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Diversity and activity of microorganisms degrading methylated sulphur compounds in terrestrial environments
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Eyice, Özge (2012) Diversity and activity of microorganisms degrading methylated sulphur compounds in terrestrial environments. PhD thesis, University of Warwick.
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Official URL: http://webcat.warwick.ac.uk/record=b2606801~S1
Abstract
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.
Item Type: | Thesis (PhD) | ||||
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Subjects: | Q Science > QD Chemistry Q Science > QR Microbiology |
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Library of Congress Subject Headings (LCSH): | Sulfur compounds -- Biodegradation, Methylotrophic bacteria, Microbial diversity, Soil microbiology | ||||
Official Date: | January 2012 | ||||
Dates: |
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Institution: | University of Warwick | ||||
Theses Department: | School of Life Sciences | ||||
Thesis Type: | PhD | ||||
Publication Status: | Unpublished | ||||
Supervisor(s)/Advisor: | Schäfer, Hendrik | ||||
Extent: | xiv, 207 leaves : illustrations, charts. | ||||
Language: | eng |
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