Methane and Methanol Utilizers

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A complication of such an approach is the retrieval of two datasets one with sequences starting with forward and one starting with the reverse primer, but minimizes bias during amplicon amplification Stacheter et al. When mxaF -targeting primers were used, also xoxF -like genes were detected in various grassland and forest soils by amplicon pyrosequencing Stacheter et al.

Analysis of non-methanotrophic methylotrophs by mxaF genotyping has been employed in several studies. All other amplicon-based NGS studies addressed methanotrophs and mostly analyzed pmoA i. The use of amplicon pyrosequencing is a great step forward toward complete coverage of the real diversity that exists in a given habitat. In this review, the authors argue in favor to target structural genes of methanol utilizers. One advantage of the use of structural genes is the increased sensitivity since rare groups, such as methylotrophs in soil communities, can be more reliably detected than by a 16S rRNA gene-based survey.

Several methylotrophs occur in taxa of which only some members are capable of methylotrophy e. The detection of such methylotrophs by 16S rRNA genes can be misleading, and thus, another advantage of the use of genes encoding a methanol-oxidizing enzyme is that the detection of the gene marker is linked with the potential phenotype of MUT. Nonetheless, gene marker-based phylogenies are not always congruent with organismal phylogenies i. In general, mxaF -based phylogenies correlate with organismal phylogenies on the level of families of methylotrophs Kist and Tate, a , b ; Lau et al.

However, for other genes mdh2 , mdo , mdh , mod1 , mod2 , mtaC of methanol-oxidizing enzymes, congruence with organismal phylogenies needs to be evaluated. Recent evaluation of phylogenetic resolution of mxaF compared to organismal phylogenies revealed contradicting results Kist and Tate, a , b ; Lau et al. Nonetheless, strain-level identification is not possible and requires the analysis of more variable genomic regions Knief et al.

Some alphaproteobacterial genera harbor mxaF -like genes that are similar to those of Methylobacterium suggesting the occurrence horizontal gene transfer events in evolution of methylotrophs; Methylobacterium nodulans ORS A carries a plasmid with methylotrophy genes including mxaF , suggesting that this species has acquired this gene from another PPFM bacterium Kist and Tate, a.

Using mxaF as a phylogenetic marker of methanotrophic Proteobacteria revealed that the three major families Methylococcaceae, Methylocystaceae, and Beijerinckiaceae can be unambiguously reconstructed Lau et al. This low mxaF cut-off level even decreases when more species are considered Stacheter et al. A frequently detected mxaF genotype in temperate aerated soils is closely related to the methanotroph Methyloferula stellata AR4.

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Nonetheless, due to lack of congruencies between mxaF and 16S rRNA gene phylogenies in Beijerinckiaceae, it cannot be judged if this mxaF genotype was derived from a methanotroph or a non-methanotrophic methylotroph Lau et al. Thus, a more in-depth analysis of bacteria that harbor MxaFI-, XoxF-, and Mdh2-like MDHs on the level of genomes is warranted to improve the understanding of the role of horizontal gene transfer and convergences in these organisms aiming at a more correct interpretation of mxaF , xoxF -like, and mdh2 datasets retrieved from amplicon-based NGS.

An example is the detection of an actinobacterial MDO-like protein in a metaproteome of rice plants Knief et al. Since the Mdh2 or fungal MDOs have a broad substrate spectrum and may utilize alternative substrates Nakagawa et al. Moreover, many methylotrophs are capable of utilization of multicarbon compounds. Thus, the detection of a genotype does not necessarily mean that the respective microorganism was involved in methanol oxidation in situ.

Hence, approaches combining gene marker-based nucleic acid stable isotope probing SIP; Antony et al. Still not resolved issues for a comprehensive detection of methanol utilizers are a the unresolved quantitative impact of organisms that employ other methanol-oxidizing enzymes than methanol-specific oxidoreductases, and b the detection of methanol utilizers that dissimilate but do not assimilate methanol-derived carbon.

Such organisms might be detectable by SIP when using their actual carbon substrate as a source of isotope label combined with unlabeled methanol and a control, in which the labeled substrate is not supplemented. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. National Center for Biotechnology Information , U. Journal List Front Microbiol v. Front Microbiol. Published online Sep 5.

Author information Article notes Copyright and License information Disclaimer. This article was submitted to Terrestrial Microbiology, a section of the journal Frontiers in Microbiology. Received Jul 19; Accepted Aug The use, distribution or reproduction in other forums is permitted, provided the original author s or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice.

No use, distribution or reproduction is permitted which does not comply with these terms. This article has been cited by other articles in PMC. Abstract The commercial availability of next generation sequencing NGS technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility.

PREFACE The commercial launch of pyrosequencing and later on, further next generation sequencing NGS technologies for direct sequencing of complex PCR amplicons facilitated the assessment of microbial communities by geno- and ribotype composition with high coverage and resolution, and with a high number of samples e.

Table 1 Classes and phyla of Bacteria and fungi that contain methanol-utilizing methylotrophs based on previous reviews Kolb, a ; Gvozdev etal. Open in a separate window. Growth on methanol has not been tested. Table 2 List of methanol-utilizing methylotophs that are not included in a previous survey Kolb, a.

Table 3 Gene markers of methanol-utilizing microorganisms for amplicon-based pyrosequencing or as targets for homology screens in metagenome, -trancriptome, or -proteome datasets. MeOH, methanol oxidation. A Primers for this group of genes have not designed and tested in environmental surveys. B These enzymes do not oxidize methanol, but are involved in formaldehyde oxidation.

These enyzmes also occur in methylotrophs that do not use methanol and in non-methylotrophs Chistoserdova, C Homologs of unknown function are present in methanogens Ding et al. E Detect only mxaF and xoxF -like genes of Proteobacteria. Table 4 Use of amplicon pyrosequencing to analyze methylotrophic communities. Conflict of Interest Statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Isolation and molecular detection of methylotrophic bacteria occurring in the human mouth. In situ measurement of methane fluxes and analysis of transcribed particulate methane monooxygenase in desert soils.

Methanol consumption drives the bacterial chloromethane sink in a forest soil

Active methylotrophs in the sediments of Lonar Lake, a saline and alkaline ecosystem formed by meteor impact. ISME J. Molecular diversity of methanogens and identification of Methanolobus sp. FEMS Microbiol. Methylophaga lonarensis sp. Aerobic and anaerobic growth of Paracoccus denitrificans on methanol. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Methanotrophic communities in Australian woodland soils of varying salinity. Oxidation of dimethylsulfide to tetrathionate by Methylophaga thiooxidans sp.


Methanol metabolism in mutants of the methylotrophic yeast Hansenula polymorpha. QIIME allows analysis of high-throughput community sequencing data. Methods 7 — Modularity of methylotrophy, revisited. The expanding world of methylotrophic metabolism. Global sequencing: a review of current molecular data and new methods available to assess microbial diversity. Microbes Environ. Soil microbial processes involved in production and consumption of atmospheric trace gases. Contribution of methanol to the production of methane and its Cisotopic signature in anoxic rice field soil.

Biogeochemistry 73 — Methylomonas paludis sp.

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Characterization of a corrinoid protein involved in the C1 metabolism of strict anaerobic bacterium Moorella thermoacetica. Proteins 67 — Exploring methanotroph diversity in acidic northern wetlands: molecular and cultivation-based studies. Microbiology 78 — Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Aerobic methanotroph diversity in Riganqiao peatlands on the Qinghai-Tibetan plateau. Cloning, expression, and sequence analysis of the Bacillus methanolicus C1 methanol dehydrogenase gene. Isolation and characterization of Methylophaga sulfidovorans sp.

Genomic and proteomic analyses reveal multiple homologs of genes encoding enzymes of the methanol: coenzyme M methyltransferase system that are differentially expressed in methanol- and acetate-grown Methanosarcina thermophila. Microbial methanol uptake in northeast Atlantic waters.

Gradients in microbial methanol uptake: productive coastal upwelling waters to oligotrophic gyres in the Atlantic Ocean.

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    Ancylobacter dichloromethanicus sp. MAFF The production of methanol by flowering plants and the global cycle of methanol. The small genome of an abundant coastal ocean methylotroph. Methylophilus flavus sp. Methylobacillus arboreus sp nov. Quinone-dependent alcohol dehydrogenases and FAD-dependent alcohol oxidases.

    Biochemistry Moscow 77 — Insight into the mechanism of biological methanol activation based on the crystal structure of the methanol-cobalamin methyltransferase complex. Synergistic metabolism of a broad range of C1 compounds in the marine methylotrophic bacterium HTCC Regulation of methanol utilisation pathway genes in yeasts.

    Cell Fact 5 1—29 Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments.

    Distribution of dissimilatory enzymes in methane and methanol oxidizing bacteria

    Atmospheric methanol budget and ocean implication. Search Advanced. Current Journals. Archive Journals. All Journals. New Titles. Pick and Choose. Literature Updates. For Members. For Librarians. RSS Feeds. Chemistry World. Education in Chemistry.

    Methane and Methanol Utilizers Biotechnology Handbooks

    Open Access. Historical Collection. You do not have JavaScript enabled. Please enable JavaScript to access the full features of the site or access our non-JavaScript page. Issue 7, Previous Article Next Article. From the journal: RSC Advances. Guidance for engineering of synthetic methylotrophy based on methanol metabolism in methylotrophy. This article is part of the themed collection: Review articles. We have a dedicated site for Germany. Editors: Murrell , J. Colin, Dalton , Howard Eds. Methane and its oxidation product, methanol, have occupied an important position in the chemical industry for many years: the former as a feedstock, the latter as a primary chemical from which many products are produced.

    Methanol, formed as a breakdown product of plant material, is also ubiquitous and has also encouraged the growth of prokaryotes and eukaryotes alike. In an attempt to give a balanced view of how microorganisms have been able to exploit these simple carbon sources, we have asked a number ofleading scientists modesty forbids our own inclusion here to contribute chapters on their specialist areas of the subject.

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