Vol.:(0123456789) 1 3 World Journal of Microbiology and Biotechnology (2019) 35:40 https://doi.org/10.1007/s11274-019-2613-1 ORIGINAL PAPER Genome sequencing and traits analysis of Burkholderia strains reveal a promising biocontrol efect against grey mould disease in grapevine (Vitis vinifera L.) Qassim Esmaeel 1  · Cédric Jacquard 1  · Christophe Clément 1  · Lisa Sanchez 1  · Essaid Ait Barka 1 Received: 23 November 2018 / Accepted: 1 February 2019 © Springer Nature B.V. 2019 Abstract Grey mould caused by Botrytis cinerea is among the most important disease afecting the production of grapevine worldwide. The high economical loss each year has led producers to become more dependent on chemical pesticides for protection. However, environmental impacts of the pesticides overuse have sparked crescent interest in developing alternative biocontrol methods. The use of plant-associated bacteria has, thus, received many attentions as a promising strategy for sustainable agriculture. Three strains, isolated from the rhizosphere of crops cultivated in the northeast of France, were evaluated for their antagonistic efect. They were found to exhibit an antagonistic efect against a set of phytopathogenic fungi. Pheno- typic and molecular characterization showed that isolates belong to the genus Burkholderia. The genome sequencing and analysis of isolated strains revealed the presence of gene clusters coding for secondary metabolites potentially involved in the biocontrol. When the grapevine plantlets were infected with B. cinerea, all plants associated with isolated strains showed a signifcant protection against B. cinerea compared to non-inoculated plants. To understand the mechanisms contributing to the biocontrol efect of selected isolates, the production of reactive oxygen species (ROS) and the expression of several defense genes were investigated. The maximum accumulation of H 2 O 2 was detected in the inoculated cell suspension medium 30 min after the challenge with B. cinerea. After pathogen challenge, results showed that grapevine cell culture inoculated with isolated strains exhibited signifcant over expression of defense markers genes PR5, PR10, and chit4c, in response to B. cinerea, confrming their priming efect. Keywords Biocontrol · Burkholderia · Grey mould · Grapevine · Rhizosphere Introduction Grapevine is one of the most common plant cultivated worldwide in general and more particularly in France, where 786 thousands hectares of lands are planted with this plant (OIV 2018). In 2017, grapevine production was estimated to be 73.3 millions of tons (mt) worldwide and 5.5 mt in France (OIV 2018). Furthermore, the global wine produc- tion (excluding juice and musts) in 2018 was estimated at 279 millions of hectoliters (mhl) and 46.4 mhl in France (OIV 2018). However, the production is negatively afected by many environmental factors including abiotic and biotic stresses.Grey mould disease, caused by Botrytis cinerea, is considered one of the most serious diseases afecting the vineyard. The pathogen is difcult to control as it can sur- vive in soil and plant debris for long period (Elad 1994; Rupp et al. 2016). In France, the annual economic loss of B. cinerea for viticulture is estimated to be between 15 and 40% according to the climatic conditions (Cilindre et al. 2007). However, no precise statistical data are yet avail- able for 2018. The high risks and economical loss sufered each year have led producers to become more dependent on chemical pesticides as a reliable method for crop protection. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11274-019-2613-1) contains supplementary material, which is available to authorized users. * Qassim Esmaeel quassin.esmaeel@univ-reims.fr * Essaid Ait Barka ea.barka@univ-reims.fr 1 Unité de Recherche Résistance Induite et BioProtection des Plantes, UFR Sciences Exactes et Naturelles, SFR Condorcet FR CNRS 3417, Université de Reims-Champagne-Ardenne, 51687 Reims Cedex 2, France