Funding

Self-funded

Project code

BIOL5220424

Department

School of the Environment and Life Sciences,

Start dates

October, February and April

Application deadline

Applications accepted all year round

Applications are invited for a self-funded, 3 year full-time or 6 year part-time PhD project.

The PhD will be based in the School of Biological Sciences and will be supervised by Dr Kenneth Wasmund and Dr Carmen Rodriguez-Falagan.

The work on this project will:

  • Identify key microbial players involved in DNA and RNA degradation and recycling in wastewater.
  • Elucidate the identities of microbes involved in degradation of nucleic acid based metabolites
  • Study the physiology of identified and/or isolated bacteria through omics (e.g. proteomics, genomics)

Wastewater treatment plants (WWTPs) are globally important biotechnological systems that clean our wastewaters primarily through the functions of complex microbial communities. They function to degrade and remove organic material, nutrients and pollutants. Organic matter degradation is important also for driving other nutrient removal processes (e.g., nitrogen removal) through microbial interactions. Previous work has shown that extracellular DNA is very abundant in WWTPs (Dominiak et al. 2011), and therefore bacteria that degrade this DNA must be important players in this microbial ecosystem. Nevertheless, the identities of such bacteria remain unknown in WWTPs. This project therefore aims to understand and elucidate the roles of bacterial key players that live by consuming nucleic acids in wastewater. 

The project will use a combination of molecular biological to study bacterial functions under in situ conditions. For example, DNA-based stable isotope probing will be used to track isotopically labelled nucleic acids into specific taxa, and will be complemented with microbial community profiling via 16S rRNA gene sequencing (Wasmund et al. 2021). Fluorescent microscopy will be used to examine spatial structuring of specific bacteria with extracellular DNA in the sludge systems. Cultivation-based approaches will also be used to isolate novel bacteria that grow exclusively using nucleic acids, which can then be further characterised, e.g., by genomic and proteomic investigations. 

Overall, this work will contribute to a better understanding of nutrient cycling and microbial food webs in wastewater ecosystems, and to our fundamental understanding of microbes adapted to specialising on the degradation of nucleic acids. 

The student will have the opportunity to learn an array of advanced molecular methods, bioinformatics and experimental approaches in microbiology. 

 

References

  • Dominiak DM, Nielsen JL, Nielsen PH. Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms. Environ Microbiol. 2011 Mar;13(3):710-21. doi: 10.1111/j.1462-2920.2010.02375.x. 
  • Wasmund K, Pelikan C, Schintlmeister A, Wagner M, Watzka M, Richter A, Bhatnagar S, Noel A, Hubert CRJ, Rattei T, Hofmann T, Hausmann B, Herbold CW, Loy A. Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments. Nat Microbiol. 2021 Jul;6(7):885-898. doi: 10.1038/s41564-021-00917-9.

Fees and funding

Visit the research subject area page for fees and funding information for this project.

Funding availability: Self-funded PhD students only. 

PhD full-time and part-time courses are eligible for the UK  (UK and EU students only).

Bench fees

Some PhD projects may include additional fees – known as bench fees – for equipment and other consumables, and these will be added to your standard tuition fee. Speak to the supervisory team during your interview about any additional fees you may have to pay. Please note, bench fees are not eligible for discounts and are non-refundable.

Entry requirements

You'll need a good first degree from an internationally recognized university (minimum upper second class or equivalent, depending on your chosen course) or a Master’s degree in Microbiology, Genomics or Molecular Biology-related, or a related area. In exceptional cases, we may consider equivalent professional experience and/or Qualifications. English language proficiency at a minimum of IELTS band 6.5 with no component score below 6.0.

 

Experience in laboratory work is mandatory. Experience in microbiology and/or molecular techniques, or bioinformatics, is highly desirable.

 

How to apply

We’d encourage you to contact Dr Kenneth Wasmund (Kenneth.Wasmund@port.ac.uk)  to discuss your interest before you apply, quoting the project code.

When you are ready to apply, please follow the 'Apply now' link on the Biological Siences PhD subject area page and select the link for the relevant intake. Make sure you submit a personal statement, proof of your degrees and grades, details of two referees, proof of your English language proficiency and an up-to-date CV. Our ‘How to Apply’ page offers further guidance on the PhD application process.

When applying please quote project code BIOL5220424.