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Zhang WL, Lai MC, Lin S, Chen WC, Deng YC, Lai SJ, Wu SY, Hung CC, Ding JY, Chen SC. Methanooceanicella nereidis gen. nov., sp. nov., the first oceanic Methanocellaceae methanogen, isolated from potential methane hydrate bearing area offshore southwestern Taiwan. Int J Syst Evol Microbiol 2024; 74. [PMID: 38634834 DOI: 10.1099/ijsem.0.006322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
A novel mesophilic, hydrogenotrophic methanogen, strain CWC-04T, was obtained from a sediment sample extracted from a gravity core retrieved at station 22 within the KP-9 area off the southwestern coast of Taiwan during the ORIII-1368 cruise in 2009. Cells of strain CWC-04T were rod-shaped, 1.4-2.9 µm long by 0.5-0.6 µm wide, and occurred singly. Strain CWC-04Tutilized formate, H2/CO2, 2-propanol/CO2 or 2-butanol/CO2 as catabolic substrates. The optimal growth conditions were 42 °C, 0.17 M NaCl and pH 5.35. The genomic DNA G+C content calculated from the genome sequence of strain CWC-04T was 46.19 mol%. Phylogenetic analysis of 16S rRNA gene revealed that strain CWC-04T is affiliated with the genus Methanocella. The 16S rRNA gene sequences similarities within strains Methanocella arvoryzae MRE50T, Methanocella paludicola SANAET and Methanocella conradii HZ254T were 93.7, 93.0 and 91.3 %, respectively. In addition, the optical density of CWC-04T culture dropped abruptly upon entering the late-log growth phase, with virus-like particles (150 nm in diameter) being observed on and around the cells. This observation suggests that strain CWC-04T harbours a lytic virus. Based on these phenotypic, phylogenetic and genomic results, we propose that strain CWC-04T represents a novel species of a novel genus in the family Methanocellaceae, for which the name Methanooceanicella nereidis gen. nov., sp. nov. is proposed. The type strain is CWC-04T (=BCRC AR10050T=NBRC 113165T).
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Affiliation(s)
- Wei-Ling Zhang
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan, ROC
| | - Wen-Chieh Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Yu-Chen Deng
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Shu-Jung Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung City, Taiwan, ROC
- Research Center for Cancer Biology, China Medical University, Taichung City, Taiwan, ROC
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Chuan-Chuan Hung
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Jiun-Yan Ding
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, PR China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, PR China
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2
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Chien HH, Lai MC, Weng CY, Chen MF, Wu SY, Lin S, Chen SC. Methanovulcanius yangii gen. nov., sp. nov., a hydrogenotrophic methanogen, isolated from a submarine mud volcano in the offshore area of southwestern Taiwan. Int J Syst Evol Microbiol 2023; 73. [PMID: 37938098 DOI: 10.1099/ijsem.0.006164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
A novel mesophilic, hydrogenotrophic methanogen, strain CYW5T, was isolated from a sediment sample of a piston core collected from submarine mud volcano MV5 located in the offshore area of southwestern Taiwan. Cells of strain CYW5T were irregular coccids, 0.5-1.0 µm in diameter and lysed easily by 0.01 % sodium dodecyl sulphate (SDS) treatment. Strain CYW5Tutilized formate or hydrogen plus carbon dioxide as catabolic substrates for methanogenesis. The optimal growth conditions were 37 °C, 0.043-0.085 M NaCl and pH 6.02-7.32. The genomic DNA G+C content calculated from the genome sequence of strain CYW5T was 56.2 mol%. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that strain CYW5T represented a member of the family Methanomicrobiaceae in the order Methanomicrobiales, and was closely related to the members of the genus Methanogenium. The most closely related species was Methanogenium cariaci JR1T (94.9 % of 16S rRNA gene sequence identity). The average nucleotide identity and average amino acid identity values between strain CYW5T and members of the family Methanomicrobiaceae were 74.7-78.5 % and 49.1-64.9%, respectively. Although many of the morphological and physiological characteristics of strain CYW5T and the species of the genus Methanogenium were similar, they were distinguishable by the differences in genomic G+C content and temperature, NaCl and pH ranges for growth. Based on these phenotypic, phylogenetic and genomic results, we propose that strain CYW5T represents a novel species, of a novel genus, named Methanovulcanius yangii gen. nov., sp. nov. The type strain is CYW5T (=BCRC AR10048T=DSM 100756T=NBRC 111404T).
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Affiliation(s)
- Hsin-Hsin Chien
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Chieh-Yin Weng
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Mei-Fei Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan, ROC
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian 365004, PR China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian 365004, PR China
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3
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Complete Genome Sequence of Methanofollis aquaemaris BCRC 16166
T
, Isolated from a Marine Aquaculture Fishpond. Microbiol Resour Announc 2022; 11:e0074322. [PMID: 36094213 PMCID: PMC9583781 DOI: 10.1128/mra.00743-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hydrogenotrophic methanogen Methanofollis aquaemaris BCRC 16166T (= N2F9704T = DSM 14661T) was isolated from a marine aquaculture fishpond near Wang-gong (Taiwan, Republic of China). The genome of strain BCRC 16166T was selected for sequencing in order to provide further information about the species delineation and its infected virus.
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4
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Draft Genomes of Methanocalculus taiwanensis P2F9704a
T
and Methanocalculus chunghsingensis K1F9705b
T
, Hydrogenotrophic Methanogens Belonging to the Family
Methanocalculaceae. Microbiol Resour Announc 2022; 11:e0079222. [PMID: 36066251 PMCID: PMC9584218 DOI: 10.1128/mra.00792-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The family Methanocalculaceae comprises hydrogen- and formate-utilizing methanogens. Here, we report two additional draft genome sequences of Methanocalculaceae, those of Methanocalculus taiwanensis P2F9704aT (equivalent to BCRC 16182T and DSM 14663T) and Methanocalculus chunghsingensis K1F9705bT (equivalent to DSM 14646T and OCM 772T), which were selected for further species delineation and comparative genomic analyses.
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Verster A, Petronella N, Green J, Matias F, Brooks SPJ. A Bayesian method for identifying associations between response variables and bacterial community composition. PLoS Comput Biol 2022; 18:e1010108. [PMID: 35793382 PMCID: PMC9307184 DOI: 10.1371/journal.pcbi.1010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 07/22/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022] Open
Abstract
Determining associations between intestinal bacteria and continuously measured physiological outcomes is important for understanding the bacteria-host relationship but is not straightforward since abundance data (compositional data) are not normally distributed. To address this issue, we developed a fully Bayesian linear regression model (BRACoD; Bayesian Regression Analysis of Compositional Data) with physiological measurements (continuous data) as a function of a matrix of relative bacterial abundances. Bacteria can be classified as operational taxonomic units or by taxonomy (genus, family, etc.). Bacteria associated with the physiological measurement were identified using a Bayesian variable selection method: Stochastic Search Variable Selection. The output is a list of inclusion probabilities ([Formula: see text]) and coefficients that indicate the strength of the association ([Formula: see text]) for each bacterial taxa. Tests with simulated communities showed that adopting a cut point value of [Formula: see text] ≥ 0.3 for identifying included bacteria optimized the true positive rate (TPR) while maintaining a false positive rate (FPR) of ≤ 5%. At this point, the chances of identifying non-contributing bacteria were low and all well-established contributors were included. Comparison with other methods showed that BRACoD (at [Formula: see text] ≥ 0.3) had higher precision and a higher TPR than a commonly used center log transformed LASSO procedure (clr-LASSO) as well as higher TPR than an off-the-shelf Spike and Slab method after center log transformation (clr-SS). BRACoD was also less likely to include non-contributing bacteria that merely correlate with contributing bacteria. Analysis of a rat microbiome experiment identified 47 operational taxonomic units that contributed to fecal butyrate levels. Of these, 31 were positively and 16 negatively associated with butyrate. Consistent with their known role in butyrate metabolism, most of these fell within the Lachnospiraceae and Ruminococcaceae. We conclude that BRACoD provides a more precise and accurate method for determining bacteria associated with a continuous physiological outcome compared to clr-LASSO. It is more sensitive than a generalized clr-SS algorithm, although it has a higher FPR. Its ability to distinguish genuine contributors from correlated bacteria makes it better suited to discriminating bacteria that directly contribute to an outcome. The algorithm corrects for the distortions arising from compositional data making it appropriate for analysis of microbiome data.
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Affiliation(s)
- Adrian Verster
- Bureau of Food Surveillance and Science Integration, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Nicholas Petronella
- Bureau of Food Surveillance and Science Integration, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Judy Green
- Bureau of Nutritional Sciences, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Fernando Matias
- Bureau of Nutritional Sciences, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Stephen P. J. Brooks
- Bureau of Nutritional Sciences, Food Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
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6
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Chen SC, Wu CH, You YT, Wu SY, Liao CH, Wang X, Li H, Guo Y, You J, Qiu W. Complete Genome Sequence of Methanofollis formosanus DSM 15483 T, Isolated from an Aquaculture Fish Pond. Microbiol Resour Announc 2022; 11:e0006822. [PMID: 35481773 PMCID: PMC9119062 DOI: 10.1128/mra.00068-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/14/2022] [Indexed: 11/20/2022] Open
Abstract
The hydrogenotrophic strain Methanofollis formosanus DSM 15483T (= ML15T = OCM 798T) was isolated from an aquaculture fish pond near Wang-gong, Taiwan. The genome of strain DSM 15483T was selected for sequencing in order to provide further information about the species delineation and its unique habitat.
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Affiliation(s)
- Sheng-Chung Chen
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, People’s Republic of China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, People’s Republic of China
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Chih-Hung Wu
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, People’s Republic of China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, People’s Republic of China
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou, Fujian, People’s Republic of China
| | - Yi-Ting You
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Ching-Hua Liao
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, People’s Republic of China
| | - Xiang Wang
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou, Fujian, People’s Republic of China
| | - Hongduo Li
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou, Fujian, People’s Republic of China
| | - Yun Guo
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou, Fujian, People’s Republic of China
| | - Jinhui You
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, People’s Republic of China
| | - Wanling Qiu
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, People’s Republic of China
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7
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Shen Y, Chen SC, Lai MC, Huang HH, Chiu HH, Tang SL, Rogozin DY, Degermendzhy AG. Methanolobus halotolerans sp. nov., isolated from the saline Lake Tus in Siberia. Int J Syst Evol Microbiol 2020; 70:5586-5593. [PMID: 32915124 DOI: 10.1099/ijsem.0.004453] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A halotolerant, psychrotolerant and methylotrophic methanogen, strain SY-01T, was isolated from the saline Lake Tus in Siberia. Cells of strain SY-01T were non-motile, cocci and 0.8-1.0 µm in diameter. The only methanogenic substrate utilized by strain SY-01T was methanol. The temperature range of growth for strain SY-01T was from 4 to 40 °C and the optimal temperature for growth was 30 °C. The pH range of growth was from pH 7.2 to 9.0, with optimal growth at pH 8.0. The NaCl range of growth was 0-1.55 M with optimal growth at 0.51 M NaCl. The G+C content of the genome of strain SY-01T was 43.6 mol % as determined by genome sequencing. Phylogenetic analysis revealed that strain SY-01T was most closely related to Methanolobus zinderi SD1T (97.3 % 16S rRNA gene sequence similarity), and had 95.5-97.2 % similarities to other Methanolobus species with valid names. Genome relatedness between strain SY-01T and DSM 21339T was computed using average nucleotide identity and digital DNA-DNAhybridization, which yielded values of 79.7 and 21.7 %, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain SY-01T represents a novel species of the genus Methanolobus, and the name Methanolobus halotolerans sp. nov. is proposed. The type strain is SY-01T (=BCRC AR10051T=NBRC 113166 T=DSM 107642T).
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Affiliation(s)
- Ya Shen
- Department of Life Science, National Chung Hsing University, Taiwan, ROC
| | - Sheng-Chung Chen
- Department of Life Science, National Chung Hsing University, Taiwan, ROC.,Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian 365004, PR China.,School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian 365004, PR China
| | - Mei-Chin Lai
- Department of Life Science, National Chung Hsing University, Taiwan, ROC.,Agricultural Biotechnology Center, National Chung Hsing University, Taiwan, ROC
| | - Hsing-Hua Huang
- Department of Life Science, National Chung Hsing University, Taiwan, ROC
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taiwan, ROC
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taiwan, ROC
| | - Denis Yu Rogozin
- Siberian Federal University, Krasnoyarsk 660041, Russia.,Institute of Biophysics Siberian Branch of Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Andrey G Degermendzhy
- Siberian Federal University, Krasnoyarsk 660041, Russia.,Institute of Biophysics Siberian Branch of Russian Academy of Sciences, Krasnoyarsk 660036, Russia
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8
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Chen SC, Teng NH, Lin YS, Lai MC, Chen HH, Wang CC. Methanofollis fontis sp. nov., a methanogen isolated from marine sediment near a cold seep at Four-Way Closure Ridge offshore southwestern Taiwan. Int J Syst Evol Microbiol 2020; 70:5497-5502. [PMID: 32897849 DOI: 10.1099/ijsem.0.004440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, hydrogenotrophic methanogen, strain FWC-SCC2T, was isolated from deep-sea sediments collected by a real-time video multiple-corer at the C5-6 station near a cold seep at Four-Way Closure Ridge region during R/V Ocean Researcher III ORIII-1900 cruise in 2015. The cells were irregular cocci, non-motile and 0.8-1.2 µm in diameter. The methanogenic substrates utilized by strain FWC-SCC2T were formate or H2+CO2, but not acetate, methanol, ethanol or methylamines. Strain FWC-SCC2T was lysed in SDS (0.01 %, w/v). The M r of surface-layer protein was 116 400. The optimum growth conditions of strain FWC-SCC2T were 37 °C, 0.17 M NaCl and pH 6.7-7.0. The genomic DNA G+C content calculated from the genome sequence of strain FWC-SCC2T was 59.5 mol %. Phylogenetic analysis revealed that strain FWC-SCC2T was a member of the genus Methanofollis, and was most closely related to Methanofollis tationis Chile 9T (97.6 % similarity of 16S rRNA gene sequence) and shared 97.4, 95.9, 95.9 and 95.4 % with Methanofollis liminatans GKZPZT, Methanofollis formosanus ML15T, Methanofollis aquaemaris N2F9704T and Methanofollis ethanolicus HASUT, respectively. The genome relatedness values between strain FWC-SCC2T and M. tationis DSM 2702T were estimated by average nucleotide identity and digital DNA-DNA hybridization analyses and the results were 79.4 and 21.2 %, respectively. Based on the differences in physiological and biochemical properties, 16S rRNA gene phylogeny and genome relatedness presented here, it is suggested that strain FWC-SCC2T represents a novel species of the genus Methanofollis, and the name Methanofollis fontis sp. nov. is proposed. The type strain is FWC-SCC2T (=BCRC AR10052T=DSM 107935T= NBRC 113164T).
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Affiliation(s)
- Sheng-Chung Chen
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, PR China.,Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Nai-Hsuan Teng
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Yu-Shih Lin
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Mei-Chin Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, ROC.,Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hsin-Hung Chen
- Institute of Undersea Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Chau-Chang Wang
- Institute of Undersea Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
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9
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Chen SC, Huang HH, Lai MC, Weng CY, Chiu HH, Tang SL, Rogozin DY, Degermendzhy AG. Methanolobus psychrotolerans sp. nov., a psychrotolerant methanoarchaeon isolated from a saline meromictic lake in Siberia. Int J Syst Evol Microbiol 2018; 68:1378-1383. [DOI: 10.1099/ijsem.0.002685] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sheng-Chung Chen
- Department of Life Science, National Chung Hsing University, Taiwan, ROC
| | - Hsing-Hua Huang
- Department of Life Science, National Chung Hsing University, Taiwan, ROC
| | - Mei-Chin Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taiwan, ROC
- Department of Life Science, National Chung Hsing University, Taiwan, ROC
| | - Chieh-Yin Weng
- Department of Life Science, National Chung Hsing University, Taiwan, ROC
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taiwan, ROC
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taiwan, ROC
| | - Denis Yu Rogozin
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Andrey G. Degermendzhy
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Siberian Federal University, Krasnoyarsk 660041, Russia
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10
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Biases during DNA extraction affect bacterial and archaeal community profile of anaerobic digestion samples. 3 Biotech 2017; 7:375. [PMID: 29071172 DOI: 10.1007/s13205-017-1009-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 10/09/2017] [Indexed: 01/01/2023] Open
Abstract
The anaerobic digestion (AD) of organic waste for biogas production has received much attention in recent years due to the increasing need for renewable energy and environmentally friendly waste management systems. Identification of the microbial community involved in AD aids in better understanding and optimising of the process. The choice of DNA extraction method is an integral step in any molecular biodiversity study. In the present study, potential biases introduced by DNA extraction methods were examined by comparing quality, quantity and representability of DNA extracted from AD samples using various extraction methods. In spite of the non-kit based method (cetyltrimethylammonium bromide) yielding the largest quantity of DNA (approximately 44 µg DNA per gram dry weight), the extracted DNA contained PCR inhibitors. Furthermore, the quantity of extracted DNA was not proportional to species diversity. Diversity, determined using denaturing gradient gel electrophoresis (DGGE), was strongly linked to the type of extraction method used. The spin-column filter-based kit that incorporated mechanical and chemical lysis (Macherey-Nagel kit) gave the best results in terms of bacterial and archaeal diversity (Shannon-Wiener indices: average 2.5 and 2.6, respectively). Furthermore, this kit was the most effective at lysing hard-to-lyse bacterial and archaeal cells. The choice of DNA extraction method significantly influences the reliability and comparability of results obtained during AD microbial ecology investigations. Moreover, the careful selection of the DNA extraction method is of particular importance when analysing AD samples since these samples are rich in PCR inhibitors and hard-to-lyse cells such as archaea and gram-positive bacteria.
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11
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Haloterrigena mahii sp. nov., an extremely halophilic archaeon from a solar saltern. Int J Syst Evol Microbiol 2017; 67:1333-1338. [DOI: 10.1099/ijsem.0.001811] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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12
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Li Y, Leahy SC, Jeyanathan J, Henderson G, Cox F, Altermann E, Kelly WJ, Lambie SC, Janssen PH, Rakonjac J, Attwood GT. The complete genome sequence of the methanogenic archaeon ISO4-H5 provides insights into the methylotrophic lifestyle of a ruminal representative of the Methanomassiliicoccales. Stand Genomic Sci 2016; 11:59. [PMID: 27602181 PMCID: PMC5011839 DOI: 10.1186/s40793-016-0183-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/22/2016] [Indexed: 12/03/2022] Open
Abstract
Methane emissions from agriculture represent around 9 % of global anthropogenic greenhouse emissions. The single largest source of this methane is animal enteric fermentation, predominantly from ruminant livestock where it is produced mainly in their fermentative forestomach (or reticulo-rumen) by a group of archaea known as methanogens. In order to reduce methane emissions from ruminants, it is necessary to understand the role of methanogenic archaea in the rumen, and to identify their distinguishing characteristics that can be used to develop methane mitigation technologies. To gain insights into the role of methylotrophic methanogens in the rumen environment, the genome of a methanogenic archaeon has been sequenced. This isolate, strain ISO4-H5, was isolated from the ovine rumen and belongs to the order Methanomassiliicoccales. Genomic analysis suggests ISO4-H5 is an obligate hydrogen-dependent methylotrophic methanogen, able to use methanol and methylamines as substrates for methanogenesis. Like other organisms within this order, ISO4-H5 does not possess genes required for the first six steps of hydrogenotrophic methanogenesis. Comparison between the genomes of different members of the order Methanomassiliicoccales revealed strong conservation in energy metabolism, particularly in genes of the methylotrophic methanogenesis pathway, as well as in the biosynthesis and use of pyrrolysine. Unlike members of Methanomassiliicoccales from human sources, ISO4-H5 does not contain the genes required for production of coenzyme M, and so likely requires external coenzyme M to survive.
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Affiliation(s)
- Yang Li
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Sinead C. Leahy
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Gemma Henderson
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Faith Cox
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Eric Altermann
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - William J. Kelly
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Suzanne C. Lambie
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H. Janssen
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Jasna Rakonjac
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Graeme T. Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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Chen SC, Chen MF, Lai MC, Weng CY, Wu SY, Lin S, Yang TF, Chen PC. Methanoculleus sediminis sp. nov., a methanogen from sediments near a submarine mud volcano. Int J Syst Evol Microbiol 2015; 65:2141-2147. [PMID: 25855623 DOI: 10.1099/ijs.0.000233] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, hydrogenotrophic methanogen, strain S3Fa(T), was isolated from sediments collected by Ocean Researcher I cruise ORI-934 in 2010 near the submarine mud volcano MV4 located at the upper slope of south-west Taiwan. The methanogenic substrates utilized by strain S3Fa(T) were formate and H2/CO2 but not acetate, secondary alcohols, methylamines, methanol or ethanol. Cells of strain S3Fa(T) were non-motile, irregular cocci, 0.5-1.0 μm in diameter. The surface-layer protein showed an Mr of 128,000.The optimum growth conditions were 37 °C, pH 7.1 and 0.17 M NaCl. The DNA G+C content of the genome of strain S3Fa(T) was 62.3 mol%. Phylogenetic analysis revealed that strain S3Fa(T) was most closely related to Methanoculleus marisnigri JR1(T) (99.3% 16S rRNA gene sequence similarity). Genome relatedness between strain S3Fa(T) and Methanoculleus marisnigri JR1(T) was computed using both genome-to-genome distance analysis (GGDA) and average nucleotide identity (ANI) with values of 46.3-55.5% and 93.08%, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data, it is evident that strain S3Fa(T) represents a novel species of the genus Methanoculleus, for which the name Methanoculleus sediminis sp. nov. is proposed. The type strain is S3Fa(T) ( = BCRC AR10044(T) = DSM 29354(T)).
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Affiliation(s)
- Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Mei-Fei Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chieh-Yin Weng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan, ROC
| | - Tsanyao F Yang
- Department of Geosciences, National Taiwan University, Taipei, Taiwan, ROC
| | - Po-Chun Chen
- Central Geological Survey, MOEA, Taipei, Taiwan, ROC
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14
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Weng CY, Chen SC, Lai MC, Wu SY, Lin S, Yang TF, Chen PC. Methanoculleus taiwanensis sp. nov., a methanogen isolated from deep marine sediment at the deformation front area near Taiwan. Int J Syst Evol Microbiol 2015; 65:1044-1049. [DOI: 10.1099/ijs.0.000062] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, hydrogenotrophic methanogen, strain CYW4T, was isolated from deep-sea sediment obtained by the Ocean Researcher I cruiser, ORI-961, in 2011. The sediment was from the deformation front area offshore of south-western Taiwan. Here, seismic reflections indicated that methane hydrates were abundant. The methanogenic substrates utilized by strain CYW4T were formate and H2/CO2, but not acetate, secondary alcohols, methylamines, methanol and ethanol. Cells of strain CYW4T were non-motile, irregular cocci and 0.6–1.5 µm in diameter. The S-layer protein had an M
r of 112 000. The optimum growth conditions were at 37 °C, pH 8.1 and 0.08 M NaCl. Growth of the strain was stimulated by acetate. The G+C content of the chromosomal DNA of strain CYW4T was 61 mol%. Phylogenetic analysis revealed that strain CYW4T was most closely related to
Methanoculleus marisnigri
JR1T (96.82 % 16S rRNA gene sequence similarity). Based on the morphological, phenotypic and phylogenetic characteristics presented here, it is evident that strain CYW4T represents a novel species of the genus
Methanoculleus
, and the name Methanoculleus taiwanensis sp. nov. is proposed. The type strain is CYW4T ( = BCRC AR10043T = NBRC 110782T). The optical density of cultures of strain CYW4T dropped abruptly upon entering the stationary growth phase. During this time numerous particles of approximately 50 nm in diameter were observed on and around the cells. This suggests that strain CYW4T harbours a lytic virus that is induced in the stationary phase, which is of interest because only a few lytic viruses have been reported in methanogens.
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Affiliation(s)
- Chieh-Yin Weng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chin Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Tsanyao F. Yang
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
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15
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Kelly WJ, Leahy SC, Li D, Perry R, Lambie SC, Attwood GT, Altermann E. The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9. Stand Genomic Sci 2014; 9:15. [PMID: 25780506 PMCID: PMC4335013 DOI: 10.1186/1944-3277-9-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 10/29/2014] [Indexed: 01/09/2023] Open
Abstract
Methanobacterium formicicum BRM9 was isolated from the rumen of a New Zealand Friesan cow grazing a ryegrass/clover pasture, and its genome has been sequenced to provide information on the phylogenetic diversity of rumen methanogens with a view to developing technologies for methane mitigation. The 2.45 Mb BRM9 chromosome has an average G + C content of 41%, and encodes 2,352 protein-coding genes. The genes involved in methanogenesis are comparable to those found in other members of the Methanobacteriaceae with the exception that there is no [Fe]-hydrogenase dehydrogenase (Hmd) which links the methenyl-H4MPT reduction directly with the oxidation of H2. Compared to the rumen Methanobrevibacter strains, BRM9 has a much larger complement of genes involved in determining oxidative stress response, signal transduction and nitrogen fixation. BRM9 also has genes for the biosynthesis of the compatible solute ectoine that has not been reported to be produced by methanogens. The BRM9 genome has a prophage and two CRISPR repeat regions. Comparison to the genomes of other Methanobacterium strains shows a core genome of ~1,350 coding sequences and 190 strain-specific genes in BRM9, most of which are hypothetical proteins or prophage related.
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Affiliation(s)
- William J Kelly
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Sinead C Leahy
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
- New Zealand Agricultural Greenhouse Gas Research Centre, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Dong Li
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Rechelle Perry
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Suzanne C Lambie
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Graeme T Attwood
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
- New Zealand Agricultural Greenhouse Gas Research Centre, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
| | - Eric Altermann
- Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand
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16
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Zhou L, Liu X, Dong X. Methanospirillum psychrodurum sp. nov., isolated from wetland soil. Int J Syst Evol Microbiol 2014; 64:638-641. [DOI: 10.1099/ijs.0.057299-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A psychrotolerant methanogenic strain, X-18T, was isolated from the soil of the Madoi wetland at Qinghai, Tibetan plateau, China. Cells were wavy rods (11–62 µm long) with blunt tapered ends and Gram-stain-negative. Strain X-18T grew strictly anaerobically and produced methane exclusively from H2/CO2. Growth occurred in the temperature range of 4–32 °C and optimally at 25 °C. Growth pH ranged from 6.5 to 8.0 and the optimum was 7.0. The G+C content of the genomic DNA of strain X-18T was 44.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and the alpha subunit of methyl-coenzyme M reductase indicated that strain X-18T was affiliated to the genus
Methanospirillum
and was most closely related to
Methanospirillum lacunae
Ki8-1T, with 96.3 % 16S rRNA gene sequence similarity. However, strain X-18T could be distinguished from the existing species of the genus
Methanospirillum
by its lower growth temperature and obligate hydrogenotrophic methanogenesis. On the basis of phenotypic characteristics and phylogenetic analysis, strain X-18T represents a novel species of the genus
Methanospirillum
, for which the name Methanospirillum psychrodurum sp. nov. is proposed and strain X-18T is assigned as the type strain ( = CGMCC 1.5186T = JCM 19216T).
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Affiliation(s)
- Liguang Zhou
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiaoli Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Leahy SC, Kelly WJ, Li D, Li Y, Altermann E, Lambie SC, Cox F, Attwood GT. The Complete Genome Sequence of Methanobrevibacter sp. AbM4. Stand Genomic Sci 2013; 8:215-27. [PMID: 23991254 PMCID: PMC3746419 DOI: 10.4056/sigs.3977691] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Methanobrevibacter sp. AbM4 was originally isolated from the abomasal contents of a sheep and was chosen as a representative of the Methanobrevibacter wolinii clade for genome sequencing. The AbM4 genome is smaller than that of the rumen methanogen M. ruminantium M1 (2.0 Mb versus 2.93 Mb), encodes fewer open reading frames (ORFs) (1,671 versus 2,217) and has a lower G+C percentage (29% versus 33%). Overall, the composition of the AbM4 genome is very similar to that of M1 suggesting that the methanogenesis pathway and central metabolism of these strains are highly similar, and both organisms are likely to be amenable to inhibition by small molecule inhibitors and vaccine-based methane mitigation technologies targeting these conserved features. The main differences compared to M1 are that AbM4 has a complete coenzyme M biosynthesis pathway and does not contain a prophage or non-ribosomal peptide synthase genes. However, AbM4 has a large CRISPR region and several type I and type II restriction-modification system components. Unusually, DNA-directed RNA polymerase B' and B'' subunits of AbM4 are joined, a feature only previously observed in some thermophilic archaea. AbM4 has a much reduced complement of genes encoding adhesin-like proteins which suggests it occupies a ruminal niche different from that of M1.
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Affiliation(s)
- S C Leahy
- New Zealand Agricultural Greenhouse Gas Research Centre ; Rumen Microbiology, Animal Nutrition and Health, AgResearch Limited, Grasslands Research Centre, New Zealand
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18
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Carbonero F, Nava GM, Benefiel AC, Greenberg E, Gaskins HR. Microbial DNA extraction from intestinal biopsies is improved by avoiding mechanical cell disruption. J Microbiol Methods 2011; 87:125-7. [PMID: 21820015 DOI: 10.1016/j.mimet.2011.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 07/14/2011] [Accepted: 07/16/2011] [Indexed: 12/28/2022]
Abstract
Currently, standard protocols for microbial DNA extraction from intestinal tissues do not exist. We assessed the efficiency of a commercial kit with and without mechanical disruption. Better quality DNA was obtained without mechanical disruption. Thus, it appears that bead-beating is not required for efficient microbial DNA extraction from intestinal biopsies.
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Affiliation(s)
- Franck Carbonero
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, IL 61801, USA
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19
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Isolation and characterization of Methanothermobacter crinale sp. nov., a novel hydrogenotrophic methanogen from the Shengli oil field. Appl Environ Microbiol 2011; 77:5212-9. [PMID: 21705537 DOI: 10.1128/aem.00210-11] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis is an alternative methanogenic pathway in certain thermophilic anaerobic environments such as high-temperature oil reservoirs and thermophilic biogas reactors. In these environments, the dominant thermophilic methanogens were generally related to uncultured organisms of the genus Methanothermobacter. Here we isolated two representative strains, Tm2(T) and HMD, from the oil sands and oil production water in the Shengli oil field in the People's Republic of China. The type strain, Tm2(T), was nonmotile and stained Gram positive. The cells were straight to slightly curved rods (0.3 μm in width and 2.2 to 5.9 μm in length), but some of them possessed a coccal shape connecting with the rods at the ends. Strain Tm2(T) grew with H(2)-CO(2), but acetate is required. Optimum growth of strain Tm2(T) occurred in the presence of 0.025 g/liter NaCl at pH 6.9 and a temperature of 65°C. The G+C content of the genomic DNA was 40.1 mol% ± 1.3 mol% (by the thermal denaturation method) or 41.1 mol% (by high-performance liquid chromatography). Analysis of the 16S rRNA gene sequence indicated that Tm2(T) was most closely related to Methanothermobacter thermautotrophicus ΔH(T) and Methanothermobacter wolfeii VKM B-1829(T) (both with a sequence similarity of 96.4%). Based on these phenotypic and phylogenic characteristics, a novel species was proposed and named Methanothermobacter crinale sp. nov. The type strain is Tm2(T) (ACCC 00699(T) = JCM 17393(T)).
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20
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Zhu J, Liu X, Dong X. Methanobacterium movens sp. nov. and Methanobacterium flexile sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2011; 61:2974-2978. [PMID: 21278411 DOI: 10.1099/ijs.0.027540-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two mesophilic methanogenic strains, designated TS-2(T) and GH(T), were isolated from sediments of Tuosu lake and Gahai lake, respectively, in the Qaidam basin, Qinghai province, China. Cells of both isolates were rods (about 0.3-0.5×2-5 µm) with blunt rounded ends and Gram-staining-positive. Strain TS-2(T) was motile with one or two polar flagella and used only H(2)/CO(2) for growth and methanogenesis. Strain GH(T) was non-motile, used both H(2)/CO(2) and formate and displayed a variable cell arrangement depending on the substrate: long chains when growing in formate (50 mM) or under high pressure H(2) and single cells under low pressure H(2). Phylogenetic analysis based on 16S rRNA gene sequences placed the two isolates in the genus Methanobacterium. Strain TS-2(T) was most closely related to Methanobacterium alcaliphilum NBRC 105226(T) (96% 16S rRNA gene sequence similarity). Phylogenetic analysis based on the alpha subunit of methyl-coenzyme M reductase also supported the affiliation of the two isolates with the genus Methanobacterium. DNA-DNA relatedness between the isolates and M. alcaliphilum DSM 3387(T) was 39-53%. Hence we propose two novel species, Methanobacterium movens sp. nov. (type strain TS-2(T)=AS 1.5093(T)=JCM 15415(T)) and Methanobacterium flexile sp. nov. (type strain GH(T)=AS 1.5092(T)=JCM 15416(T)).
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Affiliation(s)
- Jinxing Zhu
- Graduate University, Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiaoli Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Gorkin R, Park J, Siegrist J, Amasia M, Lee BS, Park JM, Kim J, Kim H, Madou M, Cho YK. Centrifugal microfluidics for biomedical applications. LAB ON A CHIP 2010; 10:1758-73. [PMID: 20512178 DOI: 10.1039/b924109d] [Citation(s) in RCA: 404] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The centrifugal microfluidic platform has been a focus of academic and industrial research efforts for almost 40 years. Primarily targeting biomedical applications, a range of assays have been adapted on the system; however, the platform has found limited commercial success as a research or clinical tool. Nonetheless, new developments in centrifugal microfluidic technologies have the potential to establish wide-spread utilization of the platform. This paper presents an in-depth review of the centrifugal microfluidic platform, while highlighting recent progress in the field and outlining the potential for future applications. An overview of centrifugal microfluidic technologies is presented, including descriptions of advantages of the platform as a microfluidic handling system and the principles behind centrifugal fluidic manipulation. The paper also discusses a history of significant centrifugal microfluidic platform developments with an explanation of the evolution of the platform as it pertains to academia and industry. Lastly, we review the few centrifugal microfluidic-based sample-to-answer analysis systems shown to date and examine the challenges to be tackled before the centrifugal platform can be more broadly accepted as a new diagnostic platform. In particular, fully integrated, easy to operate, inexpensive and accurate microfluidic tools in the area of in vitro nucleic acid diagnostics are discussed.
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Affiliation(s)
- Robert Gorkin
- University of California, Irvine, Irvine, CA 92697, USA
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22
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Ding JY, Lai MC. The biotechnological potential of the extreme halophilic archaea Haloterrigena sp. H13 in xenobiotic metabolism using a comparative genomics approach. ENVIRONMENTAL TECHNOLOGY 2010; 31:905-914. [PMID: 20662380 DOI: 10.1080/09593331003734210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Extreme halophilic archaea are thriving and dominant populations within hypersaline environments. Because of the extreme properties of the enzymes of halophilic archaea and similar metabolic abilities to their bacterial counterparts, our interests focus on their potential biotechnological applications. In this study, the partial genome of a newly isolated extreme halophilic archaeon, Haloterrigena sp. H13, was investigated. The genome size was estimated to be about 3.9 MB, and a genomic shotgun library was constructed. A total of 1479 clones from the library were sequenced once, and 1186 contigs were obtained. From these contigs, 580 open reading frames (ORFs) were identified, and 394 ORFs were annotated. From the partial genome of strain H13, we identified genes that may be involved in 1,2-dichloroethane degradation, naphthalene/anthracene degradation, gamma-hexachlorocyclohexane degradation, 1-/2-methylnaphthalene degradation and benzoate degradation via CoA ligation. Among the identified ORFs, gene homologs of (S)-2-haloacid dehalogenase (EC 3.8.1.2) and salicylate hydroxylase (EC 1.14.13.1), which might be involved in the degradation of dichloroethane, gamma-hexachlorocyclohexane and naphthalene, were found in the partial genome sequence of strain H13. According to the current genome annotation of peripheral metabolic pathways and the putative xenobiotic-degrading enzymes, the potential of extreme haloarchaea in bioremediation applications is proposed.
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Affiliation(s)
- Jiun-Yan Ding
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227 Taiwan, ROC
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Siegrist J, Gorkin R, Bastien M, Stewart G, Peytavi R, Kido H, Bergeron M, Madou M. Validation of a centrifugal microfluidic sample lysis and homogenization platform for nucleic acid extraction with clinical samples. LAB ON A CHIP 2010; 10:363-71. [PMID: 20091009 DOI: 10.1039/b913219h] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The applications of microfluidic technologies in medical diagnostics continue to increase, particularly in the field of nucleic acid diagnostics. While much attention has been focused on the development of nucleic acid amplification and detection platforms, sample preparation is often taken for granted or ignored all together. Specifically, little or no consideration is paid to the development of microfluidic systems that efficiently extract nucleic acids from biological samples. Here, a centrifugal microfluidic platform for mechanical sample lysis and homogenization is presented. The system performs sample lysis through a magnetically actuated bead-beating system followed by a centrifugal clarification step. The supernatant is then transferred for extraction using a unique siphon. Several other new microfluidic functions are implemented on this centrifugal platform as well, including sample distribution, a unique hydraulic capillary valve, and self-venting. Additionally, the improved system has features with a small footprint designed specifically for integration with further downstream processing steps. Biological validation of the platform is performed using Bacillus subtilis spores and clinical samples (nasopharyngeal aspirates) for respiratory virus detection. The platform was found to be as efficient as in-tube bead-beating lysis and homogenization for nucleic acid extraction, and capable of processing 4 samples in batch to near PCR-ready products in under 6 min.
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Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ, Pacheco DM, Li D, Kong Z, McTavish S, Sang C, Lambie SC, Janssen PH, Dey D, Attwood GT. The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One 2010; 5:e8926. [PMID: 20126622 PMCID: PMC2812497 DOI: 10.1371/journal.pone.0008926] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 12/07/2009] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Methane (CH(4)) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO(2)). Methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are lacking. Ruminant methane is formed by the action of methanogenic archaea typified by Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed. METHODOLOGY/PRINCIPAL FINDINGS The M1 genome was sequenced, annotated and subjected to comparative genomic and metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified. The feasibility of using a synthetic peptide-directed vaccinology approach to target epitopes of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated up-regulation of methanogenesis genes during co-culture with a hydrogen (H(2)) producing rumen bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium M1, the first reported in archaeal species. CONCLUSIONS/SIGNIFICANCE The M1 genome sequence provides new insights into the lifestyle and cellular processes of this important rumen methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases.
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Affiliation(s)
- Sinead C. Leahy
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - William J. Kelly
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Eric Altermann
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Ron S. Ronimus
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Carl J. Yeoman
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Diana M. Pacheco
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Dong Li
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Zhanhao Kong
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Sharla McTavish
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Carrie Sang
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Suzanne C. Lambie
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Peter H. Janssen
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Debjit Dey
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Graeme T. Attwood
- Rumen Microbial Genomics, Food Metabolism and Microbiology Section, Food and Textiles Group, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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Ding X, Yang WJ, Min H, Peng XT, Zhou HY, Lu ZM. Isolation and characterization of a new strain of Methanothermobacter marburgensis DX01 from hot springs in China. Anaerobe 2009; 16:54-9. [PMID: 19376257 DOI: 10.1016/j.anaerobe.2009.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 03/02/2009] [Accepted: 04/01/2009] [Indexed: 11/27/2022]
Abstract
Strain DX01, a thermophilic methanogen, was isolated from a hot spring in China. Strain DX01 grew only on H2/CO2. The DNA G+C content is 52 mol% and optimal growth temperature is 65 degrees C. The cell pellet is brick red. By analyzing 16S rRNA sequence, methyl-coenzyme M reductase I, gamma subunit protein sequences, we determined the DX01 strain to be closely related to the species of Methanothermobacter marburgensis. In addition, Methanothermobacter thermautotrophicus delta H(T) and strain DX01 had clear differences in their biochemical composition and protein expression profiles. Based on the above analysis, we propose that strain DX01 is a novel strain within thermoautotrophicus the species of M. marburgensis, namely M. marburgensis DX01. The isolation and characterization of the new M. marburgensis DX01 strain expands the known range of the Methanothermobacter genus.
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Affiliation(s)
- Xia Ding
- College of Life Sciences, Nanchang University, Nanchang, Jiangxi 337000, China
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Li E, Reich CI, Olsen GJ. A whole-genome approach to identifying protein binding sites: promoters in Methanocaldococcus (Methanococcus) jannaschii. Nucleic Acids Res 2008; 36:6948-58. [PMID: 18981048 PMCID: PMC2602779 DOI: 10.1093/nar/gkm499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have adapted an electrophoretic mobility shift assay (EMSA) to isolate genomic DNA fragments that bind the archaeal transcription initiation factors TATA-binding protein (TBP) and transcription factor B (TFB) to perform a genome-wide search for promoters. Mobility-shifted fragments were cloned, tested for their ability to compete with known promoter-containing fragments for a limited concentration of transcription factors, and sequenced. We applied the method to search for promoters in the genome of Methanocaldococcus jannaschii. Selection was most efficient for promoters of tRNA genes and genes for several presumed small non-coding RNAs (ncRNA). Protein-coding gene promoters were dramatically underrepresented relative to their frequency in the genome. The repeated isolation of these genomic regions was partially rectified by including a hybridization-based screening. Sequence alignment of the affinity-selected promoters revealed previously identified TATA box, BRE, and the putative initiator element. In addition, the conserved bases immediately upstream and downstream of the BRE and TATA box suggest that the composition and structure of archaeal natural promoters are more complicated.
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Affiliation(s)
- Enhu Li
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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Cheng L, Qiu TL, Li X, Wang WD, Deng Y, Yin XB, Zhang H. Isolation and characterization of Methanoculleus receptaculi sp. nov. from Shengli oil field, China. FEMS Microbiol Lett 2008; 285:65-71. [PMID: 18557787 DOI: 10.1111/j.1574-6968.2008.01212.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Three strictly anaerobic, thermophilic methanogens (ZC-2T, ZC-3 and ZC-6) were isolated from Shengli oil field, China. The 16S rRNA gene sequences of the three strains were nearly identical, possessing > 99.8% sequence similarity. They also possessed high sequence similarity, 97.4%, to Methanoculleus palmolei strain INSLUZ(T) (97.4% and 97.5%, respectively), indicating that they represented a novel species within the genus Methanoculleus. Cells of strain ZC-2T were nonmotile cocci, 0.8-1.7 microm in diameter, and always occurred singly or in pairs. The three strains used H2/CO2 or sodium formate as substrates for methanogenesis but not sodium acetate, trimethylamine, monomethylamine, ethanol, dimethyl sulfide, isopropanol, isobutanol, butan-2-ol or H2/CO. Optimum growth of strain ZC-2T occurred in the presence of 0.2 M NaCl, pH 7.5-7.8 and temperature 50-55 degrees C with a specific growth rate of 0.084 h(-1). The mol% G+C content of the genomic DNA was 55.2 mol%. Based on these phenotypic and phylogenetic characteristics, strains ZC-2T, ZC-3 and ZC-6 are proposed to represent a novel species in the genus Methanoculleus and named Methanoculleus receptaculi sp. nov. The type strain is ZC-2T (CGMCC 1.5087T=DSM 18860T).
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Affiliation(s)
- Lei Cheng
- Biogas Institute of Ministry of Agriculture, Chengdu, China
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Cheng L, Qiu TL, Yin XB, Wu XL, Hu GQ, Deng Y, Zhang H. Methermicoccus shengliensis gen. nov., sp. nov., a thermophilic, methylotrophic methanogen isolated from oil-production water, and proposal of Methermicoccaceae fam. nov. Int J Syst Evol Microbiol 2007; 57:2964-2969. [DOI: 10.1099/ijs.0.65049-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, methylotrophic methanogen, strain ZC-1T, was isolated from the Shengli oilfield, China. Cells of strain ZC-1T were motile cocci, 0.7–1.0 μm in diameter and always occurred in clusters of two to four cells. Lysis-susceptibility experiments and analysis of transmission electron micrographs of strain ZC-1T suggested the presence of a proteinaceous cell wall. Strain ZC-1T used methanol, methylamine and trimethylamine as substrates for methanogenesis. Optimal growth, with a doubling time of around 5 h, occurred at pH 6.0–6.5, 65 °C, 0.3–0.5 M NaCl and 0.05–0.20 M MgCl2. The DNA G+C content of this organism was 56 mol%. Analysis of 16S rRNA gene sequence and the inferred amino acid sequence of the mcrA gene of strain ZC-1T indicated that it is related specifically to members of the family Methanosaetaceae (90.6 and 76.6 % sequence similarity, respectively). However, strain ZC-1T failed to grow with acetate as substrate for methanogenesis, which is a special characteristic of the family Methanosaetaceae. Based on these phenotypic and phylogenic characteristics, strain ZC-1T is proposed to represent a novel genus and species, for which the name Methermicoccus shengliensis gen. nov., sp. nov. is proposed. The type strain is ZC-1T (=CGMCC 1.5056T=DSM 18856T). Methermicoccaceae fam. nov. is also proposed.
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Affiliation(s)
- Lei Cheng
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Tian-Lei Qiu
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Xiao-Bo Yin
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Xiao-Lei Wu
- Center for Environmental Biotechnology, Department of Environmental Science and Engineering, Tsinghua University, Beijing 100084, PR China
| | - Guo-Quan Hu
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Yu Deng
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
| | - Hui Zhang
- Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China
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Shih CJ, Lai MC. Analysis of the AAA+ chaperone clpB gene and stress-response expression in the halophilic methanogenic archaeon Methanohalophilus portucalensis. MICROBIOLOGY-SGM 2007; 153:2572-2583. [PMID: 17660421 DOI: 10.1099/mic.0.2007/007633-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
ClpB is a member of the protein-disaggregating chaperone machinery belonging to the AAA+ superfamily. This paper describes a new clpB gene from the halophilic methanoarchaeon Methanohalophilus portucalensis, which has not been reported previously in Archaea. The partial sequence of clpB was identified from the investigation of the salt-stress response of Meh. portucalensis by differential-display RT-PCR (DDRT-PCR). Furthermore, the complete clpB sequence (2610 nt) and its upstream genes encoding the type I chaperonin GroEL/ES were obtained through inverse PCR, Southern hybridization and sequencing. The G+C ratio of clpB is 49.6 mol%. The predicted ClpB polypeptide contains 869 aa and possesses a long central domain and a predicted distinctly discontinuous coiled-coil motif separating two nucleotide-binding domains (NBD1 and NBD2). NBD1 has a single Walker A and two Walker B motifs and NBD2 has only one of each Walker motif, a characteristic of HSP100 proteins. Two repeated Clp amino-terminal domain motifs (ClpN) were identified in ClpB. The putative amino acid sequence shared 75.6 % identity with the predicted clpB homologue annotated as ATPase AAA-2 of Methanococcoides burtonii DSM 6242. Preliminary phylogenetic analysis clustered Meh. portucalensis ClpB (MpClpB) with the low G+C Gram-positive bacteria. Stress response analysis of clpB by Northern blotting showed up to 1.5-fold increased transcription levels in response to both salt up-shock (from 2.1 to 3.1 M NaCl) and down-shock (from 2.1 to 0.9 M NaCl). Both clpB and groEL/ES transcript levels increased when the temperature was shifted from 37 degrees C to 55 degrees C. Under heat stress clpB transcription was repressed by the addition of the osmolyte betaine (1 mM). In conclusion, a novel AAA+ chaperone clpB gene from a halophilic methanogen that responded to the fluctuations in temperature, salt concentration and betaine has been identified and analysed for the first time.
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MESH Headings
- Adaptation, Physiological/genetics
- Adenosine Triphosphatases/genetics
- Amino Acid Motifs
- Archaeal Proteins/biosynthesis
- Archaeal Proteins/genetics
- Base Composition
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Chaperonin 10/genetics
- Chaperonin 60/genetics
- Chaperonins/biosynthesis
- Chaperonins/genetics
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Archaeal
- Heat-Shock Proteins/biosynthesis
- Heat-Shock Proteins/genetics
- Hot Temperature
- Methanosarcinaceae/genetics
- Methanosarcinaceae/metabolism
- Molecular Sequence Data
- Phylogeny
- Protein Structure, Tertiary
- RNA, Messenger/biosynthesis
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sodium Chloride/metabolism
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Affiliation(s)
- Chao-Jen Shih
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
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30
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Wu C, Zhang G, Liu X, Dong X. Bicarbonate is a stimulus in the inter-species induced sporulation of strict anaerobic Syntrophomonas erecta subsp. sporosyntropha. Extremophiles 2007; 11:827-32. [PMID: 17704894 DOI: 10.1007/s00792-007-0104-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Accepted: 07/17/2007] [Indexed: 11/29/2022]
Abstract
Previously Syntrophomonas species had been described as the bacteria those did not form spores, however, in our previous studies, a newly isolated S. erecta subsp. sporosyntropha JCM13344(T) was found to form spores in the co-culture with methanogens, while not in mono-culture or in co-culture with sulfate reducer. In this study, we examined the sporulation stimulus conferred by methanogens in the co-culture. By reducing bicarbonate in mono-culture and sulfate-reducing co-culture, we could induce S. erecta subsp. sporosyntropha JCM13344(T) to form spores, so that bicarbonate at lower concentration was determined as another stimulus for sporulation. Based on the substrate degradation by strain JCM13344(T) in different concentration of bicarbonate vs at different pHs, it was suggested that bicarbonate could stimulate the sporulation by mediating a nutrient deprivation but not pH drop. To further confirm the sporulation potential of this group of bacteria, spo0A fragments were amplified from strain JCM13344(T) as well as all the recognized Syntrophomonas species, confirming that they were members of the spore-forming group. Since sporulation is a kind of response of spore-forming bacteria to environmental stresses, the observation in this work implies that stresses can be created even between the mutual beneficial partners, in this case, inducing sporulation.
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Affiliation(s)
- Chenggang Wu
- Institute of Microbiology, Chinese Academy of Sciences, Chao Yang District, Beijing, 100101, People's Republic of China
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31
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Kido H, Micic M, Smith D, Zoval J, Norton J, Madou M. A novel, compact disk-like centrifugal microfluidics system for cell lysis and sample homogenization. Colloids Surf B Biointerfaces 2007; 58:44-51. [PMID: 17499489 DOI: 10.1016/j.colsurfb.2007.03.015] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2007] [Accepted: 03/19/2007] [Indexed: 11/29/2022]
Abstract
In this paper, we present the design and characterization of a novel platform for mechanical cell lysis of even the most difficult to lyse cell types on a micro or nanoscale (maximum 70 microL total volume). The system incorporates a machined plastic circular disk assembly, magnetic field actuated microfluidics, centrifugal cells and tissue homogenizer and centrifugation system. The mechanism of tissue disruption of this novel cell homogenization apparatus derives from the relative motion of ferromagnetic metal disks and grinding matrices in a liquid medium within individual chambers of the disk in the presence of an oscillating magnetic field. The oscillation of the ferromagnetic disks or blades produces mechanical impaction and shear forces capable of disrupting cells within the chamber both by direct action of the blade and by the motion of the surrounding lysis matrix, and by motion induced vortexing of buffer fluid. Glass beads or other grinding media are integrated into each lysis chamber within the disk to enhance the transfer of energy from the oscillating metal blade to the cells. The system also achieves the centrifugal elimination of solids from each liquid sample and allows the elution of clarified supernatants via siphoning into a collection chamber fabricated into the plastic disk assembly. This article describes system design, implementation and validation of proof of concept on two samples--Escherichia coli and Saccharomyces cerevisiae representing model systems for cells that are easy and difficult to lyse, respectively.
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Affiliation(s)
- Horacio Kido
- Department of Mechanical and Aerospace Engineering, University of California, Irvine, Irvine, CA 92697-3975, USA.
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32
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Gourgue-Jeannot C, Kalmokoff ML, Kheradpir E, Kwan J, Lampi BJ, McAllister M, Brooks SPJ. Dietary fructooligosaccharides alter the cultivable faecal population of rats but do not stimulate the growth of intestinal bifidobacteria. Can J Microbiol 2006; 52:924-33. [PMID: 17110960 DOI: 10.1139/w06-053] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effect of fructans on the cultivable faecal community of Bio Breeding rats fed diets containing 5% (m/v) food-grade fructooligosaccharide (FOS) was investigated. Culturing of faecal material using chicory inulin as the sole carbohydrate source revealed the presence of a greater diversity of inulin-utilizing bacterial species in FOS-fed rats as compared with the control rats, although both contained species which effectively utilized inulin. The majority of cultivable inulin-utilizing species fell within the Clostridium coccoides group and Clostridium leptum subgroup, some of which were related to previously cultured butyrate-producing bacteria from the intestines of various animals. The impact of FOS on the growth of the indigenous bifidobacteria community and three inulin-utilizing isolates was assessed using real-time polymerase chain reaction. While dietary FOS was found to stimulate the growth of all three inulin-utilizing isolates, no growth stimulation of the indigenous bifidobacteria community occurred over the duration of the feeding trial.
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Affiliation(s)
- C Gourgue-Jeannot
- Bureau of Nutritional Research, Food Directorate, Health Products and Foods Branch, Health Canada, Banting Research Centre, Ottawa, ON, Canada
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33
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Brioukhanov AL, Netrusov AI, Eggen RIL. The catalase and superoxide dismutase genes are transcriptionally up-regulated upon oxidative stress in the strictly anaerobic archaeon Methanosarcina barkeri. Microbiology (Reading) 2006; 152:1671-1677. [PMID: 16735730 DOI: 10.1099/mic.0.28542-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methanosarcina barkeriis a strictly anaerobic methanogenic archaeon, which can survive oxidative stress. The oxidative stress agent paraquat (PQ) suppressed growth ofM. barkeriat concentrations of 50–200 μM. Hydrogen peroxide (H2O2) inhibited growth at concentrations of 0.4–1.6 mM. Catalase activity in cell-free extracts ofM. barkeriincreased about threefold during H2O2stress (1.3 mM H2O2, 2–4 h exposure) and nearly twofold during superoxide stress (160 μM PQ, 2 h exposure). PQ (160 μM, 2–4 h exposure) and H2O2(1.3 mM, 2 h exposure) also influenced superoxide dismutase activity in cell-free extracts ofM. barkeri. Dot-blot analysis was performed on total RNA isolated from H2O2- and PQ-exposed cultures, using labelled internal DNA fragments of thesodandkatgenes. It was shown that H2O2but not PQ strongly induced up-regulation of thekatgene. PQ and to a lesser degree H2O2induced the expression of superoxide dismutase. The results indicate the regulation of the adaptive response ofM. barkerito different oxidative stresses.
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Affiliation(s)
- Andrei L Brioukhanov
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
- Department of Microbiology, Biological Faculty, Lomonosov Moscow State University, Vorob'evy Hills 1/12, 119992 Moscow, Russia
| | - Alexander I Netrusov
- Department of Microbiology, Biological Faculty, Lomonosov Moscow State University, Vorob'evy Hills 1/12, 119992 Moscow, Russia
| | - Rik I L Eggen
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
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Jaki BU, Franzblau SG, Cho SH, Pauli GF. Development of an extraction method for mycobacterial metabolome analysis. J Pharm Biomed Anal 2005; 41:196-200. [PMID: 16314064 PMCID: PMC3384498 DOI: 10.1016/j.jpba.2005.10.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 10/13/2005] [Accepted: 10/13/2005] [Indexed: 11/23/2022]
Abstract
As a prerequisite for studying the intracellular metabolome of mycobacteria, several methods were evaluated for efficient breakage of the cell using Mycobacterium bovis (BCG) as a model microorganism. Several pulping methods, treating with an Ultra-Turax, deep-freezing in liquid nitrogen followed by mechanical grinding, sonicating with probe head or cup horn and bead beating prior to solvent extraction were applied and compared. Gravimetry, electron microscopy, and nuclear magnetic resonance spectrometry were used to analyze the extracts. All analytical methods prove that sonicating is superior to mechanical grinding of deep-frozen cells. Two methods indicated that sonicating with a probe head enhances the efficiency of cell disruption compared to sonicating with a cup horn. The highest extract yield and chemical diversity were achieved by a combination of mechanical grinding and sonicating. Within the scope of a metabolomic analysis, the method of choice to treat mycobacterial cells is a combination of deep-freezing in liquid nitrogen and mechanical grinding followed by sonicating with a probe head.
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Affiliation(s)
- B U Jaki
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL 60612-7231, USA
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35
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Wu SY, Chen SC, Lai MC. Methanofollis formosanus sp. nov., isolated from a fish pond. Int J Syst Evol Microbiol 2005; 55:837-842. [PMID: 15774671 DOI: 10.1099/ijs.0.63475-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, hydrogenotrophic methanogen, strain ML15T, was isolated from an aquaculture fish pond near Wang-gong, Taiwan. The cells were irregular cocci, non-motile, 1·5–2·0 μm in diameter and Gram-negative. Cells of strain ML15Tlysed easily in the presence of SDS (0·1 g l−1) and the S-layer protein had anMrof 138 800. The catabolic substrates utilized by this strain included formate and H2/CO2, but not acetate, methanol, trimethylamine or secondary alcohols. Growth did not occur in minimal medium, but was observed when yeast extract and tryptone were added. Strain ML15Tgrew fastest at 37 °C, pH 6·6–7·0 and with 3 % NaCl. Acetate was not required for cell growth. Trace amounts of tungstate promoted cell growth. The G+C contents of DNA ofMethanofollis aquaemarisN2F9704Tand strain ML15Twere 59·1 and 58·4 mol%, respectively. Sequence analysis of the 16S rRNA genes of strain ML15Tand selectedMethanofollisspecies revealed similarities of 95–97 %. Based on the data presented here, it is proposed that strain ML15T(=OCM 789T=DSM 15483T) represents a novel species,Methanofollis formosanussp. nov.
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Affiliation(s)
- Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
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36
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Ma K, Liu X, Dong X. Methanobacterium beijingense sp. nov., a novel methanogen isolated from anaerobic digesters. Int J Syst Evol Microbiol 2005; 55:325-329. [PMID: 15653895 DOI: 10.1099/ijs.0.63254-0] [Citation(s) in RCA: 108] [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
Two methanogenic strains, 8-2T and 4-1, with rod-shaped (0·4–0·5×3–5 μm), non-motile cells, sometimes observed in chains, were isolated from two anaerobic digesters in Beijing, China. The two strains used H2/CO2 and formate for growth and produced methane. The temperature range for growth was 25–50 °C, with fastest growth at 37 °C. The pH ranges for growth and methane production were 6·5–8·0 for strain 8-2T and 6·8–8·6 for strain 4-1, with the fastest growth at pH 7·2 for strain 8-2T and pH 7·5–7·7 for strain 4-1. The G+C content of genomic DNA for strain 8-2T was 38·9 mol%. The similarity levels of the 16S rRNA sequence of strain 8-2T with other species of the genus Methanobacterium ranged from 93·8 to 96·0 %. Based on the phylogenetic analysis and phenotypic characteristics, the novel species Methanobacterium beijingense sp. nov. is proposed, with the type strain 8-2T (=DSM 15999T=CGMCC 1.5011T).
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Affiliation(s)
- Kai Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Xiaoli Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
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37
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Lai MC, Lin CC, Yu PH, Huang YF, Chen SC. Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan. Int J Syst Evol Microbiol 2004; 54:183-189. [PMID: 14742478 DOI: 10.1099/ijs.0.02761-0] [Citation(s) in RCA: 44] [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
Three novel halotolerant, hydrogenotrophic methanogens, designated strains K1F9705bT, K1F9705c and O1F9704a, were isolated from an estuary in Eriln Shi, Taiwan, and from a nearby marine water aquaculture fishpond. These isolates were irregular cocci that stained Gram-negative. Strains K1F9705bT and K1F9705c were non-motile, but strain O1F9704a was weakly motile with flagella. They were able to use formate and H2/CO2 to form methane, but they could not catabolize acetate, methanol, trimethylamine or secondary alcohols. Acetate was required for cell growth. Tungsten greatly stimulated the growth of strains K1F9705bT and K1F9705c, but did not affect the growth of strain O1F9704a. Optimal pH and temperature for growth of these three isolates were respectively 7.2 and 37 degrees C. Optimal NaCl concentration for growth was 0.5% for strain O1F9704a and 1.0% for strains K1F9705c and K1F9705bT. Moreover, all strains grew well at up to 8-12% NaCl. Analysis of the 16S rRNA gene revealed that these isolates are members of the genus Methanocalculus, but are distinct from Methanocalculus taiwanensis, Methanocalculus pumilus and Methanocalculus halotolerans, with sequence similarities of 98.4, 98.3 and 98.2%, respectively. In addition, strain K1F9705bT possessed 85, 80, 37, 29 and 10% DNA-DNA relatedness to strain K1F9705c, strain O1F9704a, M. pumilus, M. halotolerans and M. taiwanensis, respectively. Analysis of protein profiles and the Mr of surface (S)-layer glycoprotein subunits showed that these three new isolates are closely related to, but distinct from, known Methanocalculus species. A novel species, Methanocalculus chunghsingensis sp. nov., is proposed for strains K1F9705bT, K1F9705c and O1F9704a. The type strain is K1F9705bT (=OCM 772T=DSM 14646T).
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Affiliation(s)
- Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chih-Chien Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Ping-Hung Yu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Feng Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
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38
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Lange M, Ahring BK. A comprehensive study into the molecular methodology and molecular biology of methanogenic Archaea. FEMS Microbiol Rev 2001; 25:553-71. [PMID: 11742691 DOI: 10.1111/j.1574-6976.2001.tb00591.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Methanogens belong to the kingdom of Euryarchaeota in the domain of Archaea. The Archaea differ from Bacteria in many aspects important to molecular work. Among these are cell wall composition, their sensitivity to antibiotics, their translation and transcription machinery, and their very strict demands to anaerobic culture conditions. These differences may, at least partly, be responsible for the delay in availability of genetic research tools for methanogens. At present, however, the research within genetics of methanogens and their gene regulation and expression is in rapid progress. Two complete methanogenic genomes have been sequenced and published and more are underway. Besides, sequences are known from a multitude of individual genes from methanogens. Standard methods for simple DNA and RNA work can normally be employed, but permeabilization of the cell wall may demand special procedures. Efficient genetic manipulation systems, including shuttle and integration vector systems, have appeared for mesophilic, but not for thermophilic species within the last few years and will have a major impact on future investigations of methanogenic molecular biology.
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Affiliation(s)
- M Lange
- Biocentrum-DTU, Technical University of Denmark, Building 227, DK-2800 Lyngby, Denmark
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Lomans BP, Maas R, Luderer R, Op den Camp HJ, Pol A, van der Drift C, Vogels GD. Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. Appl Environ Microbiol 1999; 65:3641-50. [PMID: 10427061 PMCID: PMC91546 DOI: 10.1128/aem.65.8.3641-3650.1999] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A newly isolated methanogen, strain DMS1(T), is the first obligately anaerobic archaeon which was directly enriched and isolated from a freshwater sediment in defined minimal medium containing dimethyl sulfide (DMS) as the sole carbon and energy source. The use of a chemostat with a continuous DMS-containing gas stream as a method of enrichment, followed by cultivation in deep agar tubes, resulted in a pure culture. Since the only substrates utilized by strain DMS1(T) are methanol, methylamines, methanethiol (MT), and DMS, this organism is considered an obligately methylotrophic methanogen like most other DMS-degrading methanogens. Strain DMS1(T) differs from all other DMS-degrading methanogens, since it was isolated from a freshwater pond and requires NaCl concentrations (0 to 0.04 M) typical of the NaCl concentrations required by freshwater microorganisms for growth. DMS was degraded effectively only in a chemostat culture in the presence of low hydrogen sulfide and MT concentrations. Addition of MT or sulfide to the chemostat significantly decreased degradation of DMS. Transient accumulation of DMS in MT-amended cultures indicated that transfer of the first methyl group during DMS degradation is a reversible process. On the basis of its low level of homology with the most closely related methanogen, Methanococcoides burtonii (94.5%), its position on the phylogenetic tree, its morphology (which is different from that of members of the genera Methanolobus, Methanococcoides, and Methanohalophilus), and its salt tolerance and optimum (which are characteristic of freshwater bacteria), we propose that strain DMS1(T) is a representative of a novel genus. This isolate was named Methanomethylovorans hollandica. Analysis of DMS-amended sediment slurries with a fluorescence microscope revealed the presence of methanogens which were morphologically identical to M. hollandica, as described in this study. Considering its physiological properties, M. hollandica DMS1(T) is probably responsible for degradation of MT and DMS in freshwater sediments in situ. Due to the reversibility of the DMS conversion, methanogens like strain DMS1(T) can also be involved in the formation of DMS through methylation of MT. This phenomenon, which previously has been shown to occur in sediment slurries of freshwater origin, might affect the steady-state concentrations and, consequently, the total flux of DMS and MT in these systems.
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Affiliation(s)
- B P Lomans
- Department of Microbiology and Evolutionary Biology, Faculty of Science, University of Nijmegen, NL-6525 ED Nijmegen, The Netherlands
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Sauer J, Nygaard P. Expression of the Methanobacterium thermoautotrophicum hpt gene, encoding hypoxanthine (Guanine) phosphoribosyltransferase, in Escherichia coli. J Bacteriol 1999; 181:1958-62. [PMID: 10074097 PMCID: PMC93603 DOI: 10.1128/jb.181.6.1958-1962.1999] [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: 11/20/2022] Open
Abstract
The hpt gene from the archaeon Methanobacterium thermoautotrophicum, encoding hypoxanthine (guanine) phosphoribosyltransferase, was cloned by functional complementation into Escherichia coli. The hpt-encoded amino acid sequence is most similar to adenine phosphoribosyltransferases, but the encoded enzyme has activity only with hypoxanthine and guanine. The synthesis of the recombinant enzyme is apparently limited by the presence of the rare arginine codons AGA and AGG and the rare isoleucine AUA codon on the hpt gene. The recombinant enzyme was purified to apparent homogeneity.
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Affiliation(s)
- J Sauer
- Department of Biological Chemistry, University of Copenhagen, 1307 Copenhagen K, Denmark
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Abstract
Bias introduced by the simultaneous amplification of specific genes from complex mixtures of templates remains poorly understood. To explore potential causes and the extent of bias in PCR amplification of 16S ribosomal DNAs (rDNAs), genomic DNAs of two closely and one distantly related bacterial species were mixed and amplified with universal, degenerate primers. Quantification and comparison of template and product ratios showed that there was considerable and reproducible overamplification of specific templates. Variability between replicates also contributed to the observed bias but in a comparatively minor way. Based on these initial observations, template dosage and differences in binding energies of permutations of the degenerate, universal primers were tested as two likely causes of this template-specific bias by using 16S rDNA templates modified by site-directed mutagenesis. When mixtures of mutagenized templates containing AT- and GC-rich priming sites were used, templates containing the GC-rich permutation amplified with higher efficiency, indicating that different primer binding energies may to a large extent be responsible for overamplification. In contrast, gene copy number was found to be an unlikely cause of the observed bias. Similarly, amplification from DNA extracted from a natural community to which different amounts of genomic DNA of a single bacterial species were added did not affect relative product ratios. Bias was reduced considerably by using high template concentrations, by performing fewer cycles, and by mixing replicate reaction preparations.
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Affiliation(s)
- M F Polz
- The Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
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Pennings JL, de Wijs JL, Keltjens JT, van der Drift C. Medium-reductant directed expression of methyl coenzyme M reductase isoenzymes in Methanobacterium thermoautotrophicum (strain deltaH). FEBS Lett 1997; 410:235-7. [PMID: 9237636 DOI: 10.1016/s0014-5793(97)00595-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Methanobacterium thermoautotrophicum was grown in a chemostat under various controlled conditions in the presence of either sodium sulfide or sodium thiosulfate. After establishment of the steady state, cells were taken and examined for expression of the mRNA transcripts coding for the different forms of methyl coenzyme M reductase (MCR) and methylene tetrahydomethanopterin dehydrogenase (MDH). MCR isoenzyme II expression varied most markedly. Expression was found not only to depend on known parameters temperature, pH and gassing rate, but also on the medium composition, especially the reductant present.
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Affiliation(s)
- J L Pennings
- Department of Microbiology, University of Nijmegen, The Netherlands.
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Polz MF, Cavanaugh CM. A simple method for quantification of uncultured microorganisms in the environment based on in vitro transcription of 16S rRNA. Appl Environ Microbiol 1997; 63:1028-33. [PMID: 9055419 PMCID: PMC168394 DOI: 10.1128/aem.63.3.1028-1033.1997] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A simple method for the quantification of uncultured microorganisms in the environment was developed. In vitro-transcribed 16S rRNA is used as a template for midpoint dissociation temperature (Td) determinations of specific oligonucleotide probes and as a standard in quantitative probing. It replaces the need for total nucleic acids extracted from pure cultures of the organisms to be quantified. A sense RNA of a size almost identical to that of native 16S rRNA can be transcribed from ribosomal DNA clones recovered in studies of the phylogenetic diversity of microbial communities. This in vitro-transcribed rRNA yields dissociation curves typical of oligonucleotides. They parallel curves determined with total nucleic acids but yield slightly higher Td values. Neither unspecific sticking of the probe nor probe washing off the DNA template at low temperatures fully accounted for the discrepancy in probe release from the two templates. This suggests that the native rRNA itself has melting characteristics different from those of its in vitro-transcribed counterpart. However, this difference does not affect the performance of in vitro-transcribed rRNA compared with total nucleic acids as a standard in quantitative hybridizations. No difference was found between the estimates of the relative quantity of a single bacterial species in a mixed community obtained with the two standards, regardless of whether DNA was removed from the samples. This protocol will allow the large-scale quantification of the ecological importance of uncultured microorganisms in natural environments for the first time.
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Affiliation(s)
- M F Polz
- Biological Laboratories, Harvard University, Cambridge, Massachusetts 02138, USA
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Künkel A, Vaupel M, Heim S, Thauer RK, Hedderich R. Heterodisulfide reductase from methanol-grown cells of Methanosarcina barkeri is not a flavoenzyme. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 244:226-34. [PMID: 9063468 DOI: 10.1111/j.1432-1033.1997.00226.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Heterodisulfide reductase from methanol-grown cells of Methanosarcina barkeri (MbHdrDE) is a membrane-bound enzyme composed of a 46-kDa subunit MbHdrD and a 23-kDa subunit MbHdrE. The enzyme has been shown to contain 0.6 mol heme and 20 mol Fe/S per mol heterodimer. In addition, substoichiometric amounts of FAD, thought to be an essential component of the active enzyme, were detected. We have now obtained preparations of active heterodisulfide reductase in high yields completely devoid of a flavin. Cloning and sequencing of the genes encoding MbHdrD and MbHdrE, which were found to form a transcription unit hdrED, revealed that both subunits also lack an FAD-binding motif. MbHdr thus differs from heterodisulifde reductase from Methanobacterium thermoautotrophicum (MtHdr), which is a flavo iron-sulfur protein composed of the subunits MtHdrA (80 kDa), MtHdrB (36 kDa) and MtHdrC (21 kDa), the subunit HdrA harboring the flavin-binding site. Sequence comparisons revealed that the N-terminal third of MbHdrD, which contained two sequence motifs for [4Fe-4S] clusters, is similar to MtHdrC and that the C-terminal two thirds of MbHdrD are similar to MtHdrB. Thus, MbHdrD and MtHdrC are structurally equivalent subunits. MbHdrE shows sequence similarity to b-type cytochromes, in agreement with the finding that this subunit contains a heme. These and other results indicate that MbHdrD harbors the active site of heterodisulfide reduction and that a flavin is not involved in catalysis. Since MbHdrD contains only iron-sulfur clusters, a mechanism of disulfide reduction involving one electron rather than two electron-transfer reactions has to be considered such as operative in ferredoxin :thioredoxin reductases from chloroplasts and cyanobacteria.
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Affiliation(s)
- A Künkel
- Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany
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Abstract
An efficient system for electroporation of the methylotrophic bacteria Hyphomicrobium facilis, Hyphomicrobium denitrificans, Methylobacillus glycogenes, Methylobacterium extorquens, and Methylophilus methylotrophus is described. It could be demonstrated that vectors based on the broad-host-range plasmid pBBR1 could be transferred into these strains. Plasmid pBBR1KAN (3.9 kb), a kanamycin-resistant derivative of pBBR1, was suitable for transformation experiments in these methylotrophic bacteria. Transformation efficiencies up to 10(4) transformants/microgram plasmid pBBR1KAN were obtained. The broad-host-range plasmid pLA2917 was transferred into Hyphomicrobium species by a triparental mating. However, this plasmid was integrated into the genome of Hyphomicrobium spp. Plasmids pLA2917, pKT231, pSUP2021, pRZ705, and phage DNA could not be transferred in Hyphomicrobium spp. by electroporation under the conditions applied.
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Affiliation(s)
- C G Gliesche
- Institut für Allgemeine Mikrobiologie, Universität Kiel, Germany.
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Fesefeldt A, Poetsch M, Gliesche CG. Development of a species-specific gene probe for Hyphomicrobium facilis with the inverse PCR. Appl Environ Microbiol 1997; 63:335-7. [PMID: 8979362 PMCID: PMC168326 DOI: 10.1128/aem.63.1.335-337.1997] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A species-specific gene probe for Hyphomicrobium facilis was generated from a transposon Tn5-132 insertion mutant defective in methanol oxidation by the inverse PCR. With this probe, the abundance of H. facilis in a garden soil was determined as a subfraction of the total cultivable hyphomicrobia.
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Affiliation(s)
- A Fesefeldt
- Institut für Allgemeine Mikrobiologie, Universität Kiel, Germany
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Chien YT, Zinder SH. Cloning, functional organization, transcript studies, and phylogenetic analysis of the complete nitrogenase structural genes (nifHDK2) and associated genes in the archaeon Methanosarcina barkeri 227. J Bacteriol 1996; 178:143-8. [PMID: 8550408 PMCID: PMC177631 DOI: 10.1128/jb.178.1.143-148.1996] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Determination of the nucleotide sequence of the nitrogenase structural genes (nifHDK2) from Methanosarcina barkeri 227 was completed in this study by cloning and sequencing a 2.7-kb BamHI fragment containing the 3' end of nifK2 and 1,390 bp of the nifE2-homologous genes. Open reading frame nifK2 is 1,371 bp long including the stop codon TAA and encodes a polypeptide of 456 amino acids. Phylogenetic analysis of the deduced amino acid sequences of the nifK2 and nifE2 gene products from M. barkeri showed that both genes cluster most closely with the corresponding nif-1 gene products from Clostridium pasteurianum, consistent with our previous analyses of nifH2 and nifD2. The nifE gene product is known to be homologous to that of nifD, and our analysis shows that the branching pattern for the nifE proteins resembles that for the nifD product (with the exception of vnfE from Azotobacter vinelandii), suggesting that a gene duplication occurred before the divergence of nitrogenases. Primer extension showed that nifH2 had a single transcription start site located 34 nucleotides upstream of the ATG translation start site for nifH2, and a sequence resembling the archaeal consensus promoter sequence [TTTA(A/T)ATA] was found 32 nucleotides upstream from that transcription start site. A tract of four T's, previously identified as a transcription termination site in archaea, was found immediately downstream of the nifK2 gene, and a potential promoter was located upstream of the nifE2 gene. Hybridization with nifH2 and nifDK2 probes with M. barkeri RNA revealed a 4.6-kb transcript from N2-grown cells, large enough to harbor nifHDK genes and their internal open reading frames, while no transcript was detected from NH4(+)-grown cells. These results support a model in which the nitrogenase structural genes in M. barkeri are cotranscribed in a single NH4(+)-repressed operon.
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Affiliation(s)
- Y T Chien
- Section of Microbiology, Cornell University, Ithaca, New York 14853, USA
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van den Bergh ER, van der Kooij TA, Dijkhuizen L, Meijer WG. Fructosebisphosphatase isoenzymes of the chemoautotroph Xanthobacter flavus. J Bacteriol 1995; 177:5860-4. [PMID: 7592335 PMCID: PMC177410 DOI: 10.1128/jb.177.20.5860-5864.1995] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Xanthobacter flavus employs two fructosebisphosphatase (FBPase)-sedoheptulosebisphosphatase (SBPase) enzymes. One of these is constitutively expressed and has a high FBPase-to-SBPase ratio. The alternative enzyme, which is encoded by cbbF, is induced during autotrophic growth. The cbbF gene was expressed in Escherichia coli, and the FBPase was purified to homogeneity. The purified enzyme has a specific FBPase activity of 114 mumol/min/mg of protein, a Michaelis constant for fructosebisphosphate of 3 microM, and a low FBPase-to-SBPase ratio. CbbF was activated by ATP and inhibited by Ca2+.
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Affiliation(s)
- E R van den Bergh
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Haren, The Netherlands
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Isolation and Characterization of Novel Alkaliphiles from Bauxite-Processing Waste and Description of Bacillus vedderi sp. nov., a New Obligate Alkaliphile. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80392-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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