Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds

ABSTRACT Mangroves, as important and special ecosystems, create unique ecological environments for examining the microbial gene capacity and potential for producing bioactive compounds. However, little is known about the biogeochemical implications of microbiomes in mangrove ecosystems, especially t...

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Autores principales:	Shuilin Liao, Yayu Wang, Huan Liu, Guangyi Fan, Sunil Kumar Sahu, Tao Jin, Jianwei Chen, Pengfan Zhang, Lone Gram, Mikael Lenz Strube, Qiong Shi, Simon Ming Yuen Lee, Xin Liu
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	metagenomics rhizosphere biosynthesis gene clusters antibiotic resistance genes mangroves Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/685957329e63452e8efb971454598afa
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spelling	oai:doaj.org-article:685957329e63452e8efb971454598afa2021-12-02T18:15:47ZDeciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds10.1128/mSystems.00851-192379-5077https://doaj.org/article/685957329e63452e8efb971454598afa2020-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00851-19https://doaj.org/toc/2379-5077ABSTRACT Mangroves, as important and special ecosystems, create unique ecological environments for examining the microbial gene capacity and potential for producing bioactive compounds. However, little is known about the biogeochemical implications of microbiomes in mangrove ecosystems, especially the variations between pristine and anthropogenic mangroves. To elucidate this, we investigated the microbial taxonomic and functional shifts of the mangrove microbiomes and their potential for bioactive compounds in two different coastal mangrove ecosystems in southern China. A gene catalogue, including 87 million unique genes, was constructed, based on deep shotgun metagenomic sequencing. Differentially enriched bacterial and archaeal taxa between pristine mangroves (Guangxi) and anthropogenic mangroves (Shenzhen) were found. The Nitrospira and ammonia-oxidizing archaea, specifically, were more abundant in Shenzhen mangroves, while sulfate-reducing bacteria and methanogens were more abundant in Guangxi mangroves. The results of functional analysis were consistent with the taxonomic results, indicating that the Shenzhen mangrove microbiome has a higher abundance of genes involved in nitrogen metabolism while the Guangxi mangrove microbiome has a higher capacity for sulfur metabolism and methanogenesis. Biosynthetic gene clusters were identified in the metagenome data and in hundreds of de novo reconstructed nonredundant microbial genomes, respectively. Notably, we found different biosynthetic potential in different taxa, and we identified three high quality and novel Acidobacteria genomes with a large number of BGCs. In total, 67,278 unique genes were annotated with antibiotic resistance, indicating the prevalence and persistence in multidrug-resistant genes in the mangrove microbiome. IMPORTANCE This study comprehensively described the taxonomy and functionality of mangrove microbiomes, including their capacity for secondary metabolite biosynthesis and their ability to resist antibiotics. The microbial taxonomic and functional characteristics differed between geographical locations, corresponding to the environmental condition of two diverse mangrove regions. A large number of microbial biosynthetic gene clusters encoding novel bioactivities were found, and this can serve as a valuable resource to guide novel bioactive compound discovery for potential clinical uses.Shuilin LiaoYayu WangHuan LiuGuangyi FanSunil Kumar SahuTao JinJianwei ChenPengfan ZhangLone GramMikael Lenz StrubeQiong ShiSimon Ming Yuen LeeXin LiuAmerican Society for Microbiologyarticlemetagenomicsrhizospherebiosynthesis gene clustersantibiotic resistance genesmangrovesMicrobiologyQR1-502ENmSystems, Vol 5, Iss 5 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	metagenomics rhizosphere biosynthesis gene clusters antibiotic resistance genes mangroves Microbiology QR1-502
spellingShingle	metagenomics rhizosphere biosynthesis gene clusters antibiotic resistance genes mangroves Microbiology QR1-502 Shuilin Liao Yayu Wang Huan Liu Guangyi Fan Sunil Kumar Sahu Tao Jin Jianwei Chen Pengfan Zhang Lone Gram Mikael Lenz Strube Qiong Shi Simon Ming Yuen Lee Xin Liu Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds
description	ABSTRACT Mangroves, as important and special ecosystems, create unique ecological environments for examining the microbial gene capacity and potential for producing bioactive compounds. However, little is known about the biogeochemical implications of microbiomes in mangrove ecosystems, especially the variations between pristine and anthropogenic mangroves. To elucidate this, we investigated the microbial taxonomic and functional shifts of the mangrove microbiomes and their potential for bioactive compounds in two different coastal mangrove ecosystems in southern China. A gene catalogue, including 87 million unique genes, was constructed, based on deep shotgun metagenomic sequencing. Differentially enriched bacterial and archaeal taxa between pristine mangroves (Guangxi) and anthropogenic mangroves (Shenzhen) were found. The Nitrospira and ammonia-oxidizing archaea, specifically, were more abundant in Shenzhen mangroves, while sulfate-reducing bacteria and methanogens were more abundant in Guangxi mangroves. The results of functional analysis were consistent with the taxonomic results, indicating that the Shenzhen mangrove microbiome has a higher abundance of genes involved in nitrogen metabolism while the Guangxi mangrove microbiome has a higher capacity for sulfur metabolism and methanogenesis. Biosynthetic gene clusters were identified in the metagenome data and in hundreds of de novo reconstructed nonredundant microbial genomes, respectively. Notably, we found different biosynthetic potential in different taxa, and we identified three high quality and novel Acidobacteria genomes with a large number of BGCs. In total, 67,278 unique genes were annotated with antibiotic resistance, indicating the prevalence and persistence in multidrug-resistant genes in the mangrove microbiome. IMPORTANCE This study comprehensively described the taxonomy and functionality of mangrove microbiomes, including their capacity for secondary metabolite biosynthesis and their ability to resist antibiotics. The microbial taxonomic and functional characteristics differed between geographical locations, corresponding to the environmental condition of two diverse mangrove regions. A large number of microbial biosynthetic gene clusters encoding novel bioactivities were found, and this can serve as a valuable resource to guide novel bioactive compound discovery for potential clinical uses.
format	article
author	Shuilin Liao Yayu Wang Huan Liu Guangyi Fan Sunil Kumar Sahu Tao Jin Jianwei Chen Pengfan Zhang Lone Gram Mikael Lenz Strube Qiong Shi Simon Ming Yuen Lee Xin Liu
author_facet	Shuilin Liao Yayu Wang Huan Liu Guangyi Fan Sunil Kumar Sahu Tao Jin Jianwei Chen Pengfan Zhang Lone Gram Mikael Lenz Strube Qiong Shi Simon Ming Yuen Lee Xin Liu
author_sort	Shuilin Liao
title	Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds
title_short	Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds
title_full	Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds
title_fullStr	Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds
title_full_unstemmed	Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds
title_sort	deciphering the microbial taxonomy and functionality of two diverse mangrove ecosystems and their potential abilities to produce bioactive compounds
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/685957329e63452e8efb971454598afa
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Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds

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