The Hyphal Tip

A quick post of some recent comparative genomics papers on our desk that are worth a look.

• Khaldi N, Wolfe KH (2008) Elusive Origins of the Extra Genes in Aspergillus oryzae. PLoS ONE 3(8): e3036. doi:10.1371/journal.pone.0003036. This was a cool but somewhat controversal finding presented at Fungal Genetics last year.
• Casselton, LA. Fungal sex genes - searching for the ancestors. doi: 10.1002/bies.20782. A review of recent findings about the Zygomycete MAT locus.
• Soanes DM, Alam I, Cornell M, Wong HM, Hedeler C, et al. (2008) Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis. PLoS ONE 3(6): e2300. doi:10.1371/journal.pone.0002300
• Lee DW, Freitag M, Selker EU, Aramayo R (2008) A Cytosine Methyltransferase Homologue Is Essential for Sexual Development in Aspergillus nidulans. PLoS ONE 3(6): e2531. doi:10.1371/journal.pone.0002531

I found the headline today, "Biofuels: Fungus Use Improves Corn-to-ethanol Process" and I was curious to find out what fungus they were talking about in the article. It turns out that researchers at Iowa State University found that Rhizopus microsporus is able to grow off part of the leftovers of ethanol production called thin stillage. The reason this is so exciting is explained below:

(Rhizopus sporangium, picture taking during PMB 110L @ UC Berkeley)

The fuel is recovered by distillation, but there are about six gallons of leftovers for every gallon of fuel that's produced. Those leftovers, known as stillage, contain solids and other organic material. Most of the solids are removed by centrifugation and dried into distillers dried grains that are sold as livestock feed, primarily for cattle.
The remaining liquid, known as thin stillage, still contains some solids, a variety of organic compounds from corn and fermentation as well as enzymes. Because the compounds and solids can interfere with ethanol production, only about 50 percent of thin stillage can be recycled back into ethanol production. The rest is evaporated and blended with distillers dried grains to produce distillers dried grains with solubles.
The researchers added a fungus, Rhizopus microsporus, to the thin stillage and found it would feed and grow. The fungus removes about 80 percent of the organic material and all of the solids in the thin stillage, allowing the water and enzymes in the thin stillage to be recycled back into production.
The fungus can also be harvested. It's a food-grade organism that's rich in protein, certain essential amino acids and other nutrients. It can be dried and sold as a livestock feed supplement. Or it can be blended with distillers dried grains to boost its value as a livestock feed and make it more suitable for feeding hogs and chickens.

The idea of being more efficient by saving water and producing nutritious animal feed that can produce healthier animals that produce more meat is very interesting and worthwhile. But the article never mentions that many Rhizopus species are considered pathogens and R. microsporus when paired with Burkholderia rhizoxinia, a endosymbiont that produces rhizoxin, essentially becomes the pathogen responsible for rice seedling blight. Rhizopus also can cause serious mycoses in humans (The non squeamish can search for rhizopus mycoses on google).

I am curious if this Rhizopus has any endosymbionts that could be helping it grow on stillage or what other fungi that may not be potential pathogens might be out there that could also grow on the thin stillage.

Lots of papers in Mycologia (subscription required) this month of different groups analyzing the fine-scale relationships of many different fungal clades using the loads of sequences that were generated as part of the Fungal Tree of Life project.

I'm including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.

If there was any theme in the conference it was "Hey we are all using these genome sequences".

The JGI has released the Phycomyces blakesleeanus genome. This represents the second Zygomycete genome sequence that has been released in addition to Rhizopus oryzae that was released by the Broad Institute last year. We are now getting a better look at the basal fungal genomes including the Chytrids and Zygomycetes.