Soil, rhizosphere, and root microbiome in kiwifruit vine decline, emerging multifactorial disease

Woody plant declines are impacting productivity of crops, requiring studies on the synergistic effects of the combination of biotic, environmental, or soil-associated stresses caused by climate change. Kiwifruit vine decline syndrome (KVDS), defined as multifactorial syndrome where both biotic and abiotic components act synergically, is proposed as an emerging model to unveil the role of the microbiota in complex pathosystems. KVDS symptoms include severe root system impairment which leads to irreversible wilting and plants usually die rapidly from the appearance of the first above ground symptoms. Investigation of the biotic component associated with decline development using metabarcoding, in the main producing area of Northwest Italy, together with the investigation of the associations among the taxonomic groups and between the taxa and the physicochemical characteristics of the soils was performed for the first time in this pathosystem to unveil potential functions of the involved communities. Both bacterial and fungal communities resulted in a high richness of genera among considered matrices. Bacterial composition was mainly influenced by the matrix, whereas fungi by sampling location. The oomycete genus Phytopythium, previously reported as associated to the syndrome, was present both in diseased and healthy fields, but with different abundances underlining the possibility of a dysbiosis phenomenon in the syndrome onset. Association networks of co-occurrence and co-exclusion between taxa showed the negative correlation of Phytopythium spp. with the diseased status of orchards in soil and negatively associated with growth promoting fungal genera and arbuscular mycorrhizal (AM) fungi associated with kiwifruit in the rhizosphere.