The Hyphal Tip: Fungal Genomes and Comparative Genomics

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.

Science has a section dedicated to Microbial Ecology including a review describing microbial biogeography studying communities on the basis of trait rather than taxonomic diversity. Certainly this interlinks with metagenomic approaches well, something I've been thinking about more after visiting some of the folks at Montana State Thermal Biology Institute and all the increasingly massive datasets like what CAMERA provides.

This month's Genetics has a series of articles exploring the genome (published last year & freely available at Science) of the green algae [[Chlamydomonas reinhardtii]]. These manuscripts are primarily genome analyses making for a very bioinformatics focused issue of Genetics. Some of the highlights include:

(Truffle picture from BBC.com) The BBC (link) has an interesting article about a  Chinese Black truffle being found as an invasive species in Italy. The Italian's and European truffle aficionados are worried that the Chinese Black Truffle will outcompete the Perigord Black truffle, which is supposed to be very tasty and the second most expensive truffle by weight, behind only the Piedmont White Truffle.

The [[Trichoderma reesei]] genome paper was recently published in Nature Biotechnology from Diego Martinez at [[LANL]] with collaborators at [[JGI]], [[LBNL]], and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol production.

Paul Stamets thinks so and he's done work to make this happen.  The founder of FungiPerfecti and author many books on mushroom cultivation spoke at a TED talk recently that is worth taking a look. 

The genome of Podospora anserina S mat+ strain was sequenced by Genoscope and CNRS and published recently in Genome Biology. The genome sequence data has been available for several years, but it is great to see a publication describing the findings.  The 10X genome assembly with ~10,000 genes provides an important dataset for comparisons

Depleted uranium (DU) from spent ammunition used in the conflicts in Iraq and the Balkans poses a health risk to the inhabitants of those regions. This paper in Current Biology from Marina Fomina et al shows that several species of fungi including one from the mycorrhizal genus Rhizopogon

Neil has a great summary of the results from the Platypus genome sequencing project.

The transcriptional landscape of yeast has been (further) defined with [[Solexa]] sequencing in a method deemed "RNA-Seq", but what I would call "deep EST sequencing".  This approach for transcriptional profiling by sequencing alone is sure to be used by many labs looking for lower and more complete ways to describe and quantitate the full population of transcripts in an organism.