Author: Emma Kerr
Kerr, Emma, 2025 Impacts of host and environment on Elasmobranch microbiomes, Flinders University, College of Science and Engineering
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Elasmobranchs are critical for regulating prey populations, structuring coastal habitats, and maintaining biodiversity. Unfortunately, Elasmobranchs are susceptible to overfishing, climate change, and pollution leading to global declines in their populations. Microbiomes are important for Elasmobranch health and ecology, but few host species’ microbiomes have been described. My thesis expands current knowledge of Elasmobranch microbial ecology by describing novel relationships between hosts and their microbiomes. I explore host and environmental influences on wild Elasmobranch microbiomes using a combination of shotgun metagenomic sequencing, High Performance Liquid Chromatography (HPLC), and long read sequencing of bacterial isolates.
I explore the skin, gill, and cloaca microbiomes of two hosts (Myliobatis tenuicaudatus and Heterodontus portusjacksoni) living in the same environment. Both hosts have unique microbiomes, indicating host shapes taxonomic communities at all body sites. Microbiome functions were also unique between hosts, except for skin, indicating skin microbes are adapted to host and environment. A Metagenome Assembled Genome (MAG) of Photobacterium damselae, with novel prophage sequences was reconstructed from M. tenuicaudatus. Photobacterium damselae is consistently found in shark gut samples and this MAG is closely related to P. damselae originating from other Elasmobranchs.
I compare skin microbiomes of four juvenile host species across two sampling events to determine environmental influence on the microbiome. Juvenile host microbiomes were similar, but microbiomes were different between sampling events. Juvenile Elasmobranchs are influenced by the environment more than adults. To describe environmental influence across locations, I compare microbiomes of two species (Urobatis halleri and Myliobatis californica) in San Diego and Los Angeles California. Myliobatis californica had highly variable skin microbiomes that were similar across locations, likely due to the thick epidermal mucus layer. Despite their shared environment, hosts maintain distinct microbial communities from each other, and the water column indicating host is driving microbial community diversity.
To explore the mechanisms of microbiome selectivity on Elasmobranchs, I quantified the monosaccharide composition of mucus from four host species. Hosts had unique mucus monosaccharide composition. Host microbiomes had carbohydrate metabolism genes to utilize mucus monosaccharides. I described for the first time, Elasmobranch microbial genes selected by host mucus composition. I also describe genomic adaptations of bacteria isolated from white sharks (Carcharodon carcharias), including mobile genetic elements and plasmids.
Finally, I compare microbiomes of sixteen host species from South Australia and California. I compare metagenome similarity across and within host clades. Within the genus Myliobatis two species (Myliobatis tenuicaudatus and Myliobatis californica) have the most similar microbiomes, even when sampled from across the world indicating phylosymbiosis is strongest within a clade.
Overall, I described host (mucus composition, evolutionary history) and environmental (habitat, season) factors that influence Elasmobranch microbiomes. I describe the microbiome of an additional eight Elasmobranch host species from South Australia, almost doubling the number of Elasmobranch host microbiomes described previously. I contribute novel insights into Elasmobranch microbiome functions in the gill and cloaca and make the first link between microbiome and host mucus in Elasmobranchs. These findings will inform future efforts to describe host-microbiome relationships in Elasmobranchs and how this relationship will change with anthropogenic stress.
Keywords: Elasmobranch microbiome, shark, stingray, metagenomics, marine microbiology, microbiome
Subject: Biology thesis
Thesis type: Doctor of Philosophy
Completed: 2025
School: College of Science and Engineering
Supervisor: Elizabeth Dinsdale