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Yousaf T, Saleem F, Andleeb S, Ali M, Farhan Ul Haque M. Methylotrophic bacteria from rice paddy soils: mineral-nitrogen-utilizing isolates richness in bulk soil and rhizosphere. World J Microbiol Biotechnol 2024; 40:188. [PMID: 38702590 DOI: 10.1007/s11274-024-04000-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Methanol, the second most abundant volatile organic compound, primarily released from plants, is a major culprit disturbing atmospheric chemistry. Interestingly, ubiquitously found methanol-utilizing bacteria, play a vital role in mitigating atmospheric methanol effects. Despite being extensively characterized, the effect of nitrogen sources on the richness of methanol-utilizers in the bulk soil and rhizosphere is largely unknown. Therefore, the current study was planned to isolate, characterize and explore the richness of cultivable methylotrophs from the bulk soil and rhizosphere of a paddy field using media with varying nitrogen sources. Our data revealed that more genera of methylotrophs, including Methylobacterium, Ancylobacter, Achromobacter, Xanthobacter, Moraxella, and Klebsiella were enriched with the nitrate-based medium compared to only two genera, Hyphomicrobium and Methylobacterium, enriched with the ammonium-based medium. The richness of methylotrophic bacteria also differed substantially in the bulk soil as compared to the rhizosphere. Growth characterization revealed that majority of the newly isolated methanol-utilizing strains in this study exhibited better growth at 37 °C instead of 30 or 45 °C. Moreover, Hyphomicrobium sp. FSA2 was the only strain capable of utilizing methanol even at elevated temperature 45 °C, showing its adaptability to a wide range of temperatures. Differential carbon substrate utilization profiling revealed the facultative nature of all isolated methanol-utilizer strains with Xanthobacter sp. TS3, being an important methanol-utilizer capable of degrading toxic compounds such as acetone and ethylene glycol. Overall, our study suggests the role of nutrients and plant-microbial interaction in shaping the composition of methanol-utilizers in terrestrial environment.
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Affiliation(s)
- Tabassum Yousaf
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Fatima Saleem
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Sahar Andleeb
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Muhammad Ali
- Faculty of Agriculture Sciences, University of the Punjab, Lahore, 54590, Pakistan
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2
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Bedekar AA, Deewan A, Jagtap SS, Parker DA, Liu P, Mackie RI, Rao CV. Transcriptional and metabolomic responses of Methylococcus capsulatus Bath to nitrogen source and temperature downshift. Front Microbiol 2023; 14:1259015. [PMID: 37928661 PMCID: PMC10623323 DOI: 10.3389/fmicb.2023.1259015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Methanotrophs play a significant role in methane oxidation, because they are the only biological methane sink present in nature. The methane monooxygenase enzyme oxidizes methane or ammonia into methanol or hydroxylamine, respectively. While much is known about central carbon metabolism in methanotrophs, far less is known about nitrogen metabolism. In this study, we investigated how Methylococcus capsulatus Bath, a methane-oxidizing bacterium, responds to nitrogen source and temperature. Batch culture experiments were conducted using nitrate or ammonium as nitrogen sources at both 37°C and 42°C. While growth rates with nitrate and ammonium were comparable at 42°C, a significant growth advantage was observed with ammonium at 37°C. Utilization of nitrate was higher at 42°C than at 37°C, especially in the first 24 h. Use of ammonium remained constant between 42°C and 37°C; however, nitrite buildup and conversion to ammonia were found to be temperature-dependent processes. We performed RNA-seq to understand the underlying molecular mechanisms, and the results revealed complex transcriptional changes in response to varying conditions. Different gene expression patterns connected to respiration, nitrate and ammonia metabolism, methane oxidation, and amino acid biosynthesis were identified using gene ontology analysis. Notably, key pathways with variable expression profiles included oxidative phosphorylation and methane and methanol oxidation. Additionally, there were transcription levels that varied for genes related to nitrogen metabolism, particularly for ammonia oxidation, nitrate reduction, and transporters. Quantitative PCR was used to validate these transcriptional changes. Analyses of intracellular metabolites revealed changes in fatty acids, amino acids, central carbon intermediates, and nitrogen bases in response to various nitrogen sources and temperatures. Overall, our results offer improved understanding of the intricate interactions between nitrogen availability, temperature, and gene expression in M. capsulatus Bath. This study enhances our understanding of microbial adaptation strategies, offering potential applications in biotechnological and environmental contexts.
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Affiliation(s)
- Ashwini Ashok Bedekar
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Anshu Deewan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Sujit S. Jagtap
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - David A. Parker
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Shell Exploration and Production Inc., Westhollow Technology Center, Houston, TX, United States
| | - Ping Liu
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Shell Exploration and Production Inc., Westhollow Technology Center, Houston, TX, United States
| | - Roderick I. Mackie
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Christopher V. Rao
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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3
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Kim J, Chhetri G, Kim I, Lee B, Jang W, Kim MK, Seo T. Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil. Int J Syst Evol Microbiol 2020; 70:2449-2456. [DOI: 10.1099/ijsem.0.004054] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A gamma radiation-resistant and pink-pigmented bacterial strain, designated as 17Sr1-39T, was isolated from a gamma ray-irradiated soil sample collected in the Republic of Korea. Cells were Gram-stain-negative, strictly aerobic, flagellated, asporogenous, rod-shaped and methylotrophic. Results of 16S rRNA gene sequence analysis showed that strain 17Sr1-39T was phylogenetically related to
Methylobacterium currus
PR1016AT (97.3 %),
Methylobacterium aquaticum
DSM 16371T (97.2 %),
Methylobacterium platani
PMB02T (97.0 %),
Methylobacterium frigidaeris
IER25-16T (96.6 %), Methylobacterium terrae 17Sr1-28T (96.6 %) and
Methylobacterium organophilum
JCM 2833T (93.4 %). The G+C content calculated based on the genome sequence was 70.4 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain 17Sr1-39T and
M. currus
,
M. aquaticum
,
M. platani
,
M. frigidaeris
, M. terrae and
M. organophilum
were 77.3–89.9 and 22–38.2 %, respectively. The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on the data from phenotypic tests and genotypic differences between strain 17Sr1-39T and its close phylogenetic relatives, strain 17Sr1-39T represented a new species belonging to the genus
Methylobacterium
, for which the name Methylobacterium terricola sp. nov. (=KACC 52905T=NBRC 112874T) is proposed.
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Affiliation(s)
- Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Byungjo Lee
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Wonhee Jang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, Seoul Women’s University, Seoul 01797, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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4
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Bird LR, Dawson KS, Chadwick GL, Fulton JM, Orphan VJ, Freeman KH. Carbon isotopic heterogeneity of coenzyme F430 and membrane lipids in methane-oxidizing archaea. GEOBIOLOGY 2019; 17:611-627. [PMID: 31364272 DOI: 10.1111/gbi.12354] [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: 08/20/2018] [Revised: 06/17/2019] [Accepted: 06/23/2019] [Indexed: 06/10/2023]
Abstract
Archaeal ANaerobic MEthanotrophs (ANME) facilitate the anaerobic oxidation of methane (AOM), a process that is believed to proceed via the reversal of the methanogenesis pathway. Carbon isotopic composition studies indicate that ANME are metabolically diverse and able to assimilate metabolites including methane, methanol, acetate, and dissolved inorganic carbon (DIC). Our data support the interpretation that ANME in marine sediments at methane seeps assimilate both methane and DIC, and the carbon isotopic compositions of the tetrapyrrole coenzyme F430 and the membrane lipids archaeol and hydroxy-archaeol reflect their relative proportions of carbon from these substrates. Methane is assimilated via the methyl group of CH3 -tetrahydromethanopterin (H4 MPT) and DIC from carboxylation reactions that incorporate free intracellular DIC. F430 was enriched in 13 C (mean δ13 C = -27‰ for Hydrate Ridge and -80‰ for the Santa Monica Basin) compared to the archaeal lipids (mean δ13 C = -97‰ for Hydrate Ridge and -122‰ for the Santa Monica Basin). We propose that depending on the side of the tricarboxylic acid (TCA) cycle used to synthesize F430, its carbon was derived from 76% DIC and 24% methane via the reductive side or 57% DIC and 43% methane via the oxidative side. ANME lipids are predicted to contain 42% DIC and 58% methane, reflecting the amount of each assimilated into acetyl-CoA. With isotope models that include variable fractionation during biosynthesis for different carbon substrates, we show the estimated amounts of DIC and methane can result in carbon isotopic compositions of - 73‰ to - 77‰ for F430 and - 105‰ for archaeal lipids, values close to those for Santa Monica Basin. The F430 δ13 C value for Hydrate Ridge was 13 C-enriched compared with the modeled value, suggesting there is divergence from the predicted two carbon source models.
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Affiliation(s)
- Laurence R Bird
- Department of Geosciences, the Pennsylvania State University, University Park, PA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Grayson L Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - James M Fulton
- Department of Geosciences, the Pennsylvania State University, University Park, PA, USA
- Department of Geosciences, Baylor University, Waco, TX, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Katherine H Freeman
- Department of Geosciences, the Pennsylvania State University, University Park, PA, USA
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5
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Kim J, Chhetri G, Kim I, Kim H, Kim MK, Seo T. Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. J Microbiol 2019; 57:959-966. [PMID: 31463788 DOI: 10.1007/s12275-019-9007-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/09/2019] [Accepted: 07/09/2019] [Indexed: 01/05/2023]
Abstract
A Gram-stain-negative, asporogenous, aerobic rods, motile by means of a single polar flagellum, catalase- and oxidase-positive, methylotrophic bacterium, designated 17Sr1-28T, was isolated from gamma ray-irradiated soil. The 16S rRNA gene sequence analysis showed that strain 17Sr1-28T was phylogenetically related to Methylobacterium currus PR1016AT (96.8%), Methylobacterium platani PMB02T (96.2%), Methylobacterium aquaticum DSM 16371T (96.3%), Methylobacterium tarhaniae N4211T (96.4%), Methylobacterium frigidaeris IER25-16T (95.8%), and Methylobacterium organophilum JCM 2833T (92.7%). The G+C content calculated based on genome sequence was 71.6%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain 17Sr1- 28T and M. currus, M. platani, M. aquaticum, M. tarhaniae, M. frigidaeris, and M. organophilum were 77.7-90.4% and 22-39.6%, respectively. The major fatty acids of strain 17Sr1-28T were summed feature 8 (C18:1ω7c and/or C18:1ω6c), and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. On the basis of the data from phenotypic tests and genotypic differences between strain 17Sr1-28T and its close phylogenetic relatives, strain 17Sr1-28T represents a new species belonging to the genus Methylobacterium, for which the name Methylobacterium terrae sp. nov. (= KCTC 52904T = NBRC 112873T) is proposed.
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Affiliation(s)
- Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Hyungdong Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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6
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Park C, Lee YS, Park SY, Park W. Methylobacterium currus sp. nov., isolated from a car air conditioning system. Int J Syst Evol Microbiol 2018; 68:3621-3626. [DOI: 10.1099/ijsem.0.003045] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Chulwoo Park
- 1Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Yun Suk Lee
- 1Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - So-yoon Park
- 2Thermal Management Research Lab, Hyundai Motor Group, Seoul, Republic of Korea
| | - Woojun Park
- 1Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
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7
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Vekeman B, Kerckhof FM, Cremers G, de Vos P, Vandamme P, Boon N, Op den Camp HJM, Heylen K. New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase. Environ Microbiol 2016; 18:4523-4536. [PMID: 27501305 DOI: 10.1111/1462-2920.13485] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/04/2016] [Indexed: 12/14/2022]
Abstract
Marine methylotrophs play a key role in the global carbon cycle by metabolizing reduced one-carbon compounds that are found in high concentrations in marine environments. Genome, physiology and diversity studies have been greatly facilitated by the numerous model organisms brought into culture. However, the availability of marine representatives remains poor. Here, we report the isolation of four novel species from North Sea sediment enrichments closely related to the Alphaproteobacterium Methyloceanibacter caenitepidi. Each of the newly isolated Methyloceanibacter species exhibited a clear genome sequence divergence which was reflected in physiological differences. Notably one strain R-67174 was capable of oxidizing methane as sole source of carbon and energy using solely a soluble methane monooxygenase and represents the first marine Alphaproteobacterial methanotroph brought into culture. Differences in maximum cell density of >1.5 orders of magnitude were observed. Furthermore, three strains were capable of producing nitrous oxide from nitrate. Together, these findings highlight the metabolic and physiologic variability within closely related Methyloceanibacter species and provide a new understanding of the physiological basis of marine methylotrophy.
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Affiliation(s)
- Bram Vekeman
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, Gent, 9000, Belgium
| | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Geert Cremers
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, AJ Nijmegen, 6525, The Netherlands
| | - Paul de Vos
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, Gent, 9000, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, Gent, 9000, Belgium.,BCCM/LMG Bacteria Collection, Ghent University, Karel Lodewijck Ledeganckstraat 35, Gent, 9000, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, Gent, 9000, Belgium
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, AJ Nijmegen, 6525, The Netherlands
| | - Kim Heylen
- Department of Biochemistry and Microbiology, Laboratory of Microbiology (LM-UGent), Ghent University, Karel Lodewijck Ledeganckstraat 35, Gent, 9000, Belgium
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8
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Meena KK, Kumar M, Mishra S, Ojha SK, Wakchaure GC, Sarkar B. Phylogenetic study of methanol oxidizers from chilika-lake sediments using genomic and metagenomic approaches. Indian J Microbiol 2015; 55:151-62. [PMID: 25805901 DOI: 10.1007/s12088-015-0510-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/03/2015] [Indexed: 01/13/2023] Open
Abstract
Group-wise diversity of sediment methylotrophs of Chilika lake (Lat. 19°28'-19°54'N; Long. 85°06'-85°35'E) Odisha, India at various identified sites was studied. Both the culturable and unculturable (metagenome) methylotrophs were investigated in the lake sediments employing both mxaF and 16S rRNA genes as markers. ARDRA profiling, 16S rRNA gene sequencing, PAGE profiling of HaeIII, EcoRI restricted mxaF gene and the mxaF gene sequences using culture-dependent approach revealed the relatedness of α-proteobacteria and Methylobacterium, Hyphomicrobium and Ancyclobacter sp. The total viable counts of the culturable aerobic methylotrophs were relatively higher in sediments near the sea mouth (S3; Panaspada), also demonstrated relatively high salinity (0.1 M NaCl) tolerance. Metagenomic DNA from the sediments, amplified using GC clamp mxaF primers and resolved through DGGE, revealed the diversity within the unculturable methylotrophic bacterium Methylobacterium organophilum, Ancyclobacter aquaticus, Burkholderiales and Hyphomicrobium sp. Culture-independent analyses revealed that up to 90 % of the methylotrophs were unculturable. The study enhances the general understandings of the metagenomic methylotrophs from such a special ecological niche.
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Affiliation(s)
- Kamlesh K Meena
- National Bureau of Agriculturally Important Microorganisms, Mau Nath Bhanjan, 275 101 UP India ; National Institute of Abiotic Stress Management, Malegaon, Baramati, Pune, Maharashtra India
| | - Manish Kumar
- National Bureau of Agriculturally Important Microorganisms, Mau Nath Bhanjan, 275 101 UP India
| | - Snehasish Mishra
- School of Biotechnology, KIIT University, Campus-11, Bhubaneswar, 751024 Odisha India
| | - Sanjay Kumar Ojha
- School of Biotechnology, KIIT University, Campus-11, Bhubaneswar, 751024 Odisha India
| | - Goraksha C Wakchaure
- National Institute of Abiotic Stress Management, Baramati, Pune, 413115 Maharashtra India
| | - Biplab Sarkar
- National Institute of Abiotic Stress Management, Baramati, Pune, 413115 Maharashtra India
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Wellner S, Lodders N, Glaeser SP, Kämpfer P. Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces. Int J Syst Evol Microbiol 2013; 63:2690-2699. [PMID: 23291886 DOI: 10.1099/ijs.0.047787-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three pink-pigmented, aerobic, Gram-stain-negative, rod-shaped and facultatively methylotrophic strains were isolated from the phyllosphere of Trifolium repens and Cerastium holosteoides. 16S rRNA gene sequence analysis support the affiliation of all strains to the genus Methylobacterium. The closest relatives of strains C34(T) and T5 were Methylobacterium gnaphalii 23e(T) (98.0 and 98.5 % sequence similarity, respectively) and Methylobacterium organophilum JCM 2833(T) (97.0 and 97.2 %, respectively). Strain TA73(T) showed the highest sequence similarities to Methylobacterium marchantiae JT1(T) and Methylobacterium bullatum F3.2(T) (both 97.9 %), followed by Methylobacterium phyllosphaerae CBMB27(T) and Methylobacterium brachiatum DSM 19569(T) (both 97.8 %), Methylobacterium cerastii C15(T) and Methylobacterium radiotolerans JCM 2831(T) (both 97.7 %). The major components in the fatty acid profiles were C18 : 1ω7c, C16 : 0 and one unknown fatty acid for strain TA73(T) and C18 : 1ω7c, C16 : 1ω7c/iso-C15 : 0 2-OH, C18 : 0 and C16 : 0 for strains C34(T) and T5. Physiological and biochemical analysis, including DNA-DNA hybridization, revealed clear differences between the investigated strains and their closest phylogenetic neighbours. DNA-DNA hybridization studies also showed high similarities between strains C34(T) and T5 (59.6-100 %). Therefore, the isolates represent two novel species within the genus Methylobacterium, for which the names Methylobacterium trifolii sp. nov. (type strain TA73(T) = LMG 25778(T) = CCM 7786(T)) and Methylobacterium thuringiense sp. nov. (type strain C34(T) = LMG 25777(T) = CCM 7787(T)) are proposed.
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Affiliation(s)
- S Wellner
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - N Lodders
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - S P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - P Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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10
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Borrel G, Jézéquel D, Biderre-Petit C, Morel-Desrosiers N, Morel JP, Peyret P, Fonty G, Lehours AC. Production and consumption of methane in freshwater lake ecosystems. Res Microbiol 2011; 162:832-47. [DOI: 10.1016/j.resmic.2011.06.004] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
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11
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Semrau JD, DiSpirito AA, Vuilleumier S. Facultative methanotrophy: false leads, true results, and suggestions for future research. FEMS Microbiol Lett 2011; 323:1-12. [DOI: 10.1111/j.1574-6968.2011.02315.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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12
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Wellner S, Lodders N, Kämpfer P. Methylobacterium cerastii sp. nov., isolated from the leaf surface of Cerastium holosteoides. Int J Syst Evol Microbiol 2011; 62:917-924. [PMID: 21669927 DOI: 10.1099/ijs.0.030767-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Two Gram-stain-negative, non-endospore-forming, rod-like strains, designated C15T and C44, were isolated from the phyllosphere of Cerastium holosteoides and were studied in detail in order to assess their taxonomic position. 16S rRNA gene sequence analysis allocated both isolates clearly to the genus Methylobacterium. Both strains showed the highest 16S rRNA gene sequence similarity to Methylobacterium marchantiae JT1T (97.5 %) and Methylobacterium jeotgali S2R03-9T (97.4 %). The fatty acid profiles contained major amounts of C16:0, C18:1ω7c and C16:1ω7c/iso-C15:0 2-OH (summed feature 3), which supported the grouping of the isolates in the genus Methylobacterium. Physiological/biochemical characterization and DNA-DNA hybridizations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of the strains. For this reason, we propose for strain C15T (=DSM 23679T=CCUG 60040T=CCM 7788T) a novel species with the name Methylobacterium cerastii sp. nov. Strain C44 (=DSM 23675=CCM 7789) is an additional strain of M. cerastii.
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Affiliation(s)
- S Wellner
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - N Lodders
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - P Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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13
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Benstead J, King GM, Williams HG. Methanol promotes atmospheric methane oxidation by methanotrophic cultures and soils. Appl Environ Microbiol 2010; 64:1091-8. [PMID: 16349514 PMCID: PMC106373 DOI: 10.1128/aem.64.3.1091-1098.1998] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two methanotrophic bacteria, Methylobacter albus BG8 and Methylosinus trichosporium OB3b, oxidized atmospheric methane during batch growth on methanol. Methane consumption was rapidly and substantially diminished (95% over 9 days) when washed cell suspensions were incubated without methanol in the presence of atmospheric methane (1.7 ppm). Methanotrophic activity was stimulated after methanol (10 mM) but not methane (1,000 ppm) addition. M. albus BG8 grown in continuous culture for 80 days with methanol retained the ability to oxidize atmospheric methane and oxidized methane in a chemostat air supply. Methane oxidation during growth on methanol was not affected by methane deprivation. Differences in the kinetics of methane uptake (apparent K(m) and V(max)) were observed between batch- and chemostat-grown cultures. The V(max) and apparent K(m) values (means +/- standard errors) for methanol-limited chemostat cultures were 133 +/- 46 nmol of methane 10 cells h and 916 +/- 235 ppm of methane (1.2 muM), respectively. These values were significantly lower than those determined with batch-grown cultures (V(max) of 648 +/- 195 nmol of methane 10 cells h and apparent K(m) of 5,025 +/- 1,234 ppm of methane [6.3 muM]). Methane consumption by soils was stimulated by the addition of methanol. These results suggest that methanol or other nonmethane substrates may promote atmospheric methane oxidation in situ.
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Affiliation(s)
- J Benstead
- Darling Marine Center, University of Maine, Walpole, Maine 04573
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14
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Griffiths RP, Caldwell BA, Cline JD, Broich WA, Morita RY. Field observations of methane concentrations and oxidation rates in the southeastern bering sea. Appl Environ Microbiol 2010; 44:435-46. [PMID: 16346078 PMCID: PMC242029 DOI: 10.1128/aem.44.2.435-446.1982] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Measurements of methane oxidation rates were made in southeastern Bering Sea water samples with [C]methane. The rate at which CO(2) evolved from samples exposed to one methane concentration was defined as the relative methane oxidation rate. Rate determinations at three methane concentrations were used to estimate methane oxidation kinetics. The rate constant calculated from the kinetics and the observed methane concentration in the same water sample were used to calculate an in situ methane oxidation rate and the turnover time. First-order kinetics were observed in essentially all experiments in which methane oxidation kinetics were measured. Relative methane oxidation rates were greater in waters collected at inshore stations than at the offshore stations and were greater in bottom samples than in surface samples. In most water samples analyzed, there was essentially no radioactivity associated with the cells. The resulting respiration percentages were therefore very high with a mean of >98%. These data suggest that most of the methane was used by the microflora as an energy source and that very little of it was used in biosynthesis. The relative methane oxidation rates were not closely correlated with methane concentrations and did not appear to be linked to either oxygen or dissolved inorganic nitrogen concentrations. However, there was a significant correlation with relative microbial activity. Our data suggest that the methane oxidizers were associated with the general microbial heterotrophic community. Since these organisms did not appear to be using methane as a carbon source, it is unlikely that they have been isolated and identified as methane oxidizers in the past.
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Affiliation(s)
- R P Griffiths
- Department of Microbiology and School of Oceanography, Oregon State University, Corvallis, Oregon 97331-3804, and Pacific Marine Environmental Laboratory, National Oceanic and Atmospheric Administration, Seattle, Washington 98115
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15
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Zhao SJ, Hanson RS. Isolate 761M: a New Type I Methanotroph That Possesses a Complete Tricarboxylic Acid Cycle. Appl Environ Microbiol 2010; 48:1237-42. [PMID: 16346683 PMCID: PMC241715 DOI: 10.1128/aem.48.6.1237-1242.1984] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A methanotrophic bacterium, isolate 761M, grows slowly with methane as the sole carbon and energy source. Growth was stimulated by peptone, casein hydrolysate, glucose, and acetate plus malate. Sugars other than glucose did not stimulate growth. Growth yields, based on the amount of methane consumed, increased when other carbon sources were present, and less methane carbon was assimilated under these conditions. Methane was obligately required for growth of isolate 761M. This bacterium does not grow on rich media. Isolate 761M was found to possess hexulose phosphate synthase and intracytoplasmic membranes characteristic of other type I methanotrophs. Unlike other type I methanotrophs, this bacterium possessed alpha-ketoglutarate dehydrogenase and oxidized [2-C]acetate to carbon dioxide.
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Affiliation(s)
- S J Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, People's Republic of China, and Gray Freshwater Biological Institute, University of Minnesota, Navarre, Minnesota 55392
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16
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Abstract
Anoxic sediments and digested sewage sludge anaerobically oxidized methane to carbon dioxide while producing methane. This strictly anaerobic process showed a temperature optimum between 25 and 37 degrees C, indicating an active microbial participation in this reaction. Methane oxidation in these anaerobic habitats was inhibited by oxygen. The rate of the oxidation followed the rate of methane production. The observed anoxic methane oxidation in Lake Mendota and digested sewage sludge was more sensitive to 2-bromoethanesulfonic acid than the simultaneous methane formation. Sulfate diminished methane formation as well as methane oxidation. However, in the presence of iron and sulfate the ratio of methane oxidized to methane formed increased markedly. Manganese dioxide and higher partial pressures of methane also stimulated the oxidation. The rate of methane oxidation in untreated samples was approximately 2% of the CH(4) production rate in Lake Mendota sediments and 8% of that in digested sludge. This percentage could be increased up to 90% in sludge in the presence of 10 mM ferrous sulfate and at a partial pressure of methane of 20 atm (2,027 kPa).
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Affiliation(s)
- A J Zehnder
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
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17
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Zhao SJ, Hanson RS. Variants of the Obligate Methanotroph Isolate 761M Capable of Growth on Glucose in the Absence of Methane. Appl Environ Microbiol 2010; 48:807-12. [PMID: 16346647 PMCID: PMC241618 DOI: 10.1128/aem.48.4.807-812.1984] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Isolate 761M is an unusual type I methanotroph that possesses a complete tricarboxylic acid cycle. Variants of this methanotroph that were capable of growth with methanol (isolate 761AR) or glucose (isolate 761H) have been isolated. Cultures of isolate 761H grown with glucose and casein hydrolysate as the sole carbon and energy sources retained the ability to grow on methane, contained methane monooxygenase and 3-hexulose phosphate synthase, and possessed intracytoplasmic membranes similar to those found in thin sections of isolate 761M grown on methane. Methane monooxygenase was also present in cultures of isolate 761AR grown on methanol and casein hydrolysate.
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Affiliation(s)
- S J Zhao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, People's Republic of China, and Gray Freshwater Biological Institute, University of Minnesota, Navaree, Minnesota 55392
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18
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Schauer S, Kämpfer P, Wellner S, Spröer C, Kutschera U. Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort. Int J Syst Evol Microbiol 2010; 61:870-876. [PMID: 20495043 DOI: 10.1099/ijs.0.021915-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pink-pigmented, facultatively methylotrophic bacterium, designated strain JT1(T), was isolated from a thallus of the liverwort Marchantia polymorpha L. and was analysed by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis placed the strain in a clade with Methylobacterium adhaesivum AR27(T), Methylobacterium fujisawaense DSM 5686(T), Methylobacterium radiotolerans JCM 2831(T) and Methylobacterium jeotgali S2R03-9(T), with which it showed sequence similarities of 97.8, 97.7, 97.2 and 97.4 %, respectively. However, levels of DNA-DNA relatedness between strain JT1(T) and these and the type strains of other closely related species were lower than 70 %. Cells of JT1(T) stained Gram-negative and were motile, rod-shaped and characterized by numerous fimbriae-like appendages on the outer surface of their wall (density up to 200 µm(-2)). Major fatty acids were C(18 : 1)ω7c and C(16 : 0). Based on the morphological, physiological and biochemical data presented, strain JT1(T) is considered to represent a novel species of the genus Methylobacterium, for which the name Methylobacterium marchantiae sp. nov. is proposed. The type strain is JT1(T) ( = DSM 21328(T) = CCUG 56108(T)).
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Affiliation(s)
- S Schauer
- Institut für Biologie, Universität Kassel, Heinrich-Plett-Str. 40, D-34109 Kassel, Germany
| | - P Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig Universität Giessen, Heinrich-Buff-Ring 26-32 (IFZ), D-35392 Giessen, Germany
| | - S Wellner
- Institut für Angewandte Mikrobiologie, Justus-Liebig Universität Giessen, Heinrich-Buff-Ring 26-32 (IFZ), D-35392 Giessen, Germany
| | - C Spröer
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - U Kutschera
- Institut für Biologie, Universität Kassel, Heinrich-Plett-Str. 40, D-34109 Kassel, Germany
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19
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Abstract
AbstractMethanol has recently attracted significant interest in the energetic field. Current technology for the conversion of methane to methanol is based on energy intensive endothermic steam reforming followed by catalytic conversion into methanol. The one-step method performed at very low temperatures (35°C) is methane oxidation to methanol via bacteria. The aim of this work was to examine the role of copper in the one-step methane oxidation to methanol by utilizing whole cells of Methylosinus trichosporium OB3b bacteria. From the results obtained it was found that copper concentration in the medium influences the rate of bacterial biomass growth or methanol production during the process of methane oxidation to methanol. The presented results indicate that the process of methane oxidation to methanol by Methylosinus trichosporium OB3b bacteria is most efficient when the mineral medium contains 1.0 × 10−6 mol dm−3 of copper. Under these conditions, a satisfactory growth of biomass was also achieved.
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20
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Aslam Z, Lee CS, Kim KH, Im WT, Ten LN, Lee ST. Methylobacterium jeotgali sp. nov., a non-pigmented, facultatively methylotrophic bacterium isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 2007; 57:566-571. [PMID: 17329786 DOI: 10.1099/ijs.0.64625-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel facultatively methylotrophic, Gram-negative, rod-shaped bacterium, designated strain S2R03-9(T), was isolated from jeotgal, a traditional Korean fermented seafood. The organism was strictly aerobic, motile by means of a single polar flagellum, non-sporulating and catalase- and oxidase-positive. Strain S2R03-9(T) grew in the presence of 0-1 % (w/v) NaCl and at pH 6.0-10.0, with optimum growth in the absence of NaCl and at pH 7.0. It grew at temperatures in the range 20.0-30.0 degrees C, with optimum growth at 30 degrees C. Colonies grown on R2A medium were non-pigmented, opaque and creamy white. Phylogenetic analysis based on 16S rRNA gene sequences indicated that it was most closely related to Methylobacterium organophilum JCM 2833(T) (96.6 % similarity) and the phylogenetic similarities to all other Methylobacterium species with validly published names were less than 95.0 %. The DNA G+C content was 64.9 mol%. The phylogenetic analysis, the phenotypic assessment and the chemotaxonomic data (major ubiquinone, Q-10; major fatty acids, C(18 : 1) and C(18 : 0)) showed that S2R03-9(T) represents a novel species within the genus Methylobacterium in the class Alphaproteobacteria, for which the name Methylobacterium jeotgali sp. nov. is proposed. The type strain is S2R03-9(T) (=KCTC 12671(T)=LMG 23639(T)).
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Affiliation(s)
- Zubair Aslam
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Chang Soo Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Kyoung-Ho Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Wan-Taek Im
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Leonid N Ten
- Department of Biology and Medicinal Science, Pai Chai University, Daejeon 302-735, Republic of Korea
| | - Sung-Taik Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Republic of Korea
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21
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Affiliation(s)
- Andreas R Theisen
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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22
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Dedysh SN, Dunfield PF, Trotsenko YA. Methane utilization by Methylobacterium species: new evidence but still no proof for an old controversy. Int J Syst Evol Microbiol 2005; 54:1919-1920. [PMID: 15545410 DOI: 10.1099/ijs.0.63493-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Svetlana N Dedysh
- Winogradski Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Peter F Dunfield
- Max-Planck-Institut für Terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Yuri A Trotsenko
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow region, 142292, Russia
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23
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Waki M, Suzuki K, Osada T, Tanaka Y. Methane-dependent denitrification by a semi-partitioned reactor supplied separately with methane and oxygen. BIORESOURCE TECHNOLOGY 2005; 96:921-927. [PMID: 15627563 DOI: 10.1016/j.biortech.2004.08.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2003] [Revised: 08/06/2004] [Accepted: 08/12/2004] [Indexed: 05/24/2023]
Abstract
Methane (CH4) can be used as an alternative carbon source for denitrification with added oxygen (O2). However, the off-gas of denitrification reactors using a CH4-O2 mixture contains unused CH4 and O2 in proportions that make it unusable for fuel, carry explosion risks, and, if released into the atmosphere, contribute to the greenhouse effect. This study tested a novel reactor with a partition dividing the headspace completely and extending partly into the liquid layer. When CH4 and O2 were supplied separately to the liquid layer on opposite sides of the partition, the methane-dependent denitrification (MDD) activity was similar to that when the two gases were supplied as a mixture. In reactors with separate gas supplies, the off-gas from the CH4 supply side was high in CH4 and low in O2, and was usable for fuel, and that from the O2 supply side was very low in CH4, and might be released into the atmosphere. MDD activity increased with the O2 supply rate, and separate discharge of CH4 and O2 was maintained. The concentration of dissolved methane in the effluent was decreased by lowering the CH4/O2 supply ratio to 1.0 and drawing the effluent from the O2 supply side. This novel reactor enhances the safety of MDD, allows reuse of methane as fuel, and reduces methane leakage to the atmosphere.
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Affiliation(s)
- M Waki
- Department of Livestock Industry Environment, National Institute of Livestock and Grassland Science, 2 Ikenodai, Tsukuba, Ibaraki 305-0901, Japan.
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24
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Christner BC, Mosley-Thompson E, Thompson LG, Reeve JN. Isolation of bacteria and 16S rDNAs from Lake Vostok accretion ice. Environ Microbiol 2001; 3:570-7. [PMID: 11683867 DOI: 10.1046/j.1462-2920.2001.00226.x] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lake Vostok, the largest subglacial lake in Antarctica, is separated from the surface by approximately 4 km of glacial ice. It has been isolated from direct surface input for at least 420 000 years, and the possibility of a novel environment and ecosystem therefore exists. Lake Vostok water has not been sampled, but an ice core has been recovered that extends into the ice accreted below glacial ice by freezing of Lake Vostok water. Here, we report the recovery of bacterial isolates belonging to the Brachybacteria, Methylobacterium, Paenibacillus and Sphingomonas lineages from a sample of melt water from this accretion ice that originated 3593 m below the surface. We have also amplified small-subunit ribosomal RNA-encoding DNA molecules (16S rDNAs) directly from this melt water that originated from alpha- and beta-proteobacteria, low- and high-G+C Gram-positive bacteria and a member of the Cytophaga/Flavobacterium/Bacteroides lineage.
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MESH Headings
- Antarctic Regions
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/ultrastructure
- Bacterial Physiological Phenomena
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Fresh Water/chemistry
- Fresh Water/microbiology
- Genes, rRNA
- Ice
- Microscopy, Electron, Scanning
- Microscopy, Fluorescence
- Phylogeny
- Proteobacteria/classification
- Proteobacteria/genetics
- Proteobacteria/isolation & purification
- Proteobacteria/physiology
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Water Microbiology
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Affiliation(s)
- B C Christner
- Department of Microbiology, Byrd Polar Research Center, Ohio State University, Columbus, OH 43210-1292, USA
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25
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Sukesan S, Watwood ME. Effects of hydrocarbon enrichment on trichloroethylene biodegradation and microbial populations in finished compost. J Appl Microbiol 1998; 85:635-42. [PMID: 9812376 DOI: 10.1111/j.1365-2672.1998.00565.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This study focused on the capacity of finished compost, often used as packing material in biofiltration units, to support microbial biodegradation of trichloroethylene (TCE). Finished compost was enriched with methane or propane (10% head space) to stimulate cometabolic biodegradation of gaseous TCE. Successful hydrocarbon enrichment, as indicated by rapid depletion of hydrocarbon gas and measurable growth of hydrocarbon-utilizing micro-organisms, occurred within a week. Within batch reactor flasks, approximately 75% of head space TCE (1-40 ppmv) was rapidly sorbed onto compost material. Up to 99% of the remaining head space TCE was removed via biodegradation in compost enriched with either hydrocarbon. Hydrocarbon enrichment with methane or propane corresponded to 10-fold increases in methanotrophic or propanotrophic populations, respectively. Based on growth assessment under different nutritional regimes, there appeared to be complex metabolic interactions within the microbial community in enriched compost. Five separate bacterial cultures were derived from the hydrocarbon-enriched compost and assayed for the ability to degrade TCE.
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Affiliation(s)
- S Sukesan
- Department of Biological Sciences, Idaho State University, Pocatello 83209, USA
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26
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Abstract
Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene.
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Affiliation(s)
- R S Hanson
- Department of Microbiology, University of Minnesota, Minneapolis 55455, USA.
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27
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Schnell S, King GM. Stability of methane oxidation capacity to variations in methane and nutrient concentrations. FEMS Microbiol Ecol 1995. [DOI: 10.1111/j.1574-6941.1995.tb00153.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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28
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Corpe WA, Jensen TE. An electron microscopic study of picoplanktonic organisms from a Small Lake. MICROBIAL ECOLOGY 1992; 24:181-197. [PMID: 24193136 DOI: 10.1007/bf00174454] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/1991] [Revised: 03/17/1992] [Indexed: 06/02/2023]
Abstract
Picoplankton, both prokaryotic and eukaryotic, are distinguished from other aquatic organisms by their small size (0.1-2.0 μm). Such organisms were recovered from waters of a small oligotrophic lake using screens, filters, and high-speed centrifugation. The majority of the picoplankton were unable to form visible colonies on common media. Cells examined in thin sections by electron microscopy showed that 60-75% of the cells had an average diameter after dehydration of 0.48-0.51 μm. The maximum dimensions of the rest of the cells ranged from 0.56-1.81 μm. Using details of ultrastructure, cells were classified as prokaryotic or eukaryotic. Phototrophs present included two cyanobacterial morphotypes (5-6%) and two eukaryotic algae (less than I%). The arrays of intracytoplasmic membranes in 18-20% of the cells were suggestive of methanotrophic rods and chemoautotrophs. Relatively few prosthecate bacteria were observed in the water column samples. The smallest cells (1-2%) contained magnetosomes, the presence of which were confirmed by x-ray spectroscopy. Iron was also detected in the envelopes of some rod shaped cells by the same technique. The study of in situ picoplankton populations using TEM coupled with other techniques may provide better understanding of picoplankton biomass.
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Affiliation(s)
- W A Corpe
- Department of Biological Sciences, Columbia University, 10027, New York, New York, USA
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29
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Alvarez-Cohen L, McCarty PL, Boulygina E, Hanson RS, Brusseau GA, Tsien HC. Characterization of a methane-utilizing bacterium from a bacterial consortium that rapidly degrades trichloroethylene and chloroform. Appl Environ Microbiol 1992; 58:1886-93. [PMID: 1377902 PMCID: PMC195700 DOI: 10.1128/aem.58.6.1886-1893.1992] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A mixed culture of bacteria grown in a bioreactor with methane as a carbon and energy source rapidly oxidized trichloroethylene and chloroform. The most abundant organism was a crescent-shaped bacterium that bound the fluorescent oligonucleotide signature probes that specifically hybridize to serine pathway methylotrophs. The 5S rRNA from this bacterium was found to be 93.5% homologous to the Methylosinus trichosporium OB3b 5S RNA sequence. A type II methanotrophic bacterium, isolated in pure culture from the bioreactor, synthesized soluble methane monooxygenase during growth in a copper-limited medium and was also capable of rapid trichloroethylene oxidation. The bacterium contained the gene that encodes the soluble methane monooxygenase B component on an AseI restriction fragment identical in size to a restriction fragment present in AseI digests of DNA from bacteria in the mixed culture. The sequence of the 16S rRNA from the pure culture was found to be 92 and 94% homologous to the 16S rRNAs of M. trichosporium OB3b and M. sporium, respectively. Both the pure and mixed cultures oxidized naphthalene to naphthol, indicating the presence of soluble methane monooxygenase. The mixed culture also synthesized soluble methane monooxygenase, as evidenced by the presence of proteins that cross-reacted with antibodies prepared against purified soluble methane monooxygenase components from M. trichosporium OB3b on Western blots (immunoblots). It was concluded that a type II methanotrophic bacterium phylogenetically related to Methylosinus species synthesizes soluble methane monooxygenase and is responsible for trichloroethylene oxidation in the bioreactor.
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Affiliation(s)
- L Alvarez-Cohen
- Department of Civil Engineering, University of California, Berkeley 94720
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30
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Delmas RA, Marenco A, Tathy JP, Cros B, Baudet JGR. Sources and sinks of methane in the African savanna. CH4emissions from biomass burning. ACTA ACUST UNITED AC 1991. [DOI: 10.1029/90jd02496] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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32
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Tsien HC, Bratina BJ, Tsuji K, Hanson RS. Use of oligodeoxynucleotide signature probes for identification of physiological groups of methylotrophic bacteria. Appl Environ Microbiol 1990; 56:2858-65. [PMID: 1967116 PMCID: PMC184855 DOI: 10.1128/aem.56.9.2858-2865.1990] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Oligodeoxynucleotide sequences that uniquely complemented 16S rRNAs of each group of methylotrophs were synthesized and used as hybridization probes for the identification of methylotrophic bacteria possessing the serine and ribulose monophosphate (RuMP) pathways for formaldehyde fixation. The specificity of the probes was determined by hybridizing radiolabeled probes with slot-blotted RNAs of methylotrophs and other eubacteria followed by autoradiography. The washing temperature was determined experimentally to be 50 and 52 degrees C for 9-alpha (serine pathway) and 10-gamma (RuMP pathway) probes, respectively. RNAs isolated from serine pathway methylotrophs bound to probe 9-alpha, and RNAs from RuMP pathway methylotrophs bound to probe 10-gamma. Nonmethylotrophic eubacterial RNAs did not bind to either probe. The probes were also labeled with fluorescent dyes. Cells fixed to microscope slides were hybridized with these probes, washed, and examined in a fluorescence microscope equipped with appropriate filter sets. Cells of methylotrophic bacteria possessing the serine or RuMP pathway specifically bind probes designed for each group. Samples with a mixture of cells of type I and II methanotrophs were detected and differentiated with single probes or mixed probes labeled with different fluorescent dyes, which enabled the detection of both types of cells in the same microscopic field.
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Affiliation(s)
- H C Tsien
- Gray Freshwater Biological Institute, University of Minnesota, Navarre 55392
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Brusseau GA, Tsien HC, Hanson RS, Wackett LP. Optimization of trichloroethylene oxidation by methanotrophs and the use of a colorimetric assay to detect soluble methane monooxygenase activity. Biodegradation 1990; 1:19-29. [PMID: 1368139 DOI: 10.1007/bf00117048] [Citation(s) in RCA: 172] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Methylosinus trichosporium OB3b biosynthesizes a broad specificity soluble methane monooxygenase that rapidly oxidizes trichloroethylene (TCE). The selective expression of the soluble methane monooxygenase was followed in vivo by a rapid colorimetric assay. Naphthalene was oxidized by purified soluble methane monooxygenase or by cells grown in copper-deficient media to a mixture of 1-naphthol and 2-naphthol. The naphthols were detected by reaction with tetrazotized o-dianisidine to form purple diazo dyes with large molar absorptivities. The rate of color formation with the rapid assay correlated with the velocity of TCE oxidation that was determined by gas chromatography. Both assays were used to optimize conditions for TCE oxidation by M. trichosporium OB3b and to test several methanotrophic bacteria for the ability to oxidize TCE and naphthalene.
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Affiliation(s)
- G A Brusseau
- Gray Freshwater Biological Institute, University of Minnesota, Navarre 55392
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Tsien HC, Brusseau GA, Hanson RS, Waclett LP. Biodegradation of trichloroethylene by Methylosinus trichosporium OB3b. Appl Environ Microbiol 1989; 55:3155-61. [PMID: 2515801 PMCID: PMC203239 DOI: 10.1128/aem.55.12.3155-3161.1989] [Citation(s) in RCA: 153] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The methanotroph Methylosinus trichosporium OB3b, a type II methanotroph, degraded trichloroethylene at rates exceeding 1.2 mmol/h per g (dry weight) following the appearance of soluble methane monooxygenase in continuous and batch cultures. Cells capable oxidizing trichloroethylene contained components of soluble methane monooxygenase as demonstrated by Western blot (immunoblot) analysis with antibodies prepared against the purified enzyme. Growth of cultures in a medium containing 0.25 microM or less copper sulfate caused derepression of the synthesis of soluble methane monooxygenase. In these cultures, the specific rates of methane and methanol oxidation did not change during growth, while trichloroethylene oxidation increased with the appearance of soluble methane monooxygenase. M. trichosporium OB3b cells that contained soluble methane monooxygenase also degraded vinyl chloride, 1,1-dichloroethylene, cis-1,2-dichloroethylene, and trans-1,2-dichloroethylene.
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Affiliation(s)
- H C Tsien
- Gray Freshwater Biological Institute, University of Minnesota, Navarre 55392
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Henson JM, Yates MV, Cochran JW. Metabolism of chlorinated methanes, ethanes, and ethylenes by a mixed bacterial culture growing on methane. ACTA ACUST UNITED AC 1989. [DOI: 10.1007/bf01569690] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Cochran JW, Yates MV, Henson J. A modified purge-and-trap/gas chromatography method for analysis of volatile halocarbons in microbiological degradation studies. METHODS IN MICROBIOLOGY 1988. [DOI: 10.1016/0167-7012(88)90033-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Stephens RL, Haygood MG, Lidstrom ME. Identification of putative methanol dehydrogenase (moxF) structural genes in methylotrophs and cloning of moxF genes from Methylococcus capsulatus bath and Methylomonas albus BG8. J Bacteriol 1988; 170:2063-9. [PMID: 3129400 PMCID: PMC211087 DOI: 10.1128/jb.170.5.2063-2069.1988] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
An open-reading-frame fragment of a Methylobacterium sp. strain AM1 gene (moxF) encoding a portion of the methanol dehydrogenase structural protein has been used as a hybridization probe to detect similar sequences in a variety of methylotrophic bacteria. This hybridization was used to isolate clones containing putative moxF genes from two obligate methanotrophic bacteria, Methylococcus capsulatus Bath and Methylomonas albus BG8. The identity of these genes was confirmed in two ways. A T7 expression vector was used to produce methanol dehydrogenase protein in Escherichia coli from the cloned genes, and in each case the protein was identified by immunoblotting with antiserum against the Methylomonas albus methanol dehydrogenase. In addition, a moxF mutant of Methylobacterium strain AM1 was complemented to a methanol-positive phenotype that partially restored methanol dehydrogenase activity, using broad-host-range plasmids containing the moxF genes from each methanotroph. The partial complementation of a moxF mutant in a facultative serine pathway methanol utilizer by moxF genes from type I and type X obligate methane utilizers suggests broad functional conservation of the methanol oxidation system among gram-negative methylotrophs.
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Affiliation(s)
- R L Stephens
- W. M. Keck Laboratories, California Institute of Technology, Pasadena 91125
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Michael Henson J, Yates M, Cochran J, Shackleford D. Microbial removal of halogenated methanes, ethanes, and ethylenes in an aerobic soil exposed to methane. FEMS Microbiol Lett 1988. [DOI: 10.1111/j.1574-6968.1988.tb02664.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Nichols PD, Glen A S, Antworth CP, Hanson RS, White DC. Phospholipid and lipopolysaccharide normal and hydroxy fatty acids as potential signatures for methane-oxidizing bacteria. FEMS Microbiol Lett 1985. [DOI: 10.1111/j.1574-6968.1985.tb01168.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Renoux JM, Rohmer M. Prokaryotic triterpenoids. New bacteriohopanetetrol cyclitol ethers from the methylotrophic bacterium Methylobacterium organophilum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 151:405-10. [PMID: 3928379 DOI: 10.1111/j.1432-1033.1985.tb09116.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Together with bacteriohopanetetrol, which is identical to bacteriohopanetetrol isolated from Bacillus acidocaldarius, three other bacteriohopane derivatives were isolated from the methylotrophic bacterium Methylobacterium organophilum. Three different kinds of polar moieties were found linked to the C-35 hydroxyl group of bacteriohopanetetrol: glucosamine linked through a glycosidic bond and two new polyhydroxylated methylcyclopentanoids differing one from each other by the presence of an amino or a guanidino group and linked through an ether bond. The significance of the presence of these compounds in terms of membrane reinforcement and DNA/triterpenoid interactions is discussed.
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Microbial Utilization of Gaseous Alkanes. ACTA ACUST UNITED AC 1984. [DOI: 10.1016/b978-0-12-040307-3.50007-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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White SA, Claus GW. Effect of intracytoplasmic membrane development on oxidation of sorbitol and other polyols by Gluconobacter oxydans. J Bacteriol 1982; 150:934-43. [PMID: 7068538 PMCID: PMC216447 DOI: 10.1128/jb.150.2.934-943.1982] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
By using membrane-bound dehydrogenases, Gluconobacter oxydans characteristically accomplishes single-step oxidation of many polyols and quantitative release of the oxidation product into the medium. These cells typically differentiate by forming intracytoplasmic membranes (ICM) after exponential growth on glycerol. Earlier experiments demonstrated that glycerol-grown cells containing ICM oxidized glycerol more rapidly than cells which were harvested during exponential growth and lacked ICM (Claus et al., J. Bacteriol. 123:1169-1183). This report demonstrates that ICM are also formed after growth on sorbitol. Sorbitol-grown, ICM-containing maximum stationary-phase (MSP) cells showed from 50 to 300% greater oxidation (respiration) rates on mannitol, glycerol, glucose, meso-erythritol, and meso-inositol than did exponential-phase (EXP) cells which lacked ICM. Both EXP and MSP cells exhibited maximum sorbitol oxidation at pH 5.0, 38 degrees C, and 5% (wt/vol) sorbitol. When assayed under these optimum conditions, ICM-containing MSP cells demonstrated a 72% increase in respiration on sorbitol compared with that of EXP cells lacking ICM (oxygen quotients of 3,100 and 1,800, respectively). Gas chromatographic studies showed that sorbose was the only detectable product released from cells during oxygen quotient analysis. The specific activity of particulate-bound sorbitol dehydrogenase from ICM-containing MSP cells was twice that obtained from particulate fractions prepared from EXP cells lacking ICM. These results show that neither ICM formation after exponential growth nor increased respiration of other polyols is dependent upon the polyol used to grow cells. Our results suggest that increased respiratory activity of MSP cells is caused both by ICM formation and by increased synthesis (or activity) of the polyol dehydrogenases found in these membranes.
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Higgins IJ, Best DJ, Scott D. Generation of products by methanotrophs. BASIC LIFE SCIENCES 1982; 19:383-402. [PMID: 6802126 DOI: 10.1007/978-1-4684-4142-0_29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Mazodier P, Giraud E, Gasser F. Tn5dependent streptomycin resistance inMethylobacterium organophilum. FEMS Microbiol Lett 1982. [DOI: 10.1111/j.1574-6968.1982.tb08220.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Patel RN, Hou CT, Derelanko P, Felix A. Purification and properties of a heme-containing aldehyde dehydrogenase from Methylosinus trichosporium. Arch Biochem Biophys 1980; 203:654-62. [PMID: 6779711 DOI: 10.1016/0003-9861(80)90223-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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