Characterization of the soil, rhizosphere and root microbiome associated to kiwifruit vine decline syndrome in Italy.

Kiwifruit vine decline syndrome (KVDS) has been threatening kiwifruit cultivation in Italy for the last decade. Symptoms lead to severe root decay and plants usually die within a few weeks. Aboveground symptoms include leaf curl, necrosis, and twig wilting, which appear long after root impairment. KVDS is commonly identified as a multifactorial disease, caused both by abiotic and biotic factors. The copresence of different stresses impacts plant growth and yield, leading to rapid decline. Pathogens associated to disease development are soilborne oomycetes. This work focused on defining the microbial communities characterizing soil, rhizosphere, and root population present both in affected and healthy fields in North-West Italy, by analyzing the whole pathobiome, as bacteria, fungi, and oomycetes, through metabarcoding. Bacteria and fungi showed a wide diversity, even when grouped by sampling location. Focusing on oomycetes, Phytopythium spp. was the main genus across all infected matrices. Phytopythium spp. was present in significantly higher abundances in diseased orchards, compared to healthy ones, showing a statistically significant correlation with the occurrence of the syndrome. From the same sites, isolation was performed through the years revealing the presence of Phytopythium spp. mainly associated to symptomatic roots. Bacteria, fungi, and oomycetes were considered together for the first time, reinforcing the role of Phytopythium spp. in KVDS.