Comparative Analysis of Endophytic Bacterial Microbiomes in Healthy and Phytoplasma-Infected European Blueberry Plants

Phytoplasma infections pose a significant threat to the ecological balance and economic value of Vaccinium myrtillus L., affecting the plant's overall health and capacity for fruit production. This study used next-generation sequencing techniques targeting the V3-V4 region of 16S rRNA genes to examine the endophytic bacterial communities present in both healthy samples and samples infected with 'Candidatus Phytoplasma pruni' and 'Candidatus Phytoplasma trifolii' strains. Our findings revealed a total of 1.286 million raw paired-end reads across groups, which, after quality filtering, resulted in 58,492 high-quality reads and 1,670 amplicon sequence variants (ASVs). Infected plants exhibited statistically higher ASV richness (325 +/- 71.5) than healthy plants (231 +/- 21.9). However, other alpha diversity metrics did not show significant differences between the groups. Beta diversity analyses also indicated no significant differences in community composition between healthy and infected samples. The taxonomic analysis revealed that both groups were dominated by the Pseudomonadota phylum (~47.6%). However, infected plants showed a higher prevalence of the Acidobacteriota and Myxococcota phyla, whereas healthy plants showed a higher prevalence of the Actinomycetota phylum. The data presented in this study suggests that 'Candidatus Phytoplasma' infection may result in mild changes to the bacterial community structure within V. myrtillus. This data provides insights into phytoplasma disease-related dynamics.