Characterisation of the endomicrobiome of grapevine nursery plants in Australia

The plant microbiota is the community of microorganisms that naturally reside within plants. These microorganisms may form symbiotic, commensal, or pathogenic relationships with their host (1-2). A well-balanced and diverse population of microbiota play a very important role in increasing plant fitness by facilitating adaptation to changing environmental conditions. The aim of this study was to characterise the endophytic microorganisms present in grapevine nursery plants and develop an understanding of their dynamics associated with the health and fitness of planting materials and young vines in vineyards. Dormant grafted and own-rooted vines were collected from four grapevine nurseries in Australia. Total DNA from wood tissues and roots were analysed by metagenomic next-generation sequencing using the 16S rRNA gene and ITS sequences. Preliminary results demonstrate microbial communities varied greatly between nurseries, varieties, and tissue-type. One nursery had higher overall microbial populations compared to the other three nurseries. Ramsey had the highest microbial population among rootstocks, while microbial populations were similar for Shiraz and Chardonnay. Microbial populations were also higher in the roots than in the above ground tissues. For the bacteria, the most predominant families were Pseudomonadaceae (30%) and Enterobacteriaceae (22%) some of which are considered harmless or symbionts, although some species are also known to be animal or plant pathogens. The most abundant fungal taxa are considered common environmental species and beneficial fungi including Trichoderma spp., which were detected in 17% of samples tested. Also detected at lower levels were grapevine trunk disease pathogens (9%) and bunch rot fungi (5%) . Understanding the diversity of endophytic microbiota associated with grapevine plant materials may provide information on the overall health status of young vines and assist producers in understanding the impact of these endophytic organisms on the quality of their vines.


References

1) Pinto C, Pinho D, Sousa S, Pinheiro M, Egas C, Gomes AC (2014) Unravelling the Diversity of Grapevine Microbiome. PLoS ONE 9(1): e85622. doi:10.1371/journal.pone.0085622
2) Niem J, Billones-Baaijens R, Stodart B, Savocchia S (2020). Diversity profiling of grapevine microbial endosphere and antagonistic potential of endophytic Pseudomonas against grapevine trunk diseases. Front. Microbiol. 11:477. doi: 10.3389/fmicb.2020.00477.