Characterising Antarctic marine invertebrate microbiomes and their antimicrobial potential

Abstract

The West Antarctic Peninsula is experiencing rapid regional warming that will negatively impact endemic marine biodiversity. Antarctic marine invertebrates living in the near-shore are likely to be affected profoundly by warming-related changes, and microbes could help their hosts respond to the demands of environmental change. Moreover, their associated microbiomes may be untapped reservoirs of novel antimicrobial natural products. However, only a handful of the over 17,000 marine invertebrate species in the Southern Ocean have been characterised for the taxonomic identities of their microbiomes, or their antimicrobial potential. Therefore, the research in this doctoral thesis aimed to characterise bacterial diversity in the gut microbiomes of common marine invertebrates using a non-culture dependent method (16S rRNA amplicon sequencing). Furthermore, a culture dependent method was used to produce a bank of diverse host-associated bacteria, which were then assessed for their antimicrobial activity, with whole genomes sequenced from the two most promising candidates. Finally, chemical extracts of two species of Antarctic marine invertebrates were examined for antimicrobial potential, on account of their potential to harbour novel chemical defences. This research provided pilot data that suggested a strong influence of diet on gut microbiome status and revealed the surprisingly high temperature resilience of the culturable gut bacteria. Additionally, the assessment of varied culture conditions led to the successful identification of antimicrobial activity from a potentially novel strain of Psychrobacter and Antarctic strain of Pseudomonas, with in silico genome mining identifying multiple biosynthetic gene clusters. The antimicrobial potential of the chemical extracts harvested from the Antarctic marine invertebrates was also identified, particularly from lipophilic extracts targeted against Gram positive pathogens. Overall, this thesis demonstrated the rich and biodiverse nature of the Antarctic marine invertebrate microbiome and metabolome, both with potential for antimicrobial capacity. Using advanced sequencing methodologies, alongside antimicrobial assays, I was able to demonstrate the untapped potential for the discovery of novel antimicrobials in an extreme and poorly explored environment, whilst providing a first glimpse of a more functional understanding of the ecological and biotechnological significance of the bacterial metabolites, and genes identified.

Date of Award	2026
Original language	English
Awarding Institution	University of Plymouth
Sponsors	Natural Environment Research Council (NERC) and ARIES Doctoral Training Partnership (DTP), grant ref: NE/S007334/1
Supervisor	Melody Clark (Director of Studies (First Supervisor)), Mathew Upton (Other Supervisor), Kerry Howell (Other Supervisor) & Lloyd Peck (Other Supervisor)