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Guo K, Glatter T, Paczia N, Liesack W. Asparagine Uptake: a Cellular Strategy of Methylocystis to Combat Severe Salt Stress. Appl Environ Microbiol 2023; 89:e0011323. [PMID: 37184406 PMCID: PMC10305061 DOI: 10.1128/aem.00113-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023] Open
Abstract
Methylocystis spp. are known to have a low salt tolerance (≤1.0% NaCl). Therefore, we tested various amino acids and other well-known osmolytes for their potential to act as an osmoprotectant under otherwise growth-inhibiting NaCl conditions. Adjustment of the medium to 10 mM asparagine had the greatest osmoprotective effect under severe salinity (1.50% NaCl), leading to partial growth recovery of strain SC2. The intracellular concentration of asparagine increased to 264 ± 57 mM, with a certain portion hydrolyzed to aspartate (4.20 ± 1.41 mM). In addition to general and oxidative stress responses, the uptake of asparagine specifically induced major proteome rearrangements related to the KEGG level 3 categories of "methane metabolism," "pyruvate metabolism," "amino acid turnover," and "cell division." In particular, various proteins involved in cell division (e.g., ChpT, CtrA, PleC, FtsA, FtsH1) and peptidoglycan synthesis showed a positive expression response. Asparagine-derived 13C-carbon was incorporated into nearly all amino acids. Both the exometabolome and the 13C-labeling pattern suggest that in addition to aspartate, the amino acids glutamate, glycine, serine, and alanine, but also pyruvate and malate, were most crucially involved in the osmoprotective effect of asparagine, with glutamate being a major hub between the central carbon and amino acid pathways. In summary, asparagine induced significant proteome rearrangements, leading to major changes in central metabolic pathway activity and the sizes of free amino acid pools. In consequence, asparagine acted, in part, as a carbon source for the growth recovery of strain SC2 under severe salinity. IMPORTANCE Methylocystis spp. play a major role in reducing methane emissions into the atmosphere from methanogenic wetlands. In addition, they contribute to atmospheric methane oxidation in upland soils. Although these bacteria are typical soil inhabitants, Methylocystis spp. are thought to have limited capacity to acclimate to salt stress. This called for a thorough study into potential osmoprotectants, which revealed asparagine as the most promising candidate. Intriguingly, asparagine was taken up quantitatively and acted, at least in part, as an intracellular carbon source under severe salt stress. The effect of asparagine as an osmoprotectant for Methylocystis spp. is an unexpected finding. It may provide Methylocystis spp. with an ecological advantage in wetlands, where these methanotrophs colonize the roots of submerged vascular plants. Collectively, our study offers a new avenue into research on compounds that may increase the resilience of Methylocystis spp. to environmental change.
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Affiliation(s)
- Kangli Guo
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Werner Liesack
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
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2
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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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Zhang S, Yan L, Cao J, Wang K, Luo Y, Hu H, Wang L, Yu R, Pan B, Yu K, Zhao J, Bao Z. Salinity significantly affects methane oxidation and methanotrophic community in Inner Mongolia lake sediments. Front Microbiol 2023; 13:1067017. [PMID: 36687579 PMCID: PMC9853545 DOI: 10.3389/fmicb.2022.1067017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Methanotrophs oxidize methane (CH4) and greatly help in mitigating greenhouse effect. Increased temperatures due to global climate change can facilitate lake salinization, particularly in the regions with cold semiarid climate. However, the effects of salinity on the CH4 oxidation activity and diversity and composition of methanotrophic community in the sediment of natural lakes at a regional scale are still unclear. Therefore, we collected lake sediment samples from 13 sites in Mongolian Plateau; CH4 oxidation activities of methanotrophs were investigated, and the diversity and abundance of methanotrophs were analyzed using real-time quantitative polymerase chain reaction and high throughput sequencing approach. The results revealed that the diversity of methanotrophic community decreased with increasing salinity, and community structure of methanotrophs was clearly different between the hypersaline sediment samples (HRS; salinity > 0.69%) and hyposaline sediment samples (HOS; salinity < 0.69%). Types II and I methanotrophs were predominant in HRS and HOS, respectively. Salinity was significantly positively correlated with the relative abundance of Methylosinus and negatively correlated with that of Methylococcus. In addition, CH4 oxidation rate and pmoA gene abundance decreased with increasing salinity, and salinity directly and indirectly affected CH4 oxidation rate via regulating the community diversity. Moreover, high salinity decreased cooperative association among methanotrophs and number of key methanotrophic species (Methylosinus and Methylococcus, e.g). These results suggested that salinity is a major driver of CH4 oxidation in lake sediments and acts by regulating the diversity of methanotrophic community and accociation among the methanotrophic species.
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Affiliation(s)
- Shaohua Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lei Yan
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jiahui Cao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Kexin Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Ying Luo
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Haiyang Hu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lixin Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Ruihong Yu
- Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Baozhu Pan
- Institute of Water Resources and Hydro-electric Engineering, Xi’an University of Technology, Xi’an, Shaanxi, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Ji Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China
| | - Zhihua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University, Hohhot, China,*Correspondence: Zhihua Bao, ✉
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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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5
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Gu Z, Feng K, Li Y, Li Q. Microbial characteristics of the leachate contaminated soil of an informal landfill site. CHEMOSPHERE 2022; 287:132155. [PMID: 34517241 DOI: 10.1016/j.chemosphere.2021.132155] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Because informal landfills are not constructed in a regulated manner, they will inevitably become a source of leachate pollution to the surrounding environment over time. Microbes are an important part of the soil system, playing a vital role in maintaining the normal functionality of soil. This study investigated the microbial composition and co-occurrence pattern in the leachate contaminated soil of an informal landfill site. The landfill leachate underwent horizontal and vertical migration through the contaminated soil, resulting in significant differences in the microbial compositions of horizontal surface soil (CS) and vertical subsurface soil (DS and ES) compared to uncontaminated soil (S). The microbial diversity of CS, DS, and ES was lower than that of S. Due to the migration of landfill leachate, the microbial composition of the surface soil was substantially changed. The dominant phyla in S included Proteobacteria (26.88%), Chloroflexi (23.68%), Actinobacteroita (17.36%), and Acidobacteroita (16.86%), but in contaminated soils, Firmicutes (35.27-86.68%) were the dominant bacteria. A network analysis indicated that Bacilli, Clostridia, and Thermacetogeniazai of the Firmicutes were the keystone taxa and played a vital role in maintaining the stability of the soil ecosystem. A functional annotation of prokaryotic taxa (FAPROTAX) analysis showed that the microbes involved in the C-, N-, and S-cycles in contaminated soil were significantly different to those in uncontaminated soil. The proportion of (aerobic)-chemoheterotrophy and cellulolysis functional communities in contaminated soils was significantly reduced, while there was an increase in functional communities, such as anammox and denitrification, which are not conducive to soil nitrogen fixation. This negatively affected the maintenance of normal soil ecological functions. This study identified the microbial characteristics in leachate contaminated soil and the results will be beneficial for the remediation of contaminated soil in informal landfill sites.
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Affiliation(s)
- Zhepei Gu
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, 611756, China
| | - Ke Feng
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, 611756, China
| | - Yihui Li
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, 611756, China
| | - Qibin Li
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, 611756, China.
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6
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Houghton KM, Stewart LC. Temperature-gradient incubation isolates multiple competitive species from a single environmental sample. Access Microbiol 2020; 2:acmi000081. [PMID: 32974564 PMCID: PMC7470311 DOI: 10.1099/acmi.0.000081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
High-throughput sequencing has allowed culture-independent investigation into a wide variety of microbiomes, but sequencing studies still require axenic culture experiments to determine ecological roles, confirm functional predictions and identify useful compounds and pathways. We have developed a new method for culturing and isolating multiple microbial species with overlapping ecological niches from a single environmental sample, using temperature-gradient incubation. This method was more effective than standard serial dilution-to-extinction at isolating methanotrophic bacteria. It also highlighted discrepancies between culture-dependent and -independent techniques; 16S rRNA gene amplicon sequencing of the same sample did not accurately reflect cultivatable strains using this method. We propose that temperature-gradient incubation could be used to separate out and study previously ‘unculturable’ strains, which co-exist in both natural and artificial environments.
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Affiliation(s)
- Karen M Houghton
- GNS Science, Wairakei Research Centre, 114 Karetoto Rd, Taupō 3384, New Zealand
| | - Lucy C Stewart
- GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5010, New Zealand
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7
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Hakobyan A, Zhu J, Glatter T, Paczia N, Liesack W. Hydrogen utilization by Methylocystis sp. strain SC2 expands the known metabolic versatility of type IIa methanotrophs. Metab Eng 2020; 61:181-196. [PMID: 32479801 DOI: 10.1016/j.ymben.2020.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/20/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022]
Abstract
Methane, a non-expensive natural substrate, is used by Methylocystis spp. as a sole source of carbon and energy. Here, we assessed whether Methylocystis sp. strain SC2 is able to also utilize hydrogen as an energy source. The addition of 2% H2 to the culture headspace had the most significant positive effect on the growth yield under CH4 (6%) and O2 (3%) limited conditions. The SC2 biomass yield doubled from 6.41 (±0.52) to 13.82 (±0.69) mg cell dry weight per mmol CH4, while CH4 consumption was significantly reduced. Regardless of H2 addition, CH4 utilization was increasingly redirected from respiration to fermentation-based pathways with decreasing O2/CH4 mixing ratios. Theoretical thermodynamic calculations confirmed that hydrogen utilization under oxygen-limited conditions doubles the maximum biomass yield compared to fully aerobic conditions without H2 addition. Hydrogen utilization was linked to significant changes in the SC2 proteome. In addition to hydrogenase accessory proteins, the production of Group 1d and Group 2b hydrogenases was significantly increased in both short- and long-term incubations. Both long-term incubation with H2 (37 d) and treatments with chemical inhibitors revealed that SC2 growth under hydrogen-utilizing conditions does not require the activity of complex I. Apparently, strain SC2 has the metabolic capacity to channel hydrogen-derived electrons into the quinone pool, which provides a link between hydrogen oxidation and energy production. In summary, H2 may be a promising alternative energy source in biotechnologically oriented methanotroph projects that aim to maximize biomass yield from CH4, such as the production of high-quality feed protein.
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Affiliation(s)
- Anna Hakobyan
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jing Zhu
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, China
| | - Timo Glatter
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Werner Liesack
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.
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8
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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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Diversity of active root-associated methanotrophs of three emergent plants in a eutrophic wetland in northern China. AMB Express 2020; 10:48. [PMID: 32170424 PMCID: PMC7070141 DOI: 10.1186/s13568-020-00984-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 03/03/2020] [Indexed: 02/02/2023] Open
Abstract
Root-associated aerobic methanotrophs play an important role in regulating methane emissions from the wetlands. However, the influences of the plant genotype on root-associated methanotrophic structures, especially on active flora, remain poorly understood. Transcription of the pmoA gene, encoding particulate methane monooxygenase in methanotrophs, was analyzed by reverse transcription PCR (RT-PCR) of mRNA isolated from root samples of three emergent macrophytes, including Phragmites australis, Typha angustifolia, and Schoenoplectus triqueter (syn. Scirpus triqueter L.) from a eutrophic wetland. High-throughput sequencing of pmoA based on DNA and cDNA was used to analyze the methanotrophic community. Sequencing of cDNA pmoA amplicons confirmed that the structure of active methanotrophic was not always consistent with DNA. A type I methanotroph, Methylomonas, was the most active group in P. australis, whereas Methylocystis, a type II methanotroph, was the dominant group in S. triqueter. In T. angustifolia, these two types of methanotroph existed in similar proportions. However, at the DNA level, Methylomonas was predominant in the roots of all three plants. In addition, vegetation type could have a profound impact on root-associated methanotrophic community at both DNA and cDNA levels. These results indicate that members of the genera Methylomonas (type I) and Methylocystis (type II) can significantly contribute to aerobic methane oxidation in a eutrophic wetland.
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Liu JM, Bao ZH, Cao WW, Han JJ, Zhao J, Kang ZZ, Wang LX, Zhao J. Enrichment of Type I Methanotrophs with nirS Genes of Three Emergent Macrophytes in a Eutrophic Wetland in China. Microbes Environ 2020; 35. [PMID: 31969532 PMCID: PMC7104278 DOI: 10.1264/jsme2.me19098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The pmoA gene, encoding particulate methane monooxygenase in methanotrophs, and nirS and nirK genes, encoding bacterial nitrite reductases, were examined in the root and rhizosphere sediment of three common emergent macrophytes (Phragmites australis, Typha angustifolia, and Scirpus triqueter) and unvegetated sediment from eutrophic Wuliangsuhai Lake in China. Sequencing analyses indicated that 334 out of 351 cloned pmoA sequences were phylogenetically the most closely related to type I methanotrophs (Gammaproteobacteria), and Methylomonas denitrificans-like organisms accounted for 44.4% of the total community. In addition, 244 out of 250 cloned nirS gene sequences belonged to type I methanotrophs, and 31.2% of nirS genes were the most closely related to paddy rice soil clone SP-2-12 in Methylomonas of the total community. Three genera of type I methanotrophs, Methylomonas, Methylobacter, and Methylovulum, were common in both pmoA and nirS clone libraries in each sample. A quantitative PCR (qPCR) analysis demonstrated that the copy numbers of the nirS and nirK genes were significantly higher in rhizosphere sediments than in unvegetated sediments in P. australis and T. angustifolia plants. In the same sample, the nirS gene copy number was significantly higher than that of nirK. Furthermore, type I methanotrophs were localized in the root tissues according to catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Thus, nirS-carrying type I methanotrophs were enriched in macrophyte root and rhizosphere sediment and are expected to play important roles in carbon/nitrogen cycles in a eutrophic wetland.
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Affiliation(s)
- Ju-Mei Liu
- College of Life Sciences, Inner Mongolia University.,College of Chemistry and Environmental Engineering, Chongqing Key Laboratory of Environmental Materials & Remediation Technologies, Chongqing University of Arts and Sciences
| | - Zhi-Hua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University.,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University
| | - Wei-Wei Cao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Jing-Jing Han
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Jun Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Zhen-Zhong Kang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Li-Xin Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Ji Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University.,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University
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11
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Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria. ISME JOURNAL 2019; 14:714-726. [PMID: 31796935 DOI: 10.1038/s41396-019-0561-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/09/2019] [Accepted: 11/14/2019] [Indexed: 11/08/2022]
Abstract
Copper-containing membrane monooxygenases (CuMMOs) are encoded by xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, or some short-chain alkanes and alkenes. In a metagenome constructed from an oilsands tailings pond we detected an xmoCABD gene cluster with <59% derived protein sequence identity to genes from known bacteria. Stable isotope probing experiments combined with a specific xmoA qPCR assay demonstrated that the bacteria possessing these genes were incapable of methane assimilation, but did grow on ethane and propane. Single-cell amplified genomes (SAGs) from propane-enriched samples were screened with the specific PCR assay to identify bacteria possessing the target gene cluster. Multiple SAGs of Betaproteobacteria belonging to the genera Rhodoferax and Polaromonas possessed homologues of the metagenomic xmoCABD gene cluster. Unexpectedly, each of these two genera also possessed other xmoCABD paralogs, representing two additional lineages in phylogenetic analyses. Metabolic reconstructions from SAGs predicted that neither bacterium encoded enzymes with the potential to support catabolic methane or ammonia oxidation, but that both were capable of higher n-alkane degradation. The involvement of the encoded CuMMOs in alkane oxidation was further suggested by reverse transcription PCR analyses, which detected elevated transcription of the xmoA genes upon enrichment of water samples with propane as the sole energy source. Enrichments, isotope incorporation studies, genome reconstructions, and gene expression studies therefore all agreed that the unknown xmoCABD operons did not encode methane or ammonia monooxygenases, but rather n-alkane monooxygenases. This study broadens the known diversity of CuMMOs and identifies these enzymes in non-nitrifying Betaproteobacteria.
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12
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Bodelier PLE, Pérez G, Veraart AJ, Krause SMB. Methanotroph Ecology, Environmental Distribution and Functioning. METHANOTROPHS 2019. [DOI: 10.1007/978-3-030-23261-0_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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13
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Watsuji TO, Motoki K, Hada E, Nagai Y, Takaki Y, Yamamoto A, Ueda K, Toyofuku T, Yamamoto H, Takai K. Compositional and Functional Shifts in the Epibiotic Bacterial Community of Shinkaia crosnieri Baba & Williams (a Squat Lobster from Hydrothermal Vents) during Methane-Fed Rearing. Microbes Environ 2018; 33:348-356. [PMID: 30333383 PMCID: PMC6308002 DOI: 10.1264/jsme2.me18072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The hydrothermal vent squat lobster Shinkaia crosnieri Baba & Williams harbors an epibiotic bacterial community, which is numerically and functionally dominated by methanotrophs affiliated with Methylococcaceae and thioautotrophs affiliated with Sulfurovum and Thiotrichaceae. In the present study, shifts in the phylogenetic composition and metabolic function of the epibiont community were investigated using S. crosnieri individuals, which were reared for one year in a tank fed with methane as the energy and carbon source. The results obtained indicated that indigenous predominant thioautotrophic populations, such as Sulfurovum and Thiotrichaceae members, became absent, possibly due to the lack of an energy source, and epibiotic communities were dominated by indigenous Methylococcaceae and betaproteobacterial methylotrophic members that adapted to the conditions present during rearing for 12 months with a supply of methane. Furthermore, the overall phylogenetic composition of the epibiotic community markedly changed from a composition dominated by chemolithotrophs to one enriched with cross-feeding heterotrophs in addition to methanotrophs and methylotrophs. Thus, the composition and function of the S. crosnieri epibiotic bacterial community were strongly affected by the balance between the energy and carbon sources supplied for chemosynthetic production as well as that between the production and consumption of organic compounds.
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Affiliation(s)
- Tomo-O Watsuji
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Kaori Motoki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Life Science Research Center, College of Bioresource Sciences, Nihon University.,Present Address: Department of Biological Sciences, Graduate School of Science, the University of Tokyo
| | - Emi Hada
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yukiko Nagai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Asami Yamamoto
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC).,Life Science Research Center, College of Bioresource Sciences, Nihon University
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University
| | | | | | - Ken Takai
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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14
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Hakobyan A, Liesack W, Glatter T. Crude-MS Strategy for in-Depth Proteome Analysis of the Methane-Oxidizing Methylocystis sp. strain SC2. J Proteome Res 2018; 17:3086-3103. [DOI: 10.1021/acs.jproteome.8b00216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Werner Liesack
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 16, D-35043 Marburg, Germany
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15
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Rahalkar MC, Bahulikar RA. Hemerythrins are widespread and conserved for methanotrophic guilds. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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Rochman FF, Kim JJ, Rijpstra WIC, Sinninghe Damsté JS, Schumann P, Verbeke TJ, Dunfield PF. Oleiharenicola alkalitolerans gen. nov., sp. nov., a new member of the phylum Verrucomicrobia isolated from an oilsands tailings pond. Int J Syst Evol Microbiol 2018; 68:1078-1084. [PMID: 29461179 DOI: 10.1099/ijsem.0.002624] [Citation(s) in RCA: 11] [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 novel member of the phylum Verrucomicrobia was isolated from an oilsands tailings pond in Alberta, Canada. Cells of isolate NVTT are Gram-negative, strictly aerobic, non-pigmented, non-motile cocci to diplococci 0.5-1.0 µm in diameter. The bacterium is neutrophilic (optimum pH 6.0-8.0) but alkalitolerant, capable of growth between pH 5.5 and 11.0. The temperature range for growth is 15-40 °C (optimum 25-37 °C). Carbon and energy sources include sugars and organic acids. Nitrogen sources include nitrate, urea, l-glycine, l-alanine, l-proline and l-serine. Does not fix atmospheric nitrogen. Does not require NaCl and is inhibited at NaCl concentrations above 3.0 % (w/v). The DNA G+C content of strain NVTT, based on a draft genome sequence, is 66.1 mol%. MK-6 and MK-7 are the major respiratory quinones. Major cellular fatty acids are anteiso-C15 : 0 and iso-C15 : 0. Phylogenetic analysis of 16S rRNA gene sequences revealed that the strain belongs to the family Opitutaceae of the phylum Verrucomicrobia. The most closely related validated species is Opitutus terrae (93.7 % 16S rRNA gene sequence identity to its type strain PB90-1T). Based on genotypic, phenotypic and chemotaxonomic characteristics, it was concluded that this strain represents a novel genus and species, for which the name Oleiharenicola alkalitolerans gen. nov., sp. nov. is proposed. The type strain of this novel species is NVTT (=ATCC BAA-2697T;=DSM 29249T).
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Affiliation(s)
- Fauziah F Rochman
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Joong-Jae Kim
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - W Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry, Utrecht University, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Utrecht University, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands.,Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tobin J Verbeke
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Canada
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17
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Al-Karablieh N. Antimicrobial Activity of Bacillus Persicus 24-DSM Isolated from Dead Sea Mud. Open Microbiol J 2018; 11:372-383. [PMID: 29399218 PMCID: PMC5759096 DOI: 10.2174/1874285801711010372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 11/22/2022] Open
Abstract
Intorduction: Dead Sea is a hypersaline lake with 34% salinity, gains its name due to the absence of any living macroscopic creatures. Despite the extreme hypersaline environment, it is a unique ecosystem for various halophilic microorganisms adapted to this environment. Aims & Objectives: Halophilic microorganisms are known for various potential biotechnological applications, the purpose of the current research is isolation and screening of halophilic bacteria from Dead Sea mud for potential antimicrobial applications. Methods & Materials: Screening for antagonistic bacteria was conducted by bacterial isolation from Dead Sea mud samples and agar plate antagonistic assay. The potential antagonistic isolates were subjected to biochemical characterization and identification by 16S-rRNA sequencing. Among the collected isolates, four isolates showed potential antagonistic activity against Bacillus subtilis 6633 and Escherichia coli 8739. The most active isolate (24-DSM) was subjected for antagonistic activity and minimal inhibitory concentration against different gram positive and negative bacterial strains after cultivation in different salt concentration media. Results: The results of 16S-rRNA analysis revealed that 24-DSM is very closely related to Bacillus persicus strain B48, which was isolated from hypersaline lake in Iran. Conclusion: Therefore, the isolate 24-DSM is assigned as a new strain of B. persicusi isolated from the Dead Sea mud. B. persicusi 24-DSM showed higher antimicrobial activity, when it was cultivated with saline medium, against all tested bacterial strains, where the most sensitive bacterial strain was Corynebacterium diphtheria 51696.
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Affiliation(s)
- Nehaya Al-Karablieh
- Hamdi mango center for scientific research, The University of Jordan, Amman, Jordan
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18
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Frindte K, Maarastawi SA, Lipski A, Hamacher J, Knief C. Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai. Int J Syst Evol Microbiol 2017; 67:4507-4514. [PMID: 28984554 DOI: 10.1099/ijsem.0.002319] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three gammaproteobacterial methanotrophic strains (73aT, 175 and 114) were isolated from stems of rice plants. All strains are Gram-negative, motile and grow on methane or methanol as sole carbon sources. They oxidize methane using the particulate methane monooxygenase. Strains 114 and 175 possess additionally a soluble methane monooxygenase. All strains contain significant amounts of the cellular fatty acids C16 : 0, C16 : 1ω6c and C16 : 1ω7c, typical for type Ib methanotrophs. Characteristic for strains 114 and 175 are high amounts of C14 : 0 and C16 : 1ω6c , while strain 73aT contains high quantities of C16 : 1ω5c. 16S rRNA gene sequence analyses showed that strains 114 and 175 are most closely related to Methylomagnum ishizawai (≥99.6 % sequence identity). Strain 73aT is representing a new genus within the family Methylococcaceae, most closely related to Methylococcus capsulatus (94.3 % sequence identity). Phylogenetic analysis of the PmoA sequence indicates that strain 73aT represents rice paddy cluster I (RPCI), which has almost exclusively been detected in rice ecosystems. The G+C content of strain 73aT is 61.0 mol%, while strains 114 and 175 have a G+C content of 63.3 mol%. Strain 73aT (=LMG 29185T, =VKM B-2986T) represents the type strain of a novel species and genus, for which the name Methyloterricola oryzae gen. nov., sp. nov. is proposed and a description is provided. Strains 175 (=LMG 28717, VKM B-2989) and 114 are members of the species Methylomagnum ishizawai. This genus was so far only represented by one isolate, so an amended description of the species is given.
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Affiliation(s)
- Katharina Frindte
- Molecular Biology of the Rhizosphere, Institute of Crop Science and Resource Conservation, University of Bonn, Nussallee 13, 53115 Bonn, Germany
| | - Sarah A Maarastawi
- Molecular Biology of the Rhizosphere, Institute of Crop Science and Resource Conservation, University of Bonn, Nussallee 13, 53115 Bonn, Germany
| | - André Lipski
- Food Microbiology and Hygiene, Institute of Nutritional and Food Sciences, University of Bonn, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Joachim Hamacher
- Plant Diseases and Crop Protection, Institute of Crop Science and Resource Conservation, University of Bonn, Nussallee 9, 53115 Bonn, Germany
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Institute of Crop Science and Resource Conservation, University of Bonn, Nussallee 13, 53115 Bonn, Germany
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19
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Response of Methylocystis sp. Strain SC2 to Salt Stress: Physiology, Global Transcriptome, and Amino Acid Profiles. Appl Environ Microbiol 2017; 83:AEM.00866-17. [PMID: 28802275 DOI: 10.1128/aem.00866-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 08/09/2017] [Indexed: 12/18/2022] Open
Abstract
Soil microorganisms have to rapidly respond to salt-induced osmotic stress. Type II methanotrophs of the genus Methylocystis are widely distributed in upland soils but are known to have a low salt tolerance. Here, we tested the ability of Methylocystis sp. strain SC2 to adapt to increased salinity. When exposed to 0.75% NaCl, methane oxidation was completely inhibited for 2.25 h and fully recovered within 6 h. Growth was inhibited for 23.5 h and then fully recovered. Its transcriptome was profiled after 0 min (control), 45 min (early response), and 14 h (late response) of stress exposure. Physiological and transcriptomic stress responses corresponded well. Salt stress induced the differential expression of 301 genes, with sigma factor σ32 being a major controller of the transcriptional stress response. The transcript levels of nearly all the genes involved in oxidizing CH4 to CO2 remained unaffected, while gene expression involved in energy-yielding reactions (nuoA-N) recovered concomitantly with methane oxidation from salt stress shock. Glutamate acted as an osmoprotectant. Its accumulation in late stress response corresponded to increased production of glutamate dehydrogenase 1. Chromosomal genes whose products (stress-induced protein, DNA-binding protein from starved cells, and CsbD family protein) are known to confer stress tolerance showed increased expression. On plasmid pBSC2-1, genes encoding type IV secretion system and single-strand DNA-binding protein were upregulated in late response, suggesting stress-induced activation of the plasmid-borne conjugation machinery. Collectively, our results show that Methylocystis sp. strain SC2 is able to adapt to salt stress, but only within a narrow range of salinities.IMPORTANCE Besides the oxic interface of methanogenic environments, Methylocystis spp. are widely distributed in upland soils, where they may contribute to the oxidation of atmospheric methane. However, little is known about their ability to cope with changes in soil salinity. Growth and methane oxidation of Methylocystis sp. strain SC2 were not affected by the presence of 0.5% NaCl, while 1% NaCl completely inhibited its activity. This places strain SC2 into the low-salt-tolerance range reported for other Methylocystis species. Our results show that, albeit in a narrow range, strain SC2 is able to respond and adapt to salinity changes. It possesses various stress response mechanisms, which allow resumption of growth within 24 h when exposed to 0.75% NaCl. Presumably, these mechanisms allow Methylocystis spp., such as strain SC2, to thrive in upland soils and to adapt to certain fluctuations in soil salinity.
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20
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Rochman FF, Sheremet A, Tamas I, Saidi-Mehrabad A, Kim JJ, Dong X, Sensen CW, Gieg LM, Dunfield PF. Benzene and Naphthalene Degrading Bacterial Communities in an Oil Sands Tailings Pond. Front Microbiol 2017; 8:1845. [PMID: 29033909 PMCID: PMC5627004 DOI: 10.3389/fmicb.2017.01845] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/08/2017] [Indexed: 11/13/2022] Open
Abstract
Oil sands process-affected water (OSPW), produced by surface-mining of oil sands in Canada, is alkaline and contains high concentrations of salts, metals, naphthenic acids, and polycyclic aromatic compounds (PAHs). Residual hydrocarbon biodegradation occurs naturally, but little is known about the hydrocarbon-degrading microbial communities present in OSPW. In this study, aerobic oxidation of benzene and naphthalene in the surface layer of an oil sands tailings pond were measured. The potential oxidation rates were 4.3 μmol L-1 OSPW d-1 for benzene and 21.4 μmol L-1 OSPW d-1 for naphthalene. To identify benzene and naphthalene-degrading microbial communities, metagenomics was combined with stable isotope probing (SIP), high-throughput sequencing of 16S rRNA gene amplicons, and isolation of microbial strains. SIP using 13C-benzene and 13C-naphthalene detected strains of the genera Methyloversatilis and Zavarzinia as the main benzene degraders, while strains belonging to the family Chromatiaceae and the genus Thauera were the main naphthalene degraders. Metagenomic analysis revealed a diversity of genes encoding oxygenases active against aromatic compounds. Although these genes apparently belonged to many phylogenetically diverse taxa, only a few of these taxa were predominant in the SIP experiments. This suggested that many members of the community are adapted to consuming other aromatic compounds, or are active only under specific conditions. 16S rRNA gene sequence datasets have been submitted to the Sequence Read Archive (SRA) under accession number SRP109130. The Gold Study and Project submission ID number in Joint Genome Institute IMG/M for the metagenome is Gs0047444 and Gp0055765.
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Affiliation(s)
- Fauziah F Rochman
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Andriy Sheremet
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Ivica Tamas
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.,Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Alireza Saidi-Mehrabad
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Joong-Jae Kim
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Xiaoli Dong
- Department of Biochemistry and Molecular Biology in the Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Christoph W Sensen
- Department of Biochemistry and Molecular Biology in the Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria
| | - Lisa M Gieg
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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21
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Tláskal V, Voříšková J, Baldrian P. Bacterial succession on decomposing leaf litter exhibits a specific occurrence pattern of cellulolytic taxa and potential decomposers of fungal mycelia. FEMS Microbiol Ecol 2016; 92:fiw177. [DOI: 10.1093/femsec/fiw177] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 11/13/2022] Open
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22
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Bornemann M, Bussmann I, Tichy L, Deutzmann J, Schink B, Pester M. Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance. FEMS Microbiol Ecol 2016; 92:fiw123. [PMID: 27267930 DOI: 10.1093/femsec/fiw123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 11/14/2022] Open
Abstract
Methane emissions from freshwater environments contribute substantially to global warming but are under strong control of aerobic methane-oxidizing bacteria. Recently discovered methane seeps (pockmarks) in freshwater lake sediments have the potential to bypass this control by their strong outgassing activity. Whether this is counteracted by pelagic methanotrophs is not well understood yet. We used a (3)H-CH4-radiotracer technique and pmoA-based molecular approaches to assess the activity, abundance and community structure of pelagic methanotrophs above active pockmarks in deep oligotrophic Lake Constance. Above profundal pockmarks, methane oxidation rates (up to 458 nmol CH4 l(-1) d(-1)) exceeded those of the surrounding water column by two orders of magnitude and coincided with maximum methanotroph abundances of 0.6% of the microbial community. Phylogenetic analysis indicated a dominance of members of the Methylococcaceae in the water column of both, pockmark and reference sites, with most of the retrieved sequences being associated with a water-column specific clade. Communities at pockmark and reference locations also differed in parts, which was likely caused by entrainment of sediment-hosted methanotrophs at pockmark sites. Our results show that the release of seep-derived methane to the atmosphere is counteracted by a distinct methanotrophic community with a pronounced activity throughout bottom waters.
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Affiliation(s)
- Maren Bornemann
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Ingeborg Bussmann
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Meeresstation Helgoland, Kurpromenade 201, D-27498 Helgoland, Germany
| | - Lucas Tichy
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Jörg Deutzmann
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany Department of Civil and Environmental Engineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Bernhard Schink
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Michael Pester
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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23
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Wen X, Yang S, Liebner S. Evaluation and update of cutoff values for methanotrophic pmoA gene sequences. Arch Microbiol 2016; 198:629-36. [PMID: 27098810 DOI: 10.1007/s00203-016-1222-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/30/2016] [Accepted: 04/06/2016] [Indexed: 01/16/2023]
Abstract
The functional pmoA gene is frequently used to probe the diversity and phylogeny of methane-oxidizing bacteria (MOB) in various environments. Here, we compared the similarities between the pmoA gene and the corresponding 16S rRNA gene sequences of 77 described species covering gamma- and alphaproteobacterial methanotrophs (type I and type II MOB, respectively) as well as methanotrophs from the phylum Verrucomicrobia. We updated and established the weighted mean pmoA gene cutoff values on the nucleotide level at 86, 82, and 71 % corresponding to the 97, 95, and 90 % similarity of the 16S rRNA gene. Based on these cutoffs, the functional gene fragments can be entirely processed at the nucleotide level throughout software platforms such as Mothur or QIIME which provide a user-friendly and command-based alternative to amino acid-based pipelines. Type II methanotrophs are less divergent than type I both with regard to ribosomal and functional gene sequence similarity and GC content. We suggest that this agrees with the theory of different life strategies proposed for type I and type II MOB.
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Affiliation(s)
- Xi Wen
- Helmholtz Center Potsdam, GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Telegrafenberg, 14473, Potsdam, Germany.,College of Electrical Engineering, Northwest University for Nationalities, Lanzhou, 730030, China
| | - Sizhong Yang
- Helmholtz Center Potsdam, GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Telegrafenberg, 14473, Potsdam, Germany. .,State Key Laboratory of Frozen Soils Engineering, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Susanne Liebner
- Helmholtz Center Potsdam, GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Telegrafenberg, 14473, Potsdam, Germany
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24
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Knief C. Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker. Front Microbiol 2015; 6:1346. [PMID: 26696968 PMCID: PMC4678205 DOI: 10.3389/fmicb.2015.01346] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing "unknown methanotrophic bacteria." This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.
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Affiliation(s)
- Claudia Knief
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of BonnBonn, Germany
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25
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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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Laas P, Simm J, Lips I, Lips U, Kisand V, Metsis M. Redox-specialized bacterioplankton metacommunity in a temperate estuary. PLoS One 2015; 10:e0122304. [PMID: 25860812 PMCID: PMC4393233 DOI: 10.1371/journal.pone.0122304] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 02/19/2015] [Indexed: 11/30/2022] Open
Abstract
This study explored the spatiotemporal dynamics of the bacterioplankton community composition in the Gulf of Finland (easternmost sub-basin of the Baltic Sea) based on phylogenetic analysis of 16S rDNA sequences acquired from community samples via pyrosequencing. Investigations of bacterioplankton in hydrographically complex systems provide good insight into the strategies by which microbes deal with spatiotemporal hydrographic gradients, as demonstrated by our research. Many ribotypes were closely affiliated with sequences isolated from environments with similar steep physiochemical gradients and/or seasonal changes, including seasonally anoxic estuaries. Hence, one of the main conclusions of this study is that marine ecosystems where oxygen and salinity gradients co-occur can be considered a habitat for a cosmopolitan metacommunity consisting of specialized groups occupying niches universal to such environments throughout the world. These niches revolve around functional capabilities to utilize different electron receptors and donors (including trace metal and single carbon compounds). On the other hand, temporal shifts in the bacterioplankton community composition at the surface layer were mainly connected to the seasonal succession of phytoplankton and the inflow of freshwater species. We also conclude that many relatively abundant populations are indigenous and well-established in the area.
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Affiliation(s)
- Peeter Laas
- Marine Systems Institute at Tallinn University of Technology, Tallinn, Estonia
- * E-mail:
| | - Jaak Simm
- Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, KU Leuven, Leuven, Belgium
- iMinds Medical IT, Leuven, Belgium
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Inga Lips
- Marine Systems Institute at Tallinn University of Technology, Tallinn, Estonia
| | - Urmas Lips
- Marine Systems Institute at Tallinn University of Technology, Tallinn, Estonia
| | - Veljo Kisand
- Institute of Technology at University of Tartu, Tartu, Estonia
| | - Madis Metsis
- Institute of Mathematics and Natural Sciences, Tallinn University, Tallinn, Estonia
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Lebrero R, Hernández L, Pérez R, Estrada JM, Muñoz R. Two-liquid phase partitioning biotrickling filters for methane abatement: exploring the potential of hydrophobic methanotrophs. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2015; 151:124-131. [PMID: 25555135 DOI: 10.1016/j.jenvman.2014.12.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/03/2014] [Accepted: 12/05/2014] [Indexed: 06/04/2023]
Abstract
The potential of two-liquid phase biotrickling filters (BTFs) to overcome mass transfer limitations derived from the poor aqueous solubility of CH4 has been scarcely investigated to date. In this context, the abatement of diluted methane emissions in two-liquid phase BTFs was evaluated using two different inocula: a type II methanotrophs culture in BTF 1 and a hydrophobic microbial consortium capable of growing inside silicone oil in BTF 2. Both BTFs supported stable elimination capacities above 45 g m(-3) h(-1) regardless of the inoculum, whereas no improvement derived from the presence of hydrophobic microorganisms compared to the type II metanotrophs culture was observed. Interestingly, the addition of silicone oil mediated a reduced metabolites concentration in the recycling aqueous phase, thus decreasing the needs for mineral medium renewal. Moreover, a 78% similarity was recorded between the microbial communities enriched in both BTFs at the end of the experimental period in spite of the differences in the initial inoculum structure. The results obtained confirmed the superior performance of two-liquid phase BTFs for CH4 abatement compared with conventional biotrickling filters.
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Affiliation(s)
- Raquel Lebrero
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Spain
| | - Laura Hernández
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Spain
| | - Rebeca Pérez
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Spain
| | - José M Estrada
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Spain
| | - Raúl Muñoz
- Department of Chemical Engineering and Environmental Technology, University of Valladolid, Spain.
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Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed. ISME JOURNAL 2014; 9:1693-9. [PMID: 25535936 DOI: 10.1038/ismej.2014.252] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 11/21/2014] [Accepted: 11/21/2014] [Indexed: 11/08/2022]
Abstract
For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes.
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Abdallah RZ, Adel M, Ouf A, Sayed A, Ghazy MA, Alam I, Essack M, Lafi FF, Bajic VB, El-Dorry H, Siam R. Aerobic methanotrophic communities at the Red Sea brine-seawater interface. Front Microbiol 2014; 5:487. [PMID: 25295031 PMCID: PMC4172156 DOI: 10.3389/fmicb.2014.00487] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/28/2014] [Indexed: 01/16/2023] Open
Abstract
The central rift of the Red Sea contains 25 brine pools with different physicochemical conditions, dictating the diversity and abundance of the microbial community. Three of these pools, the Atlantis II, Kebrit and Discovery Deeps, are uniquely characterized by a high concentration of hydrocarbons. The brine-seawater interface, described as an anoxic-oxic (brine-seawater) boundary, is characterized by a high methane concentration, thus favoring aerobic methane oxidation. The current study analyzed the aerobic free–living methane-oxidizing bacterial communities that potentially contribute to methane oxidation at the brine-seawater interfaces of the three aforementioned brine pools, using metagenomic pyrosequencing, 16S rRNA pyrotags and pmoA library constructs. The sequencing of 16S rRNA pyrotags revealed that these interfaces are characterized by high microbial community diversity. Signatures of aerobic methane-oxidizing bacteria were detected in the Atlantis II Interface (ATII-I) and the Kebrit Deep Upper (KB-U) and Lower (KB-L) brine-seawater interfaces. Through phylogenetic analysis of pmoA, we further demonstrated that the ATII-I aerobic methanotroph community is highly diverse. We propose four ATII-I pmoA clusters. Most importantly, cluster 2 groups with marine methane seep methanotrophs, and cluster 4 represent a unique lineage of an uncultured bacterium with divergent alkane monooxygenases. Moreover, non-metric multidimensional scaling (NMDS) based on the ordination of putative enzymes involved in methane metabolism showed that the Kebrit interface layers were distinct from the ATII-I and DD-I brine-seawater interfaces.
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Affiliation(s)
- Rehab Z Abdallah
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt
| | - Mustafa Adel
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Amged Ouf
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Ahmed Sayed
- Department of Biology, American University in Cairo Cairo, Egypt
| | - Mohamed A Ghazy
- Department of Biology, American University in Cairo Cairo, Egypt
| | - Intikhab Alam
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Feras F Lafi
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Vladimir B Bajic
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Hamza El-Dorry
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Rania Siam
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt ; YJ-Science and Technology Research Center, American University in Cairo Cairo, Egypt
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Tiodjio RE, Sakatoku A, Nakamura A, Tanaka D, Fantong WY, Tchakam KB, Tanyileke G, Ohba T, Hell VJ, Kusakabe M, Nakamura S, Ueda A. Bacterial and archaeal communities in Lake Nyos (Cameroon, Central Africa). Sci Rep 2014; 4:6151. [PMID: 25141868 PMCID: PMC4139950 DOI: 10.1038/srep06151] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/04/2014] [Indexed: 11/21/2022] Open
Abstract
The aim of this study was to assess the microbial diversity associated with Lake Nyos, a lake with an unusual chemistry in Cameroon. Water samples were collected during the dry season on March 2013. Bacterial and archaeal communities were profiled using Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) approach of the 16S rRNA gene. The results indicate a stratification of both communities along the water column. Altogether, the physico-chemical data and microbial sequences suggest a close correspondence of the potential microbial functions to the physico-chemical pattern of the lake. We also obtained evidence of a rich microbial diversity likely to include several novel microorganisms of environmental importance in the large unexplored microbial reservoir of Lake Nyos.
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Affiliation(s)
- Rosine E. Tiodjio
- Department of Environmental and Energy Sciences, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Akihiro Sakatoku
- Department of Environmental and Energy Sciences, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Akihiro Nakamura
- Department of Environmental and Energy Sciences, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Daisuke Tanaka
- Department of Environmental and Energy Sciences, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Wilson Y. Fantong
- Institute of Mining and Geological Research, P.O. Box 4110, Yaoundé, Cameroon
| | - Kamtchueng B. Tchakam
- Department of Environmental and Energy Sciences, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Gregory Tanyileke
- Institute of Mining and Geological Research, P.O. Box 4110, Yaoundé, Cameroon
| | - Takeshi Ohba
- Department of Chemistry, School of Science, University of Tokai, Kanagawa 259-1292, Japan
| | - Victor J. Hell
- Institute of Mining and Geological Research, P.O. Box 4110, Yaoundé, Cameroon
| | - Minoru Kusakabe
- Department of Environmental and Energy Sciences, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Shogo Nakamura
- Department of Environmental and Energy Sciences, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Akira Ueda
- Department of Environmental and Energy Sciences, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
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Sharp CE, Martínez-Lorenzo A, Brady AL, Grasby SE, Dunfield PF. Methanotrophic bacteria in warm geothermal spring sediments identified using stable-isotope probing. FEMS Microbiol Ecol 2014; 90:92-102. [DOI: 10.1111/1574-6941.12375] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 06/11/2014] [Accepted: 06/22/2014] [Indexed: 01/06/2023] Open
Affiliation(s)
- Christine E. Sharp
- Department of Biological Sciences; University of Calgary; Calgary AB Canada
| | | | - Allyson L. Brady
- Department of Biological Sciences; University of Calgary; Calgary AB Canada
| | | | - Peter F. Dunfield
- Department of Biological Sciences; University of Calgary; Calgary AB Canada
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Draft Genome Sequence of Methanol-Utilizing Methylophilus sp. Strain OH31, Isolated from Pond Sediment in Hokkaido, Japan. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00274-14. [PMID: 24723716 PMCID: PMC3983305 DOI: 10.1128/genomea.00274-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Methylophilus sp. strain OH31 was isolated from the sediment of the Ohno pond at Hokkaido University. Strain OH31 utilizes methanol as its energy source. Here, we present the draft genome sequence of Methylophilus sp. strain OH31.
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Bao Z, Watanabe A, Sasaki K, Okubo T, Tokida T, Liu D, Ikeda S, Imaizumi-Anraku H, Asakawa S, Sato T, Mitsui H, Minamisawa K. A rice gene for microbial symbiosis, Oryza sativa CCaMK, reduces CH4 flux in a paddy field with low nitrogen input. Appl Environ Microbiol 2014; 80:1995-2003. [PMID: 24441161 PMCID: PMC3957643 DOI: 10.1128/aem.03646-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/10/2014] [Indexed: 11/20/2022] Open
Abstract
Plants have mutualistic symbiotic relationships with rhizobia and fungi by the common symbiosis pathway, of which Ca(2+)/calmodulin-dependent protein kinase (encoded by CCaMK) is a central component. Although Oryza sativa CCaMK (OsCCaMK) is required for fungal accommodation in rice roots, little is known about the role of OsCCaMK in rice symbiosis with bacteria. Here, we report the effect of a Tos17-induced OsCCaMK mutant (NE1115) on CH4 flux in low-nitrogen (LN) and standard-nitrogen (SN) paddy fields compared with wild-type (WT) Nipponbare. The growth of NE1115 was significantly decreased compared with that of the WT, especially in the LN field. The CH4 flux of NE1115 in the LN field was significantly greater (156 to 407% in 2011 and 170 to 816% in 2012) than that of the WT, although no difference was observed in the SN field. The copy number of pmoA (encodes methane monooxygenase in methanotrophs) was significantly higher in the roots and rhizosphere soil of the WT than in those of NE1115. However, the mcrA (encodes methyl coenzyme M reductase in methanogens) copy number did not differ between the WT and NE1115. These results were supported by a (13)C-labeled CH4-feeding experiment. In addition, the natural abundance of (15)N in WT shoots (3.05‰) was significantly lower than in NE1115 shoots (3.45‰), suggesting greater N2 fixation in the WT because of dilution with atmospheric N2 (0.00‰). Thus, CH4 oxidation and N2 fixation were simultaneously activated in the root zone of WT rice in the LN field and both processes are likely controlled by OsCCaMK.
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Affiliation(s)
- Zhihua Bao
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Aya Watanabe
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Kazuhiro Sasaki
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Takashi Okubo
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Takeshi Tokida
- National Institute for Agro-Environmental Sciences, Tsukuba, Japan
| | - Dongyan Liu
- Graduate School of Agricultural Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Japan
| | - Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
- Memuro Research Station, National Agricultural Research Center for Hokkaido Region, Shinsei, Memuro-cho, Kasaigun, Hokkaido, Japan
| | - Haruko Imaizumi-Anraku
- Department of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Susumu Asakawa
- Graduate School of Agricultural Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Japan
| | - Tadashi Sato
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Miyagi, Japan
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Dam B, Dam S, Kim Y, Liesack W. Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2. Environ Microbiol 2014; 16:3115-27. [PMID: 24373058 DOI: 10.1111/1462-2920.12367] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/14/2013] [Indexed: 11/30/2022]
Abstract
Nitrogen source and concentration are major determinants of methanotrophic activity, but their effect on global gene expression is poorly studied. Methylocystis sp. strain SC2 produces two isozymes of particulate methane monooxygenase. These are encoded by pmoCAB1 (low-affinity pMMO1) and pmoCAB2 (high-affinity pMMO2). We used RNA-Seq to identify strain SC2 genes that respond to standard (10 mM) and high (30 mM) NH4(+) concentrations in the medium, compared with 10 mM NO3(-). While the expression of pmoCAB1 was unaffected, pmoCAB2 was significantly downregulated (log2 fold changes of -5.0 to -6.0). Among nitrogen metabolism-related processes, genes involved in hydroxylamine detoxification (haoAB) were highly upregulated, while those for assimilatory nitrate/nitrite reduction, high-affinity ammonium uptake and nitrogen regulatory protein PII were downregulated. Differential expression of pmoCAB2 and haoAB was independently validated by end-point reverse transcription polymerase chain reaction. Methane oxidation by SC2 cells exposed to 30 mM NH4(+) was inhibited at ≤ 400 ppmv CH4 , where pMMO2 but not pMMO1 is functional. When transferred back to standard nitrogen concentration, methane oxidation capability and pmoCAB2 expression were restored. Given that Methylocystis contributes to atmospheric methane oxidation in upland soils, differential expression of pmoCAB2 explains, at least to some extent, the strong inhibitory effect of ammonium fertilizers on this activity.
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Affiliation(s)
- Bomba Dam
- Max Planck Institute for Terrestrial Microbiology, D-35043, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35043, Marburg, Germany
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Watsuji TO, Yamamoto A, Takaki Y, Ueda K, Kawagucci S, Takai K. Diversity and methane oxidation of active epibiotic methanotrophs on live Shinkaia crosnieri. ISME JOURNAL 2014; 8:1020-31. [PMID: 24401859 DOI: 10.1038/ismej.2013.226] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 11/12/2013] [Accepted: 11/17/2013] [Indexed: 11/09/2022]
Abstract
Shinkaia crosnieri is a galatheid crab that predominantly dwells in deep-sea hydrothermal systems in the Okinawa Trough, Japan. In this study, the phylogenetic diversity of active methanotrophs in the epibiotic microbial community on the setae of S. crosnieri was characterized by reverse transcription-polymerase chain reaction (RT-PCR) of a functional gene (pmoA) encoding a subunit of particulate methane monooxygenase. Phylogenetic analysis of pmoA transcript sequences revealed that the active epibiotic methanotrophs on S. crosnieri setae consisted of gammaproteobacterial type Ia and Ib methanotrophs. The effect of different RNA stabilization procedures on the abundance of pmoA and 16S rRNA transcripts in the epibiotic community was estimated by quantitative RT-PCR. Our novel RNA fixation method performed immediately after sampling effectively preserved cellular RNA assemblages, particularly labile mRNA populations, including pmoA mRNA. Methane consumption in live S. crosnieri was also estimated by continuous-flow incubation under atmospheric and in situ hydrostatic pressures, and provided a clear evidence of methane oxidation activity of the epibiotic microbial community, which was not significantly affected by hydrostatic pressure. Our study revealed the significant ecological function and nutritional contribution of epibiotic methanotrophs to the predominant S. crosnieri populations in the Okinawa Trough deep-sea hydrothermal systems. In conclusion, our study gave clear facts about diversity and methane oxidation of active methanotrophs in the epibiotic community associated with invertebrates.
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Affiliation(s)
- Tomo-o Watsuji
- Subsurface Geobiology Advanced Research (SUGAR) Project, Extremobiosphere Research Program (XBR), Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Asami Yamamoto
- 1] Subsurface Geobiology Advanced Research (SUGAR) Project, Extremobiosphere Research Program (XBR), Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan [2] Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Yoshihiro Takaki
- Chemosymbiosis System Genomics Team, XBR, Institute of Biogeosciences, JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Kenji Ueda
- Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Shinsuke Kawagucci
- Subsurface Geobiology Advanced Research (SUGAR) Project, Extremobiosphere Research Program (XBR), Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Subsurface Geobiology Advanced Research (SUGAR) Project, Extremobiosphere Research Program (XBR), Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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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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The (d)evolution of methanotrophy in the Beijerinckiaceae--a comparative genomics analysis. ISME JOURNAL 2013; 8:369-82. [PMID: 23985741 DOI: 10.1038/ismej.2013.145] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 07/17/2013] [Accepted: 07/24/2013] [Indexed: 01/26/2023]
Abstract
The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. This was supported by a compositional analysis suggesting that all MMOs in Alphaproteobacteria methanotrophs are foreign in origin. Some members of the Beijerinckiaceae subsequently lost methanotrophic functions and regained the ability to grow on multicarbon energy substrates. We conclude that B. indica is a recidivist multitroph, the only known example of a bacterium having completely abandoned an evolved lifestyle of specialized methanotrophy.
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Lüke C, Frenzel P, Ho A, Fiantis D, Schad P, Schneider B, Schwark L, Utami SR. Macroecology of methane-oxidizing bacteria: the β-diversity ofpmoAgenotypes in tropical and subtropical rice paddies. Environ Microbiol 2013; 16:72-83. [DOI: 10.1111/1462-2920.12190] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Claudia Lüke
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
- Radboud University Nijmegen; Heyendaalsweg 135 Nijmegen 6525 AJ The Netherlands
| | - Peter Frenzel
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
| | - Adrian Ho
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
- Laboratory for Microbial Ecology and Technology (LabMET); Faculty of Bioscience Engineering; Coupure Links 653 Ghent 9000 Belgium
| | - Dian Fiantis
- Department of Soil Science; Faculty of Agriculture; Andalas University; Kampus Unand Limau Manis Padang 25163 Indonesia
| | - Peter Schad
- Department Ecology and Ecosystem Management; Center of Life and Food Sciences Weihenstephan; Technische Universität München; Lehrstuhl für Bodenkunde Freising-Weihenstephan D-85350 Germany
| | - Bellinda Schneider
- Max Planck Institute for Terrestrial Microbiology; Karl-von-Frisch-Str.10 Marburg D-35043 Germany
| | - Lorenz Schwark
- Institute of Geosciences; University Kiel; Ludewig-Meyn-Straße 10 Kiel 24118 Germany
- WA-OIGC; Curtin University; Perth WA 6845 Australia
| | - Sri Rahayu Utami
- Department of Soil Science; Faculty of Agriculture; Brawijaya University; Jalan Veteran Malang 65145 East Java Indonesia
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Aerobic Methanotrophs in Natural and Agricultural Soils of European Russia. DIVERSITY 2013. [DOI: 10.3390/d5030541] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Lau E, Fisher MC, Steudler PA, Cavanaugh CM. The methanol dehydrogenase gene, mxaF, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments. PLoS One 2013; 8:e56993. [PMID: 23451130 PMCID: PMC3579938 DOI: 10.1371/journal.pone.0056993] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/16/2013] [Indexed: 11/27/2022] Open
Abstract
The mxaF gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the Alpha-, Beta- and Gammaproteobacteria. It is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoA and mmoX genes, which are absent in some methanotrophic proteobacterial genera. This study examined the potential for using the mxaF gene as a functional and phylogenetic marker for methanotrophs. mxaF and 16S rRNA gene phylogenies were constructed based on over 100 database sequences of known proteobacterial methanotrophs and other methylotrophs to assess their evolutionary histories. Topology tests revealed that mxaF and 16S rDNA genes of methanotrophs do not show congruent evolutionary histories, with incongruencies in methanotrophic taxa in the Methylococcaceae, Methylocystaceae, and Beijerinckiacea. However, known methanotrophs generally formed coherent clades based on mxaF gene sequences, allowing for phylogenetic discrimination of major taxa. This feature highlights the mxaF gene's usefulness as a biomarker in studying the molecular diversity of proteobacterial methanotrophs in nature. To verify this, PCR-directed assays targeting this gene were used to detect novel methanotrophs from diverse environments including soil, peatland, hydrothermal vent mussel tissues, and methanotroph isolates. The placement of the majority of environmental mxaF gene sequences in distinct methanotroph-specific clades (Methylocystaceae and Methylococcaceae) detected in this study supports the use of mxaF as a biomarker for methanotrophic proteobacteria.
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Affiliation(s)
- Evan Lau
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America.
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Dedysh SN, Dunfield PF, Derakshani M, Stubner S, Heyer J, Liesack W. Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes. FEMS Microbiol Ecol 2012; 43:299-308. [PMID: 19719661 DOI: 10.1111/j.1574-6941.2003.tb01070.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Abstract Based on an extensive 16S rRNA sequence database for type II methanotrophic bacteria, a set of 16S rRNA-targeted oligonucleotide probes was developed for differential detection of specific phylogenetic groups of these bacteria by fluorescence in situ hybridisation (FISH). This set of oligonucleotides included a genus-specific probe for Methylocystis (Mcyst-1432) and three species-specific probes for Methylosinus sporium (Msins-647), Methylosinus trichosporium (Msint-1268) and the recently described acidophilic methanotroph Methylocapsa acidiphila (Mcaps-1032). These novel probes were applied to further characterise the type II methanotroph community that was detected in an acidic Sphagnum peat from West Siberia in a previous study (Dedysh et al. (2001) Appl. Environ. Microbiol. 67, 4850-4857). The largest detectable population of indigenous methanotrophs simultaneously hybridised with a group-specific probe targeting all currently known Methylosinus/Methylocystis spp. (M-450), with a genus-specific probe for Methylocystis spp. (Mcyst-1432), and with an additional probe (Mcyst-1261) that had been designed to target a defined phylogenetic subgroup of Methylocystis spp. The same subgroup of Methylocystis was also detected in acidic peat sampled from Sphagnum-dominated wetland in northern Germany. The population size of this peat-inhabiting Methylocystis subgroup was 2.0+/-0.1x10(6) cells g(-1) (wet weight) of peat from Siberia and 5.5+/-0.5x10(6) cells g(-1) of peat from northern Germany. This represented 60 and 95%, respectively, of the total number of methanotroph cells detected by FISH in these two wetland sites. Other major methanotroph populations were M. acidiphila and Methylocella palustris. Type I methanotrophs accounted for not more than 1% of total methanotroph cells. Neither M. trichosporium nor M. sporium were detected in acidic Sphagnum peat.
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Affiliation(s)
- Svetlana N Dedysh
- Institute of Microbiology, Russian Academy of Sciences, Moscow 117811, Russia
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43
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Chauhan A, Pathak A, Ogram A. Composition of methane-oxidizing bacterial communities as a function of nutrient loading in the Florida everglades. MICROBIAL ECOLOGY 2012; 64:750-759. [PMID: 22544346 DOI: 10.1007/s00248-012-0058-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 04/11/2012] [Indexed: 05/31/2023]
Abstract
Agricultural runoff of phosphorus (P) in the northern Florida Everglades has resulted in several ecosystem level changes, including shifts in the microbial ecology of carbon cycling, with significantly higher methane being produced in the nutrient-enriched soils. Little is, however, known of the structure and activities of methane-oxidizing bacteria (MOB) in these environments. To address this, 0 to 10 cm plant-associated soil cores were collected from nutrient-impacted (F1), transition (F4), and unimpacted (U3) areas, sectioned in 2-cm increments, and methane oxidation rates were measured. F1 soils consumed approximately two-fold higher methane than U3 soils; additionally, most probable numbers of methanotrophs were 4-log higher in F1 than U3 soils. Metabolically active MOB containing pmoA sequences were characterized by stable-isotope probing using 10 % (v/v) (13)CH(4). pmoA sequences, encoding the alpha subunit of methane monooxygenase and related to type I methanotrophs, were identified from both impacted and unimpacted soils. Additionally, impacted soils also harbored type II methanotrophs, which have been shown to exhibit preferences for high methane concentrations. Additionally, across all soils, novel pmoA-type sequences were also detected, indicating presence of MOB specific to the Everglades. Multivariate statistical analyses confirmed that eutrophic soils consisted of metabolically distinct MOB community that is likely driven by nutrient enrichment. This study enhances our understanding on the biological fate of methane being produced in productive wetland soils of the Florida Everglades and how nutrient-enrichment affects the composition of methanotroph bacterial communities.
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Affiliation(s)
- Ashvini Chauhan
- School of the Environment, Florida A&M University, Tallahassee, FL 32307, 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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45
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Function and limits of biofilters for the removal of methane in exhaust gases from the pig industry. Appl Microbiol Biotechnol 2012; 94:601-11. [DOI: 10.1007/s00253-012-3998-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/24/2012] [Accepted: 02/27/2012] [Indexed: 10/28/2022]
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Dourado MN, Andreote FD, Dini-Andreote F, Conti R, Araújo JM, Araújo WL. Analysis of 16S rRNA and mxaF genes revealing insights into Methylobacterium niche-specific plant association. Genet Mol Biol 2012; 35:142-8. [PMID: 22481887 PMCID: PMC3313503 DOI: 10.1590/s1415-47572012005000017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 12/09/2011] [Indexed: 11/21/2022] Open
Abstract
The genus Methylobacterium comprises pink-pigmented facultative methylotrophic (PPFM) bacteria, known to be an important plant-associated bacterial group. Species of this group, described as plant-nodulating, have the dual capacity of producing cytokinin and enzymes, such as pectinase and cellulase, involved in systemic resistance induction and nitrogen fixation under specific plant environmental conditions. The aim hereby was to evaluate the phylogenetic distribution of Methylobacterium spp. isolates from different host plants. Thus, a comparative analysis between sequences from structural (16S rRNA) and functional mxaF (which codifies for a subunit of the enzyme methanol dehydrogenase) ubiquitous genes, was undertaken. Notably, some Methylobacterium spp. isolates are generalists through colonizing more than one host plant, whereas others are exclusively found in certain specific plant-species. Congruency between phylogeny and specific host inhabitance was higher in the mxaF gene than in the 16S rRNA, a possible indication of function-based selection in this niche. Therefore, in a first stage, plant colonization by Methylobacterium spp. could represent generalist behavior, possibly related to microbial competition and adaptation to a plant environment. Otherwise, niche-specific colonization is apparently impelled by the host plant.
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Affiliation(s)
- Manuella Nóbrega Dourado
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, Brazil
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Meena KK, Kumar M, Kalyuzhnaya MG, Yandigeri MS, Singh DP, Saxena AK, Arora DK. Epiphytic pink-pigmented methylotrophic bacteria enhance germination and seedling growth of wheat (Triticum aestivum) by producing phytohormone. Antonie van Leeuwenhoek 2011; 101:777-86. [PMID: 22200783 DOI: 10.1007/s10482-011-9692-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 12/15/2011] [Indexed: 10/14/2022]
Abstract
Methylotrophic bacteria were isolated from the phyllosphere of different crop plants such as sugarcane, pigeonpea, mustard, potato and radish. The methylotrophic isolates were differentiated based on growth characteristics and colony morphology on methanol supplemented ammonium mineral salts medium. Amplification of the mxaF gene helped in the identification of the methylotrophic isolates as belonging to the genus Methylobacterium. Cell-free culture filtrates of these strains enhanced seed germination of wheat (Triticum aestivum) with highest values of 98.3% observed using Methylobacterium sp. (NC4). Highest values of seedling length and vigour were recorded with Methylobacterium sp. (NC28). HPLC analysis of production by bacterial strains ranged from 1.09 to 9.89 μg ml(-1) of cytokinins in the culture filtrate. Such cytokinin producing beneficial methylotrophs can be useful in developing bio-inoculants through co-inoculation of pink-pigmented facultative methylotrophs with other compatible bacterial strains, for improving plant growth and productivity, in an environment-friendly manner.
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Affiliation(s)
- Kamlesh K Meena
- National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, India.
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Borrel G, Jézéquel D, Biderre-Petit C, Morel-Desrosiers N, Morel JP, Peyret P, Fonty G, Lehours AC. Production and consumption of methane in freshwater lake ecosystems. Res Microbiol 2011; 162:832-47. [DOI: 10.1016/j.resmic.2011.06.004] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
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Graef C, Hestnes AG, Svenning MM, Frenzel P. The active methanotrophic community in a wetland from the High Arctic. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:466-472. [PMID: 23761309 DOI: 10.1111/j.1758-2229.2010.00237.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The dominant terminal process of carbon mineralization in most freshwater wetlands is methanogenesis. With methane being an important greenhouse gas, the predicted warming of the Arctic may provide a positive feedback. However, the amount of methane released to the atmosphere may be controlled by the activity of methane-oxidizing bacteria (methanotrophs) living in the oxic surface layer of wetlands. Previously, methanotrophs have been isolated and identified by genetic profiling in High Arctic wetlands showing the presence of only a few genotypes. Two isolates from Solvatnet (Ny-Ålesund, Spitsbergen; 79°N) are available: Methylobacter tundripaludum (type I) and Methylocystis rosea (type II), raising the question whether the low diversity is a cultivation effect. We have revisited Solvatnet applying stable isotope probing (SIP) with (13) C-labelled methane. 16S rRNA profiling revealed active type I methanotrophs including M. tundripaludum, while no active type II methanotrophs were identified. These results indicate that the extant M. tundripaludum is an active methane oxidizer at its locus typicus; furthermore, Methylobacter seems to be the dominant active genus. Diversity of methanotrophs was low as compared, e.g. to wetland rice fields in the Mediterranean. This low diversity suggests a high vulnerability of Arctic methanotroph communities, which deserves more attention.
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Affiliation(s)
- Christiane Graef
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, University of Tromsø, N-9037 Tromsø, Norway. Max-Planck-Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
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Biderre-Petit C, Jézéquel D, Dugat-Bony E, Lopes F, Kuever J, Borrel G, Viollier E, Fonty G, Peyret P. Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake. FEMS Microbiol Ecol 2011; 77:533-45. [PMID: 21595728 DOI: 10.1111/j.1574-6941.2011.01134.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Lake Pavin is a meromictic crater lake located in the French Massif Central area. In this ecosystem, most methane (CH(4)) produced in high quantity in the anoxic bottom layers, and especially in sediments, is consumed in the water column, with only a small fraction of annual production reaching the atmosphere. This study assessed the diversity of methanogenic and methanotrophic populations along the water column and in sediments using PCR and reverse transcription-PCR-based approaches targeting functional genes, i.e. pmoA (α-subunit of the particulate methane monooxygenase) for methanotrophy and mcrA (α-subunit of the methyl-coenzyme M reductase) for methanogenesis as well as the phylogenetic 16S rRNA genes. Although methanogenesis rates were much higher in sediments, our results confirm that CH(4) production also occurs in the water column where methanogens were almost exclusively composed of hydrogenotrophic methanogens, whereas both hydrogenotrophs and acetotrophs were almost equivalent in the sediments. Sequence analysis of markers, pmoA and the 16S rRNA gene, suggested that Methylobacter may be an important group actively involved in CH(4) oxidation in the water column. Two main phylotypes were characterized, one of which could consume CH(4) under conditions where the oxygen amount is undetectable.
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Affiliation(s)
- Corinne Biderre-Petit
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université, Université Blaise Pascal, BP 10448, Clermont-Ferrand, France
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