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A requiem for the reprint

This is the Friday Afternoon Mycologist

One of my favorite things is a 161 page reprint of a 1929 paper by D.H. Linder published in the Annals of the Missouri Botanical Garden, called “A monograph of Helicosporous Hyphomycetes.” It has a brown paper cover, and when I got it the signatures had not yet been cut; the book had never been read or used. With wonderful drawings grouped at the back, it is a relic of a different time. The title part of the cover of Linder's monograph It was published by the author’s institution, before scientific publishing was a big commercial concern. Over the years, I have seen many copies, some with the original paper cover, many rebound, some immaculate, others obviously heavily used, some autographed by the author. Imagine Dr. Linder receiving reprint request cards (no one would have dared use his first name) and responding with this impressive tome. Imagine getting this present in the mail, months after requesting it. Unlike most mycological books published today, Linder’s monograph was an original work, not a recapitulation or review of work published elsewhere. It was not carved into twenty smaller papers. And perhaps surprisingly, it is still useful today and is cited regularly.

I got it when I was an undergrad, and an elder colleague let me loose in his filing cabinets to remove reprints that interested me. There is nobody greedier than someone who has decided to start a reprint collection. At first, any reprint will do, even something from an unrelated field. It takes time to become discerning, to know immediately what might be useful, and what will only take up space. My reprint collection became a gluttonous monster that had to be hauled along whenever I moved. By some phagocytotic process, it absorbed several other collections from retirees and grad students who abandoned science. Now, the collection is confined to two filing cabinets, but inserting new reprints requires prying apart existing folders and cramming the new paper in… surely someone has invented some kind of special tool for this.

A plate from the Linder monographOnce you have more than 20 reprints, organization is required. Most scientists file the papers by author, which is fine if you easily remember people’s names. The maintenance of the index card catalogues associated with many reprint collections consumed many hours, typing on manual typewriters, cutting and pasting in the old fashioned, pre-computerized way. My old office had a secretary’s nook just outside. In the old days, almost every scientist had a secretary, who counted among her tasks the filing and mailing of reprints, and the maintenance of the index card reprint catalogue. Lacking my own secretary, who would intuitively know how to do these things, I tried many experimental organizational systems for my reprint collection. Eventually, the collection reached a size where any further resorting was impractical. If something wasn’t in the expected place, there were always several other files to check. Misfiled papers showed up eventually, tucked away in the wrong file following some cryptic logic.

Sending and receiving reprint requests was a solemn ritual. Postcards with preprinted return postage labels were beyond the financial means of the average graduate student, and far too impersonal. We addressed our cards by hand, and transcribed the entire citation of the article requested. It was unthinkable to write “et al.” instead of the whole list of coauthors. Omitting the title was a sacrilege. And when the reprints finally arrived, usually addressed to Dr. FAM (although I had no such credentials), there was always a guilty thrill… should I write back and tell them?

Photocopies were never as satisfying as real reprints. For one thing, we had to pay for our own photocopies. Each grad student had a counter that plugged into the photocopier. We became adept at the subtleties of page reduction and squashing two pages onto one, before photocopiers did this automatically. Each page was 5 cents. For anything longer than five pages, a real reprint saved money, not to mention the infinitely higher aesthetic quality.

As photocopiers became cheaper and better, reprints started to disappear. A colleague told me that when photocopies became affordable, scientists stopped reading, planning to do that “later.” As The World’s Funniest Mycologist put it, he felt like his PhD should stand for “Doctor of Photocopying”.

We now live in a paperless scientific society and the pdf file rules the day. My laptop is crammed with them, most of which I have never read and probably never will. Now I have my own research budget but don’t spend money buying reprints or on postage to send them out (although journals try to sell me pdfs of my own work at laughable prices).

I’ve even got Linder’s 1929 monograph in pdf form. But who can be bothered to open this monster when the original thing sits on the bookshelf, still ready to serve?

First Annual Blogger Bioblitz in Ithaca

Blogger Bioblitz logoDespite the snowy weekend to come, Spring has come to Ithaca, and Ithacans are itching to get outside. In that spirit, the Cornell Mushroom Blog announces our participation in the First Annual Blogger Bioblitz. Jeremy Bruno of The Voltage Gate conceived the idea, and he challenges science and natural history bloggers to sign up in honor of National Wildlife Week. It took a little goading from Dan (fellow-Ithacan and Migrations blogger), but now we’re on board.

On April 28 2007 I’m convening a group of naturalists, biologists, and biodiversitologists (both amateurs and professionals) to complete a one-day bioinventory of a handy 5 acre patch of Ellis Hollow (just east of Ithaca, New York). The point of a Bioblitz is to see how many different species we can find in a single day, not omitting the small and interesting things. April isn’t a great time for fungi, but I’m sure we’ll find some, as well as some charismatic megafauna, creepy crawlies, and leafy green things. We’ll also get to know each other a bit, transcending our taxonomic biases. Our data will join those generated by a growing community of bloggers across North America.

If you’re in the Ithaca area and you’d like to participate on April 28, contact me for details.

The lovely Blogger Bioblitz graphic was created by Jenn of the Invasive Species Weblog.

An adventure with Omphalotus

I was wandering through the Fall woods near Ithaca, New York when I stumbled upon what looked like a delicious surprise. Growing from a stump in the middle of the woods was what appeared to be a giant bunch of delectable chanterelle mushrooms. I greedily picked the entire clump, which must have weighed at least 5 pounds. The mushrooms smelled slightly fruity and inviting, and I was excited to bring them home and fry them up. However upon closer inspection (and the observations of a trained mycologist), I realized that I had made the amateur mistake of confusing the tasty Chanterelle with the poisonous Jack O’Lantern mushroom Omphalotus illudens.1

A clump of poisonous Jack O'Lantern mushrooms

The Jack O’Lantern is a mushroom of note in mycological circles largely for two reasons. First because of the tendency for mushroom hunting novices to mistake it for a Chanterelle (and consequently become quite sick for a day or so) and second because of the mushroom’s unusual ability to bioluminesce (glow in the dark).

The tendency for people to confuse the Chanterelle with the Jack O’Lantern is understandable because of their similar color and general appearance. Both are some shade of yellow-orange (more orange than yellow for Jack O’Lanterns), and both have decurrent gills that ease their way down the stalks. However the mistake can be quite uncomfortable as Jack O’Lanterns induce painful stomach cramps, diarrhea and vomiting. The symptoms pass within a day or two, but are pretty awful and most victims end up in the emergency room. Checking for several key characters can save you from confusing the two mushrooms. First, Chanterelles grow singly on the forest floor, whereas Jack O’Lanterns grow on rotting wood, usually in distinct clumps (tricky if the clump is small, or the wood is a buried root). Secondly, the gills of the Jack O’Lantern are clearly defined and have sharp, thin edges, whereas the gills on Chanterelles are blocky or fat or at least not so sharp.

The Jack O’Lantern’s ability to create luminescence is another factor which makes the mushroom interesting to mycologists (and anyone else who likes things that glow in the dark!). The specific molecules responsible for the glow of Jack O’Lanterns haven’t been characterized yet, and why a mushroom might bother to glow at all is another unanswered question. We took a long-exposure photo of my clump of mushrooms, revealing the yellow-green glow of their gills. To see the glow in real time, locate a living clump of Jack O’Lanterns, and sit with them in the woods on a dark night. Give your eyes 5 or 10 minutes to adjust (that’s how faint it is).2 Don’t rely on the glow to distinguish Jacks from Chanterelles, because it fades after the mushrooms are picked, and, as Michael Kuo can tell you, it can be hard to see.

Jack O'Lantern mushrooms glowing in the dark


Jack O'Lantern mushrooms in the light


Editor’s Notes

  1. Jack O’Lantern poisoning is my most common mushroom poisoning call here in the Northeast. Happily, it tends to pass without any lasting effects.
  2. A couple of years ago, I went out at night to sit with a clump of jack o’lanterns around a stump in my neighbor’s lawn. It took about 10 minutes for my eyes to be able to make out the glow. During that time, I counted shooting stars, meditated on the answer to the ultimate question (42), and listened to night sounds. Among those sounds was a persistent shushing, coming from all around me. When I had basked long enough in the glow and switched on my flashlight, I found I was surrounded by hungry giant slugs, slithering softly through the grass as they homed in on the Jack O’Lanterns, which apparently don’t upset slug tummies at all.

Photos by Kathie Hodge (in the field) and Kent Loeffler (glow/no glow). Kent explains that the long exposure (5 minutes) needed to capture the groovy glow results in a snowy effect when using a digital camera.

The fungus in my maple syrup

Last week an uninvited guest showed up for breakfast. As I poured maple syrup over my son’s waffle, Plop! A perfect dime-sized fungus colony spilled out to crown that waffle like a malevolent pat of butter. The maple syrup had been sitting out, unrefrigerated for, um, quite a while.

A cup of maple syrup (yum), with Wallemia sebi colonies (yuck)

A 10 cm custard cup of maple syrup, with guest (click for a closer look)

What would you do? I asked my 4-year-old whether he could touch his nose with his tongue, and used mommy stealth to swiftly replace the contaminated waffle with a new one (with honey on it). Crisis averted. Finally, and I’m sure you would’ve done the same, I packed up the offending maple syrup for a rendezvous with my microscope. Sometimes uninvited guests turn out to be pretty darned interesting, if you take the trouble to get to know them.

A fungus that can grow in maple syrup is not your average everyday mold, it’s a xerophile. Xerophiles grow in places that are too dry and hostile for your average fungus. OK, maple syrup is wet, but it’s also extremely high in sugar. All that sugar has the effect of pulling water out of cells, and the vast majority of fungi can’t grow in maple syrup at all. No matter how much they might like it in smaller quantities–the water in maple syrup isn’t “available” to them.

Water activity (aw) is a measure of “available water.” Water itself has an aw of 1.0 (all the water in water is available!); for dried milk powder aw=0.2 (hardly any water is available). To protect food from spoilage by molds and bacteria without refrigeration, you want to reduce water activity below 0.8. You can do that by drying out the food, or brining it with either a high salt or a high sugar treatment. According to this site, maple syrup typically has a water activity of about 0.87 to 0.88, pretty hostile to most molds. Only a few xerophiles can live in it,1 including our surprise guest, Wallemia sebi.

Wallemia sebi busily making spores. The scale bar is 5 µm long.

What a handsome fungus! Wallemia sebi is a xerophilic mold that specializes in growing on things of low water activity, like dried fruits and jams, and salted meats and nuts. It grows in salterns (the evaporating beds in which sea salt is produced), and its bumpy little spores are found fairly often in indoor air.

A nice study by Zalar and colleagues2 reveals that Wallemia is a distinctly weird mold. It’s so weird, and so distantly related to most other molds, the authors erected a whole new class of fungi just for it, class Wallemiomycetes. Within this entire class there are only three species, Wallemia sebi, W. muriae, and W. ichthyophaga. Just for reference, you and I and my dog and almost every furry creature in the world are Mammals–that’s a class too.

The Wallemiomycetes are distantly related to the usual xerophilic suspects, Aspergillus and Penicillium. In fact, they’re distantly related to just about every other fungus we know. Zalar et al. found that they’re out there by themselves on a very long evolutionary branch. They emerged very early, just as the major basidiomycete groups were evolving. It’s hard to imagine Wallemia as a basidiomycete, because it has never been seen make a sexual fruiting body, and that’s how most basidiomycetes are classified. Mysterious and beautiful, that’s Wallemia.

A lot of people think that a mold is a mold is a mold, but that’s just not so. The mold that’s rotting your lemon is not the same one that’s growing in your maple syrup, or eating your strawberries. In fact, your lemon, maple, and strawberry molds each belong to a different phylum of fungi. Proust said it:

The real voyage of discovery consists not in seeking new landscapes but in having new eyes.

What happens if you leave your maple syrup out for way too long


  1. To avoid moldy maple syrup, producers heat-sterilize it before selling it to you. Once you open the bottle, the fridge is your friend. The fridge doesn’t change the aw, but the low temperatures in there slow or stop the growth of most fungi. By the way, fake maple syrup resists molds through the miracle of chemical preservatives (usually sodium benzoate and sorbic acid). You don’t use fake maple syrup, do you?
  2. Zalar, P., G.S. de Hoog, H.-J. Shroers, J.M. Frank, N. Gunde-Cimerman. 2005. Taxonomy and phylogeny of the xerophilic genus Wallemia (Wallemiomycetes and Wallemiales, cl. et ord. nov.) Antonie van Leeuwenhoek 87: 311-328.
  3. ERRATUM: When I first wrote the article, I overlooked an important new publication on Wallemia (thanks, Else). It sheds a little more light on Wallemia’s relationships, and includes a thorough discussion of Wallemia’s strange characteristics. Here’s the citation: PB Matheny, JA Gossmann, P Zalar, TKA Kumar, and DS Hibbett. 2006. Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota. Can. J. Bot. 84: 1794-1805.

Thanks to Kent Loeffler, who took the photos of Wallemia growing in little 10 cm custard cups full of maple syrup.

Mystery liverwort fungus, chapter 5

This is the Friday Afternoon Mycologist

New to the Mushroom Blog? Check out the FAM’s earlier installments, which lay out the taxonomic process for all to see:

  • chapter 1, in which we meet the FAM and the fungus on his liverwort
  • chapter 2, in which the liverwort fungus is found to be vexing
  • chapter 3, in which we meet Molecule Man and a sheep
  • chapter 4, in which we take aim with the big gun of DNA forensics

Eventually, you have to stop studying your own fungus, and start looking at fungi found by other people. If a first scan of the literature doesn’t give a match for morphology or cultures, and the DNA sequences don’t get the answer, you have to examine other species, other cultures, and generate new DNA sequences of potentially related fungi. Sensible people stop at this point. But this is the frightening bridge you have to cross when you stop playing at identification, and begin scientific, taxonomic study. Whatever the liverwort fungus is, it sits in taxonomic mist. To describe a new species and genus now would just thicken the fog. We need to dive deeper into history, and find specimens left behind by previous mycologists.

Recently, we were introduced to the Cornell Herbarium and the surprising things sometimes found in such institutional collections of dried specimens. When I was a grad student, I had the chance to examine many specimens from a different herbarium that must remain anonymous, made by a scientist who must also remain anonymous. I couldn’t find anything on these dried twigs and leaves, but my feelings of ineptitude lessened when a colleague told me that this particular mycologist was an obsessive-compulsive confined to a lunatic asylum following a Significant World Conflict. He was allowed into the garden for an hour every week to collect fungi but had no microscope and his keepers only allowed him paper that he could fold into herbarium packets. So he pretended to find and identify fungi, and the specimens are preserved for posterity in a Significant International Collection. They are borrowed mostly by naïve graduate students; everyone else knows better.

The Friday Afternoon Mycologist must bare his soul here. I skipped over the sooty moulds too quickly last December, hoping for an easy answer. Now is the time to reconsider some neglected fungi, starting with something called Microxiphium. Probably fewer than ten living people have seen the type species of this genus, M. footii,1 and known what they were looking at. The existing illustrations are rather cartoonish, so it is hard to guess whether it might be a close relative of the liverwort fungus. In the herbarium of my home institution, there are many specimens of this species. I rehydrate a bit of one specimen to make it easier to make a slide, using a wet piece of KimWipe (a highly scientific lab tissue perhaps invented to deal with a particularly messy baby named Kim). Micromycologists have many gadgets for making slides.2 Today’s tool was a gift from a student, a tiny diamond-shaped blade designed for eye surgery, and with it, it is easy to scrape up the dark needle-like structures of M. footii jutting out of the Rhododendron leaves.

Microxiphium footii is not the liverwort fungus

So here’s Microxiphium footii. The main feature of this fungus is the dark, thick-walled central spine that runs up the middle of the hyphal bundle, something lacking in the liverwort fungus. The little round cells near the top are apparently the cells that make the spores rather than the spores themselves. Despite a lot of slide making, I cannot find any spores. But the spore-producing cells of the liverwort fungus are cylinders, not round. So M. footii is very different from the liverwort fungus, and this is certainly not a genus for our fungus.

But there’s a trick. Other species of Microxiphium have been described, and an inconsistent concept was applied as species were added. Some species are hyphomycetes, other coelomycetes, others even sexual Ascomycetes. What’s more, the generic name is spelled in two different ways, with Microxyphium the alternative, and sometimes these are treated as distinct genera rather than different spellings. Perhaps somewhere in this mess of about 42 described species, lies the liverwort fungus. The only way to find out is to sort through all the descriptions, all the literature, and try to eliminate as many species as possible on the basis of reliable reclassifications and existing illustrations. We know the spore size and shape for our fungus… these are characters that are difficult to get wrong. For the remaining species, it will be necessary to try to find specimens for comparison. Rather than try to revise (i.e. re-describe and re-illustrate) everything, I will just move on looking for our fungus. But I’m not optimistic. Just stubborn.

  1. Microxiphium footii has as its sexual state something called Dennisiella babingtonii, but we don’t need to worry about that because we are interested in things asexual.
  2. One famous mycologist told me he used his own thick eyebrow hair, mounted in metal handles, to remove delicate structures from specimens. Jewelers’ forceps are wonderful for tearing tiny structures off twigs and leaves, but the tools are aerodynamically designed to fall to the floor, where they always land on the very soft tips… I have many pairs with gnarled ends, and sometimes when I am bored or frustrated, I try to fix them (LAUGHTER).Mangled tips of fine forceps, the detritus of half a career

Daisuke Goto – The first to cultivate mushrooms in Samoa

For my winter vacation and to escape the cold of Ithaca, I visited my mother in Samoa. She is a pharmacist who is doing volunteer work there through an organization called Japan International Cooperation Agency (JICA). JICA is analogous to the American Peace Corps — they send volunteers to less developed countries to help with economic and social development (JICA, 1995).

Where is Samoa?Samoa (formally The Independent State of Samoa) is located in the South Pacific just east of the International Date Line and north of New Zealand. The country comprises two main islands and eight smaller islands with a total land area of 2934 km2 and a population of approximately 180,000. Samoa was, famously, the adopted home of Robert Louis Stevenson, author of Treasure Island and other novels. (Map courtesy of the Samoa Tourism Authority, 2005).

Before I got there, my mother had told me of a man who had come to Samoa to develop mushroom cultivation as a means of generating local income. Since I am interested in mushrooms, the idea sounded interesting, and I asked her to arrange a meeting with the volunteer during my stay. The volunteer, Daisuke Goto, was very kind to take me on a tour of his facilities on Upolu and tell me about his project.

Bags of colonized fruiting substrate; jars of spawn


The project was initiated by the Chinese government in 1999, but as they failed to produce mushrooms, JICA came to the rescue and has been involved since 2001. The first JICA volunteer was also unable to produce mushrooms, but Daisuke, who came next, has succeeded in producing the first cultivated mushrooms in Samoa. Daisuke says, “This has taken way too long!” Daisuke’s goal in Samoa is to establish a mushroom cultivation protocol and to transmit mushroom-growing skills to local farmers.

Daisuke Goto's poster to teach locals about mushroom cultivation in Samoa

click for a larger view

It turns out that growing mushrooms in Samoa is not as easy as you might think. The hot tropical climate is hard on mushrooms, and few conventional substrates are available locally. Farmers lack elaborate laboratory facilities with cooled growth chambers, and grain and hardwoods generally used for mushroom cultivation are not grown in Samoa. Daisuke has overcome these obstacles with his creative ideas. Rather than cultivating the common oyster mushroom, Pleurotus ostreatus, he uses P. pulmonarius, an oyster mushroom more tolerant of higher temperatures. Other species he has had success with are Auricularia polytricha (wood ear mushroom), Ganoderma lucidum (reishi), and Pleurotus citrinopileatus (golden oyster mushroom). The Auricularia and Ganoderma strains he is using were found in the native forests of Samoa, and other cultures have been sent from Japan. Daisuke has also experimented with Lentinula edodes (shiitake), however, he has found that the climate and available substrates limit its production.

Mana's mother outside the mushroom hut in SamoaDaisuke’s predecessor dug out a big hole and built an underground hut with the idea that mushrooms might grow better where it is cooler. At right is Mana’s mother with the mushroom hut. Unfortunately, Daisuke has found that there is not enough light in the hut for fruiting and some watering is required. He still has some ongoing experiments in there using Auricularia and Pleurotus when there is too much rain outside.

Spawn is typically made from inoculated grain, but grain is not produced on Samoa, so Daisuke uses sawdust from a native broadleaf lumber tree, the Kava tree. In case anybody is confused, this is not the same Kava (Piper methysticum) that people make into mind-altering drinks! He also tried using coconut meat pressings, but says the sweet smell attracts mice and cockroaches, so he has had to stop using it. Kava sawdust works well for generating spawn but results in poor fruiting when used as substrate material. Therefore, for the fruiting substrate, Daisuke has come up with an interesting recipe that calls for mowed weeds and beer waste at an 8:1 ratio. Weeds are abundant everywhere and Samoans have a large beer industry relative to the size of their country (a legacy of German colonization). Thus, these materials are easily accessible and, better yet, free. You may wonder where the barley for beer comes from–in fact, it is imported. The substrate is packed in autoclavable bags with filter patches and sterilized in a pressure cooker, because large autoclaves are not available. Then, a hole is made in the middle of the substrate and inoculated with the spawn. Spawn production and spawn run takes place indoors, but fruiting takes place outdoors. Daisuke takes the colonized substrate bags out under the trees and makes good use of the highly humid climate and natural shade for fruiting. He said the mushrooms fruit better outdoors—the only problem is that now he is in competition with the slugs.

Daisuke with his fruiting blocks planted in a shady grove


Big oil drum used to pasteurize fruiting substrateIn this way, Daisuke has established a standard protocol that the local people can follow to cultivate mushrooms. His next step is to scale up the production and teach the farmers how to do it. One problem he faces is the inability to mass sterilize using the pressure cooker and the high costs of the autoclavable bags. He is currently experimenting with using a large oil drum to boil and pasteurize the fruiting substrate.

The word for mushroom in Samoan is “pulou aitu” where “pulou” means “hat” and “aitu” means “ghost.” Despite the mycophobic sound of the word, Daisuke says that the local people are optimistic about accepting mushrooms as a new food source. With Daisuke’s perseverance, the project looks promising and will be interesting to follow up on. I could go on bragging about the beautiful snorkeling and diving Samoa had to offer as well, but I guess I will stop here, because my vacation is complete as long as I see mushrooms!

Acknowledgment

Daisuke Goto with the author, Mana OhkuraI am very grateful to Daisuke Goto for his time and effort to show me around the facilities and tell me about his project. In addition, his frequent correspondence has been very helpful in answering the many questions that kept arising as I wrote this post.

When strawberries go bad

Rhizopus stolonifer is an awesome mold. You’ve probably seen it before, on the peaches in your fruit bowl, or on your bagel, or (hopefully not) attacking your body. It’s a versatile and ubiquitous thing, and it makes great hairy colonies that grow astonishingly quickly.

Here is it causing a post-harvest disease of strawberries. You’re seeing seven days of growth and subsidence.

Quicktime 5+ movie

Time lapse video of delicious strawberries inoculated with the evil mold Rhizopus stolonifer by Kent Loeffler.

The little hairs that seem to be clawing their way up are the sporangiophores. If you squint a bit you can almost see a little grey pinhead (sporangium) atop each one. Those pinheads are filled with fungal spores, each hoping to find its very own strawberry.

  • DoctorFungus has a good discussion of Rhizopus spp. implicated in nasty, invasive human disease (zygomycosis). In general, don’t worry about catching a fungal infection from rotten fruit. However, if your immune system is not working right because of HIV or immune-suppressing drugs, be wary of fungi.
  • Rhizopus oligosporus, a friendlier cousin of the strawberry mold, is used to produce tempeh. You know, tempeh, that meat-like substance made from fermented soybeans. Buy some from your local grocer or health food store and stir fry it up for dinner.
  • The strawberries? No, don’t eat them once they’ve become hairy.

Mystery liverwort fungus, chapter 4

This is the Friday Afternoon Mycologist

New to the Mushroom Blog? You’ll want to catch up on our earlier FAM installments, because it’s becoming clear that something exciting is happening. Maybe something new is being discovered…

  • chapter 1, in which we meet the FAM and the fungus on his liverwort
  • chapter 2, in which the liverwort fungus is found to be vexing
  • chapter 3, in which we meet Molecule Man and a sheep


Big news! Molecule Man got lucky with the DNA!

As you recall, we took a pinch of dead liverwort tissue with structures of our fungus and sacrificed it to a DNA extraction kit. From there it was mixed with enzymes, shaken up, spun down, extracted, precipitated, suspended, dissolved, electrophoresed and subjected to the most wonderful of biochemical reactions, the polymerase chain reaction (PCR).

Molecule Man used PCR to amplify two adjacent bits of DNA, specifically the ‘small subunit of the nuclear ribosomal DNA’ (SSU, often also called the 18S) and its neighbor, the ‘internal transcribed spacer’ (ITS). He was successful in amplifying DNA from two of the three samples, and both the SSU and ITS were successfully amplified in at least some of the samples.

A diagram helps sometimes.  Good science always rhymes.

The bands on this agarose gel mean PCR successPCR is usually the tricky part, so we’ve done well to have PCR products that we can try to sequence. DNA sequencing involves more enzymes, shaking, spinning, precipitating, suspending, dissolving, and another mysterious biochemical reaction, and then the passage of the resulting solution through a long, thin column in an automated DNA sequencer. The resulting multicolored pattern of peaks and valleys represents the sequence of bases in the DNA fragment. After some editing with software, the DNA sequence emerges as a series of the letters A C T and G.

Output from the DNA sequencer: Peaks of different colours=different bases

Molecule Man was successful in getting two different SSU sequences, but the ITS sequences failed.

Read more

Something funny in the herbarium

There are thousands upon thousands of interesting specimens contained in the Cornell Plant Pathology Herbarium. Every now and then, an extraordinary specimen is uncovered — an apocryphal specimen, if you will.

The suspect label

I was adding data for Aleurodiscus specimens to our database and decided to add the few remaining specimens in the same drawer. When I came to CUP 25787, I found a wonderful surprise. The label seemed ordinary enough; I expected to find a typical Stereum specimen in the box.

Instead, I found the unexpected (below). This is, of course, a joke. Stereum is a genus of bracket fungi with a smooth undersurface lacking gills or pores. The epithet “seashellia” gives away the actual identity of the specimens in the box. And Fagus is the genus name of beech trees (beech. beach. get it?).

A surprise awaits inside the box.


For the specimen to have been accessioned into the Herbarium, Dr. Stewart must have had the cooperation of H.H. Whetzel or H.M. Fitzpatrick. In Stewart’s obituary we learn: “He had a pleasant disposition, a well developed sense of humor, and thoroughly enjoyed a good joke, especially when it dealt with human interest or reaction.”

Fred Carleton Stewart was a native of French Creek, New York, who got his BS (1892) and MS (1894) degrees from Iowa State University.1 He was Assistant Botanist of the Iowa Agricultural Experiment Station from 1891 to 1894 where he worked with Professor L. H. Pammel, Botanist of the Station. Stewart’s training with Prof. Pammel strengthened his interest in plant diseases.

F.C Stewart himselfStewart next took the position of Mycologist at the new Long Island Branch Station at Jamaica, New York (Dec. 1894-1897). His main accomplishments there were his field experiments in controlling diseases of potato and market-garden crops, and his demonstration of the bacterial nature of a newly discovered wilt disease of sweet corn. Back then, bacteria weren’t believed to be major causes of plant diseases, and Plant Pathology was a brash new discipline that arose from Applied Mycology. In 1898, Erwin F. Smith dubbed the disease “Stewart’s disease of sweet corn,” and named the causal organism Pseudomonas stewartii. Nowadays, we call the disease “Stewart’s wilt” and the bacterium has recently been renamed Pantoea stewartii to better reflect its affinities. We now know it is transmitted mainly by the diminutive but voracious corn flea beetle.2

After a year off for additional training in plant pathology at Cornell and in Europe, in 1898 Stewart became Botanist and the Head of the Department of Botany of the New York Agricultural Experiment Station at Geneva. In 1923, the Station became part of Cornell University, and Stewart became a Professor of Botany at Cornell. Despite his duties as a plant pathologist, he also managed to publish a handful of papers on edible wild mushrooms and mushroom cultivation.e.g., 3 When he finally retired in 1936 he was granted the distinguished title of Professor Emeritus. Just a year later he sent us a message from retirement–a lovely box of seashells.

We are currently pursuing a rumor that a mustache removed from a Victorian-era mycologist is somewhere in the herbarium. We’re sure Stewart would appreciate the humor in this, even if it turns out to be a scurrilous rumor. We’ll keep you posted.

  1. Fitzpatrick, Harry M. 1947. Fred Carleton Stewart: 1868-1946. Phytopathology 37: 687-697.
  2. Pataky, Jerald K. 2003. Stewart’s Wilt of Corn. APSnet Feature Story, July-Aug 2003. American Phytopathological Society.
  3. Stewart, F.C. 1936. The uncertain Hypholoma. NY State Ag. Experiment Stn. Bulletin 666. [on the edibility of the mushroom now known as Psathyrella incerta]
  4. Stereum seashellia portraits by Kent Loeffler
  5. Photo of F.C. Stewart from the Cornell Plant Pathology Herbarium Photo Archives. CUP 31762a.

Mushroom Fever

Happy shiitake logs on display right here on campus

What does the word fungi make you think of? For many, it conjures up images of athlete’s foot and mold, and not money in the bank. But mushroom cultivation can be a profitable and enjoyable endeavor for those willing to take the time and space to grow edible gourmet mushrooms on their property. Many Ithacans have recently discovered this agroforestry project and are diving in to the world of mushroom cultivation.

Mushroom cultivation has been around for centuries, so the question remains: What is contributing to the recent mushroom craze in Ithaca? What has prompted this sudden fungal fever in upstate New York, an area that has been bursting with mushrooms long before humans inhabited it?

Public education and demonstrations have played a big role, with organizations such as the Cornell Mushroom Collectors, Cultivators, and Connoisseurs Club demonstrating different methods of growing mushrooms to the people of Ithaca.

“It’s a matter of showing people that it’s something that can be done” says Peter Hobbs, a professor in the Crop and Soil Science department at Cornell and an independent mushroom cultivator. “Once somebody interacts with a person who grows mushrooms, they realize it is a viable thing to try and start on their own.”

The demonstrations are having a noticeable affect around town, sparking interest that before circulated only among a select group of mycological enthusiasts.

“I’ve been impressed with how many inquiries we get, and the attendance at extension programs,” said Kenneth Mudge, a Horticulture professor at Cornell, advisor to the Cornell Mushroom Club, and supervisor of the MacDaniel’s Nut Grove Research and Teaching Forest. “The interest is surprisingly big; I certainly think it’s more than it was 6 years ago. I would say it’s quickly growing.”

Mudge was actually responsible for teaching Hobbs how to perfect the art of at-home mushroom cultivation, and he is an example of how the knowledge and interest is spreading around Ithaca.

“I wasn’t successful at first,” Hobbs said, “and then I started helping Ken Mudge with his forest farming class. In it, they teach the students how to grow mushrooms. Apparently there was a few little things my previous instructions had left out, so I did some things wrong. But once I got to where I was successful, my interests were stimulated more. Seeing them grow first, trying myself, and working with people who knew what they were doing, that is how I really got interested.”

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