Quantitative reduction of soil bacteria and qualitative microbial changes: biotic components associated to kiwifruit decline

Purpose This study aimed at elucidating the biotic components of crop decline affecting kiwifruit ( Actinidia deliciosa ) orchards. Methods The study was carried out on soil samples originating from an over twenty-year-old orchard showing typical yield decline (Old), one in full production phase (Adult), one fallow after a kiwifruit cultivation (Fallow), an abandoned one (Virgin). Soil health of those soil samples was assessed with an in-pot growth assay using kiwifruit plantlets in which root endophytic fungi and rhizosphere bacteria communities were assessed using qPCR and NGS analysis. Results Plant growth in the Old field was significantly lower than the others, in line with the crop decline of that field. The Old treatment differed from the others in the following soil features: i. a great reduction of total bacteria, Pseudomonas , actinomycetes and Bacillus compared to the Adult orchard; ii. a significant increase of Nitrosospira and other nitrifying bacteria which persisted in kiwifruit rhizosphere even under the optimal conditions; iii. a reduction of potentially beneficial genera among which Massilia , Rubrobacter and Kaistobacter . Old, Adult and Fallow were similar in root fungal community composition, with Dactylonectria as dominant genus (about 50%); whilst in the Virgin prevailed saprophytic non-pathogenic fungi. Conclusions Bacterial communities in over-30-year-old kiwifruit orchards were greatly reduced and modified, thus suggesting being a cause of the reduced ability of soil to support plant growth. In addition, kiwifruit manifested a legacy effect on soil-borne fungal communities, including root endophytes.