Project title: Modelling Metabolic Stress Response of Whole Microbial Communities to Environmental Cues
Project description:
Microbial communities underpin the major biogeochemical cycles of Earth’s soil, oceans, and atmosphere, providing ecosystem services and functions for plants, animals, and humans. However, our understanding of their structure-function relationships remains highly limited. An ongoing challenge remains to determine and model the response of microbial communities to environmental change, including changing climates. Biotechnological applications, in which mixed-species consortia are applied for specific functions, provide useful model systems, having clear functional parameters and offering controlled environments. Methanogenic granules, formed spontaneously during high-rate anaerobic wastewater treatment, are unique in their abilities to transform organic wastewater pollutants to biogas and are also highly adaptive and complex whole microbial communities.
This proposal seeks to leverage their interesting and unique properties to study how whole communities of bacteria, archaea, viruses, and fungi interact and respond to a wide range of environmental stresses at the genetic level. This project combines a unique incubation set-up with cutting-edge ‘omics strategies and community modelling to identify patterns and gradients in community stress response. This set-up provides a high-throughput means of testing stress-response in whole microbial communities from the whole-community level down to the level of individual metabolic pathways and even genes.
Objectives:
1. Development and operation of a novel experimental platform of micro-batch reactors (μBRs) which expose single granules to a set of prescribed environmental stresses.
2. Sequence select samples for 16S rRNA genes, whole genome shotgun metagenomics, and meta-transcriptomes of these whole microbial communities using Illumina MiSeq & NovaSeqX.
3. Use amplicon sequences to track overall diversity profiles, elucidate microbial community members that persist and that change with respect to the chosen hypothesis design, and explore how these communities are assembled in response to biotic and abiotic stressors.
4. Use the metagenomes and meta-transcriptomes to perform targeted genomic analysis of specific stress-related genes and metabolic pathways important to the anaerobic digestion (AD) process.
To answer these questions, the student will use a multidisciplinary approach. For example, building and operating innovative μBRs for the incubation of individual methanogenic granules (whole communities). The student will also use genetic approaches (e.g., cloning), molecular tools (e.g., metagenomics/metatranscriptomics), bioinformatics, and ecological modelling tools.
The student will be supervised by lead supervisor Dr Anna Trego (expert in microbial ecology and environmental engineering) and co-supervisors Prof. Vincent O’Flaherty (expert in microbial ecology and environmental engineering) and Dr Umer Zeeshan Ijaz (expert in integrative omics).
Qualifications
* Proficiency in gaining insights into molecular techniques.
* Proficiency in applying numerical ecology and machine learning principles, particularly those that offer dimensionality reductions in multi-omics datasets and find correlations across them.
* Proficiency in scripting 16S rRNA, metagenomics, and transcriptomics workflows on a high-performance computing environment (Orion Cluster: http://userweb.eng.gla.ac.uk/umer.ijaz/#orion).
* Proficiency in developing methods and visualisation tools in R.
Essential:
* Good Degree in a Natural Science discipline (or other discipline with evidence of wet-lab expertise).
* Excellent communication skills (written, spoken).
* Wet-lab experience.
Desirable:
* Research masters completed.
* Expertise in statistical analysis.
* Expertise in molecular biology.
Working Environment
The University of Galway is ranked Ireland’s #1 university for sustainable development in the Times Higher Education World Rankings (THE). At the University of Galway, you’ll not only find excellence in teaching, but a commitment to shaping a better world. Ranked in the top 2% of universities worldwide, you can be sure to receive comprehensive training and education. The Department of Microbiology is inviting applications for a fully-funded PhD studentship to start September 2025 to work jointly within the Microbial Ecology Laboratory (https://www.oflahertylab.com/home) and the Environmental ‘Omics Laboratory (https://userweb.eng.gla.ac.uk/umer.ijaz/). The successful candidate will have access to all the facilities available within the College of Science and Engineering. The student will receive comprehensive training in wet lab experimentation and computational research. They will also have access to the University of Galway’s Research and Development Program. The University of Galway provides a wide variety of training courses, ranging from paper/thesis support writing to project management. In addition, the student will be registered as a visiting post-graduate student at the University of Glasgow and have access to their network and resources.
University of Galway supervisors: Dr Anna Trego & Prof. Vincent O’Flaherty
University of Glasgow supervisor: Dr Umer Zeeshan Ijaz (http://userweb.eng.gla.ac.uk/umer.ijaz)
Funding Body: Science Foundation Ireland/Research Ireland
Project Start Date: September 1st 2025
Funding duration: 4 Years (Sept 2025 – Aug 2029)
University fees: €5,500 p.a.
Student stipend: €25,000 p.a.
Application process:
In the first instance (or for informal discussion), contact Dr Anna Trego (annachristine.trego@universityofgalway.ie). Applications can then be formally submitted through the online postgraduate (research) application system.
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