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.