Core and Variable Fractions of the Rhizosphere Microbiome Across Five Field-Grown Mentha Accessions

Rhizosphere microbiomes contain both conserved and variable community components, but the balance between these fractions may differ between bacteria and fungi. We compared bacterial and fungal rhizosphere communities associated with five field-grown Mentha accession plots (Mentha spicata B1, Mentha × villosa B10, Mentha longifolia B12, Mentha × piperita B20, and Mentha suaveolens J17) and managed inter-row soil using 16S rRNA gene and ITS amplicon sequencing, together with soil physicochemical characterization. Bacterial and fungal community composition differed significantly among the Mentha accession plots, while bacterial and fungal Bray–Curtis dissimilarities were moderately correlated. Because the five plant materials were represented by one field plot each, the observed between-group differences should be interpreted as plot-level patterns rather than replicated accession- or species-level effects. Prevalence-based analysis revealed a pronounced contrast between kingdoms: at the primary ≥2/3 within-plot prevalence threshold, 96.07% of bacterial amplicon sequence variants (ASVs) were shared across all five Mentha accession plots and accounted for 98.65% of bacterial reads, whereas only 21.89% of fungal ASVs were shared, although these still represented 72.83% of fungal reads. This contrast remained after rarefaction and under alternative prevalence thresholds. Soil physicochemical models were significant overall for both communities, but no individual soil variable showed a significant marginal effect. These results indicate that across the five sampled Mentha accession plots, bacterial communities were characterized by a highly shared ASV pool, whereas fungal communities showed substantially greater ASV-level variability.