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), methyl halides and methane important as climate active gases or ozone depleting compounds.

Previous work in the Schäfer group has identified methylotrophic bacterial populations in the Stiffkey saltmarsh (Norfolk, UK) that utilise DMS as a carbon and energy source (Schäfer, personal communication). Another fate of DMS degradation is its oxidation to dimethylsulfoxide. Bacterial groups that have been shown capable of DMS to DMSO oxidation including anoxygenic phototrophs such as Rhodovulum sulfidophilum,(using DMS dehydrogenase ddhA) heterotrophs that utilise DMS as an energy source (eg Sagittula stellata) 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.

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. Despite many years of study of DMSO reductases and closely related (and functionally equivalent) trimethylamine N-oxide (TMAO) reductases, very little is known about the role of DMSO reduction as a terminal pathway of carbon turnover in anoxic sediments.

Although the potential for DMSO (and TMAO) reduction in anoxic habitats is widely distributed, neither the populations responsible for DMSO/TMA reduction nor the relative importance of this pathway to overall anaerobic respiration in sediments has been determined previously, constituting another area of fundamental lack of understanding related to DMSO reduction. Given that DMSO reduction under anaerobic conditions produces DMS, it is conceivable that the DMS thus formed may undergo re-oxidation to DMSO in the surface sediment constituting a full cycle of DMS to DMSO oxidation and DMSO to DMS reduction.

The aim of this is to investigate how taxonomically and functionally diverse bacteria contribute to DMS/DMSO cycling in saltmarsh sediments, and how they contributes to organic carbon degradation under anaerobic conditions.

Characteristic saltmarsh environment of the lower marsh at Stiffkey (at low tide) with tidal creeks and pools, illustrating a hotspot for organic súlfur cycling.

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 rate of environmental processes such as DMS and DMSO degradation using gas chromatography as required.

You will receive training in a wide range of environmental microbiology approaches including assessment of metabolic potential of communities in environmental samples, DNA and RNA based assessment of community composition and function, processing and bioinformatic analysis of next generation high throughput sequencing data, metagenomics and related approaches, as well as analytical techniques such as gas and ion chromatography

 

Training and Skills

CENTA students are required to complete 45 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 the student's projects and themes. 

 

Timeline

Year 1: Assessment of potential to degrade DMS and DMSO under aerobic and anaerobic conditions in surface sediments and in the rhizosphere of saltmarsh vegetation.  Characterisation of DMSO producing and respiring bacteria from surface saltmarsh sediments by enrichment, isolation and physiological characterisation and genome sequencing. Analysis of taxonomic diversity of microbial communities using ribosomal marker genes and measurement of metabolic potential/process rates.

Years 2 & 3:  Analysis of the functional diversity of microbial communities in the saltmarsh using analysis of functional genetic markers directly retrieved from saltmarsh sediment DNA (including ddhA and tmm, see above) by PCR and the analysis of ddhA and tmm diversity in saltmarsh sediment and rhizosphere metagenomes.

Partners and collaboration (including CASE)

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.

Further Details

If you would like to discuss any aspects of this project or get additional information, please do get in touch:

Dr Hendrik Schäfer, School of Life Sciences

University of Warwick, Coventry, CV4 7AL

Phone: 024 765 75052

H.Schaefer@warwick.ac.uk

Dr Yin Chen, School of Life Sciences

University of Warwick, Coventry, CV4 7AL

Phone: 024 765 28976

Y.Chen.25@warwick.ac.uk