Investigation of mold fungi, nature’s substances, to replace pesticides

DTU is helping a large international company to find nature’s substances to combat fungal diseases in crops. The University’s large collection of molds and a small collection of bacteria are part of the project – and one of them may hold the solution. Thirty-eight thousand, four hundred isolates of mold fungi take the leading role in the major research project “Smarter AgroBiological Screening” (SABS). In the project, DTU is collaborating with the international company FMC, which produces crop protection such as pesticides for agriculture.

The elusive ‘lead actors’ are stored in plastic tubes with red screw caps at exactly 9°C in a basement at DTU and form an internationally recognized collection of fungi started in 1988 by university researchers storing the first isolates.

Now, 35 years later, they will be carefully studied along with a small collection of bacteria. Perhaps, these microorganisms can be used to produce biofungicides, i.e. natural substances that can fight fungal diseases in cereal crops. Expectations are particularly high for mold fungi.

“Biotechnologically speaking, the mold fungus is a really fascinating organism because each fungus has anywhere from 50 to 80 biosynthetic pathways. A biosynthetic pathway is a series of reactions within the organism that allow the production of a bioactive substance. By comparison, a normal bacterium can it has six to seven biosynthesis pathways while a yeast cell has none. It makes fungi really rich but also very complex to study. So the exploration of fungi has great potential and maybe we can find substances that can be used to control diseases in agriculture. ” says Rasmus John Normand Frandsen, Associate Professor at DTU and coordinator of DTU’s participation in the project.

In detail, “For the vast majority of substances—probably as many as 95%—we have no idea what they’re used for or why microorganisms make them. But they’re made in nature for a reason, and maybe with a purpose we can benefit from.”

Pesticide use must be halved

Finding alternatives to chemical-based pesticides is urgent, with the EU proposing to halve use by member states by 2030 and a complete ban in sensitive areas.

But pesticides – despite their bad reputation – have ensured that crop yields are not destroyed by plant diseases and insects. According to a note from Aarhus University, phasing out pesticides will result in significant production losses, and total phasing out will cause an average reduction in grain yields of 23%, as well as large losses—up to 50%—in sugar beet and potato production.

With increasing global food demand, we need to find other ways to ensure good crop yields to make a green transition in plant breeding that does not require including more land for cultivation and thus emitting more CO₂.

Preparing fungal collection for robots

So how do you screen 38,400 mold isolates? Right now, there is only one, slow method. the portable, says Niels Bjerg Jensen, project manager on the project and liaison with FMC. However, as a key part of the SABS project, DTU’s entire fungal collection will be “modernized” so that we can avoid the manual part in the future and use robots to check the collection.

The modernization means that two lab technicians currently retrieve the isolates from the basement and unscrew the red cap, one by one, to siphon the spores from the fungus and transfer them to an agar plate where they can be grown in the lab. After 8–10 days, lab technicians can collect the fresh spores and transfer them to a 24-well plastic tray (or wells, as they’re actually called) where each well houses its own fungal isolate.

The robot then takes over and finally transfers the fungi to a plastic 96-well plate. Now the shape of the fungi fits the automated process where a robot can pipette spores from 96 fungi at once.

“In the future, this means that we will be able to examine around 100 times more molds at the same time we are looking for an organism to help us,” says Niels Bjerg Jensen, who explains that collecting fungi in the new robot-friendly format will stored at minus 80°C so that isolates can be retrieved again and again for future testing.

High performance laboratories

The automated process, where slow and portable pipetting is omitted, means that both speed and amount of data are increased tremendously. It’s a trend that’s being seen worldwide and it’s called high performance labs.

“It’s clear from biotech research articles around the world that data sets are getting bigger and bigger. Just a few years ago, it was normal for a data set to consist of maybe a dozen microorganisms. Now it’s possible to include hundreds of microorganisms,” he says. Rasmus John Nordmand Frandsen.

It also places demands on the staffing of biotechnology laboratories, which now also have a need for profiles that can program robots and create data warehouses to structure the vast amounts of biological data.

As fungal tests at DTU generate data, it will also be possible to use artificial intelligence in fungal tests.

“Artificial intelligence can find connections and patterns in huge amounts of data that humans simply cannot search and can facilitate faster identification of fungi that have the potential to help us,” says Rasmus John Nordmand Frandsen.

Promising fungi discovered

In the SABS project, DTU has already screened and identified some promising fungi that have succeeded in producing the desired bioactive substances in the laboratory. The candidates have been handed over to the FMC for further investigation. If the promising results continue, the next step is to test the substances under controlled conditions in field experiments where grains are grown using natural fungicides.

For FMC, the project is an opportunity to develop solutions that meet the needs of agriculture to complete a green transition.

“Biopesticides provide new methods to combat plant diseases and help extend the usefulness of existing chemistry. They are a sustainable tool that satisfies plant growers’ need for new solutions and neutralizes resistance, which helps extend shelf life of chemical active substances as well as protecting the environment,” says Burghard Liebmann, Director of Plant Health Research and Development at FMC’s European Innovation Center in Hørsholm, Denmark.

“FMC is excited to be working with DTU on the SABS project. We benefit from DTU Bioengineering’s large and diverse collection of microorganisms. DTU’s expertise in microbiology, genomics, metabolism, automation and artificial intelligence is invaluable to work.”