With the availability of the complete sequences of the genomes of different microorganisms, functional genomic tools provide a powerful approach for identifying microbial genes that are expressed during association of bacteria with hosts and or in response to various environmental factors. In my current research, I am working on a project to sequence the complete genome of Erwinia chrysanthemi 3937. E. chrysanthemi is a common colonist of aerial plant surfaces and causes soft-rot, wilts and blight diseases on a wide range of plant species. Infection of plants by E. chrysanthemi serves as a model for studying the mechanism of bacterial infection. My students and I are using complementary approaches to look at gene expression in this model organism. The first involves a custom designed microarray for E. chrysanthemi that will enable us to look at sets of genes that are regulated over time during the infection process. Secondly, we are using in vivo expression techniques (IVET) to investigate specific genes of E. chrysanthemi that are up-regulated in plant hosts. Thirdly, by hrp functional cloning technology, we explore genes of E. chrysanthemi 3937 that are involved in pathogenesis. Using bioinformatic tools, the known hrp regulated genes and DNA clones identified in hrp functional screening are used as a training set for a genomewide identification of potential virulence genes in E. chrysanthemi.

2) Developing novel approaches for microbial diversity profiling

The quantitative description of microbial communities is one of the most promising areas of research in microbial ecology. Classical culture based techniques recover only a small proportion of microorganisms from environmental samples, but have provided us with a wide array of products that have benefited humanity. New techniques in molecular ecology have now opened the door for a revolutionary advance in our understanding of microbial communities in nature and identification of new microorganisms and microbial products that can be harnessed for biotechnology. My students and I have been especially interested in developing novel approaches to analyze microbial diversity that is associated with plants. Going beyond these initial descriptions of microbial communities, my most recent work has begun to focus on interactions between plants and microorganisms using genome profiling. In addition, I would like to further explore how plant pathogens are influenced by the microbial communities with which they are associated and how gene expression is modified by environmental factors that influence both the pathogen and leaf bacterial communities. This research may lead to improved understanding of disease and methods for biocontrol by promoting disease suppressive bacterial communities on plant leaf surfaces.