Microbial diversity in cultivated and feral vanilla Vanilla planifolia orchids affected by stem and rot disease

We described the taxonomic composition of endophytic microbiomes in symptomatic, asymptomatic and feral vanilla plants using 16S and ITS rDNA metabarcoding. We compared the bacterial and fungal diversity in vanilla plants in a plantation, and from feral plants found near abandoned plantations that did not present SRD symptoms. We didn't found a difference in the species richness of the bacterial and fungal microbiome among feral, or asymptomatic and symptomatic cultivated vanilla. However, significant differences were detected in both fungal and bacterial diversity from different organs in the same plant, with roots being more diverse than stems. Two taxa of bacteria, Proteobacteria and Actinobacteria, and the fungal families Nectriaceae and Xylariaceae, constitute the core of the vanilla microbiome that inhabits the root and stem of both cultivated and feral plants. Our work provides information on the microbial diversity found in root and stem rot in vanilla and lays the groundwork for a better understanding of the role of the microbiome in fungal diseases in vanilla cultivation.