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Doctoral thesis, 2020

A dive into the coral microbiome

Gourlé, Hadrien


Coral reefs are one of the most diverse ecosystems on the planet, harbouring approximately twenty-five percent of the diverse eukaryotic life in the oceans, while also being important economically for millions of people worldwide. Despite their importance, coral reefs are menaced of a very steep decline due to pollution and anthropogenic climate change. In this thesis, we investigate the microbes that live close-by and inside coral reefs. It is believed that microbiomes, both environmental and coral-associated, play an important role in coral health, both by contributing to nutrient cycling, such as carbon and nitrogen fixation as well as photosynthesis, and by protecting the corals against environmental stressors such as pathogens. These microbiomes can be studied using targeted approaches, such as metabarcoding, or more general and powerful approaches, called metagenomics. Metagenomics is a relatively new field of study and the first part of this thesis focuses on method development for metagenomics. In paper I, we present InSilicoSeq, a software package to simulate metagenomic Illumina reads. InSilicoSeq is useful for testing new bioinformatics methods as well as benchmarking existing ones. In paper II and III, we study the composition of the coral microbiome from previously published studies, and the composition and function of the microbiome of the water and upper sediment layer from reefs of the Kenyan coast of the west Indian ocean. We define a putative coral core microbiome at the genus level and take a look at the metabolic pathways that may be active in the surrounding environment of the corals. While the coral core microbiome was largely dominated by one genus, Endozoicomonas, the surrounding environment showed great diversity both in taxonomy and in metabolism. We found evidence of antibiotics resistance in the water, which we hypothesise mainly comes from agriculture. We also publish a catalogue of putative expressed pathways and discovered 174 new bacteria in the water and sediment samples.


metagenomics; coral reefs; sequencing; bioinformatics; microbiome

Published in

Acta Universitatis Agriculturae Sueciae
2020, number: 2020:29
ISBN: 978-91-7760-576-8, eISBN: 978-91-7760-577-5
Publisher: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences

    UKÄ Subject classification

    Bioinformatics and Systems Biology
    Climate Research

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