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Nasershariat M, Pishvaie MR, Boozarjomehry RB, Waldherr S. A dynamic model of growth phase of bio-conversion of methane to polyhydroxybutyrate using dynamic flux balance analysis. Bioprocess Biosyst Eng 2024; 47:463-474. [PMID: 38492006 DOI: 10.1007/s00449-024-02966-w] [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] [Received: 10/08/2023] [Accepted: 01/06/2024] [Indexed: 03/18/2024]
Abstract
Biological conversion of waste methane to biodegradable plastics is a way of reducing their production cost. This study addresses the computational modeling of the growth phase reactor of the process of polyhydroxybutyrate production. The model was used for investigating the effect of gas recycling and inlet gas retention time on the reactor performance. The model was run by the use of a genome-scale metabolic network of Methylocystis hirsuta in a dynamic flux balance analysis framework. The reactor has been modeled for two separate feeding scenarios: a pure methane feed and a biogas feed. The mass transfer coefficient parameter was predicted as a function of superficial gas velocities by the regression of data from published experiments. The results show an increase of removal efficiency by 38% and biomass concentration by 2.8 g/L with the increase of gas recycle ratio from 0 to 30 at the empty bed residence time of 60 min .
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Affiliation(s)
- Mohadeseh Nasershariat
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran
| | - Mahmoud Reza Pishvaie
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Tehran, Iran.
| | | | - Steffen Waldherr
- Faculty of Life Sciences, Division of Molecular Systems Biology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
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2
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Zhu X, Deng Y, Liu Y. Methylocystis dominates methane oxidation in glacier foreland soil at elevated temperature. FEMS Microbiol Lett 2024; 371:fnae011. [PMID: 38366911 DOI: 10.1093/femsle/fnae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/01/2023] [Accepted: 02/15/2024] [Indexed: 02/19/2024] Open
Abstract
Methane-oxidizing bacteria (methanotrophs) play an important role in mitigating methane emissions in various ecological environments, including cold regions. However, the response of methanotrophs in these cold environments to extreme temperatures above the in-situ temperature has not been thoroughly explored. Therefore, this study collected soil samples from Longxiazailongba (LXZ) and Qiangyong (QY) glacier forelands and incubated them with 13CH4 at 35°C under different soil water conditions. The active methanotroph populations were identified using DNA stable isotope probing (DNA-SIP) and high throughput sequencing techniques. The results showed that the methane oxidation potential in LXZ and QY glacier foreland soils was significantly enhanced at an unusually high temperature of 35°C during microcosm incubations, where abundant substrate (methane and oxygen) was provided. Moreover, the influence of soil water conditions on this potential was observed. Interestingly, Methylocystis, a type II and mesophilic methanotroph, was detected in the unincubated in-situ soil samples and became the active and dominant methanotroph in methane oxidation at 35°C. This suggests that Methylocystis can survive at low temperatures for a prolonged period and thrive under suitable growth conditions. Furthermore, the presence of mesophilic methanotrophs in cold habitats could have potential implications for reducing greenhouse gas emissions in warming glacial environments.
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Affiliation(s)
- Xinshu Zhu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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Garner CT, Sankaranarayanan K, Abin CA, Garner RM, Cai H, Lawson PA, Krumholz LR. Methylocystis suflitae sp. nov., a novel type II methanotrophic bacterium isolated from landfill cover soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 38259170 DOI: 10.1099/ijsem.0.006239] [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: 01/24/2024] Open
Abstract
A bacterial strain, designated NLS-7T, was isolated through enrichment of landfill cover soil in methane-oxidizing conditions. Strain NLS-7T is a Gram-stain negative, non-motile rod, approximately 0.8 µm wide by 1.3 µm long. Phylogenetic analysis based on 16S rRNA gene sequencing places it within the genus Methylocystis, with its closest relatives being M. hirsuta, M. silviterrae and M. rosea, with 99.9, 99.7 and 99.6 % sequence similarity respectively. However, average nucleotide identity and average amino acid identity values below the 95 % threshold compared to all the close relatives and digital DNA-DNA hybridization values between 20.9 and 54.1 % demonstrate that strain NLS-7T represents a novel species. Genome sequencing generated 4.31 million reads and genome assembly resulted in the generation of 244 contigs with a total assembly length of 3 820 957 bp (N50, 37 735 bp; L50, 34). Genome completeness is 99.5 % with 3.98 % contamination. It is capable of growth on methane and methanol. It grows optimally at 30 °C between pH 6.5 and 7.0. Strain NLS-7T is capable of atmospheric dinitrogen fixation and can use ammonium (as NH4Cl), l-aspartate, l-arginine, yeast extract, nitrate, l-leucine, l-proline, l-methionine, l-lysine and l-alanine as nitrogen sources. The major fatty acids are C18:1 ω8c and C18:1 ω7c. Based upon this polyphasic taxonomic study, strain NLS-7T represents a novel species of the genus Methylocystis, for which the name Methylocystis suflitae sp. nov. is proposed. The type strain is NLS-7T (=ATCC TSD-256T=DSM 112294T). The 16S rRNA gene and genome sequences of strain NLS-7T have been deposited in GenBank under accession numbers ON715489 and GCA_024448135.1, respectively.
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Affiliation(s)
- Christopher T Garner
- School of Biological Sciences, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research, Stephenson Research and Technology Center, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK, 73019, USA
| | - Christopher A Abin
- School of Biological Sciences, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, Stephenson Research and Technology Center, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK, 73019, USA
| | - Rosa M Garner
- School of Biological Sciences, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
| | - Haiyuan Cai
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China. 73 East Beijing Road, Nanjing 210008, PR China
| | - Paul A Lawson
- School of Biological Sciences, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
| | - Lee R Krumholz
- School of Biological Sciences, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
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4
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Kaise H, Sawadogo JB, Alam MS, Ueno C, Dianou D, Shinjo R, Asakawa S. Methylocystis iwaonis sp. nov., a type II methane-oxidizing bacterium from surface soil of a rice paddy field in Japan, and emended description of the genus Methylocystis ( ex Whittenbury et al. 1970) Bowman et al. 1993. Int J Syst Evol Microbiol 2023; 73. [PMID: 37279153 DOI: 10.1099/ijsem.0.005925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Abstract
A novel methane-oxidizing bacterial strain SS37A-ReT was isolated from surface soil of a rice paddy field in Japan. Cells were Gram-stain-negative, motile rods with single polar flagellum and type II intracytoplasmic membrane arrangement. The strain grew on methane or methanol as the sole carbon and energy source. It grew at 15–37 °C (optimum 25–30 °C), pH 6.0–9.0 (optimum 7.0–8.0) and with 0–0.1 % (w/w) NaCl (no growth at 0.5 % or above). Cells formed cysts, but not exospores. The results of sequence analysis of the 16S rRNA gene indicated that SS37A-ReT represented a member of the family
Methylocystaceae
, with the highest similarity (98.9 %) to Methylocystis parva corrig. OBBPT. Phylogenetic analysis of pmoA and mxaF genes and core genes in the genome indicated that the strain was closely related to the members of the genus
Methylocystis
, while the analysis of the mmoX gene indicated the close relationships with the genus
Methylosinus
. The values of genome relatedness between SS37A-ReT and species of the genera
Methylocystis
and
Methylosinus
were 78.6–82.5% and 21.7–24.9 % estimated by the average nucleotide identity and digital DNA–DNA hybridisation, respectively, showing the highest values with
Methylocystis echinoides
LMG 27198T. The DNA G+C content was 63.2 mol% (genome). The major quinone and fatty acids were Q-8 and, C18 : 1 (C18 : 1ω8t and C18 : 1ω8c) and C18 : 2, respectively. On the basis of the phenotypic and phylogenetic features, the strain represents a novel species of the genus
Methylocystis
, for which the name Methylocystis iwaonis sp. nov. is proposed. The type strain is SS37A-ReT (=JCM 34278T =NBRC 114996T=KCTC 82710T).
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Affiliation(s)
- Hirotaka Kaise
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Joseph Benewindé Sawadogo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Université Nazi BONI, Bobo-Dioulasso, 01 BP 1091 Bobo-Dioulasso 01, Burkina Faso
| | - Mohammad Saiful Alam
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur 1706, Bangladesh
| | - Chihoko Ueno
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Dayéri Dianou
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Centre National de la Recherche Scientifique et Technologique, Ouagadougou, 03 BP 7047 Ouagadougou 03, Burkina Faso
| | - Rina Shinjo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Susumu Asakawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
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Zhuang J, Zhang R, Zeng Y, Dai T, Ye Z, Gao Q, Yang Y, Guo X, Li G, Zhou J. Petroleum pollution changes microbial diversity and network complexity of soil profile in an oil refinery. Front Microbiol 2023; 14:1193189. [PMID: 37287448 PMCID: PMC10242060 DOI: 10.3389/fmicb.2023.1193189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Introduction Petroleum pollution resulting from spills and leakages in oil refinery areas has been a significant environmental concern for decades. Despite this, the effects of petroleum pollutants on soil microbial communities and their potential for pollutant biodegradation still required further investigation. Methods In this study, we collected 75 soil samples from 0 to 5 m depths of 15 soil profiles in an abandoned refinery to analyze the effect of petroleum pollution on soil microbial diversity, community structure, and network co-occurrence patterns. Results Our results suggested soil microbial a-diversity decreased under high C10-C40 levels, coupled with significant changes in the community structure of soil profiles. However, soil microbial network complexity increased with petroleum pollution levels, suggesting more complex microbial potential interactions. A module specific for methane and methyl oxidation was also found under high C10-C40 levels of the soil profile, indicating stronger methanotrophic and methylotrophic metabolic activities at the heavily polluted soil profile. Discussion The increased network complexity observed may be due to more metabolic pathways and processes, as well as increased microbial interactions during these processes. These findings highlight the importance of considering both microbial diversity and network complexity in assessing the effects of petroleum pollution on soil ecosystems.
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Affiliation(s)
- Jugui Zhuang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Ruihuan Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yufei Zeng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Tianjiao Dai
- School of Water Resources and Environment, China University of Geosciences, Beijing, China
| | - Zhencheng Ye
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guanghe Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
- Earth and Environmental Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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6
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Naizabekov S, Hyun SW, Na JG, Yoon S, Lee OK, Lee EY. Comparative genomic analysis of Methylocystis sp. MJC1 as a platform strain for polyhydroxybutyrate biosynthesis. PLoS One 2023; 18:e0284846. [PMID: 37163531 PMCID: PMC10171618 DOI: 10.1371/journal.pone.0284846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/06/2023] [Indexed: 05/12/2023] Open
Abstract
Biodegradable polyhydroxybutyrate (PHB) can be produced from methane by some type II methanotroph such as the genus Methylocystis. This study presents the comparative genomic analysis of a newly isolated methanotroph, Methylocystis sp. MJC1 as a biodegradable PHB-producing platform strain. Methylocystis sp. MJC1 accumulates up to 44.5% of PHB based on dry cell weight under nitrogen-limiting conditions. To facilitate its development as a PHB-producing platform strain, the complete genome sequence of Methylocystis sp. MJC1 was assembled, functionally annotated, and compared with genomes of other Methylocystis species. Phylogenetic analysis has shown that Methylocystis parvus to be the closest species to Methylocystis sp. MJC1. Genome functional annotation revealed that Methylocystis sp. MJC1 contains all major type II methanotroph biochemical pathways such as the serine cycle, EMC pathway, and Krebs cycle. Interestingly, Methylocystis sp. MJC1 has both particulate and soluble methane monooxygenases, which are not commonly found among Methylocystis species. In addition, this species also possesses most of the RuMP pathway reactions, a characteristic of type I methanotrophs, and all PHB biosynthetic genes. These comparative analysis would open the possibility of future practical applications such as the development of organism-specific genome-scale models and application of metabolic engineering strategies to Methylocystis sp. MJC1.
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Affiliation(s)
- Sanzhar Naizabekov
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Seung Woon Hyun
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Republic of Korea
| | - Sukhwan Yoon
- Department of Civil & Environmental Engineering, Korea Advanced Institute of Science & Technology, Daejeon, Republic of Korea
| | - Ok Kyung Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
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7
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Methylocystis sp. Strain SC2 Acclimatizes to Increasing NH 4+ Levels by a Precise Rebalancing of Enzymes and Osmolyte Composition. mSystems 2022; 7:e0040322. [PMID: 36154142 PMCID: PMC9600857 DOI: 10.1128/msystems.00403-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A high NH4+ load is known to inhibit bacterial methane oxidation. This is due to a competition between CH4 and NH3 for the active site of particulate methane monooxygenase (pMMO), which converts CH4 to CH3OH. Here, we combined global proteomics with amino acid profiling and nitrogen oxides measurements to elucidate the cellular acclimatization response of Methylocystis sp. strain SC2 to high NH4+ levels. Relative to 1 mM NH4+, a high (50 mM and 75 mM) NH4+ load under CH4-replete conditions significantly increased the lag phase duration required for proteome adjustment. The number of differentially regulated proteins was highly significantly correlated with an increasing NH4+ load. The cellular responses to increasing ionic and osmotic stress involved a significant upregulation of stress-responsive proteins, the K+ "salt-in" strategy, the synthesis of compatible solutes (glutamate and proline), and the induction of the glutathione metabolism pathway. A significant increase in the apparent Km value for CH4 oxidation during the growth phase was indicative of increased pMMO-based oxidation of NH3 to toxic hydroxylamine. The detoxifying activity of hydroxlyamine oxidoreductase (HAO) led to a significant accumulation of NO2- and, upon decreasing O2 tension, N2O. Nitric oxide reductase and hybrid cluster proteins (Hcps) were the candidate enzymes for the production of N2O. In summary, strain SC2 has the capacity to precisely rebalance enzymes and osmolyte composition in response to increasing NH4+ exposure, but the need to simultaneously combat both ionic-osmotic stress and the toxic effects of hydroxylamine may be the reason why its acclimatization capacity is limited to 75 mM NH4+. IMPORTANCE In addition to reducing CH4 emissions from wetlands and landfills, the activity of alphaproteobacterial methane oxidizers of the genus Methylocystis contributes to the sink capacity of forest and grassland soils for atmospheric methane. The methane-oxidizing activity of Methylocystis spp. is, however, sensitive to high NH4+ concentrations. This is due to the competition of CH4 and NH3 for the active site of particulate methane monooxygenase, thereby resulting in the production of toxic hydroxylamine with an increasing NH4+ load. An understanding of the physiological and molecular response mechanisms of Methylocystis spp. is therefore of great importance. Here, we combined global proteomics with amino acid profiling and NOx measurements to disentangle the cellular mechanisms underlying the acclimatization of Methylocystis sp. strain SC2 to an increasing NH4+ load.
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8
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Tikhonova EN, Grouzdev DS, Avtukh AN, Kravchenko IK. Methylocystis silviterrae sp.nov., a high-affinity methanotrophic bacterium isolated from the boreal forest soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34913862 DOI: 10.1099/ijsem.0.005166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel species is proposed for a high-affinity methanotrophic representative of the genus Methylocystis. Strain FST was isolated from a weakly acidic (pH 5.3) mixed forest soil of the southern Moscow area. Cells of FST are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. Only methane and methanol are used as carbon sources. FST grew at a temperature range of 4-37 °C (optimum 25-30 °C) and a pH range of 4.5 to 7.5 (optimum pH 6.0-6.5). The major fatty acids were C18 : 1ω8c, C18 : 1ω7c and C18 : 0; the major quinone as Q-8. FST displays 16S rRNA gene sequences similarity to other taxonomically recognized members of the genus Methylocystis, with Methylocystis hirsuta CSC1T (99.6 % similarity) and Methylocystis rosea SV97T (99.3 % similarity) as its closest relatives. The genome comprises 3.85 Mbp and has a DNA G+C content of 62.6 mol%. Genomic analyses and DNA-DNA relatedness with genome-sequenced members of the genus Methylocystis demonstrated that FST could be separated from its closest relatives. FST possesses two particulate methane monooxygenases (pMMO): low-affinity pMMO1 and high-affinity pMMO2. In laboratory experiments, it was demonstrated that FST might oxidize methane at atmospheric concentration. The genome contained various genes for nitrogen fixation, polyhydroxybutyrate synthesis, antibiotic resistance and detoxification of arsenic, cyanide and mercury. On the basis of genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Methylocystis silviterrae sp. nov. The type strain is FST (=KCTC 82935T=VKM B-3535T).
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Affiliation(s)
- Ekaterina N Tikhonova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Denis S Grouzdev
- SciBear OU, Tartu mnt 67/1-13b, Kesklinna linnaosa, Tallin 10115, Estonia
| | - Alexander N Avtukh
- All-Russian Collection of Microorganisms - VKM, GK Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center' Puschino Scientific Center for Biological Research of the Russian Academy of Sciences, Estonia
| | - Irina K Kravchenko
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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9
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Nguyen DTN, Lee OK, Nguyen TT, Lee EY. Type II methanotrophs: A promising microbial cell-factory platform for bioconversion of methane to chemicals. Biotechnol Adv 2021; 47:107700. [PMID: 33548453 DOI: 10.1016/j.biotechadv.2021.107700] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/04/2020] [Accepted: 01/20/2021] [Indexed: 10/22/2022]
Abstract
Methane, the predominant element in natural gas and biogas, represents a promising alternative to carbon feedstocks in the biotechnological industry due to its low cost and high abundance. The bioconversion of methane to value-added products can enhance the value of gas and mitigate greenhouse gas emissions. Methanotrophs, methane-utilizing bacteria, can make a significant contribution to the production of various valuable biofuels and chemicals from methane. Type II methanotrophs in comparison with Type I methanotrophs have distinct advantages, including high acetyl-CoA flux and the co-incorporation of two important greenhouse gases (methane and CO2), making it a potential microbial cell-factory platform for methane-derived biomanufacturing. Herein, we review the most recent advances in Type II methanotrophs related to multi-omics studies and metabolic engineering. Representative examples and prospects of metabolic engineering strategies for the production of suitable products are also discussed.
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Affiliation(s)
- Diep Thi Ngoc Nguyen
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea
| | - Ok Kyung Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea
| | - Thu Thi Nguyen
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea.
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10
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Jung GY, Rhee SK, Han YS, Kim SJ. Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland. Microorganisms 2020; 8:microorganisms8111719. [PMID: 33147874 PMCID: PMC7716213 DOI: 10.3390/microorganisms8111719] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 01/07/2023] Open
Abstract
Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate synthesis, and heavy metal resistance. This metabolic versatility of strain B8 might enable its survival in wetland environments.
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Affiliation(s)
- Gi-Yong Jung
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Korea;
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea;
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea;
| | - Young-Soo Han
- Department of Environmental Engineering, Chungnam National University, Daejeon 34134, Korea;
| | - So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Korea;
- Correspondence: ; Tel.: +82-42-868-3311; Fax: +82-42-868-3414
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11
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Farhan Ul Haque M, Xu HJ, Murrell JC, Crombie A. Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review. MICROBIOLOGY (READING, ENGLAND) 2020; 166:894-908. [PMID: 33085587 PMCID: PMC7660913 DOI: 10.1099/mic.0.000977] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/20/2020] [Indexed: 12/18/2022]
Abstract
Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.
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Affiliation(s)
| | - Hui-Juan Xu
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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12
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Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus. Microorganisms 2020; 8:microorganisms8050768. [PMID: 32443820 PMCID: PMC7285482 DOI: 10.3390/microorganisms8050768] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 01/21/2023] Open
Abstract
The Methylocystis and Methylosinus are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing methane fluxes from soils and wetlands. The original separation of these methanotrophs in two distinct genera was based mainly on their differences in cell morphology. Further comparative studies that explored various single-gene-based phylogenies suggested the monophyletic nature of each of these genera. Current availability of genome sequences from members of the Methylocystis/Methylosinus clade opens the possibility for in-depth comparison of the genomic potentials of these methanotrophs. Here, we report the finished genome sequence of Methylocystis heyeri H2T and compare it to 23 currently available genomes of Methylocystis and Methylosinus species. The phylogenomic analysis confirmed that members of these genera form two separate clades. The Methylocystis/Methylosinus pan-genome core comprised 1173 genes, with the accessory genome containing 4941 and 11,192 genes in the shell and the cloud, respectively. Major differences between the genome-encoded environmental traits of these methanotrophs include a variety of enzymes for methane oxidation and dinitrogen fixation as well as genomic determinants for cell motility and photosynthesis.
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13
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Rodríguez Y, Firmino PIM, Arnáiz E, Lebrero R, Muñoz R. Elucidating the influence of environmental factors on biogas-based polyhydroxybutyrate production by Methylocystis hirsuta CSC1. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 706:135136. [PMID: 31862586 DOI: 10.1016/j.scitotenv.2019.135136] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 06/10/2023]
Abstract
The valorization of biogas as a feedstock for the generation of added-value bioproducts will play a key role on the sustainability of anaerobic digestion. The present work assessed the influence of key environmental parameters (O2:CH4 ratio, temperature and nitrogen source) on the growth and polyhydroxybutyrate (PHB) synthesis under nitrogen limiting conditions of the type II methanotroph Methylocystis hirsuta CSC1 using biogas as a feedstock. The O2:CH4 ratios tested (1:1, 1.5:1 and 2:1) did not affect significantly M. hirsuta CSC1 growth yields (~5 g TSS mol-1 CH4), although lower CH4 removal rates were reached under O2-limiting conditions (ratio 1:1). The highest PHB content (45 wt%) was achieved at a ratio 2:1 and was threefold higher than those obtained at lower ratios (~15 wt%). The increase in temperature from 15 to 25 °C resulted in increases in the growth yield (from 5 to 6 g TSS mol-1 CH4) and PHB content (from 32 to 40 wt%). Conversely, the lowest PHB content (30 wt%) was reached at 37 °C, together with a negligible growth under nutrient sufficient conditions. The nitrogen source also played a key role on both M. hirsuta CSC1 growth and PHB synthesis. Thus, ammonium resulted in the highest growth yield (7 g TSS mol-1 CH4), although the maximum PHB content was achieved when biomass was previously grown in nitrate as the nitrogen source (41 wt%). Nitrite exerted an inhibitory effect on M. hirsuta CSC1 growth.
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Affiliation(s)
- Yadira Rodríguez
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain
| | - Paulo Igor Milen Firmino
- Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain; Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Esther Arnáiz
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain
| | - Raquel Lebrero
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina s/n, 47011 Valladolid, Spain; Institute of Sustainable Processes, Dr. Mergelina s/n, 47011 Valladolid, Spain.
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14
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Xing W, Wang Y, Hao T, He Z, Jia F, Yao H. pH control and microbial community analysis with HCl or CO 2 addition in H 2-based autotrophic denitrification. WATER RESEARCH 2020; 168:115200. [PMID: 31655440 DOI: 10.1016/j.watres.2019.115200] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
H2-based autotrophic denitrification is promising to remove nitrate from water or wastewater lacking organic carbon sources, and pH is one of its most important process parameters. HCl and CO2 addition are known as adequate pH control methods for practical purposes. However, because of H2, added CO2 may participate in microbial metabolisms and affect denitrification mechanisms. Here, a combined micro-electrolysis and autotrophic denitrification (CEAD) reactor, in which H2 is generated based on galvanic-cell reactions between zero-valent iron and carbon, was optimized and continuously operated for 233 days by adding HCl or CO2 to control pH in the range of 7.2-8.2. Microbial communities were compared between the two pH-control methods through high-throughput sequencing of 16S rRNA, nirS, and nirK genes. Under a low COD/N ratio of 0.5 in the influent (with ∼36 mgNO3--N/L), when adding HCl, the total nitrogen (TN) removal efficiency reached 91.4% ± 0.9% with a 28-h hydraulic retention time (HRT). When adding CO2, the TN removal efficiency was improved to 96.5% ± 1.7% with 24-h HRT. Significant differences of 16S rRNA and nirS genes between the two pH-control stages indicated the variation of microbial communities and nirS-type denitrifiers. With HCl addition, Thiobacillus, unclassified Comamonadaceae, Arenimonas, Limnobacter, and Thermomonas, which were reported previously as likely autotrophic or heterotrophic denitrifiers, were most dominant in the biofilms. With CO2 addition, the biofilms became dominated by Anaerolineaceae and Methylocystaceae (related to organic carbon metabolism), Denitratisoma (likely heterotrophic denitrifier), and uncultured bacteria TK10 and AKYG587. The results suggest that the added CO2 not only contributed to pH control but also participated in microbial metabolisms. This study provides useful insights into microbial mechanisms and further optimization of H2-based autotrophic denitrification in water and wastewater treatment.
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Affiliation(s)
- Wei Xing
- Department of Civil and Environmental Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China.
| | - Yan Wang
- Department of Civil and Environmental Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Tianyu Hao
- Department of Civil and Environmental Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Zhenglan He
- Department of Civil and Environmental Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Fangxu Jia
- Department of Civil and Environmental Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Hong Yao
- Department of Civil and Environmental Engineering, Beijing Key Laboratory of Aqueous Typical Pollutants Control and Water Quality Safeguard, School of Civil Engineering, Beijing Jiaotong University, Beijing, 100044, China.
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15
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Bordel S, Rodríguez E, Muñoz R. Genome sequence of Methylocystis hirsuta CSC1, a polyhydroxyalkanoate producing methanotroph. Microbiologyopen 2018; 8:e00771. [PMID: 30548837 PMCID: PMC6562138 DOI: 10.1002/mbo3.771] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 01/22/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs) are biodegradable plastics that can be produced by some methanotrophic organisms such as those of the genus Methylocystis. This allows the conversion of a detrimental greenhouse gas into an environmentally friendly high added‐value bioproduct. This study presents the genome sequence of Methylocystis hirsuta CSC1 (a high yield PHB producer). The genome comprises 4,213,043 bp in 4 contigs, with the largest contig being 3,776,027 bp long. Two of the other contigs are likely to correspond to large size plasmids. A total of 4,664 coding sequences were annotated, revealing a PHA production cluster, two distinct particulate methane monooxygenases with active catalytic sites, as well as a nitrogen fixation operon and a partial denitrification pathway.
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Affiliation(s)
- Sergio Bordel
- Departamento de Ingeniería Química y Tecnología del Medio Ambiente, Escuela de Ingenierías IndustrialesUniversidad de ValladolidValladolidSpain
- Institute of Sustainable ProcessesUniversidad de ValladolidValladolidSpain
| | - Elisa Rodríguez
- Departamento de Ingeniería Química y Tecnología del Medio Ambiente, Escuela de Ingenierías IndustrialesUniversidad de ValladolidValladolidSpain
- Institute of Sustainable ProcessesUniversidad de ValladolidValladolidSpain
| | - Raúl Muñoz
- Departamento de Ingeniería Química y Tecnología del Medio Ambiente, Escuela de Ingenierías IndustrialesUniversidad de ValladolidValladolidSpain
- Institute of Sustainable ProcessesUniversidad de ValladolidValladolidSpain
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16
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Ghaz-Jahanian MA, Khoshfetrat AB, Hosseinian Rostami M, Haghighi Parapari M. An innovative bioprocess for methane conversion to methanol using an efficient methane transfer chamber coupled with an airlift bioreactor. Chem Eng Res Des 2018. [DOI: 10.1016/j.cherd.2018.03.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Drinking water microbiome assembly induced by water stagnation. ISME JOURNAL 2018; 12:1520-1531. [PMID: 29588495 PMCID: PMC5955952 DOI: 10.1038/s41396-018-0101-5] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 02/09/2018] [Accepted: 02/20/2018] [Indexed: 01/05/2023]
Abstract
What happens to tap water when you are away from home? Day-to-day water stagnation in building plumbing can potentially result in water quality deterioration (e.g., lead release or pathogen proliferation), which is a major public health concern. However, little is known about the microbial ecosystem processes in plumbing systems, hindering the development of biological monitoring strategies. Here, we track tap water microbiome assembly in situ, showing that bacterial community composition changes rapidly from the city supply following ~6-day stagnation, along with an increase in cell count from 103 cells/mL to upwards of 7.8 × 105 cells/mL. Remarkably, bacterial community assembly was highly reproducible in this built environment system (median Spearman correlation between temporal replicates = 0.78). Using an island biogeography model, we show that neutral processes arising from the microbial communities in the city water supply (i.e., migration and demographic stochasticity) explained the island community composition in proximal pipes (Goodness-of-fit = 0.48), yet declined as water approached the faucet (Goodness-of-fit = 0.21). We developed a size-effect model to simulate this process, which indicated that pipe diameter drove these changes by mediating the kinetics of hypochlorite decay and cell detachment, affecting selection, migration, and demographic stochasticity. Our study challenges current water quality monitoring practice worldwide which ignore biological growth in plumbing, and suggests the island biogeography model as a useful framework to evaluate building water system quality.
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18
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May T, Polag D, Keppler F, Greule M, Müller L, König H. Methane oxidation in industrial biogas plants—Insights in a novel methanotrophic environment evidenced by pmoA gene analyses and stable isotope labelling studies. J Biotechnol 2018; 270:77-84. [DOI: 10.1016/j.jbiotec.2018.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 01/24/2018] [Accepted: 01/31/2018] [Indexed: 02/05/2023]
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19
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Schnyder E, Bodelier PLE, Hartmann M, Henneberger R, Niklaus PA. Positive diversity-functioning relationships in model communities of methanotrophic bacteria. Ecology 2018; 99:714-723. [PMID: 29323701 DOI: 10.1002/ecy.2138] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/01/2017] [Accepted: 12/20/2017] [Indexed: 11/11/2022]
Abstract
Biodiversity enhances ecosystem functions such as biomass production and nutrient cycling. Although the majority of the terrestrial biodiversity is hidden in soils, very little is known about the importance of the diversity of microbial communities for soil functioning. Here, we tested effects of biodiversity on the functioning of methanotrophs, a specialized group of soil bacteria that plays a key role in mediating greenhouse gas emissions from soils. Using pure strains of methanotrophic bacteria, we assembled artificial communities of different diversity levels, with which we inoculated sterile soil microcosms. To assess the functioning of these communities, we measured methane oxidation by gas chromatography throughout the experiment and determined changes in community composition and community size at several time points by quantitative PCR and sequencing. We demonstrate that microbial diversity had a positive overyielding effect on methane oxidation, in particular at the beginning of the experiment. This higher assimilation of CH4 at high diversity translated into increased growth and significantly larger communities towards the end of the study. The overyielding of mixtures with respect to CH4 consumption and community size were positively correlated. The temporal CH4 consumption profiles of strain monocultures differed, raising the possibility that temporal complementarity of component strains drove the observed community-level strain richness effects; however, the community niche metric we derived from the temporal activity profiles did not explain the observed strain richness effect. The strain richness effect also was unrelated to both the phylogenetic and functional trait diversity of mixed communities. Overall, our results suggest that positive biodiversity-ecosystem-function relationships show similar patterns across different scales and may be widespread in nature. Additionally, biodiversity is probably also important in natural methanotrophic communities for the ecosystem function methane oxidation. Therefore, maintaining soil conditions that support a high diversity of methanotrophs may help to reduce the emission of the greenhouse gas methane.
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Affiliation(s)
- Elvira Schnyder
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Martin Hartmann
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903, Birmensdorf, Switzerland
| | - Ruth Henneberger
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Universitätstrasse 16, CH-8092, Zurich, Switzerland
| | - Pascal A Niklaus
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.,University of Zurich Research Priority Program Global Change and Biodiversity, University of Zürich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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20
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Tavormina PL, Kellermann MY, Antony CP, Tocheva EI, Dalleska NF, Jensen AJ, Valentine DL, Hinrichs K, Jensen GJ, Dubilier N, Orphan VJ. Starvation and recovery in the deep‐sea methanotroph
M
ethyloprofundus sedimenti. Mol Microbiol 2016; 103:242-252. [DOI: 10.1111/mmi.13553] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Patricia L. Tavormina
- Division of Geological and Planetary SciencesCalifornia Institute of Technology1200 E. California BlvdPasadena CA91125 USA
| | - Matthias Y. Kellermann
- Department of Earth Science and Marine Science InstituteUniversity of CaliforniaSanta Barbara CA93106 USA
| | | | - Elitza I. Tocheva
- Department of Stomatology and Department of Biochemistry and Molecular MedicineUniversité de MontréalP. O. Box 6128 Station Centre‐VilleMontreal QCH3C 3J7 Canada
- Division of Biology and Biological Engineering andCalifornia Institute of Technology1200 E. California BlvdPasadena CA91125 USA
| | - Nathan F. Dalleska
- Environmental Analysis CenterCalifornia Institute of Technology1200 E. California BlvdPasadena CA91125 USA
| | - Ashley J. Jensen
- Division of Biology and Biological Engineering andCalifornia Institute of Technology1200 E. California BlvdPasadena CA91125 USA
| | - David L. Valentine
- Department of Earth Science and Marine Science InstituteUniversity of CaliforniaSanta Barbara CA93106 USA
| | - Kai‐Uwe Hinrichs
- MARUM Center for Marine Environmental SciencesUniversity of Bremen, Leobener StrBremen28359 Germany
| | - Grant J. Jensen
- Division of Biology and Biological Engineering and Howard Hughes Medical InstituteCalifornia Institute of Technology1200 E. California BlvdPasadena CA91125 USA
| | - Nicole Dubilier
- Max Planck Institute for Marine MicrobiologyCelsiusstraße 1Bremen28359 Germany
| | - Victoria J. Orphan
- Division of Geological and Planetary SciencesCalifornia Institute of Technology1200 E. California BlvdPasadena CA91125 USA
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21
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Knief C. Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker. Front Microbiol 2015; 6:1346. [PMID: 26696968 PMCID: PMC4678205 DOI: 10.3389/fmicb.2015.01346] [Citation(s) in RCA: 257] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.
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Affiliation(s)
- Claudia Knief
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of BonnBonn, Germany
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22
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Isolation of methanotrophic bacteria from termite gut. Microbiol Res 2015; 179:29-37. [DOI: 10.1016/j.micres.2015.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 05/08/2015] [Accepted: 06/06/2015] [Indexed: 11/20/2022]
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23
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Methanotrophic community abundance and composition in plateau soils with different plant species and plantation ways. Appl Microbiol Biotechnol 2015; 99:9237-44. [PMID: 26142389 DOI: 10.1007/s00253-015-6782-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 06/11/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
Abstract
Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating the methane emission in soil ecosystems to the atmosphere. However, the impact of plant species and plantation ways on the distribution of MOB remains unclear. The present study investigated MOB abundance and structure in plateau soils with different plant species and plantation ways (natural and managed). Soils were collected from unmanaged wild grassland and naturally forested sites, and managed farmland and afforested sites. A large variation in MOB abundance and structure was found in these studied soils. In addition, both type I MOB (Methylocaldum) and type II MOB (Methylocystis) were detected in these soils, while type II MOB usually outnumbered type I MOB. The distribution of soil MOB community was found to be collectively regulated by plantation way, plant species, the altitude of sampling site, and soil properties.
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24
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Chidambarampadmavathy K, Obulisamy P. K, Heimann K. Role of copper and iron in methane oxidation and bacterial biopolymer accumulation. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400127] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Karthigeyan Chidambarampadmavathy
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
| | - Karthikeyan Obulisamy P.
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
| | - Kirsten Heimann
- Collegeof Marine and Environmental ScienceJames Cook University Townsville Queensland Australia
- Centre for Sustainable Fisheries and AquacultureJames Cook University Townsville Queensland Australia
- Centre for Biodiscovery and Molecular Development of TherapeuticsJames Cook University Townsville Queensland Australia
- Comparative Genomics CentreJames Cook University Townsville Queensland Australia
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25
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Németh A, Szirányi B, Krett G, Janurik E, Kosáros T, Pekár F, Márialigeti K, Borsodi A. Prokaryotic phylogenetic diversity of Hungarian deep subsurface geothermal well waters. Acta Microbiol Immunol Hung 2014; 61:363-77. [PMID: 25261947 DOI: 10.1556/amicr.61.2014.3.9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Geothermal wells characterized by thermal waters warmer than 30°C can be found in more than 65% of the area of Hungary. The examined thermal wells located nearby Szarvas are used for heating industrial and agricultural facilities because of their relatively high hydrocarbon content. The aim of this study was to reveal the prokaryotic community structure of the water of SZR18, K87 and SZR21 geothermal wells using molecular cloning methods and Denaturing Gradient Gel Electrophoresis (DGGE). Water samples from the outflow pipes were collected in 2012 and 2013. The phylogenetic distribution of archaeal molecular clones was very similar in each sample, the most abundant groups belonged to the genera Methanosaeta, Methanothermobacter and Thermofilum. In contrast, the distribution of bacterial molecular clones was very diverse. Many of them showed the closest sequence similarities to uncultured clone sequences from similar thermal environments. From the water of the SZR18 well, phylotypes closely related to genera Fictibacillus and Alicyclobacillus (Firmicutes) were only revealed, while the bacterial diversity of the K87 well water was much higher. Here, the members of the phyla Thermodesulfobacteria, Proteobacteria, Nitrospira, Chlorobi, OP1 and OPB7 were also detected besides Firmicutes.
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Affiliation(s)
- Andrea Németh
- 1 Eötvös Loránd University Department of Microbiology Pázmány P. sétány 1/C H-1117 Budapest Hungary
| | - Barbara Szirányi
- 1 Eötvös Loránd University Department of Microbiology Pázmány P. sétány 1/C H-1117 Budapest Hungary
| | - Gergely Krett
- 1 Eötvös Loránd University Department of Microbiology Pázmány P. sétány 1/C H-1117 Budapest Hungary
| | - Endre Janurik
- 2 Research Institute for Fisheries, Aquaculture and Irrigation Anna-liget 8 H-5540 Szarvas Hungary
| | - Tünde Kosáros
- 2 Research Institute for Fisheries, Aquaculture and Irrigation Anna-liget 8 H-5540 Szarvas Hungary
| | - Ferenc Pekár
- 2 Research Institute for Fisheries, Aquaculture and Irrigation Anna-liget 8 H-5540 Szarvas Hungary
| | - Károly Márialigeti
- 1 Eötvös Loránd University Department of Microbiology Pázmány P. sétány 1/C H-1117 Budapest Hungary
| | - Andrea Borsodi
- 1 Eötvös Loránd University Department of Microbiology Pázmány P. sétány 1/C H-1117 Budapest Hungary
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26
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Kizilova AK, Sukhacheva MV, Pimenov NV, Yurkov AM, Kravchenko IK. Methane oxidation activity and diversity of aerobic methanotrophs in pH-neutral and semi-neutral thermal springs of the Kunashir Island, Russian Far East. Extremophiles 2013; 18:207-18. [PMID: 24343375 DOI: 10.1007/s00792-013-0603-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 11/14/2013] [Indexed: 11/26/2022]
Abstract
Aerobic methane oxidation has been mostly studied in environments with moderate to low temperatures. However, the process also occurs in terrestrial thermal springs, where little research on the subject has been done to date. The potential activity of methane oxidation and diversity of aerobic methanotrophic bacteria were studied in sediments of thermal springs with various chemical and physical properties, sampled across the Kunashir Island, the Kuriles archipelago. Activity was measured by means of the radioisotope tracer technique utilizing (14)C-labeled methane. Biodiversity assessments were based on the particulate methane monooxygenase (pmoA) gene, which is found in all known thermophilic and thermotolerant methanotrophs. We demonstrated the possibility of methane oxidation in springs with temperature exceeding 74 °C, and the most intensive methane uptake was shown in springs with temperatures about 46 °C. PmoA was detected in 19 out of 30 springs investigated and the number of pmoA gene copies varied between 10(4) and 10(6) copies per ml of sediment. Phylogenetic analysis of PmoA sequences revealed the presence of methanotrophs from both the Alpha- and Gammaproteobacteria. Our results suggest that methanotrophs inhabiting thermal springs with temperature exceeding 50 °C may represent novel thermophilic and thermotolerant species of the genera Methylocystis and Methylothermus, as well as previously undescribed Gammaproteobacteria.
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Affiliation(s)
- A K Kizilova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117312, Moscow, Russia,
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Dam B, Dam S, Blom J, Liesack W. Genome analysis coupled with physiological studies reveals a diverse nitrogen metabolism in Methylocystis sp. strain SC2. PLoS One 2013; 8:e74767. [PMID: 24130670 PMCID: PMC3794950 DOI: 10.1371/journal.pone.0074767] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 07/28/2013] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Methylocystis sp. strain SC2 can adapt to a wide range of methane concentrations. This is due to the presence of two isozymes of particulate methane monooxygenase exhibiting different methane oxidation kinetics. To gain insight into the underlying genetic information, its genome was sequenced and found to comprise a 3.77 Mb chromosome and two large plasmids. PRINCIPAL FINDINGS We report important features of the strain SC2 genome. Its sequence is compared with those of seven other methanotroph genomes, comprising members of the Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia. While the pan-genome of all eight methanotroph genomes totals 19,358 CDS, only 154 CDS are shared. The number of core genes increased with phylogenetic relatedness: 328 CDS for proteobacterial methanotrophs and 1,853 CDS for the three alphaproteobacterial Methylocystaceae members, Methylocystis sp. strain SC2 and strain Rockwell, and Methylosinus trichosporium OB3b. The comparative study was coupled with physiological experiments to verify that strain SC2 has diverse nitrogen metabolism capabilities. In correspondence to a full complement of 34 genes involved in N2 fixation, strain SC2 was found to grow with atmospheric N2 as the sole nitrogen source, preferably at low oxygen concentrations. Denitrification-mediated accumulation of 0.7 nmol (30)N2/hr/mg dry weight of cells under anoxic conditions was detected by tracer analysis. N2 production is related to the activities of plasmid-borne nitric oxide and nitrous oxide reductases. CONCLUSIONS/PERSPECTIVES Presence of a complete denitrification pathway in strain SC2, including the plasmid-encoded nosRZDFYX operon, is unique among known methanotrophs. However, the exact ecophysiological role of this pathway still needs to be elucidated. Detoxification of toxic nitrogen compounds and energy conservation under oxygen-limiting conditions are among the possible roles. Relevant features that may stimulate further research are, for example, absence of CRISPR/Cas systems in strain SC2, high number of iron acquisition systems in strain OB3b, and large number of transposases in strain Rockwell.
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Affiliation(s)
- Bomba Dam
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Somasri Dam
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
| | - Jochen Blom
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
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Kenney GE, Rosenzweig AC. Genome mining for methanobactins. BMC Biol 2013; 11:17. [PMID: 23442874 PMCID: PMC3621798 DOI: 10.1186/1741-7007-11-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/26/2013] [Indexed: 01/27/2023] Open
Abstract
Background Methanobactins (Mbns) are a family of copper-binding natural products involved in copper uptake by methanotrophic bacteria. The few Mbns that have been structurally characterized feature copper coordination by two nitrogen-containing heterocycles next to thioamide groups embedded in a peptidic backbone of varying composition. Mbns are proposed to derive from post-translational modification of ribosomally synthesized peptides, but only a few genes encoding potential precursor peptides have been identified. Moreover, the relevance of neighboring genes in these genomes has been unclear. Results The potential for Mbn production in a wider range of bacterial species was assessed by mining microbial genomes. Operons encoding Mbn-like precursor peptides, MbnAs, were identified in 16 new species, including both methanotrophs and, surprisingly, non-methanotrophs. Along with MbnA, the core of the operon is formed by two putative biosynthetic genes denoted MbnB and MbnC. The species can be divided into five groups on the basis of their MbnA and MbnB sequences and their operon compositions. Additional biosynthetic proteins, including aminotransferases, sulfotransferases and flavin adenine dinucleotide (FAD)-dependent oxidoreductases were also identified in some families. Beyond biosynthetic machinery, a conserved set of transporters was identified, including MATE multidrug exporters and TonB-dependent transporters. Additional proteins of interest include a di-heme cytochrome c peroxidase and a partner protein, the roles of which remain a mystery. Conclusions This study indicates that Mbn-like compounds may be more widespread than previously thought, but are not present in all methanotrophs. This distribution of species suggests a broader role in metal homeostasis. These data provide a link between precursor peptide sequence and Mbn structure, facilitating predictions of new Mbn structures and supporting a post-translational modification biosynthetic pathway. In addition, testable models for Mbn transport and for methanotrophic copper regulation have emerged. Given the unusual modifications observed in Mbns characterized thus far, understanding the roles of the putative biosynthetic proteins is likely to reveal novel pathways and chemistry.
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Affiliation(s)
- Grace E Kenney
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
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Belova SE, Kulichevskaya IS, Bodelier PLE, Dedysh SN. Methylocystis bryophila sp. nov., a facultatively methanotrophic bacterium from acidic Sphagnum peat, and emended description of the genus Methylocystis (ex Whittenbury et al. 1970) Bowman et al. 1993. Int J Syst Evol Microbiol 2012; 63:1096-1104. [PMID: 22707532 DOI: 10.1099/ijs.0.043505-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A novel species is proposed for two facultatively methanotrophic representatives of the genus Methylocystis, strains H2s(T) and S284, which were isolated from an acidic (pH 4.3) Sphagnum peat-bog lake (Teufelssee, Germany) and an acidic (pH 3.8) peat bog (European North Russia), respectively. Cells of strains H2s(T) and S284 are aerobic, Gram-negative, non-motile, curved coccoids or short rods that contain an intracytoplasmic membrane system typical of type-II methanotrophs. They possess both a soluble and a particulate methane monooxygenase (MMO); the latter is represented by two isozymes, pMMO1 and pMMO2. The preferred growth substrates are methane and methanol. In the absence of C1 substrates, however, these methanotrophs are capable of slow growth on acetate. Atmospheric nitrogen is fixed by means of an aerotolerant nitrogenase. Strains H2s(T) and S284 grow between pH 4.2 and 7.6 (optimum pH 6.0-6.5) and at 8-37 °C (optimum 25-30 °C). The major fatty acids are C18 : 1ω8c, C18 : 1ω7c and C16 : 1ω7c; the major quinone is Q-8. The DNA G+C content is 62.0-62.3 mol%. Strains H2s(T) and S284 share identical 16S rRNA gene sequences, which displayed 96.6-97.3 % similarity to sequences of other taxonomically characterized members of the genus Methylocystis. Therefore, strains H2s(T) and S284 are classified as members of a novel species, for which the name Methylocystis bryophila sp. nov. is proposed; strain H2s(T) ( = DSM 21852(T) = VKM B-2545(T)) is the type strain.
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Affiliation(s)
- Svetlana E Belova
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Irina S Kulichevskaya
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Paul L E Bodelier
- Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, The Netherlands
| | - Svetlana N Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow 117312, Russia
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PHB production by Methylocystis hirsuta from natural gas in a bubble column and a vertical loop bioreactor. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.03.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Variations in methanobactin structure influences copper utilization by methane-oxidizing bacteria. Proc Natl Acad Sci U S A 2012; 109:8400-4. [PMID: 22582172 DOI: 10.1073/pnas.1112921109] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methane-oxidizing bacteria are nature's primary biological mechanism for suppressing atmospheric levels of the second-most important greenhouse gas via methane monooxygenases (MMOs). The copper-containing particulate enzyme is the most widespread and efficient MMO. Under low-copper conditions methane-oxidizing bacteria secrete the small copper-binding peptide methanobactin (mbtin) to acquire copper, but how variations in the structures of mbtins influence copper metabolism and species selection are unknown. Methanobactins have been isolated from Methylocystis strains M and hirsuta CSC1, organisms that can switch to using an iron-containing soluble MMO when copper is limiting, and the nonswitchover Methylocystis rosea. These mbtins are shorter, and have different amino acid compositions, than the characterized mbtin from Methylosinus trichosporium OB3b. A coordinating pyrazinedione ring in the Methylocystis mbtins has little influence on the Cu(I) site structure. The Methylocystis mbtins have a sulfate group that helps stabilize the Cu(I) forms, resulting in affinities of approximately 10(21) M(-1). The Cu(II) affinities vary over three orders of magnitude with reduction potentials covering approximately 250 mV, which may dictate the mechanism of intracellular copper release. Copper uptake and the switchover from using the iron-containing soluble MMO to the copper-containing particulate enzyme is faster when mediated by the native mbtin, suggesting that the amino acid sequence is important for the interaction of mbtins with receptors. The differences in structures and properties of mbtins, and their influence on copper utilization by methane-oxidizing bacteria, have important implications for the ecology and global function of these environmentally vital organisms.
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Im J, Lee SW, Yoon S, Dispirito AA, Semrau JD. Characterization of a novel facultative Methylocystis species capable of growth on methane, acetate and ethanol. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:174-181. [PMID: 23761249 DOI: 10.1111/j.1758-2229.2010.00204.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A non-motile strain of Methylocystis, strain SB2, isolated from a spring bog in southeast Michigan, had a curved rod morphology with a typical type II intracytoplasmic membrane system. This organism expressed the membrane-bound or particulate methane monooxygenase (pMMO) as well as a chalkophore with high affinity for copper and did not express the cytoplasmic or soluble methane monooxygenase (sMMO). Strain SB2 was found to grow within the pH range of 6-9, with optimal growth at 6.8. Growth was observed at temperatures ranging between 10°C and 30°C, with no growth at 37°C. The DNA G+C content was 62.9 mol%. Predominant fatty acids were 18:1ω7c (72.7%) and 18:1ω9c (24%) when grown on methane. Phylogenetic comparisons based on both pmoA and 16S rRNA sequences indicated that this organism belonged to the Methylocystis genus, and was closely related to Methylocystis rosea SV97(T) and Methylocystis echinoides IMET10491(T) (98% 16S rRNA gene sequence similarity to both strains). DNA : DNA hybridizations indicated that strain SB2 had 70% similarity with M. rosea SV97(T) . Unlike M. rosea SV97(T) , strain SB2 was able to utilize not only methane for growth, but also ethanol and acetate. Furthermore, the predominant fatty acids in strain SB2 were different from those found in M. rosea SV97(T) , i.e. 54.2% and 39.7% of fatty acids are 18:1ω8 and 18:1ω7 in M. rosea SV97(T) , while 18:1ω8 is completely absent in strain SB2.
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Affiliation(s)
- Jeongdae Im
- Department of Civil and Environmental Engineering, The University of Michigan, 1351 Beal Avenue, Ann Arbor, MI 48109-2125, USA. Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011-3211, USA
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Lee EH, Park H, Cho KS. Effect of substrate interaction on oxidation of methane and benzene in enriched microbial consortia from landfill cover soil. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2011; 46:997-1007. [PMID: 21847790 DOI: 10.1080/10934529.2011.586266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The interaction of methane and benzene during oxidation in enriched methane-oxidizing consortium (MOC) and in benzene-oxidizing consortium (BOC) from landfill cover soil was characterized. Oxidation of both methane and benzene occurred in the MOC due to the coexistence of bacteria responsible for benzene oxidation, as well as methanotrophs, whereas in the BOC, only benzene was oxidized, not methane. Methane oxidation rates in the MOC were decreased with increasing benzene/methane ratio (mol/mol), indicating its methane oxidation was inhibited by the benzene coexistence. Benzene oxidation rates in the MOC, however, were increased with increasing benzene/methane ratio. The benzene oxidation in the BOC was not affected by the coexistence of methane or by the ratio of methane/benzene ratio (mol/mol). No effect of methane or benzene was found on the dynamics of functional genes, such as particulate methane monooxygenase and toluene monooxygenase, in association with oxidation of methane and benzene in the MOC and BOC.
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Affiliation(s)
- Eun-Hee Lee
- Department of Environmental Science and Engineering, Ewha Womans University, Republic of Korea
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Eshinimaev BT, Khmelenina VN, Trotsenko YA. First isolation of a type II methanotroph from a soda lake. Microbiology (Reading) 2008. [DOI: 10.1134/s0026261708050196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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