Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment
Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment
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)CH4, 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 Methylococcaceae. Transcripts of the methane monooxygenase genes pmoCAB were the most abundant in this metatranscriptome, and the pathway of methane oxidation to CO2 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.
757-764
Dumont, Marc
afd9f08f-bdbb-4cee-b792-1a7f000ee511
Pommerenke, Bianca
b88ad6f7-3df5-46b2-ad72-395ecef447f3
Casper, Peter
90dac29d-fee3-4d8c-8b50-db661e71c80a
October 2013
Dumont, Marc
afd9f08f-bdbb-4cee-b792-1a7f000ee511
Pommerenke, Bianca
b88ad6f7-3df5-46b2-ad72-395ecef447f3
Casper, Peter
90dac29d-fee3-4d8c-8b50-db661e71c80a
Dumont, Marc, Pommerenke, Bianca and Casper, Peter
(2013)
Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment.
Environmental Microbiology Reports, 5 (5), .
(doi:10.1111/1758-2229.12078).
(PMID:24115627)
Abstract
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)CH4, 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 Methylococcaceae. Transcripts of the methane monooxygenase genes pmoCAB were the most abundant in this metatranscriptome, and the pathway of methane oxidation to CO2 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.
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e-pub ahead of print date: 22 July 2013
Published date: October 2013
Organisations:
Centre for Biological Sciences, Environmental
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Local EPrints ID: 387924
URI: http://eprints.soton.ac.uk/id/eprint/387924
ISSN: 1758-2229
PURE UUID: 91cfa32e-81c7-4985-8475-39d4a21788f6
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Date deposited: 07 Jul 2016 15:22
Last modified: 15 Mar 2024 03:53
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Author:
Bianca Pommerenke
Author:
Peter Casper
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