Posts Tagged ‘mycology’

A day in the life of a field mycologist.

Thursday, March 10th, 2011

My husband is always pestering me, “Hey, you’re a historian of science—why don’t you study the history of mycology?” Or, “You want to write about science, right? The study of mushrooms is pretty cool, why don’t you write about mushrooms?”

Well, alright. After all, these elusive, mysterious fungal reproductive organs brought us here to Borneo, it seems only fair that I finally write something about them.

There you are, then, that’s something about mushrooms: A mushroom is the reproductive structure, also called the fruit body, of a fungus. Most fungi that you or I would recognize are, like plants, multicellular organisms with stiff outer cell walls—that’s the part that’s hard for our bodies to digest when we eat uncooked vegetables or mushrooms. Like all multicellular organisms, the work of living is divided up between different cells. Most of the “body” of a fungus exists where we cannot see it. That is the mycelium, a filamentous structure that grows underground or through a decaying log—wherever the fungus resides. It absorbs nutrients, exchanges gases, and expands the fungus’ territory; it’s in charge of all the stuff of daily life. But when a mushroom appears aboveground, it’s time for reproduction.

This is why mushrooms are so important to mycologists. Like a lot of other organisms on this planet, reproductive systems provide a lot of clues about the identity of an organism, how it’s related to other organisms, and its evolutionary history. One of the really wonderful (some would even say seductive) things about biology and evolutionary theory is its intuitive appeal, and this concept is no exception! If evolution is a matter of survival and reproduction over thousands of generations, then it makes a lot of sense that many biological questions and problems would revolve around understanding how cells and organisms produce the next generation. For example, if you have ever taken a course in botany, you know that basic plant identification begins with the reproductive organs, the flowers: the number of petals and the arrangement of the pistils and stamens, which are the flower’s sex organs, these are the keys to identifying flowering plants.

Another level of “identification” is the attempt to understand what a species is. This is a knotty issue, both philosophically and practically, but an inability to interbreed is used by many as a basic criterion for separate species. If two organisms cannot mix their genes to produce viable offspring, for whatever reason—it could be physical, behavioral, or genetic—they belong to two different species. You get the picture: sex is biologically important, thus biologists are often focused on reproductive organs.

In a practical, day-to-day sense, then, my husband spends a lot of time looking at fungal sex organs. And what does he see? In order to show you, I am going to take you for a walk in the muddy wellies of a field mycologist.

Here we are in Borneo, exploring a tropical rainforest. We are on the opposite side of the biological universe from the boreal forest of northern Minnesota, where my husband Bryn grew up. So how does Bryn know where to look for mushrooms? In a sense, the answer is: he looks everywhere. It’s true, and anyone who knows him will confirm it, he never stops looking! However, like any mycologist, my husband usually has some sense of where to head first…

As you walk through the rainforest, remember that mushrooms do not live in isolation. While much is made of the work that fungi do in decomposing dead forest debris (and certainly they are amongst the most important decomposers in the forest), a lot of fungi are not decomposers. Instead, many fungi live in symbiosis with plants, called a mycorrhizal association. To put this symbiosis in perspective: If all of the fungal partners in this marriage were to file for divorce tomorrow, almost all of the forested land in the temperate Northern Hemisphere would be treeless. Luckily, however, a complex exchange of nutrients and water makes this partnership sustaining and beneficial for both sides. Thus, the first thing Bryn looks for is a type of forest. Wherever we go, he has already learned as much as he can about the kind of trees we will find, and he knows which ones are most likely to have the kind of symbiosis with mushrooms that he is looking for. Here in Gunung Mulu National Park, we are seeking lowland tropical rainforest giants: the dipterocarps. This is a group of trees that are especially abundant and diverse in Asia—and especially here in Borneo.

Of course, because these trees are gargantuan, there’s an added difficulty: you can’t see the leaves, they are too high up! And many of the leaves in the tropical forest look very similar, so they are difficult to identify anyway. As Bryn has said, to be a mycologist in the tropics, you practically have to be a botanist as well—and, indeed, he spends a lot of time trying to identify trees and detect patterns of association between trees and mushrooms.

For your purposes, though, just start by looking for some very big tree buttresses, those huge wedge-shaped roots that tropical trees use to prop themselves up because they are so shallowly rooted. Yep, that means you have to go off the trail, so watch out for pit vipers and toxic, furry urticating caterpillars! Poke around in the crevices between these buttresses and you’re bound to turn up something.

Can you spot the mycologist? This is an especially impressive example of a buttress! This photo was taken on the Osa Peninsula in Costa Rica.

Some mushrooms can be identified morphologically, that is, by examining their appearance, whether with the naked eye or under a microscope. There are all sorts of features that turn both the beautiful and the boring of the fungal world into recognizable species. Where you or I just see cap and stem and gills, Bryn makes fine distinctions. There’s an overall sense of the form of the mushroom that it takes years to develop.

 

 

Mycena. Like almost all of the mushrooms collected on this trip to Borneo, the species is thus far unidentified..

 

Before I went for a walk (or many walks, that is) in the woods with a mycologist, I wasn’t really aware of the sculptural quality of mushrooms. Now I have an appreciation for the beauty of their overall shapes and textures. But Bryn’s brain is like a code reader. From a distance he can judge if that tiny little thing on the log is a Marasmius or Mycena, based on the shape of the pileus (the cap), the width and bow of the stipe (the stem), and other general impressions that he probably cannot even articulate—the tacit knowledge that the scientist gains from years of direct experience.

 

 

 

 

The top of these Pluteus is beyond rugulous--those are some deep wrinkles.

 

Take a closer look now. Is the surface of the pileus velutinous (velvety) or glabrous (smooth)? Is it rugulose (wrinkled), pitted, or cracked? Better yet, it could be glutinous and covered in slime.

A glutinous Cortinarius.

 

 

 

 

 

 

 

 

 

 

 

 

Tylopilus nigerrimus. Note the reticulation on the stipe.

 

Does the stipe have any interesting features, like a finely netted reticulation or patchy raised “scabers”? You might break a little piece of the pileus off with your fingernail and try to peel the top surface off—whether it peels easily is yet another field character.

 

 

 

 

 

 

 

 

This is the one mushroom photo not taken in Borneo in the past 3 weeks. This was taken (like the buttress photo) on the Osa Peninsula in Costa Rica and it is (I think...I can't remember for sure and Bryn is now asleep, so I can't check) Boletus vermiculosis. I include it to illustrate the bluing color-change reaction on the pores.

 

Look under the pileus, and if there are gills, make a small slice through them with your knife: Does a white, yellow, red, or blue latex ooze out? Does it change color once the air oxidizes it? Keep an eye for color changes on the flesh of the mushroom as well. Is the pileus or stipe bruised where you have held the mushroom? Bluing reactions can be especially impressive, as you can see below.

 

 

 

 

 

 

 

 

 

Hydnum. A choice edible in this toothed genus is Hydnym repandum (this could be my wonky spelling of the species name, again, Bryn is sleeping...), known commonly as the sweet-tooth mushroom or the hedgehog mushroom.

 

Or perhaps it looks like a sponge, like you see on the left. Microscopically, the underside of the pileus is one of the most important parts of the mushroom, because this is where the reproductive cells are located. The sponge you see (look—a well-fed beetle larva just crawled out of one of the pores!) is made up of thousands of little tubes, packed in together. Like the gills, these tubes exist solely as the means to spread the mushroom’s spores. You may see a tint of color on the gills or pores here that hint at the color of the spores, which can be a very important character. The spores themselves can be extremely beautiful, but you won’t get a really good look at them until you are back in the lab with your microscope.

Leccinum, with a great view of the pores (or tubes) under the pileus.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Mushrooms may also identified using chemical characters. Some chemical tests must be done in the lab with droppers full of reagents that turn different mushrooms different colors; but there are plenty of chemical characters that can be tested right here in the field. The nose knows—and Bryn has an impressive nose, in both form and function! Does the mushroom smell raphanoid (like a radish or watermelon rind)? Or perhaps it smells like camphor or almonds or even like rotting flesh? Some mushrooms must be tasted to be understood, so beware the mycologist that hands you a tiny piece of fungus to taste in the field. It’s unlikely that he is trying to poison you, but he might be giving you a chunk of an acrid Lactarius that tastes as if you are chewing some especially hot peppercorns!

As you have learned, workaday mycology begins outside, in direct contact with the natural world. The attention that you paid to the forest around you and the detailed observations that you have made of the very fine Tylopilus that you found will pay off in dividends in the future. First, there is a cumulative benefit to be gained from today’s time in the forest. This is the practice of natural history: You draw continually from the knowledge that you’ve gained in past experiences in nature and in your study of others’ work, and you synthesize that knowledge with your immediate experience of the world around you today.

But what’s next for today? Fortunately, Bryn’s ready with a snappy mycological aphorisms for just this kind of occasion: Flash it, Smash it, and Dry it.

Tylopilus nigerrimus again.

“Flash it” is probably obvious: You must photograph your mushroom both before and after you collect it.  Get a nice picture in the field, showing the substrate on which it was growing, and later take a more artificial photo against a neutral background, to record color and scale, and morphological details.

 

“Smash it” is Bryn’s method of DNA collection.  Once upon a time we carried tiny little plastic tubes with preservative liquids into the field, into which we would plunge a fragment of each mushroom’s gills or pores.  Now the very same reproductive tissue gets smashed into a fancy kind of paper that preserves the DNA in a much more convenient form. Bryn has even made a very informative video of this method.

That last step, “Dry it,” kind of ruins the rhyme, but there’s no way around it, you can’t change what happens in a food dehydrator.  Before that lovely Tylopilus nigerrimus starts to deliquesce, better dry it out as soon as possible.

Now that you have flashed, smashed, and dried your mushroom, you’re ready to take your impressive knowledge of that mushroom’s natural history into the laboratory. Scientists who work with DNA may be derided as “gene jockeys”  when they have a myopic focus on DNA, at the expense of seeing the whole organism.  But you are already well on your way to becoming a natural historian and I know you won’t lose sight of that whole living mushroom and its associated tree when you finally get a peek at its DNA.

On really striking out and (sometimes) striking el oro

Tuesday, February 24th, 2009

About luck. The notion has been irritating me for the past few days. I’ve always been interested in how chance operates in my own life. Like most people, I usually construct a nice satisfying retrospective narrative about my life. But chance has always played an unsettling starring role, throwing a wrench in the aesthetics of that erstwhile smooth story arc—you know, the one where I make wise conscious decisions and directly control the events of my own existence?

My sense of the importance of chance has only been heightened in my dissertation research, in observing its importance in the lives of pretty prominent scientists. This is not just the historian’s impartial eye, observing how life deals different hands to different players. This is the witness borne by those players themselves! Renowned biologists—known for their brilliance and not, typically, for their humility—have repeatedly credited chance with the paths of their careers. Paul Ehrlich. Dan Janzen. These guys have taken unusual and sometimes unpopular stances on ecological issues—in other words, they give the impression of deliberately charting their own courses. And yet, Janzen loves the words “serendipity” and “serendipitous,” and applies them liberally to the story of his own career.

Of course, when Janzen speaks of “serendipitously” stumbling upon an ant acacia while roving across Costa Rica in the early 1960s, he is not talking about pure chance. He is talking about the convergence of luck and preparation; the effect of a particular experience upon a mind primed with just the right kind of knowledge and previous experiences. The true luck is almost always in the timing of that critical experience.

Like Janzen, we’ve been doing some roving across the Costa Rican landscape, hoping for such a lucky convergence. We have no concrete information directing our mushroom search at the moment; only a knowledge of the general rainfall patterns for the season and a sense of where oak trees might be found.

Walking along a forest trail during the dry season might remind you of autumn in North America. Deciduous trees lose their leaves here just as they do in the temperate zone—it just happens to be during the “summer,” the drier and sunnier time of year. According to the Costa Rican bird Bible, Skutch and Stiles’  Birds of Costa Rica, it was the Spanish that declared the dry season summer, arriving with their memories of a hot and dry verano and cool and wet invierno.

If you’re lucky enough to have made it to an oak-dominated forest, however, you might still look up and see a truly regal canopy above your head. These oaks are closely related to the evergreen live oaks of the Southern U.S. And while “regal” might seem a cliché, under the circumstances, it’s spot-on. The oaks we have seen here are hundreds of years old, many feet in diameter, and verdantly populated with mosses, lichens, and bromeliads. There’s something so vital about the silhouette of an oak tree. The leaves burst so densely from the awkward joints of its branches. Its body looks haphazardly assembled and, at the same time, absolutely coherent. Coherence is a concept, but I would even say that an oak tree is cohesive, in a purely physical sense, as if it is gathering its deep green pigmentation along with moisture and light and a body of cool air, directly from the air around it. When each branch supports a dozen bromeliads, and their bright fuchsia and maroon and yellow-green leaves glowing translucently from above, this sense of pure organic gravity, of substance and sustenance, is intensified.

Rhapsodies over the beauty of oak trees, however, do not a successful collecting trip make! Oak trees are also mycorrhizal symbionts, living in intimate collusion with fungi, whose hair-like mycelia connect with their roots underground, sharing nutrients and minerals in an exchange that sustains both tree and fungus. Finding an oak means finding its fungal symbionts, which, if we’re lucky, have fruited above ground, producing those reproductive organs that my dear husband so desperately seeks: mushrooms.

This is where serendipity comes in. There are thousands of acres of forest reserve and national park in Costa Rica. Most of this is completely inaccessible, or else only moderately accessible, especially for people that need to collect mushrooms, photograph them immaculately, in situ and against a gray background with an herbarium collection number, take DNA samples (because this is, after all, part of a DNA barcoding project), and then dry them completely in a food dehydrator. So, via various points of entry, public, private, and otherwise (meaning, we’re not quite sure who owns the land or the road by which we reach it), we try to get at this inaccessible core of forest.

For our purposes then, these roads and trails are essentially random cuts in the forest. We can steer ourselves toward higher altitudes, where oaks and other mycorrhizal tree species are more common, or toward the rainiest provinces, but the decisions made decades ago to build a trail along this ridgeline or blast a switchback for the road into that hillside, may or may not take us precisely where the mushrooms just happen to be fruiting today. As much we have prepared for this trip, there will always be the discomfiting suspicion that somewhere—maybe even just a measly kilometer to the east or the south—the mother lode of mushrooms is elbowing its way up through soil and detritus, where we will never find it.

Anyway, that’s how it feels today. Fieldwork, especially when the task is opportunistic collecting in an attempt to document fungal diversity in the region, can sometimes boil down completely to luck. And luck is not with us in other ways, as well. We are three days into this collecting trip and have yet to see the collection and export permits for the mushrooms we are supposed to be collecting. Bryn started the process of applying for these permits more than two months ago, at the moment he knew that his teaching trip would be extended into a collecting trip. Unfortunately however, the term “process” implies that there is a straightforward method for obtaining such permisos. In reality, successfully scoring a permit turns mostly upon finding a reliable contact on the ground, a contact who also has a functional working relationship with the relevant bureaucratic body. It’s not entirely clear what went wrong, but it seems to be a little bit of a failure in both aspects (maybe more heavily the former than the later, I might add).

In any case, we have not yet been able to collect in Parque Nacional Tapantí-Macizo de la Muerte, as we do not have the relevant permits. So, we are reduced to making even more random forays into the landscape, in hopes of finding mushrooms on land where park rangers are not likely to be breathing down our necks. This morning, over weak coffee (Costa Rica is a coffee-producing nation that reserves its most drinkable beans for export and tends to disappoint the palate with weak and bitter brews in person.), Bryn identified a small “protection zone” called Cuenca Rio Tuis, perhaps a couple of hours drive from our hotel in the small village of Orosi. It seemed a little far away, but also unlikely to be heavily monitored, and according to our topographical map, it reaches a peak elevation of 1963 meters and may even have oaks.

It was a lovely drive, on a fantastically sunny day, over mountainside roads that rapidly drop and fall while they and around Lake Cachí. Everywhere that we drove, a brief wave or a “Buenas!” out the window of our car transformed that standard hard-edged impersonal glance you turn toward a strange car into smiles—people are incredibly nice to strange gringos blowing unexpectedly through their tiny little hamlets.

coffee plantation

At first, at the higher elevations, we drove through coffee plantations. Coffee is Costa Rica’s grano de oro, “grain of gold,” which brought prosperity to this nation named “rich coast.” Workers alongside the road were spraying the beans with a pesticide. These workers are, reportedly, mostly Nicaraguans, since Costa Ricans are no longer willing to lower themselves to earning something like $1/bushel for picking el grano de oro. The shade-grown varieties actually appear to receive a good deal of sunlight, especially since many of the scattered trees planted to give them shade are deciduous, with only bare branches remaining, which cast crooked shadows (if not actual shade) over the coffee. Other plots are stocked with imported eucalyptus, trees that at least retain their leaves during the dry season.

dscn0249Halfway through the drive we made delicious tomate, aguacate, y queso fresco sandwiches for ourselves at the roadside. At lower elevations we began to see the sugarcane fields, where men with machetes hacked away at their stalks. Near the end of the day we passed a plant where trucks full of sugarcane stalks pulled in for processing. The men trailed down the roads slowly in the wake of the trucks, looking exhausted, machetes still in hand, while a smoggy burnt-caramel smoke filled the Orosi valley.sugarcane truck

Finally we reached our little forest reserve. Or…..we’re pretty sure that we did. After all, most of the roads are not signed and the GPS is often little help in finding our position on what seems to be a pretty imperfect map (it’s missing an entire huge lake?!). Driving into the reserve on the potholed dirt road through increasingly tiny villages (where people seemed even friendlier, in inverse proportion to the size of their towns), we started to get excited about the wooded hills that we could see ahead. When a road winds around so much, you really just have to keep faith that eventually you will reach that mirage of forest on the horizon.

abandoned houseWe passed a couple of abandoned house, one with half-collapsed porticoes and arches and windows that still contained shards of glass. We’ve tried to decipher graffiti from the side of the building, but it’s hard to read from my passing photograph: Aqui es solamente / No se aqui que / porque aqui.” Bryn says I’m wasting my time trying to read this nonsense, like a bathroom wall in the basement of some bar in Toronto. It’s something like: “Here is only / I don’t know here what / why here.” Indeed.

Anyway, eventually, we had to turn on the 4-wheel drive to cross a little river with steep embankments on either side and a little catarata (waterfall) in the center. But we never got much higher, and we never got much closer to that elusive deep core of forest. We drove as far as we could on the road, to a place where the mud was ridged so deeply in a sharp turn that we couldn’t imagine the car handling both challenges simultaneously. So we did a little bit on foot. And it was disappointing mycologically.

But for me, with the mud on my boots, and the humidity that layered my face in sweat the moment I started to climb the steep trail along the hillside, and my first glimpse of something as common as a bird-of-paradise flower—all of these started to melt that icy nucleus of Torontonian slush and snow at my center. Running my hand along a mossy boulder, I had a tempting moment of synesthesia, and I was certain that I could taste the deep green in the blade of a bromeliad just above my head. So, although we struck out mycological today, I feel finally that I have really arrived in Costa Rica, and I’m excited to try our luck again tomorrow.sunset drive back to Orosi

Striking out! or The Daunting Unknown of a Foreign Language

Saturday, February 21st, 2009

view from the Hotel CactsWhen I walked into my San Jose hotel today, it was with a totally overblown sense of pride. I had just, amazingly, completed…the simplest task. I had gotten myself from the airport to a downtown hotel, completely alone, speaking only en Español. A first sentence to the cabbie, “Sabe donde está el Hotel Cacts?” Then, later, as we were driving, “Como se dice ‘el metro’ en Costa Rica? I thought that I remembered that Costa Rican taxi meters have their own affectionate nickname. And was rewarded with the answer: “La María.”

This may not be the most impressive conversation that you’ve ever heard in Spanish, but it was a major coup for me. I am fluent in one language alone—and you are reading it. Purportedly, I have reading proficiency in both French and German. My graduate transcript attests to this far-fetched notion with a nice round pair of “A”s. In reality, if ever I were faced with a German or French text that I actually needed to, ahem, understand, well, there is no doubt that I would have to hire a translator.

I am not proud of this. In fact, I am so deeply embarrassed about it, that it actively conflicts with my ability to rectify the situation. On my flight from Toronto to San Jose, I had a layover in San Salvador. On the first leg of my trip, I sat next to an El Salvadoran ex-pat, living in Ottawa, who told me how impressed he is with people from the United States, with how “aggressively” they pursue foreign languages, unashamed of the flaws in their grammar or accent. We’re so different from Latin Americans, he told me, who are too cautious about making mistakes, crippling their ability to practice using another language.

Let’s just set aside how surprising this generalization is, how much it completely contradicts what I would otherwise have assumed to be an almost global opinion on Americans’ xenophobic ignorance of other languages and cultures. Upon accepting this extremely flattering take on American aggression, I immediately had to confess to this very sweet (and very fluent en Inglés, I should note) man that I, an otherwise aggressive American (to say the least, my Canadian friends might assert) am deeply, painfully diffident in this respect.

Given that background, you can probably see why I am so absurdly proud of my grade-school-worthy conversation with a taxi driver. It seemed like a pretty solid start to my two weeks in Costa Rica, so I decided to reward myself with una cerveza. When in Costa Rica, drink like a Tica, so now I am sitting on the hotel’s rooftop patio, drinking a bottle of Imperial, waiting for my husband Bryn’s arrival.

For the previous week, Bryn has been one of the instructors of a tropical ecology field course, leading a group of University of Toronto undergraduates around Costa Rica in what has been, for most of them, a first exposure to hot tropical rainforests and frigid cloudforests. From what I’ve heard so far, these students have been extremely lucky. They have seen a sloth, crocodiles, quetzals, an eyelash viper, a mother humpback whale nursing its baby, and much, much more.

Already I know that I am never going to get quite this lucky during my two weeks in Costa Rica. After the students leave, Bryn and I are heading off to collect mushrooms. Yeah, it’s a mycological collecting trip during the dry season. It’s a little strange, since mushrooms thrive in wet conditions. But sometimes field biologists must take what they can get. The course created an opportunity (read: plane ticket to Central America) that simply could not be refused, despite the lack of rain.

And, after all, even in the dry season, rainforests and cloudforests can hardly be parched. The Eastern slopes of central Costa Rica, descending from the Talamanca mountains down to the sea, meet gusts of warm, wet Caribbean air during the dry season, making the East the wettest side of the country at the moment. So we are heading to Tapantí-Macizo National Park, a place that receives something like 800 cm of rain annually. Only about 80 cm of that impressive total fall during the months of February and March. But—with luck—it will be just enough!

looking south over San Jose