The breakdown of lignocellulosic biomass to fermentable sugars remains a key challenge in the production of biofuels, such as hydrogen and ethanol.  To this end, microbial consortia need to be considered so that natural synergistic contributions to biomass deconstruction can be used advantageously. To develop such consortia, an understanding of the relevant molecular microbial ecology of the constituent organisms is critically important. In our lab, functional genomics approaches are being used to explore interspecies interactions between extremely thermophilic bacteria that have the capacity to degrade lignocellulosic biomass. Two gram-positive, oligotrophic, fermentative anaerobes, with growth T_opt of ~75°C, Caldicellulosiruptor saccharolyticus (Csac) and Anaerocellum thermophilum (Athe), are being investigated as model cellulolytic extreme thermophiles. Although 16S rRNA phylogeny suggests that these two bacteria are closely related, genome sequence analysis revealed that Athe contains almost 700 ORFs not present in Csac, while Csac has over 600 ORFs missing from Athe. A key objective is to determine the physiological and ecological significance of genome sequence differences as this relates to biomass deconstruction. Using whole genome oligonucleotide microarrays, both pure and co-cultures of C. saccharolyticus and A. thermophilum were monitored at various stages of growth on monosaccharides, polysaccharides and plant biomass substrates. Operons, regulons, and key protein-encoding ORFs responsive to specific substrates, growth conditions and interspecies interactions were identified. The results illustrate how strategic use of transcriptional response analysis can be a powerful tool for examining microbial biomass deconstruction by pure and co-cultures capable of consolidated bioprocessing.