Discovery of Microorganisms and Enzymes Involved in High-Solids Decomposition of Rice Straw Using Metagenomic Analyses

Abstract

High-solids incubations were performed to enrich for microbial communities and enzymes that decompose rice straw under mesophilic (35°C) and thermophilic (55°C) conditions. Thermophilic enrichments yielded a community that was 7.5 times more metabolically active on rice straw than mesophilic enrichments. Extracted xylanase and endoglucanse activities were also 2.6 and 13.4 times greater, respectively, for thermophilic enrichments. Metagenome sequencing was performed on enriched communities to determine community composition and mine for genes encoding lignocellulolytic enzymes. Proteobacteria were found to dominate the mesophilic community while Actinobacteria were most abundant in the thermophilic community. Analysis of protein family representation in each metagenome indicated that cellobiohydrolases containing carbohydrate binding module 2 (CBM2) were significantly overrepresented in the thermophilic community. Micromonospora, a member of Actinobacteria, primarily housed these genes in the thermophilic community. In light of these findings, Micromonospora and other closely related Actinobacteria genera appear to be promising sources of thermophilic lignocellulolytic enzymes for rice straw deconstruction under high-solids conditions. Furthermore, these discoveries warrant future research to determine if exoglucanases with CBM2 represent thermostable enzymes tolerant to the process conditions expected to be encountered during industrial biofuel production.

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts

“…Thus, engineered culture conditions are used to enrich for desirable traits and lead to the discovery of functional microbial consortia or specific microorganisms. For example, starting with microbial communities collected from compost and soil environments, a selection of simplified communities have been found that can deconstruct lignocellulosic biomass in extreme conditions, such as high temperature, high-solid loading, and low moisture (DeAngelis et al 2010;Jimenez et al 2014;Reddy et al 2013;Simmons et al 2014;Yu et al 2015). The enrichment process generates less complex lignocellulolytic microbial communities that can facilitate targeted discovery of potential enzymes and microorganisms for biomass deconstruction .…”

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures

“…But due to the single point analysis, the succession of microorganisms that had occurred during the enrichment period remains unknown. It is interesting to note, however, that in spite of the different incubation times in the present versus previous studies, some major features are similar: a high accumulation of Actinobacteria in compost-like enrichments or a higher proportion of Firmicutes and Chloroflexi , with a lower abundance of Gemmatimodadetes and Trueperaceae and nearly no Actinobacteria in a thermophilic liquid enrichment [9,10,14,30]. …”

Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis

“…The cumulative carbon dioxide evolution rate (cCER) decreased as the IL concentration increased (Table 1) (14). The cCER seen with switchgrass amended with 2% IL was significantly lower than the cCER from samples amended with 0% and 0.5% IL.…”

“…Incubations were conducted as described previously (14, 24). In summary, switchgrass was wetted with minimal media (25) to a moisture content of 400% (wt) dry basis (g water [g dry solid] −1 ), inoculated with 10% (wt) inoculum (g dry inoculum [g dry solid] −1 ), and then amended with IL.…”