Do trace gas oxidising bacteria help build soil on volcanic rock?


Do trace gas oxidising bacteria help build soil on volcanic rock?


Project Description


Dr Marcela Hernandez (School of Biological Sciences, University of East Anglia) – Contact me

Dr Laura Lehtovirta-Morley (School of Biological Sciences, University of East Anglia)

Dr Colin Murrell (School of Biological Sciences, University of East Anglia)


Project Background

Trace-gas metabolising microbes can produce “early” organic carbon leading to soil formation and therefore play a crucial role in soil dynamics. They are particularly important in early soil formation, where organic carbon concentration is low. Understanding the mechanisms by which these microbes consume trace gases is important as this will determine the rate and nature of initial biomass formation, providing the foundation for the development of heterotrophic microbes, microbial turnover, plant growth and root exudation. Although the relative abundance of trace-gas metabolising microbes may decrease as soil develops, the absolute amount of trace-gas metabolism is likely sustained and significant in control of the Earth’s climate. The objective of this PhD proposal is to determine the drivers influencing microbial colonisation of new volcanic soils and the importance of trace gases in supporting soil formation and restoration.

The project

The student will determine how bacteria are able to oxidise climate-active gases such as methane (CH4), carbon monoxide (CO) and hydrogen (H2) in recently-formed soils from volcanoes. Soil incubations will be performed, and trace-gases will be measured by using gas chromatography. The student will be trained in cutting-edge tools for isolation and identification of microbes, including whole genome sequencing, metagenomics and bioinformatics.


The student will receive training in experimental design and data analyses and will learn molecular microbial ecology techniques such as stable isotope probing, DNA sequencing and metagenomics. Specific training will include the cultivation of soil bacteria; quantitative PCR; amplicon-based sequencing (metagenetics); whole genome sequencing and (meta)genomic analysis. They will enrol in soft-skills workshops (e.g. how to give a presentations, how to write a fellowship application, scientific writing) at the University of East Anglia. The student will present their results at weekly lab meetings, departmental seminars, and also at national and international conferences.

Person specification

We are looking for a pro-active, highly motivated student willing to join sampling campaigns at Llaima Volcano in Chile and/or at Kilauea Volcano in Hawaii. Background knowledge on basic microbiology techniques is desirable. The successful candidate should have a strong background in Microbial, Soil or Environmental Sciences (BSc/Masters in Soil Microbiology, Environmental Microbiology, or similar).


  • 1) Hernández M, Vera-Gargallo B, Calabi-Floody M, King GM, Conrad R, Tebbe CC. Reconstructing genomes of carbon monoxide oxidisers in volcanic deposits including members of the class Ktedonobacteria. Microorganisms. 2020 Nov 27;8(12):1880. doi: 10.3390/microorganisms8121880.
  • 2) Hernández M, Calabi M, Conrad R, Dumont M. 2020b. Analysis of the microbial communities in soils of different ages following volcanic eruptions. Pedosphere. 30: 126-134. doi:10.1016/S1002-0160(19)60823-4.
  • 3) Hernández M, Dumont MG, Calabi M, Basualto D, Conrad R. Ammonia oxidizers are pioneer microorganisms in the colonization of new acidic volcanic soils from South of Chile. Environ Microbiol Rep. 2014 Feb;6(1):70-9. doi: 10.1111/1758-2229.12109.
  • 4) Radajewski S, Ineson P, Parekh NR, Murrell JC. Stable-isotope probing as a tool in microbial ecology. Nature. 2000 Feb 10;403(6770):646-9. doi: 10.1038/35001054.
  • 5) King GM, Weber CF. Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nat Rev Microbiol. 2007 Feb;5(2):107-18. doi: 10.1038/nrmicro1595. PMID: 17224920.

Key Information

  • This project has been shortlisted for funding by the ARIES NERC DTP and will start on 1st October 2022. The closing date for applications is 23:59 on 12th January 2022.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a NERC studentship, which covers fees, stipend (£15,609 p.a. for 2021-22) and research funding. International applicants (EU and non-EU) are eligible for fully-funded UKRI studentships. Please note ARIES funding does not cover visa costs (including immigration health surcharge) or other additional costs associated with relocation to the UK.
  • ARIES students benefit from bespoke graduate training and ARIES provides £2,500 to every student for access to external training, travel and conferences. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses in the subject area.
  • ARIES is committed to equality, diversity, widening participation and inclusion in all areas of its operation. We encourage enquiries and applications from all sections of the community regardless of gender, ethnicity, disability, age, sexual orientation and transgender status. Academic qualifications are considered alongside non-academic experience, and our recruitment process considers potential with the same weighting as past experience.
  • All ARIES studentships may be undertaken on a part-time or full-time basis, visa requirements notwithstanding
  • For further information, please contact the supervisor. To apply for this Studentship click on the “Apply now” link below.
  • ARIES is required by our funders to collect Equality and Diversity Information from all of our applicants. The information you provide will be used solely for monitoring and statistical purposes; it will remain confidential, and will be stored on the UEA sharepoint server. Data will not be shared with those involved in making decisions on the award of Studentships, and will have no influence on the success of your application. It will only be shared outside of this group in an anonymised and aggregated form. You will be ask to complete the form by the University to which you apply.

Applications are open

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