Exploring the genetic potential of bacteria isolated from extreme environments for use in biofuel and bioprocess industries.
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Industrial processes that employ microbes or microbial components (e.g. enzymes) to create high-value products (e.g. bioremediation agents, fuels, effective detergents, nutrients, pharmaceuticals, probiotics, etc.) can be optimized or expanded by exploring the capacity of novel microbes from extreme environments. Specifically microbes from sediment environments with high total dissolved solids (TDS) will likely tolerate product accumulation better. Microbes from thermal environments will likely tolerate higher temperatures under process conditions. Interest in utilizing extremophiles (e.g. halophiles and thermophiles) such as Bacillus and related genera for industrial processes is mounting (Niehaus et al. 1999; Demirjian et al. 2001; van den Burg 2003; Xiong et al. 2009; Tiquia and Mormile 2010).The central theme for biofuel and bioprocess research in the Wilkinson laboratory is that microbial communities from extreme environments (e.g. saline and/or thermal sediments) are pre-adapted to the conditions present in industrial processes (e.g. high product concentrations and/or high temperatures). Thus, these communities have tremendous discovery potential and can provide individual isolates or consortia ("teams" of isolates) that advance the biofuel, bioproduct, and bioprocess industries. Through more than 5 years of extensive field and laboratory work we assembled a unique collection of microbial communities and isolates from saturated sediments collected across a wide geographic and ecological range (Figure 1). In total we collected and preserved >500 sediment samples from 77 sites (most saline and/or thermal) and generated extensive datasets for both soil chemistry and fermentation performance in a 2nd generation biofuel platform (MixAlcoTM), developed by chemical engineers at Texas A&M University. The >500 samples collected span a tremendous range of soil and sediment environments (Table 1), therefore should we be interested in targeting any particular type of extremophile (e.g. acidophiles, alkaliphiles, anaerobes, halophiles, oligotrophs, thermophiles) it is highly likely we have multiple preserved samples from which to select. Furthermore, we conducted a long term project to culture individual strains from 34 of the best performing fermentation communities, resulting in an isolate library with >1900 strains falling out into at least 46 species (almost all within the Phylum Firmicutes) based on phylogenetic analysis of partial 16S rDNA gene sequences (Figure 2). All these biological materials (preserved soils, fermentation communities, and isolates) and extensive datasets (soil chemistry and fermentation performance data for all sediment samples, community pyrosequence data for targeted subsets of fermentations and soils, isolate sequence data) are in place..........