Both bacterial and fungal endophyte-plant interactions involve modifications of plant gene expression and overall plant physiology/biochemistry to beneficially impact growth and stress tolerance. While monitoring specific gene expression during beneficial endophyte-sugarcane interactions, Arencibia et al. (2006) identified 47 differentially expressed sequence tags (EST) using cDNA-AFLP analysis. The transcripts showed significant genetic homologies to major signaling pathways such as the ethylene signaling pathway. For example, PYK10 encodes for a root — and hypocotyl-specific P-glucosidase/myrosinase and is important during the endophyte P. indica and Arabidopsis beneficial bio-control against herbivores and pathogens (Sherameti et al. 2008). NoxA was found to be crucial in regulating hyphal morphogenesis and growth in the mutualistic symbiotic interaction between the fungal endophyte Epicho festucae and perennial ryegrass (Tanaka et al. 2008). Functional genomics research will help scientists understand and elucidate mechanisms under which beneficial microorganisms promote host plant growth and enhance stress tolerance. Currently we are carrying out studies of mechanisms of plant growth promotion by bacterial endophytes using the responsive switchgrass cultivar Alamo and non-responsive cultivar Cave-in-Rock to Burkholderia phytofirmans strain PsJN (Kim et al.

2012) . Comparative global gene expression profiling is being conducted using both cultivars following B. phytofirmans strain PsJN inoculation with DOE-funded switchgrass EST microarray chips by Genomics Core Facility in the Noble Foundation. Approximately 35,200 switchgrass ID probes were identified to show significant differences between switchgrass cultivars Alamo and Cave-In-Rock after B. phytofirmans strain PsJN inoculation. Using the rice genome as a model for the analysis of the data along with the MapMan (Usadel et al. 2005) and the PageMap (Usadel et al. 2006) software, we are currently analyzing this large data set. Results showed that in Alamo almost 2000 genes were unique up-regulated at 0.5 day. On the other hand, in Cave-in-Rock, the number of unique up-regulated genes for 0.5 day was only 901. The significant changes are found in transcription factor genes, plant hormone and cell wall metabolism (unpublished data).

Bacterial and Fungal endophytes exhibit a diverse range of growth promoting mechanisms. In many cases, endophytes, primarily bacteria, possess multiple mechanisms of action and differentially express these traits at different stages of plant growth and development. Under stress conditions, endophytes help the host plant survive and flourish, as in the case of ACC deaminase activity and bio-control compound production. Under normal conditions, endophytes help fix atmospheric di-nitrogen and produce plant hormones to help the plant grow to its maximum potential.

Together, under both stress and normal conditions, endophytes ensure its host plant thrives, and its nutrient rich environment is maintained.