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Revealing a cryptic organosulfur cycle in benthic marine environments using microbiology and metagenomics

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  • Full or part time
    Dr H Schaefer
    Dr Yin Chen
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Project Highlights
• Microbiology of cycling of climatically active aerosol precursors and trace gases
• Apply metagenomics approaches to organosulfur cycling
• Investigate globally significant processes linking the nitrogen and sulfur cycles

Overview
Coastal saltmarshes are important environments for the cycling of organic matter. They are a source and sink for a number of atmospheric trace gases including volatile organic sulphur compounds such as dimethylsulfide (DMS) and methanethiol (MT), volatile amines, methyl halides and methane, which play diverse roles in atmospheric chemistry.
DMS is an organic sulfur gas that has been described as the ‘smell of the sea’. It is of biogeochemical significance as a precursor for secondary organic aerosols which play a role as cloud condensation nuclei and which affect the radiative balance of the Earth. It is also an important infochemical that has an effect on species interactions and the trophic web (Curson et al 2010). Approximately 300 million tons of DMS are produced annually, most of it in marine environments, but only a relatively small amount is emitted to the atmosphere, the majority being subject to microbial degradation (Schäfer et al 2011). Our previous work in the Stiffkey saltmarsh (Norfolk, UK) has identified methylotrophic bacterial populations that utilise DMS as a carbon and energy source (Pratscher et al., in prep). Another fate of DMS degradation is its oxidation to dimethylsulfoxide (DMSO). Bacterial groups that have been shown capable of DMS to DMSO oxidation include anoxygenic phototrophs such as Rhodovulum sulfidophilum,(using DMS dehydrogenase ddhA) (McDevitt et al 2002) and aerobic heterotrophs like Ruegeria pomeroyi which co-oxidatively convert DMS to DMSO using the enzyme trimethylamine monooxygenase (Tmm) dependent on the presence of methylated amines (Lidbury et al, 2015).
DMSO produced as described above is then available to act as a terminal electron acceptor for anaerobic respiration through the action of DMSO reductases which reduce DMSO to DMS (Satoh & Kurihara, 1987) and some also trimethylamine N-oxide (TMAO) to trimethylamine. Although the potential for DMSO (and TMAO) reduction in anoxic habitats is widely distributed, the identity of the organisms responsible for DMSO/TMAO reduction and the overall contribution of DMSO reduction to organic matter degradation remain poorly characterised.

Further, the production of DMS through the reduction of DMSO under anaerobic conditions could in turn regenerate the substrate for Tmm potentially constituting a full cycle of DMS to DMSO oxidation and DMSO to DMS reduction in surface sediments. This cycle may be driven by the spatially close interaction of DMS oxidising Tmm-containing bacteria in oxic sediment layers and DMSO-reducing bacteria in anoxic sediment layers.
The aim of this is to investigate how taxonomically and functionally diverse bacteria contribute to DMS/DMSO cycling in saltmarsh sediments, and how these contribute to organic carbon degradation under anaerobic conditions.

Methodology
You will use a combination of environmental sampling and laboratory experiments to assess diversity and activity of DMS and DMSO cycling microbial populations. Samples will be obtained from Stiffkey saltmarsh. You will use a variety of molecular approaches to characterise microbial community organisation and its ecological function. This will include DNA and RNA extraction and purification, PCR, sequencing using next generation platforms and bioinformatic analysis. You will also measure the processes such as DMS and DMSO degradation using gas chromatography as required.

Training and skills
CENTA students are required to complete 50 days training throughout their PhD including a 10-day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to CENTA research themes. Discipline specific training opportunities in this project are based on the experimental approaches that will be used including microbial cultivation and characterisation, molecular microbial ecology techniques for analysis of microbial diversity and activity, including PCR based approaches, high-throughput amplicon sequencing for analysis of taxonomic and functional diversity as well as metagenomics approaches. You will also be trained in relevant analytical chemistry techniques such as ion and gas chromatography.


Partners and collaboration
There is ample potential for scientific exchange and collaboration with our network of collaborators throughout the UK and in Europe who study microbial trace gas metabolism, sulfur cycling, nitrogen cycling, and marine microbial ecology.

Funding Notes

Funding eligibility criteria apply. Please visit the School of Life Sciences NERC CENTA webpage for more information.

References

Further reading
1. Chen Y, Patel NA, Crombie A, Scrivens JH, & Murrell JC (2011) Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase. Proc Natl Acad Sci USA 108(43):17791-17796.
2. Chen Y (2012) Comparative genomics of methylated amine utilization by marine Roseobacter clade bacteria and development of functional gene markers (tmm, gmaS). Environ Microbiol 14(9):2308-2322.
3. Curson ARJ, Todd JD, Sullivan MJ, Johnston AWB (2011) Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes. Nat Rev Micro, 9(12):849-859.
4. McDevitt CA, Hugenholtz P, Hanson GR, McEwan AG (2002) Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes. Mol Microbiol, 44(6):1575-1587.
5. Satoh T, Kurihara FN (1987) Purification and properties of dimethylsulfoxide reductase containing a molybdenum cofactor from a photodenitrifier, Rhodopseudomonas sphaeroides f.s. denitrificans. J Biochem, 102(1):191-197.
6. Schäfer H, Myronova N, and R Boden (2010) Microbial degradation of dimethylsulfide and related C1-sulfur compounds: organisms and pathways controlling fluxes of sulfur in the biosphere. J Exp Bot 61, 315-334; DOI:10.1093/jxb/erp355
7. Lidbury I, Kröber E, Zhang Z, Zhu Y, Murrell JC, Chen Y, and H Schäfer (2016) A mechanism for bacterial transformation of DMS to DMSO: a missing link in the marine organic sulfur cycle. Environ Microbiol 18, 2754-2766. doi: 10.1111/1462-2920.13354.

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