Complex endophytic bacterial composition of phytoplasma-infected grapevines and coconut palms

In the last decade, several studies have been addressed to understand the dynamic microbial community associated with important plant diseases. Among others plant pathogenic bacteria that cause serious diseases for many agriculture crops, phytoplasmas are wall-less pathogenic bacteria difficult to be cultured in vitro and transmitted by various hemipteran species. Grapevine yellows and coconut palm lethal yellows are among the most damaging phytoplasma-associated diseases that cause severe yield losses worldwide. The endophytic microbial composition of phytoplasma-infected grapevines (from Italy) and coconut palms (from Ghana, Mexico, Jamaica and Cuba) was investigated in terms of abundance and variability of bacterial genera identified, and the possible positive and negative correlations with the detected phytoplasmas. After Illumina sequencing overall 431 bacterial OTUs (Organism Taxonomic Unit) were identified in the grapevine samples and more than 1,000 in the coconut palm samples monitored. The bioinformatic analyses allowed identification of the detected genera. Phytoplasmas (Acholeplasmataceae family) were detected in all the analyzed samples, however the relative amount of phytoplasma OTUs compared to other bacterial genera varied enormously according to the phytoplasma detected (in the case of grapevines samples) or to the geographic origin (in the case of coconut palms). In particular samples from “flavescence dorée” infected grapevines showed the presence of about 90% phytoplasma OTUs among all bacterial species, while from “bois noir” infected samples this percentage decreased to less than 50%. Interestingly, the percentage of phytoplasma OTUs detected in severely infected coconut palms was ranging from 2-15% of the total bacterial community in samples from Ghana, Mexico and Jamaica, and increased to 55% in Cuban plants. Furthermore, the preliminary analysis on bacterial communities showed that the Enterobacteriaceae family represents the predominant bacterial group, no matter of plant species considered. Among the bacteria detected in grapevines, Micrococcaceae, Sphingomonadaceae, Pseudomonadaceae and Beijerinckiaceae families were identified in all the Italian regions analyzed, while in the case of coconut palms a significant difference in genera was detected according to the geographic origin of the samples. In particular, while about 20/25 families were identified in samples collected from Ghana, Jamaica and Mexico, with a prevalence of Pseudomonadaceae, Rhizobiaceae, Bacillaceae and Burkholderiaceae, over 70 families were obtained from samples collected in Cuba, indicating a greater variability and complexity of the microbiota in the coconut plants. The overall results obtained in this study highlighted that phytoplasma diseases are complex pathosystems, shaped by numerous biotic and abiotic factors, including the interactions with bacteria living in the same host. More studies are then needed to better understand the mechanisms involved in the pathogenicity of these microorganisms also in relationship with their bacterial communities.