Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean.

Angus Macdonald,Oskar Karlsson-Lindsjö,Sammy Wambua,Erik Bongcam-Rudloff,Nina Wambiji,Etienne P De Villiers,Santie De Villiers,Hadrien Gourlé

doi:10.3389/fmicb.2021.673128

Abstract

Coral reefs face an increased number of environmental threats from anthropomorphic climate change and pollution from agriculture, industries and sewage. Because environmental changes lead to their compositional and functional shifts, coral reef microbial communities can serve as indicators of ecosystem impacts through development of rapid and inexpensive molecular monitoring tools. Little is known about coral reef microbial communities of the Western Indian Ocean (WIO). We compared taxonomic and functional diversity of microbial communities inhabiting near-coral seawater and sediments from Kenyan reefs exposed to varying impacts of human activities. Over 19,000 species (bacterial, viral and archaeal combined) and 4,500 clusters of orthologous groups of proteins (COGs) were annotated. The coral reefs showed variations in the relative abundances of ecologically significant taxa, especially copiotrophic bacteria and coliphages, corresponding to the magnitude of the neighboring human impacts in the respective sites. Furthermore, the near-coral seawater and sediment metagenomes had an overrepresentation of COGs for functions related to adaptation to diverse environments. Malindi and Mombasa marine parks, the coral reef sites closest to densely populated settlements were significantly enriched with genes for functions suggestive of mitigation of environment perturbations including the capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. Our study is the first metagenomic assessment of WIO coral reef microbial diversity which provides a much-needed baseline for the region, and points to a potential area for future research toward establishing indicators of environmental perturbations.

Highlights

Coastal ecosystems are some of the most dynamic and vulnerable environments under various pressures from anthropogenic activities and climate change
With its goods and services supporting over a quarter of the region’s population who live within 100 km of the shoreline (Van Der Elst et al, 2005; Obura, 2017), the Western Indian Ocean (WIO) and its coastal ecosystems are essential to the region’s economy
Other strategies extensively applied by government institutions, Non-Governmental Organizations (NGO) and communities throughout the WIO to conservation coral reefs are reviewed by Hattam et al (2020) and include the introduction of alternative livelihoods, coral gardening and payment for ecosystem services (PES) schemes

Summary

Introduction

Coastal ecosystems are some of the most dynamic and vulnerable environments under various pressures from anthropogenic activities and climate change. With its goods and services supporting over a quarter (more than 60 million people) of the region’s population who live within 100 km of the shoreline (Van Der Elst et al, 2005; Obura, 2017), the WIO and its coastal ecosystems are essential to the region’s economy. Indications of distress on the region’s ecosystems are noted with increasing frequency characterized by reduced fish catches, diminishing mangrove coverage, and declining coral reef cover (Van Der Elst et al, 2005; Obura, 2017) threatening the livelihoods of dependent coastal communities. Advancements and declining costs of high-throughput sequencing technologies aided by autonomous reef monitoring systems has improved collection of diversity data on cryptic marine communities for coral reef monitoring (Ransome et al, 2017). Marine microbes are thought to have significant potential as a cryptic community due to their rapid response to environmental change (Glasl et al, 2017)

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