Diversity and ecological function of fungi and protists in Antarctic and Arctic freshwater ecosystems

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This project aims to understand key ecological processes driven by microbes in the polar regions.

The studentship is part of the Great Western Four+ Doctoral Training Partnership, funded by NERC and starts September 2019.

Apply for this course

Read the eligibility criteria and application guidance below, then send your application to postgradoffice@nhm.ac.uk.

Application deadline: 7 January 2019

Summary

This PhD project aims to perform a comprehensive environmental DNA diversity assessment of fungi and protists in lakes, meltwater ponds and streams across the Arctic and Antarctic, and characterise phylogenetic and biogeography relationships, and evaluate the relative importance of nutritional roles (heterotrophs: grazers, predators, parasites, symbioses) and autotrophs, and microbial consortia/biofilms in freshwater microbial mat ecosystems in the Polar regions.

Key microbial players/consortia/biofilms will then be isolated from the communities and RNA-based analyses undertaken to understand metabolic and genomic adaptations to polar environments using cutting edge high throughput sequencing (including Nanopore) and bioinformatics.

The project would suit a candidate interested in microbiology, protistology, environmental and freshwater ecology and bioinformatics. It would be good for the proposed PhD student to have some experience in molecular techniques and sequence analysis.

Background

The Polar regions are characterised by perennially extreme conditions and Antarctic lakes are recognised as early detectors of environmental change, because variation in snow and ice cover affects ecological variables, while some of the polar regions has experienced some of the most rapid temperature increases on Earth.

Polar freshwater environments represent oasis of life and hotspot of biodiversity in arid polar desert and glacier ecosystems. In these freshwater habitats, cold temperatures are often accompanied by freeze-thaw cycles, extreme fluctuations in irradiance including ultraviolet radiation, and large variations in nutrient supply and salinity, and therefore the biology of these ecosystems is dominated by microbial life with plants, insects and animals being mostly absent.

Microbial communities often form microbial mats which are thick biofilms with matrix formed by filamentous cyanobacteria and internal vertical stratification of physical and chemical gradients with diverse bacterial assemblages. Recent molecular analyses have shown that fungi and protists including ciliates, amoeba and flagellates are also abundant in these extreme environments, but their taxonomic richness, diversity and biogeography remain poorly characterised.

However, the few existing relevant studies indicate that there is significant genomic and functional novelty in these systems that demand further study in order to understand key ecological processes driven by microbes in polar regions.

In temperate environments fungi and protists have been shown to be significant contributor to aquatic microbial food webs and carbon and nutrient cycling through decomposition of organic matter, predation and parasitism. However, their ecological function in polar food webs and interactions with bacterial assemblages are not known yet. 

Supervision and training

This project is cross institutional between the Natural History Museum and Bristol University.

The project will use a multi-faceted approach and provide the PhD student with training in molecular, microbiology techniques and bioinformatics, in particular environmental DNA and RNA, high throughput sequencing, microbial community structure analysis, genomics, metagenomics and phylogenetic interference.

The student will have access to an integrated programme of postgraduate transferrable skills training and professional development.

The student will also be encouraged to apply for the NERC Arctic Field course, or take part in a University of Svalbard Polar Microbiology course, to put their work in context of in-situ field setting.

Eligibility

Applications are primarily open to UK residents only (minimum residence of 3 years excluding time in further education), however, a limited number of full studentships are also available to EU residents. All applicants need to comply with the registered university's English-language requirements.

Applicants should have obtained or be about to obtain a First or Upper Second Class UK Honours degree, or equivalent qualifications gained outside the UK. Applicants with a Lower Second Class degree will be considered if they also have a master's degree. Applicants with a minimum Upper Second Class degree and significant relevant non-academic experience are encouraged to apply.

How to apply

Applications for the PhD are processed through the Natural History Museum.

To apply please send the following documents to the Postgraduate Office at postgradoffice@nhm.ac.uk:

  • Curriculum vitae.
  • Covering letter outlining your interest in the PhD position, relevant skills training, experience and qualifications for the research, and a statement of how this PhD project fits your career development plans.
  • Names of two academic referees.

The deadline for applications is 7 January 2019.

Any questions?

If you have any questions about the project please contact

Main supervisor: Dr Anne Jungblut

Supervisors

The Natural History Museum

Main supervisor: Dr Anne Jungblut

Co-supervisor: Dr David Bass

Bristol University

Co-supervisor: Dr Tom Williams

References

Bass D, Tikhonenkov DV, Foster R, Dyal P, Janouškovec J, Keeling PJ, Gardner M, Neuhauser S, Hartikainen H, Mylnikov AP, Berney C (2018) Rhizarian ‘Novel Clade 10’ Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates, including Aquavolon n. gen. The Journal of Eukaryotic Microbiology 0, 1–15

Dean, P, Sendra, KM, Williams, T, Watson, AK, Major, P, Nakjang, S, Kozhevnikova, E, Goldberg, AV, Kunji, ERS, Hirt, RP & Embley, TM, 2018, Transporter gene acquisition and innovation in the evolution of Microsporidia intracellular parasites. Nature Communications, 9: 1709

Yi Z, Berney C, Hartikainen H, Mahamdallie S, Gardner M, Boenigk J, Cavalier-Smith T, David Bass (2017) High-throughput sequencing of microbial eukaryotes in Lake Baikal reveals ecologically differentiated communities and novel evolutionary radiations, FEMS Microbilogy Ecology 93 fix073

Jungblut AD, Vincent WF, Lovejoy C (2012) Eukaryotes in Arctic and Antarctic cyanobacterial mats. FEMS Microbiology Ecology, 82 (2) : 416 - 428

Great Western Four+ Doctoral Training Partnership

Joint PhD training partnerships between the Natural History Museum and the Great Western Four, Bath, Bristol, Cardiff and Exeter universities.

Funded by 

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