Mapping Antarctic marine microbial diversity and identification of bioactive molecules with an emphasis on antimicrobials


Mapping Antarctic marine microbial diversity and identification of bioactive molecules with an emphasis on antimicrobials


Project Description


Prof Melody Clark, British Antarctic Survey (BAS)

Dr Kerry Howell, School of Biological and Marine Sciences, University of Plymouth

Prof Mat Upton, School of Biomedical Sciences, University of Plymouth

Antimicrobial resistance (AMR) is one of the most serious threats to global human health, resulting in 700,000 deaths per year. This figure is currently rising year on year. The O’Neill Report (2016) estimated that in the absence of strategies to combat AMR, by 2050 10 million lives per year will be lost, with a cumulative loss in economic output of $100 trillion. Hence, there is an urgent need to increase the number of effective antimicrobial drugs to defeat infections that have become resistant to existing medicines. 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 (Cragg & Newman, 2012). However, as the incidence of AMR has increased, new discoveries of bioactive compounds from well-known bacteria have fallen dramatically. Therefore extreme environments, such as the Antarctic, are increasingly seen as important sources of novel antimicrobials (Núñez-Montero & Barrientos, 2018).

This PhD will focus on investigation of microbial biodiversity associated with a range of Antarctic marine invertebrates (eg. Nudibranchs) and identification and characterisation of novel biomolecules. You will be joining a multidisciplinary team based in the British Antarctic Survey, Cambridge and the UoP with a strong track record in Antarctic ecology, molecular biology and discovery of novel biomolecules from marine sources (Koch et al. 2019; Fonseca et al. 2017). You will also spend a secondment of up to 6 months at the Natural Products Department at GEOMAR, Kiel University, Germany, where you will conduct further bioassays and metabolomics analyses. 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 laboratory techniques and the associated bioinformatics analysis in the UNIX environment, purification and extraction of metabolites and analysis of bioactive compounds using Mass Spectrometry.

Therefore, we are looking for a student with strong experience 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.


  • 1. O’Neill (2061) Tackling drug-resistant infections globally: Final report and recommendations. The review on antimicrobial resistance chaired by Jim O’Neill, May 2016. Available at:
  • 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. Nunez-Montero & Barrierentos (2018) Advances in Antarctic research for antimicrobial discovery: A comprehensive narrative of bacteria from Antarctic environments as potential sources of novel antibiotic compounds against human pathogens and microorganisms of industrial importance. Antibiotics 7, 90
  • 4. 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
  • 5. 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

Key Information

  • This project has been shortlisted for funding by the ARIES NERC Doctoral Training Partnership, and will involve attendance at mandatory training events throughout the course of the PhD.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a NERC studentship - UK and EU nationals who have been resident in the UK for 3 years are eligible for a full award.
  • 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 (see
  • This studentship will start on 1st October 2020, and the closing date for applications is 23:59 on 15th January 2020.
  • Shortlisted applicants will be interviewed on 18/19 February 2020.
  • For further information, please contact the supervisor.
  • Please note that the joint NERC-ESRC ARIES-SeNSS studentship projects have different deadlines and funding arrangements. For full details please visit, or contact

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