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Publication Date

Spring 2018

Degree Type

Thesis - Campus Access Only

Degree Name

Master of Science (MS)


Moss Landing Marine Laboratories


Jonathan B. Geller


Coral reef, Cryptic, Host-specific, Metagenome, Microbiome

Subject Areas

Molecular biology; Microbiology


Cryptic sponge and ascidian coral reef species are rarely studied in relation to their microbiota. 16S rRNA studies have provided taxonomic profiles but only functional inferences about invertebrate host-microbe associations. The sponge and ascidian species investigated herein grew on settling plates called autonomous reef monitoring structures (ARMS) placed at three sites around Moorea, French Polynesia and left for two years to be colonized. Sponge (N = 9) and ascidian (N = 17) tissue samples were harvested, DNA extracted, and metagenomes sequenced using Illumina MiSeq protocols. Host species were identified with mitochondrial COI barcodes. Significant differences between sponge and ascidian microbiome taxonomy and gene content were found. Invertebrate (N = 26) and seawater (N = 3) microbiomes were taxonomically and functionally significantly different. Host species was more important than sites on the reef for microbiome composition and function. This degree of host-specificity in a shared microenvironment suggests that the host-microbe relationship is likely important for these invertebrates’ metabolism and overall fitness. As the first comparison of sponges and ascidians microbiome metagenomes, this study broadens our understanding of specificity and significance of these host-microbe associations.