Metagenomics assessment of Anthropogenic impact on coral reef-associated microorganisms on the Kenyan Indian Ocean.

Abstract

The Western Indian Ocean (WIO) is the world’s second richest marine biodiversity hotspot. It is characterized by a diverse range of ecologically and nutritionally rich marine ecosystems that are increasingly under pressure from the impacts of human population growth and coastal development. A comprehensive understanding of variations of marine microbial community composition with environmental conditions is key to understanding and predicting responses to human and climate pressures because microorganisms are the main drivers of biogeographical processes, and they respond and adapt fast to climatic patterns. Also, because unique environments harbour unique microorganisms with unique properties, genomic exploration of marine microorganisms may lead to discovery of novel metabolic processes, and bioactive products with potential for novel biotechnological applications. This project aimed to assess the effect of local anthropogenic impacts on the community structure and the functional potential of microorganisms inhabiting the WIO coral reefs along the Kenyan coast by metagenomics. Reasons for low application of genomics specifically in marine research in the WIO region were examined through literature review and in-depth interviews with scientists in the region. Coral reef seawater and sediment samples were collected, for microbial assessments, along gradients of human impacts and protection regimes. Environmental variables were estimated, and microbial taxonomic and functional diversity analysed by metagenomic approaches. Comparisons were done between sites with differential human impacts, and with oceanic metagenomes from Tara Oceans expedition. Compartmentalised training of marine scientists and lack of collaboration with molecular scientists are key reasons highlighted for poor uptake of genomics in marine research. Significant differences in taxonomic and functional composition were observed between the coral reef and Tara Oceans datasets. Coral reef metagenomes had more diverse and even microbial taxa and gene groups. Tara Oceans metagenomes were enriched with groups of genes of functions in keeping with oligotrophic conditions, and reefs metagenomes with genes for functions related to adaptations to heterogenous environments. E. coli density decreased with increasing degree of protection, but physicochemical and nutrient variables did not differ across coral reefs in the protected coral reefs. Variations in relative abundances of copiotrophic bacteria and coliphages were observed in coral reefs corresponding to magnitude of the neighbouring human impacts. Malindi and Mombasa marine parks, the coral reef sites experiencing degradative human impacts, were significantly enriched with genes for functions suggestive of mitigation of environment perturbations e.g. capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. This study establishes essential baselines for microbiome studies in the WIO region and provides insights to anthropogenic impact on microbial structure and functions, and potential indicators of health status coral reef ecosystems.