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Exploring the contribution of horizontal gene transfer to greenhouse gas emissions from arable agriculture


Institute of Integrative Biology

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Dr J Hall , Prof T J Daniell No more applications being accepted Competition Funded PhD Project (European/UK Students Only)

About the Project

Nitrous oxide (N2O) is a potent and long-lived greenhouse gas, and arable agriculture is a major source of N2O due to incomplete denitrification of N-based fertilizers by microbes. Soil microbes engage in denitrification to respire under anoxic conditions, for example when soil becomes waterlogged. Unpredictable conditions under a changing climate, combined with demands for crop production by expanding populations, are likely to favour increased rates of denitrification and N2O production. Mitigating N2O emissions requires an increased understanding of the microbial evolutionary ecology driving denitrification. In particular, genetic analyses suggest that the genes responsible for denitrification can be spread between bacterial species by horizontal gene transfer (HGT). Plasmids and other mobile genetic elements can facilitate the transmission of traits by HGT, as evidenced in the spread of antimicrobial resistance, but our understanding of the role of HGT in transferring denitrification genes, and the consequences for N2O production, is limited. In this project we will use microbial ecology, experimental evolution, and genomics to unpick the role of mobile genetic elements in the evolution of denitrification across soil bacterial communities.

The student will be trained in laboratory methods including microbiology, experimental evolution, molecular biology, and bioinformatics. Background in any of these subjects would be useful, but more important are enthusiasm for soil microbiology/microbial evolution and ecology, self-motivation, and the drive to develop an independent research project. Students will also develop general research skills such as scientific writing, presentation, literature reviewing, and statistical analysis, developing skills that will place them in an excellent position for a future scientific career. The project will be jointly based in the Universities of Liverpool and Sheffield as part of the ACCE Doctoral Training Partnership.

Applicants should generally have an upper second or first class degree in biological sciences or any other relevant field. Please get in touch by email if you have any questions about this project or your application — informal pre-application enquiries are strongly encouraged.


Funding Notes

Competitive funding of tuition fee, research costs and stipend (£15,009 tax-free, 2019-20) from the NERC Doctoral Training Partnership “Adapting to the Challenges of a Changing Environment” (ACCE, http://acce.group.shef.ac.uk/ ). ACCE – a collaboration between the Universities of Liverpool, Sheffield,and York – is the only dedicated ecology/evolution/conservation Doctoral Training Partnership in the UK.

Applications (CV, letter of application, 2 referees) by email to [Email Address Removed] deadline: January 8th 2020. Interviews in or after the week commencing : 10th February 2020. Shortlisted applicants will be interviewed for only one project from the ACCE partnership.

References

Giles, Daniell & Baggs (2017) Compound driven differences in N2 and N2O emission from soil; the role of substrate use efficiency and the microbial community. Soil Biology and Biochemistry 106, 90-98

Hall, Harrison, Lilley, Paterson, Spiers & Brockhurst (2015). Environmentally co-occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context-dependent fitness effects. Environmental Microbiology, 17(12): 5008-5022.

Hall, Wood, Harrison & Brockhurst (2016) Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities. Proceedings of the National Academy of Sciences, 113: 8260-8265.

Langarica-Fuentes, Manrubia, Giles, Mitchell & Daniell (2018) Effect of model root exudate on denitrifier community dynamics and activity at different water-filled pore space levels in a fertilised soil. Soil Biology and Biochemistry 120, 70-79.
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