Project highlights

  • Fieldwork in the Makgadikgadi Salt Pans, Botswana
  • Characterising the CO-utilising metabolism that fuels life in saline environments
  • Training in state-of-the-art techniques across the fields of microbiology, molecular biology, and bioinformatics.

Overview

Extremophiles thrive in conditions at the limits of life and are thought to have been the first life on Earth.  Studying extreme environments is important to: 1) characterise the boundaries of life on Earth; 2) identify metabolisms fuelling the life at these boundaries and 3) understand the ecological principles controlling community diversity and function.

Extremophiles are believed to be critical to the evolution of the Earth’s biogeochemical cycles, including carbon monoxide (CO) oxidation, an ancient metabolic process that is widespread across the tree of life, abundant in numerous environments and upregulated under carbon starvation. CO is also an important, ubiquitous trace gas that enhances climate change. Despite this importance, CO oxidation is still poorly defined with regard to the ecology and physiology of CO-oxidising microbes. CO oxidisers can be broadly divided into two categories: Carboxydotrophs (that use CO as a carbon and energy source) and Carboxydovores (that use CO as an energy source), further complicating their identification and characterisation. CO oxidation-related genes are highly abundant in microbes in saline environments, and since these extreme environments have lower taxonomic diversity, they are ideal for the effective identification of CO-oxidising microbes and investigation into their interactions with other members of the microbial community. Studying environments across a salinity gradient allows characterisation of how the ecology of these microbes changes with increasing taxonomic diversity and reduced environmental selection pressure.

This project will therefore focus on developing our understanding of how physico-chemical factors influence the diversity and function of CO-oxidising bacteria. For this work, samples will be collected from the Makgadikgadi Salt Pans, Botswana. To answer the proposed research questions, the project will combine state-of-the-art molecular techniques and culture-based microbiology. The project will involve: 1) identifying the CO-oxidising bacteria in the two saline environments, using a microcosm and sequencing-based approach; 2) assessing the interactions between distinct microbes via Stable Isotope Probing; 3) defining the impact of CO oxidation and CO-oxidising microbes on other members of the microbial community, through isolations, genome sequencing, and growth experiments.

Image of a Salt Pan

Figure 1: The fieldwork site for this project – the salt pan in Botswana.

Host

The Open University

Theme

  • Climate and Environmental Sustainability
  • Organisms and Ecosystems

Supervisors

Project investigator

Co-investigators

How to apply

Methodology

A combination of cultivation dependant and independent techniques will be applied to investigate the role of CO oxidation in fuelling microbial community viability under saline conditions.  This will involve extracting DNA and RNA from environmental samples collected from fieldwork and identifying: 1) the diversity of CO-utilisers within the saline environments, 2) comparing the CO-communities between the saline and hypersaline water, and 3) using Stable Isotope Probing to identify the carbon flow between members of the community. This will be supported by cultivation experiments to enrich and isolate the CO-utilisers identified within these environments, and analytical techniques to understand the geochemical context of the samples (fluid and sediments). The student will have access to a range of additional techniques at the partner organisations that can be used to identify microbial interactions.

Training and skills

Students will be awarded CENTA2 Training Credits (CTCs) for participation in CENTA2-provided and ‘free choice’ external training. One CTC equates to 1⁄2 day session and students must accrue 100 CTCs across the three years of their PhD.

The student will be trained in fieldwork and specific laboratory-based techniques, e.g., molecular biology (DNA extraction, PCR, library preparation, stable isotope probing and DNA sequencing), analytical geochemistry and culture-based microbiology by members of the research team. Short placements with the project partners will enable access to laboratory facilities and training in specific laboratory techniques. The student will also be trained in computer-based techniques, including bioinformatic analysis of sequencing data.

The student will benefit from additional skills development opportunities offered by the AstrobiologyOU research group and wider faculty/university, e.g., communication skills, time management, academic writing and more.

Partners and collaboration

Dr. Michael Cunliffe (MBA – Plymouth) has expertise in environmental microbiology, including DNA sequencing and Stable Isotope Probing.

Dr. Eric Bapteste (Université Pierre et Marie Curie – Paris) has expertise in evolutionary bioinformatics. They will provide training in data mining and network analysis of metagenomic datasets.

Dr. Fulvio Franchi (Botswana International University of Science and Technology – Botswana) is an Associate Professor in Sedimentology and our contact in Botswana.

Further details

If you wish to apply to the project, applications should include:

  • A CV with the names of at least two referees (preferably three and who can comment on your academic abilities)

Applications to be received by the end of the day on Wednesday 11th January 2023.

 

Possible timeline

Year 1

Year 1: Perform a literature review and undertake fieldwork collecting samples from Botswana. Complete initial training in molecular techniques and bioinformatics (genome, amplicon and metagenome). Set up cultures for isolation and perform initial growth experiments with CO.

Year 2

Year 2: Perform metagenomic analysis of the field sites and Stable Isotope Probing experiments with environmental materials to assess mechanisms underpinning CO oxidation and its role in community diversity. Analyse the geochemistry of the field sites. Present results at a national conference (e.g. Microbiology Society annual conference).

Year 3

Year 3: Perform growth experiments to further investigate the impact of CO-oxidation on other members of the microbial community. Prepare and submit a manuscript regarding the metagenomic work and related growth experiments. Present data at an international conference (e.g. Gordon Applied and Environmental Microbiology). Write and submit thesis.

Further reading

  • Bay, S. K. et al. (2021) ‘Trace gas oxidizers are widespread and active members of soil microbial communities’, Nature Microbiology, 6(2), pp. 246–256. doi: 10.1038/s41564-020-00811-w.
  • Cordero, P. R. F. et al. (2019) ‘Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival’, ISME Journal, 13(11), pp. 2868–2881. doi: 10.1038/s41396-019-0479-8.
  • King, G. M. and Weber, C. F. (2007) ‘Distribution, diversity and ecology of aerobic CO-oxidizing bacteria’, Nature Reviews Microbiology, 5(2), pp. 107–118. doi: 10.1038/nrmicro1595.
  • Macey, M.C. et al. (2020) ‘Impact of plants on the diversity and activity of methylotrophs in soil’, Microbiome, 8(1). doi: 10.1186/s40168-020-00801-4.
  • Macey, M. C. et al. (2020) ‘The identification of sulfide oxidation as a potential metabolism driving primary production on late Noachian Mars’, Scientific Reports, 10(1), p. 10941. doi: 10.1038/s41598-020-67815-8.
  • Ortiz, M. et al. (2021) ‘Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils’, Proceedings of the National Academy of Sciences USA, p. In revision. doi: 10.1073/pnas.2025322118/-/DCSupplemental.Published.

COVID-19

Possible impacts of a pandemic would include the suspension of international travel, impacting fieldwork, and the possibility of local lockdowns, restricting lab access. To mitigate risks in the instance that fieldwork is prevented, we would have collaborators from a research institute in Botswana that would be able to collect the samples on our behalf and ship them to the UK. In the instance of local lockdowns restricting lab access, the project has been designed to include computer-based research, which would allow the project and research questions to progress.