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A dive into the coral microbiome

Gourlé, Hadrien (2020). A dive into the coral microbiome. Diss. (sammanfattning/summary) Sveriges lantbruksuniv., Acta Universitatis Agriculturae Sueciae, 1652-6880 ; 2020:29
ISBN 978-91-7760-576-8
eISBN 978-91-7760-577-5
[Doctoral thesis]

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Abstract

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.

Authors/Creators:Gourlé, Hadrien
Title:A dive into the coral microbiome
Year of publishing :2020
Number:2020:29
Number of Pages:63
Publisher:Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-7760-576-8
ISBN for electronic version:978-91-7760-577-5
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Article category:Other scientific
Version:Published version
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 105 Earth and Related Environmental Sciences > Climate Research
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Microbiology (Microbiology in the medical area to be 30109)
Keywords:metagenomics, coral reefs, sequencing, bioinformatics, microbiome
URN:NBN:urn:nbn:se:slu:epsilon-p-105415
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-105415
ID Code:16966
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:08 May 2020 13:09
Metadata Last Modified:08 May 2020 13:09

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