Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment

Kolb, Steffen; Stacheter, Astrid

doi:10.3389/fmicb.2013.00268

Cited by 34 publications

(32 citation statements)

References 132 publications

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“…Aerobic methanol-utilizers are phylogenetically diverse and affiliate with gram-negative Alpha -, Beta -, and Gammaproteobacteria and Verrucomicrobia and with gram-positive Actinobacteria and Firmicutes , as well as with some fungi, i.e., ascomycetous yeasts and molds (Kolb, 2009; Gvozdev et al, 2012; Chistoserdova and Lidstrom, 2013; Kolb and Stacheter, 2013; Sharp et al, 2014). …”

Section: Introductionmentioning

confidence: 99%

“…The sensitivity of the environmental detection of low-abundant, one-carbon (C 1 ) compound converting microorganisms has been improved by the detection of key genes of methylotrophy (Holmes et al, 1995; McDonald and Murrell, 1997; Kolb and Stacheter, 2013). The initial enzymatic step of microbial methanol utilization is the oxidation of methanol to formaldehyde.…”

Section: Introductionmentioning

confidence: 99%

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Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil

Morawe¹,

Hoeke²,

Wissenbach³

et al. 2017

Front. Microbiol.

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Methanol is an abundant atmospheric volatile organic compound that is released from both living and decaying plant material. In forest and other aerated soils, methanol can be consumed by methanol-utilizing microorganisms that constitute a known terrestrial sink. However, the environmental factors that drive the biodiversity of such methanol-utilizers have been hardly resolved. Soil-derived isolates of methanol-utilizers can also often assimilate multicarbon compounds as alternative substrates. Here, we conducted a comparative DNA stable isotope probing experiment under methylotrophic (only [13C1]-methanol was supplemented) and combined substrate conditions ([12C1]-methanol and alternative multi-carbon [13Cu]-substrates were simultaneously supplemented) to (i) identify methanol-utilizing microorganisms of a deciduous forest soil (European beech dominated temperate forest in Germany), (ii) assess their substrate range in the soil environment, and (iii) evaluate their trophic links to other soil microorganisms. The applied multi-carbon substrates represented typical intermediates of organic matter degradation, such as acetate, plant-derived sugars (xylose and glucose), and a lignin-derived aromatic compound (vanillic acid). An experimentally induced pH shift was associated with substantial changes of the diversity of active methanol-utilizers suggesting that soil pH was a niche-defining factor of these microorganisms. The main bacterial methanol-utilizers were members of the Beijerinckiaceae (Bacteria) that played a central role in a detected methanol-based food web. A clear preference for methanol or multi-carbon substrates as carbon source of different Beijerinckiaceae-affiliated phylotypes was observed suggesting a restricted substrate range of the methylotrophic representatives. Apart from Bacteria, we also identified the yeasts Cryptococcus and Trichosporon as methanol-derived carbon-utilizing fungi suggesting that further research is needed to exclude or prove methylotrophy of these fungi.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil

Morawe¹,

Hoeke²,

Wissenbach³

et al. 2017

Front. Microbiol.

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“…Methylotrophs are organisms which can use reduced organic compounds with no carbon–carbon bonds, such as methane, methanol or methylamines, as their sole source of carbon and energy (Anthony, ; Chistoserdova, ). There are over 200 described species of methylotrophs belonging mostly to the Alphaproteobacteria , Betaproteobacteria and Gammaproteobacteria , but also to Verrucomicrobia , Bacteroidetes , Firmicutes and Actinobacteria (Madhaiyan et al ., ; Kolb and Stacheter, ). The majority of methylotrophs are aerobic bacteria, and almost all are able to utilize methanol (Anthony, ; Chistoserdova, ).…”

Section: Introductionmentioning

confidence: 99%

XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments

Taubert

Grob

Howat

et al. 2015

Environmental Microbiology

105

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). (2015) XoxFencoding an alternative methanol dehydrogenase is widespread in coastal marine environments. Environmental Microbiology, 17 (10). pp. 3937-3948. Permanent WRAP URL:http://wrap.warwick.ac.uk/67990 Copyright and reuse:The Warwick Research Archive Portal (WRAP) makes this work by researchers of the University of Warwick available open access under the following conditions. Copyright © and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable the material made available in WRAP has been checked for eligibility before being made available.Copies of full items can be used for personal research or study, educational, or not-for profit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. Publisher's statement:"This is the peer reviewed version of the following article: which has been published in final form at http://dx.doi.org/10.1111/1462-2920.12896 This article may be used for noncommercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving." A note on versions:The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP url' above for details on accessing the published version and note that access may require a subscription. Abstract 22The xoxF gene, encoding a pyrroloquinoline quinone-dependent methanol dehydrogenase, is found in all 23 known proteobacterial methylotrophs. In several newly discovered methylotrophs, XoxF is the active methanol 24 dehydrogenase, catalysing the oxidation of methanol to formaldehyde. Apart from that, its potential role in 25 methylotrophy and carbon cycling is unknown. So far, the diversity of xoxF in the environment has received 26 little attention. We designed PCR primer sets targeting clades of the xoxF gene, and used 454 pyrosequencing 27 of PCR amplicons obtained from DNA of four coastal marine environments for a unique assessment of the 28 diversity of xoxF in these habitats. Phylogenetic analysis of the data obtained revealed a high diversity of xoxF 29 genes from two of the investigated clades, and substantial differences in sequence composition between 30 environments. Sequences were classified as being related to a wide range of both methylotrophs and non-31 methylotrophs from Alpha-, Beta-and Gammaproteobacteria. The most prominent sequences detected were 32 related to the family Rhodobacteraceae, the genus Methylotenera and the OM43 clade of Methylophilales, 33 and are thus related to organisms that employ XoxF for methanol oxidation. Furthermore, our analyses 34 revealed a high degree of so far undescribed sequences, suggesting a high number of unknown species in 35 these habitats. 36

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“…Methanol and dimethylsulfide (DMS) are two important methylotrophic substrates in the environment. Methanol is the second most abundant organic compound in the atmosphere after methane and affects ozone formation and the oxidizing capacity of the atmosphere (MacDonald and Fall 1993;Kolb and Stacheter 2013). In terrestrial environments, methanol is mainly released from plants during synthesis of cell wall components with an estimated amount of 100 Tg year -1 (Galbally and Kirstine 2002).…”

Section: Introductionmentioning

confidence: 99%

“…Especially, methanol-utilizing methylotrophs are considered difficult to investigate due to their broad diversity in the environment (Kolb and Stacheter 2013). Also, it is not clear whether there are distinct methylotrophic populations in different terrestrial habitats such as bulk soil and the rhizosphere.…”

Section: Introductionmentioning

confidence: 99%

Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments

Eyice

Schäfer

2015

Arch Microbiol

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Original citation:Eyice, Özge and Schäfer, Hendrik. (2015) Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments. Archives of Microbiology. Permanent WRAP url:http://wrap.warwick.ac.uk/73935 Copyright and reuse:The Warwick Research Archive Portal (WRAP) makes this work by researchers of the University of Warwick available open access under the following conditions. Copyright © and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable the material made available in WRAP has been checked for eligibility before being made available.Copies of full items can be used for personal research or study, educational, or not-for profit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. Publisher's statement:The final publication is available at Springer via http://dx.doi.org/10.1007/s00203-015-1160-x A note on versions: The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP url' above for details on accessing the published version and note that access may require a subscription. They are suggested to affect atmospheric chemistry and global climate. Methylotrophic microorganisms are considered as a significant sink for these compounds, therefore we analysed the diversity of terrestrial bacteria that utilise methanol, DMS and DMSO as carbon and energy source using culture-dependent and -independent methods. The effect of habitat type on the methylotrophic community structure was also investigated in rhizosphere and bulk soil. While thirteen strains affiliated to the genera

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Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment

Cited by 34 publications

References 132 publications

Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil

Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil

XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments

Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments

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