JYUnity

Fungal spores larger than a micrometre flow into the mouth of a cyclone sampler in the Siberian taiga in Yakutia. The same procedure is underway on Barro Colorado Island in Panama and in 50 places across the globe. Over the course of a year, billions of spores are collected in test tubes – largely from fungi still unknown to science. They provide information about ecological diversity, and Academy Professor Otso Ovaskainen and his research team are the first ones to sort through the data.

Otso Ovaskainen outlines the starting point as follows: “We are aware of the accelerating disappearance of species, but we know only a fraction about biodiversity itself and there are especially fungal species that remain unknown to science, but which may potentially serve as key indicators of ecological wellbeing. In fact, nature and humans could not cope without fungi. Fungi serve as major decomposers in ecosystems and helpers for plants both in nutrition intake and as part of the defence against diseases.

A leap in the research into fungal populations was achieved when researchers began taking into systematic consideration not only the mycelium and fruiting bodies of fungi but also the airborne spores.

Otso Ovaskainen leads ERC-synergy project LIFEPLAN.

“With Nerea Abrego and Veera Norros, we tested whether species could be identified from cyclone samples by means of DNA sequencing”, Ovaskainen says. “The results of our pilot study were encouraging and we decided to explore the global spectrum of fungal species by sending devices to our cooperation partners around the world.” The idea was originally developed at a lunch in 2017, when Ovaskainen, Abrego and Tomas Roslin were sitting at the same table.

Indeed, this combination is now producing results effectively. Fungal spores collected from the Siberian taiga are sequenced into nucleotide series in a Canadian laboratory. Information on the range of species is obtained after several computational phases pertaining to bioinformatics and statistical analysis. In 2019, the research received 12 million euros of ERC funding.

Researcher were surprised how cosmopolitan fungi are – next we will find out the seasonal impacts

The first results of the global research are now available and Ovaskainen finds them truly interesting.

“Climate is clearly a decisive explanatory factor for the existence of fungal species,” says Ovaskainen, speaking about the first findings of the ERC-synergy project LIFEPLAN that he leads.

“We expected to see an impact of geographical distance as well, so that the composition of species would be different in different continents, for instance. However, this seems not to be the case. The range of species was highly similar within the same climate zone, for example in Australia, Argentina, South Africa and Croatia.”

Fungal populations have recently been studied on a smaller scale also in Finland. Senior Researcher Nerea Abrego is working with cyclone sampler at Sipoo.

The analyses expand knowledge regarding already previously known species, even though most of the spores could be categorised on the level of fungal genera only, instead of precise species. From a total of 2,100 collected samples, a total of 100 million DNA sequences were generated. Based on the samples, the air at the test sites contained spores of hundreds of thousands of species. The overall number of fungi is estimated to be in the millions, so most of them still remained undetected.

As the research progresses, the group analyse how seasonal variation, for instance, influences the composition of species. For fungi, systematic global-level knowledge about this remains scarce.

“A specific point of interest is how long the distances are over which fungi spread.”

“Previous studies indicate that most of the spores produced actually land within the radius of a few metres from the fruiting body, whereas some of them can fly as far as the other side of the globe. Our data include direct evidence about this kind of long-distance spreading. For example, in samples collected from arctic areas in winter, we can detect hundreds of species.”

What happens to the range of species when the climate or land use changes?

Airborne fungal spores are just a part of the data collected in the LIFEPLAN study. Other research equipment has been set up at 450 sites across the world.

Fungal samples are collected from the soil as well. Insects are captured by means of tent traps, mammals are photographed by trail cameras, and bird and bat sounds are audio recorded.

The data also involves a lynx, which recently stepped into the range of a remote camera at Lammi Biological Research Station.

“This lynx will become one among the huge number of data points in our systematically collected data and appear as part of the results in a scientific article maybe a couple of years from now”, Ovaskainen says.

Overall, the dataset will comprise up to 5,000 terabytes collected over a five-year period. The Finnish IT Center for Science, CSC, plays a central role in data storage and computing for the study.

When the dataset is ready, meaning the field samples have been collected and DNA sequenced, and the species have been identified, Ovaskainen will start another, future-oriented section of the study. He is going to model how the composition of species is changing along with changes in climate or land use, for instance.

Such modelling is his area of expertise. As a top expert of his field, the Academy of Finland appointed Ovaskainen as a Research Professor for a five-year term starting from September 2021. Since the beginning of this year, he has worked as a professor of mathematical and statistical ecology at the University of Jyväskylä.

Using ecological modelling, Ovaskainen eventually seeks answers to the question of what happens to a set of species in climate change. “Before finding the answers,” Ovaskainen says, “we must first reduce uncertainties and learn more about ecological rules and patterns.”

1. The first phase comprises automatic identification of species by means of machine learning. All of the uncertainties related to identification must be considered. In general, only part of the species have been scientifically described, and even reference databases for known species contain some errors, be they about bird sounds or fungal DNA sequences.

2. The second phase: Identifying ecological rules and patterns through statistical modelling. This helps us understand how the dynamics of species depend on the climate and biotopes as well as on the interaction between different species.

3. In the third phase, this new understanding enables, for example, predictions about what will happen to various species along with climate change.

The amount of fungal spores plummeted in the Finnish urban environment

Alongside the global research, fungal populations have recently been studied on a smaller scale also in Finland. The results of a study conducted in five Finnish cities (Jyväskylä, Helsinki, Lahti, Tampere, and Joensuu) give a harsh picture of the impact of urbanisation on fungal populations.

The amount of fungal spores plummeted in the Finnish urban environment.

Looking at airborne spores and soil samples, the study obtained information about tens of thousands of fungal species. It was found that the amount of fungi has declined sharply between woods and built environment.

”We were surprised to find that the amount of airborne spores plummets to a fifth when moving just a kilometre away from a nearby forest to a built-up area”, says the main author of the research report, Senior Researcher Nerea Abrego from the University of Jyväskylä. “This supports the view that most spores travel just a very short distance, even if some of them may fly thousands of kilometres away.”

Confirmation of these findings is now being sought in the global research as well.

“Our global sample scheme involves 100 sites, each with both a more urban and a more natural-state environment”, Ovaskainen says. “It will be truly interesting to see whether we will find equally clear effects of urbanisation in all of these places. Decreased biodiversity in urban surroundings is associated with human wellbeing.”