Developing Methods for Sponge Captive Husbandry, Exploration of Genetic Diversity and Resilience to Environmental Stressors

Chakraborty, Abhiraj (2025) Developing Methods for Sponge Captive Husbandry, Exploration of Genetic Diversity and Resilience to Environmental Stressors. Masters by Research thesis (MPhil), Manchester Metropolitan University.

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Abstract

Sponges are a highly diverse and ancient phylum, integral to the ecosystems they inhabit. They host a high diversity of microbial symbionts that have significant potential commercial and scientific value and so face environmental stressors and commercial exploitation, but the effects of these are not well known. This is because sponge research can be challenging due to high levels of taxonomic ambiguity and the lack of effective captive husbandry practices limiting laboratory-based research. The first aim of this thesis was to answer the question of if methods of ex-situ sponge husbandry and mesocosm-based experimentation can be developed that future studies can use to bridge these critical knowledge gaps. Using the abundant tropical sponge Cinachyrella alloclada, I developed an effective method for sponge husbandry in closed aquaria systems, then set up a mesocosm experiment to demonstrate the potential resilience of C. alloclada to ocean acidification. I also established fragging (propagating sponges by growing smaller fragments of the parent sponge) as a reliable method of propagating C. alloclada in captivity as it regenerated quickly when fragged. This method provides the potential to supply sponges for ex-situ research and could facilitate a reduction in wild harvesting of commercially important sponges. The next aim was to test if the novel Oxford Nanopore next-generation sequencing technology can be effectively used to create Porifera genomic assemblies and thus help increase the accessibility of molecular data available for sponges. I developed a workflow to assemble and decontaminate low-coverage data from Nanopore Sequencing of the vase sponge Ircinia campana. I show that this is a cost-effective way to create de novo assemblies for non-model species like sponges that lack high-quality reference genomes, enabling the use of SNPs-based genotyping to identify cryptic species. I found that a high microbial load can make post-sequencing decontamination difficult, leading to a significant loss of data. However, the microbial sequences show potential for this type of sequencing to also provide metagenomic data for characterising microbial communities. Thus this thesis provides methods to increase the amount of molecular data available for sponges and also facilitates further study by providing effective methods of sponge husbandry and propagation, benefiting the scientific and commercial communities.