Biochemical pathways such as aerobic respiration, anaerobic respiration and fermentation within microoganisms efficiently convert organic substrates into chemicals or biofuels such as ethanol. Aerobic respiration pathways convert carbon source such as glucose to produce ATP through series of the Embden-Meyerhof pathway, the tri-carboxylic acid pathway and the electron transport chain, with oxygen acting as the terminal electron acceptor. In anaerobic respiration (absence of oxygen), the terminal electron acceptors are replaced with inorganic compounds such as sulfate or nitrate to produce ATP. In fermentation, internally balanced oxidation and reduction of organic compounds occur with the biochemical pathway under anaerobic conditions, but without utilization of the electron transport system. However, bioprocessing industries often call both aerobic and anaerobic respiration fermentation processes where the term generally entails any bioconversion process.

Cellulosic ethanol fermentation may be performed using a wide range of microorganisms. Yeast such as Sacharomyces cerevisiae and bacteria such as Zymomonas mobilis are well known for utilizing glucose, fructose and sucrose for ethanol fermentation under anaerobic conditions with higher ethanol tolerance. Z. mobilis has a higher metabolic rate with less biomass production through the Entner-Doudoroff pathway (Fig. 3) compared to S. cerevisiae through the Embden-Meyerhof-Parnas (EMP) pathway (Fig. 4). The faster rates occur from decoupling energy generation from ethanol production with the absence of the highly-regulated enzyme phosphofructokinase (PFK) present in the EMP pathway. However, a number of disadvantages

exist for use of Z. mobilis, mainly in the production of byproducts such as levan catalyzed by levansucrase and other fructose polymers that tend to foul distillation columns downstream (Drapcho et al. 2008). S. cerevisiae is the most widely used microorganism for cellulosic ethanol production due to high ethanol tolerance and the remaining biomass being more suitable for use as animal feed than biomass from Z. mobilis fermentation. The hydrolysis of lignocellulosic biomass generates a mixture of both sugars (hexoses and pentoses) during the process. The simultaneous utilization of both sugars is the most challenging part for the cellulosic ethanol production. Therefore, other strains of yeast, bacteria and fungi have been explored or genetically modified for simultaneous utilization of both glucose and xylose in cellulosic ethanol fermentation. In literature, numerous microorganisms have been studied using xylose as the carbon source (Table 4). However, the performance of these microorganisms varies on hydrolyzed lignocellulosic broth due to variations in sugar utilization from the presence of inhibitors that depends on the chemical composition of lignocellulosic feedstock, chemical pretreatment and the extent of recirculation in the process (Table 5). A preprocessing or detoxification of these inhibitors from the hydrolyzed broth before or after the fermentation could be an energy-intensive step (Olsson and Hahn-Hagerdal 1996). However, these inhibitory effects could be resolved using fermenting microorganisms with high cell densities (Olsson and Hahn-Hagerdal 1996). A list of different microorganisms with their optimal ethanol yield and productivity is given for ethanol fermentation using enzymatic hydrolysate of lignocellulosic feedstock (Table 6).

In addition, fermentation can be performed in batch, semi-batch and continuous mode. The selection of the fermentation mode for optimal ethanol yields is based on the kinetic properties of microorganisms used and the integration of the cellulosic ethanol production process.