The quarterly of the University of Helsinki

Tapio Ollikainen

Back to summer issue 2004

The purpose of modern taxonomy is to describe organisms, to name and classify them based on their evolutionary history. Currently, taxonomy is a booming field of science. People have come to realise the importance of basic taxonomic data; for example, it is needed to organise biological data which is being accumulated at increasing speed and we must understand species thoroughly to be able to protect their diversity.

A four-year research project on polymorphism involving several ministries was launched in 2003 in Finland. The Ministry of the Environment invested one million euros in the taxonomic study of poorly known Finnish species. This is an important topic.

"Of our organisms a large number are known so poorly that we cannot even assess how endangered they are," says Soili Stenroos, docent.

Opening doors to new people

Stenroos from the University of Turku's Botanical Museum heads a research project on micro-fungi found on mosses and lichens. When the German veteran of the field Peter Döbbeler from the University of Munich joined the group of researchers from Turku and Helsinki, it became the world's only team specialising in the micro-fungi of mosses.

The Ministry of the Environment provided funding for a research project concerning diptera, cortinaria, fungus gnats, aphids and ichneumons at the University of Helsinki – the only place in Finland where taxonomy is still taught.

What made Stenroos choose such a poorly known topic as micro-fungi? "Entering a completely new field is always challenging," she says. Funding was provided for the study of organisms and also to train new people.

"Among other things, we in the research group tried to think what group of organisms would open the most doors abroad to young researchers. Micro-fungi are poorly known and there is a lot to study."

Indeed, the team includes three researchers and five undergraduates working on their theses.

"They receive a thorough introduction into taxonomic research and hopefully are inspired to continue in the field," says Stenroos.

Growing mycelia

When the occasional mushroom pickers stumble in the woods and fall flat on their face in the moss, they may well have discovered a wealth of thousands of 'mushrooms'. Micro-fungi appear – when they appear at all – as tiny black specks on mosses.

The discovery is not likely to make them sing their praises, however, because micro-fungi are not much to eat. They are not much to study, either; their structure is extremely simple, which means that DNA is required for classification.

"To get enough mycelia for DNA analysis we have to grow them in the laboratory. Fortunately they are easy to grow," Stenroos says.

It may not come as a surprise that the almost invisible micro-fungi have not been studied before. In fact, only about 5% of the world's fungus varieties are known and new micro-fungi are discovered every now and then even in Finland.

The researchers did not have to pack their bags and leave for the mossy woods looking for samples straight away, however. While material grown for DNA analysis is usually and preferably kept separate from fresh samples, samples stored in botanical museums form a large part of the basis of the study.

"There are thousands of plant samples in Finnish museums that would suit our project. Fortunately for us, they have been carefully archived. Information on the precise location where a plant was found is necessary for researchers, for example," says Professor of Botany Jaakko Hyvönen.

Social entanglements of fungi and mosses

Micro-fungi are placed in the fungal 'tree of life' based on their base-pair sequences. The work has already produced some good results. During the first year of research the group has discovered a genus of micro fungi that is completely new to science and 20 species and three genera that are new in Finland.

"Our analyses also show that the symbiosis of micro-fungi and mosses has emerged independently on several occasions in the evolution of fungi and in several different ascomycetes groups," Stenroos tells us.

The team has also discovered that micro-fungi have several different forms of symbiosis with mosses. Some of the fungi harm their hosts lethally while others grow inside the moss without causing any apparent harm at all.

"Such endophytic relationships are known in conifers and deciduous trees and grasses," Stenroos says.

"It may also be that the symbiosis of fungi and mosses is based on co-evolution, meaning that both mosses and their micro-fungi have developed and specified side by side. It is interesting to try and find out how this ecological slot has been taken over, how a new way of life has emerged and from what kinds of organisms it has evolved. Why do some moss species always have a micro fungus with them, do they benefit from it and how? Or why do certain micro fungi always grow on particular moss species or only in a particular place on the moss," Stenroos wonders.

"Peter Döbbeler has studied micro-fungi in Tierra del Fuego and found as many as six on a single specimen of hair-cap moss. Thanks to Döbbeler's study and our own rich material we can in future compare the micro-fungi of hair-cap mosses from, for example, Tierra del Fuego and Finland," Jaakko Hyvönen says.

There are ambitious, massive taxonomic projects underway around the world. In Sweden, a 20-year project following in the footsteps of Linnaeus was launched in 2003 to collect comprehensive data on every organism found in Sweden. Everything is obviously bigger in the United States where several programmes funded by the National Science Foundation have been launched, including Partnership in Enhancing Expertise in Taxonomy, Planetary Biodiversity Inventories and Assembling the Tree of Life.

The goal of Assembling the Tree of Life is no less than to resolve the evolutionary history of all living and extinct organisms.

"The programme's fungus project entitled Assembling the Fungal Tree of Life includes a large number of European taxonomists, too," Stenroos says.

A similar project is being set up in Europe. European taxonomists have been working on it for 18 months now and EU funding is all but approved. Stenroos and Hyvönen are included in the European project.

"Completing this project is of immense importance to the future of taxonomy in Europe. Most of the diversity of the world's organisms has been stored in the natural science museums of Europe but this enormous wealth of information may be left unused and partly destroyed if we are unable to train new taxonomists. Today, young European researchers go to the United States, in particular because there is so much more money over there than in Europe," says Stenroos.

Computers work as we sleep

Every year, the University of Helsinki spends two million euros on personal computers. This resource usually sits idle for the better part of each day, mostly used only during the day. In the evenings, at night and during weekends the machines are unused. Instead, the idling computers could be put to work on calculations which would take months to complete on a single computer.

Professor Jaakko Hyvönen and Jyrki Muona from the Finnish Museum of Natural History have received 100,000 euros from the University’s own research funds for a three-year project using the existing computing resources of the University in large phylogenetic - evolutionary history - analyses.

The phylogenetic study of organisms requires massive computing capacity.

"For instance, 10 species may be linked to each other in more than two million ways and for 100 species there are 2x10182 such diagrams. In other words, we cannot test every possibility when we search for the most simple diagram despite efficient algorithms and there is still more than enough to compute," says Hyvönen.

Taxonomists do use the supercomputers of CSC, the Finnish IT centre for science, but even their capacity is not always enough. They have had to go as far as New York for their computations because the largest datasets have been too large to be run within the batch processing timeframe provided by the CSC.

CSC’s batch processing system means that a number of a supercomputers’ several processors is dedicated to a specific calculation for a specified time and the calculations end automatically when that time runs out if there are other calculations waiting in line.

In Hyvönen and Muona’s project - entitled Everclades - the calculations are divided into bits which are sent out to different machines and then returned to the host machine. Initially some 200 processors at the Finnish Museum of Natural Science and the University’s Viikki campus will be used. The purpose is to make the computers compute sequence data of the DNA of micro fungi, for example, after the user of a computer linked to the University’s network ends his workday.

"In decentralized computation calculations proceed without interruption on the Ôhost machine’ and the number of Ôslaves’ in use may vary radically. In other words, calculation makes slow progress during the daytime but on a Saturday evening, for example, when there may be as many as 200 processors available, the work proceeds very rapidly," Hyvönen explains.

"Such use of computing resources is rare in Europe and the University of Helsinki stands a chance of becoming the leader in large phylogenetic analyses," Hyvönen adds.