Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities

ABSTRACT While functional gene arrays (FGAs) have greatly expanded our understanding of complex microbial systems, specificity, sensitivity, and quantitation challenges remain. We developed a new generation of FGA, GeoChip 5.0, using the Agilent platform. Two formats were created, a smaller format (...

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Autores principales:	Zhou Shi, Huaqun Yin, Joy D. Van Nostrand, James W. Voordeckers, Qichao Tu, Ye Deng, Mengting Yuan, Aifen Zhou, Ping Zhang, Naijia Xiao, Daliang Ning, Zhili He, Liyou Wu, Jizhong Zhou
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	functional gene array microarrays microbial communities Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b8695d1276da4134beceeb6dadaea7b6
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spelling	oai:doaj.org-article:b8695d1276da4134beceeb6dadaea7b62021-12-02T19:47:34ZFunctional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities10.1128/mSystems.00296-192379-5077https://doaj.org/article/b8695d1276da4134beceeb6dadaea7b62019-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00296-19https://doaj.org/toc/2379-5077ABSTRACT While functional gene arrays (FGAs) have greatly expanded our understanding of complex microbial systems, specificity, sensitivity, and quantitation challenges remain. We developed a new generation of FGA, GeoChip 5.0, using the Agilent platform. Two formats were created, a smaller format (GeoChip 5.0S), primarily covering carbon-, nitrogen-, sulfur-, and phosphorus-cycling genes and others providing ecological services, and a larger format (GeoChip 5.0M) containing the functional categories involved in biogeochemical cycling of C, N, S, and P and various metals, stress response, microbial defense, electron transport, plant growth promotion, virulence, gyrB, and fungus-, protozoan-, and virus-specific genes. GeoChip 5.0M contains 161,961 oligonucleotide probes covering >365,000 genes of 1,447 gene families from broad, functionally divergent taxonomic groups, including bacteria (2,721 genera), archaea (101 genera), fungi (297 genera), protists (219 genera), and viruses (167 genera), mainly phages. Computational and experimental evaluation indicated that designed probes were highly specific and could detect as little as 0.05 ng of pure culture DNAs within a background of 1 μg community DNA (equivalent to 0.005% of the population). Additionally, strong quantitative linear relationships were observed between signal intensity and amount of pure genomic (∼99% of probes detected; r > 0.9) or soil (∼97%; r > 0.9) DNAs. Application of the GeoChip to a contaminated groundwater microbial community indicated that environmental contaminants (primarily heavy metals) had significant impacts on the biodiversity of the communities. This is the most comprehensive FGA to date, capable of directly linking microbial genes/populations to ecosystem functions. IMPORTANCE The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities.Zhou ShiHuaqun YinJoy D. Van NostrandJames W. VoordeckersQichao TuYe DengMengting YuanAifen ZhouPing ZhangNaijia XiaoDaliang NingZhili HeLiyou WuJizhong ZhouAmerican Society for Microbiologyarticlefunctional gene arraymicroarraysmicrobial communitiesMicrobiologyQR1-502ENmSystems, Vol 4, Iss 4 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	functional gene array microarrays microbial communities Microbiology QR1-502
spellingShingle	functional gene array microarrays microbial communities Microbiology QR1-502 Zhou Shi Huaqun Yin Joy D. Van Nostrand James W. Voordeckers Qichao Tu Ye Deng Mengting Yuan Aifen Zhou Ping Zhang Naijia Xiao Daliang Ning Zhili He Liyou Wu Jizhong Zhou Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities
description	ABSTRACT While functional gene arrays (FGAs) have greatly expanded our understanding of complex microbial systems, specificity, sensitivity, and quantitation challenges remain. We developed a new generation of FGA, GeoChip 5.0, using the Agilent platform. Two formats were created, a smaller format (GeoChip 5.0S), primarily covering carbon-, nitrogen-, sulfur-, and phosphorus-cycling genes and others providing ecological services, and a larger format (GeoChip 5.0M) containing the functional categories involved in biogeochemical cycling of C, N, S, and P and various metals, stress response, microbial defense, electron transport, plant growth promotion, virulence, gyrB, and fungus-, protozoan-, and virus-specific genes. GeoChip 5.0M contains 161,961 oligonucleotide probes covering >365,000 genes of 1,447 gene families from broad, functionally divergent taxonomic groups, including bacteria (2,721 genera), archaea (101 genera), fungi (297 genera), protists (219 genera), and viruses (167 genera), mainly phages. Computational and experimental evaluation indicated that designed probes were highly specific and could detect as little as 0.05 ng of pure culture DNAs within a background of 1 μg community DNA (equivalent to 0.005% of the population). Additionally, strong quantitative linear relationships were observed between signal intensity and amount of pure genomic (∼99% of probes detected; r > 0.9) or soil (∼97%; r > 0.9) DNAs. Application of the GeoChip to a contaminated groundwater microbial community indicated that environmental contaminants (primarily heavy metals) had significant impacts on the biodiversity of the communities. This is the most comprehensive FGA to date, capable of directly linking microbial genes/populations to ecosystem functions. IMPORTANCE The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities.
format	article
author	Zhou Shi Huaqun Yin Joy D. Van Nostrand James W. Voordeckers Qichao Tu Ye Deng Mengting Yuan Aifen Zhou Ping Zhang Naijia Xiao Daliang Ning Zhili He Liyou Wu Jizhong Zhou
author_facet	Zhou Shi Huaqun Yin Joy D. Van Nostrand James W. Voordeckers Qichao Tu Ye Deng Mengting Yuan Aifen Zhou Ping Zhang Naijia Xiao Daliang Ning Zhili He Liyou Wu Jizhong Zhou
author_sort	Zhou Shi
title	Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities
title_short	Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities
title_full	Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities
title_fullStr	Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities
title_full_unstemmed	Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities
title_sort	functional gene array-based ultrasensitive and quantitative detection of microbial populations in complex communities
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/b8695d1276da4134beceeb6dadaea7b6
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Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities

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