Abstract
Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.
Highlights
Plant biomass is one of the most abundant renewable energy sources on Earth and a largely underutilized feedstock for biofuels [1]
C. phytofermentans is distinct from other well-studied solventogenic and cellulolytic species found within clostridial Clusters I (Clostridiaceae), III (Ruminococcaceae), and X (Thermoanaerobacteraceae) (Fig 1)
A member of Cluster XIV (Lachnospiraceae), C. phytofermentans is closely related to human commensals that have been sequenced as part of the International Human Microbiome Consortium [53], and to bacteria isolated from rice paddy soils, earthworm intestines and other anaerobic, carbon rich environments (Fig 1)
Summary
Plant biomass is one of the most abundant renewable energy sources on Earth and a largely underutilized feedstock for biofuels [1]. Production of biofuels from the lignocellulose fraction of plant biomass differs from production from grains in two fundamental aspects: (1) different types of saccharolytic enzymes are required to break down lignocellulose into soluble carbohydrates; and (2) fermentation of pentose sugars, in addition to hexoses, is required to harvest the majority of energy stored in lignocellulose [2]. One potential solution is the use of microbes that produce lignocellulose-decomposing enzymes and simultaneously ferment the resulting hexose and pentose carbohydrates to products such as ethanol. Merging these processes in a single microbe could substantially reduce the costs of lignocellulosic biofuel production [4]. Primarily members of the Clostridiales, are found in natural anoxic environments where vast quantities of cellulose and other plant cell wall components are decomposed
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