title: SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment.
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 (13)C-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.
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, UK.
authors.forename: Özge
authors.initials: Ö
authors.lastname: Eyice
authors.affiliation: MOAC Doctoral Training Centre, University of Warwick, Coventry, UK.
authors.forename: Motonobu
authors.initials: M
authors.lastname: Namura
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, UK.
authors.forename: Yin
authors.initials: Y
authors.lastname: Chen
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Mead
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, UK.
authors.forename: Siva
authors.initials: S
authors.lastname: Samavedam
authors.affiliation: School of Life Sciences, University of Warwick, Coventry, UK.
authors.forename: Hendrik
authors.initials: H
authors.lastname: Schäfer
mesh_terms: D002247:Carbon Isotopes / Q000737:chemistry; D017753:Ecosystem; D016680:Genome, Bacterial; D019015:Geologic Sediments / Q000382:microbiology*; D060106:Lakes; D056186:Metagenomics; D008745:Methylation; D042762:Methylophilaceae / Q000235:genetics*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012987:Soil; D012988:Soil Microbiology; D013440:Sulfides
chemical_list: D002247:Carbon Isotopes; D012336:RNA, Ribosomal, 16S; D012987:Soil; D013440:Sulfides; C004784:dimethyl sulfide
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