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SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment
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Eyice, Özge, Namura, Motonobu, Chen, Yin, Mead, A. (Andrew), Samavedam, Siva and Schäfer, Hendrik (2015) SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment. The ISME Journal . pp. 1-13. doi:10.1038/ismej.2015.37
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Official URL: http://dx.doi.org/10.1038/ismej.2015.37
Abstract
Dimethylsulphide (DMS) has an important role in the global sulphur cycle and atmospheric chemistry. Microorganisms using DMS as sole carbon, sulphur or energy source, contribute to the cycling of DMS in a wide variety of ecosystems. The diversity of microbial populations degrading DMS in terrestrial environments is poorly understood. Based on cultivation studies, a wide range of bacteria isolated from terrestrial ecosystems were shown to be able to degrade DMS, yet it remains unknown whether any of these have important roles in situ. In this study, we identified bacteria using DMS as a carbon and energy source in terrestrial environments, an agricultural soil and a lake sediment, by DNA stable isotope probing (SIP). Microbial communities involved in DMS degradation were analysed by denaturing gradient gel electrophoresis, high-throughput sequencing of SIP gradient fractions and metagenomic sequencing of phi29-amplified community DNA. Labelling patterns of time course SIP experiments identified members of the Methylophilaceae family, not previously implicated in DMS degradation, as dominant DMS-degrading populations in soil and lake sediment. Thiobacillus spp. were also detected in 13C-DNA from SIP incubations. Metagenomic sequencing also suggested involvement of Methylophilaceae in DMS degradation and further indicated shifts in the functional profile of the DMS-assimilating communities in line with methylotrophy and oxidation of inorganic sulphur compounds. Overall, these data suggest that unlike in the marine environment where gammaproteobacterial populations were identified by SIP as DMS degraders, betaproteobacterial Methylophilaceae may have a key role in DMS cycling in terrestrial environments.
| Item Type: | Journal Article | ||||||||
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| Subjects: | Q Science > QH Natural history > QH301 Biology | ||||||||
| Divisions: | Faculty of Science > Life Sciences (2010- ) | ||||||||
| Library of Congress Subject Headings (LCSH): | Atmospheric dimethyl sulfide, Sulfur cycle | ||||||||
| Journal or Publication Title: | The ISME Journal | ||||||||
| Publisher: | Nature Publishing Group | ||||||||
| ISSN: | 1751-7362 | ||||||||
| Official Date: | 27 March 2015 | ||||||||
| Dates: |
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| Date of first compliant deposit: | 28 July 2016 | ||||||||
| Number of Pages: | 13 | ||||||||
| Page Range: | pp. 1-13 | ||||||||
| DOI: | 10.1038/ismej.2015.37 | ||||||||
| Status: | Peer Reviewed | ||||||||
| Publication Status: | Published | ||||||||
| Access rights to Published version: | Open Access | ||||||||
| Funder: | Natural Environment Research Council (Great Britain) (NERC), University of Warwick Postgraduate Research Scholarship | ||||||||
| Grant number: | NE/E013333/1 (NERC) |
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