Tue - February 8, 2005
Mushroom DNA sequences online at NCBI
For the modern biologist who happens to be
interested in mushrooms: There's a treasure trove of taxonomic and DNA sequence
data online. Almost every species that has been described has had at least a few
genes sequenced.
The results are online and freely available at NCBI, where you can also find out about the full classification system by using the "taxonomy" search option. Just another one of the things that PubMed makes possible.
The results are online and freely available at NCBI, where you can also find out about the full classification system by using the "taxonomy" search option. Just another one of the things that PubMed makes possible.
One day as I lamented the challenges of
unambiguous identification of closely related or morphologically similar
species, I wondered whether one could use DNA sequence to make an authoritative
ID.
Of course, this would take a lot of legwork. First, one would have to choose a sequence that was similar enough across all mushrooms that it would be straightforward to sequence it. Fortunately, this is already solved: ribosomal RNAs are the industry standard for this kind of cross-species comparison).
More importantly, one would have to sequence these genes in pre-identified samples, in order to create a reference. This requires the samples themselves and an unambiguous identification, presumably performed by someone else. Hence, I reasoned, this wasn't ultimately a useful approach.
Unless someone else would, you know, go ahead and sequence every mushroom for me.
I was thrilled to learn that this has been done.
Taxonomy searching at NCBI ((choose "Taxonomy" on the pulldown menu) allows a search by full scientific name, genus alone, or indeed any higher-level taxonomic category. Hits are linked to all sequences recorded for the species of interest. So far I haven't found a single species that isn't described.
This is a valuable tool, not just for difficult identifications, but for educating the amateur mycologist about the relationships between various mushroom species.
Also, in the unlikely event that one finds a previously undescribed fungus, a DNA sequence will serve as an important part both of the proof of novelty and in the initial characterization and classification of the species.
P.S.: OK, granted that this requires one to have access to DNA sequencing facilities, but I'm guessing that among those who read this blog, I'm not the only biologist.
Of course, this would take a lot of legwork. First, one would have to choose a sequence that was similar enough across all mushrooms that it would be straightforward to sequence it. Fortunately, this is already solved: ribosomal RNAs are the industry standard for this kind of cross-species comparison).
More importantly, one would have to sequence these genes in pre-identified samples, in order to create a reference. This requires the samples themselves and an unambiguous identification, presumably performed by someone else. Hence, I reasoned, this wasn't ultimately a useful approach.
Unless someone else would, you know, go ahead and sequence every mushroom for me.
I was thrilled to learn that this has been done.
Taxonomy searching at NCBI ((choose "Taxonomy" on the pulldown menu) allows a search by full scientific name, genus alone, or indeed any higher-level taxonomic category. Hits are linked to all sequences recorded for the species of interest. So far I haven't found a single species that isn't described.
This is a valuable tool, not just for difficult identifications, but for educating the amateur mycologist about the relationships between various mushroom species.
Also, in the unlikely event that one finds a previously undescribed fungus, a DNA sequence will serve as an important part both of the proof of novelty and in the initial characterization and classification of the species.
P.S.: OK, granted that this requires one to have access to DNA sequencing facilities, but I'm guessing that among those who read this blog, I'm not the only biologist.
Posted at 10:00 AM
Mon - February 7, 2005
Hobo Joe
Forever an hour ahead of me on every mushroom
walk I've ever taken. Does he ever sleep?
It's a great day for a mushroom hike -- recent
rain but firm ground, sun filtering down through the trees, early morning. The
barely visible trail takes me deep into the woods, into ground that I'm certain
will be perfect for exotic and prized finds.
The trail breaks into a clearing of slightly canted, well-drained but moist ground. The dappled light is so gorgeous I feel like kissing myself. I might be the first person in this clearing in a week. Maybe I'm the first one ever. At least that's how it feels.
And then I see the tracks: two-inch holes in the leaf bed, exposing bare soil and a few thread of mycelium. There's one, there's two, there's...twelve. A little bit of rummaging through the leaves reveals a single sad bolete or maggoty chanterelle, too small for a proper ID, much less for collection. I have to assume that the twelve holes had once been filled with beautiful specimens of the same species. Someone else got to them first.
(It's never long ago: You can tell how long a hole has been in loose soil by tapping the ground nearby. If crumbs of soil settle, then it's only been a few hours. Even the dew cycle overnight will generally cause loose soil to settle. Call me Aragorn.)
We gave him a name, so that we could curse it: Hobo Joe.
Every time, every perfect walking day, he's just ahead, getting the best and most prized specimens. Sometimes he leaves broken stems or caps of imperfect carpophores, just in case we missed the less obvious signs.
I don't know much else about him. He has no life; he never rests; he eats well...
...and he'd better hope I never catch up.
The trail breaks into a clearing of slightly canted, well-drained but moist ground. The dappled light is so gorgeous I feel like kissing myself. I might be the first person in this clearing in a week. Maybe I'm the first one ever. At least that's how it feels.
And then I see the tracks: two-inch holes in the leaf bed, exposing bare soil and a few thread of mycelium. There's one, there's two, there's...twelve. A little bit of rummaging through the leaves reveals a single sad bolete or maggoty chanterelle, too small for a proper ID, much less for collection. I have to assume that the twelve holes had once been filled with beautiful specimens of the same species. Someone else got to them first.
(It's never long ago: You can tell how long a hole has been in loose soil by tapping the ground nearby. If crumbs of soil settle, then it's only been a few hours. Even the dew cycle overnight will generally cause loose soil to settle. Call me Aragorn.)
We gave him a name, so that we could curse it: Hobo Joe.
Every time, every perfect walking day, he's just ahead, getting the best and most prized specimens. Sometimes he leaves broken stems or caps of imperfect carpophores, just in case we missed the less obvious signs.
I don't know much else about him. He has no life; he never rests; he eats well...
...and he'd better hope I never catch up.
Posted at 10:44 AM
Fri - February 4, 2005
Pleurotus ostreatus (Tree oyster)
This arboreal fungus is unmistakable, and a
welcome find on an otherwise soggy day.
Date:
December 2004
Nearest city: Stinson Beach, CA
Local climate: Wooded; coastal
Location: Dead tree trunk
Recent weather: Very heavy rain
On a walk that had uncovered nothing but death caps and rare, waterlogged, maggoty boletes, a tree covered with oysters was a sight for sore eyes.
After oven-drying them overnight (they were a bit damp) we made omelets. This wasn't the best thing for their consistency but they were still delicious.
More Pleurotus ostreatus on the web
- Mykoweb: Fungi of California
- Tom Volk's Fungus of the Month
Nearest city: Stinson Beach, CA
Local climate: Wooded; coastal
Location: Dead tree trunk
Recent weather: Very heavy rain
On a walk that had uncovered nothing but death caps and rare, waterlogged, maggoty boletes, a tree covered with oysters was a sight for sore eyes.
After oven-drying them overnight (they were a bit damp) we made omelets. This wasn't the best thing for their consistency but they were still delicious.
More Pleurotus ostreatus on the web
- Mykoweb: Fungi of California
- Tom Volk's Fungus of the Month
Posted at 09:44 AM
Thu - February 3, 2005
Required gear
Any list of the essential items one must take on
a mushroom walk...
...must include toilet
paper.
Any list that is prioritized by the paradigm "Of what item, if I need it and don't have it, will I most feel the lack?"...
...must start with toilet paper.
You're lucky that I'm not telling you the story.
Any list that is prioritized by the paradigm "Of what item, if I need it and don't have it, will I most feel the lack?"...
...must start with toilet paper.
You're lucky that I'm not telling you the story.
Posted at 09:23 AM
Wed - February 2, 2005
Boletus flaviporus
While I certainly wish I could someday find and
identify an edible bolete, I was still happy to find a few samples of this
beautiful yellow-pored member of the genus.
Date:
January 2005
Nearest city: Berkeley, CA
Local climate: Wooded
Location: Roadside, dense fallen leaves
Recent weather: One week after several weeks of rain
This is a pretty easy ID and I'm just including these pictures because they capture the striking yellow color of the tubes, in the context of the place where the mushroom actually grows:
Here's a close-up:
We took a few home to do a more careful characterization (mostly because we thought they might be something else).
More Boletus flaviporus on the web:
- Mykoweb: Fungi of California
Nearest city: Berkeley, CA
Local climate: Wooded
Location: Roadside, dense fallen leaves
Recent weather: One week after several weeks of rain
This is a pretty easy ID and I'm just including these pictures because they capture the striking yellow color of the tubes, in the context of the place where the mushroom actually grows:
Here's a close-up:
We took a few home to do a more careful characterization (mostly because we thought they might be something else).
More Boletus flaviporus on the web:
- Mykoweb: Fungi of California
Posted at 11:34 AM
Wed - January 26, 2005
Helvella lacunosa (Black elfin saddle)
The "black elfin saddle" out in force in
January.
Date:
January 2005
Nearest city: Berkeley, CA
Local climate: Hillside, near a wood
Location: Berry bramble
Recent weather: One week after several weeks of rain
Unless my hiking partner had known what he was looking for on this particular day (having just been clued in by a French colleague who used to hunt mushrooms in this area), we would have missed these exotic-looking edibles.
The black hood makes this mushroom very hard to spot, and the irregularity of its shape makes repeated spots hard even after you know that you're in an area that has them. Plus, these don't match my intuition about what an edible mushroom "ought to look like" -- I realize this is utterly nonsensical, but there you have it. I would have walked on by.
As it turns out, there were quite a few Helvella lacunosa growing in the area where we found this first one, but they were sparse -- no more than one or two per square meter. The ground in which they grew was fairly well typified by the photo above: lots of dead leaves covering fertile soil in an area that's probably covered by a berry bush during the summer. (It looked like blackberry, but without the leaves or any remnants of flowers and berries it's impossible for us to be sure.)
Since multiple references say that this mushroom likes pine, I want to point out that there were no conifers anywhere to be found.
The black elfin saddle is reputed to be edible, so you'd better believe that we took some home:
We plan to dry them down and use them at some point in the future, after we've accumulated more.
More Helvella lacunosa on the web:
- Mykoweb: Fungi of California
Nearest city: Berkeley, CA
Local climate: Hillside, near a wood
Location: Berry bramble
Recent weather: One week after several weeks of rain
Unless my hiking partner had known what he was looking for on this particular day (having just been clued in by a French colleague who used to hunt mushrooms in this area), we would have missed these exotic-looking edibles.
The black hood makes this mushroom very hard to spot, and the irregularity of its shape makes repeated spots hard even after you know that you're in an area that has them. Plus, these don't match my intuition about what an edible mushroom "ought to look like" -- I realize this is utterly nonsensical, but there you have it. I would have walked on by.
As it turns out, there were quite a few Helvella lacunosa growing in the area where we found this first one, but they were sparse -- no more than one or two per square meter. The ground in which they grew was fairly well typified by the photo above: lots of dead leaves covering fertile soil in an area that's probably covered by a berry bush during the summer. (It looked like blackberry, but without the leaves or any remnants of flowers and berries it's impossible for us to be sure.)
Since multiple references say that this mushroom likes pine, I want to point out that there were no conifers anywhere to be found.
The black elfin saddle is reputed to be edible, so you'd better believe that we took some home:
We plan to dry them down and use them at some point in the future, after we've accumulated more.
More Helvella lacunosa on the web:
- Mykoweb: Fungi of California
Posted at 03:59 PM
Mykoweb
Mushrooms, fungi and mycology -- with lots of
great pictures to aid in identification.
Mykoweb is a treasure trove of information for
the amateur mycologist. The image bank is priceless, especially for those of us
who are doing our hunting in Northern California.
In the author's own words:
In the author's own words:
Welcome to MykoWeb, WWW pages devoted to the science of mycology (the study of the fungi) and the hobby of mushrooming (the pursuit of mushrooms). It is a production of Michael Wood, a past president of the Mycological Society of San Francisco. MykoWeb was started in the fall of 1995 and since then has garnered several web Awards. The biggest attraction at MykoWeb is The Fungi of California, an expanded version of the former "Fungi of the San Francisco Bay Area". The Fungi of California contains photographs and descriptions of over 400 species of fungi found in California (with over 1780 total photographs). Included are links to other online descriptions and photos of the species treated plus references to common field guides. Also included is a Glossary of mycological terms and a Bibliography of useful mycological references. The Fungi of California is a joint project of Michael Wood and Fred Stevens. MykoWeb has republished two books that are mycological treasures, but long out of print in book form. The first appears here as The Boletes of California. This is an online reprint of California Mushrooms: A Field Guide to the Boletes by Dr. Harry D. Thiers. Here you will find keys and descriptions of the 85 species and varieties of Boletes known from California when the book was published in 1975. The Boletes of California was done with the permission of Dr. Harry Thiers and the assistance of Fred Stevens and Michael Boom.
Posted at 03:43 PM
Tue - January 25, 2005
"Shaft"
Who's the baddest of them all? We found this
gorgeous black-skinned mushroom in a hilly wooded area in the East Bay. After
combing through Arora and Simon and Schuster, we came up empty. Does
anyone have any idea what it might be?
Date:
January 2005
Nearest city: Berkeley, CA
Local climate: Sparse woodland, hillside
Location: Amidst the leaves
Recent weather: One week after several weeks of rain
As we tramped through a shady but sparsely treed hillside, we stumbled across these black beauties. Since we'd been finding the black elfin saddle (Helvella lacunosa) all over the place on the same day, I initially thought I was finding large versions of the same. An only slightly closer inspection revealed that I was being silly -- other than the black color, they're totally different.
These mushrooms have deeply bladed gills and a smooth stalk. The skin is a glossy black.
We took one home for further study. Upon getting it on the table for closer inspection, we noticed that the flesh of the stipe is quite fibrous, and splits apart quite easily. Furthermore, the flesh of the mushroom is greyish-white, with the black color limited to the outermost "skin". The gills are quite "tall" (they go up all the way to the skin on the cap) and are the same gray-white in color, except for the edges, which are black. The flesh has a tendency to stain yellow, especially in the cap.
We tried working a few keys but came up empty. If you know what this mushroom is, feel free to drop me a line.
Nearest city: Berkeley, CA
Local climate: Sparse woodland, hillside
Location: Amidst the leaves
Recent weather: One week after several weeks of rain
As we tramped through a shady but sparsely treed hillside, we stumbled across these black beauties. Since we'd been finding the black elfin saddle (Helvella lacunosa) all over the place on the same day, I initially thought I was finding large versions of the same. An only slightly closer inspection revealed that I was being silly -- other than the black color, they're totally different.
These mushrooms have deeply bladed gills and a smooth stalk. The skin is a glossy black.
We took one home for further study. Upon getting it on the table for closer inspection, we noticed that the flesh of the stipe is quite fibrous, and splits apart quite easily. Furthermore, the flesh of the mushroom is greyish-white, with the black color limited to the outermost "skin". The gills are quite "tall" (they go up all the way to the skin on the cap) and are the same gray-white in color, except for the edges, which are black. The flesh has a tendency to stain yellow, especially in the cap.
We tried working a few keys but came up empty. If you know what this mushroom is, feel free to drop me a line.
Posted at 10:02 AM
Thu - January 6, 2005
Mycological Society of San Francisco
A great resource for the Northern Californian
mushroom hunter.
(I detest blogrolls, which is why I'm making an
entry for every link that I think is worth linking
to.)
Events, recipes, nice pictures and a veritable fungal cornucopia of other stuff can be found at
Mycological Society of San Francisco
I find a couple of things about the organization of the pages a little annoying (it's impossible to link to sub-pages, so I can't sic Google Alerts on their Events page), but it's generally a well-designed and informative site.
Not a whole lot of information about the challenges of identification, but then, that's why we started Mycoblog.
Events, recipes, nice pictures and a veritable fungal cornucopia of other stuff can be found at
Mycological Society of San Francisco
I find a couple of things about the organization of the pages a little annoying (it's impossible to link to sub-pages, so I can't sic Google Alerts on their Events page), but it's generally a well-designed and informative site.
Not a whole lot of information about the challenges of identification, but then, that's why we started Mycoblog.
Posted at 10:03 AM
Wed - January 5, 2005
Gymnopilus spectabilis
The "big laughing mushroom" of Japan, found
en
masse near a lake in the East
Bay.
Date:
November 2004
Nearest city: Hayward, CA
Local climate: Riparian woodland
Location: Base of a living tree
Recent weather: Relatively dry
We found this large cluster (~2-3' across) in a low-lying area near the bottom of a steep valley. The host tree appears to be alive and well.
The largest of these caps is probably 10" in diameter:
Note, in the pictures above and below, the huge quantities of bright orange spores that have been dropped on the wood and soil surrounding the base of the tree:
The ID:
Per David Arora's Mushrooms Demystified:
I can't remember just now how we stumbled over the initial idea that it was Gymnopilus to begin with. Once you see it, though, it's hard to forget.
More Gymnopilus spectabilis on the web:
- Mykoweb: The Fungi of California
Nearest city: Hayward, CA
Local climate: Riparian woodland
Location: Base of a living tree
Recent weather: Relatively dry
We found this large cluster (~2-3' across) in a low-lying area near the bottom of a steep valley. The host tree appears to be alive and well.
The largest of these caps is probably 10" in diameter:
Note, in the pictures above and below, the huge quantities of bright orange spores that have been dropped on the wood and soil surrounding the base of the tree:
The ID:
Per David Arora's Mushrooms Demystified:
CAP 5-40 cm or more board, convex becoming broadly convex or nearly plane; surface dry...bright yellow-orange to yellowish-buff when young...often somewhat darker in age (rust-orange to holden-tawny to orange-brown or reddish brown).,.SPORE PRINT bright rusty-orange
I can't remember just now how we stumbled over the initial idea that it was Gymnopilus to begin with. Once you see it, though, it's hard to forget.
More Gymnopilus spectabilis on the web:
- Mykoweb: The Fungi of California
Posted at 10:08 AM
Sat - January 1, 2005
Launch Entry
"To boldly go out into damp fields, find and
identify fungi, and quite possibly eat
them."
Ten bucks and a free T-shirt to the first person who can translate that into graceful Latin.
Ten bucks and a free T-shirt to the first person who can translate that into graceful Latin.
Largely as a result of the near-spastic energy
and logistical legerdemain of my friend and former colleague Jess Leber,
I've been out mushrooming a few times in the past few months. (Despite the fact
that we both used to be yeast biologists, our love of fungus is mostly culinary
and secondarily aesthetic, rather than strictly scientific -- certainly it's
true that some of the fungi of scientific interest have lousy, even frightful,
reputations.)
It's been a lot of fun: There's something very peaceful about going into the woods and looking for the subtle quiet things of the world, what one famed mycologist calls All That the Rain Promises.
After we go out, we return home to look at our digital pictures and the occasional sample that we take with us. I've been amazed by the challenge of identifying the mushrooms that we find -- even with the use of excellent books and the (dubious) intellectual power of two biology Ph.D.'s, we can identify far less than half of what we find.
So the idea for Mycoblog emerged largely as an idea about how to train people (meaning, mostly, ourselves) about how to identify mushrooms. My plan is to post images of the mushrooms we find, along with descriptions of the locations in which we find them, and share our thoughts with the sprawling mycological blogosphere. If you think we could do a better job of making ID's, let us know.
Eventually, we hope to have forums up, so that readers can publicly post about images and discuss issues pertaining to amateur mycology and mushroom identification.
The ultimate dream is to move to a real server and set up a system that would allow users to post their own images -- even from the field -- and benefit from the expertise of the world mycological community.
But, you know, baby steps.
It's been a lot of fun: There's something very peaceful about going into the woods and looking for the subtle quiet things of the world, what one famed mycologist calls All That the Rain Promises.
After we go out, we return home to look at our digital pictures and the occasional sample that we take with us. I've been amazed by the challenge of identifying the mushrooms that we find -- even with the use of excellent books and the (dubious) intellectual power of two biology Ph.D.'s, we can identify far less than half of what we find.
So the idea for Mycoblog emerged largely as an idea about how to train people (meaning, mostly, ourselves) about how to identify mushrooms. My plan is to post images of the mushrooms we find, along with descriptions of the locations in which we find them, and share our thoughts with the sprawling mycological blogosphere. If you think we could do a better job of making ID's, let us know.
Eventually, we hope to have forums up, so that readers can publicly post about images and discuss issues pertaining to amateur mycology and mushroom identification.
The ultimate dream is to move to a real server and set up a system that would allow users to post their own images -- even from the field -- and benefit from the expertise of the world mycological community.
But, you know, baby steps.
Posted at 10:06 AM