Hi, Rui. When you say genetic transformation, do you mean you like to genetically engineering the bacterial strain, or to transform foreign DNA into your strain? I've done some work to improve yield of secondary metabolites by genetic engineering. Generally, you can increase pool size of precursors of your final products, or block pathways that compete for the precursors. You can also use stronger promoters to improve protein expression, or increase gene dosage of positive regulators. On the other hand, you can also optimize components of your ferment ion media and other conditions for fermentation such as temperature, pH, and aeration.

Strain improvement by transformation (if not genetic engineering) is the last resort in improving the productivity of fermentation. It is not just the increase in the yield of product, it may be reduction in cost like energy, time, manpower etc and finally interfering substances which can increase the cost of down stream processing. In your case of biodiesel or biohydrogen, these are more important factors that genetically improved (transformed - in your words). Think over it carefully.