Citric acid production by the filamentous ascomycete fungus, Aspergillus niger represents the most efficient, highest yielding bioprocess in practice. This process is a model for other filamentous fungal fermentation processes that will become a key part of DOE's vision of the biorefinery, where multiple products such as organic acids and ethanol, are produced from renewable biomass. These products can be further refined for use as plastic monomers, solvents, or fuels, thereby decreasing dependence on petroleum, the traditional source of these products. The strain chosen for sequencing (ATCC 1015) is also the wildtype strain used in the first patented citric acid process nearly 90 years ago.

As a common member of the microbial communities found in soils, A. niger also plays a significant role in the global carbon cycle. It is a soil saprobe with a wide array of hydrolytic and oxidative enzymes involved in the breakdown of plant lignocellulose. An increased understanding of the molecular mechanisms controlling carbon flux in fungi will be gained from study of the A. niger genome. Finally, A. niger is an important model fungus for the study of eukaryotic protein secretion in general, the effects of various environmental factors on suppressing or triggering the export of various biomass degrading enzymes, molecular mechanisms critical to fermentation process development, and mechanisms involved in the control of fungal morphology.