Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph

Grob, C; Taubert, M; Howat, AM; Burns, OJ; Dixon, JL; Richnow, HH; Jehmlich, N; von Bergen, M; Chen, Y; Murrell, JC. 2015 Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph. Environmental Microbiology. 10.1111/1462-2920.12935

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Abstract/Summary

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: Publication - Article
Subjects: Ecology and Environment
Marine Sciences
Oceanography
Divisions: Plymouth Marine Laboratory > Science Areas > Cycling in the Sunlit Ocean
Depositing User: Jo Dixon
Date made live: 30 Jun 2015 10:29
Last Modified: 06 Jun 2017 16:13
URI: http://plymsea.ac.uk/id/eprint/6400

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