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Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph
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Grob, Carolina, Taubert, Martin, Howat, Alexandra M., Burns, Oliver J., Dixon, Joanna L., Richnow, Hans H., Jehmlich, Nico, von Bergen, Martin, Chen, Yin and Murrell, J. C. (J. Colin) (2015) Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph. Environmental Microbiology, 17 (10). pp. 4007-4018. doi:10.1111/1462-2920.12935
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Official URL: http://dx.doi.org/10.1111/1462-2920.12935
Abstract
A variety of culture-independent techniques have been developed that can be used in conjunction with culture-dependent physiological and metabolic studies of key microbial organisms, in order to better understand how the activity of natural populations influences and regulates all major biogeochemical cycles. In this study, we combined DNA-stable isotope probing with metagenomics and metaproteomics to characterize an as yet uncultivated marine methylotroph that actively incorporated carbon from 13C-labeled methanol into biomass. By metagenomic sequencing of the heavy DNA, we retrieved virtually the whole genome of this bacterium and determined its metabolic potential. Through protein-stable isotope probing, the RuMP cycle was established as the main carbon assimilation pathway, and the classical methanol dehydrogenase-encoding gene mxaF, as well as three out of four identified xoxF homologues were found to be expressed. This proof-of-concept study is the first in which theculture-independent techniques of DNA- and protein-stable isotope probing have been used to characterize the metabolism of a naturally-ocurring Methylophaga-like bacterium in the marine environment (i.e. M. thiooxydans L4) and thus provides a powerful approach to access the genome and proteome of uncultivated microbes involved in key processes in the environment.
| Item Type: | Journal Article | ||||||||
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| Subjects: | Q Science > QH Natural history Q Science > QR Microbiology |
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| Divisions: | Faculty of Science > Life Sciences (2010- ) | ||||||||
| Library of Congress Subject Headings (LCSH): | Metagenomics , Methylotrophic microorganisms , Biogeochemical cycles , Marine bacteria, Methylotrophic bacteria | ||||||||
| Journal or Publication Title: | Environmental Microbiology | ||||||||
| Publisher: | Wiley-Blackwell Publishing Ltd. | ||||||||
| ISSN: | 1462-2912 | ||||||||
| Official Date: | 22 October 2015 | ||||||||
| Dates: |
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| Date of first compliant deposit: | 29 December 2015 | ||||||||
| Volume: | 17 | ||||||||
| Number: | 10 | ||||||||
| Page Range: | pp. 4007-4018 | ||||||||
| DOI: | 10.1111/1462-2920.12935 | ||||||||
| Status: | Peer Reviewed | ||||||||
| Publication Status: | Published | ||||||||
| Access rights to Published version: | Restricted or Subscription Access | ||||||||
| Funder: | Gordon and Betty Moore Foundation (GBMF), Earth & Life Systems Alliance (ELSA) | ||||||||
| Grant number: | GBMF3303 (GBMF) | ||||||||
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