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Metabolic interactions between fungi and bacteria in the rumen microbiome

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  Dr Jolanda van Munster  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Sustainable ruminant farming is required to ensure global food security while mitigating environmental impacts. Ruminant performance, including greenhouse-gas emission, is critically impacted by activity of the microbiome.

The microbiome contains bacteria, archaea, fungi and protozoa, who’s joint metabolism converts animal feed to nutrients. Primary degraders, including anaerobic gut fungi (AGF), break down feed polysaccharides to soluble sugars, consumers grow on such sugars, and cross-feeders rely on metabolites (e.g. acetate) produced by the others. Importance of metabolic interactions across trophic levels is exemplified by how hydrogen, produced by AGF and protozoa, drives production of GHG methane by archaea. Other metabolic interactions of AGF remain largely unknown.

This project aims to uncover metabolic pathways that enable a recently discovered fungal-bacterial cross-feeding interaction, and to explore the existence of other fungal-bacterial interactions.

Project objectives are:

1. Establish a data analysis workflow for stable isotope-based labelled untargeted metabolomics.

We identified a novel fungal-bacterial cross-feeding interaction. To understand the fate of the responsible metabolite in AGF, stable isotope labelled metabolite will be traced during fungal metabolism. Ion mobility mass spectrometry-based untargeted metabolomics methods, including data analysis workflows, are established within EdinOmics. You will develop a data analysis workflow that enables deployment of the current methods for stable isotope-based labelled untargeted metabolomics.

 2. Elucidate bacterial and fungal metabolic pathways that enable a novel cross-feeding interaction mechanism.

You’ll offer stable isotope labelled metabolite to AGF, detect breakdown products and thereby elucidate fungal metabolic pathway(s) underlying consumption of this compound. In a complementary approach, assessing gene expression in AGF and the bacterial partner will elucidate their (metabolic) activity during cross-feeding interaction.

3. Explore other fungal-bacterial cross-feeding interactions during lignocellulose degradation.

You’ll screen for cross-feeding interactions employing synthetic co-cultures of AGF and bacteria under rumen-mimicking conditions. You will isolate responsible bacteria, identify candidate metabolites, and test if these support microbial growth.

This project builds on expertise in fungal biology and rumen microbiology at Scotland’s Rural College (SRUC), and untargeted metabolomics at University of Edinburgh (UoE). You’ll benefit from training across microbiology, biochemistry, mass spectrometry and liquid chromatography. You will develop skills in univariate and multivariate statistics, experimental design for ‘omics and interpretation of complex biological datasets.

You will be registered at UoE, based at SRUC and work closely with EdinOmics, at King’s Buildings Campus, Edinburgh. The supervisory team is committed to, and expects your active contribution to, an inclusive work environment and professional development of all research team members.


Application instructions can be found on the SRUC website- PhD opportunities | SRUC

  1. Download and complete the Equal opportunities survey and note the completion reference
  2. Download and complete the SRUC Application form
  3. Download the Academic Reference Request and send to two referees requesting they submit to [Email Address Removed] by the closing date.

Send your application including the following to [Email Address Removed]:

  • Completed Application form quoting REF SRUC/JVM
  • Academic Qualifications
  • English Language Qualification (if applicable)

Unfortunately, due to workload constraints, we cannot consider incomplete applications. Please ensure your application is complete by Thursday 5th January 2023.

Funding Notes

This 3.5 year PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

How good is research at SRUC - Scotland’s Rural College in Agriculture, Food and Veterinary Sciences?

Research output data provided by the Research Excellence Framework (REF)

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