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

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

doi:10.1128/mSystems.00296-19

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

mSystems. 2019 Jun 18;4(4):e00296-19. doi: 10.1128/mSystems.00296-19.

Authors

Zhou Shi¹, Huaqun Yin², Joy D Van Nostrand¹, James W Voordeckers¹, Qichao Tu³, Ye Deng³, Mengting Yuan¹, Aifen Zhou¹, Ping Zhang¹, Naijia Xiao¹, Daliang Ning¹, Zhili He⁴, Liyou Wu¹, Jizhong Zhou^{5

6

7}

Affiliations

¹ Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA.
² Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China.
³ Institute of Marine Science and Technology, Shandong University, Qingdao, China.
⁴ School of Environmental Science and Engineering, Environmental Microbiomics Research Center, Sun Yat-sen University, Guangzhou, China.
⁵ Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA jzhou@ou.edu.
⁶ Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
⁷ School of Environment, Tsinghua University, Beijing, China.

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.

Keywords: functional gene array; microarrays; microbial communities.