The released sugars can now be converted into a broad spectrum of biochemicals and biofu­els through fermentation. An enormous variety of microorganisms, such as yeasts, bacteria, or fungi, exist that can be added to the mixture of free sugars to be fermented into advanced biochemicals, including biofuels. Although organisms exist to break down virtually any organic material, six-carbon sugars, and especially glucose, are widely available in the plant and animal world. Hence, there is more experience fermenting six-carbon sugars (as present in cellulose) than the five-carbon sugars (as present in hemicellulose), but both are valuable fermentation feedstock, especially with recent advances in fermenting five-carbon sugars. Cost-effective processes will require the rapid, complete and simultaneous fermentation of all sugars. Therefore, new developments are focusing on optimizing the biochemical conversion pathway by integrating several processing steps. In the Simultaneous Saccha­rification and Fermentation process (SSF), cellulose hydrolysis and C6 fermentation are performed in one step. In the Simultaneous Saccharification and Cocurrent Fermentation process (SSCF), cellulose hydrolysis and the fermentation of both C5 and C6 sugars is performed. The ultimate step is the Consolidated BioProcessing (CBP), combining C5 and C6 hydrolysis and fermentation in one single process step (Figure 2.2).

Challenges faced are the inhibition of the yeast by the end-product, so lowering the yield, high distillation cost, formation of un-productive by-products such as acetates or furfural that cause inhibition of the fermentation process. In addition, hydrolysates of lignocellulose contain compounds that are inhibitory to most microorganisms. Tolerance to harsh environments, including elevated temperatures, high salt, and low pH, will be essential. Currently available strains are severely limited in pentose utilization and exhibit poor hydrolysate tolerance. New genetically modified microorganisms are being developed, designed in such a way that they are able to ferment different sugars, get round inhibition or tolerate harsh environments, as such leading to a higher overall yield [30].