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

Project description

Skin is the first line in defence between an animal and its environment, with skin associated microbes strongly linked to defence 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 agriculture(1). 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 years(2). 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. 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 biomolecules(3-5). 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. 

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.

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. Al-Mahrous & Upton M (2011) Discovery and development of lantibiotics: Antimicrobial agents that have significant potential for medical applications. Expert Opin. Drug Discov. 6, 155-170.
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.

Supplementary information 

Hypothesis - soft-bodied Antarctic marine invertebrates host novel microbiomes, which are a rich source of microbial biomolecules that can be exploited for societal gain.   

The student will investigate the microbial biodiversity associated with a range of Antarctic marine invertebrates using 16S rDNA barcoding and sophisticated cultivation techniques. In parallel, the epidermal layers of the target species will be investigated for novel chemical defences. This study will specifically target soft-bodied Antarctic invertebrates such as nudibranchs, nemerteans, soft corals, ascidians etc, which have an enhanced requirement for a robust immune and chemical defence system when compared with more physically protected species with hard exoskeletons, such as molluscs(1-3). There are a number of questions associated with these species: What chemical defences do they use to avoid predation? How do their immune and digestive systems work at 0°C? How much of this is mediated by the microbiome? What are the bioactive compounds involved? 

The characterisation of bioactive compounds from Antarctic marine invertebrates is very limited to date, the associated microbiomes, even more so(4). This project offers great potential to close these knowledge gaps. 

The collaboration between the British Antarctic Survey (BAS) and the University of Plymouth (UoP) will ensure that the student will benefit from a wide range of expertise from Antarctic ecology and physiology, molecular biology, active compound purification and evaluation in bioassays. There is also the potential to spend a secondment at the Marine Natural Products Chemistry Department at GEOMAR, Kiel (a world-leader in marine natural product discovery and metabolomics), if suitable sources of funding can be provided. This secondment is not critical to the success of the project.   

Specifically, training will be provided in laboratory techniques of microbiological sampling and processing, amplicon sequencing and bioinformatics analysis (e.g. QIIME) and metabolomics. Microbes will be isolated using standard techniques and iChip technologies will be trialled to increase microbial diversity. Microbial populations will be characterised at via metagenetic 16S rDNA sequence analysis (V3-5 regions) using the Minion platform. Culture supernatants from isolated bacteria and novel metabolites from invertebrate protein extractions will be taken through a pipeline of chromatographic purification and subjected to a wide range of bioassays, primarily to detect antimicrobial activity, but also anticancer, immunomodulatory, wound healing and quorum sensing/biofilm disruption. Fractions containing significant biological activities will be analysed using MS-based methods and compounds evaluated for future progression towards possible clinical use(5). 

UoP has an exemplary commitment to post‐graduate training and support. Compulsory training in transferable skills include; experimental design and critique, statistics, data management, health and safety, bioethics (ARRIVE guidelines), IP and publication/exploitation of results (UK and European skills gaps). BAS has an excellent Communications Department, which regularly provides media and presentation training. The student will have full access to Aurora, the BAS Innovation Centre providing opportunities to interact with a wide range of industry partners and stakeholders.   

The unique cross-disciplinary skills sets developed during this PhD will produce an excellent candidate for employment within the environmental/biodiscovery sector. 

References:

1. Butala et al. (2015) Toxicon 108, 32-37
2. Diyabalange et al. (2010) J. Nat. Prod. 73, 416-421.
3. McClintock & Baker (1997) Amer. Zool. 37, 329-342.
4. Núñez-Montero & Barrientos (2018) Antibiotics 7, 90.
5. Sandiford & Upton (2012) Antimicrob Agents Chemother 56. 1539-47.