Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
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. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle.
Keywords: methylotroph, PQQ MDH, PQQ MDH2, NAD MDH, FAD AO, mtaC, xoxF, mxaF′
Citation: Kolb S and Stacheter A (2013) Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment. Front. Microbiol. 4:268. doi: 10.3389/fmicb.2013.00268
Received: 19 July 2013; Accepted: 19 August 2013;
Published online: 05 September 2013.
Edited by:Marc Gregory Dumont, Max Planck Institute for Terrestrial Microbiology, Germany
Reviewed by:Marina Kalyuzhnaya, University of Washington, USA
Svetlana N. Dedysh, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Russia
Copyright © 2013 Kolb and Stacheter. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). 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.
*Correspondence: Steffen Kolb, Department of Ecological Microbiology, University of Bayreuth, Dr.-Hans-Frisch-Str. 1-3, 95448 Bayreuth, Germany e-mail: firstname.lastname@example.org