Projects / Programmes
Genomic / transcriptomic approaches to fungus-pest interactions and biological control
| Code |
Science |
Field |
Subfield |
| 4.03.05 |
Biotechnical sciences |
Plant production |
Phytomedicine |
| Code |
Science |
Field |
| B230 |
Biomedical sciences |
Microbiology, bacteriology, virology, mycology |
| Code |
Science |
Field |
| 4.01 |
Agricultural and Veterinary Sciences |
Agriculture, Forestry and Fisheries |
Biodiversity, biological control, fungi, nematodes, plant growth promotion, soil, soil-borne pests, sustainable food production, genomics, transcriptomics
Researchers (12)
Organisations (2)
Abstract
Agricultural production has been and is relying on external, artificially produced pesticides and fertilizers that cause pressures on ecological services, on which human societies depend. Invasive species and the changed behaviour of indigenous pest species (specifically nematodes and insects), emerging as a consequence of climatic changes, present other pressures. Soil systems are of primary concern. An increase in soil temperature during spring can significantly affect the behaviour of soil borne pests. No pesticide is currently accredited for the use against subterranean nematodes but partly invasive species of the nematode genus Meloidogyne emerged recently as important pests in Europe. New or improved concepts are therefore required to deal with the growing threat of soil borne animal pests and to promote plant growth without or with limited amounts of fertilizers.
The proposed research aims at strengthening knowledge on fungi that have beneficial traits as biological control agents (BCAs) against soil borne nematodes & insects in general. Specifically, however, it aims at the identification of agents that can use an animal pest as prey and at the same time promote plant growth as rhizosphere colonizers and/or endophytes. These traits have been described already for species of the fungal genera Clonostachys and Trichoderma. Although they are best known as BCAs for the control of other fungal plant pathogens, representative species of both genera are also known as soil saprotrophs, rhizophere colonizers, endophytes and plant growth promoters. They were recently also encountered as potential control agents of nematodes and a Clonostachys sp. was also described as potentially effective against insects. Accordingly we suggest additional inventories for targeting fungi that inhabit (1) the rhizosphere of plants infected with nematodes (root knot nematode Meloidogyne sp. and potato cyst nematode Globodera rostochiensis); (2) inner parts of Meloidogyne infected roots as endophytes; (3) inner parts of cysts of G. rostochiensis; and (4) free living or as baits introduced insect larvae.
Fungi are characterized and identified on the bases of sets of DNA sequences allowing fine tuned taxon recognition and the discovery of potentially new beneficial microbes. A tomato or, respectively, a tomato-Meloidogyne system is then implemented for the identification of plant growth promoters and effective BCAs parasitizing eggs and/or the free living juvenile nematode stage.
Although Clonostachys and Trichoderma are only distantly related because they belong to different families of the Hypocreales, their species have similarly diverse and frequently beneficial traits. A genomic and transcriptomic comparison of Clonostachys and Trichoderma should therefore lead to better understanding the underlying molecular mechanisms for biological control and the involved genes and regulatory systems. Understanding these mechanisms is a prerequisite for an optimized exploitation and to manipulate their behaviour towards human benefit in sustainable applications. We aim therefore at sequencing the genomes of Clonostachys species and to compare these genomes with already available Trichoderma genome data. Through sequencing transcriptomes retrieved from defined fungal nematode interactions, major factors (proteins and peptides) involved in the interaction will be identified. The specific role of selected genes will then be analyzed through reversed genetics on the basis of mutants with altered gene expressions.
Significance for science
Many agriculturally important fungi are found in the fungal order Hypocreales that accommodates important plant pathogens, mycotoxin producers and opportunistic human pathogens (e.g., Fusarium), and biological control agents (e.g., Beauveria, Metarhizium, Trichoderma and Clonostachys). The project’s findings improve our current understanding of species that belong to this important order. Providing taxonomic solutions that clarify species boundaries allowed recognition and assignment of biological traits to individual fungi. Also, study of narrowly defined ecological niches allowed to understand the ecological features associated with the isolated resident microbial species. The selected isolation approach of fungi from natural ecological niches influenced the research hypotheses we were proposing. The study of either undescribed, potentially rarely encountered species showing pest control abilities, and others that are known to interact with pests, provided insights into nematode and insect control approaches. Clonostachys rosea (Bionectriaceae) accommodates commonly encountered saprotrophic strains. However, the same strains can also possess a wide range of additional traits, including fungal parasitism, ability to associate plants as endophytes, and rhizosphere colonizers. Results from experiments showed that C. rosea can destructively interact with Meloidogyne nematode eggs and reduce the reproduction of this pest on tomato plants. A similar nematode related behaviour was observed in a currently undescribed species of the Nectriaceae isolated from tomato in Slovenia. Although this species shows a Fusarium-like morphology, it is unlikely plant pathogenic, because phylogenetically it is unrelated to Fusarium plant pathogens. Trichoderma longibrachiatum (Hypocreaceae) had no effect on nematode reproduction in plant experiments but parasitized nematode eggs in slide culture tests. The observed similar ecological behaviour of the species belonging to different Hypocreales families may have evolved independently. Transcriptomic analyses of genes expressed during parasitism on Meloidogyne nematode eggs can contribute to our understanding of different parasitism strategies that evolved in three different families of the Hypocreales (Bionectriaceae, Hypocreaceae, Nectriaceae). Chemical pesticides and biopesticides contribute to crop health and quality, however, both often do not selectively target pest species only, but also other living components in agro-ecosystems. This is the case for several biopesticide agents that are currently marketed for insect and also nematode control. Results obtained during the project imply that some common soil fungi may contribute to the natural control of soil pests. Even common and frequent plant pathogens showing a wide ecological amplitude and possessing also saprotrophic abilities can destructively parasite nematode eggs. Research development towards sustainable approaches in agro-ecosystems may thus shift focus from development and improvement of biopesticides to microbial diversity and species abundance in soil. We gained insight into destructive parasitism of fungi on agriculturally relevant insect pests, like Delia radicum on cauliflower. The tested fungi inoculated on roots of seedlings can become established in the rhizosphere. Plant roots inoculated with beneficial fungi may thus disseminate beneficial agents. Dissemination of ecological service providers by using plant as a vector for beneficial fungi is an attractive concept, and may reduce frequency of seasonal crop spraying with biopesticide formulations.
Significance for the country
Inventories of entomopathogenic and nematode parasitizing fungi clearly stimulated and implemented research that is of high applicability in agriculture. So-called biopesticides that are based on living microorganisms are considered to present environmentally more acceptable or at least alternative tools for controlling plant pests. They have the potential to add sustainability to crop production. Molecular barcode based identifications of retrieved species showed that agents of some, already available commercial biopesticides are also naturally present in agro-ecosystems in Slovenia. Resolving such problems is not trivial because of unresolved taxonomic problems and confusions. The results help to understand the biogeographic distribution and ecological traits of already identified or novel beneficial fungi, of which some are used in already existing biopesticide formulations. Knowledge about biogeography and ecological traits of these species is one of several requirements that may lead to the development of new or registrations of available formulations in countries of the EU. Results are thus of interest for decision makers and were provided to the Ministry of Agriculture Forestry and Food (MKGP). Applied aspects of the project were implemented and are conform with integrated pest management strategies and the demand to increase sustainability in agriculture. The reduction in dependence on chemical pesticides is a directive expressed by the agenda for agriculture in Slovenia (Resolution on the strategic orientations of development of Slovenian agriculture and food industry until 2020, ReSURSKŽ). Beneficial fungi can be implemented in Integrated Pest Management Strategies only if these fungi are well studied. Adopting Integrated Pest Management Strategies and developing more sustainable approaches in agriculture are of utmost importance for human as they can reduce pressures to natural resources societies increasingly depend on.
Most important scientific results
Annual report
2013,
2014,
2015,
final report
Most important socioeconomically and culturally relevant results
Annual report
2013,
2014,
2015,
final report
