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Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment
Author(s) -
Dumont Marc G.,
Pommerenke Bianca,
Casper Peter
Publication year - 2013
Publication title -
environmental microbiology reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.229
H-Index - 69
ISSN - 1758-2229
DOI - 10.1111/1758-2229.12078
Subject(s) - methanotroph , biology , pyrosequencing , archaea , stable isotope probing , methane monooxygenase , gene , rna , methanogen , metagenomics , microorganism , bacteria , methane , ecology , biochemistry , anaerobic oxidation of methane , genetics
Summary In this study, we demonstrate the possibility of obtaining a targeted metatranscriptome from a functional group of microorganisms using a stable isotope probing ( SIP ) approach. Methanotrophs in lake sediment were labelled using 13 CH 4 , and both labelled and unlabelled‐ RNA were isolated and sequenced by 454 pyrosequencing. The unlabelled metatranscriptome had a large diversity of bacterial, archaeal, eukaryotic and viral sequences as expected from a diverse sediment community. In contrast, the labelled‐ RNA metatranscriptome was dominated by methanotroph sequences, particularly from M ethylococcaceae . Transcripts of the methane monooxygenase genes pmo CAB were the most abundant in this metatranscriptome, and the pathway of methane oxidation to CO 2 could be traced, as well as many steps in the ribulose monophosphate pathway for carbon assimilation. A high abundance of mRNA transcripts for proteins related to motility was detected, suggesting an importance for methanotrophs in lake sediments. This combination of SIP and metatranscriptomics should be broadly applicable, and will enhance the detection and identification of mRNA from target organisms.