Abstract

Deaths attributable to antimicrobial resistance (AMR) are predicted to rise from 700,000 per year now to 10 million by 2050. There is an urgent need for new antibiotics to meet the threat posed by AMR; the WHO recently reported that there are not enough antibiotics in development to meet this need. The sponge microbiota has emerged as one of the most prolific sources of novel antimicrobial candidates from marine environments in recent decades. The majority of work on sponge microbiology, however, has been carried out on shallow-water sponges of the Demosponge Class. This work explores the cultivable diversity and antimicrobial potential of bacteria from two species of Hexactinellid sponge (Pheronema carpenteri and Hertwigia sp.). Bacteria were cultured using a variety of methods including the novel use of pressurised environments, revealing bacteria belonging to the Proteobacteria, Actinobacteria and Firmicutes. Bacteria were screened for antimicrobial activity, revealing a higher proportion of active isolates from Pheronema carpenteri, leading to the purification of an antimicrobial with protease inhibitory activity, and further genomic characterisation of a potentially novel species of Streptomyces displaying inhibitory activity against Gram-positive and Gram-negative organisms. Culture-independent methods were used in order to provide the first characterisation of the microbiota of the deep-sea Hexactinellid sponge Pheronema carpenteri, as well as supporting a comparison of its microbiota to that of the surrounding sediment and seawater. Taxonomic classification of the microbiota of these samples revealed the following: that P. carpenteri has a microbiota that is generally congruent with that of the global sponge and Hexactinellid microbiota; it contains a smaller core microbiota; has a smaller sample-specific microbiota; and is comprised of distinct phyla when compared to sediment samples. Differences were also observed in P. carpenteri replicates that were collected from two separate sampling sites. The presence of cultivated isolates within the P. carpenteri metagenome was also demonstrated, indicating that culture-dependent studies are to some extent successful in obtaining sponge-associated bacteria for the purposes of natural product discovery. Overall, this work displays that the Hexactinellid sponges investigated are a promising source for the discovery of novel bacterial species and antimicrobial candidates.

Keywords

Antimicrobial resistance, Sponge, Microbiology, Antimicrobial, Natural product, Discovery, 16S, Microbiome, Streptomyces

Document Type

Thesis

Publication Date

2022

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