Prospective PhD projects

Investigating the geomicrobiology of mercury methylation in northern peatlands

NERC IAPETUS2 project – full details will soon be available at www.iapetus2.ac.uk.

University of Glasgow application portal www.gla.ac.uk/ScholarshipApp will open in November 2020. Contact primary supervisor (john.moreau [at] gla.ac.uk) in the interim for more information.

Scotland’s ombrotrophic peatlands have accumulated atmospherically-deposited mercury (Hg) for over two millennia [Farmer et al. 2009], originally from mining and fossil fuel burning during Roman times, and later from 19th– and 20th-century industrialisation. A combination of the high organic matter content of peat with elevated sulphate levels in rainfall promotes environmental conditions conducive for native microorganisms to transform Hg into methylmercury (MeHg) [Blythe 2020], a neurotoxin that can bioaccumulate through ecosystem food webs [e.g., Liu et al. 2019]. However, little is known about the MeHg content, the potential for MeHg formation, or the putative microorganisms methylating Hg in peatlands. Based on climate change modelling [e.g., Chen et al. 2018], we hypothesize that peatlands could be potential MeHg sources under forecast environmental conditions. In contrast, we also hypothesize that changes in Hg association with organic matter over time could act to decrease the bioavailability of Hg for methylation [e.g., Moreau et al. 2015]. 

The aim of the proposed research is to apply field- and lab-based experiments, stable mercury isotope geochemistry, molecular microbiology, and bioinformatics to:

  • test hypotheses regarding peatland MeHg generation
  • determine potential microbial (phylogenetic) sources for MeHg production
  • understand effects of varying environmental conditions on Hg methylation activity.

We will visit several Scottish peatland study areas to take peat cores for total Hg (HgT) and MeHg quantification, DNA/RNA extraction, and laboratory experiments. Measurements of HgT and MeHg will be performed at the University of Glasgow, using cold-vapour atomic fluorescence spectrometry (CVAFS). Microcosm experiments under anaerobic conditions, with varying temperatures and partial pressures of CO2representative of current and plausible climate warming scenarios, will be conducted at Heriot-Watt University. Hg stable isotope tracer measurements will be made at the U.S. Geological Survey Water Lab in WI, USA. Whole microbial community DNA/RNA will be extracted and sequenced at the University of Glasgow, and bioinformatic analyses will be performed on the CLIMB HPC cluster to search for genes encoding for mercury methylation [e.g., Podar et al. 2015]) in both field and lab samples.Integrating these results and their interpretations from the above workflows will allow us to construct a conceptual model for Hg methylation potential in peatlands. We will be able to test hypotheses about the potential for Scotland’s peat bogs to act as a net contributor to environmental MeHg levels, in the context of Hg interaction with organic matter over time, and to understand how this process may be affected by plausible climate change scenarios. Given recent discoveries of new and non-canonical pathways for microbial Hg methylation [e.g., Gionfriddo et al. 2016], we envision that novel Hg-methylating microorganisms will be discovered, which will help to elucidate yet unknown biochemical pathways for Hg methylation.

The PhD student will conduct ground-breaking research on the biogeochemistry of mercury in Scottish peatlands, a landscape that plays a key role in carbon storage and climate change mitigation. The PhD student will be trained in all aspects of the project by leaders in the fields of geomicrobiology and geochemistry. S/he will learn fieldwork planning, sampling and sample processing, mercury analytical chemistry, molecular biology, metagenomics, bioinformatics, experiment design, anaerobic culturing, conceptual modelling, data archiving, scientific writing and science communication. The student will have the opportunity to present her/his work at national and international scientific conferences.

Supervisors

Dr. John W Moreau, University of Glasgow

Dr. Julia de Rezende, Heriot-Watt University

References

Blythe, J.L., 2020. The effects of legacy sulphur deposition on methylmercury production in northern peatlands; geochemical and biological considerations.

Chen, C.Y., Driscoll, C.T., Eagles-Smith, C.A., Eckley, C.S., Gay, D.A., Hsu-Kim, H., Keane, S.E., Kirk, J.L., Mason, R.P., Obrist, D. and Selin, H., 2018. A critical time for mercury science to inform global policy.

Farmer, J.G., Anderson, P., Cloy, J.M., Graham, M.C., MacKenzie, A.B. and Cook, G.T., 2009. Historical accumulation rates of mercury in four Scottish ombrotrophic peat bogs over the past 2000 years. Science of the Total Environment407(21), pp.5578-5588.

Gionfriddo, C.M., Tate, M.T., Wick, R.R., Schultz, M.B., Zemla, A., Thelen, M.P., Schofield, R., Krabbenhoft, D.P., Holt, K.E. and Moreau, J.W., 2016. Microbial mercury methylation in Antarctic sea ice. Nature microbiology1(10), p.16127.

Liu, M., Zhang, Q., Cheng, M., He, Y., Chen, L., Zhang, H., Cao, H., Shen, H., Zhang, W., Tao, S. and Wang, X., 2019. Rice life cycle-based global mercury biotransport and human methylmercury exposure. Nature communications10(1), pp.1-14.

Moreau, J.W., Gionfriddo, C.M., Krabbenhoft, D.P., Ogorek, J.M., DeWild, J.F., Aiken, G.R. and Roden, E.E., 2015. The effect of natural organic matter on mercury methylation by Desulfobulbus propionicus 1pr3. Frontiers in microbiology6, p.1389.

Podar, M., Gilmour, C.C., Brandt, C.C., Soren, A., Brown, S.D., Crable, B.R., Palumbo, A.V., Somenahally, A.C. and Elias, D.A., 2015. Global prevalence and distribution of genes and microorganisms involved in mercury methylation. Science advances1(9), p.e1500675.


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

NERC IAPETUS2 project – full details will soon be available at www.iapetus2.ac.uk.

University of Glasgow application portal www.gla.ac.uk/ScholarshipApp will open in November 2020. Contact primary supervisor (john.moreau [at] gla.ac.uk) in the interim for more information.

Fig. 1. Schematic representation of SCNbiodegradation by terrestrial and marine microbial communities, both of which produce the atmospheric trace gas carbonyl sulfide (COS) and aqueous CNO.

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, CNOacts as a significant source of N for nitrification [5], suggesting CNOplays 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, CNOand COS in wetland sediments.

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, CNOand COS degrading enzymes. A novel SIP metagenomics approach, utilizing stable isotope labelled substrates, will be used to get time resolved data on SCN, CNOand 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 CNObiodegradation in natural environments.

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.

  1. Watts, S.F., 2000. The mass budgets of carbonyl sulfide, dimethyl sulfide, carbon disulfide and hydrogen sulfide. Atmospheric Environment34(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. Nature524(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 Letters3(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 research158, 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. Nature524(7563), pp.105-108.

Supervisors

Dr. John W Moreau, University of Glasgow

Dr. Julia de Rezende, Heriot-Watt University

References

  1. Watts, S.F., 2000. The mass budgets of carbonyl sulfide, dimethyl sulfide, carbon disulfide and hydrogen sulfide. Atmospheric Environment34(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. Nature524(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 Letters3(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 research158, 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. Nature524(7563), pp.105-108.
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