cAnaerobic gut fungi represent a distinct early-branching fungal phylum (Neocallimastigomycota) and reside in the rumen, hindgut, and feces of ruminant and nonruminant herbivores. The genome of an anaerobic fungal isolate, Orpinomyces sp. strain C1A, was sequenced using a combination of Illumina and PacBio single-molecule real-time (SMRT) technologies. The large genome (100.95 Mb, 16,347 genes) displayed extremely low G؉C content (17.0%), large noncoding intergenic regions (73.1%), proliferation of microsatellite repeats (4.9%), and multiple gene duplications. Comparative genomic analysis identified multiple genes and pathways that are absent in Dikarya genomes but present in early-branching fungal lineages and/or nonfungal Opisthokonta. These included genes for posttranslational fucosylation, the production of specific intramembrane proteases and extracellular protease inhibitors, the formation of a complete axoneme and intraflagellar trafficking machinery, and a near-complete focal adhesion machinery. Analysis of the lignocellulolytic machinery in the C1A genome revealed an extremely rich repertoire, with evidence of horizontal gene acquisition from multiple bacterial lineages. Experimental analysis indicated that strain C1A is a remarkable biomass degrader, capable of simultaneous saccharification and fermentation of the cellulosic and hemicellulosic fractions in multiple untreated grasses and crop residues examined, with the process significantly enhanced by mild pretreatments. This capability, acquired during its separate evolutionary trajectory in the rumen, along with its resilience and invasiveness compared to prokaryotic anaerobes, renders anaerobic fungi promising agents for consolidated bioprocessing schemes in biofuels production.

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Biomass and other carbonaceous materials can be gasified to produce syngas with high concentrations of CO and H 2 . Feedstock materials include wood, dedicated energy crops, grain wastes, manufacturing or municipal wastes, natural gas, petroleum and chemical wastes, lignin, coal and tires. Syngas fermentation converts CO and H 2 to alcohols and organic acids and uses concepts applicable in fermentation of gas phase substrates. The growth of chemoautotrophic microbes produces a wide range of chemicals from the enzyme platform of native organisms. In this review paper, the Wood-Ljungdahl biochemical pathway used by chemoautotrophs is described including balanced reactions, reaction sites physically located within the cell and cell mechanisms for energy conservation that govern production. Important concepts discussed include gas solubility, mass transfer, thermodynamics of enzyme-catalyzed reactions, electrochemistry and cellular electron carriers and fermentation kinetics. Potential applications of these concepts include acid and alcohol production, hydrogen generation and conversion of methane to liquids or hydrogen.

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