Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities
Abstract
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. Applicationmore »
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1526650
- Alternate Identifier(s):
- OSTI ID: 1580884
- Grant/Contract Number:
- SC0004730; SC0010570; SC0004601; SC0010715; AC02-05CH11231; SC0016247; SC0014079
- Resource Type:
- Published Article
- Journal Name:
- mSystems
- Additional Journal Information:
- Journal Name: mSystems Journal Volume: 4 Journal Issue: 4; Journal ID: ISSN 2379-5077
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; functional gene array; microarrays; microbial communities
Citation Formats
Shi, Zhou, Yin, Huaqun, Van Nostrand, Joy D., Voordeckers, James W., Tu, Qichao, Deng, Ye, Yuan, Mengting, Zhou, Aifen, Zhang, Ping, Xiao, Naijia, Ning, Daliang, He, Zhili, Wu, Liyou, Zhou, Jizhong, and Gibbons, ed., Sean M. Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities. United States: N. p., 2019.
Web. doi:10.1128/mSystems.00296-19.
Shi, Zhou, Yin, Huaqun, Van Nostrand, Joy D., Voordeckers, James W., Tu, Qichao, Deng, Ye, Yuan, Mengting, Zhou, Aifen, Zhang, Ping, Xiao, Naijia, Ning, Daliang, He, Zhili, Wu, Liyou, Zhou, Jizhong, & Gibbons, ed., Sean M. Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities. United States. https://doi.org/10.1128/mSystems.00296-19
Shi, Zhou, Yin, Huaqun, Van Nostrand, Joy D., Voordeckers, James W., Tu, Qichao, Deng, Ye, Yuan, Mengting, Zhou, Aifen, Zhang, Ping, Xiao, Naijia, Ning, Daliang, He, Zhili, Wu, Liyou, Zhou, Jizhong, and Gibbons, ed., Sean M. Tue .
"Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities". United States. https://doi.org/10.1128/mSystems.00296-19.
@article{osti_1526650,
title = {Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities},
author = {Shi, Zhou and Yin, Huaqun and Van Nostrand, Joy D. and Voordeckers, James W. and Tu, Qichao and Deng, Ye and Yuan, Mengting and Zhou, Aifen and Zhang, Ping and Xiao, Naijia and Ning, Daliang and He, Zhili and Wu, Liyou and Zhou, Jizhong and Gibbons, ed., Sean M.},
abstractNote = {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.},
doi = {10.1128/mSystems.00296-19},
journal = {mSystems},
number = 4,
volume = 4,
place = {United States},
year = {Tue Jun 18 00:00:00 EDT 2019},
month = {Tue Jun 18 00:00:00 EDT 2019}
}
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