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Comparative genomics study of industrial fungus seeks to better harness potential for biofuels applications

Aspergillus niger, shown here with its DNA lit up in green, is a fungus that can be used on an industrial scale to produce enzymes or chemicals such as citric acid. Source: PNNL. Click to enlarge.

An international team led by Scott Baker of the Pacific Northwest National Laboratory has compared the genome sequences of two strains of the fungus Aspergillus niger to, among other things, better harness its industrial potential in biofuels applications.

A. niger is an industrial workhorse, with different strains efficient in producing polysaccharide-degrading enzymes (particularly amylases, pectinases, and xylanases) or organic acids (mainly citric acid) in high amounts. (As of 2007, the global market for citric acid was estimated to be approximately $1.2 billion with more than 500,000 tons produced annually by fermentation.) The production process involving A. niger is thus a well understood fungal fermentation process. The PNNL-led study compares the genomes of an enzyme-producing strain and a citric-acid-producing strain.

Learning more about the genetic bases of the behaviors and abilities of these two industrially relevant fungal strains, wrote senior author Baker and his colleagues in a paper published in the journal Genome Research, will allow researchers to exploit their genomes towards the more efficient production of organic acids and other compounds, including biofuels.

Aspergillus niger is an industrial workhorse for enzymes and small molecules such as organic acids. We know that this single organism is used for production of organic acids and for enzymes, and it can degrade plant cell wall matter for sugar production. For biofuels it’s a highly relevant organism since it’s already been scaled up, shown to be safe, and used for enzyme production. That’s why it was such an important organism to further characterize through DNA sequencing.

—Scott Baker

The US Department of Energy (DOE) Joint Genome Institute (JGI) generated the 35-million base genome of A. niger ATCC 1015, the wild-type strain that was used in research that led to the first patented citric acid process. The other A. niger strain used in the study (A. niger CBS 513.88, an industrial strain derived from A. niger NRRL 3122, a strain developed for enzyme production by classical mutagenesis and screening methods) was sequenced by DSM in the Netherlands and reported in the journal Nature Biotechnology in January 2007.

The PNNL-led study determined the genetic diversity of these two A. niger strains 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 enzyme–producing strain.

By analyzing the genomes on several levels—DNA, chromosome, gene and protein—Baker and his colleagues found several hundred unique genes in each strain that are key to their predominant characteristics. For example, A. niger ATCC 1015 had a higher expression of traits involved in high citric acid yields. On the other hand, the induced mutant strain had more elements related to efficient enzyme production. The team also noted that the genes involved in boosting enzyme production in the induced mutant strain of A. niger may have come from another Aspergillus strain via horizontal gene transfer, which allows one organism to acquire and use genes from other organisms.

In this study, we provide and compare the genomes of two strains of A. niger. These two strains have different phenotypes: one, the predecessor to efficient enzyme-producing strains having undergone some level of mutagenesis and selection, and the other a wild-type parent strain of high citric-acid-producing strains. This makes the comparison interesting both in terms of genomic research and industrial applications. We have supported the conclusions of our comparison with further experiments, allowing us to propose new hypotheses and conclusions within three main areas: (1) genetic diversity of the A. niger group, (2) horizontal gene transfer in fungi, and (3) fungal biotechnology.

—Andersen et al.

Nearly a dozen additional Aspergillus strains that are used in industry are either being sequenced or in the queue to be at the DOE JGI, said study co-author Igor Grigoriev, head of the DOE JGI Fungal Genomics Program. Grigoriev noted that a better understanding of genomic content and organization and how rearrangements and mutations lead to desired traits should facilitate further optimization of these strains for different bio-products.

Having the genetic blueprint for a citric acid-producing fungus will increase our understanding of the organism’s metabolic pathways that can be fine-tuned to enhance productivity or alter its metabolism to generate other green chemicals and fuels from renewable and sustainable plant-derived sugars.

—Randy Berka, Director, Novozymes, Inc., and co-author

The US Department of Energy Joint Genome Institute, supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup.


  • Mikael R Andersen et al. (2011) Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Res. doi: 10.1101/gr.112169.110

  • Herman J Pel et al. (2007) Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88. Nature Biotechnology 25, 221 – 231 doi: 10.1038/nbt1282



Years ago they looked at "jungle rot" fungus, it was very good at destroying materials. These findings show how it can be done through nature. They also made breakthroughs in lowering the cost of enzyme production. That is what led to the Iogen announcements about wheat straw to fuels.

Henry Gibson

All of the large original forests that existed 2000 years surrounding the Mediterranian sea have been almost completely destroyed along with the soil that supported them for foods and biofuels.

But to appease the BIOFUEL god and its supporters. I would personally feed the final bits of the last US Redwood tree into the biodigester or just simple flames.

Do the arithmetic folks! how many square miles does the UK or the US have. What is the maximum production of biomass possible with the solar energy and growth efficiency. Do not even consider how much water is needed to produce the petrol to fill a tank with processes plants. The cost of the land for solar energy is too much and their is not enough of it. And it is wasted for producing biofuels. Use Infinia parabolic generators! ..HG..


I have to agree with HG.

1. One e-car uses 10 Kwh/day = 8600 cal = food for 4 persons/day.

2. One ICE uses 3 gal/day = 372,000 BTU = food for 46 persons/day

3. Our inefficient gas guzzlers use 11.5 times as much energy as an electrified vehicle and consume enough energy to feed 46 people.

4. Feeding our 240 million inefficient gas guzzlers with biomass derived liquid fuels would consume as much food energy as 240 M x 46 = 11 billion people.

5. USA's total land mass could never produce enough biomass to produce liquid fuel for 240 M vehicles and food for 330+ million people. If so, it could feed 11.5 billion people. Many would doubt that.

6. USA could easily produce enough clean electrical energy for 240 million electrified vehicles and food for 330+ million people. A proper e-energy national conservation program could contribute for about half of it. The other half could be produced with solar and wind. No new nuclear or coal fired power plants would be required. A few new NG power plants could be used for peak demands until such times as V2G and battery technologies have evolved.


All or nothing at all is ridiculous. If corn stalks, cobs and wheat straw can replace even a fraction of petroleum based transportation fuels, we are ahead of the game.

The corn and wheat are already grown for the grain to provide feed/food, we are just using the cellulose for fuels. Enough can be left on the land for future crops and no extra land nor water is needed.


SJC... biomass could hardly supply more 10% to 15% of the liquid fuels consumed by the current fleet and enough food for 300 to 400 million people. With a normal fleet and population growth of 3%/yr, biomass produced liquid fuels would not make much of a lasting dent.

Extremely high liquid fuel consumption is the problem to be solved. Progressive, partial and full, vehicle/train electrification will be required to maintain a fast growing fleet in operation.


E10 replaced a lot of petroleum. Synthetic fuels can replace a lot of petroleum. Electrification will not happen over night and if we wait for that we will be in a bind LONG before that happens.


One billion tons of biomass can make 50 billion gallons of synthetic gasoline. That is 1/3 of the gasoline consumed in the U.S. each year.

That is using just the agricultural and forest waste. That leaves ALL of the 100 million acres now planted in corn for feed/food. That is just cellulose biofuel using existing land, water and fertilizer.

If we can feed 300+ million Americans with the land and crops like we do now, we will when we turn the waste biomass into biofuels. People are not eating corn stalks nor cobs and they are not eating wheat straw nor sawdust.


Typically, EVs have/would have been able to handle my to-to-day driving for a dozen years, but recently I had to drive from the mid-west to DC overnight.

No affordable battery car in our immediate future is going to grind away ~300 miles/4 hours between 10 minute stops without a liquid fuel assist.

As SJC writes, "That is 1/3 of the gasoline consumed in the U.S. each year.. That is just cellulose biofuel using existing land, water and fertilizer.". With this fuel, we could produce the fuel for these atypical events. Then maybe we wouldn't be training US kids to be Moslem killers at $2700/day occupation financed by 75 years of elderly social security deductions.

I would have taken a "Europass/EV rental", but US oil/auto greed crushs that option with big(7 lobbiests/"representative") lobby dollars for the past and all foreseeable decades.


This is all part of the alternative, conserve and efficiency idea. If we do not use as much fuel and the fuel we use is produced domestically, then we are in a much better national security and economic position.

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