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.
Highlights
Methylated sulphur compounds are significant intermediates in the global biogeochemical sulphur cycle owing to their role in transferring sulphur between the atmosphere, terrestrial and marine ecosystems (Lomans et al, 1997; Bentley and Chasteen, 2004; Schäfer et al, 2010)
While Thiobacillus spp. detected by DGGE band sequencing in the lake sediment ‘heavy’ DNA were detected by 454 amplicon sequencing, the read abundance remained fairly constant and they were not found as one of the operational taxonomical units (OTUs) contributing to the differences protein annotation sources (M5NR database) used between the data sets according to the principal components analysis (PCA) which by MG-RAST, the ‘heavy’ and ‘light’ metagenomes suggests that these did not proliferate significantly. were dominated by bacteria (74.9 and 76.9%)
The methylotrophy and sulphur compound oxidation genes in the ‘heavy’ metagenomes were mainly related to Methylophilaceae and Thiobacillus species, while those detected in the ‘light’ fractions were affiliated with more diverse bacteria including members of the Bacteroidetes group that was abundant based on 454 read data
Summary
Methylated sulphur compounds are significant intermediates in the global biogeochemical sulphur cycle owing to their role in transferring sulphur between the atmosphere, terrestrial and marine ecosystems (Lomans et al, 1997; Bentley and Chasteen, 2004; Schäfer et al, 2010). OTUs in different DNA fractions and across the time second and third time-point (days 17 and 20, course of the incubations suggested the degradation respectively) samples (Figure 1a; Supplementary and assimilation of 13C-labelled DMS by specific Table 2a).
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