A Metabarcoding Approach to Investigate Fungal and Oomycete Communities Associated with Kiwifruit Vine Decline Syndrome in Italy

Since 2012, kiwifruit vine decline syndrome (KVDS) has severely compromised all major kiwifruit-growing areas in Italy. Thus far, etiological studies were mainly focused on waterlogging effects or on the isolation of microorganisms from diseased plants; therefore, an all-encompassing picture of KVDS microbiota is still missing. This work aims to describe oomycete and fungal communities associated with KVDS and to identify key taxa potentially involved in the disease through a metabarcoding approach on root endosphere and rhizosphere samples. Two nearby fields with similar pedoclimatic conditions were identified based on KVDS spreading during a 4-year survey (2016 to 2019). In total, four sampling areas were selected, one from the control field with no sign of KVDS (asymptomatic site) and three from the KVDS-affected field (diseased site): (i) asymptomatic until the sampling date in 2018, (ii) symptomatic since 2018, and (iii) symptomatic since 2017. Total genomic DNA samples were subjected to a nested PCR approach separately targeting the internal transcribes spacer 2 regions of fungal and oomycete communities. The communities were compared in terms of α- and β-diversities, and key taxa were identified using univariate differential abundance tests. Major differences in taxa distribution were observed between samples from the different sites (asymptomatic and diseased) and were mostly linked to the oomycete community. Phytophthora sojae was the main taxa characterizing the diseased site and supposed to be involved in the disease and Phytopythium spp. were found related to the different plant health status. Finally, Dactylonectria macrodidyma, Phytopythium citrinum, and Thielaviopsis basicola were also proposed as new KVDS-related pathogens.