Microorganisms to Control Phytopathogenic Fungi

Research motivation

Due to the climatic changes of our time, extreme weather events increase. This leads to multidimensional plant stress. Under the influence of hot spells and droughts as well as extreme rainfalls, indigenous and foreign crop pests gain ground. These include fungal pathogens, which impair crop yields in conventional agriculture and organic farming. The agricultural sector is facing increasing problems due to resistance developments of these pests. Therefore, alternative fungicides are needed. 

Chances and Challenges of Agriculture 

Approximately 35 percent of the area of Germany are used for the cultivation of agricultural commodities. Thereby, conventional farming systems achieve high crop yields, particularly by using chemical-synthetically produced pesticides and agrochemicals. Due to that, the conventional agriculture is responsible for almost the entire environmental pollution, based on plant protection products. This results in a serious loss of biodiversity, the destruction of habitats and the manifestation of pesticides in food chains. The constant and unilateral application of these agents cause a misguided selection pressure and finally the resistances of harmful organisms. To counteract these current developments, a realignment of the agricultural systems towards bio-economically compatible, sustainable food production is indispensable. In the »strategy for the future of organic farming« the German federal government aims to double the area of organic farming from 2019 until 2030. However, this form of cultivation reaches 20 percent less yield than the conventional agriculture. Moreover, the yield stability is subject to substantial fluctuations.

Consequently, throughout the transformation to environmentally compatible agricultural systems, the organic cultivation needs to maintain or increase its productivity and its resilience towards factors associated with the climate change. An essential factor for yield loss are fungal diseases. However, especially for organic farming systems, there is a lack of eradication tools. Consequently, the specific need for suitable, bio-based antifungal products really exists. Their development must be based on scientifically secured foundations that comply with the ecological and sanitary application standards of the EU.

Biocontrol agents based on natural products as solution

One possible solution is the usage of biocontrol agents, which are approved as a future oriented technology in ecological agriculture. These agents are plant protection products that are not of chemical-synthetic origin. Instead, they are applied in form of isolated natural products or strain-preparations of microorganisms, for plant stimulation and pathogen defense.

Biocontrol agents with an antifungal activity already available are based on bacterial or fungal strains. These products contain inter alia Bacilli and Actinobacteria as active components and function based on their bacterial natural mechanisms. The bacterial groups are united by a complex lifecycle that leads to the formulation of spores to survive rough environmental conditions. Microorganisms that produce heat- and dehydration-resistant spores provide a natural solution for the product formulation. This facilitates an important step during the development from the living organism towards an applicable product.

Both soil living groups of microorganisms produce a broad range of bioactive natural products. These include substances, which promote plant health. Yet, strains of these two bacterial groups are also known producers of medicine-associated agents as antibiotics, or toxic compounds. The application of medicinally relevant substances contradicts the common scientific understandings and has to be avoided with regard to resistance developments. Moreover, toxic substances as insecticides or herbicides can have devastating effects on the sensitive ecosystems of the agricultural landscape.

Therefore, potential producer strains have a wide-ranging feature profile that has to be determined in case of an agricultural application.

The published knowledge on metabolic potentials of such strains, already available on the market, is poor. Additionally, the range of strains used is not satisfactory.

For a safe application of this type of products, it is decisive to identify the specific mode of actions that are responsible for their functionality. This way the risk for the environment and us humans can be assessed on a scientific fundament. In addition, the potential for resistance development can be determined.

Strain collection of the Fraunhofer IME: a valuable resource for the development of antifungal natural products

In a three-phased project, Actinobacteria and bacteria of the genus Bacillus, from the 120,000 microorganisms counting strain collection of the Fraunhofer IME, are tested for a potential antifungal activity, against Septoria tritici in wheat and Colletitrichum coccodes in potatoes. Guided by antifungal bioactivity data, the overall metabolite profile of every active strain is assessed due to metabolomic technologies. Moreover, the antifungally active substance is identified. Along with the genomic-driven analysis of the biosynthetic potentials, the production of plant growth promoting agents as phytohormones, complexing agents or organic acids, as well as undesired metabolites can be examined.

This way, strains with low-risk feature profiles can be identified. They are tested as strain preparations or isolated natural products on their toxicity towards mammalian cells, insects and plants.

In final plant experiments, the potential for the application as a bio control agent is assessed.

Due to this process, a global risk-assessment of potential bio control strains can be performed before their further application as bio control agents in the organic farming research.