Mapping Antarctic marine microbial diversity

Project background

Skin is the first line in defense between an animal and its environment, with skin associated microbes strongly linked to defense and animal-environment interactions. An understanding of microbiomes is key to meeting many of the challenges that face humanity in the 21st Century from energy to infection to agriculture1. For example, antimicrobial resistance (AMR) is one of the most serious threats to global human health, resulting in 700,000 deaths per year and rapidly increasing with a huge consequential loss in economic output. Over the past three decades, over 70% of antibiotics and over 60% of anticancer agents in the clinic have been based on organism-derived compounds, mainly from microbial resources. However, new discoveries of bioactive compounds from well-known bacteria have fallen dramatically in recent years2. Therefore extreme environments, such as the Antarctic, are increasingly seen as important sources of novel bioactive molecules. The PhD will have two complementary aspects, the major one is ecological: describing the microbial biodiversity of both skin and gut of Antarctic marine invertebrates; the secondary focus is pharmacological: identifying novel bioactive compounds, characterising these bacteria using a whole range of in-house bioassays (many for antimicrobial compounds) and characterisation of any identified inhibitory compounds.

Training

You will be joining a multidisciplinary team based in the British Antarctic Survey, Cambridge and the University of Plymouth with a strong track record in Antarctic and marine ecology, molecular biology and discovery of novel microbial biomolecules3-5. There is also the potential to spend a secondment at the Natural Products Department (GEOMAR, Kiel, Germany) with access to different analytical techniques and bioassays. In this PhD, you will screen and analyse diversity in Antarctic microbiomes and characterise associated metabolites to identify significant biological activities. You will be trained in microbial isolation, bioassays, amplicon sequencing and the associated bioinformatics analysis in the UNIX environment, purification and extraction of metabolites and analysis of bioactive compounds using Mass Spectrometry.

This studentship will be based at the British Antarctic Survey, and registered at the University of Plymouth.

Person specification

Therefore, we are looking for a candidate with strong experience/a degree in molecular biology and/or biochemistry. An interest in marine biology is desirable. Some experience of the UNIX operating system is desirable, but full training will be provided.

References

  • 1. Dubilier et al (2015) Create a global microbiome effort. Nature 526, 631-632.
  • 2. Cragg & Newman (2012) Natural products as sources of new drugs over the 30 years from 1981 to 2010. Journal of Natural Products 75, 311.
  • 3. Koch et al including Howell K and Upton M (2019) Characterisation of the microbiome for two hexactinellid sponges and purification of associated antimicrobial agents from their resident microbes. Access Microbiology 1, doi: 10.1099/acmi.ac2019.po0410
  • 4. Fonseca et al, including Peck LS, Clark MS (2017) Revealing higher than expected meiofaunal diversity in Antarctic sediments: a metabarcoding approach. Scientific Reports 7, 6094
  • 5. Vause et al including Clark MS, Peck LS (2019) Spatial and temporal dynamics of Antarctic shallow soft-bottom benthic communities: Ecological drivers under climate change. BMC Ecology. 19: 27.

Key information

  • This project has been shortlisted for funding by the ARIES NERC DTP and will start on 1 October 2021. The closing date for applications is 23:59 on 12 January 2021.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a NERC studentship, which covers fees, stipend (£15,285 p.a. for 2020-21) and research funding. For the first time in 2021/22 international applicants (EU and non-EU) will be eligible for fully-funded UKRI studentships. Please note ARIES funding does not cover visa costs (including immigration health surcharge) or other additional costs associated with relocation to the UK.
  • ARIES students benefit from bespoke graduate training and ARIES provides £2,500 to every student for access to external training, travel and conferences. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses in the subject area.
  • ARIES is committed to equality, diversity, widening participation and inclusion in all areas of its operation. We encourage enquiries and applications from all sections of the community regardless of gender, ethnicity, disability, age, sexual orientation and transgender status. Academic qualifications are considered alongside significant relevant non-academic experience.
  • All ARIES studentships may be undertaken on a part-time or full-time basis, visa requirements notwithstanding
  • For further information, please contact the supervisor.