Molecular Ecology of Coral Reef Microorganisms in the Western Indian Ocean coast of Kenya

Coral reefs face increased environmental threats from anthropomorphic climate change and pollution, from agriculture, industries and tourism. They are economically vital for many people worldwide, and harbour a fantastically diverse ecosystem, being the home for many species of fish and algae. Surprisingly little is known about the microbial communities living in and in the surrounding of coral reefs. Here we employ high throughput sequencing for investigating the bacteria living in the water column and upper sediment layer in close proximity to coral reefs on the Kenyan coast of the West Indian Ocean. We show that while the read-level taxonomic distribution of bacteria is similar with ones obtained from 16S metabarcoding, whole metagenome sequencing provides valuable functional insights not available with 16S metabarcoding. We find evidence of pollution, marked by the presence of Vibrio and more importantly the presence of antibiotic resistance notably to vancomycin, that we attribute to the use of avoparcin in agriculture. Additionally, 175 bacterial genomes not previously sequenced were discovered. Our study is the first whole-metagenome study from the West Indian Ocean, provides a much-needed baseline to study microbes surrounding coral reefs under different conditions as well as the microbiome of coral reefs.