This Article Full Text Full Text (PDF) Supplemental material Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Wu, L. Articles by Zhou, J. Search for Related Content PubMed PubMed Citation Articles by Wu, L. Articles by Zhou, J. Agricola Articles by Wu, L. Articles by Zhou, J.

Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification

Liyou Wu ,^1,, Xueduan Liu,^1,2,3,, Christopher W. Schadt,¹ and Jizhong Zhou^1*,

Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6038,¹ Department of Plant Pathology, Hunan Agricultural University,² School of Minerals Processing & Bioengineering, Central South University, Changsha 410083 Hunan, People’s Republic of China³

Received 18 November 2005/ Accepted 15 April 2006

Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (r² = 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (r² = 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (r² = 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment.

Supplemental material for this article may be found at http://aem.asm.org/.

L.W., X.L., and J.Z. contributed equally to this work.

Present address: Institute for Environmental Genomics and Department of Botary and Microbiology, University of Oklahoma, Norman, OK 73019.

This article has been cited by other articles:

• Zhou, J., Kang, S., Schadt, C. W., Garten, C. T. Jr. (2008). Spatial scaling of functional gene diversity across various microbial taxa. Proc. Natl. Acad. Sci. USA 105: 7768-7773 [Abstract] [Full Text]  
• Liu, Y., Gilchrist, A., Zhang, J., Li, X.-F. (2008). Detection of Viable but Nonculturable Escherichia coli O157:H7 Bacteria in Drinking Water and River Water. Appl. Environ. Microbiol. 74: 1502-1507 [Abstract] [Full Text]  
• Maligoy, M., Mercade, M., Cocaign-Bousquet, M., Loubiere, P. (2008). Transcriptome Analysis of Lactococcus lactis in Coculture with Saccharomyces cerevisiae. Appl. Environ. Microbiol. 74: 485-494 [Abstract] [Full Text]  
• Han, W., Liu, B., Cao, B., Beutin, L., Kruger, U., Liu, H., Li, Y., Liu, Y., Feng, L., Wang, L. (2007). DNA Microarray-Based Identification of Serogroups and Virulence Gene Patterns of Escherichia coli Isolates Associated with Porcine Postweaning Diarrhea and Edema Disease. Appl. Environ. Microbiol. 73: 4082-4088 [Abstract] [Full Text]  
• Smolina, I., Lee, C., Frank-Kamenetskii, M. (2007). Detection of Low-Copy-Number Genomic DNA Sequences in Individual Bacterial Cells by Using Peptide Nucleic Acid-Assisted Rolling-Circle Amplification and Fluorescence In Situ Hybridization. Appl. Environ. Microbiol. 73: 2324-2328 [Abstract] [Full Text]  
• Gao, H., Yang, Z. K., Gentry, T. J., Wu, L., Schadt, C. W., Zhou, J. (2007). Microarray-Based Analysis of Microbial Community RNAs by Whole-Community RNA Amplification. Appl. Environ. Microbiol. 73: 563-571 [Abstract] [Full Text]