Microbial thiocyanate biodegradation: an unexplored nexus for the sulphur, nitrogen and carbon biogeochemical cycles

Biogeochemical Cycles

IAP2-20-031

Overview

In wetlands and estuarine sediments, microorganisms degrade thiocyanate (SCN-) to form carbonyl sulphide (COS) and cyanate (CNO-) (Fig. 1). These molecules represent an unexplored and critical nexus of three major elemental cycles [1-3]: sulphur (S), nitrogen (N) and carbon (C), which:

• strongly influences atmospheric, terrestrial and ocean chemistry,
• provides critical requirements for primary productivity, cell growth and metabolic energy, and
• sustains diverse and highly interconnected sedimentary microbial communities.

Despite the importance of COS as a major S-bearing trace gas with a central role in stratospheric sulphate aerosol production, the process of microbial COS degradation is very poorly understood [4]. Microbial cycling of COS in the open ocean and coastal waters is even less understood, as are fluxes of COS in the global S cycle. Likewise, a recent study found that, in oligotrophic seawater, CNO- acts as a significant source of N for nitrification [5], suggesting CNO- plays a more important role in the global N cycle than previously realised. This project aims to: increase our knowledge of the distribution, phylogeny and metabolic role(s) of microorganisms responsible for the biodegradation of SCN-, CNO- and COS in wetland sediments.

Click on an image to expand

Image Captions

Schematic representation of SCN- biodegradation by terrestrial and marine microbial communities, both of which produce the atmospheric trace gas carbonyl sulfide (COS) and aqueous CNO-.
Photo of North Sea salt marsh, Creative Commons license CC0 (public domain).

Methodology

Sediment samples will be taken from salt marsh sites chosen from the Scottish Wetland Inventory (https://map.environment.gov.scot), focusing on the Clyde Estuary. The materials will undergo extensive chemical analyses to determine SCN-, CNO- and COS concentrations, pH, organic and organic carbon content, major and trace element abundance, S and N speciation, chlorophyll- concentration and major anions. These analyses will be performed at Glasgow University using existing or newly acquired equipment maintained by the PI and/or colleagues.

Samples will then be used to set up microcosm experiments monitored for changes in SCN-, CNO-, COS concentrations, S and N speciation and pH. Microcosms will be sampled over a time course to assess changes in the geochemistry and at key points samples will be removed for microbial community analysis. These experiments will be conducted in the lab of the PI.

Samples taken from microcosm experiments will be DNA-extracted for sequencing. The data will be binned to reconstruct individual genomes. Bioinformatic analyses will be used to identify sequences encoding for known SCN-, CNO- and COS degrading enzymes. A novel SIP metagenomics approach, utilizing stable isotope labelled substrates, will be used to get time resolved data on SCN-, CNO- and COS degradation and subsequent elemental cycling. SIP experiments will be performed in the lab of the PI at Glasgow University.

The results and interpretations will be integrated to develop a new, phylum-resolved, mechanistic, conceptual model for SCN-, COS and CNO- biodegradation in natural environments.

Project Timeline

Year 1

1a) Sampling and processing of sediment samples
1b) Quantification of (bio)geochemical analytes
1c) Sediment microcosm experiments (with acquisition and storage of subsamples for DNA sequencing/analysis)
1d) Write-up first manuscript

Year 2

2a) DNA sequencing and genome-resolved metagenomics/bioinformatics analyses of sediment microcosm experiments
2b) Setup of stable isotope probing (SIP) microcosm experiments
2c) Write-up 2nd manuscript
2d) Attend 1st scientific conference (domestic, likely Geomicrobiology Network Meeting, UK)

Year 3

3a) SIP microcosm experiments and consequent geochemical analyses/molecular microbiological studies

Year 3.5

3b) Write-up 3rd manuscript
3c) Present culmination of doctoral research at 2nd scientific conference (international; likely ISME Conference, location TBA))

Training
& Skills

The PhD student will learn fieldwork skills, sample handling and processing techniques, analytical geochemistry methods, molecular biology and bioinformatics approaches, experimental design, scientific writing and science communication.

References & further reading

1. Watts, S.F., 2000. The mass budgets of carbonyl sulfide, dimethyl sulfide, carbon disulfide and hydrogen sulfide. Atmospheric Environment, 34(5), pp.761-779.
2. Palatinszky, M., Herbold, C., Jehmlich, N., Pogoda, M., Han, P., von Bergen, M., Lagkouvardos, I., Karst, S.M., Galushko, A., Koch, H. and Berry, D., 2015. Cyanate as an energy source for nitrifiers. Nature, 524(7563), pp.105-108.
3. Widner, B., Mulholland, M.R. and Mopper, K., 2016. Distribution, sources, and sinks of cyanate in the coastal North Atlantic Ocean. Environmental Science & Technology Letters, 3(8), pp.297-302.
4. Watts, M.P., Spurr, L.P., Lê Cao, K.A., Wick, R., Banfield, J.F. and Moreau, J.W., 2019. Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium. Water research, 158, pp.106-117.
5. Palatinszky, M., Herbold, C., Jehmlich, N., Pogoda, M., Han, P., von Bergen, M., Lagkouvardos, I., Karst, S.M., Galushko, A., Koch, H. and Berry, D., 2015. Cyanate as an energy source for nitrifiers. Nature, 524(7563), pp.105-108.

Further Information

Application procedure: For IAPETUS2 applications to the University of Glasgow please use the dedicated application portal: www.gla.ac.uk/ScholarshipApp (you will still need to submit your administrative details to the IAPETUS2 website as well).

John Moreau, john.moreau@glasgow.ac.uk, +44 141 330 5461

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