Thursday, January 3, 2013

Numbers of Fungi

The part of my brain that deals with numbers is quite well-developed (in contrast, some would say, with other more important areas).  (Though some physicists suggest that the Universe is actually made up entirely of numbers). However, I am grateful that it didn't decide to turn me into an accountant.  At least I get to play with numbers of my own choice.  I also decided, a long time ago, to play with fungi.  So today’s blog melds the two. 

Numbers of Fungi

How many fungi exist on Earth?  We don’t know, since we have so far described only about 100,000.  That may sound like a fairly big number, and it does represent a lot of work, as I can attest from having been involved in describing about 300 of them for the first time.
However, a comparison of the numbers of plants and fungi in the British Isles suggests that there are about six times as many fungi as plants.  Since there are about 250,000 plants in the world (they are big enough to see and we have searched for them pretty thoroughly) there should be about 1.5 million fungi.  We were more or less happy with that estimate, despite the mountain of work that lay before us in describing them all.  Then rapid means of sequencing loose DNA lying about in the environment came along.  Now if we sequence what is in, for example, a rain or soil sample, we will obtain about 20 times as many kinds of fungal DNA as there are culturable specimens  This changes the arithmetic, suggesting that there may actually be as many as 30 million fungi, most of them unculturable, so for all effects invisible.
Well, that’s fungal astronomy.  Now for some more down-to-Earth studies.  A few of us have been listing fungi found in a forested mountain park (John Dean Provincial Park) just behind where I live.  We have so far found just over 300 mushrooms and other fungi, including the one shown below, which is a colourful species of Nectria.  We brought a sample home and I photographed it through my dissecting microscope with my Galaxy Android phone (Now, there’s a relatively new phenomenon for you).

If you look carefully, you should be able to see the little apical point on each perithecial ascoma, which is where the ascospores are shot out.

Another less local study was 5-year attempt to produce a catalogue of the fungi of Haida Gwaii (formerly known as the Queen Charlotte Islands), an archipelago of the west coast of Canada.  This study produced a list of 615 species.  This number was limited by weather and funds, which permitted access to the Islands only in certain months of the year, and limited our over-all number of collecting trips.

Nevertheless, the study showed clearly some differences between the mycota of the Islands and the Mainland.  These differences may have been accentuated by the fact that such trees as the Arbutus, true firs and Douglas fir don’t grow there.

Now, moving close to home again, two distinguished local Botanists, Oluna and Adolf Ceska, who happen to be a couple, have been collecting fungi on another nearby forested hill called Observatory Hill just north of Victoria.  They have so far, over seven years, and about 200 visits, compiled just over 1100 species, including some rare and undescribed taxa. 

Next time I will discuss the periodicity of fungal fruiting, as revealed in these and other studies.

Sunday, October 21, 2012

We have just come to the end of a two-month drought on our island. We were very worried about the fire risk in the old-growth forest on the mountain. The first picture shows how the so-called Emerald Pool in the forest had shrunk to a puddle. But in our driveway, things were very different, as the second picture shows - our well continued to overflow, apparently being fed by an inexhaustible aquifer. 

So we were able to water our garden liberally throughout the drought, knowing that if we didn't use the water, it would just flow into the ocean.  An interesting contrast. From now on we have to persuade the excess water to flow into our creek, (which never dries up either).

Thursday, September 6, 2012

Correlation and Causation

These are not words most of us use every day (unless we are scientists, that is).

I recently read a fascinating news item telling me that people who had cataract operations were less likely to break their pelvis.

Now, one could spend time trying to find a physiological link between the replacement of cloudy lenses in the eye and increased strength of pelvic bone.

But a little thought will show us that once people can see better, they are less likely to trip and fall.

There is a strong correlation between these two events, but one does not physiologically cause the other.

The world is full of apparent links, some of them true, some not.

We were pretty sure that smoking caused lung disease, but because we could not do controlled experiments on people, it was much more difficult to come up with proof that one caused the other (though it accumulated eventually). Note however, that though people are not allowed to smoke on planes, Governments and private investors still reap huge profits from the sale of tobacco. Addictions are extremely difficult to cure. We don’t seem to know what causes gambling addiction, but it is another one that brings huge amounts of money into Government (and private) coffers. Makes one wonder if a real cure would be welcome, or whether enough research is being done into the causes.

We are now optimistic about ASA (acetyl salicylic acid) [sometimes called by the trade name of Aspirin] and its preventive effects on many important threats to our health – heart attacks, colon cancer and others. But we are not sure of these effects, partly because there are not enough truly scientific double blind studies behind the claims, and partly because people’s lifestyles are so diverse that it is almost impossible to unravel the effects of ASA from many other substances they take on board, or many other of their behaviours. Again, this is because we cannot do truly controlled experiments on people (they have to be the worst possible subjects!) and must wait for the truth to gradually become clear after innumerable studies seem to add up, and meta-analyses finally lead us to a reasonable conclusion.

We should always be cautious about accepting supposed causations that may just be correlations.

Monday, July 16, 2012

We have been compiling the fungi in John Dean Park for years, and have listed hundreds.  But the other day I found a new one - a leaf-curl fungus that attacks Poplar leaves.  The pictures tell the story:
the third is a photomicrograph I took of some of the asci, which cover the surface of the yellow areas of the leaves. Asci contain lots of yellow oil, which explains the colour. This is a very unusual ascomycete, in that it does not make any fruit bodies. Members of the same genus, Taphrina, cause peach leaf curl, a fairly serious disease.

Thursday, June 14, 2012

Geopora cooperi

On a recent mushroom foray in Washington State we found a wonderful fungus that shows evolution in action. We now know that underground truffles started out as cup fungi fruiting on the surface of the soil, then retreated below as the climate dried out. This fungus, Geopora cooperi, shows the process part of the way through. What was once a large cup fungus has folded in on itself and become like a ball of scrunched up newspaper (look at the first picture), with the spore-bearing surfaces on the inside, as the second picture shows.
I had never seen this before and it was an exciting discovery for a mycologist/evolutionist. If you are fascinated by natural history and biodiversity, as I am, this shows that you never run out of new things to see and wonder at.

Tuesday, May 29, 2012

Calypso Orchids

Recently, when walking on the mountain, I found some calypso orchids. These are supposed to be a sign that Spring is here, and morels are up. So I went to my little secret morel patch and found that they had indeed popped, almost overnight (there had been none the previous week). 

The photo shows a cluster of six, exactly as they were when I found them.
So I picked some, left some to propagate themselves, and we had a tasty dinner.
Delicious! This is one of very few mushrooms Laurie has any time for.

Thursday, April 19, 2012

Stormy Weather!

During a recent storm we were awoken at 4 am by a huge bang and a brilliant flash.
It wasn't thunder and lightning (which almost never happen here). No, our multi-trunked 70-foot tall poplar tree had blown down across our stream and into the park next door (picture 1), taking out our hydro pole on the way. Three days and one new pole later we got our power back.

Why did this happen? Looking at the aftermath, I noted that the hole where the roots had been was half full of water (picture 2). When we were able to cut up the main trunk, I saw extensive white rot at the base (right hand side of picture 3). So the fungi were largely to blame...

Tuesday, April 3, 2012


It is an amazing experience to be lying flat in the water, and then have two dolphins come up from behind you and push with their noses, one on the sole of each foot, until you are projected forward and raised high in the air before they dump you.  This happened recently in Mexico to my twin granddaughters (who weigh about 60 pounds each), and to me (I weigh in at 145 pounds).  Somehow or other, the dolphins were able to communicate to each other exactly how hard each of them had to push to achieve the desired effect.  They did this successfully to eight people of varying heights and weights while we all watched, and never made a mistake.  I have no idea how they can synchronize their efforts so precisely - clever beasts indeed - or how they could be trained to do that.

                                         The picture shows Skylar just after being 'released'

Tuesday, February 7, 2012

Sand Dollars

We tend to think that sandy beaches are more or less sterile, but it isn't true. Life exists everywhere. During our walks along the gorgeous beach at Riviera Nayarit at low tide, we found Keyhole sand dollars. Those we have here on Vancouver Island have complete discs, with no holes, but those in Mexico have 5 slits through the disc. They move about slowly
just below the surface of the sand, and I could watch them sieving the sand through the slits
as they filtered it and the water for food particles. The trails they left were often quite amusing, because they had a little 'owl face' at the end, as you can see in some of the photos.
Or sometimes they looked a bit like an animal footprint. Their name is Mellita (not spelled like the coffee), and there are thousands of them, all along the shoreline.

Thursday, January 26, 2012

January 24, 2012

On the endless beach at Riviera Nayarit in December Laurie and I found clusters of turtle egg shells. We also came across a few wire mesh enclosures in which turtle eggs were clearly being incubated (each 'nest' was marked with a date). Eventually I unearthed the secret and got to participate in the action. These were Ridley’s turtles, which we had never seen before, and volunteers cruise the beach on ATVs every night looking for laying turtles. I got to go along on a bumpy ride with a volunteer by the name of Memo. We found a nesting turtle and stole her almost 100 eggs as she laid them. She, being busy, was quite unaware of this. After she had spent several minutes smoothing over the now empty nest, she headed for the water. We watched until she was back home in the ocean, then took the eggs away and dug a surrogate nest in one of the enclosures. The other end of the story comes at sunset every day, when the turtle people release hundreds of newly hatched babies on the beach, and they head into the surf.  I got two of my own to launch.

Friday, December 2, 2011

Here is a photo of something I never thought I'd see, let alone have it happen in my own bathroom!
This is the handle of a Braun Oral-B electric toothbrush that I bought some time in the past year.
It developed spreading dark areas which resisted removal.
Though the brush was never left in water, and was kept dry, the areas grew and amalgamated.
Being an environmental mycologist, I eventually made a tape-lift, and was rather surprised to see
that the dark areas were colonies of a sporulating mould - probably a species of Phoma.
When I phoned Braun, they suggested I send it to their depot somewhere in Vancouver,
which would get it back to me in 3 weeks.
You'd think they could do better than that.   I don't want it back!
It doesn't look as if there's any mould-retardant in the plastic.
But perhaps more importantly, I may have inadvertently discovered a mould that can eat plastic...

It's November, and mushrooms are popping up everywhere (so why are a Rhodo and an Azalea in our garden flowering?) However, this message is to show off one of the more spectacular mushrooms, Gymnopilus spectabilis, which pops out, not up.  Our local mountainside Park has many thousands of trees, but I have seen this beautiful big, bright yellow mushroom on only one. It tends to produce a group of fruit bodies, but as you can see in the pictures, it has outdone itself here...

How Do We Come Up With Research Problems in Mycology?

How do we come up with research problems in Mycology?
(This is an excerpt from Chapter 25 of the new 4th Edition of The Fifth Kingdom)
During a 3 km hike in late March up a steep trail to Spirit Lake near Skidegate, Haida Gwaii (formerly Queen Charlotte Islands), fruiting colonies of a little lichenized mushroom, Lichenomphalia (Omphalinaericetorum, drew my attention no fewer than 27 times.

Perhaps the most interesting thing about this was that almost no other mushrooms were in evidence (though there was lots of a beautiful yellow jelly fungus called Heterotextus (formerly Guepiniopsisalpinus (Dacrymycetales), fruiting on rotting branches). Swamp candles and salmonberry (and dandelions) were in flower.

Science always begins with an accumulation of observations. As I saw the little mushrooms again and again (they are also illustrated on the front cover of The Fifth Kingdom), I began to ask myself questions about this successful little fungus.

(1) Why was it so common in early Spring when so few others were to be seen?

(2) What gave it a competitive edge over all the other macrofungi, enabling it to fruit even before the usual Spring discomycetes? Perhaps the answer lay in the fact that it is a lichenized fungus, even though the mushrooms themselves contain no algal cells. I imagined that its symbiosis with the unicellular dark green alga Coccomyxa, which covered the surface of the wood around the little agarics, had given it a boost of photosynthesis-derived energy. But that was mere conjecture. More questions bubbled up in my mind as I walked.

(3) How long does the mushroom take to develop?

(4) How long does it go on producing mushrooms (and how long does each mushroom last)? This would call for repeated visits to the trail, but could be answered in a reasonable time-span (It has been suggested to me that this species can probably fruit in all months of the year, given the right conditions - that would make it a rare breed).

(5) How extensive are the individual colonies? Judging by the occurrence of the fruit bodies - and those I saw bore from one to almost 50 mushrooms - they seemed to range in extent from about 10cm to about 2m. This could easily be quantified and expressed statistically.  It would need to be related to climatic data on temperature (degree days?) and moisture (see 7 below).

(6) How much algal biomass does it take to support each mushroom? Some tricky observations and manipulations called for here.

(7) What conditions stimulated it to fruit? I realized immediately that this could be broken down or analyzed into a number of factors. (A) Over what range of temperature will it fruit? (B) What level of moisture does it require in the substrate? (C) What kind of climatic (seasonal) history encourages it to fruit? (D) What range of pH will it tolerate? (E) What levels of inorganic nutrients, such as nitrogen and phosphorus, does it require? Wood is notoriously low in nitrogen, and is presumably not replete with phosphorus either. (F) Since the lichen seemed to prefer better-lit locations near the path, what light levels does it (or its alga, Coccomyxa) need? This could be quantified, and might also lead to a consideration of day-length and degree days, which are already known to influence many flowering plants.

(8) Which substrates does it prefer? It seems clear that the alga must precede the fungus, and seemed to grow here only on well-rotted wood, probably of conifers, though I have seen it fruiting on the ground among mosses on Vancouver Island.

(9) Which wood-rotting fungi precede the alga - Do they represent particular taxa or could they be any among many?

(10) How long after the woody substrate becomes available does the mushroom fruit? Long-term question, hard to answer.

(11) Which locations permit growth and fruiting? I have already mentioned rotten wood, in fairly well-lit places, but to be more specific, most of the colonies were on rotten stumps, and within 50cm of ground level.  Why not higher as well?

(12) I saw many patches of algae without mushrooms: Did this mean that the fungus was absent, or just that it wasn't yet fruiting?

(13) Can the basidiomycetous fungus be grown in axenic culture (that means, without its domesticated alga)?  The mycobionts of many ascolichens have been brought into axenic culture (they look weird, and don't produce ascomata).

(14) Can the lichen be synthesized in the lab.? Under what conditions and from what kind of materials can the symbiosis be initiated?

You can come up with hypotheses on many of these issues, which could be falsified or proven correct. Many of these questions could be answered by prolonged and repetitive observations.  Some would require experiments. Some would require long-term studies that might well be beyond the purview of a PhD thesis project.

Those are just the questions that occurred to me during and soon after a morning hike. Perhaps some of them have already been answered. But what I have just written is a (fairly primitive) example of how scientists look at the world. (1) Make observations. (2) Analyze them and make connections among those observations. (3) Using the new database, think of possible explanations for some or all of the observed phenomena. These Ĺ’explanations‚ may be presented in the form of hypotheses. Some of the hypotheses will probably be shown to be wrong. Others may fit all of the available data, and may be accepted for the time being as probably true. But these may still be shown to be false if newly acquired data do not fit. So goes the process of science. Observe. Question. Hypothesize. Test. Re-hypothesize. And so on.

It is now apparent to me that Lichenomphalia ericetorum could easily form the subject of one or more Ph.D. theses, or of many experiments. Possibly, some of them have been done - after all, we already know that it is a lichen, even though that isn't obvious to the naked eye. But there are very few basidiolichens, and I would be surprised if we had the answers to all the questions I have raised. Would you like to find some of those answers, or to answer other questions about fungi (and believe me, there are lots)? If so, mycology is for you. 

Monday, November 7, 2011

October 29, 2011

I have ten fairy rings in my courtyard. Do I live in the Magic Kingdom? No, I just happen to have an abundant fruiting of a tiny mushroom called Arrhenia retiruga growing on the moss that covers the bricks. I have seen it in the past two years, but never as numerous as it is now, at the end of October 2011.  Although it sounds as if you are clearing your throat when you say it, this genus was actually named in honour of a botanist called J.P. Arrhenius.

The fruit bodies are tiny - mostly only a few millimetres across - and tend to be one-sided, thin and rather petal-like, without a stipe. The hymenium is almost smooth, with shallow veins, but nothing resembling gills. The main reason it is growing at my house is the moss that covers much of our small courtyard - this fungus is almost always associated with mosses, and doesn't seem to be a particularly congenial companion, since the moss looks a bit faded wherever the Arrhenia is growing.

Monday, July 25, 2011

What are “saprophytic” plants all about?

Those of us who penetrate the depths of our local forests in Summer inevitably come across plants which have no chlorophyll. They are always white. Indian pipe (Monotropa uniflora) is the most common of these in B.C., and is just flowering now in late July of 2011. But there are others, including the rare phantom orchid (which is also flowering now in one of our local forest Parks). Such plants, having no chlorophyll, have generally been called saprophytic plants, the assumption being that since they can’t make their own food by photosynthesis, they must be absorbing nutrition from the decaying remains of other organisms in the soil (as, for example, many fungi do). We have recently learned that this is not the case, and that none of these achlorophyllous plants are, in fact, saprophytic. So what is really going on?

The somewhat weird relationships between the non-photosynthesizing flowering plants in a strange sub-group of the heather, Arbutus and Rhododendron family (Ericaceae), known as the Monotropoideae, and others like the phantom orchid, have recently been clarified, in particular by the work of Martin Bidartondo and his associates in California.

The roots of Monotropa have a fungal mantle outside and something resembling a Hartig net of fungal hyphae inside. The one distinguishing morphological feature is that the fungus sends a single haustorium-like peg into each root cell. So you might think that the plant was in a normal mycorrhizal relationship (such as that between many fungi and Douglas-fir). But since this plant cannot photosynthesize, it has no energy-rich carbon compounds to give the fungus. This eventually led mycologists to suspect that the plant might in fact be parasitic on the fungus. This turned out to be the case. The plant is indeed taking food from the fungus.

The main fungi so far identified as being associated with Monotropa are species of the mushroom genus Russula and some other mushrooms in the Family Russulaceae, and the association is often extremely specific and exclusive.
The monotropoid genera Allotropa and Pityopus have victims in the mushroom genus Tricholoma, and other monotropoid genera are tied to different fungi. For example, the genus Pleuricospora has associates in Gautieria, while Sarcodes and Pterospora have associates in Rhizopogon (Gautieria and Rhizopogon are both hypogeous basidiomycetes - genera which fruit underground). Hemitomes and Monotropopsis associate with Hydnellum,(a tooth fungus) while Cheilotheca and Monotropastrum are associated with members of the Russulaceae.
Whatever the morphology suggests, the fact is that the achlorophyllous Monotropaceae are taking food from the fungi, and no-one knows if they are giving anything at all in exchange.

The key to the situation is that the food in question has been found to be coming from a large neighbouring plant (a green one this time) with which the fungus in question has a normal ectomycorrhizal relationship. So we are looking at a tripartite relationship. Coniferous trees, such as Douglas-fir, make sugars and pass them to Russula. Russula translocates them through its mycelium in the soil, and then, for reasons unknown, hands over part to the Monotropa, which thus seems to exploit the fungus directly, and the conifer at second hand as an epiparasite.
Pseudotsuga ---> Russula ---> Monotropa

So, despite what you read in even the most up-to-date dictionary (and the one I have, the Canadian Oxford Dictionary, was published in 1998), Monotropa is not a saprophyte, and can more correctly be described as parasitic on its associated fungus. Interestingly, mycologists have known this since 1960. It makes me wonder about lexicologists.

How did this strange group of plants and its even stranger fungal relationships evolve? I suspect that it all began in a regular ectomycorrhizal relationship (to judge by the way the fungus still grows around and into the roots of the plant) and somehow became turned around, possibly when the ancestor of the plant group lost its ability to produce chlorophyll, and found that the fungus had another source of food, and could be exploited. Even in normal ectomycorrhizal fungi, food moves back and forth between plant and fungus depending on the needs of each partner. Sometimes the mycorrhizal mantle is a food bank for the tree, and sometimes the root is a food bank for the fungus. So you can see how it might start...

J.R. Leake (2005) presented a wide-ranging discussion of plants which are now known to be parasitic on fungi - the antithesis of a mycorrhizal symbiosis. Leake notes that this phenomenon extends to over 400 achlorophyllous plants in 87 genera. The fungi exploited by these plants represent a wide taxonomic spectrum: Glomeromycota (arbuscular mycorrhizal fungi), basidiomycetes in the Ceratobasidiales, Sebacinales, Tulasnellales, resupinate Aphyllophorales, Russulales, Boletales and Agaricales, as well as ascomycetes in the Pezizales (cup fungi and truffles).

Wednesday, June 15, 2011

June 7, 2011

The plant kingdom never ceases to spring little visual surprises.
The two photographs came from the garden and the kitchen.
I like the patterns and symmetry that emerge when you look closely...
(a young Sedum infloresecence and a bit of a broccoli head, in case you're interested)

May 31, 2011

I spent a good chunk of yesterday using a folding handsaw to 'fell' a whole bunch (hundreds...) of large broom bushes
which were flowering happily on a rocky knoll in our local Provincial Park.  Why would I want to cut down such wonderful masses of glowing yellow blooms?
Because broom is an invasive alien plant here on the west coast, having been introduced from Europe by a sea captain,
and having subsequently spread all along the Pacific coast.  We can never hope to get rid of it, but I and a few others are trying to extirpate it in our Park,
so that the native wildflowers will be able to take over their space again.
One problem is that broom is a legume: it has nitrogen-fixing bacteria in its roots, so it can grow rapidly in poor soil, thuggishly taking over the space
and out-competing the native plants, which evolved to grow in low-nitrogen soil, and are thus at a double disadvantage.
Other plants we have problems with here are English ivy, leather-leaf daphne and holly - invasive aliens all,
and hard to get rid of (I have had sweaty experiences with all of them). 

Interestingly, when I was in Australia, the local biologists were complaining about invasive alien plants - but their problematic species came from South Africa.
When I was in South Africa, the locals complained about yet other invasive aliens, but these came from Australia.

Of course, plants do move around by themselves, and Humans are not to blame for all introductions.
Yet in most cases we are the villains, and those of us who care about our local floras must protect them with the sweat of our brow, and a few aching muscles..

Thursday, May 5, 2011

May 5, 2011

I am going to interrupt my happy meanderings through the fungi of Haida Gwaii to mark two unique events, both of which happened yesterday, 2nd May 2011.

The first (and possibly the more important) was the election in my Federal riding,
Saanich and Gulf Islands, of Elizabeth May, National Leader of the Green Party of Canada, to Parliament, handily defeating the long-standing Conservative incumbent (and Cabinet Minister) Gary Lunn. She is the first Green to be elected in a Canadian Federal election, and I feel proud to have played a small part in her campaign.

The second event was the arrival of four copies of our new book, The Genera of Hyphomycetes. These copies are to be signed by all four authors and distributed among them. This book, the product of 20 years' work, looks just as fine as I thought it would, and I look forward to getting copies to my friends and colleagues as soon as I can. The book is just over 1,000 pages long, and has thousands of illustrations. It will be the standard work for years to come, and I am proud to have been part of the team that produced it.
Here is the cover...

Monday, May 2, 2011

May 2, 2011

For the past 5 years several local mycologists including yours truly have been making extended visits to a group of islands off the Northwest coast of British Columbia called Haida Gwaii (they were called the Queen Charlotte Islands until recently, when the ancestral rights of the Haida Nation were recognized). Haida Gwaii is an archipelago of more than 150 islands with a total land area of just over 10,000 square kilometres.

Our visits were undertaken to collect and identify as many of the fungi of the islands as possible. 
Over the five years, we made eight field trips to Haida Gwaii of ten to fourteen days. In all, 113 areas were visited (53 in Gwaii Haanas National Park Reserve, 12 in Naikoon Provincial Park),
and we made and preserved 2906 collections representing 615 species, and documented 812 species of fungi (not including lichens) from all available sources. We collected on nineteen islands, 17 of which lie entirely within Gwaii Haanas National Park Reserve. The islands range in size from 0.5 hectares to the over 648,000 hectares of Graham Island.

In this blog entry, I show pictures of several of the more unusual fungi we found.
We have now compiled our information and pictures into a book 'The Outer Spores - Mushrooms of Haida Gwaii' which will be published very soon and will be available from my little publishing house, Mycologue.

There are lots (hundreds) of pictures, so I have enough to illustrate quite a few blogs...
Here are the first 4 - a rather diverse bunch!

Friday, March 18, 2011

March 18, 2011

On November 4th 2010, Adolf and Oluna Ceska and I climbed slowly up the
Slektain Trail in John Dean Park. looking for fungi.

Over the course of several hours we found no fewer than 168 species,
a few still unidentified and very rare.  Most were basidiomycetes, though there were 7 ascomycetes.

Here are pictures of some of the most interesting species.
The most conspicuous is the green and yellow parrot mushroom,
but the other more drab pictures are of even more unusual species.
If anyone wants the names, they can E-mail me.