The application of molecular tools to microbial community structure analysis pro­vides insight about the development of a mature microbial community, its response to changes in substrate loading rate, and the influence of environmental factors [414]. This knowledge allows us to improve the design and control of the ADP.

Metabolic and Genetic Engineering of Anaerobic Microorganisms

Classical strain improvement is an evolutionary engineering technique that has been used for decades for the production of penicillin, amino acids, and many other industrial products, but it is time consuming and has limited applications [415, 416]. Attractive opportunities exist with metabolic and genetic engineering techniques to enhance biofuel production. Studies have been conducted with several organisms including Escherichia coli [417-420], Zymomonas mobilis [421-423], Klebsiella oxytoca [424,425], and S. cerevisiae [426-429].

Cellulolytic Clostridium is one of the prospective organisms for metabolic engi­neering in an anaerobic digester. Hydrolysis of polymeric organic compounds is often the limiting step during biodegradation of algal biomass. Hydrolysis of algal cell walls is difficult due to its heterogeneous structure composed of carbohydrates, glycoproteins, and lipids. Guedon and colleagues applied metabolic engineering to produce a recombinant Clostridium cellulolyticum that exhibited 150% higher cel­lulose consumption and 180% larger cell dry weight in comparison to the wild strain [430]. Another possible strategy is the expression in Clostridia of the algal cell wall degrading enzymes from wild strains that naturally use algal biomass as a substrate. Saccharophagus degradans is able to degrade at least ten distinct com­plex polysaccharides from diverse algal, plant, and invertebrate sources and can be an outstanding source of degrading enzymes [431, 432].