Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass. Files of RNA expression for Clostridium phytofermentans growing on D-+-Xylose.. BED

Plant-fermenting bacteria are important for the global carbon cycle, human nutrition, and industrial production of renewable fuels and commodities from cellulosic biomass. Plants are primarily composed of heterogeneous polysaccharides, requiring plant-degrading microbes to encode many carbohydrate-active enzymes (CAZymes) to cleave different sugar linkages. Here we develop a broadly applicable method to study how microbes catabolize plant biomass by determining the combination of CAZymes that depolymerize each polysaccharide into sugars, how the cell alters global mRNA expression, and the efficiency with which each polysaccharide is metabolized. We apply this method to investigate how Clostridium phytofermentans, a bacterium encoding 171 CAZymes, ferments polysaccharides. We assimilate our results into a genetic model of how this bacterium metabolizes plant biomass and discuss how these results advance our understanding of microbial plant fermentation.