The general scheme of "Biomass to ethanol" process is presented elsewhere in this book. Our purpose in this section is to highlight the numerous and various ways to optimize the whole process from biomass to ethanol at different steps: choice of the biomass, pretreatment, enzyme productions, enzymatic hydrolysis, and ethanol fermentation. First of all, as discussed earlier, in the second generation of biofuels, biomass collection should not compete with food plants. Biomass should be abundant and cultural practices as

sustainable as possible. Interest was recently focused on plants providing good yields of biomass for a given surface as the tall Miscanthus. Reduction of lignin cell wall content is another interesting approach to enhance sugar recovery from biomass, lignin being an abundant and resistant polymer limiting the digestion of biomass in biofuels processes. With anti-sense technology, tobacco plants lines were obtained with 20% lower lignin content (Kavousi et al., 2010). The modified lines displayed a threefold increase of saccharification efficiency compared to wild type. Of course, the application of such studies in larger scales depends on the acceptance of transgenic plants by the society. Decision to use these plants has to be supported by studies of environmental risks and potential benefits (Talukder, 2006). Literature about pretreatment is very abundant, describing various methods: physical, chemical or combination of both (Soccol et al. 2010). Fine optimization of conditions should be performed individually depending on biomass. Among innovative method proposed, dry wheat straw has been treated successfully with supercritical CO2. After treatment, 1kg biomass yields to 149 g sugars (Alinia et al., 2010). Another currently emerging feature for bioethanol process amelioration is protein engineering. For instance, a cellulase from the filamentous bacterium Thermobifida fusca has been modified both in its catalytic domain and in its carbohydrate binding module (Li et al., 2010). A mutant enzyme displays a two fold increase activity, and a better synergy with other enzymes, leading it to be very useful for biomass digestion. At the next step, i. e. sugar fermentation to ethanol, many efforts have been run to allow yeast to perform both hexoses and pentoses fermentations. Industrial yeast Saccharomyces cerevisiae strains, fermenting only hexoses have been modified by addition of xylose degradation enzymes (Hector et al., 2010). Finally the outcome of engineering could be the use of synthetic biology, which is creating cell systems able to convert biomass to sugars and also to ferment them to ethanol. This strategy needs better fundamental knowledge to be developed (Elkins et al., 2010).

As discussed above, the step following the pretreatment of the biomass could be performed via the enzymatic hydrolysis of the cell wall polysaccharides into fermentescible, monomeric sugars. Unfortunately, it is well known that recalcitrance of plant cell wall to enzymatic digestion impairs the process. The behavior and the efficiency of the cell wall degrading enzymes (CWDE) in situ and in vitro with isolated polysaccharides are completely different. The properties of the CWDE, as conformation, hydrophobicity, capacity of adsorption onto the cell wall, interaction with the lignins, and catalytic efficiency in heterogeneous catalysis, are major parameters which should be considered and studied.

This chapter focuses on biomass degradation enzymes. What is the best strategy to produce the most efficient enzymes? What is the best choice depending of up — and downstream steps: commercial enzyme cocktail, enzymes produced by a given microorganism or heterologous production of individual enzymes? Efficiencies and cost of enzymes, two bottlenecks in the process, will be discussed. For some authors, the improvements of the conversion of biomass to sugar offer larger cost-saving potential than those concerning the step from sugar to biofuels (Lynd et al., 2008). These authors evaluated two scenarios; the first based on current technology and the second one including advanced nonbiological steps. In both cases, conversion of polysaccharides from biomass could be improved by increasing polysaccharides hydrolysis yields combined by lowered enzyme inputs. On-site enzyme production was also identified as beneficial for cost of the whole ethanol production process.