Metatranscriptomics Analysis of Coral Mucus-Associated Microbiome in the Kenyan Coast

Abstract

Coral reefs are significant marine ecosystems located in shallow tropical and subtropical seas that provide important services. More than 25% of all marine species depend on coral reefs as breeding and feeding sites, as well as about 500 million people globally, for food and income. Coral mucus, tissue and skeleton form different coral microcompartments. The mucus compartment contains a diverse range of microorganisms that serve as the first line of defense against pathogens and environmental change. Despite its advantages, global climatic change and human activities have had a significant impact on corals; since 1950, the world has lost 19% of its coral cover and projections indicate a loss of more than 90% of total coral cover by 2050 if no appropriate action will be taken. This study utilized metatranscriptomics data from coral mucus microbiome associated with Acropora digitifera in coastal Kenya to assess the impacts of human activities on corals so as to provide an early indication of environmental perturbation on coral health. Taxonomic classification was conducted by kraken2 software with minikraken2 database, and host RNA and rRNA removal was conducted by BBsplit and SortMeRNA software respectively. Transcripts assembly and differential transcripts expression was conducted by Trinity and Deseq2 respectively. Function annotation and pathways were performed by blast2Go and KEGG pathways. The results of taxonomic classification indicated microbial diversity and composition patterns that predispose Malindi and Mombasa corals to risk of coral diseases. A decrease in bacteria from genus Endozoicomonas in Malindi and Mombasa corals, which are beneficial coral microbiomes, indicates a decreased coral defense against opportunistic and pathogenic bacteria. The pattern observed in cyanobacteria phylum and classes of proteobacteria suggests a risk of corals to black band, white band, and white plaque disease at the Malindi and Mombasa coral reefs. Differential transcripts expression results showed similar expression patterns in Mombasa and Kisite-Mpunguti samples in contrast to Malindi, suggesting a risk of disease and bleaching in Malindi corals. Malindi and Mombasa samples were significantly enriched in energy acquisition and nitrogen metabolism-related microbial functions and pathways. The upregulation of these microbial function and pathways has been linked to coral stress due to nutrient imbalance caused by anthropogenic activities. Overall, microbial diversity, compositions, functions and biological pathways patterns observed revealed risk of diseases and bleaching in the Mombasa and Malindi coral reefs compared to Kisite-Mpunguti due to human activities. However, the influence of River Sabaki at Malindi may provide additional stressors to Malindi corals due to sedimentation and nutrient enrichment. This study demonstrates the utilization of metatranscriptome to assess the impact of human activities as well as provide baseline information for active microbial composition, functions and pathways of Acropora corals mucus microbiome