Project Description
This project aims to analyse the microevolutionary mechanisms responsible for the creation and maintenance of microbial diversity across several terrestrial ecosystems. Understanding how biological diversity is created and maintained has been a key challenge for biologists for more than a century. Diversity is greatest in bacteria and archaea and its description has been dramatically improved by high-throughput sequencing which has been applied to a large range of land-use ecosystems. Large public genomic repositories now provide a fantastic opportunity to move beyond description and to solve some of the mysteries concerning the physiological and evolutionary mechanisms involved in biological diversification. Lateral gene transfer has been proposed as a key mechanism driving prokaryotic adaptation and this mechanism occurs within microbial populations, including both closely related or more distant organisms.
Microevolutionary mechanisms within microbial populations have been largely ignored by microbiologists partly due to the species concept debate and to the previously poor genetic diversity recovered from highly diverse natural microbial populations. However, the release of ultra-deep metagenomic sequencing technology now opens new opportunities for microbial population analyses, such as population metagenomics, which allows exploration and interpretation of the myriad of individual haplotypes that provide the population-level diversity of natural microbiomes (Nicholls et al., 2020).
The proposed research will therefore use available deep metagenomics sequencing from a range of soils to establish a population metagenomics bioinformatics pipeline. Once established, the student will generate some novel deep metagenomics sequencing across a range of soil ecosystems to test specific hypotheses relating to the physiological and evolutionary microbial adaptation required in different land-use soils and across several environmental gradients (either pH, temperature, moisture or other abiotic factors) (e.g. Sheridan et al., 2022). In particular, soils of different structural complexity (including diverse pore sizes, moisture content) will be analysed as such complexity impact microbial diversity (Hallett et al., 2022). This project will also involve some in vivo experimental environmental perturbations to determine the effect of several environmental changes (including drought and rewetting treatments) on the existing standing variation in the native and perturbed populations as well as their consequences for ecosystem services, processes, function and resilience.
Essential and desirable skills:
Essential: This innovative and cutting-edge project will require strong interest from the student in bioinformatics approaches and ecological theory. A strong motivation to deliver new insight in global change ecology is also required.
Desirable: Skills in bioinformatics and microbial ecology are rarely developed during MSc studies so the supervisor team will engage to train the student in the various bioinformatics and evolutionary approaches required (including metagenomics assembly and annotation, comparative genomics, selection detection, population metagenomics). A student holding a MSc in bioinformatics, microbial ecology and/or evolutionary biology would be preferred for this position.
Supervisors
Cécile Gubry-RanginPrimary Supervisor: | Profile: Cécile Gubry-Rangin Email: c.rangin@abdn.ac.uk Institution: University of Aberdeen Department/School: School of Biological Sciences |
Chris CreeveySecondary Supervisor: | Profile: Chris Creevey Email: chris.creevey@qub.ac.uk Institution: Queen's University, Belfast Department/School: School of Biological Sciences |
Paul HallettAdditional Supervisor: | Profile: Paul Hallett Email: paul.hallett@abdn.ac.uk Institution: University of Aberdeen Department/School: School of Biological Sciences |
References
Nicholls SM, Aubrey W, Edwards A, de Grave K, Huws S, Schietgat L, Soares A, Creevey CJ, Clare A (2020) Recovery of gene haplotypes from a metagenome. BioArxiv, https://doi.org/10.1101/223404
Sheridan PO, Meng Y, Williams TA, Gubry-Rangin C. (2022) Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat Com 13:1-13. https://doi.org/10.1038/s41467-022-31847-7
Hallett, P.D., Marin, M., Bending, G.D., George, T.S., Collins, C.D. & Otten, W. 2022. Building soil sustainability from root–soil interface traits. Trends in Plant Science. 27. https://doi.org/10.1016/j.tplants.2022.01.010
Research Methods
Some metagenomics data are already available in the host laboratory but also in many public databases. In addition, soil sampling will be performed in Scotland in different field stations, and natural (grassland, forest) or managed (agricultural, pasture) ecosystems. The supervisors also have a collaborative network in place to investigate a range of abiotic gradients using long-term established international field stations (US, Spain, France…).
Expected Training Provision
This project benefits from four existing grants on the impact of environmental change on microbial community combining empirical and bioinformatics analyses on soil ecosystems (one Royal Society University Research Fellowship, two Royal Society Enhancement Grants and one Marie Curie fellowship), totalling £1.5M. The student will work in collaboration with the postdoctoral fellows and PhD students working on the complementary aspects of this research, and will benefit from additional training and support.
Impact
This ambitious research is important and is likely to attract both academic (from diverse disciplines) and general audience interest given the urgency of understanding the impact of environmental change on biodiversity.
The impact of environmental change on biodiversity will be analysed through the use of different land-use ecosystems including peatlands, forest or agricultural soils for example. This will be analysed through an innovative fine molecular and genomic level, which has never been applied before. As such, it will produce significant scientific results for the academic community but will also impact on our understanding of maintenance of microbial biodiversity in terrestrial ecosystems. Results to be obtained will be disseminated to a wide community through public engagement.
In parallel to the impact on biodiversity, this project will also determine the impact of environmental change on the ecosystem services, processes, function and resilience. It will therefore be of interest for environmental management policy. These results will be transmitted to end-user community and policy-makers interested in environmental change.
This research will have a strong impact on the fundamental research and this project is expected to deliver several high-impact publications of international quality, including on:
- Metagenome assembled genomes (MAGs) reconstruction and evolutionary mechanisms associated to different soil ecosystems
- Bioinformatics pipeline analysing the microevolutionary diversity
- Impact of environmental change on fine-scale microbial biodiversity.
The novel MAGs assembled during the project will be deposited on public databases for use by other researchers, either in academy or in industry. They may be of interest for their potential industrial interest and may lead to the discovery of novel pharmaceutical/antibiotic compounds, especially for the previously underexplored acidic soils.
The outcome of this research will also be disseminated to the general public through several local dissemination events (in Aberdeen and Belfast), such as primary/secondary school workshops, Techfest, Explorathon.
Proposed Supervision
The student will primarily be based at University of Aberdeen under the supervision of Prof. Cecile Gubry-Rangin (CGR), Royal Society University Research Fellowship, with access to lab and facilities for research and training at the School of Biological Sciences. CGR’s research is directed toward understanding ecological, physiological and evolutionary adaptation of microbial populations. The research of co-supervisor Prof. Chris Creevey (CC) at Queen’s University Belfast focuses on computational biology with an interest in applying ecological and evolutionary principals to microbial communities. His research primarily focusses on bioinformatic analyses, including the development of novel open source computational approaches for evolutionary analyses of microbial data. The third supervisor, Prof. Paul Hallett, will bring his expertise on soil science and terrestrial land-use management. All supervisors will be involved in providing advice and guidance as well as monitoring project progress through periodic meetings. The supervisory team has highly relevant and complementary expertise which will ensure a safe delivery of the project.
Proposed Timetable
During the first 6-months, the student will complete an induction process at UoA and QUB and will spend time in the laboratories of all supervisors to get familiarised with the research environment. The student will review the literature on the impact of environmental change on microbial diversity at multiple phylogenetic levels and on metagenomics. The student will also gain technical skills and hands-on experience in using the relevant approaches, including bioinformatics, soil sampling and molecular biology.
The student will then focus on learning to use the bioinformatics tools and generate a pipeline to analyse the microevolutionary diversity and apply it on a range of soil metagenomes available from the UoA lab and from public databases. This will be performed over 12 months and these results will be fully analysed and presented in a national conference (MMEG or SAM).
The following year will be dedicated to selecting a range of soils to perform the deep-sequencing metagenomics approach. DNA extraction optimisation, sequencing (outsourced in an external company), MAGs assembly and annotation and application of the microevolutionary diversity pipeline will likely require 12 months. The student will also perform a policy-driven non-HEI placement.
In parallel to the bioinformatics analyses, the experimental incubation experiment will be established, and both molecular and bioinformatics analyses will also be applied. Analysis of ecosystem function and resilience (as well as statistical implementation) will require another 6 months. These results will be fully analysed by the end of the PhD and presented in an international conference (ISME).
While this schedule does not take into account the periods required for training, non-HEI placement and leave, the remaining time will be required to write the thesis and finalise associated publications. Manuscripts will be drafted throughout the PhD and at least one high impact manuscript will be submitted before thesis submission.
QUADRAT Themes
- biodiversity
- earth-systems
Partners
Not applicable at this time.
