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Kröber E, Kanukollu S, Wende S, Bringel F, Kolb S. A putatively new family of alphaproteobacterial chloromethane degraders from a deciduous forest soil revealed by stable isotope probing and metagenomics. ENVIRONMENTAL MICROBIOME 2022; 17:24. [PMID: 35527282 PMCID: PMC9080209 DOI: 10.1186/s40793-022-00416-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/19/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Chloromethane (CH3Cl) is the most abundant halogenated organic compound in the atmosphere and substantially responsible for the destruction of the stratospheric ozone layer. Since anthropogenic CH3Cl sources have become negligible with the application of the Montreal Protocol (1987), natural sources, such as vegetation and soils, have increased proportionally in the global budget. CH3Cl-degrading methylotrophs occurring in soils might be an important and overlooked sink. RESULTS AND CONCLUSIONS The objective of our study was to link the biotic CH3Cl sink with the identity of active microorganisms and their biochemical pathways for CH3Cl degradation in a deciduous forest soil. When tested in laboratory microcosms, biological CH3Cl consumption occurred in leaf litter, senescent leaves, and organic and mineral soil horizons. Highest consumption rates, around 2 mmol CH3Cl g-1 dry weight h-1, were measured in organic soil and senescent leaves, suggesting that top soil layers are active (micro-)biological CH3Cl degradation compartments of forest ecosystems. The DNA of these [13C]-CH3Cl-degrading microbial communities was labelled using stable isotope probing (SIP), and the corresponding taxa and their metabolic pathways studied using high-throughput metagenomics sequencing analysis. [13C]-labelled Metagenome-Assembled Genome closely related to the family Beijerinckiaceae may represent a new methylotroph family of Alphaproteobacteria, which is found in metagenome databases of forest soils samples worldwide. Gene markers of the only known pathway for aerobic CH3Cl degradation, via the methyltransferase system encoded by the CH3Cl utilisation genes (cmu), were undetected in the DNA-SIP metagenome data, suggesting that biological CH3Cl sink in this deciduous forest soil operates by a cmu-independent metabolism.
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Affiliation(s)
- Eileen Kröber
- Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Saranya Kanukollu
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Sonja Wende
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Françoise Bringel
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
| | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
- Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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2
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Bashir I, War AF, Rafiq I, Reshi ZA, Rashid I, Shouche YS. Phyllosphere microbiome: Diversity and functions. Microbiol Res 2021; 254:126888. [PMID: 34700185 DOI: 10.1016/j.micres.2021.126888] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.
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Affiliation(s)
- Iqra Bashir
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India.
| | - Aadil Farooq War
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Iflah Rafiq
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Irfan Rashid
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
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3
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Kröber E, Wende S, Kanukollu S, Buchen-Tschiskale C, Besaury L, Keppler F, Vuilleumier S, Kolb S, Bringel F. 13 C-chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern. Environ Microbiol 2021; 23:4450-4465. [PMID: 34121306 DOI: 10.1111/1462-2920.15638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/20/2022]
Abstract
Chloromethane (CH3 Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH3 Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH3 Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH3 Cl-degrading bacteria associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with 13 C-labelled CH3 Cl combined with metagenomics. Metagenome-assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH3 Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH3 Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH3 Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterized methylotrophic cmuA-independent pathway may drive CH3 Cl degradation in the investigated tree ferns.
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Affiliation(s)
- Eileen Kröber
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Sonja Wende
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Saranya Kanukollu
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Caroline Buchen-Tschiskale
- Isotope Biogeochemistry and Gas Fluxes, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Ludovic Besaury
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
| | - Frank Keppler
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Stéphane Vuilleumier
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
| | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Françoise Bringel
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
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4
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Horst A, Bonifacie M, Bardoux G, Richnow HH. Isotopic Characterization ( 2H, 13C, 37Cl, 81Br) of Abiotic Degradation of Methyl Bromide and Methyl Chloride in Water and Implications for Future Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:8813-8822. [PMID: 31286766 DOI: 10.1021/acs.est.9b02165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Methyl bromide (CH3Br) and methyl chloride (CH3Cl) significantly contribute to stratospheric ozone depletion. The atmospheric budgets of both compounds are unbalanced with known degradation processes outweighing known emissions. Stable isotope analysis may be capable to identify and quantify emissions and to achieve a balanced budget. Degradation processes do, however, cause isotope fractionation in methyl halides after emission and hence knowledge about these processes is a crucial prerequisite for any isotopic mass balance approach. In the current study, triple-element isotope analysis (2H, 13C, 37Cl/81Br) was applied to investigate the two main abiotic degradation processes of methyl halides (CH3X) in fresh and seawater: hydrolysis and halide exchange. For CH3Br, nucleophilic attack by both H2O and Cl- caused significant primary carbon and bromine isotope effects accompanied by a secondary inverse hydrogen isotope effect. For CH3Cl only nucleophilic substitution by H2O was observed at significant rates causing large primary carbon and chlorine isotope effects and a secondary inverse hydrogen isotope effect. Observed dual-element isotope ratios differed slightly from literature values for microbial degradation in water and hugely from radical reactions in the troposphere. This bodes well for successfully distinguishing and quantifying degradation processes in atmospheric methyl halides using triple-element isotope analysis.
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Affiliation(s)
- Axel Horst
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research - UFZ , Permoserstr.15 , 04318 Leipzig , Germany
| | - Magali Bonifacie
- Institut de Physique du Globe de Paris , Sorbonne Paris Cité, Université Paris-Diderot, UMR 7154 CNRS , 1 rue Jussieu , F-75005 Paris , France
| | - Gérard Bardoux
- Institut de Physique du Globe de Paris , Sorbonne Paris Cité, Université Paris-Diderot, UMR 7154 CNRS , 1 rue Jussieu , F-75005 Paris , France
| | - Hans Hermann Richnow
- Department of Isotope Biogeochemistry , Helmholtz Centre for Environmental Research - UFZ , Permoserstr.15 , 04318 Leipzig , Germany
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5
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Bhatt P, Pal K, Bhandari G, Barh A. Modelling of the methyl halide biodegradation in bacteria and its effect on environmental systems. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 158:88-100. [PMID: 31378365 DOI: 10.1016/j.pestbp.2019.04.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 06/10/2023]
Abstract
Methyl halide group of pesticides are being used widely in past decades as fumigant but due to their hazardous effect, these pesticides are not sold directly. They are volatile and gaseous in nature and may easily come in the contact of trophosphere and stratosphere. In troposphere, they are harmful to the living beings; nevertheless, in stratosphere they react with ozone and degrade the ozone layers. In this study, we have investigated the in-silico pathways of methyl halide and its toxic effect on living systems like pest, humans and environment. Till date, limited studies provide the understanding of degradation of methyl halide and its effect on the environment. This leads to availability of scanty information for overall bio-magnifications of methyl halides at molecular and cellular level. The model developed in the present study explains how a volatile toxic compound not only affects living systems on earth but also on environmental layers. Hub nodes were also evaluated by investigating the developed model topologically. Methyl transferase system is identified as promising enzyme in response to degradation of methyl halides.
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Affiliation(s)
- Pankaj Bhatt
- Department of Microbiology, Dolphin (P.G) Institute of Biomedical and Natural Sciences Dehradun, Uttarakhand, India.
| | - Kalyanbrata Pal
- Department of Microbiology, Dolphin (P.G) Institute of Biomedical and Natural Sciences Dehradun, Uttarakhand, India
| | - Geeta Bhandari
- Sardar Bhagwan Singh University, Dehradun, Uttarakhand, India
| | - Anupam Barh
- ICAR-Directorate of Mushroom Research, Solan, H.P, India
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6
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Chaignaud P, Morawe M, Besaury L, Kröber E, Vuilleumier S, Bringel F, Kolb S. Methanol consumption drives the bacterial chloromethane sink in a forest soil. ISME JOURNAL 2018; 12:2681-2693. [PMID: 29991765 PMCID: PMC6194010 DOI: 10.1038/s41396-018-0228-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/01/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022]
Abstract
Halogenated volatile organic compounds (VOCs) emitted by terrestrial ecosystems, such as chloromethane (CH3Cl), have pronounced effects on troposphere and stratosphere chemistry and climate. The magnitude of the global CH3Cl sink is uncertain since it involves a largely uncharacterized microbial sink. CH3Cl represents a growth substrate for some specialized methylotrophs, while methanol (CH3OH), formed in much larger amounts in terrestrial environments, may be more widely used by such microorganisms. Direct measurements of CH3Cl degradation rates in two field campaigns and in microcosms allowed the identification of top soil horizons (i.e., organic plus mineral A horizon) as the major biotic sink in a deciduous forest. Metabolically active members of Alphaproteobacteria and Actinobacteria were identified by taxonomic and functional gene biomarkers following stable isotope labeling (SIP) of microcosms with CH3Cl and CH3OH, added alone or together as the [13C]-isotopologue. Well-studied reference CH3Cl degraders, such as Methylobacterium extorquens CM4, were not involved in the sink activity of the studied soil. Nonetheless, only sequences of the cmuA chloromethane dehalogenase gene highly similar to those of known strains were detected, suggesting the relevance of horizontal gene transfer for CH3Cl degradation in forest soil. Further, CH3Cl consumption rate increased in the presence of CH3OH. Members of Alphaproteobacteria and Actinobacteria were also 13C-labeled upon [13C]-CH3OH amendment. These findings suggest that key bacterial CH3Cl degraders in forest soil benefit from CH3OH as an alternative substrate. For soil CH3Cl-utilizing methylotrophs, utilization of several one-carbon compounds may represent a competitive advantage over heterotrophs that cannot utilize one-carbon compounds.
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Affiliation(s)
- Pauline Chaignaud
- Department of Microbiology, Genomics and the Environment, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Mareen Morawe
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Ludovic Besaury
- Department of Microbiology, Genomics and the Environment, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,UMR FARE 614 Fractionnement des AgroRessources et Environnement, Chaire AFERE, INRA, Université de Reims Champagne-Ardenne, Reims, France
| | - Eileen Kröber
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Landscape Research, Müncheberg, Germany
| | - Stéphane Vuilleumier
- Department of Microbiology, Genomics and the Environment, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Françoise Bringel
- Department of Microbiology, Genomics and the Environment, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.
| | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Landscape Research, Müncheberg, Germany.
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7
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Correlated production and consumption of chloromethane in the Arabidopsis thaliana phyllosphere. Sci Rep 2017; 7:17589. [PMID: 29242530 PMCID: PMC5730606 DOI: 10.1038/s41598-017-17421-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/24/2017] [Indexed: 11/24/2022] Open
Abstract
Chloromethane (CH3Cl) is a toxic gas mainly produced naturally, in particular by plants, and its emissions contribute to ozone destruction in the stratosphere. Conversely, CH3Cl can be degraded and used as the sole carbon and energy source by specialised methylotrophic bacteria, isolated from a variety of environments including the phyllosphere, i.e. the aerial parts of vegetation. The potential role of phyllospheric CH3Cl-degrading bacteria as a filter for plant emissions of CH3Cl was investigated using variants of Arabidopsis thaliana with low, wild-type and high expression of HOL1 methyltransferase previously shown to be responsible for most of CH3Cl emissions by A. thaliana. Presence and expression of the bacterial chloromethane dehalogenase cmuA gene in the A. thaliana phyllosphere correlated with HOL1 genotype, as shown by qPCR and RT-qPCR. Production of CH3Cl by A. thaliana paralleled HOL1 expression, as assessed by a fluorescence-based bioreporter. The relation between plant production of CH3Cl and relative abundance of CH3Cl-degrading bacteria in the phyllosphere suggests that CH3Cl-degrading bacteria co-determine the extent of plant emissions of CH3Cl to the atmosphere.
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8
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Eyice Ö, Schäfer H. Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments. Arch Microbiol 2015; 198:17-26. [DOI: 10.1007/s00203-015-1160-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 09/27/2015] [Accepted: 10/03/2015] [Indexed: 10/22/2022]
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9
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Doronina NV, Torgonskaya ML, Fedorov DN, Trotsenko YA. Aerobic methylobacteria as promising objects of modern biotechnology (Review). APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815020052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Nadalig T, Greule M, Bringel F, Keppler F, Vuilleumier S. Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation. Front Microbiol 2014; 5:523. [PMID: 25360131 PMCID: PMC4197683 DOI: 10.3389/fmicb.2014.00523] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/19/2014] [Indexed: 11/13/2022] Open
Abstract
Chloromethane (CH3Cl) is produced on earth by a variety of abiotic and biological processes. It is the most important halogenated trace gas in the atmosphere, where it contributes to ozone destruction. Current estimates of the global CH3Cl budget are uncertain and suggest that microorganisms might play a more important role in degrading atmospheric CH3Cl than previously thought. Its degradation by bacteria has been demonstrated in marine, terrestrial, and phyllospheric environments. Improving our knowledge of these degradation processes and their magnitude is thus highly relevant for a better understanding of the global budget of CH3Cl. The cmu pathway, for chloromethane utilisation, is the only microbial pathway for CH3Cl degradation elucidated so far, and was characterized in detail in aerobic methylotrophic Alphaproteobacteria. Here, we reveal the potential of using a two-pronged approach involving a combination of comparative genomics and isotopic fractionation during CH3Cl degradation to newly address the question of the diversity of chloromethane-degrading bacteria in the environment. Analysis of available bacterial genome sequences reveals that several bacteria not yet known to degrade CH3Cl contain part or all of the complement of cmu genes required for CH3Cl degradation. These organisms, unlike bacteria shown to grow with CH3Cl using the cmu pathway, are obligate anaerobes. On the other hand, analysis of the complete genome of the chloromethane-degrading bacterium Leisingera methylohalidivorans MB2 showed that this bacterium does not contain cmu genes. Isotope fractionation experiments with L. methylohalidivorans MB2 suggest that the unknown pathway used by this bacterium for growth with CH3Cl can be differentiated from the cmu pathway. This result opens the prospect that contributions from bacteria with the cmu and Leisingera-type pathways to the atmospheric CH3Cl budget may be teased apart in the future.
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Affiliation(s)
- Thierry Nadalig
- Université de Strasbourg, Equipe Adaptations et Interactions Microbiennes dans l'Environnement, Unitès Mixtes de Recherche 7156 Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie Strasbourg, France
| | - Markus Greule
- Institute of Earth Sciences, Ruprecht Karls University Heidelberg Heidelberg, Germany
| | - Françoise Bringel
- Université de Strasbourg, Equipe Adaptations et Interactions Microbiennes dans l'Environnement, Unitès Mixtes de Recherche 7156 Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie Strasbourg, France
| | - Frank Keppler
- Institute of Earth Sciences, Ruprecht Karls University Heidelberg Heidelberg, Germany
| | - Stéphane Vuilleumier
- Université de Strasbourg, Equipe Adaptations et Interactions Microbiennes dans l'Environnement, Unitès Mixtes de Recherche 7156 Centre National de la Recherche Scientifique, Génétique Moléculaire, Génomique, Microbiologie Strasbourg, France
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11
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Madhaiyan M, Poonguzhali S. Methylobacterium pseudosasicola sp. nov. and Methylobacterium phyllostachyos sp. nov., isolated from bamboo leaf surfaces. Int J Syst Evol Microbiol 2014; 64:2376-2384. [DOI: 10.1099/ijs.0.057232-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Two strains of Gram-negative, methylotrophic bacteria, isolated because of their abilities to promote plant growth, were subjected to a polyphasic taxonomic study. The isolates were strictly aerobic, motile, pink-pigmented, facultatively methylotrophic, non-spore-forming rods. The chemotaxonomic characteristics of the isolates included the presence of C18 : 1ω7c as the major cellular fatty acid. The DNA G+C contents of strains BL36T and BL47T were 69.4 and 69.8 mol%, respectively. 16S rRNA gene sequence analysis of strains BL36T and BL47T placed them under the genus
Methylobacterium,
with the pairwise sequence similarity between them and the type strains of closely related species ranging from 97.2 to 99.0 %. On the basis of their phenotypic and phylogenetic distinctiveness and the results of DNA–DNA hybridization analysis, the isolates represent two novel species within the genus
Methylobacterium
, for which the names Methylobacterium pseudosasicola sp. nov. (type strain BL36T = NBRC 105203T = ICMP 17621T) and Methylobacterium phyllostachyos sp. nov. (type strain BL47T = NBRC 105206T = ICMP 17619T) are proposed.
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Affiliation(s)
- Munusamy Madhaiyan
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
| | - Selvaraj Poonguzhali
- Department of Agricultural Microbiology, Tamilnadu Agricultural University, Coimbatore 641 003, Tamilnadu, India
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12
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Roselli S, Nadalig T, Vuilleumier S, Bringel F. The 380 kb pCMU01 plasmid encodes chloromethane utilization genes and redundant genes for vitamin B12- and tetrahydrofolate-dependent chloromethane metabolism in Methylobacterium extorquens CM4: a proteomic and bioinformatics study. PLoS One 2013; 8:e56598. [PMID: 23593113 PMCID: PMC3621897 DOI: 10.1371/journal.pone.0056598] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/11/2013] [Indexed: 12/24/2022] Open
Abstract
Chloromethane (CH3Cl) is the most abundant volatile halocarbon in the atmosphere and contributes to the destruction of stratospheric ozone. The only known pathway for bacterial chloromethane utilization (cmu) was characterized in Methylobacterium extorquens CM4, a methylotrophic bacterium able to utilize compounds without carbon-carbon bonds such as methanol and chloromethane as the sole carbon source for growth. Previous work demonstrated that tetrahydrofolate and vitamin B12 are essential cofactors of cmuA- and cmuB-encoded methyltransferases of chloromethane dehalogenase, and that the pathway for chloromethane utilization is distinct from that for methanol. This work reports genomic and proteomic data demonstrating that cognate cmu genes are located on the 380 kb pCMU01 plasmid, which drives the previously defined pathway for tetrahydrofolate-mediated chloromethane dehalogenation. Comparison of complete genome sequences of strain CM4 and that of four other M. extorquens strains unable to grow with chloromethane showed that plasmid pCMU01 harbors unique genes without homologs in the compared genomes (bluB2, btuB, cobA, cbiD), as well as 13 duplicated genes with homologs of chromosome-borne genes involved in vitamin B12-associated biosynthesis and transport, or in tetrahydrofolate-dependent metabolism (folC2). In addition, the presence of both chromosomal and plasmid-borne genes for corrinoid salvaging pathways may ensure corrinoid coenzyme supply in challenging environments. Proteomes of M. extorquens CM4 grown with one-carbon substrates chloromethane and methanol were compared. Of the 49 proteins with differential abundance identified, only five (CmuA, CmuB, PurU, CobH2 and a PaaE-like uncharacterized putative oxidoreductase) are encoded by the pCMU01 plasmid. The mainly chromosome-encoded response to chloromethane involves gene clusters associated with oxidative stress, production of reducing equivalents (PntAA, Nuo complex), conversion of tetrahydrofolate-bound one-carbon units, and central metabolism. The mosaic organization of plasmid pCMU01 and the clustering of genes coding for dehalogenase enzymes and for biosynthesis of associated cofactors suggests a history of gene acquisition related to chloromethane utilization.
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Affiliation(s)
- Sandro Roselli
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Thierry Nadalig
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Stéphane Vuilleumier
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
| | - Françoise Bringel
- Département Génétique Moléculaire, Génomique, Microbiologie, Université de Strasbourg, UMR7156, Centre national de la recherche scientifique, Strasbourg, France
- * E-mail:
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13
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Elucidation of the role of the methylene-tetrahydromethanopterin dehydrogenase MtdA in the tetrahydromethanopterin-dependent oxidation pathway in Methylobacterium extorquens AM1. J Bacteriol 2013; 195:2359-67. [PMID: 23504017 DOI: 10.1128/jb.00029-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The methylotroph Methylobacterium extorquens AM1 oxidizes methanol and methylamine to formaldehyde and subsequently to formate, an intermediate that serves as the branch point between assimilation (formation of biomass) and dissimilation (oxidation to CO₂). The oxidation of formaldehyde to formate is dephosphotetrahydromethanopterin (dH₄MPT) dependent, while the assimilation of carbon into biomass is tetrahydrofolate (H₄F) dependent. This bacterium contains two different enzymes, MtdA and MtdB, both of which are dehydrogenases able to use methylene-dH₄MPT, an intermediate in the oxidation of formaldehyde to formate. Unique to MtdA is a second enzymatic activity with methylene-H₄F. Since methylene-H₄F is the entry point into the biomass pathways, MtdA plays a key role in assimilatory metabolism. However, its role in oxidative metabolism via the dH₄MPT-dependent pathway and its apparent inability to replace MtdB in vivo on methanol growth are not understood. Here, we have shown that an mtdB mutant is able to grow on methylamine, providing a system to study the role of MtdA. We demonstrate that the absence of MtdB results in the accumulation of methenyl-dH₄MPT. Methenyl-dH₄MPT is shown to be a competitive inhibitor of the reduction of methenyl-H₄F to methylene-H₄F catalyzed by MtdA, with an estimated Ki of 10 μM. Thus, methenyl-dH₄MPT accumulation inhibits H₄F-dependent assimilation. Overexpression of mch in the mtdB mutant strain, predicted to reduce methenyl-dH₄MPT accumulation, enhances growth on methylamine. Our model proposes that MtdA regulates carbon flux due to differences in its kinetic properties for methylene-dH₄MPT and for methenyl-H₄F during growth on single-carbon compounds.
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Cox MJ, Schäfer H, Nightingale PD, McDonald IR, Murrell JC. Diversity of methyl halide-degrading microorganisms in oceanic and coastal waters. FEMS Microbiol Lett 2012; 334:111-8. [DOI: 10.1111/j.1574-6968.2012.02624.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 06/19/2012] [Accepted: 06/20/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Michael J. Cox
- School of Life Sciences; University of Warwick; Coventry; UK
| | - Hendrik Schäfer
- School of Life Sciences; University of Warwick; Coventry; UK
| | | | - Ian R. McDonald
- Department of Biological Sciences; University of Waikato; Hamilton; New Zealand
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Knief C, Dengler V, Bodelier PLE, Vorholt JA. Characterization of Methylobacterium strains isolated from the phyllosphere and description of Methylobacterium longum sp. nov. Antonie van Leeuwenhoek 2011; 101:169-83. [DOI: 10.1007/s10482-011-9650-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 09/24/2011] [Indexed: 11/27/2022]
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Nadalig T, Farhan Ul Haque M, Roselli S, Schaller H, Bringel F, Vuilleumier S. Detection and isolation of chloromethane-degrading bacteria from the Arabidopsis thaliana phyllosphere, and characterization of chloromethane utilization genes. FEMS Microbiol Ecol 2011; 77:438-48. [PMID: 21545604 DOI: 10.1111/j.1574-6941.2011.01125.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Chloromethane gas is produced naturally in the phyllosphere, the compartment defined as the aboveground parts of vegetation, which hosts a rich bacterial flora. Chloromethane may serve as a growth substrate for specialized aerobic methylotrophic bacteria, which have been isolated from soil and water environments, and use cmu genes for chloromethane utilization. Evidence for the presence of chloromethane-degrading bacteria on the leaf surfaces of Arabidopsis thaliana was obtained by specific quantitative PCR of the cmuA gene encoding the two-domain methyltransferase corrinoid protein of chloromethane dehalogenase. Bacterial strains were isolated on a solid mineral medium with chloromethane as the sole carbon source from liquid mineral medium enrichment cultures inoculated with leaves of A. thaliana. Restriction analysis-based genotyping of cmuA PCR products was used to evaluate the diversity of chloromethane-degrading bacteria during enrichment and after strain isolation. The isolates obtained, affiliated to the genus Hyphomicrobium based on their 16S rRNA gene sequence and the presence of characteristic hyphae, dehalogenate chloromethane, and grow in a liquid culture with chloromethane as the sole carbon and energy source. The cmu genes of these isolates were analysed using new PCR primers, and their sequences were compared with those of previously reported aerobic chloromethane-degrading strains. The three isolates featured a colinear cmuBCA gene arrangement similar to that of all previously characterized strains, except Methylobacterium extorquens CM4 of known genome sequence.
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Affiliation(s)
- Thierry Nadalig
- Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France.
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Methylotrophy in a lake: from metagenomics to single-organism physiology. Appl Environ Microbiol 2011; 77:4705-11. [PMID: 21622781 DOI: 10.1128/aem.00314-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This review provides a brief summary of ongoing studies in Lake Washington (Seattle, WA) directed at an understanding of the content and activities of microbial communities involved in methylotrophy. One of the findings from culture-independent approaches, including functional metagenomics, is the prominent presence of Methylotenera species in the site and their inferred activity in C(1) metabolism, highlighting the local environmental importance of this group. Comparative analyses of individual genomes of Methylophilaceae from Lake Washington provide insights into their genomic divergence and suggest significant metabolic flexibility.
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Oelgeschläger E, Rother M. In vivo role of three fused corrinoid/methyl transfer proteins in Methanosarcina acetivorans. Mol Microbiol 2009; 72:1260-72. [PMID: 19432805 DOI: 10.1111/j.1365-2958.2009.06723.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methanosarcina acetivorans is able to use carbon monoxide (CO) as the sole source of energy for growth. Its carboxidotrophic growth is peculiar as it involves formation of acetate, formate and methylated thiols, besides methane. Under this condition three proteins homologous to both corrinoid proteins and methyltransferases (MA0859, MA4384 and MA4558) are highly abundant. To address their role in M. acetivorans, a set of single and double mutants, and the triple mutant, was constructed by deletion/disruption of the encoding genes. Phenotypic analysis of the mutants rules out an important role of the methyltransferase homologues in the CO(2) reduction pathway of methanogenesis. Instead, the single and double mutants were affected to various degrees in their capacity to generate dimethylsulphide (DMS) from CO and to form methane from DMS. The triple mutant was unable to produce or metabolize DMS, and could not grow with DMS as the sole energy source, which demonstrates that MA0859, MA4384 and MA4558 are involved in, and required for, methylsulphide metabolism of M. acetivorans. Based on these findings we propose to designate MA0859, MA4384 and MA4558 as methyltransferases specific for methylsulphides, MtsD, MtsF and MtsH respectively.
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Affiliation(s)
- Ellen Oelgeschläger
- Molekulare Mikrobiologie und Bioenergetik, Institut für Molekulare Biowissenschaften, Goethe-Universität, Frankfurt am Main, Germany
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Substrate-specific clades of active marine methylotrophs associated with a phytoplankton bloom in a temperate coastal environment. Appl Environ Microbiol 2008; 74:7321-8. [PMID: 18849453 DOI: 10.1128/aem.01266-08] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine microorganisms that consume one-carbon (C(1)) compounds are poorly described, despite their impact on global climate via an influence on aquatic and atmospheric chemistry. This study investigated marine bacterial communities involved in the metabolism of C(1) compounds. These communities were of relevance to surface seawater and atmospheric chemistry in the context of a bloom that was dominated by phytoplankton known to produce dimethylsulfoniopropionate. In addition to using 16S rRNA gene fingerprinting and clone libraries to characterize samples taken from a bloom transect in July 2006, seawater samples from the phytoplankton bloom were incubated with (13)C-labeled methanol, monomethylamine, dimethylamine, methyl bromide, and dimethyl sulfide to identify microbial populations involved in the turnover of C(1) compounds, using DNA stable isotope probing. The [(13)C]DNA samples from a single time point were characterized and compared using denaturing gradient gel electrophoresis (DGGE), fingerprint cluster analysis, and 16S rRNA gene clone library analysis. Bacterial community DGGE fingerprints from (13)C-labeled DNA were distinct from those obtained with the DNA of the nonlabeled community DNA and suggested some overlap in substrate utilization between active methylotroph populations growing on different C(1) substrates. Active methylotrophs were affiliated with Methylophaga spp. and several clades of undescribed Gammaproteobacteria that utilized methanol, methylamines (both monomethylamine and dimethylamine), and dimethyl sulfide. rRNA gene sequences corresponding to populations assimilating (13)C-labeled methyl bromide and other substrates were associated with members of the Alphaproteobacteria (e.g., the family Rhodobacteraceae), the Cytophaga-Flexibacter-Bacteroides group, and unknown taxa. This study expands the known diversity of marine methylotrophs in surface seawater and provides a comprehensive data set for focused cultivation and metagenomic analyses in the future.
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