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FUNGI


20,000 cultures from 1,600 species of fungi


Getting to Know You ENCYCLOPEDIA 1000 Fungal Genome Project Begins Encyclopedia of Fungi


By Dr. Daniel Lindner, Research Plant Pathologist, U.S. Forest Service, Northern Research Station And Jane Hodgins, Public Affairs Specialist, U.S. Forest Service, Northern Research Station


The next time you see a mushroom glowing like stained glass on the forest floor, or even a layer of grey-green fuzz over a dish of leftovers in a corner of the refrigerator, have a little respect. You are looking at an organism that is part of a scientific kingdom that is neither animal nor plant, that contributes mightily to the health and happiness of human beings, and that we know very little about.


The ‘1000 Fungal Genomes’ project is an ambitious start in getting to know fungi. Scientists with the U.S. Forest Service’s Northern Research Station, the U.S. Department of Agriculture’s Agricultural Research Service, and universities in the U.S., the Netherlands and France are collaborating with the Department of Energy’s Joint Genome Institute to sequence two species from every known fungal family in the next 5 years. The project is the first step in creating an encyclopedia of all fungi, which will one day help researchers understand not only what these amazing organisms do, but how they operate. The ‘1000 Fungal Genomes’ project is one of 41 research projects that will receive funding through the Department of Energy’s 2012 Community Sequencing Program.


Approximately 200 of the 1,000 species sequenced will come from a 79-year-old fungal culture collection maintained by the Northern Research Station’s Center for Forest Mycology Research in Madison, Wis. The remaining 800 species will come from other major culture collections from around the world and from many smaller labs that will contribute individual species of interest.


Established in 1932, the Center for Forest Mycology Research’s fungal culture collection includes 20,000 cultures from 1,600 species of fungi. The collection is comprised mainly of Basidiomycetes, or club fungi, which includes the types of fungi that form mushrooms. These fungi play many critical roles in forests, from species that protect tree roots to species that decompose wood to destructive forest pathogens that actively kill trees.


“It’s an incredible resource,” according to Dan Lindner, a Forest Service research plant pathologist at the Center for Forest Mycology Research. “As far as we know, it’s the world’s largest collection of wood-inhabiting fungi.”


Fungi that are needed on a day-to-day basis are kept in cold sterile water– cold to the tune of 4 degrees Celsius or about 39 degrees Fahrenheit – because it is relatively easy to move fungi in and out of cold-water storage. A fungus can remain alive in cold water for about 7 years, after which time it needs to be taken out of storage, warmed up and allowed to grow. Afterward, the fungal culture is tucked away into cold storage for another 7 years. It takes the Center’s technicians about 7 years to work their way through the entire collection of cold- water isolates, “waking” them up from their slumber and putting them back to sleep again, just to start back at the beginning of the collection in a never ending cycle. The entire collection of isolates is kept in cold-water storage for immediate access, and is “backed up” in liquid nitrogen storage at -195 Celsius, or -320 degrees Fahrenheit. The extreme cold of liquid nitrogen can keep fungi in “suspended animation” for many decades.


For the 1000 Fungal Genome project, Forest Service scientists will grow the fungal cultures coming from their collection and isolate the DNA for sequencing by the DOE’s Joint Genome Institute. Lindner expects to send a first batch of 10 species to the Joint Genome Institute by next spring. Isolating the high quality DNA needed for this project is complicated, and the DNA is subject to a series of exacting quality reviews before it is sequenced. At the Center for Forest Mycology Research, Lindner will work with three other scientists and technicians to isolate the DNA and perform quality reviews.


Very high quality DNA is needed because the goal of the 1000 Fungal Genomes Project is to read the entire genetic “blue print” of each species. Sequencing of DNA is essentially reading the code of the DNA, which is made up of four bases: A, T, C and G. The order of these bases makes up the genetic code for building the organism. To "whole genome sequence" a fungus, scientists read every base in the organism's DNA, resulting in a very long string of A, T, C and G's. For most fungi, each genome contains about 43 "megabases," or 43 million bases. So, for each fungus, there is a string of about 43 million A, T, C and G's. Getting this information is just the start of the process, since then scientists have to "read" the code and try to make sense of it.


Making sense of fungi is worth the effort, whether you want to survive an organ transplant or just grab a pint of beer. Fungi are important to everything from carbon cycling to production of life-saving drugs, including “old-fashioned” wonder drugs such as penicillin, and the new cholesterol-lowering statins and immunosuppresant cyclosporins, which made organ transplants possible. They are also needed for the production of quality-of-life products like chocolate, beer and specialty cheeses, such as brie and gorgonzola.


There are an estimated 1 million to 1.5 million species of fungi; only about 100,000 species have a name. “They are so important in so many ways, and we have so much to learn about them,” Lindner said. “We know the tip of the iceberg.”


Throughout history, discovery has often been about vast spaces, like continents and galaxies. The 1000 Fungal Genome project involves discovery on a tiny scale with vast implications. Strings of genetic code will expand our knowledge of fungi and fine tune our ability to apply them to challenges confronting both forests and people.


KNOWLEDGE


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