Fungal endophytic communities in grapevines (Vitis vinifera L.) respond to crop management

We studied the distribution of fungal endophytes of grapevine (V. vinifera L.) plants in a subalpine area of Northern Italy where viticulture is of high economic relevance. We adopted both cultivation-based and cultivation-independent approaches, to address how various anthropic and non-anthropic factors shape microbial communities. Grapevine stems were harvested from several locations considering organic and integrated pest management (IPM) and from cultivars Merlot and Chardonnay. Cultivable fungi were isolated and identified by ITS sequence analysis, using a novel colony-PCR method, to amplify DNA from fungal specimens. The composition of fungal communities was assessed through a cultivation-independent approach: Automated Ribosomal Intergenic Spacer Analysis (ARISA). Multivariate statistical analysis of both culture-dependent and culture-independent datasets was convergent and indicated that fungal endophytic communities in grapevines from organically managed farms were different from those from IPM farms. Fungal communities in plants of cv. Merlot and cv. Chardonnay overlapped when analysed using culture-dependent approaches, but could be partially resolved using ARISA fingerprinting.