Into the dark: diversity and ecology of fungi and protists in the twilight zone of polar freshwaters environments

Project Background

Polar freshwater environments represent oasis of life and hotspot of biodiversity in arid polar desert and in these freshwater habitats, cold temperature can be accompanied by freeze-thawing cycling, darkness and large variations in nutrients and salinity, and therefore the biology of these ecosystems is dominated by microbial life with plants, insects and animals being mostly absent.

Microbial communities from diverse communities in the water column and biofilms along the bottom of freshwater environments. The water column of lakes and meltwater ponds can be highly stratified with illuminated oxygen containing water at the surface but dark and anoxic layers at the bottom.

Recent molecular analyses have shown that fungi and protists including ciliates, amoeba and flagellates are abundant and can even be detected in the more extremer deeper water layers that lack of oxygen, but their taxonomic richness, diversity and biogeography remain poorly characterised.

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. 

Project Aims and Methods

Anaerobic protists have specialist mitochondria for their energy metabolism in the absence of oxygen and they have been shown to be major predator of bacteria in aquatic environments. However, polar environments have received little attention, and their ecological function in food webs and interactions with bacterial assemblages are not known yet.

The aims of the project are therefore to perform a comprehensive environmental DNA diversity assessment of fungi and protists in low oxygen and anoxic waters in lakes and meltwater ponds across the Arctic and Antarctic, and characterise phylogenetic and biogeography relationships, and evaluate the relative importance of nutritional roles (heterotrophs: grazers, predators, parasites, symbioses) in the Polar regions.

Genomic adaptations of key microbial players to polar environments could be studied using cutting edge high throughput sequencing and bioinformatics. The research outcomes will also be relevant for the evolution of eukaryotes on Early Earth.

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.

Candidate requirements

The project would suit a candidate interested in microbiology, protistology, environmental and freshwater ecology and bioinformatics. Basic molecular and sequence analysis skills would be beneficial for the project.

Project partners 

This project is cross-institutional between the Natural History Museum, University of Exeter and University of Stavanger and University of Quebec at Chicoutimi.

he prospective students will benefit from ongoing collaborations with the wider international research community in the field of polar microbiology in the Arctic and Antarctic.

The student will also have access to GW4+ training courses and wider development opportunities, including cohort induction and bespoke training courses. The project might also provide opportunities for field work. The NHM postgraduate office offers regular workshops for PhD students designed to support their research and communication skills and career development. 

Molecular and microbiology techniques: DNA and RNA extraction methodologies from environmental samples and enrichment cultures, PCR, high throughput sequencing, microscopy techniques. 

Bioinformatic and phylogenetic inference analysis: Computational biology for eukaryote genome diversity and evolution; genome assembly and annotation, phylogenetics using maximum likelihood.

Science communication skills: The PhD student will have opportunities to training in communication skills and participate at NHM public engagement events 

How to apply

Apply for this project here.

The application deadline is Tuesday 9 January 2024 at 23.59 GMT.

Interviews will take place from 26 February to 8 March 2024. For more information about the NERC GW4+ Doctoral Training Partnership please visit https://www.nercgw4plus.ac.uk.

If you are interested in applying, you must complete the Personal Statement form.

Please also complete the applicant's questionnaire GW4+ DTP PhD applicants questionnaire - 2023-24.

For more information on who can apply please visit the GW4+ page: Apply - NERC GW4+.

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