The structural and functional shift in the soil rhizosphere and raspberry shoot microbiomes underlies changes caused by phytopathogens contamination and naturalization strategies implementation

Abstract

Biopreparations based on an inoculum of beneficial bacteria may become an essential tool in the prevention of fungal and fungal-like phytopathogens with cause a decrease in the yield of raspberries, especially in organic farming, in which the use of conventional plant protection products is prohibited. The research is based on a pot experiment which includes 4 different naturalization strategies and 5 different pathosystems. The application of environmental isolates of plant beneficial bacteria belonging to genera Arthrobacter, Pseudomonas, and Rhodococcus to the raspberry plant was performed in order to characterize their effect on the microbial communities surrounding the raspberry plant. The application of pathosystems consisting of fungal and fungal-like pathogens belonging to the Botrytis, Colletotrichum, Phytophthora, and Verticillium genera allowed for an analysis to be conducted with regard to the effect of naturalization treatments on microbial communities of raspberry plants infected with phytopathogens. Rhizosphere and shoots samples were subjected to a functional profiling analysis of their microbial communities with the use of Biolog® EcoPlates. Furthermore the DNA was isolated from the rhizosphere and shoots of raspberries and sequenced using the Illumina MiSeq platform. The application of a bacterial inoculum resulted in a decrease in the substrate stress index of raspberry shoots microbiota. Over 95 % of the fungal phyla found in the rhizosphere consisted of 3 phyla: Ascomycota, Mortierellomycota, and Basidiomycota. The results obtained indicated, that the application of plant beneficial bacteria to raspberry plants roots during planting, and afterwards during the watering, may be an important way of inhibiting the negative effect of plant pathogens and enhancing the functional abilities of microbial communities.