Periodic Reporting for period 2 - VIROPLANT (VIROME NGS ANALYSIS OF PESTS AND PATHOGENS FOR PLANT PROTECTION)
Période du rapport: 2019-11-01 au 2021-10-31
The general objective of VIROPLANT is to study and propose integrated biocontrol strategies based on viruses. Growing conflicts between farmers and general society about the use of pesticides in highly urbanized areas of grapevine and fruit cultivation are a cause of major concern. Safer alternatives must be found.
VIROPLANT has the following specific objectives:
I) Finding biocontrol tools for bacterial diseases of plants to replace copper, the only available chemical approach routinely allowed in Europe against bacteria.
II) Finding alternatives to the use of chemical fungicides for the control of plant diseases caused by fungi.
III) Reducing the use of insecticides to control pests causing direct and indirect damage to plants.
IV) Exploring the potential of recent technology (RNA interference=RNAi) to limit the use of fungicides and pesticides in agriculture.
V) Evaluating the possible “resilience” to biotic stresses caused by the presence of covert/cryptic viruses in model crops (tomato), and in one specific experimental system.
VI) Assessing the environmental risk of phage therapy against bacterial plant pathogens.
VII) Identifying and measuring generational and gender-specific drivers for social acceptance of natural and biotechnologically manipulated virome-based tools.
VIII) Identifying new business and market opportunities on a regional and European scale for virus-based biological control agents (BCAs).
In summary, VIROPLANT was able to identify and characterize molecularly a large number of new viruses infecting bacteria, fungi and insects. Some of them were characterized also biologically, and their potential for biocontrol was evaluated. Some encouraging results were obtained specifically for the bacteriophages to be used for control of bacterial plant diseases. Virus-induced gene silencing (VIGS) approaches did not result in feasible biocontrol tools, both for technical and regulatory reasons. A potential market and communication strategy to overcome reluctance to adopt virus-based biocontrol agents were identified. The regulatory burden together with low social acceptability remains a major hurdle to develop further steps.
VIROPLANT has the following specific objectives:
I) Finding biocontrol tools for bacterial diseases of plants to replace copper, the only available chemical approach routinely allowed in Europe against bacteria.
II) Finding alternatives to the use of chemical fungicides for the control of plant diseases caused by fungi.
III) Reducing the use of insecticides to control pests causing direct and indirect damage to plants.
IV) Exploring the potential of recent technology (RNA interference=RNAi) to limit the use of fungicides and pesticides in agriculture.
V) Evaluating the possible “resilience” to biotic stresses caused by the presence of covert/cryptic viruses in model crops (tomato), and in one specific experimental system.
VI) Assessing the environmental risk of phage therapy against bacterial plant pathogens.
VII) Identifying and measuring generational and gender-specific drivers for social acceptance of natural and biotechnologically manipulated virome-based tools.
VIII) Identifying new business and market opportunities on a regional and European scale for virus-based biological control agents (BCAs).
In summary, VIROPLANT was able to identify and characterize molecularly a large number of new viruses infecting bacteria, fungi and insects. Some of them were characterized also biologically, and their potential for biocontrol was evaluated. Some encouraging results were obtained specifically for the bacteriophages to be used for control of bacterial plant diseases. Virus-induced gene silencing (VIGS) approaches did not result in feasible biocontrol tools, both for technical and regulatory reasons. A potential market and communication strategy to overcome reluctance to adopt virus-based biocontrol agents were identified. The regulatory burden together with low social acceptability remains a major hurdle to develop further steps.
VIROPLANT isolated and characterized 33 new bacteriophages that are good candidates for a phage biocontrol approach for some important bacterial plant diseases, such as bacterial wilt of roses, bacterial canker of cherry and kiwi vine and crazy root diseases of cucurbits. For some of them, such as the bacterial canker of kiwi vine, the translation to a specific in vivo application still remains to be ascertained due to issues defining a correct delivery method. However, for the cherry pathogens and for the rose system, the phage cocktails are ready to approach interested companies to bring them to the market. The standardized methodology for environmental risk assessment for phage therapy tested in VIROPLANT could be further exploited by stakeholders involved in regulation (e.g. EFSA).
Regarding the use of mycovirus to limit biotrophic fungal/oomycetes diseases, the main exploitable results obtained in VIROPLANT are:
• The description of the viromes can be exploited for new theories of virus evolution by scientists.
• We have characterized more than new 1000 virus segments corresponding to circa 600 new mycovirus species. Their sequences are deposited in public repositories (GenBank) and described in peer-reviewed publications, and these could be potentially exploited for specific biocontrol applications.
• Several hypovirulent strains of B. cinerea with biocontrol potential were identified and some mycoviral candidates inducing hypovirulence were also characterized. An infectious clone of Botrytis virus F has been successfully developed and will be exploited for the construction of a viral expression and VIGS vector.
• A VIGS vector with potential to produce dsRNA to be used for RNAi approaches against fungi has been developed. The one based on CHV1 infectious clone was shown to work on endogenous silencing and can be exploited for reverse genetic approaches by other scientists.
Regarding the search of new viruses to control insect pests and vectors, VIROPLANT exploitable results are:
• A “turnkey” approach for virus identification/survey in agrosystems.
• Two new VIGS insect virus vectors.
• The development and breed of thrips populations with specific persistent virus that can interfere with tospovirus transmission (synergy or antagonism).
• For the plant mitovirus, the virus-associated resilience to abiotic stress could become a strategy for improving plant performance, i.e. breeding for resistance with mitochondrial viruses.
VIROPLANT also conducted an inquiry in the economical/regulatory landscape to accompany virus-based plant protection products (PPPs) to the market. The potential exploitable results of this analysis are:
• The results of the techno-economic system analysis can guide companies wanting to invest in virus-based PPPs and inspire funding agencies about the necessity and urgency of supporting research in this field.
• Gaps in the regulation and research to bring phage-based PPPs to the EU market have been identified and should be considered by the regulatory agencies.
• Preliminary three-tier protocol is proposed for the environmental impact of phage-based PPPs.
VIROPLANT also considered ways to monitor, and possibly improve, social acceptance of virus-based PPPs.
The results are of utmost important to policy makers and whoever is involved in technological innovation in the biotechnological field. A roadmap towards conditions to improve the “process” of acceptability is paved.
The dissemination activities implemented in the project are: 24 open access peer-reviewed scientific publications (that obtained a total of 246 citations), 4 articles published in local magazines for farmers, 25 participations to national and international scientific conferences (9 posters and 16 oral presentations), 13 seminars to academics and 16 meetings with stakeholders.
Regarding the use of mycovirus to limit biotrophic fungal/oomycetes diseases, the main exploitable results obtained in VIROPLANT are:
• The description of the viromes can be exploited for new theories of virus evolution by scientists.
• We have characterized more than new 1000 virus segments corresponding to circa 600 new mycovirus species. Their sequences are deposited in public repositories (GenBank) and described in peer-reviewed publications, and these could be potentially exploited for specific biocontrol applications.
• Several hypovirulent strains of B. cinerea with biocontrol potential were identified and some mycoviral candidates inducing hypovirulence were also characterized. An infectious clone of Botrytis virus F has been successfully developed and will be exploited for the construction of a viral expression and VIGS vector.
• A VIGS vector with potential to produce dsRNA to be used for RNAi approaches against fungi has been developed. The one based on CHV1 infectious clone was shown to work on endogenous silencing and can be exploited for reverse genetic approaches by other scientists.
Regarding the search of new viruses to control insect pests and vectors, VIROPLANT exploitable results are:
• A “turnkey” approach for virus identification/survey in agrosystems.
• Two new VIGS insect virus vectors.
• The development and breed of thrips populations with specific persistent virus that can interfere with tospovirus transmission (synergy or antagonism).
• For the plant mitovirus, the virus-associated resilience to abiotic stress could become a strategy for improving plant performance, i.e. breeding for resistance with mitochondrial viruses.
VIROPLANT also conducted an inquiry in the economical/regulatory landscape to accompany virus-based plant protection products (PPPs) to the market. The potential exploitable results of this analysis are:
• The results of the techno-economic system analysis can guide companies wanting to invest in virus-based PPPs and inspire funding agencies about the necessity and urgency of supporting research in this field.
• Gaps in the regulation and research to bring phage-based PPPs to the EU market have been identified and should be considered by the regulatory agencies.
• Preliminary three-tier protocol is proposed for the environmental impact of phage-based PPPs.
VIROPLANT also considered ways to monitor, and possibly improve, social acceptance of virus-based PPPs.
The results are of utmost important to policy makers and whoever is involved in technological innovation in the biotechnological field. A roadmap towards conditions to improve the “process” of acceptability is paved.
The dissemination activities implemented in the project are: 24 open access peer-reviewed scientific publications (that obtained a total of 246 citations), 4 articles published in local magazines for farmers, 25 participations to national and international scientific conferences (9 posters and 16 oral presentations), 13 seminars to academics and 16 meetings with stakeholders.
VIROPLANT accomplished initial steps to bring to the European market the first phage cocktail for a crop disease; has looked at the possibility of using circular ssDNA mycoviruses directly as fungicides against Botrytis cinerea; has developed the first mycovirus-based vector for successful VIGS in fungi; has broadened the arsenal of virus-based tools available for bio control of insect pests beyond the limited host range of baculoviruses; has looked at the specific aspects behind gender/generational bias acceptance, and has provided specific communication strategies to overcome reluctance to adopt virus-based products.
IMPACTS
- VIROPLANT had a major impact in re-shaping the evolutionary history of mycovirus
- VIROPLANT identified a new insect virus-based strategy to interfere with tospovirus transmission
- potentially reduce reliance on chemical plant protection products
- introduce novel products with increased specificity and improved environmental performance
IMPACTS ON SOCIETY
- improve societal awareness, i.e. to improve the general acceptance of gene therapy based on viruses.
- improve perception of viruses and virus-based products in the learning process in school curricula.
IMPACTS
- VIROPLANT had a major impact in re-shaping the evolutionary history of mycovirus
- VIROPLANT identified a new insect virus-based strategy to interfere with tospovirus transmission
- potentially reduce reliance on chemical plant protection products
- introduce novel products with increased specificity and improved environmental performance
IMPACTS ON SOCIETY
- improve societal awareness, i.e. to improve the general acceptance of gene therapy based on viruses.
- improve perception of viruses and virus-based products in the learning process in school curricula.