Projects / Programmes
Transcriptomics of fungal pathogens in the bark beetle-fungi symbiosis
| Code |
Science |
Field |
Subfield |
| 4.06.04 |
Biotechnical sciences |
Biotechnology |
Microbe biotechnology |
| Code |
Science |
Field |
| B230 |
Biomedical sciences |
Microbiology, bacteriology, virology, mycology |
| Code |
Science |
Field |
| 1.06 |
Natural Sciences |
Biological sciences |
climate change, Ophiostoma, sapstain fungi, Ips typographus, European spruce bark beetle, Picea abies, Norway spruce, cytochrome P450, PKS, NRPS
Researchers (1)
| no. |
Code |
Name and surname |
Research area |
Role |
Period |
No. of publicationsNo. of publications |
| 1. |
23473 |
PhD Ljerka Lah |
Biotechnology |
Head |
2010 - 2012 |
60 |
Organisations (1)
| no. |
Code |
Research organisation |
City |
Registration number |
No. of publicationsNo. of publications |
| 1. |
0104 |
National Institute of Chemistry |
Ljubljana |
5051592000 |
20,982 |
Abstract
Transcriptomics of fungal pathogens in the bark beetle-fungi symbiosis
Background: The predisposition of coniferous forests to bark beetle outbreaks is increasing as a consequence of climate change. Despite the fact that the European spruce bark beetle, Ips typographus, is an integral part of forest ecosystems, it is also considered a highly destructive pest. The bark beetle epidemic involves interactions between three principal biological components: host spruce trees (Picea abies), the bark beetle, and fungi associated by the beetle. I. typographus is a vector for Ophiostomatoid fungi (e.g. Ophiostoma bicolor) which destroy trees and decrease timber value. They weaken and detoxify spruce defenses (terpenoids, phenolics), thus granting successful colonization by the beetle and associated fungi. To overcome host defeses, pathogenic fungi evolved several resistance mechanisms. Among those are virulence factors, which are host-specific, and include enzymes involved in toxin biosynthesis, xenobiotic detoxification and (secreted) proteins.
Problem: Genes involved in fungal pathogenicity are virulence factors and importantly define the host-pathogen interaction through concerted action warranted by joint expression regulation. Key enzyme families involved in secondary metabolite biosynthesis include cytochromes P450, polyketide synthases and non-ribosomal peptide synthases. These genes are often arranged in gene clusters, and regulated by the combination of several transcription factors. Cytochromes P450 also detoxify xenobiotics, whereas efflux transporters function in their elimination. It is unknown exactly which genes are present in pathogenic expression profiles of non-sequenced ophiostomatoid fungi, and how those genes are regulated.
Aims: Through systematic focus on pathogenicity expression profiles this project aims to identify pathogenicity genes, to determine in which metabolic pathways they function, and to discover regulatory transcription factors in bark beetle-associated fungi. We intend to:
1. Identify ophiostomatoid genes involved in infection of spruce host trees using transcriptome sequencing and comparative genomics.
2. Establish phylogenetic relationships of selected genes in O. bicolor and related species.
3. Establish preliminary functional characterization studies for selected O. bicolor genes/proteins.
Methods: Standard molecular biology techniques will be used in cDNA library preparation of defense compound-treated mycelia. Transcriptomes obtained by next generation sequencing (Roche's 454 GS FLX Titanium) will be analyzed to identify genes important in O. bicolor pathogenicity using comparative genomics. Phylogenetic analyses of identified pathogenicity genes will be used to clarify evolutionary relationships between (closely) related pathogenic and/or saprophytic fungi. Preliminary studies of function will encompass gene selection and appropriate choice of method (deletion mutant studies/RNA interference or heterologous gene expression and further biochemical characterization).
Impact: Impacts of climate change on forest ecosystems will be manifold, and will effect abiotic and biotic disturbances (frequency of pathogen outbreaks). There is a great lack of comprehensive genomic studies of bark beetle system components, especially in Europe. A strong genomic background would be partly established with the proposed study, and would undoubtedly contribute to a deeper understanding of host-pathogen dynamics. It would warrant development of genomics enhanced environmental risk modeling predictions which would ensure sustainable management of commercial forests, and preservation of natural forest ecosystems and biodiversity.
Significance for science
In Europe, where bark beetle outbreaks have become more frequent in recent years, also as a consequence of a changing climate, there is a great lack of comprehensive genomic studies of bark beetle system components. The main aim of the project, which was successfully accomplished, was to create genomic and transcriptomic resources for two species of phytopathogenic fungi, Ceratocystis polonica and Ophiostoma bicolor, which are fungal associates of the European spruce bark beetle (Ips typographus). These resources are a firm background for further evolutionary and laboratory-based studies. In our proposed research we identified and phylogenetically characterized, and began to functionally caracterize key genes (with a focus on cytochromes P450)in the process of pathogenesis of bluestain fungi associated with bark beetles.
The project was partially based and supported with studies of a North-American species of fungal bark beetle associates, Grosmannia clavigera, which were part of a large scale project (www.thetriaproject.ca) on the genomics of system components of the mountain pine beetle (Dendroctonus ponderosae) partly conducted by the project leader. She has successfully transfered new knowledge on the latest genome and transcritpome sequencing methodologies, bioinformatic analyses of large sequencing data-sets (genome/transcriptome assembly and annotation) as well as knowledge on the biology of the North American symbiosis. New insights and results were twofold. Firstly, we were able to discover species-specific pathogenicity genes, through comparative genomic analyses of closely related pathogenic and/or saprophytic fungi. Subjected to further study, these can be characterized for their functional role in the fungus. Alternatively, their properties can be used in biotechnology (e.g. genes involved in secondary metabolite biosynthesis) or pharmacology (e.g. detoxifying enzymes as novel drug targets). Secondly, such an analysis yields information on the more general principles and mechanisms of host-pathogen interactions, which can be extended beyond the bark-beetle system interactions.
Microbial symbionts represent an internal control of the bark beetle system that regulates the surpassing of thresholds which lead to epidemic eruptions. Studying the genomic background of the bark beetle system is a bottom-up approach to the study of system dynamics at endemic and epidemic levels. It should be recognized, considered and integrated into studies of pathogen outbreaks on higher levels of scale, such as environmental studies or generating genomics-enhanced modeling tools for environmental risk predictions.
Significance for the country
The impacts of climate change on forests and forestry in the Europe will be manifold and complex. These changes will of course further effect social well-being through economy and international competitiveness. Higher temperatures, increasing atmospheric CO2 concentration, and changes in precipitation and droughts will have associated consequences for abiotic (e.g. fires, storms) and biotic disturbances (frequency and consequences of pathogen outbreaks). All consequent environmental changes will have strong implications for forest ecosystems. The above are introductory statements of a November 2008 report to the European Commission Directorate-General for Agriculture and Rural Development: Impacts of Climate Change on European Forests and Options for Adaptation (Lindner et al., 2008).
Currently, measures against damage by Ips typographus and other bark beetle species seek to control beetle activity with comprehensive salvage logging and large-scale commercial harvesting of infested stands in order to remove all potential breeding materials such as weakened trees, windthrows and logs with bark before the new generation of adult beetles emerge. Additionally, silvicultural techniques are adopted, aimed at increasing the stability and vitality of forest stands. The use of pheromone-baited traps or trap trees has also been used to trap and suppress beetle populations and prevent outbreak conditions. Several of these measures, however, have negative effects on forest ecosystems (e.g. salvage logging delays forest recovery). Uniform measures throughout Europe are difficult to administer because of the varied bioclimactic zonations and different forest types.
There is a great lack of comprehensive genomic studies of bark beetle system components, especially in Europe. A strong genomic background of bark beetles associated pathogenic fungi and host conifer trees would without a doubt contribute to a deeper understanding of host-pathogen dynamics. It would allow for the development of genomics enhanced environmental risk modeling predictions and sustainable development and management of commercial forests and preservation of non-commercial forest ecosystems and biodiversity.
The proposed research agrees completely with the national research and development program. The field of life sciences and health is a priority field with great economic promises and the highest added value, as already designated in the Slovenian National and Developmental Resolution program. Investment in genomic and biotechnology research for health is the priority of the public appeal, and the proposed project fulfils it entirely.
In the proposed project we have established a firm cooperation with distinguished international research groups. Our collaborators from the University of British Columbia in Vancouver and University of Guelph (Ontario), Canada, head world leading research in forest health genomics. We intend to integrate the results of our studies also in the future which will add depth to our understanding of the genomic background of the bark beetle system across continents, as well as strengthen our collaboration efforts.
Most important scientific results
Annual report
2011,
final report,
complete report on dLib.si
Most important socioeconomically and culturally relevant results
Final report,
complete report on dLib.si
