Environmental Sciences Division
Microbial Genomics Group

Funded Projects Lab Equipment Genomics Staff Functional Genomics Microbial Ecology Publications

Microbial Ecology

Genomic Technologies for Microbial Community Analysis

DNA microarray technology has been used primarily to monitor gene expression and regulation on a genome-wide scale. By contrast, the use of microarray hybridization for microbial community detection and analysis has not been previously explored in a rigorous manner. A major focus of the ESD Genomics Laboratory concerns the application of microarray-based genomic technology for the analysis of the composition, function, and dynamics of microbial communities in natural environments. In the laboratory, we have developed three kinds of glass-based microarrays for addressing specific research questions in microbial ecology (below).

Functional Gene Arrays (FGAs)

Comprehensive Microbial Functional Gene Microarrays (FGAs) for the Study of
Microbial Diversity and Processes in the Environment
Christopher W. Schadt, Jost Liebich, Song C. Chong, Terry J. Gentry, Zhili He and Jizhong Zhou

Based on our previous studies (Wu et al. 2001; Zhou 2003; Schadt et al 2004; Rhee et al. 2004) we have designed a comprehensive functional gene microarray (FGA) for use in the study microorganisms in environmental samples. The designed probes encompass the variation in >14,000 known microbial functional genes involved in nitrogen (e.g. denitirification and nitrogen fixation), carbon (e.g. carbon dioxide fixation and cellulose degradation) and sulfur (e.g.dissimaltory sulfur reduction) cycling processes, as well as methane oxidation and reduction, organic contaminant degradation and metals reduction and resistance (Table 1).

These consist of gene specific probes as well as group probes that encompass the variation in closely related sequences for which specific probe design was not possible. In most cases we were able to design multiple probes for each target sequence, bringing the total number of designed probes to 23,864. We have been able to incorporate the design probes in several potential microarray layouts, such that we may create arrays in different formats. For example one design incorporates single probes for each gene for a wide variety of functional process (all design categories) genes can be arrayed together (Figure 1). Such arrays are useful for a broad overview of the functional capabilities of any given microbial community. Additionally more exhaustive and detailed probe sets may be used to create arrays with multiple probes for any given target gene. We have incorporated this strategy into to layout an array that contains up to three probes for each gene involved in carbon, nitrogen and sulfur cycling processes. Thus these arrays may be used to thoroughly and robustly characterize microbial functional diversity between samples for a particular process using DNA or RNA hybridizations.

  • Rhee, S.K., Liu, X., Wu, L., Chong, S.C., Wan, X., and Zhou, J. (2004). Detection of biodegradation and biotransformation genes in microbial communities using 50-mer oligonucleotide microarrays. Appl. Environ. Microl. 70:4303-4317.
  • Schadt C., Leibich J, Chong S., Gentry T., He Z., Pan H., and J. Zhou. (2004) Design and Use of Functional Gene Microarrays (FGAs) for the Characterization of Microbial Communities. In Methods in Microbiology Volume 33: Microbial Imaging, (Savidge & Pothoulakis, eds). Academic Press, Pp 331-368.
  • Wu, L. Y., Thompson, D. K., Li, G., Hurt, R. A., Tiedje, J. M., and Zhou, J. (2001). Development and evaluation of functional gene arrays for detection of selected gene in the environment. Applied and Environmental Microbiology 67, 5780-5790.
  • Zhou, J. (2003). Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol. 6, 288-294.

Community Genome Arrays (CGAs)

A prototype glass-based microarray, termed the Community Genome Array, was constructed to evaluate the utility of microarray hybridization for assessing microbial community composition. CGAs contained pure whole genomic DNA from many different formally characterized reference organisms (e.g., various species within the genus Shewanella and strains of Azoarcus clastics and Pseudomonas stutzeri) as well as environmental isolates. Work evaluating the specificity, sensitivity, quantitation potential, and applicability of CGAs is ongoing.

Phylogenetic Oligonucleotide Arrays (POAs)

We are currently in the process of developing a Phylogenetic Oligonucleotide Array that contains 16S rDNA oligonucleotide probes targeting bacteria at different taxonomic levels (e.g., kingdom, phyla, family, genus, species, and even strains). However, achieving hybridization specificity has been a major challenge in the ongoing development of POAs because of the potential cross-hybridization of oligonucleotide probes to 16S rRNA genes from non-targeted organisms. So far, work in this area has focused on oligonucleotide probe attachment to glass slides and the optimization of hybridization conditions for achieving single nucleotide mismatch discrimination (specificity).


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Last Modified: May 20, 2005