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

Phytoplasma infections pose a significant threat to the ecological equilibrium and economic worth of Vaccinium myrtillus L., the plant’s overall well-being and capacity for fruit production. This study utilized next-generation sequencing techniques targeting the V3–V4 region of 16S rRNA genes to examine the endophytic bacterial communities present in both healthy and infected samples with ‘Candidatus Phytoplasma pruni’ and ‘Candidatus Phytoplasma trifolii’ related strains. Our findings revealed a total of 1.286 million raw paired-end reads across sequenced samples, which, after quality filtering, resulted in 58,492 high-quality reads without chloroplasts and 1670 amplicon sequence variants (ASVs). Infected plants exhibited statistically higher ASV richness (325 ± 71.5) than healthy plants (231 ± 21.9). This divergence suggests that, although more unique taxa were present in infected plants, their distribution was uneven or phylogenetically clustered, resulting in no significant differences in other diversity indices. 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 displayed a higher prevalence of the Acidobacteriota and Myxococcota phyla, whereas healthy plants exhibited a higher prevalence of the Actinomycetota phylum. The data presented in this study suggest that ‘Candidatus Phytoplasma’ infection may result in mild changes to the bacterial community structure within V. myrtillus. These data provide insights into phytoplasma disease-related changes in the microbial diversity of the plant host.