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EASTBIO The impact of gut fungal morphology on digestion of plant material

PHD Opportunities

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Dr Jolanda van Munster , Prof S C Fry , Prof J Newbold No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

Sustainable food sources are urgently required to support the growing world population. Increased production of meat and milk from ruminants can help meet these nutritional needs and contributes to food security. However, more sustainable livestock farming is required to minimize environmental impacts. Cattle health and performance, including emission of greenhouse gasses, is impacted by activity of the rumen microbiome. This consortium of bacteria, archaea, protozoa and fungi is critical in ruminant feed digestion. The anaerobic gut fungi effectively degrade hard-to-digest plant biomass, and thereby increase ruminant feed conversion. Despite their importance, the degradative capacities of these gut fungi are still poorly understood. This project focusses on the degradative mechanisms employed by gut fungi in plant biomass degradation, the fundamental understanding of which is critical to their subsequent exploitation in improvement of animal nutrition and sustainable livestock farming.

Anaerobic gut fungi, Neocallimastigomycota, are thought to derive their effective degradative capacity from a combination of degradative enzyme complexes and physical force exerted by the fungal cells in and on the plant material. However, gut fungal species have been identified both with and without the filamentous structures that penetrate plant biomass during its degradation.

This project will assess the impact of these different morphologies on degradative strategies of gut fungi. You will assess how gut fungi with filamentous structures compare to fungi that form only bulbous structures, in their capacity to degrade plant material relevant as animal feeds or renewable feedstock. You will assess differences in genome content between filamentous and bulbous fungal species, and via cultivations of the fungi with plant biomass, assess their degradative response via identification of gene expression and enzyme production. You will investigate the performance of fungi in a complex microbiome environment via fermentation of fungi with rumen fluid in vitro. The ability of fungal species to degrade the plant material itself will be assessed via detailed analysis of the plant biomass substrate, using a combination of biochemical assays, and detection of specific carbohydrate structures via immunohistochemistry, mass spectrometry and radiolabelling. Combining the information uncovered above with biochemical assays, you’ll aim to identify enzymes that are located on the filamentous rhizoids of gut fungi, as opposed to the enzymes that are soluble or located on bulbous fungal structures that are external to the plant material.

This project will give the student an opportunity to develop a broad, interdisciplinary skill set covering anaerobic microbiology, fermentation, molecular biology including transcriptomics and proteomics as well as biochemical analysis and state of the art mass spectrometry techniques. Training in specialist techniques unfamiliar to the student will be provided by the supervisors.

Within SRUC the project falls in the remit of the recently established challenge-driven research centres for safe and improved food and climate emergency, and links in with a well-established program of activities around the role of the microbiome in sustainable farming of ruminants, thus ensuring research embedding and opportunities to collaborate. The project will involve collaboration with a polysaccharide expert in the Institute of Molecular Plant Sciences, University of Edinburgh.

Applicants should download the required forms from and send the following documents to [Email Address Removed]:
a. EASTBIO Application Form
b. EASTBIO DTP Equality Form
c. CV
d. Academic transcripts (a minimum of an upper second class or first class honours degree or equivalent is required for PhD study
e. Two references should be provided by the deadline using the EASTBIO reference form ( Please advise your referees to return the reference form to [Email Address Removed].
f. If you are nominated by the supervisor(s) of the EASTBIO PhD project you wish to apply for, they will provide a Supervisor Support Statement.

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition (Please state if your institution will provide funding to cover the difference in fees). Please refer to UKRI website and Annex B of the UKRI Training Grant Terms and Conditions for full eligibility criteria.


Two references should be provided by the deadline using the EASTBIO reference form ( Please advise your referees to return the reference form to

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