=DSMZ DSM 27269=ATCC TSD-186) is the type strain.
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Affiliation(s)
- Alireza Saidi-Mehrabad
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2E9, Canada
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Dimitri K. Kits
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2E9, Canada
| | - Joong-Jae Kim
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Ivica Tamas
- Departman Za Biologiju I Ekologiju, Prirodno-Matematicki Fakultet, Univerzitet u Novom Sadu, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Peter Schumann
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures. Inhoffenstr. 7 B 38124 Braunschweig, Germany
| | - Roshan Khadka
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - Tania Strilets
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2E9, Canada
| | - Angela V. Smirnova
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Jaap S. Sinninghe Damsté
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Peter F. Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, T2N 1N4, Canada
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Tavakoli G, Armstrong JE, Naapuri JM, Deska J, Prechtl MHG. Chemoenzymatic Hydrogen Production from Methanol through the Interplay of Metal Complexes and Biocatalysts. Chemistry 2019; 25:6474-6481. [PMID: 30648769 DOI: 10.1002/chem.201806351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Indexed: 01/26/2023]
Abstract
Microbial methylotrophic organisms can serve as great inspiration in the development of biomimetic strategies for the dehydrogenative conversion of C1 molecules under ambient conditions. In this Concept article, a concise personal perspective on the recent advancements in the field of biomimetic catalytic models for methanol and formaldehyde conversion, in the presence and absence of enzymes and co-factors, towards the formation of hydrogen under ambient conditions is given. In particular, formaldehyde dehydrogenase mimics have been introduced in stand-alone C1 -interconversion networks. Recently, coupled systems with alcohol oxidase and dehydrogenase enzymes have been also developed for in situ formation and decomposition of formaldehyde and/or reduced/oxidized nicotinamide adenine dinucleotide (NADH/ NAD+ ). Although C1 molecules are already used in many industries for hydrogen production, these conceptual bioinspired low-temperature energy conversion processes may lead one day to more efficient energy storage systems enabling renewable and sustainable hydrogen generation for hydrogen fuel cells under ambient conditions using C1 molecules as fuels for mobile and miniaturized energy storage solutions in which harsh conditions like those in industrial plants are not applicable.
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Affiliation(s)
- Ghazal Tavakoli
- Department of Chemistry, University of Cologne, Greinstr. 6, 50939, Köln, Germany
| | - Jessica E Armstrong
- Department of Chemistry, University of Cologne, Greinstr. 6, 50939, Köln, Germany.,Department of Chemistry, Yale University, 225 Prospect St, New Haven, CT, 06511-8499, USA
| | - Janne M Naapuri
- Department of Chemistry & Materials Science, Aalto University, Kemistintie 1, FI-02150, Espoo, Finland
| | - Jan Deska
- Department of Chemistry & Materials Science, Aalto University, Kemistintie 1, FI-02150, Espoo, Finland
| | - Martin H G Prechtl
- Department of Chemistry, University of Cologne, Greinstr. 6, 50939, Köln, Germany.,Institute of Natural Science and Environment, Roskilde University, 4000, Roskilde, Denmark
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9
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Shao Y, Hatzinger PB, Streger SH, Rezes RT, Chu KH. Evaluation of methanotrophic bacterial communities capable of biodegrading trichloroethene (TCE) in acidic aquifers. Biodegradation 2019; 30:173-190. [DOI: 10.1007/s10532-019-09875-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 04/04/2019] [Indexed: 10/27/2022]
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10
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Bale NJ, Rijpstra WIC, Sahonero-Canavesi DX, Oshkin IY, Belova SE, Dedysh SN, Sinninghe Damsté JS. Fatty Acid and Hopanoid Adaption to Cold in the Methanotroph Methylovulum psychrotolerans. Front Microbiol 2019; 10:589. [PMID: 31024466 PMCID: PMC6460317 DOI: 10.3389/fmicb.2019.00589] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/07/2019] [Indexed: 12/31/2022] Open
Abstract
Three strains of aerobic psychrotolerant methanotrophic bacteria Methylovulum psychrotolerans, isolated from geographically remote low-temperature environments in Northern Russia, were grown at three different growth temperatures, 20, 10 and 4°C and were found to be capable of oxidizing methane at all temperatures. The three M. psychrotolerans strains adapted their membranes to decreasing growth temperature by increasing the percent of unsaturated fatty acid (FAs), both for the bulk and intact polar lipid (IPL)-bound FAs. Furthermore, the ratio of βOH-C16:0 to n-C16:0 increased as growth temperature decreased. The IPL head group composition did not change as an adaption to temperature. The most notable hopanoid temperature adaptation of M. psychrotolerans was an increase in unsaturated hopanols with decreasing temperature. As the growth temperature decreased from 20 to 4°C, the percent of unsaturated M. psychrotolerans bulk-FAs increased from 79 to 89 % while the total percent of unsaturated hopanoids increased from 27 to 49 %. While increased FA unsaturation in response to decreased temperature is a commonly observed response in order to maintain the liquid-crystalline character of bacterial membranes, hopanoid unsaturation upon cold exposition has not previously been described. In order to investigate the mechanisms of both FA and hopanoid cold-adaption in M. psychrotolerans we identified genes in the genome of M. psychrotolerans that potentially code for FA and hopanoid desaturases. The unsaturation of hopanoids represents a novel membrane adaption to maintain homeostasis upon cold adaptation.
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Affiliation(s)
- Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, and Utrecht University, Texel, Netherlands
| | - W Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, and Utrecht University, Texel, Netherlands
| | - Diana X Sahonero-Canavesi
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, and Utrecht University, Texel, Netherlands
| | - Igor Y Oshkin
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Svetlana E Belova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Svetlana N Dedysh
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, Russia
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, and Utrecht University, Texel, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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11
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Orata FD, Meier-Kolthoff JP, Sauvageau D, Stein LY. Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels. Front Microbiol 2018; 9:3162. [PMID: 30631317 PMCID: PMC6315193 DOI: 10.3389/fmicb.2018.03162] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/06/2018] [Indexed: 11/13/2022] Open
Abstract
The order Methylococcales constitutes the methanotrophs – bacteria that can metabolize methane, a potent greenhouse gas, as their sole source of energy. These bacteria are significant players in the global carbon cycle and can produce value-added products from methane, such as biopolymers, biofuels, and single-cell proteins for animal feed, among others. Previous studies using single-gene phylogenies have shown inconsistencies in the currently established taxonomic structure of this group. This study aimed to determine and resolve these issues by using whole-genome sequence analyses. Phylogenomic analysis and the use of similarity indexes for genomic comparisons – average amino acid identity, digital DNA–DNA hybridization (dDDH), and average nucleotide identity (ANI) – were performed on 91 Methylococcales genomes. Results suggest the reclassification of members at the genus and species levels. Firstly, to resolve polyphyly of the genus Methylomicrobium, Methylomicrobium alcaliphilum, “Methylomicrobium buryatense,” Methylomicrobium japanense, Methylomicrobium kenyense, and Methylomicrobium pelagicum are reclassified to a newly proposed genus, Methylotuvimicrobium gen. nov.; they are therefore renamed to Methylotuvimicrobium alcaliphilum comb. nov., “Methylotuvimicrobium buryatense” comb. nov., Methylotuvimicrobium japanense comb. nov., Methylotuvimicrobium kenyense comb. nov., and Methylotuvimicrobium pelagicum comb. nov., respectively. Secondly, due to the phylogenetic affinity and phenotypic similarities of Methylosarcina lacus with Methylomicrobium agile and Methylomicrobium album, the reclassification of the former species to Methylomicrobium lacus comb. nov. is proposed. Thirdly, using established same-species delineation thresholds (70% dDDH and 95% ANI), Methylobacter whittenburyi is proposed to be a later heterotypic synonym of Methylobacter marinus (89% dDDH and 99% ANI). Also, the effectively but not validly published “Methylomonas denitrificans” was identified as Methylomonas methanica (92% dDDH and 100% ANI), indicating that the former is a later heterotypic synonym of the latter. Lastly, strains MC09, R-45363, and R-45371, currently identified as M. methanica, each represent a putative novel species of the genus Methylomonas (21–35% dDDH and 74–88% ANI against M. methanica) and were reclassified as Methylomonas sp. strains. It is imperative to resolve taxonomic inconsistencies within this group, first and foremost, to avoid confusion with ecological and evolutionary interpretations in subsequent studies.
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Affiliation(s)
- Fabini D Orata
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jan P Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Dominic Sauvageau
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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12
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Description of ‘Candidatus Methylocucumis oryzae’, a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field. Antonie van Leeuwenhoek 2018; 111:2473-2484. [DOI: 10.1007/s10482-018-1136-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/26/2018] [Indexed: 11/25/2022]
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13
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Mateos-Rivera A, Islam T, Marshall IPG, Schreiber L, Øvreås L. High-quality draft genome of the methanotroph Methylovulum psychrotolerans Str. HV10-M2 isolated from plant material at a high-altitude environment. Stand Genomic Sci 2018; 13:10. [PMID: 29686747 PMCID: PMC5898042 DOI: 10.1186/s40793-018-0314-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 04/04/2018] [Indexed: 11/10/2022] Open
Abstract
Here we present the genome of Methylovulum psychrotolerans strain HV10-M2, a methanotroph isolated from Hardangervidda national park (Norway). This strain represents the second of the two validly published species genus with a sequenced genome. The other is M. miyakonense HT12, which is the type strain of the species and the type species of the genus Methylovulum. We present the genome of M. psychrotolerants str. HV10-M2 and discuss the differences between M. psychrotolerans and M. miyakonense. The genome size of M. psychrotolerans str. HV10-M2 is 4,923,400 bp and contains 4415 protein-coding genes, 50 RNA genes and an average GC content of 50.88%.
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Affiliation(s)
- Alejandro Mateos-Rivera
- 1Department of Biology, University of Bergen, Bergen, Norway.,2Faculty of Engineering and Science, Western Norway University of Applied Sciences, Sogndal, Norway
| | - Tajul Islam
- 1Department of Biology, University of Bergen, Bergen, Norway
| | - Ian P G Marshall
- 3Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- 3Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,5Present address: Energy, Mining and Environment, National Research Council, Montreal, QC Canada
| | - Lise Øvreås
- 1Department of Biology, University of Bergen, Bergen, Norway.,4UNIS, the University Centre in Svalbard, Longyearbyen, Norway
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Islam T, Torsvik V, Larsen Ø, Bodrossy L, Øvreås L, Birkeland NK. Acid-Tolerant Moderately Thermophilic Methanotrophs of the Class Gammaproteobacteria Isolated From Tropical Topsoil with Methane Seeps. Front Microbiol 2016; 7:851. [PMID: 27379029 PMCID: PMC4908921 DOI: 10.3389/fmicb.2016.00851] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 05/23/2016] [Indexed: 11/13/2022] Open
Abstract
Terrestrial tropical methane seep habitats are important ecosystems in the methane cycle. Methane oxidizing bacteria play a key role in these ecosystems as they reduce methane emissions to the atmosphere. Here, we describe the isolation and initial characterization of two novel moderately thermophilic and acid-tolerant obligate methanotrophs, assigned BFH1 and BFH2 recovered from a tropical methane seep topsoil habitat. The new isolates were strictly aerobic, non-motile, coccus-shaped and utilized methane and methanol as sole carbon and energy source. Isolates grew at pH range 4.2–7.5 (optimal 5.5–6.0) and at a temperature range of 30–60°C (optimal 51–55°C). 16S rRNA gene phylogeny placed them in a well-separated branch forming a cluster together with the genus Methylocaldum as the closest relatives (93.1–94.1% sequence similarity). The genes pmoA, mxaF, and cbbL were detected, but mmoX was absent. Strains BFH1 and BFH2 are, to our knowledge, the first isolated acid-tolerant moderately thermophilic methane oxidizers of the class Gammaproteobacteria. Each strain probably denotes a novel species and they most likely represent a novel genus within the family Methylococcaceae of type I methanotrophs. Furthermore, the isolates increase our knowledge of acid-tolerant aerobic methanotrophs and signify a previously unrecognized biological methane sink in tropical ecosystems.
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Affiliation(s)
- Tajul Islam
- Department of Biology, University of Bergen Bergen, Norway
| | - Vigdis Torsvik
- Department of Biology, University of Bergen Bergen, Norway
| | - Øivind Larsen
- Department of Biology, University of BergenBergen, Norway; Uni Environment, Uni ResearchBergen, Norway
| | | | - Lise Øvreås
- Department of Biology, University of Bergen Bergen, Norway
| | - Nils-Kåre Birkeland
- Department of Biology, University of BergenBergen, Norway; Centre for Geobiology, University of BergenBergen, Norway
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Oshkin IY, Belova SE, Danilova OV, Miroshnikov KK, Rijpstra WIC, Sinninghe Damsté JS, Liesack W, Dedysh SN. Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum. Int J Syst Evol Microbiol 2016; 66:2417-2423. [DOI: 10.1099/ijsem.0.001046] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Igor Y. Oshkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Svetlana E. Belova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Olga V. Danilova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | | | - W. Irene C. Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S. Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, PO Box 59, 1790 AB Den Burg, The Netherlands
- Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Werner Liesack
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog. Appl Environ Microbiol 2016; 82:2363-2371. [PMID: 26873322 DOI: 10.1128/aem.03640-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/03/2016] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, in Minnesota. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing (SIP), expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14 to 17 μmol of CH4g dry weight soil(-1)day(-1) Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4% in situ to 25 to 36% after 8 to 14 days. Phylogenetic analysis of the(13)C-enriched DNA fractions revealed that the active methanotrophs were dominated by the genera Methylocystis(type II;Alphaproteobacteria),Methylomonas, and Methylovulum(both, type I;Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in surface peat layers, which attenuated rapidly with depth, indicating that the highest methane consumption was associated with a depth of 0 to 10 cm. Metagenomes and sequencing of cDNA pmoA amplicons from field samples confirmed that the dominant active methanotrophs were Methylocystis and Methylomonas Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the genera Methylomonas and Methylovulum(type I) can significantly contribute to aerobic methane oxidation in these ecosystems.
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Knief C. Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker. Front Microbiol 2015; 6:1346. [PMID: 26696968 PMCID: PMC4678205 DOI: 10.3389/fmicb.2015.01346] [Citation(s) in RCA: 278] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.
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Affiliation(s)
- Claudia Knief
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of BonnBonn, Germany
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Chidambarampadmavathy K, Karthikeyan OP, Heimann K. Biopolymers made from methane in bioreactors. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400203] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Karthigeyan Chidambarampadmavathy
- College of Marine and Environmental Science; James Cook University; Townsville Queensland Australia
- Centre for Sustainable Fisheries and Aquaculture; James Cook University; Townsville Queensland Australia
| | - Obulisamy P. Karthikeyan
- College of Marine and Environmental Science; James Cook University; Townsville Queensland Australia
- Centre for Sustainable Fisheries and Aquaculture; James Cook University; Townsville Queensland Australia
| | - Kirsten Heimann
- College of Marine and Environmental Science; James Cook University; Townsville Queensland Australia
- Centre for Sustainable Fisheries and Aquaculture; James Cook University; Townsville Queensland Australia
- Centre for Biodiscovery and Molecular Development of Therapeutics; James Cook University; Townsville Queensland Australia
- Comparative Genomics Centre; James Cook University; Townsville Queensland Australia
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Hamilton R, Kits KD, Ramonovskaya VA, Rozova ON, Yurimoto H, Iguchi H, Khmelenina VN, Sakai Y, Dunfield PF, Klotz MG, Knief C, Op den Camp HJM, Jetten MSM, Bringel F, Vuilleumier S, Svenning MM, Shapiro N, Woyke T, Trotsenko YA, Stein LY, Kalyuzhnaya MG. Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. GENOME ANNOUNCEMENTS 2015; 3:e00515-15. [PMID: 26044417 PMCID: PMC4457054 DOI: 10.1128/genomea.00515-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 11/20/2022]
Abstract
Genome sequences of Methylobacter luteus, Methylobacter whittenburyi, Methylosarcina fibrata, Methylomicrobium agile, and Methylovulum miyakonense were generated. The strains represent aerobic methanotrophs typically isolated from various terrestrial ecosystems.
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Affiliation(s)
| | - K Dimitri Kits
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Victoria A Ramonovskaya
- Department of Biology of Extremophilic Microorganisms, Institute of Microbiology and Virology of National Academy of Science, Kyiv, Ukraine
| | - Olga N Rozova
- GK Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Japan
| | - Hiroyuki Iguchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Japan
| | - Valentina N Khmelenina
- GK Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Japan
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Martin G Klotz
- Department of Biological Sciences, University of North Carolina, Charlotte, North Carolina, USA
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation-Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Huub J M Op den Camp
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Françoise Bringel
- Department of Microbiology, Genomics and the Environment, Université de Strasbourg, CNRS, Strasbourg, France
| | - Stéphane Vuilleumier
- Department of Microbiology, Genomics and the Environment, Université de Strasbourg, CNRS, Strasbourg, France
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Yuri A Trotsenko
- GK Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Chidambarampadmavathy K, Obulisamy P. K, Heimann K. Role of copper and iron in methane oxidation and bacterial biopolymer accumulation. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400127] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Karthigeyan Chidambarampadmavathy
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
| | - Karthikeyan Obulisamy P.
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
| | - Kirsten Heimann
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
- Centre for Biodiscovery and Molecular Development of TherapeuticsJames Cook University Townsville Queensland Australia
- Comparative Genomics CentreJames Cook University Townsville Queensland Australia
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21
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Tavormina PL, Hatzenpichler R, McGlynn S, Chadwick G, Dawson KS, Connon SA, Orphan VJ. Methyloprofundus sedimenti gen. nov., sp. nov., an obligate methanotroph from ocean sediment belonging to the 'deep sea-1' clade of marine methanotrophs. Int J Syst Evol Microbiol 2014; 65:251-259. [PMID: 25342114 DOI: 10.1099/ijs.0.062927-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We report the isolation and growth characteristics of a gammaproteobacterial methane-oxidizing bacterium (Methylococcaceae strain WF1(T), 'whale fall 1') that shares 98 % 16S rRNA gene sequence identity with uncultivated free-living methanotrophs and the methanotrophic endosymbionts of deep-sea mussels, ≤94.6 % 16S rRNA gene sequence identity with species of the genus Methylobacter and ≤93.6 % 16S rRNA gene sequence identity with species of the genera Methylomonas and Methylosarcina. Strain WF1(T) represents the first cultivar from the 'deep sea-1' clade of marine methanotrophs, which includes members that participate in methane oxidation in sediments and the water column in addition to mussel endosymbionts. Cells of strain WF1(T) were elongated cocci, approximately 1.5 µm in diameter, and occurred singly, in pairs and in clumps. The cell wall was Gram-negative, and stacked intracytoplasmic membranes and storage granules were evident. The genomic DNA G+C content of WF1(T) was 40.5 mol%, significantly lower than that of currently described cultivars, and the major fatty acids were 16 : 0, 16 : 1ω9c, 16 : 1ω9t, 16 : 1ω8c and 16 : 2ω9,14. Growth occurred in liquid media at an optimal temperature of 23 °C, and was dependent on the presence of methane or methanol. Atmospheric nitrogen could serve as the sole nitrogen source for WF1(T), a capacity that had not been functionally demonstrated previously in members of Methylobacter. On the basis of its unique morphological, physiological and phylogenetic properties, this strain represents the type species within a new genus, and we propose the name Methyloprofundus sedimenti gen. nov., sp. nov. The type strain of Methyloprofundus sedimenti is WF1(T) ( = LMG 28393(T) = ATCC BAA-2619(T)).
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Affiliation(s)
- Patricia L Tavormina
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Shawn McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Grayson Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Stephanie A Connon
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA
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Gammaproteobacterial methanotrophs dominate cold methane seeps in floodplains of West Siberian rivers. Appl Environ Microbiol 2014; 80:5944-54. [PMID: 25063667 DOI: 10.1128/aem.01539-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A complex system of muddy fluid-discharging and methane (CH4)-releasing seeps was discovered in a valley of the river Mukhrinskaya, one of the small rivers of the Irtysh Basin, West Siberia. CH4 flux from most (90%) of these gas ebullition sites did not exceed 1.45 g CH4 h(-1), while some seeps emitted up to 5.54 g CH4 h(-1). The δ(13)C value of methane released from these seeps varied between -71.1 and -71.3‰, suggesting its biogenic origin. Although the seeps were characterized by low in situ temperatures (3.5 to 5°C), relatively high rates of methane oxidation (15.5 to 15.9 nmol CH4 ml(-1) day(-1)) were measured in mud samples. Fluorescence in situ hybridization detected 10(7) methanotrophic bacteria (MB) per g of mud (dry weight), which accounted for up to 20.5% of total bacterial cell counts. Most (95.8 to 99.3%) methanotroph cells were type I (gammaproteobacterial) MB. The diversity of methanotrophs in this habitat was further assessed by pyrosequencing of pmoA genes, encoding particulate methane monooxygenase. A total of 53,828 pmoA gene sequences of seep-inhabiting methanotrophs were retrieved and analyzed. Nearly all of these sequences affiliated with type I MB, including the Methylobacter-Methylovulum-Methylosoma group, lake cluster 2, and several as-yet-uncharacterized methanotroph clades. Apparently, microbial communities attenuating methane fluxes from these local but strong CH4 sources in floodplains of high-latitude rivers have a large proportion of potentially novel, psychrotolerant methanotrophs, thereby providing a challenge for future isolation studies.
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Danilova OV, Dedysh SN. Abundance and diversity of methanotrophic Gammaproteobacteria in northern wetlands. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714020040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Krause S, van Bodegom PM, Cornwell WK, Bodelier PLE. Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria. J Evol Biol 2014; 27:1240-7. [DOI: 10.1111/jeb.12401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 04/01/2014] [Accepted: 04/04/2014] [Indexed: 11/29/2022]
Affiliation(s)
- S. Krause
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
- Department of Chemical Engineering; University of Washington; Seattle WA USA
| | - P. M. van Bodegom
- Department of Ecological Sciences; Subdepartment of Systems Ecology; VU University of Amsterdam; Amsterdam The Netherlands
| | - W. K. Cornwell
- Department of Ecological Sciences; Subdepartment of Systems Ecology; VU University of Amsterdam; Amsterdam The Netherlands
| | - P. L. E. Bodelier
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
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25
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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: 4.3] [Reference Citation Analysis] [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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Wang PL, Chiu YP, Cheng TW, Chang YH, Tu WX, Lin LH. Spatial variations of community structures and methane cycling across a transect of Lei-Gong-Hou mud volcanoes in eastern Taiwan. Front Microbiol 2014; 5:121. [PMID: 24723919 PMCID: PMC3971192 DOI: 10.3389/fmicb.2014.00121] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 03/10/2014] [Indexed: 12/04/2022] Open
Abstract
This study analyzed cored sediments retrieved from sites distributed across a transect of the Lei-Gong-Hou mud volcanoes in eastern Taiwan to uncover the spatial distributions of biogeochemical processes and community assemblages involved in methane cycling. The profiles of methane concentration and carbon isotopic composition revealed various orders of the predominance of specific methane-related metabolisms along depth. At a site proximal to the bubbling pool, the methanogenic zone was sandwiched by the anaerobic methanotrophic zones. For two sites distributed toward the topographic depression, the methanogenic zone overlaid the anaerobic methanotrophic zone. The predominance of anaerobic methanotrophy at specific depth intervals is supported by the enhanced copy numbers of the ANME-2a 16S rRNA gene and coincides with high dissolved Fe/Mn concentrations and copy numbers of the Desulfuromonas/Pelobacter 16S rRNA gene. Assemblages of 16S rRNA and mcrA genes revealed that methanogenesis was mediated by Methanococcoides and Methanosarcina. pmoA genes and a few 16S rRNA genes related to aerobic methanotrophs were detected in limited numbers of subsurface samples. While dissolved Fe/Mn signifies the presence of anaerobic metabolisms near the surface, the correlations between geochemical characteristics and gene abundances, and the absence of aerobic methanotrophs in top sediments suggest that anaerobic methanotrophy is potentially dependent on iron/manganese reduction and dominates over aerobic methanotrophy for the removal of methane produced in situ or from a deep source. Near-surface methanogenesis contributes to the methane emissions from mud platform. The alternating arrangements of methanogenic and methanotrophic zones at different sites suggest that the interactions between mud deposition, evaporation, oxidation and fluid transport modulate the assemblages of microbial communities and methane cycling in different compartments of terrestrial mud volcanoes.
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Affiliation(s)
- Pei-Ling Wang
- Institute of Oceanography, National Taiwan University Taipei, Taiwan
| | - Yi-Ping Chiu
- Institute of Oceanography, National Taiwan University Taipei, Taiwan ; Department of Geosciences, National Taiwan University Taipei, Taiwan
| | - Ting-Wen Cheng
- Department of Geosciences, National Taiwan University Taipei, Taiwan
| | - Yung-Hsin Chang
- Department of Geosciences, National Taiwan University Taipei, Taiwan
| | - Wei-Xain Tu
- Department of Geosciences, National Taiwan University Taipei, Taiwan
| | - Li-Hung Lin
- Department of Geosciences, National Taiwan University Taipei, Taiwan
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Kim TG, Jeong SY, Cho KS. Characterization of tobermolite as a bed material for selective growth of methanotrophs in biofiltration. J Biotechnol 2014; 173:90-7. [DOI: 10.1016/j.jbiotec.2014.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 01/06/2014] [Accepted: 01/08/2014] [Indexed: 11/16/2022]
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Kallistova AY, Montonen L, Jurgens G, Münster U, Kevbrina MV, Nozhevnikova AN. Culturable psychrotolerant methanotrophic bacteria in landfill cover soil. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714010044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Hirayama H, Abe M, Miyazaki M, Nunoura T, Furushima Y, Yamamoto H, Takai K. Methylomarinovum caldicuralii gen. nov., sp. nov., a moderately thermophilic methanotroph isolated from a shallow submarine hydrothermal system, and proposal of the family Methylothermaceae fam. nov. Int J Syst Evol Microbiol 2013; 64:989-999. [PMID: 24425820 DOI: 10.1099/ijs.0.058172-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel methane-oxidizing bacterium, strain IT-9(T), was isolated from a shallow submarine hydrothermal system occurring in a coral reef in Japan. Strain IT-9(T) was a Gram-negative, aerobic, motile, coccoid or oval-shaped bacterium with the distinctive intracytoplasmic membrane arrangement of a type I methanotroph. Strain IT-9(T) was a moderately thermophilic, obligate methanotroph that grew on methane and methanol at 30-55 °C (optimum 45-50 °C). The strain possessed the particulate methane monooxygenase (pMMO). The ribulose monophosphate pathway was operative for carbon assimilation. NaCl was required for growth within a concentration range of 1-5 % (optimum 3 %). The hao gene encoding hydroxylamine oxidoreductase (HAO) involved in nitrification was detected by a PCR experiment. The major phospholipid fatty acids were C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The DNA G+C content was 66.0 mol%. The 16S rRNA gene sequence of strain IT-9(T) was only moderately related to the sequences of members of the closest genera Methylohalobius (94.1 % similarity) and Methylothermus (91.7-91.9 % similarity); however, those sequences formed a deeply branching monophyletic group within the order Methylococcales. Phylogenies based on 16S rRNA gene sequences, deduced partial PmoA sequences and deduced partial Hao sequences and physiological and chemotaxonomic characteristics revealed that strain IT-9(T) represents a novel species of a new genus, for which the name Methylomarinovum caldicuralii gen. nov., sp. nov. is proposed. The type strain of Methylomarinovum caldicuralii is IT-9(T) ( = JCM 13666(T) = DSM 19749(T)). In addition, we propose a new family, Methylothermaceae fam. nov., in the order Methylococcales, to accommodate the genera Methylothermus, Methylohalobius and Methylomarinovum. The genera Methylothermus and Methylohalobius have been recognized as being distinct from other genera in the methane-oxidizing order Methylococcales in the class Gammaproteobacteria. These genera form a distinctive monophyletic lineage within the order on the basis of 16S rRNA gene sequence phylogeny. This seems consistent with their distinctive physiological traits; the genus Methylothermus includes the most thermophilic species, and the genus Methylohalobius includes the most halophilic species, within the order. Although these two genera include only three species at the time of writing, similar sequences of 16S rRNA genes and pmoA genes encoding pMMO have been detected in a geothermal area or deep-sea hydrothermal vent fields by studies using culture-independent techniques. This suggests that unknown methanotrophs of this lineage inhabit various extreme environments.
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Affiliation(s)
- Hisako Hirayama
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Mariko Abe
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masayuki Miyazaki
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Takuro Nunoura
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yasuo Furushima
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hiroyuki Yamamoto
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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Kong JY, Su Y, Zhang QQ, Bai Y, Xia FF, Fang CR, He R. Vertical profiles of community and activity of methanotrophs in landfill cover soils of different age. J Appl Microbiol 2013; 115:756-65. [DOI: 10.1111/jam.12263] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/29/2013] [Accepted: 05/24/2013] [Indexed: 11/30/2022]
Affiliation(s)
- J.-Y. Kong
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Y. Su
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Q.-Q. Zhang
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - Y. Bai
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - F.-F. Xia
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
| | - C.-R. Fang
- School of Civil Engineering and Architecture; Zhejiang University of Science and Technology; Hangzhou China
| | - R. He
- Department of Environmental Engineering; Zhejiang University; Hangzhou China
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Nazaries L, Murrell JC, Millard P, Baggs L, Singh BK. Methane, microbes and models: fundamental understanding of the soil methane cycle for future predictions. Environ Microbiol 2013; 15:2395-417. [DOI: 10.1111/1462-2920.12149] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Loïc Nazaries
- Hawkesbury Institute for the Environment; University of Western Sydney; Building L9; Locked Bag 1797; Penrith South; NSW; 2751; Australia
| | - J. Colin Murrell
- School of Environmental Sciences; University of East Anglia; Norwich Research Park; Norwich; NR4 7TJ; UK
| | - Pete Millard
- Landcare Research; PO Box 40; Lincoln; 7604; New Zealand
| | - Liz Baggs
- Institute of Biological and Environmental Sciences; University of Aberdeen; Zoology Building; Tillydrone Avenue; Aberdeen; AB24 2TZ; Scotland; UK
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment; University of Western Sydney; Building L9; Locked Bag 1797; Penrith South; NSW; 2751; Australia
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Beck DAC, Kalyuzhnaya MG, Malfatti S, Tringe SG, Glavina Del Rio T, Ivanova N, Lidstrom ME, Chistoserdova L. A metagenomic insight into freshwater methane-utilizing communities and evidence for cooperation between the Methylococcaceae and the Methylophilaceae. PeerJ 2013; 1:e23. [PMID: 23638358 PMCID: PMC3628875 DOI: 10.7717/peerj.23] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 01/09/2013] [Indexed: 11/20/2022] Open
Abstract
We investigated microbial communities active in methane oxidation in lake sediment at different oxygen tensions and their response to the addition of nitrate, via stable isotope probing combined with deep metagenomic sequencing. Communities from a total of four manipulated microcosms were analyzed, supplied with 13C-methane in, respectively, ambient air, ambient air with the addition of nitrate, nitrogen atmosphere and nitrogen atmosphere with the addition of nitrate, and these were compared to the community from an unamended sediment sample. We found that the major group involved in methane oxidation in both aerobic and microaerobic conditions were members of the family Methylococcaceae, dominated by species of the genus Methylobacter, and these were stimulated by nitrate in aerobic but not microaerobic conditions. In aerobic conditions, we also noted a pronounced response to both methane and nitrate by members of the family Methylophilaceae that are non-methane-oxidizing methylotrophs, and predominantly by the members of the genus Methylotenera. The relevant abundances of the Methylococcaceae and the Methylophilaceae and their coordinated response to methane and nitrate suggest that these species may be engaged in cooperative behavior, the nature of which remains unknown.
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Affiliation(s)
- David A C Beck
- Department of Chemical Engineering and eScience Institute, University of Washington , Seattle, WA , USA
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Lee JH, Kim TG, Cho KS. Isolation and characterization of a facultative methanotroph degrading malodor-causing volatile sulfur compounds. JOURNAL OF HAZARDOUS MATERIALS 2012; 235-236:224-229. [PMID: 22884733 DOI: 10.1016/j.jhazmat.2012.07.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 07/02/2012] [Accepted: 07/25/2012] [Indexed: 06/01/2023]
Abstract
Simultaneous removal of methane and malodor-causing volatile sulfur compounds (MVSCs), both emitted from landfills, is a desirable characteristic for methane-mitigation approaches. A methanotrophic bacterium was isolated from a microbial consortium, enriched with methane and dimethyl sulfide (DMS). It grew in the complex nutrient medium R2A without methane, and stably exhibited methanotrophic activity after facultative growth. It was identified as Sphingopyxis sp. MD2 by comparison of the 16S rRNA gene. It belongs to Sphingomonadales, whose members have not shown methanotrophic activity, phylogenetically distinct from orders of known methanotrophs. The MD2 biomass increased at a growth rate of 1.18d(-1) when methane was used as the sole growth substrate. An inhibition test with allylthiourea and PCR/sequencing confirmed the presence of particulate methane monooxygenase in MD2. DMS decreased the methane oxidation rate (2634±146 μmole g DCW(-1) h(-1)) by 12%, while H(2)S had no effect on the methane oxidation rate. Interestingly, methanethiol (MT) enhanced the methane oxidation rate by more than 50%. MD2 degraded H(2)S and MT, regardless of the presence of methane. MD2 also degraded DMS in the presence of methane, indicating co-metabolism. These combined results indicate that MD2 may be a promising biological resource for simultaneous removal of methane and MVSCs.
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Affiliation(s)
- Jung-Hee Lee
- Department of Environmental Science and Engineering, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul 120-750, Republic of Korea
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Effects of nonmethane volatile organic compounds on microbial community of methanotrophic biofilter. Appl Microbiol Biotechnol 2012; 97:6549-59. [DOI: 10.1007/s00253-012-4443-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 10/27/2022]
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Hirayama H, Fuse H, Abe M, Miyazaki M, Nakamura T, Nunoura T, Furushima Y, Yamamoto H, Takai K. Methylomarinum vadi gen. nov., sp. nov., a methanotroph isolated from two distinct marine environments. Int J Syst Evol Microbiol 2012; 63:1073-1082. [PMID: 22707534 DOI: 10.1099/ijs.0.040568-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Two aerobic methane-oxidizing bacterial strains were isolated from distinct marine environments in Japan. Strains IT-4(T) and T2-1 were Gram-stain-negative, aerobic, motile, plump short rods or oval-shaped bacteria with a single polar flagellum and type I intracytoplasmic membranes. They were obligate methanotrophs that grew only on methane or methanol. Each strain possessed the particulate methane monooxygenase (pMMO). The ribulose monophosphate pathway was operative for carbon assimilation. The strains grew best at 37 °C, and did not grow at 45 °C. NaCl was required for growth within a concentration range of 1-8 % (w/v). The major phospholipid fatty acids were C16 : 0, C16 : 1ω7c, and C16 : 1ω5t. The major isoprenoid quinone was MQ-8. The DNA G+C content was 50.9-51.7 mol%. The 16S rRNA gene sequences of the strains showed 99.4 % similarity to each other, and DNA-DNA hybridization analysis indicated that the strains were representatives of the same species. The 16S rRNA gene sequences were highly similar to some marine environmental sequences (94.0-97.7 % similarity), but did not show similarities more than 94 % with sequences of members of other related genera, such as Methylomicrobium, Methylobacter, Methylomonas and Methylosarcina. Phylogenies based on 16S rRNA gene sequences and deduced partial PmoA sequences, and the physiological and chemotaxonomic characteristics revealed that strains IT-4(T) and T2-1 represent a novel species of a new genus in the family Methylococcaceae, for which the name Methylomarinum vadi gen. nov., sp. nov. is proposed. The type strain is IT-4(T) ( = JCM 13665(T) = DSM 18976(T)).
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Affiliation(s)
- Hisako Hirayama
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hiroyuki Fuse
- College of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama-city, Saitama 337-8570, Japan
| | - Mariko Abe
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masayuki Miyazaki
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Takamichi Nakamura
- Chugai Technos Corp., 9-12 Yokogawa Shinmachi Nishi-ku, Hiroshima-City 733-0013, Japan
| | - Takuro Nunoura
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yasuo Furushima
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hiroyuki Yamamoto
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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Kim TG, Moon KE, Yun J, Cho KS. Comparison of RNA- and DNA-based bacterial communities in a lab-scale methane-degrading biocover. Appl Microbiol Biotechnol 2012; 97:3171-81. [DOI: 10.1007/s00253-012-4123-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 04/16/2012] [Accepted: 04/17/2012] [Indexed: 11/30/2022]
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He R, Wooller MJ, Pohlman JW, Catranis C, Quensen J, Tiedje JM, Leigh MB. Identification of functionally active aerobic methanotrophs in sediments from an arctic lake using stable isotope probing. Environ Microbiol 2012; 14:1403-19. [PMID: 22429394 DOI: 10.1111/j.1462-2920.2012.02725.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Arctic lakes are a significant source of the greenhouse gas methane (CH(4) ), but the role that methane oxidizing bacteria (methanotrophs) play in limiting the overall CH(4) flux is poorly understood. Here, we used stable isotope probing (SIP) techniques to identify the metabolically active aerobic methanotrophs in upper sediments (0-1 cm) from an arctic lake in northern Alaska sampled during ice-free summer conditions. The highest CH(4) oxidation potential was observed in the upper sediment (0-1 cm depth) with 1.59 µmol g wet weight(-1) day(-1) compared with the deeper sediment samples (1-3 cm, 3-5 cm and 5-10 cm), which exhibited CH(4) oxidation potentials below 0.4 µmol g wet weight(-1) day(-1) . Both type I and type II methanotrophs were directly detected in the upper sediment total communities using targeted primer sets based on 16S rRNA genes. Sequencing of 16S rRNA genes and functional genes (pmoA and mxaF) in the (13) C-DNA from the upper sediment indicated that type I methanotrophs, mainly Methylobacter, Methylosoma, Methylomonas and Methylovulum miyakonense, dominated the assimilation of CH(4) . Methylotrophs, including the genera Methylophilus and/or Methylotenera, were also abundant in the (13) C-DNA. Our results show that a diverse microbial consortium acquired carbon from CH(4) in the sediments of this arctic lake.
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Affiliation(s)
- Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
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Hoefman S, van der Ha D, De Vos P, Boon N, Heylen K. Miniaturized extinction culturing is the preferred strategy for rapid isolation of fast-growing methane-oxidizing bacteria. Microb Biotechnol 2011; 5:368-78. [PMID: 22070783 PMCID: PMC3821679 DOI: 10.1111/j.1751-7915.2011.00314.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Methane‐oxidizing bacteria (MOB) have a large potential as a microbial sink for the greenhouse gas methane as well as for biotechnological purposes. However, their application in biotechnology has so far been hampered, in part due to the relative slow growth rate of the available strains. To enable the availability of novel strains, this study compares the isolation of MOB by conventional dilution plating with miniaturized extinction culturing, both performed after an initial enrichment step. The extinction approach rendered 22 MOB isolates from four environmental samples, while no MOB could be isolated by plating. In most cases, extinction culturing immediately yielded MOB monocultures making laborious purification redundant. Both type I (Methylomonas spp.) and type II (Methylosinus sp.) MOB were isolated. The isolated methanotrophic diversity represented at least 11 different strains and several novel species based on 16S rRNA gene sequence dissimilarity. These strains possessed the particulate (100%) and soluble (64%) methane monooxygenase gene. Also, 73% of the strains could be linked to a highly active fast‐growing mixed MOB community. In conclusion, miniaturized extinction culturing was more efficient in rapidly isolating numerous MOB requiring little effort and fewer materials, compared with the more widely applied plating procedure. This miniaturized approach allowed straightforward isolation and could be very useful for subsequent screening of desired characteristics, in view of their future biotechnological potential.
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Affiliation(s)
- Sven Hoefman
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, KL Ledeganckstraat 35, B-9000 Gent, Belgium
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Geymonat E, Ferrando L, Tarlera SE. Methylogaea oryzae gen. nov., sp. nov., a mesophilic methanotroph isolated from a rice paddy field. Int J Syst Evol Microbiol 2011; 61:2568-2572. [DOI: 10.1099/ijs.0.028274-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel methanotroph, designated strain E10T, was isolated from a rice paddy field in Uruguay. Strain E10T grew on methane and methanol as sole carbon and energy sources. Cells were Gram-negative, non-motile, non-pigmented, slightly curved rods showing type I intracytoplasmic membranes arranged in stacks. The strain was neutrophilic and mesophilic; optimum growth occurred at 30–35 °C with no growth above 37 °C. The strain possessed only a particulate methane monooxygenase (pmoA). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the moderately thermophilic strains Methylocaldum szegediense OR2T (91.6 % sequence similarity) and Methylococcus capsulatus Bath (91.5 %). Comparative sequence analysis of pmoA genes also confirmed that strain E10T formed a new lineage among the genera Methylocaldum and Methylococcus with 89 and 84 % derived amino acid sequence identity to Methylococcus capsulatus Bath and Methylocaldum gracile VKM-14LT, respectively. The DNA G+C content was 63.1 mol% and the major cellular fatty acid was C16 : 0 (62.05 %). Thus, strain E10T ( = JCM 16910T = DSM 23452T) represents the type strain of a novel species within a new genus, for which the name Methylogaea oryzae gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Estefanía Geymonat
- Cátedra de Microbiología, Facultad de Química y Facultad de Ciencias, Universidad de la República-UDELAR, CC1157 Montevideo, Uruguay
| | - Lucía Ferrando
- Cátedra de Microbiología, Facultad de Química y Facultad de Ciencias, Universidad de la República-UDELAR, CC1157 Montevideo, Uruguay
| | - Silvana E. Tarlera
- Cátedra de Microbiología, Facultad de Química y Facultad de Ciencias, Universidad de la República-UDELAR, CC1157 Montevideo, Uruguay
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Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia. Appl Environ Microbiol 2011; 77:8509-15. [PMID: 21984248 DOI: 10.1128/aem.05834-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanotrophs play a key role in the global carbon cycle, in which they affect methane emissions and help to sustain diverse microbial communities through the conversion of methane to organic compounds. To investigate the microbial interactions that cause positive effects on methanotrophs, cocultures were constructed using Methylovulum miyakonense HT12 and each of nine nonmethanotrophic bacteria, which were isolated from a methane-utilizing microbial consortium culture established from forest soil. Three rhizobial strains were found to strongly stimulate the growth and methane oxidation of M. miyakonense HT12 in cocultures. We purified the stimulating factor produced by Rhizobium sp. Rb122 and identified it as cobalamin. Growth stimulation by cobalamin was also observed for three other gammaproteobacterial methanotrophs. These results suggest that microbial interactions through cobalamin play an important role in methane oxidation in various ecosystems.
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Detection, isolation, and characterization of acidophilic methanotrophs from Sphagnum mosses. Appl Environ Microbiol 2011; 77:5643-54. [PMID: 21724892 DOI: 10.1128/aem.05017-11] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sphagnum peatlands are important ecosystems in the methane cycle. Methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. Yet little is known about the diversity and identity of the methanotrophs present in and on Sphagnum mosses of peatlands, and only a few isolates are known. The methanotrophic community in Sphagnum mosses, originating from a Dutch peat bog, was investigated using a pmoA microarray. A high biodiversity of both gamma- and alphaproteobacterial methanotrophs was found. With Sphagnum mosses as the inoculum, alpha- and gammaproteobacterial acidophilic methanotrophs were isolated using established and newly designed media. The 16S rRNA, pmoA, pxmA, and mmoX gene sequences showed that the alphaproteobacterial isolates belonged to the Methylocystis and Methylosinus genera. The Methylosinus species isolated are the first acid-tolerant members of this genus. Of the acidophilic gammaproteobacterial strains isolated, strain M5 was affiliated with the Methylomonas genus, and the other strain, M200, may represent a novel genus, most closely related to the genera Methylosoma and Methylovulum. So far, no acidophilic or acid-tolerant methanotrophs in the Gammaproteobacteria class are known. All strains showed the typical features of either type I or II methanotrophs and are, to the best of our knowledge, the first isolated (acidophilic or acid-tolerant) methanotrophs from Sphagnum mosses.
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