Friday, December 2, 2011

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. 

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