1
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Wu H, Nie WB, Tan X, Xie GJ, Qu H, Zhang X, Xian Z, Dai J, Yang C, Chen Y. Different oxygen affinities of methanotrophs and Comammox Nitrospira inform an electrically induced symbiosis for nitrogen loss. WATER RESEARCH 2024; 256:121606. [PMID: 38631236 DOI: 10.1016/j.watres.2024.121606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
Aerobic methanotrophs establish a symbiotic association with denitrifiers to facilitate the process of aerobic methane oxidation coupled with denitrification (AME-D). However, the symbiosis has been frequently observed in hypoxic conditions continuing to pose an enigma. The present study has firstly characterized an electrically induced symbiosis primarily governed by Methylosarcina and Hyphomicrobium for the AME-D process in a hypoxic niche caused by Comammox Nitrospira. The kinetic analysis revealed that Comammox Nitrospira exhibited a higher apparent oxygen affinity compared to Methylosarcina. While the coexistence of comammox and AME-D resulted in an increase in methane oxidation and nitrogen loss rates, from 0.82 ± 0.10 to 1.72 ± 0.09 mmol CH4 d-1 and from 0.59 ± 0.04 to 1.30 ± 0.15 mmol N2 d-1, respectively. Furthermore, the constructed microbial fuel cells demonstrated a pronounced dependence of the biocurrents on AME-D due to oxygen competition, suggesting the involvement of direct interspecies electron transfer in the AME-D process under hypoxic conditions. Metagenomic and metatranscriptomic analysis revealed that Methylosarcina efficiently oxidized methane to formaldehyde, subsequently generating abundant NAD(P)H for nitrate reduction by Hyphomicrobium through the dissimilatory RuMP pathway, leading to CO2 production. This study challenges the conventional understanding of survival mechanism employed by AME-D symbionts, thereby contributing to the characterization responsible for limiting methane emissions and promoting nitrogen removal in hypoxic regions.
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Affiliation(s)
- Hao Wu
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Wen-Bo Nie
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Xin Tan
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Han Qu
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Xin Zhang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Zhihao Xian
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Jingyi Dai
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Chun Yang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Yi Chen
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
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2
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Cao W, Zhao J, Cai Y, Mo Y, Ma J, Zhang G, Jiang X, Jia Z. Ridge with no-tillage facilitates microbial N 2 fixation associated with methane oxidation in rice soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171172. [PMID: 38402982 DOI: 10.1016/j.scitotenv.2024.171172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Aerobic methane-oxidizing bacteria (MOB) play a crucial role in mitigating the greenhouse gas methane emission, particularly prevalent in flooded wetlands. The implementation of ridge with no-tillage practices within a rice-rape rotation system proves effective in overcoming the restrictive redox conditions associated with waterlogging. This approach enhances capillary water availability from furrows, especially during periods of low rainfall, thereby supporting plant growth on the ridges. However, the microbe-mediated accumulation of soil organic carbon and nitrogen remains insufficiently understood under this agricultural practice, particularly concerning methane oxidation, which holds ecological and agricultural significance in the rice fields. In this study, the ridge and ditch soils from a 28-year-old ridge with no-tillage rice field experiment were utilized for incubation with 13C-CH4 and 15NN2 to estimate the methane-oxidizing and N2-fixing potentials. Our findings reveal a significantly higher net production of fresh soil organic carbon in the ridge compared to the ditch soil during methane oxidation, with values of 626 and 543 μg 13C g-1 dry weight soil, respectively. Additionally, the fixed 15N exhibited a twofold increase in the ridge soil (14.1 μg 15N g-1 dry weight soil) compared to the ditch soil. Interestingly, the result of DNA-based stable isotope probing indicated no significant differences in active MOB and N2 fixers between ridge and ditch soils. Both Methylocystis-like type II and Methylosarcina/Methylomonas-like type I MOB catalyzed methane into organic biomass carbon pools. Soil N2-fixing activity was associated with the 15N-labeling of methane oxidizers and non-MOB, such as methanol oxidizers (Hyphomicrobium) and conventional N2 fixers (Burkholderia). Methane oxidation also fostered microbial interactions, as evidenced by co-occurrence patterns. These results underscore the dual role of microbial methane oxidation - not only as a recognized sink for the potent greenhouse gas methane but also as a source of soil organic carbon and bioavailable nitrogen. This emphasizes the pivotal role of microbial methane metabolism in contributing to soil carbon and nitrogen accumulation in ridge with no-tillage systems.
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Affiliation(s)
- Weiwei Cao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; Institute for Food and Agricultural Sciences (IFAS), Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL 33314, USA
| | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Yongliang Mo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; College of Environmental Science and Engineering, China West Normal University, Nanchong 637002, PR China
| | - Jingjing Ma
- Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun 130102, PR China
| | - Guangbin Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xianjun Jiang
- College of Resources and Environment, Southwest University, Chongqing 400715, PR China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun 130102, PR China.
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3
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Seo Y, Cho KS. Effects of Plant and Soil Amendment on Remediation Performance and Methane Mitigation in Petroleum-Contaminated Soil. J Microbiol Biotechnol 2021; 31:104-114. [PMID: 33144544 PMCID: PMC9705697 DOI: 10.4014/jmb.2006.06023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
Petroleum-contaminated soil is considered among the most important potential anthropogenic atmospheric methane sources. Additionally, various rhizoremediation factors can affect methane emissions by altering soil ecosystem carbon cycles. Nonetheless, greenhouse gas emissions from soil have not been given due importance as a potentially relevant parameter in rhizoremediation techniques. Therefore, in this study we sought to investigate the effects of different plant and soil amendments on both remediation efficiencies and methane emission characteristics in dieselcontaminated soil. An indoor pot experiment consisting of three plant treatments (control, maize, tall fescue) and two soil amendments (chemical nutrient, compost) was performed for 95 days. Total petroleum hydrocarbon (TPH) removal efficiency, dehydrogenase activity, and alkB (i.e., an alkane compound-degrading enzyme) gene abundance were the highest in the tall fescue and maize soil system amended with compost. Compost addition enhanced both the overall remediation efficiencies, as well as pmoA (i.e., a methane-oxidizing enzyme) gene abundance in soils. Moreover, the potential methane emission of diesel-contaminated soil was relatively low when maize was introduced to the soil system. After microbial community analysis, various TPH-degrading microorganisms (Nocardioides, Marinobacter, Immitisolibacter, Acinetobacter, Kocuria, Mycobacterium, Pseudomonas, Alcanivorax) and methane-oxidizing microorganisms (Methylocapsa, Methylosarcina) were observed in the rhizosphere soil. The effects of major rhizoremediation factors on soil remediation efficiency and greenhouse gas emissions discussed herein are expected to contribute to the development of sustainable biological remediation technologies in response to global climate change.
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Affiliation(s)
- Yoonjoo Seo
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kyung-Suk Cho
- Department of Environmental Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea,Corresponding author Phone: +82-2-3277-2393 Fax: +82-2-3277-3275 E-mail:
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4
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Awala SI, Bellosillo LA, Gwak JH, Nguyen NL, Kim SJ, Lee BH, Rhee SK. Methylococcus geothermalis sp. nov., a methanotroph isolated from a geothermal field in the Republic of Korea. Int J Syst Evol Microbiol 2020; 70:5520-5530. [PMID: 32910751 DOI: 10.1099/ijsem.0.004442] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and coccoid methanotroph, strain IM1T, was isolated from hot spring soil. Cells of strain IM1T were catalase-negative, oxidase-positive and displayed a characteristic intracytoplasmic membrane arrangement of type I methanotrophs. The strain possessed genes encoding both membrane-bound and soluble methane monooxygenases and grew only on methane or methanol. The strain was capable of growth at temperatures between 15 and 48 °C (optimum, 30-45 °C) and pH values between pH 4.8 and 8.2 (optimum, pH 6.2-7.0). Based on phylogenetic analysis of 16S rRNA gene and PmoA sequences, strain IM1T was demonstrated to be affiliated to the genus Methylococcus. The 16S rRNA gene sequence of this strain was most closely related to the sequences of an uncultured bacterium clone FD09 (100 %) and a partially described cultured Methylococcus sp. GDS2.4 (99.78 %). The most closely related taxonomically described strains were Methylococcus capsulatus TexasT (97.92 %), Methylococcus capsulatus Bath (97.86 %) and Methyloterricola oryzae 73aT (94.21 %). Strain IM1T shared average nucleotide identity values of 85.93 and 85.62 % with Methylococcus capsulatus strains TexasT and Bath, respectively. The digital DNA-DNA hybridization value with the closest type strain was 29.90 %. The DNA G+C content of strain IM1T was 63.3 mol% and the major cellular fatty acids were C16 : 0 (39.0 %), C16 : 1 ω7c (24.0 %), C16 : 1 ω6c (13.6 %) and C16 : 1 ω5c (12.0 %). The major ubiquinone was methylene-ubiquinone-8. On the basis of phenotypic, genetic and phylogenetic data, strain IM1T represents a novel species of the genus Methylococcus for which the name Methylococcus geothermalis sp. nov. is proposed, with strain IM1T (=JCM 33941T=KCTC 72677T) as the type strain.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Lorraine Araza Bellosillo
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ngoc-Loi Nguyen
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, 34132 Daejeon, Republic of Korea
| | - Byoung-Hee Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
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5
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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: 2.5] [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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6
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Mayr MJ, Zimmermann M, Dey J, Brand A, Wehrli B, Bürgmann H. Growth and rapid succession of methanotrophs effectively limit methane release during lake overturn. Commun Biol 2020; 3:108. [PMID: 32144394 PMCID: PMC7060174 DOI: 10.1038/s42003-020-0838-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/19/2020] [Indexed: 11/09/2022] Open
Abstract
Lakes and reservoirs contribute substantially to atmospheric concentrations of the potent greenhouse gas methane. Lake sediments produce large amounts of methane, which accumulate in the oxygen-depleted bottom waters of stratified lakes. Climate change and eutrophication may increase the number of lakes with methane storage in the future. Whether stored methane escapes to the atmosphere during annual lake overturn is a matter of controversy and depends critically on the response of the methanotroph assemblage. Here we show, by combining 16S rRNA gene and pmoA mRNA amplicon sequencing, qPCR, CARD-FISH and potential methane-oxidation rate measurements, that the methanotroph assemblage in a mixing lake underwent both a substantial bloom and ecological succession. As a result, methane oxidation kept pace with the methane supplied from methane-rich bottom water and most methane was oxidized. This aspect of freshwater methanotroph ecology represents an effective mechanism limiting methane transfer from lakes to the atmosphere.
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Affiliation(s)
- Magdalena J Mayr
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Matthias Zimmermann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Jason Dey
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland
| | - Andreas Brand
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Bernhard Wehrli
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland.,Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047, Kastanienbaum, Switzerland.
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7
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Wang M, Wang C, Lan X, Abid AA, Xu X, Singla A, Sardans J, Llusià J, Peñuelas J, Wang W. Coupled steel slag and biochar amendment correlated with higher methanotrophic abundance and lower CH 4 emission in subtropical paddies. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2020; 42:483-497. [PMID: 31342217 DOI: 10.1007/s10653-019-00378-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
Aerobic methanotrophs in paddies serve as methane (CH4) filters and thereby reduce CH4 emissions. Amending soil with waste products can mitigate CH4 emissions in crops, but little is known about the impacts of amendments with steel slag and biochar on the populations and activities of aerobic methanotrophs in rice cropland. We used real-time quantitative PCR detecting system and high-throughput sequencing to determine the effects of slag and biochar amendments on CH4 emission, abundance, and community structure of methanotrophs, and the relationships between soil properties and the abundance and community composition of methanotrophs during the rice growing season in both early and late paddies. Soil salinity and pH were significantly higher for an amendment with both slag and biochar than the control in both the early and late paddies, and pH was significantly higher for a slag amendment in the late paddy. Cumulative CH4 emission was lower for the slag and slag + biochar amendments than the control in early paddy by-34.1%. Methanotrophic abundance was three- and sixfold higher for the slag + biochar amendment than the control in the early and late paddies (p < 0.05), respectively. The abundance of different groups of methanotrophs varied among the treatments. The relative abundance of Methylosarcina was higher for the slag amendment than the control, and the relative abundance of Methylomonas was lower for biochar, and slag + biochar amendments than the control. The relative abundance of Methylocystis was higher for the slag and slag + biochar amendments than the control in the early paddy, and the relative abundance of Methylocystis was higher for the slag, biochar, and slag + biochar amendments in the late paddy. Univariate and multivariate analyses indicated that the higher abundance of methanotrophic bacteria for the slag and slag + biochar amendments was correlated with soil pH, salinity, soil organic carbon, and C/N ratio, and the relative abundances of Methylocystis, Methylomonas, and Methylosarcina were associated with the effective mitigation of CH4 emission in the paddies. A discriminant general analysis indicated that the total population of methanotrophs was larger for the slag + biochar amendment than the control, and that this effect was only weakly correlated with changes in the soil properties, demonstrating that this effect on the size and species composition of methanotrophic soil populations was mostly associated with a direct effect of the slag + biochar amendment.
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Affiliation(s)
- Miaoying Wang
- College of Life Science, Fujian Normal University, Fuzhou, 350108, China
| | - Chun Wang
- Key Laboratory of Humid Sub-tropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou, 350007, China
| | - Xingfu Lan
- College of Life Science, Fujian Normal University, Fuzhou, 350108, China
| | - Abbas Ali Abid
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xuping Xu
- College of Life Science, Fujian Normal University, Fuzhou, 350108, China.
| | - Ankit Singla
- Regional Centre of Organic Farming, Ministry of Agriculture and Farmers Welfare, Bhubaneswar, Odisha, 751-021, India
| | - Jordi Sardans
- Global Ecology Unit, CREAF-CSIC-UAB, CSIC, 08193, Bellaterra, Catalonia, Spain.
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain.
| | - Joan Llusià
- Global Ecology Unit, CREAF-CSIC-UAB, CSIC, 08193, Bellaterra, Catalonia, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
| | - Josep Peñuelas
- Global Ecology Unit, CREAF-CSIC-UAB, CSIC, 08193, Bellaterra, Catalonia, Spain
- CREAF, 08193, Cerdanyola del Vallès, Catalonia, Spain
| | - Weiqi Wang
- Key Laboratory of Humid Sub-tropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou, 350007, China.
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8
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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: 83] [Impact Index Per Article: 13.8] [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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Chidambarampadmavathy K, Karthikeyan OP, Huerlimann R, Maes GE, Heimann K. Response of mixed methanotrophic consortia to different methane to oxygen ratios. WASTE MANAGEMENT (NEW YORK, N.Y.) 2017; 61:220-228. [PMID: 27876290 DOI: 10.1016/j.wasman.2016.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 08/31/2016] [Accepted: 11/04/2016] [Indexed: 05/22/2023]
Abstract
Methane (CH4) and oxygen (air) concentrations affect the CH4 oxidation capacity (MOC) and mixed methanotrophic community structures in compost (fresh) and landfill (age old) top cover soils. A change in the mixed methanotrophic community structure in response has implications for landfill CH4 bio-filter remediation and possible bio-product outcomes (i.e., fatty acid methyl esters (FAME) content and profiles and polyhydroxybutyrate (PHB) contents). Therefore the study aimed to evaluate the effect of variable CH4 to oxygen ratios (10-50% CH4 in air) on mixed methanotrophic community structures enriched from landfill top cover (LB) and compost soils (CB) and to quantify flow on impacts on MOC, total FAME contents and profiles, and PHB accumulation. A stable consortium developed achieving average MOCs of 3.0±0.12, 4.1±0.26, 6.9±0.7, 7.6±1.3 and 9.2±1.2mgCH4g-1DWbiomassh-1 in LB and 2.9±0.04, 5.05±0.32, 6.7±0.31, 7.9±0.61 and 8.6±0.48mgCH4g-1DWbiomassh-1 in CB for a 20day cultivation period at 10, 20, 30, 40 and 50% CH4, respectively. CB at 10% CH4 had a maximal FAME content of 40.5±0.8mgFAMEg-1DWbiomass, while maximal PHB contents (25mgg-1DWbiomass) was observed at 40% CH4 in LB. Despite variable CH4/O2 ratios, the mixed methanotrophic community structures in both LB and CB were relatively stable, dominated by Methylosarcina sp., and Chryseobacterium, suggesting that a resilient consortium had formed which can now be tested in bio-filter operations for CH4 mitigations in landfills.
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Affiliation(s)
- K Chidambarampadmavathy
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - O P Karthikeyan
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Sino-Forest Applied Research Centre for Pearl River Delta Environment (ARCPE), Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region
| | - R Huerlimann
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - G E Maes
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Center for Human Genetics, Genomics Core, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - K Heimann
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Centre for Bio-discovery and Molecular Development of Therapeutics, James Cook University, Townsville 4811, Queensland, Australia.
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10
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Thoetkiattikul H, Mhuantong W, Pinyakong O, Wisawapipat W, Yamazoe A, Fujita N, Eurwilaichitr L, Champreda V. Culture-independent study of bacterial communities in tropical river sediment. Biosci Biotechnol Biochem 2017; 81:200-209. [DOI: 10.1080/09168451.2016.1234927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
Ubiquitous microbial communities in river sediments actively govern organic matter decomposition, nutrient recycling, and remediation of toxic compounds. In this study, prokaryotic diversity in two major rivers in central Thailand, the Chao Phraya (CP) and the Tha Chin (TC) distributary was investigated. Significant differences in sediment physicochemical properties, particularly silt content, were noted between the two rivers. Tagged 16S rRNA sequencing on a 454 platform showed that the sediment microbiomes were dominated by Gammaproteobacteria and sulfur/sulfate reducing Deltaproteobacteria, represented by orders Desulfobacteriales and Desulfluromonadales together with organic degraders Betaproteobacteria (orders Burkholderiales and Rhodocyclales) together with the co-existence of Bacteroidetes predominated by Sphingobacteriales. Enrichment of specific bacterial orders was found in the clayey CP and silt-rich TC sediments, including various genera with known metabolic capability on decomposition of organic matter and xenobiotic compounds. The data represent one of the pioneered works revealing heterogeneity of bacteria in river sediments in the tropics.
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Affiliation(s)
- Honglada Thoetkiattikul
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Onruthai Pinyakong
- Faculty of Science, Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Worachart Wisawapipat
- Faculty of Agriculture, Department of Soil Science, Kasetsart University, Bangkok, Thailand
| | - Atsushi Yamazoe
- Biological Resource Center (BRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Nobuyuki Fujita
- Biological Resource Center (BRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Lily Eurwilaichitr
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Verawat Champreda
- Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
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11
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Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils. Nat Commun 2016; 7:11728. [PMID: 27248847 PMCID: PMC4895445 DOI: 10.1038/ncomms11728] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/25/2016] [Indexed: 01/30/2023] Open
Abstract
Soils serve as the biological sink of the potent greenhouse gas methane with exceptionally low concentrations of ∼1.84 p.p.m.v. in the atmosphere. The as-yet-uncultivated methane-consuming bacteria have long been proposed to be responsible for this ‘high-affinity' methane oxidation (HAMO). Here we show an emerging HAMO activity arising from conventional methanotrophs in paddy soil. HAMO activity was quickly induced during the low-affinity oxidation of high-concentration methane. Activity was lost gradually over 2 weeks, but could be repeatedly regained by flush-feeding the soil with elevated methane. The induction of HAMO activity occurred only after the rapid growth of methanotrophic populations, and a metatranscriptome-wide association study suggests that the concurrent high- and low-affinity methane oxidation was catalysed by known methanotrophs rather than by the proposed novel atmospheric methane oxidizers. These results provide evidence of atmospheric methane uptake in periodically drained ecosystems that are typically considered to be a source of atmospheric methane. Atmospheric methane may be consumed by microorganisms in soil, but the mechanisms behind high-affinity methane oxidization remain poorly understood. Here, Jia et al. show that known methanotrophic bacteria are responsible for atmospheric methane uptake in periodically drained wetland ecosystems.
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12
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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: 256] [Impact Index Per Article: 28.4] [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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13
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Posadas E, Serejo M, Blanco S, Pérez R, García-Encina P, Muñoz R. Minimization of biomethane oxygen concentration during biogas upgrading in algal–bacterial photobioreactors. ALGAL RES 2015. [DOI: 10.1016/j.algal.2015.09.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Oswald K, Milucka J, Brand A, Littmann S, Wehrli B, Kuypers MMM, Schubert CJ. Light-Dependent Aerobic Methane Oxidation Reduces Methane Emissions from Seasonally Stratified Lakes. PLoS One 2015; 10:e0132574. [PMID: 26193458 PMCID: PMC4508055 DOI: 10.1371/journal.pone.0132574] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 06/17/2015] [Indexed: 11/18/2022] Open
Abstract
Lakes are a natural source of methane to the atmosphere and contribute significantly to total emissions compared to the oceans. Controls on methane emissions from lake surfaces, particularly biotic processes within anoxic hypolimnia, are only partially understood. Here we investigated biological methane oxidation in the water column of the seasonally stratified Lake Rotsee. A zone of methane oxidation extending from the oxic/anoxic interface into anoxic waters was identified by chemical profiling of oxygen, methane and δ13C of methane. Incubation experiments with 13C-methane yielded highest oxidation rates within the oxycline, and comparable rates were measured in anoxic waters. Despite predominantly anoxic conditions within the zone of methane oxidation, known groups of anaerobic methanotrophic archaea were conspicuously absent. Instead, aerobic gammaproteobacterial methanotrophs were identified as the active methane oxidizers. In addition, continuous oxidation and maximum rates always occurred under light conditions. These findings, along with the detection of chlorophyll a, suggest that aerobic methane oxidation is tightly coupled to light-dependent photosynthetic oxygen production both at the oxycline and in the anoxic bottom layer. It is likely that this interaction between oxygenic phototrophs and aerobic methanotrophs represents a widespread mechanism by which methane is oxidized in lake water, thus diminishing its release into the atmosphere.
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Affiliation(s)
- Kirsten Oswald
- Department of Surface Waters—Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
- * E-mail:
| | - Jana Milucka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Andreas Brand
- Department of Surface Waters—Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Sten Littmann
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bernhard Wehrli
- Department of Surface Waters—Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Marcel M. M. Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carsten J. Schubert
- Department of Surface Waters—Research and Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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15
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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: 1.9] [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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16
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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: 66] [Impact Index Per Article: 6.6] [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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17
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Biological conversion of methane to liquid fuels: status and opportunities. Biotechnol Adv 2014; 32:1460-75. [PMID: 25281583 DOI: 10.1016/j.biotechadv.2014.09.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 09/01/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022]
Abstract
Methane is the main component of natural gas and biogas. As an abundant energy source, methane is crucial not only to meet current energy needs but also to achieve a sustainable energy future. Conversion of methane to liquid fuels provides energy-dense products and therefore reduces costs for storage, transportation, and distribution. Compared to thermochemical processes, biological conversion has advantages such as high conversion efficiency and using environmentally friendly processes. This paper is a comprehensive review of studies on three promising groups of microorganisms (methanotrophs, ammonia-oxidizing bacteria, and acetogens) that hold potential in converting methane to liquid fuels; their habitats, biochemical conversion mechanisms, performance in liquid fuels production, and genetic modification to enhance the conversion are also discussed. To date, methane-to-methanol conversion efficiencies (moles of methanol produced per mole methane consumed) of up to 80% have been reported. A number of issues that impede scale-up of this technology, such as mass transfer limitations of methane, inhibitory effects of H2S in biogas, usage of expensive chemicals as electron donors, and lack of native strains capable of converting methane to liquid fuels other than methanol, are discussed. Future perspectives and strategies in addressing these challenges are also discussed.
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18
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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: 1.3] [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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19
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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] [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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20
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Jhala YK, Vyas RV, Shelat HN, Patel HK, Patel HK, Patel KT. Isolation and characterization of methane utilizing bacteria from wetland paddy ecosystem. World J Microbiol Biotechnol 2014; 30:1845-60. [PMID: 24469547 DOI: 10.1007/s11274-014-1606-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 01/17/2014] [Indexed: 11/30/2022]
Abstract
Methylotrophic bacteria which are known to utilize C1 compounds including methane. Research during past few decades increased the interest in finding out novel genera of methane degrading bacteria to efficiently utilize methane to decrease global warming effect. Moreover, evaluation of certain known plant growth promoting strains for their methane degrading potential may open up a new direction for multiple utility of such cultures. In this study, efficient methylotrophic cultures were isolated from wetland paddy fields of Gujarat. From the overall morphological, biochemical and molecular characterization studies, the isolates were identified and designated as Bacillus aerius AAU M 8; Rhizobium sp. AAU M 10; B. subtilis AAU M 14; Paenibacillus illinoisensis AAU M 17 and B. megaterium AAU M 29. Gene specific PCR analysis of the isolates, P. illinoisensis, B. aerius, Rhizobium sp. and B. subtilis showed presence of pmoA gene encoding α subunit particulate methane monooxygenase cluster. B. megaterium, P. illinoisensis, Rhizobium sp. and Methylobacterium extrorquens showed presence of mmoX gene encoding α subunit of the hydroxylase component of the soluble methane monooxygenase cluster. P. illinoisensis and Rhizobium sp. showed presence mxaF gene encoding α subunit region of methanol dehydrogenase gene cluster showing that both isolates are efficient utilizers of methane. To the best of our knowledge, this is the first time report showing presence of methane degradation enzymes and genes within the known PGPB group of organisms from wet land paddy agro-ecosystem, which is considered as one of the leading methane producer.
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Affiliation(s)
- Y K Jhala
- Department of Microbiology, Anand Agricultural University, Anand, Gujarat, India,
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21
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Krause S, Meima-Franke M, Hefting MM, Bodelier PLE. Spatial patterns of methanotrophic communities along a hydrological gradient in a riparian wetland. FEMS Microbiol Ecol 2013; 86:59-70. [PMID: 23397906 DOI: 10.1111/1574-6941.12091] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 02/06/2013] [Accepted: 02/06/2013] [Indexed: 11/30/2022] Open
Abstract
Microbial communities display a variety of biogeographical patterns mainly driven by large-scale environmental gradients. Here, we analysed the spatial distribution of methane-oxidizing bacteria (MOB) and methane oxidation in a strongly fluctuating environment. We investigated whether the spatial variability of the MOB community can be explained by an environmental gradient and whether this changes with different plot sizes. We applied a pmoA-specific microarray to detect MOB, measured methane oxidation, methane emissions and soil properties. All variables were measured in a 10 × 10 m, 1 × 1 m and 20 × 20 cm plot and interpreted using a geostatistical approach. Methane oxidation as well as MOB displayed spatial patterns reflected in the underlying flooding gradient. Overlapping and contrasting spatial patterns for type I and type II MOB suggested different ecological life strategies. With smaller plot size, the environmental gradient could not explain the variability in the data and local factors became more important. In conclusion, environmental gradients can generally explain variability in microbial spatial patterns; however, we think that this does not contribute to a mechanistic explanation for microbial diversity because the relevant scales for microorganisms are much smaller than those normally measured.
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Affiliation(s)
- Sascha Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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22
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Forget NL, Kim Juniper S. Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge. Microbiologyopen 2013; 2:259-75. [PMID: 23401293 PMCID: PMC3633350 DOI: 10.1002/mbo3.70] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 12/19/2012] [Accepted: 01/07/2013] [Indexed: 02/01/2023] Open
Abstract
We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobacteria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus–Thermus. Statistically significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, available energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities.
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Affiliation(s)
- Nathalie L Forget
- Department of Biology, University of Victoria, 3800 Finnerty Rd, Victoria, British Columbia, Canada V8P 5C2.
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Methane carbon supports aquatic food webs to the fish level. PLoS One 2012; 7:e42723. [PMID: 22880091 PMCID: PMC3413669 DOI: 10.1371/journal.pone.0042723] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 07/10/2012] [Indexed: 01/08/2023] Open
Abstract
Large amounts of the greenhouse gas methane (CH4) are produced by anaerobic mineralization of organic matter in lakes. In spite of extensive freshwater CH4 emissions, most of the CH4 is typically oxidized by methane oxidizing bacteria (MOB) before it can reach the lake surface and be emitted to the atmosphere. In turn, it has been shown that the CH4-derived biomass of MOB can provide the energy and carbon for zooplankton and macroinvertebrates. In this study, we demonstrate the presence of specific fatty acids synthesized by MOB in fish tissues having low carbon stable isotope ratios. Fish species, zooplankton, macroinvertebrates and the water hyacinth Eichhornia crassipes were collected from a shallow lake in Brazil and analyzed for fatty acids (FA) and carbon stable isotope ratios (δ13C). The fatty acids 16∶1ω8c, 16∶1ω8t, 16∶1ω6c, 16∶1ω5t, 18∶1ω8c and 18∶1ω8t were used as signature for MOB. The δ13C ratios varied from −27.7‰ to −42.0‰ and the contribution of MOB FA ranged from 0.05% to 0.84% of total FA. Organisms with higher total content of MOB FAs presented lower δ13C values (i.e. they were more depleted in 13C), while organisms with lower content of MOB signature FAs showed higher δ13C values. An UPGMA cluster analysis was carried out to distinguish grouping of organisms in relation to their MOB FA contents. This combination of stable isotope and fatty acid tracers provides new evidence that assimilation of methane-derived carbon can be an important carbon source for the whole aquatic food web, up to the fish level.
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One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic-anoxic interface in a flooded paddy soil. ISME JOURNAL 2012; 6:2128-39. [PMID: 22695859 DOI: 10.1038/ismej.2012.57] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aerobic methane-oxidizing bacteria (MOB) use a restricted substrate range, yet >30 species-equivalent operational taxonomical units (OTUs) are found in one paddy soil. How these OTUs physically share their microhabitat is unknown. Here we highly resolved the vertical distribution of MOB and their activity. Using microcosms and cryosectioning, we sub-sampled the top 3-mm of a water-saturated soil at near in situ conditions in 100-μm steps. We assessed the community structure and activity using the particulate methane monooxygenase gene pmoA as a functional and phylogenetic marker by terminal restriction fragment length polymorphism (t-RFLP), a pmoA-specific diagnostic microarray, and cloning and sequencing. pmoA genes and transcripts were quantified using competitive reverse transcriptase PCR combined with t-RFLP. Only a subset of the methanotroph community was active. Oxygen microprofiles showed that 89% of total respiration was confined to a 0.67-mm-thick zone immediately above the oxic-anoxic interface, most probably driven by methane oxidation. In this zone, a Methylobacter-affiliated OTU was highly active with up to 18 pmoA transcripts per cell and seemed to be adapted to oxygen and methane concentrations in the micromolar range. Analysis of transcripts with a pmoA-specific microarray found a Methylosarcina-affiliated OTU associated with the surface zone. High oxygen but only nanomolar methane concentrations at the surface suggested an adaptation of this OTU to oligotrophic conditions. No transcripts of type II methanotrophs (Methylosinus, Methylocystis) were found, which indicated that this group was represented by resting stages only. Hence, different OTUs within a single guild shared the same microenvironment and exploited different niches.
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Henneberger R, Lüke C, Mosberger L, Schroth MH. Structure and function of methanotrophic communities in a landfill-cover soil. FEMS Microbiol Ecol 2012; 81:52-65. [PMID: 22172054 DOI: 10.1111/j.1574-6941.2011.01278.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/23/2011] [Accepted: 12/05/2011] [Indexed: 11/30/2022] Open
Abstract
In landfill-cover soils, aerobic methane-oxidizing bacteria (MOB) convert CH(4) to CO(2), mitigating emissions of the greenhouse gas CH(4) to the atmosphere. We investigated overall MOB community structure and assessed spatial differences in MOB diversity, abundance and activity in a Swiss landfill-cover soil. Molecular cloning, terminal restriction-fragment length polymorphism (T-RFLP) and quantitative PCR of pmoA genes were applied to soil collected from 16 locations at three different depths to study MOB community structure, diversity and abundance; MOB activity was measured in the field using gas push-pull tests. The MOB community was highly diverse but dominated by Type Ia MOB, with novel pmoA sequences present. Type II MOB were detected mainly in deeper soil with lower nutrient and higher CH(4) concentrations. Substantial differences in MOB community structure were observed between one high- and one low-activity location. MOB abundance was highly variable across the site [4.0 × 10(4) to 1.1 × 10(7) (g soil dry weight)(-1)]. Potential CH(4) oxidation rates were high [1.8-58.2 mmol CH(4) (L soil air)(-1) day(-1) ] but showed significant lateral variation and were positively correlated with mean CH(4) concentrations (P < 0.01), MOB abundance (P < 0.05) and MOB diversity (weak correlation, P < 0.17). Our findings indicate that Methylosarcina and closely related MOB are key players and that MOB abundance and community structure are driving factors in CH(4) oxidation at this landfill.
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Affiliation(s)
- Ruth Henneberger
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland
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26
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Abstract
Methanotrophs, cells that consume methane (CH(4)) as their sole source of carbon and energy, play key roles in the global carbon cycle, including controlling anthropogenic and natural emissions of CH(4), the second-most important greenhouse gas after carbon dioxide. These cells have also been widely used for bioremediation of chlorinated solvents, and help sustain diverse microbial communities as well as higher organisms through the conversion of CH(4) to complex organic compounds (e.g. in deep ocean and subterranean environments with substantial CH(4) fluxes). It has been well-known for over 30 years that copper (Cu) plays a key role in the physiology and activity of methanotrophs, but it is only recently that we have begun to understand how these cells collect Cu, the role Cu plays in CH(4) oxidation by the particulate CH(4) monooxygenase, the effect of Cu on the proteome, and how Cu affects the ability of methanotrophs to oxidize different substrates. Here we summarize the current state of knowledge of the phylogeny, environmental distribution, and potential applications of methanotrophs for regional and global issues, as well as the role of Cu in regulating gene expression and proteome in these cells, its effects on enzymatic and whole-cell activity, and the novel Cu uptake system used by methanotrophs.
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Affiliation(s)
- Jeremy D Semrau
- Department of Civil and Environmental Engineering, The University of Michigan, Ann Arbor, MI, USA.
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27
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Horz HP, Raghubanshi AS, Heyer J, Kammann C, Conrad R, Dunfield PF. Activity and community structure of methane-oxidising bacteria in a wet meadow soil. FEMS Microbiol Ecol 2009; 41:247-57. [PMID: 19709259 DOI: 10.1111/j.1574-6941.2002.tb00986.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The structure and activity of the methane-oxidising microbial community in a wet meadow soil in Germany were investigated using biogeochemical, cultivation, and molecular fingerprinting techniques. Both methane from the atmosphere and methane produced in anaerobic subsurface soil were oxidised. The specific affinity (first-order rate constant) for methane consumption was highest in the top 20 cm of soil and the apparent half-saturation constant was 137-300 nM CH(4), a value intermediate to measured values in wetland soils versus well-aerated upland soils. Most-probable-number (MPN) counting of methane-oxidising bacteria followed by isolation and characterisation of strains from the highest positive dilution steps suggested that the most abundant member of the methane-oxidising community was a Methylocystis strain (10(5)-10(7) cells g(-1) d.w. soil). Calculations based on kinetic data suggested that this cell density was sufficient to account for the observed methane oxidation activity in the soil. DNA extraction directly from the same soil samples, followed by PCR amplification and comparative sequence analyses of the pmoA gene, also detected Methylocystis. However, molecular community fingerprinting analyses revealed a more diverse and dynamic picture of the methane-oxidising community. Retrieved pmoA sequences included, besides those closely related to Methylocystis spp., others related to the genera Methylomicrobium and Methylocapsa, and there were differences across samples which were not evident in MPN analyses.
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Affiliation(s)
- Hans-Peter Horz
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse, 35043 Marburg, Germany
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28
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Abell GCJ, Stralis-Pavese N, Sessitsch A, Bodrossy L. Grazing affects methanotroph activity and diversity in an alpine meadow soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:457-465. [PMID: 23765900 DOI: 10.1111/j.1758-2229.2009.00078.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The role of methane-oxidizing bacteria (MOB) in alpine environments is poorly understood, but is of importance given the abundance of alpine environments and the role of MOB in the global carbon cycle. Using a combination of approaches we examined both seasonal and land usage effects on the ecology of microbial methane oxidation in an alpine meadow soil. Analysis of the abundance and diversity of MOB demonstrated that the abundance and diversity of the dominant type II MOB, predominantly Metylocystis and relatives, was only influenced by season. Conversely type Ia MOB abundance was significantly affected by season and land usage, while diversity changes were effected predominantly by land use. Assessment of methane oxidation potential and soil physical properties demonstrated a strong link between type Ia MOB abundance and methane oxidation potential as well as a complex series of relationships between soil moisture, pH and MOB abundance, changing with season. The results of this study suggest that, while type II MOB, unaffected by land use, represent the dominant MOB, Methylobacter-related type Ia MOB appear to be responsible for the majority of methane oxidation and are strongly affected by the grazing of cattle.
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Affiliation(s)
- Guy C J Abell
- Austrian Research Centers, Department of Bioresources, A-2444 Seibersdorf, Austria
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29
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Op den Camp HJM, Islam T, Stott MB, Harhangi HR, Hynes A, Schouten S, Jetten MSM, Birkeland NK, Pol A, Dunfield PF. Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:293-306. [PMID: 23765882 DOI: 10.1111/j.1758-2229.2009.00022.x] [Citation(s) in RCA: 280] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Aerobic methanotrophic bacteria are capable of utilizing methane as their sole energy source. They are commonly found at the oxic/anoxic interfaces of environments such as wetlands, aquatic sediments, and landfills, where they feed on methane produced in anoxic zones of these environments. Until recently, all known species of aerobic methanotrophs belonged to the phylum Proteobacteria, in the classes Gammaproteobacteria and Alphaproteobacteria. However, in 2007-2008 three research groups independently described the isolation of thermoacidophilic methanotrophs that represented a distinct lineage within the bacterial phylum Verrucomicrobia. Isolates were obtained from geothermal areas in Italy, New Zealand and Russia. They are by far the most acidophilic methanotrophs known, with a lower growth limit below pH 1. Here we summarize the properties of these novel methanotrophic Verrucomicrobia, compare them with the proteobacterial methanotrophs, propose a unified taxonomic framework for them and speculate on their potential environmental significance. New genomic and physiological data are combined with existing information to allow detailed comparison of the three strains. We propose the new genus Methylacidiphilum to encompass all three newly discovered bacteria.
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Affiliation(s)
- Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands. Department of Biology and Centre for Geobiology, University of Bergen, P.O. Box 7800, N-5020 Bergen, Norway. GNS Science, Extremophile Research Group, Private Bag 2000, 3352 Taupo, New Zealand. Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada, T2N 1N4. NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, P.O. Box 59, 1790 AB Den Burg, Texel, The Netherlands
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30
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Bussmann I, Pester M, Brune A, Schink B. Preferential cultivation of type II methanotrophic bacteria from littoral sediments (Lake Constance). FEMS Microbiol Ecol 2009; 47:179-89. [PMID: 19712333 DOI: 10.1016/s0168-6496(03)00260-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Most widely used medium for cultivation of methanotrophic bacteria from various environments is that proposed in 1970 by Whittenbury. In order to adapt and optimize medium for culturing of methanotrophs from freshwater sediment, media with varying concentrations of substrates, phosphate, nitrate, and other mineral salts were used to enumerate methanotrophs by the most probable number method. High concentrations (>1 mM) of magnesium and sulfate, and high concentrations of nitrate (>500 microM) significantly reduced the number of cultured methanotrophs, whereas phosphate in the range of 15-1500 microM had no influence. Also oxygen and carbon dioxide influenced the culturing efficiency, with an optimal mixing ratio of 17% O(2) and 3% CO(2); the mixing ratio of methane (6-32%) had no effect. A clone library of pmoA genes amplified by PCR from DNA extracted from sediment revealed the presence of both type I and type II methanotrophs. Nonetheless, the cultivation of methanotrophs, also with the improved medium, clearly favored growth of type II methanotrophs of the Methylosinus/Methylocystis group. Although significantly more methanotrophs could be cultured with the modified medium, their diversity did not mirror the diversity of methanotrophs in the sediment sample detected by molecular biology method.
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Affiliation(s)
- Ingeborg Bussmann
- LS Mikrobielle Okologie, Fachbereich Biologie, Universität Konstanz, Germany.
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31
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Scheutz C, Kjeldsen P, Bogner JE, De Visscher A, Gebert J, Hilger HA, Huber-Humer M, Spokas K. Microbial methane oxidation processes and technologies for mitigation of landfill gas emissions. WASTE MANAGEMENT & RESEARCH : THE JOURNAL OF THE INTERNATIONAL SOLID WASTES AND PUBLIC CLEANSING ASSOCIATION, ISWA 2009; 27:409-455. [PMID: 19584243 DOI: 10.1177/0734242x09339325] [Citation(s) in RCA: 231] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Landfill gas containing methane is produced by anaerobic degradation of organic waste. Methane is a strong greenhouse gas and landfills are one of the major anthropogenic sources of atmospheric methane. Landfill methane may be oxidized by methanotrophic microorganisms in soils or waste materials utilizing oxygen that diffuses into the cover layer from the atmosphere. The methane oxidation process, which is governed by several environmental factors, can be exploited in engineered systems developed for methane emission mitigation. Mathematical models that account for methane oxidation can be used to predict methane emissions from landfills. Additional research and technology development is needed before methane mitigation technologies utilizing microbial methane oxidation processes can become commercially viable and widely deployed.
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Affiliation(s)
- Charlotte Scheutz
- Department of Environmental Engineering, Technical University of Denmark, Lyngby, Denmark.
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32
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Na H, Kim S, Moon EY, Chun J. Marinifilum fragile gen. nov., sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2009; 59:2241-6. [DOI: 10.1099/ijs.0.009027-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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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. MICROBIAL ECOLOGY 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] [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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Trotsenko YA, Murrell JC. Metabolic aspects of aerobic obligate methanotrophy. ADVANCES IN APPLIED MICROBIOLOGY 2008; 63:183-229. [PMID: 18395128 DOI: 10.1016/s0065-2164(07)00005-6] [Citation(s) in RCA: 245] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Yuri A Trotsenko
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow 142290, Russia
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35
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Kalyuzhnaya MG, Khmelenina V, Eshinimaev B, Sorokin D, Fuse H, Lidstrom M, Trotsenko Y. Classification of halo(alkali)philic and halo(alkali)tolerant methanotrophs provisionally assigned to the genera Methylomicrobium and Methylobacter and emended description of the genus Methylomicrobium. Int J Syst Evol Microbiol 2008; 58:591-6. [PMID: 18319461 DOI: 10.1099/ijs.0.65317-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of four aerobic, obligately halo(alkali)philic/-tolerant, methanotrophic bacteria previously affiliated with the genera Methylobacter ('Methylobacter alcaliphilus' strains 20Z and 5Z) and Methylomicrobium (Methylomicrobium strains AMO1 and NI) were investigated. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strains form a separate branch within the type I methanotrophic bacteria and are closely related to Methylomicrobium pelagicum. DNA-DNA hybridization data revealed relatively low levels of relatedness of Methylomicrobium sp. AMO1 and Methylomicrobium sp. N1 with each other and with previously described species of the genera Methylomicrobium and Methylobacter (<55 %), indicating that they may represent novel species. Based on the results presented here and on previously reported morphological and physiological characteristics, we classify these halotolerant and halophilic methanotrophic strains as representing novel species within the genus Methylomicrobium: Methylomicrobium alcaliphilum sp. nov. (type strain 20Z(T) =VKM B-2133(T) =NCIMB 14124(T); reference strain 5Z =VKM B-2180), Methylomicrobium japanense sp. nov. (type strain NI(T) =VKM B-2462(T) =FERM BP-5633(T) =NBRC 103677(T)) and Methylomicrobium kenyense sp. nov. (type strain AMO1(T) =NCCB 97157(T) =NCIMB 13566(T) =VKM B-2464(T)). The genus Methylomicrobium has been emended in its description.
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Affiliation(s)
- Marina G Kalyuzhnaya
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia.
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Effect of earthworms on the community structure of active methanotrophic bacteria in a landfill cover soil. ISME JOURNAL 2007; 2:92-104. [PMID: 18049457 DOI: 10.1038/ismej.2007.66] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the United Kingdom, landfills are the primary anthropogenic source of methane emissions. Methanotrophic bacteria present in landfill biocovers can significantly reduce methane emissions via their capacity to oxidize up to 100% of the methane produced. Several biotic and abiotic parameters regulate methane oxidation in soil, such as oxygen, moisture, methane concentration and temperature. Earthworm-mediated bioturbation has been linked to an increase in methanotrophy in a landfill biocover soil (AC Singer et al., unpublished), but the mechanism of this trophic interaction remains unclear. The aims of this study were to determine the composition of the active methanotroph community and to investigate the interactions between earthworms and bacteria in this landfill biocover soil where the methane oxidation activity was significantly increased by the earthworms. Soil microcosms were incubated with 13C-CH4 and with or without earthworms. DNA and RNA were extracted to characterize the soil bacterial communities, with a particular emphasis on methanotroph populations, using phylogenetic (16S ribosomal RNA) and functional methane monooxygenase (pmoA and mmoX) gene probes, coupled with denaturing gradient-gel electrophoresis, clone libraries and pmoA microarray analyses. Stable isotope probing (SIP) using 13C-CH4 substrate allowed us to link microbial function with identity of bacteria via selective recovery of 'heavy' 13C-labelled DNA or RNA and to assess the effect of earthworms on the active methanotroph populations. Both types I and II methanotrophs actively oxidized methane in the landfill soil studied. Results suggested that the earthworm-mediated increase in methane oxidation rate in the landfill soil was more likely to be due to the stimulation of bacterial growth or activity than to substantial shifts in the methanotroph community structure. A Bacteroidetes-related bacterium was identified only in the active bacterial community of earthworm-incubated soil but its capacity to actually oxidize methane has to be proven.
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Chen Y, Dumont MG, Cébron A, Murrell JC. Identification of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes. Environ Microbiol 2007; 9:2855-69. [DOI: 10.1111/j.1462-2920.2007.01401.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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] [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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Romanovskaya VA, Rokitko PV, Shilin SO, Malashenko YR. Emended description of Methylomonas rubra sp. nov. Microbiology (Reading) 2006. [DOI: 10.1134/s0026261706060117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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40
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Sundh I, Bastviken D, Tranvik LJ. Abundance, activity, and community structure of pelagic methane-oxidizing bacteria in temperate lakes. Appl Environ Microbiol 2005; 71:6746-52. [PMID: 16269705 PMCID: PMC1287661 DOI: 10.1128/aem.71.11.6746-6752.2005] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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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41
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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] [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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42
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Wagner D, Lipski A, Embacher A, Gattinger A. Methane fluxes in permafrost habitats of the Lena Delta: effects of microbial community structure and organic matter quality. Environ Microbiol 2005; 7:1582-92. [PMID: 16156731 DOI: 10.1111/j.1462-2920.2005.00849.x] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For the understanding and assessment of recent and future carbon dynamics of arctic permafrost soils the processes of CH(4) production and oxidation, the community structure and the quality of dissolved organic matter (DOM) were studied in two soils of a polygonal tundra. Activities of methanogens and methanotrophs differed significantly in their rates and distribution patterns among the two investigated profiles. Community structure analysis showed similarities between both soils for ester-linked phospholipid fatty acids (PLFAs) and differences in the fraction of unsaponifiable PLFAs and phospholipid ether lipids. Furthermore, a shift of the overall composition of the microbiota with depth at both sites was indicated by an increasing portion of iso- and anteiso-branched fatty acids related to the amount of straight-chain fatty acids. Although permafrost soils represent a large carbon pool, it was shown that the reduced quality of organic matter leads to a substrate limitation of the microbial metabolism. It can be concluded from our and previous findings first that microbial communities in the active layer of an Arctic polygon tundra are composed by members of all three domains of life, with a total biomass comparable to temperate soil ecosystems, and second that these microorganisms are well adapted to the extreme temperature gradient of their environment.
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Affiliation(s)
- Dirk Wagner
- Alfred Wegener Institute for Polar and Marine Research, Telegrafenberg A43, 14469 Potsdam, Germany.
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43
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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] [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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Berger J, Fornés LV, Ott C, Jager J, Wawra B, Zanke U. Methane oxidation in a landfill cover with capillary barrier. WASTE MANAGEMENT (NEW YORK, N.Y.) 2005; 25:369-73. [PMID: 15869979 DOI: 10.1016/j.wasman.2005.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/14/2005] [Indexed: 05/02/2023]
Abstract
The methane oxidation potential of a landfill cover with capillary barrier was investigated in an experimental plant (4.8 m x 0.8 m x 2.1m). The cover soil consisted of two layers, a mixture of compost plus sand (0.3 m) over a layer of loamy sand (0.9 m). Four different climatic conditions (summer, winter, spring and fall) were simulated. In and outgoing fluxes were measured. Gas composition, temperature, humidity, matrix potential and gas pressure were monitored in two profiles. CH4 oxidation rate within the investigated top cover ranged from 98% to 57%. The minimum was observed for a short time after irrigation. Temperature distribution, gas concentration profiles and lab-scaled batch experiments indicate that before irrigation the highest oxidising activity took place in a depth of about 30 cm. After irrigation the oxidising horizon seemed to migrate upwards since methanotrophic bacteria develop better there due to an adequate supply with oxygen. It can be assumed that the absence of oxygen is one of the most important limiting factors for the CH4 oxidation process. Abrupt cross-overs between horizons of different soil material may lead to zones of increased water saturation and decreased soil respiration.
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Affiliation(s)
- J Berger
- Darmstadt University of Technology, Institute for Water Supply and Groundwater Protection, Wastewater Technology, Waste Management, Industrial Material Flows and Environmental Planning, Germany.
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Stralis-Pavese N, Sessitsch A, Weilharter A, Reichenauer T, Riesing J, Csontos J, Murrell JC, Bodrossy L. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ Microbiol 2004; 6:347-63. [PMID: 15008813 DOI: 10.1111/j.1462-2920.2004.00582.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Landfill sites are responsible for 6-12% of global methane emission. Methanotrophs play a very important role in decreasing landfill site methane emissions. We investigated the methane oxidation capacity and methanotroph diversity in lysimeters simulating landfill sites with different plant vegetations. Methane oxidation rates were 35 g methane m-2 day-1 or higher for planted lysimeters and 18 g methane m-2 day-1 or less for bare soil controls. Best methane oxidation, as displayed by gas depth profiles, was found under a vegetation of grass and alfalfa. Methanotroph communities were analysed at high throughput and resolution using a microbial diagnostic microarray targeting the particulate methane monooxygenase (pmoA) gene of methanotrophs and functionally related bacteria. Members of the genera Methylocystis and Methylocaldum were found to be the dominant members in landfill site simulating lysimeters. Soil bacterial communities in biogas free control lysimeters, which were less abundant in methanotrophs, were dominated by Methylocaldum. Type Ia methanotrophs were found only in the top layers of bare soil lysimeters with relatively high oxygen and low methane concentrations. A competetive advantage of type II methanotrophs over type Ia methanotrophs was indicated under all plant covers investigated. Analysis of average and individual results from parallel samples was used to identify general trends and variations in methanotroph community structures in relation to depth, methane supply and plant cover. The applicability of the technology for the detection of environmental perturbations was proven by an erroneous result, where an unexpected community composition detected with the microarray indicated a potential gas leakage in the lysimeter being investigated.
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Affiliation(s)
- Nancy Stralis-Pavese
- Department of Biotechnology, ARC Seibersdorf research GmbH, A-2444 Seibersdorf, Austria
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46
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Morris SA, Radajewski S, Willison TW, Murrell JC. Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing. Appl Environ Microbiol 2002; 68:1446-53. [PMID: 11872500 PMCID: PMC123758 DOI: 10.1128/aem.68.3.1446-1453.2002] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The active population of low-affinity methanotrophs in a peat soil microcosm was characterized by stable-isotope probing. "Heavy" (13)C-labeled DNA, produced after microbial growth on (13)CH(4), was separated from naturally abundant (12)C-DNA by cesium chloride density gradient centrifugation and used as a template for the PCR. Amplification products of 16S rRNA genes and pmoA, mxaF, and mmoX, which encode key enzymes in the CH(4) oxidation pathway, were analyzed. Sequences related to extant type I and type II methanotrophs were identified, indicating that these methanotrophs were active in peat exposed to 8% (vol/vol) CH(4). The (13)C-DNA libraries also contained clones that were related to beta-subclass Proteobacteria, suggesting that novel groups of bacteria may also be involved in CH(4) cycling in this soil.
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Affiliation(s)
- Samantha A Morris
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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47
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Gulledge J, Ahmad A, Steudler PA, Pomerantz WJ, Cavanaugh CM. Family- and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria. Appl Environ Microbiol 2001; 67:4726-33. [PMID: 11571178 PMCID: PMC93225 DOI: 10.1128/aem.67.10.4726-4733.2001] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. To facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes target methanotrophs in the family Methylocystaceae (type II methanotrophs) as a group. No oligonucleotide signatures that distinguish between the two genera in this family, Methylocystis and Methylosinus, were identified. Two other probes target, as a single group, a majority of the known methanotrophs belonging to the family Methylococcaceae (type I/X methanotrophs). The remaining probes target members of individual genera of the Methylococcaceae, including Methylobacter, Methylomonas, Methylomicrobium, Methylococcus, and Methylocaldum. One of the family-level probes also covers all methanotrophic endosymbionts of marine mollusks for which 16S rRNA sequences have been published. The two known species of the newly described genus Methylosarcina gen. nov. are covered by a probe that otherwise targets only members of the closely related genus Methylomicrobium. None of the probes covers strains of the newly proposed genera Methylocella and "Methylothermus," which are polyphyletic with respect to the recognized methanotrophic families. Empirically determined midpoint dissociation temperatures were 49 to 57 degrees C for all probes. In dot blot screening against RNA from positive- and negative-control strains, the probes were specific to their intended targets. The broad coverage and high degree of specificity of this new suite of probes will provide more detailed, quantitative information about the community structure of methanotrophs in environmental samples than was previously available.
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Affiliation(s)
- J Gulledge
- The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
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48
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Horz HP, Yimga MT, Liesack W. Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling. Appl Environ Microbiol 2001; 67:4177-85. [PMID: 11526021 PMCID: PMC93145 DOI: 10.1128/aem.67.9.4177-4185.2001] [Citation(s) in RCA: 172] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity of methanotrophic bacteria associated with roots of submerged rice plants was assessed using cultivation-independent techniques. The research focused mainly on the retrieval of pmoA, which encodes the alpha subunit of the particulate methane monooxygenase. A novel methanotroph-specific community-profiling method was established using the terminal restriction fragment length polymorphism (T-RFLP) technique. The T-RFLP profiles clearly revealed a more complex root-associated methanotrophic community than did banding patterns obtained by pmoA-based denaturing gradient gel electrophoresis. The comparison of pmoA-based T-RFLP profiles obtained from rice roots and bulk soil of flooded rice microcosms suggested that there was a substantially higher abundance of type I methanotrophs on rice roots than in the bulk soil. These were affiliated to the genera Methylomonas, Methylobacter, Methylococcus, and to a novel type I methanotroph sublineage. By contrast, type II methanotrophs of the Methylocystis-Methylosinus group could be detected with high relative signal intensity in both soil and root compartments. Phylogenetic treeing analyses and a set of substrate-diagnostic amino acid residues provided evidence that a novel pmoA lineage was detected. This branched distinctly from all currently known methanotrophs. To examine whether the retrieval of pmoA provided a complete view of root-associated methanotroph diversity, we also assessed the diversity detectable by recovery of genes coding for subunits of soluble methane monooxygenase (mmoX) and methanol dehydrogenase (mxaF). In addition, both 16S rRNA and 16S ribosomal DNA (rDNA) were retrieved using a PCR primer set specific to type I methanotrophs. The overall methanotroph diversity detected by recovery of mmoX, mxaF, and 16S rRNA and 16S rDNA corresponded well to the diversity detectable by retrieval of pmoA.
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Affiliation(s)
- H P Horz
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
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