Analysis of Microbial Communities by Functional Gene Arrays

A major hurdle to the study of microbial communities is that only about 1% of microorganisms are cultivated (Whitman et al. 1998). As such, cultureindependent approaches are necessary in order to examine the vast majority of environmental microorganisms. Many molecular techniques are available for community analysis, and most of these techniques utilize phylogenetic markers such as the 16S rRNA or the DNA gyrase gene (gyrB) (Wilson et al. 1990; Yamamoto and Harayama 1995; Hugenholtz et al. 1998; Brodie et al. 2006). While the use of these genes provides information regarding phylogenic diversity and structure of a microbial community, they don’t provide much, if any information relating to the functional potential and/or activity of the community. Functional genes have been used to examine both phylogenetic and functional diversities (e.g., McDonald et al. 1995; Braker et al. 1998). However, even if multiple functional genes are examined, conventional molecular techniques only provide information on a small fraction of the community. This is because conserved PCR primers cannot be designed for many functional genes of interest due to a lack of sequence homology or a lack of a sufficient number of sequences. Consequently, conventional PCRbased approaches cannot be used to detect and quantify many functional genes of interest. As such, a more comprehensive technique is required to provide a full picture of microbial community activity and dynamics in a rapid, parallel, and high-through-put manner. Use of microarrays is one way to overcome these limitations. Microarrays provide a rapid and high-throughput method of examining thousands of functional Chapter 5 Analysis of Microbial Communities by Functional Gene Arrays