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SIP/metagenomics of terrestrial DMS degrading microorganisms

ABSTRACT: Stable isotope probing/metagenomics of terrestrial dimethylsulfide degrading microorganisms

PROVIDER: PRJEB6310 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR505054_1.fastq.gz	Fastqsanger.gz
	ERR505054_2.fastq.gz	Fastqsanger.gz
	ERR505055_1.fastq.gz	Fastqsanger.gz
	ERR505055_2.fastq.gz	Fastqsanger.gz
	ERR505056_1.fastq.gz	Fastqsanger.gz

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SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment.

Project description: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.

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Project description:identifying the denitrifying bacteria in the deep vadose zone by stable isotope probing

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Project description:By using metagenome resolved protein stable isotope probing (protein-SIP) through incubations of identical reactors with 13C labelled bicarbonate over a period of 48 hours, the study aims to map differences in the metabolic behaviour of the microbial community during anaerobic digestion.

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