Fungal Lesson in Improving Large-Scale Chemical Production

Filamentous fungus Aspergillus niger exhibits great diversity in its phenotype.

The Science

The chemical compound citric acid has been produced on a large-scale basis for decades with the help of the filamentous fungus Aspergillus niger. The fungus also has enzymes that can be used to help break down plant cell walls for biofuel production, and it plays a key role in the carbon cycle.

For biofuels, A. niger is a highly relevant organism since it has already been scaled up, shown to be safe, and used for enzyme production. An A. niger strain was selected for sequencing by the DOE Joint Genome Institute (JGI) in 2005.

In a recent paper, an international team of collaborators including JGI compared the genome of the citric-acid producing A. niger strain with another strain that had undergone mutagenesis for enzyme production. The genetic diversity of these two A. niger strains was determined by applying systems biology tools as well as new bioinformatics methods to examine multi-level differences that distinguish the wild-type citric-acid-producing strain from the mutagenized glucoamylase A–producing strain.

The fungal genomes are expected to help industry generate green chemicals and fuels from sustainable sources. The comparative analysis allowed the team to identify the key genes to each strain’s predominant characteristics. This information, along with genomic data from additional Aspergillus strains being sequenced at the DOE JGI should facilitate further optimization of these strains for different bio-products.

BER Program Manager

Ramana Madupu

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Andersen, M. R., Grigoriev, I. V., Baker, S. E., Salazar, M. P., Schaap, P. J., Culley, D.; Thykaer, J., Frisvad, J. C., Nielsen, K. F., Albang, R., Albermann, K., Berka, R. M., Braus, G. H., Braus-Stromeyer, S. A., Corrochano, L. M., Dai, Zi., Hofmann, G., Lasure, L. L., Magnusson, J. K., Meijer, S. L., Nielsen, J. B., Nielsen, M., Panther, K., Pel, H. J., Poulsen, L., Samson, R., Stam, H. Tsang, A., Brink, J. M. van den, Atkins, A., Aerts, A., Shapiro, H., Pangilinan, J., Salamov, A., Lou, Y., Lindquist, E., Lucas, S., Grimwood, J., Kubicek, C. P., Martinez, D., Roubos, J. A., Nielsen, J. 2011. “Comparative Genomics of Citric-Acid-Producing Aspergillus niger ATCC 1015 Versus Enzyme-Producing CBS 513.88,” Genome Research. DOI:10.1101/gr.112169.110.