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

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 ecosys...

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Autores principales: Wambua, Sammy, Gourlé, Hadrien, de Villiers, Etienne P., Karlsson-Lindsjö, Oskar, Wambiji, Nina, Macdonald, Angus, Bongcam-Rudloff, Erik, de Villiers, Santie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8260691/
https://www.ncbi.nlm.nih.gov/pubmed/34248882
http://dx.doi.org/10.3389/fmicb.2021.673128
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author Wambua, Sammy
Gourlé, Hadrien
de Villiers, Etienne P.
Karlsson-Lindsjö, Oskar
Wambiji, Nina
Macdonald, Angus
Bongcam-Rudloff, Erik
de Villiers, Santie
author_facet Wambua, Sammy
Gourlé, Hadrien
de Villiers, Etienne P.
Karlsson-Lindsjö, Oskar
Wambiji, Nina
Macdonald, Angus
Bongcam-Rudloff, Erik
de Villiers, Santie
author_sort Wambua, Sammy
collection PubMed
description 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.
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spelling pubmed-82606912021-07-08 Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean Wambua, Sammy Gourlé, Hadrien de Villiers, Etienne P. Karlsson-Lindsjö, Oskar Wambiji, Nina Macdonald, Angus Bongcam-Rudloff, Erik de Villiers, Santie Front Microbiol Microbiology 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. Frontiers Media S.A. 2021-06-23 /pmc/articles/PMC8260691/ /pubmed/34248882 http://dx.doi.org/10.3389/fmicb.2021.673128 Text en Copyright © 2021 Wambua, Gourlé, de Villiers, Karlsson-Lindsjö, Wambiji, Macdonald, Bongcam-Rudloff and de Villiers. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Wambua, Sammy
Gourlé, Hadrien
de Villiers, Etienne P.
Karlsson-Lindsjö, Oskar
Wambiji, Nina
Macdonald, Angus
Bongcam-Rudloff, Erik
de Villiers, Santie
Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean
title Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean
title_full Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean
title_fullStr Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean
title_full_unstemmed Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean
title_short Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean
title_sort cross-sectional variations in structure and function of coral reef microbiome with local anthropogenic impacts on the kenyan coast of the indian ocean
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8260691/
https://www.ncbi.nlm.nih.gov/pubmed/34248882
http://dx.doi.org/10.3389/fmicb.2021.673128
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