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Title: Diversity and activity of microorganisms degrading methylated sulphur compounds in terrestrial environments
Author: Eyice, Özge
ISNI:       0000 0004 2739 8047
Awarding Body: University of Warwick
Current Institution: University of Warwick
Date of Award: 2012
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Dimethylsulphide (DMS) and methanethiol (MT) play a crucial role in the biogeochemical sulphur cycle, atmospheric chemistry and global climate. Bacteria are a major sink of DMS in the global cycle and a number of bacteria that can utilise DMS as sole carbon and energy source have been isolated. This study investigated the diversity and activity of microorganisms degrading methylated sulphur compounds (mainly DMS and DMSO) in terrestrial environments. Initially, methylotrophic strains were isolated from soil and plant enrichments, with Hyphomicrobium being the most dominant genus. However, denaturing gradient gel electrophoresis (DGGE) analysis of the enrichment cultures revealed the dominance of bacteria related to Thiobacillus, Rhodococcus and the Cytophaga-Flavobacterium-Bacteroides group. The diversity of methanol- and DMS-degrading bacteria in the rhizosphere of Brassica oleracea and surrounding bulk soil was also assessed by enrichment culture. DGGE analysis suggested the dominance of members of the Methylophilaceae in methanol enrichments whereas bacterial populations related to Cytophaga, Pseudomonas and Thiobacillus were predominant in DMS enrichments. There was no significant difference between the bacterial diversity of enrichments obtained from rhizosphere and bulk soil. A functional gene marker was developed to determine the diversity of bacteria degrading methylated sulphur comounds. The gene encoding methanethiol oxidase (mto), a key enzyme in DMS degradation pathways, was identified for the first time in Hyphomicrobium sp. VS; it is a member of the selenium-binding protein family with closely related genes detected in a number of bacterial genomes. A primer pair targeting putative bacterial mto genes was designed and successfully applied on DMS/MT degrading isolates and terrestrial samples. mto PCR products from DMS-enriched rhizosphere were cloned and the mto genes found to be related to those of Thiobacillus strains and unidentified bacteria. Stable-isotope probing (SIP) combined with metagenomics was carried out to identify the active DMS degraders in soil. DGGE analysis of the SIP experiment revealed the dominance of Methylophilaceae family members and Thiobacillus genus. mto clone libraries from SIP-DNA fractions resulted in two clades. One of these clades includes Mto of Thiobacillus spp., the other clade could not be matched to any known bacteria. Those sequences might belong to Methylophilaceae or undiscovered DMS or MT oxidisers. High-throughput sequencing was applied to 13C-DNA, results showed the dominance of Burkholderia, Thiobacillus and Methylophilaceae. Overall results suggest that diversity of DMS-degrading populations in terrestrial environments is greater than previously realised and mto specific PCR is an efficient method for the analysis of microbial diversity of DMS degrading bacteria. It was found that Thiobacillus and potentially Methylophilaceae strains have significant roles in soil DMS cycling. Although metagenomics analysis needs further improvement, it was shown that SIP combined with high throughput sequencing is a useful approach to investigate active DMS/MT degraders in soil.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: QD Chemistry ; QR Microbiology