High Throughput sequencing technologies complemented by growers’ perceptions highlight the impact of tomato virome in diversified vegetable farms and a lack of awareness of emerging virus threats
Belgium; grower’s perception; high throughput sequencing; small-scale vegetable farms; tomato; virome; Global and Planetary Change; Food Science; Ecology; Agronomy and Crop Science; Management, Monitoring, Policy and Law; Horticulture
Abstract :
[en] The number of small-scale diversified vegetable growers in industrialized countries has risen sharply over the last 10 years. The risks associated with plant viruses in these systems have been barely studied in Europe, yet dramatic virus emergence events, such as tomato brown fruit rugose virus (ToBRFV), sometimes occur. We developed a methodology that aimed to understand better the implications related to viruses for tomato production in Belgian’s vegetable farms by comparing growers’ perception and the presence of plant-viral-like symptoms (visual inspection) with non-targeting detection of nearly all viruses present in the plants by high throughput sequencing technologies (HTS). Virus presence and impact were interpreted considering the farm’s typology and cultural practices, and the grower’s professional profiles. Overall, the data indicated that most growers have limited understanding of tomato viruses and are not concerned about them. Field observations were correlated to this perception as the prevalence of symptomatic plants was usually lower than 1%. However, important and potentially emergent viruses, mainly transmitted by insects, were detected in several farms. Notably, the presence of these viruses tended to be associated with the number of plant species grown per site (diversity) but not with a higher awareness of the growers regarding plant viral diseases, or a higher number of symptomatic plants. In addition, both HTS and perception analysis underlined the rising incidence and importance of an emergent virus: Physostegia chlorotic mottle virus. This study also revealed a notable lack of knowledge among producers regarding the highly contagious quarantine virus ToBRFV. Overall, the original methodology developed here, involving the integration of two separate fields of study (social science with phytopathology using HTS technologies), could be applied to other crops in other systems to identify emergent risks associated with plant viruses, and can highlight the communication needed with growers to mitigate epidemics. This exploratory investigation provides relevant insights, which, ideally, would be further tested on wider samples to allow finer statistical treatment to be performed.
Disciplines :
Biotechnology
Author, co-author :
Temple, Coline ; Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux, Belgium
Tindale, Sophie; School of Natural and Environmental Sciences, Newcastle University, Newcastle, United Kingdom
Steyer, Stephan; Crops and Forest Health Unit, Walloon Agricultural Research Center (CRA-W), Gembloux, Belgium
Marechal, Kevin ; Modelization and Development Department, University of Liège, Gembloux Agro-Bio Tech, Gembloux, Belgium
Massart, Sébastien ; Université de Liège - ULiège > TERRA Research Centre > Gestion durable des bio-agresseurs
Language :
English
Title :
High Throughput sequencing technologies complemented by growers’ perceptions highlight the impact of tomato virome in diversified vegetable farms and a lack of awareness of emerging virus threats
The authors would like to thank the National Institute of Biology of Slovenia and especially Denis Kutnjak and Mark Paul Selda Rivarez for their help in bioinformatic analysis. We also acknowledge the Phytopathology team of ULiege Gembloux Agro-biotech (Gbx) Laurent Minet (Hortiforum asbl/Center Technique Horticole de Gembloux), and the members of the extension services (Center Interprofessionel Maraicher) for their support and brainstorming effort in designing the survey and the questionnaire. Elisabeth Demonty and Pierre Hellin (Plant Virology Lab, CRA-W) are also thanks for their support in the laboratory analyzes. We are also very grateful to the growers who took the time to reply to the questions, allowed us to access their properties and collect samples. We thank Johan Rollin, Nuria Fontdevila, François Maclot (Gbx), and Sandrine Dury (CIRAD) for their support on analyzing the data and their helped in improving the manuscript.This work was supported by European Union’s Horizon 2020 Research and Innovation program under the Marie Sklodowska-Curie, Grant Agreement no. 813542 and Federal public service, public health, Belgium, Grant Agreement no. RT 18/3 SEVIPLANT 55.
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