Microbial ecology of early stage colonisers in the digestive tracts of large herbivores (PhD Scholarship)

Applications for this scholarship are now closed.

Microbial ecology of early stage colonisers in the digestive tracts of large herbivores.

Aberystwyth University, IBERS

Project ID: AU20018
Annual Stipend: £14,340
Application Deadline: 1st November 2017

Animals are unable to degrade plant polymers and are thus reliant on consortia of microbes to secrete cellulose and other fibre-degrading enzymes to access the nutritional value contained within plant biomass. These anaerobic microbial consortia comprise not only bacteria and fungi which form biofilms on the surface of ingested plant material but also ciliate protozoa and methanogenic archaea. These ciliates form a second level in the food chain, with different species variously adapted to graze on fungal zoospores, free-swimming bacterial cells or plant plastids.

The enzymes secreted by these microbes are of interest, not only because of their high activity against plant fibre (eg anaerobic fungi secrete the most powerful cellulose found to date) but also because of their biotechnological potential. One area where this has been exploited is in enzymatic pre-treatment of animal feeds, which has been shown to have beneficial effects in ruminants, horses etc.


The current proposal aims to investigate the initial stage of colonisation of freshly ingested feed particles and the formation of the degradative biofilms, where it is believed that the zoospores of anaerobic fungi play a particularly important role. In addition to investigating the dynamics of initial colonisation, the effects of various enzyme pre-treatments of feeds on the rate of feed particle colonisation and degradation will be investigated. It is hoped to identify additional enzymes capable of digesting plant material, with a view to possibly exploiting them as alternative pre-digestion sources to supplement the existing market. Development of an increasing number of potential enzymes with a relevance to the feed industry is critical to the work of the commercial partner within this application.


Within this project a range of approaches will be deployed to investigate the processes of initial feed particle colonisation, including the construction of metagenomic libraries from digesta samples at different stages of colonisation, screening of microbes isolated from feed particles for fibrolytic properties. Enzymes with novel properties (e.g. unusual optimal pH values) will be selected for more detailed enzymatic characterisation.


In order to better understand why enzymatic pre-treatment is effective, the dynamics of feed particle colonisation will also be investigated by microscopy (confocal, scanning electron and epifluorescence), as well as fluorescent in situ hybridisation (FISH) to localise particular microbes as they attach to freshly ingested feed particles.

This studentship offers the opportunity to address fundamental questions in microbial ecology using the latest technological tools, and additionally to deploy the results of such investigations in an applied context.


The prospective applicant should have a minimum of a 1st or good 2:1 in a relevant degree, and be available to take up the studentship by January 2018. The project is part-funded by the European Social Fund (ESF) through the European Union’s Convergence programme administered by the Welsh Government. KESS II PhD scholarships are collaborative awards with external partners. (Applicants need to only apply, they do not need to search for partners).


To apply, please submit the following to the Postgraduate Admissions Office (address below) by Wednesday 1st November 2017:

  1. A completed Research Programme Application Form, two references. Application and reference forms may be downloaded from http://www.aber.ac.uk/en/postgrad/howtoapply/
  2. A completed KESS II Participant proposal form (put the reference number AU20018 in the top right hand box of the application form) and an up-to-date CV. KESS II application forms are available to download at the link below.


  1. A PhD proposal of up to 1,000 words where you expand on your experience and interests and describe why you are a good candidate for this research studentship. Please refer to the Project Description.


Value of Award: A stipend of £14,340 (rising in accordance with inflation for the remaining two years). Each scholarship has an additional budget for travel, equipment/consumables and training to support your research. KESS II PhD Scholarship holders do not pay fees.

Length: Full-time for 3 years. (Theses must be submitted 6 months after the funded three year study period.)

Training: The achievement of a Postgraduate Skills Development Award (PSDA) is compulsory for each KESS II scholar (The PSDA is based on a 60 credit award, which is an additional award to the PhD).

Eligibility: To be eligible to apply for a KESS II award, you must be resident, upon starting the scholarship, in the Convergence Area of Wales and you must be able to take paid employment in the Convergence area on completion of the scholarship.

The Convergence Area means the following counties of Wales:

Isle of Anglesey
Neath Port Talbot
Rhondda Cynon Taff

For further student eligibility criteria related to the individual projects, please view the details of the individual project above.

Informal enquiries should be made to Dr Gareth Griffith at gwg@aber.ac.uk or 01970 622325

Address for applications:

Postgraduate Admissions Office
Recruitment & Admissions
Student Welcome Centre
Aberystwyth University
SY23 3FB

Quote Reference AU20018

Closing date for applications 1st November 2017