Endophytic Diversity in Vitis vinifera with Different Vineyard Managements and Vitis sylvestris Populations from Northern Italy: A Comparative Study of Culture-Dependent and Amplicon Sequencing Methods

This study aimed to investigate the endophytic microbial populations associated with wild and domesticated grapevines using both culture-based and culture-independent methods. Through culture-based methods, 148 endophytes were identified. The dominant fungal species included <i>Aureobasidium pullulans</i>, <i>Alternaria alternata</i>, and <i>Cladosporium allicinum</i>, while predominant bacterial species were <i>Ralstonia pikettii</i>, <i>Nocardia niigatensis</i>, and <i>Sphingomonas echinoides</i>. Culture-independent methods employed metagenomic techniques to explore microbial biodiversity, focusing on targeted amplification of bacterial 16S rRNA as well as fungal ITS and 26S rRNA gene regions. The main bacterial species identified included <i>Halomonas</i> sp., <i>Sphingomonas</i> sp. and <i>Massilia</i> sp., whereas the fungal population was dominated by <i>Cladosporium</i> sp., <i>Malassezia</i> sp. and <i>Mucor</i> sp. The findings revealed that vineyard management practices did not lead to statistically significant variations in microbial communities. The consistent presence of these genera across all samples suggests that they are stable components of the grapevine endophytic microbiota, remaining relatively unaffected by external environmental factors.