Soil microbiomes play a central role in nutrient cycling and ecosystem stability in forestry ecosystems. We performed a high-resolution amplicon-based analysis of rhizosphere soils from eucalyptus plantations in two ecologically distinct Brazilian regions. Following ASV inference and phylogenetic reconstruction, we observed pronounced taxonomic divergence: Eldorado do Sul (ES) showed higher richness (1,221 vs. 755 ASVs) and phylogenetic diversity, whereas Três Lagoas (TL) exhibited greater evenness. Beta diversity revealed strong compositional dissimilarity (Jaccard = 0.915; Bray–Curtis = 0.843), largely driven by site-specific rare taxa, with only 8.1% of ASVs forming a shared core microbiome. Despite this turnover, PICRUSt2-based functional prediction indicated substantial conservation of dominant metabolic pathways. Core MetaCyc pathways were highly similar across sites and centered on central carbon metabolism, amino acid biosynthesis, and energy production, while weighted UniFrac distances were low (0.067), indicating phylogenetic similarity among abundant taxa. Region-specific metabolic enrichments were detected: ES showed greater predicted potential for chitin degradation, purine turnover, and nitrifier denitrification, whereas TL was enriched in alternative TCA variants, glyoxylate pathways, menaquinol biosynthesis, and aromatic compound degradation. These findings demonstrate the coexistence of pronounced taxonomic turnover with a relatively conserved predicted functional framework across contrasting eucalyptus systems.

Soil microbiomes play a central role in nutrient cycling and ecosystem stability in forestry ecosystems. Here, we present an exploratory analysis of rhizosphere bacterial communities from eucalyptus plantations in two ecologically distinct Brazilian regions. Using 16S rRNA amplicon sequencing followed by ASV inference and phylogenetic reconstruction, we observed distinct taxonomic composition pattern between samples. Dominant phyla across both samples were Actinomycetota, Pseudomonadota, Acidobacteriota, and Bacillota, with Actinomycetota more abundant in TL (44.0%) than in ES (26.5%), and Acidobacteriota and Verrucomicrobiota more represented in ES. The family Streptomycetaceae and the genus Streptantibioticus were strongly enriched in ES (19.6% and 18.6%, respectively), whereas Solirubrobacteraceae, Pseudonocardiaceae, and Nocardiaceae were preferentially associated with TL. The Eldorado do Sul (ES) sample was characterized by higher observed richness and phylogenetic diversity, whereas Três Lagoas (TL) sample displayed relatively greater community evenness. Beta diversity metrics were consistent with high compositional dissimilarity between samples, with a limited fraction of ASVs forming a shared core microbiome. Despite this taxonomic variation, PICRUSt2-based predictions suggested a broadly conserved set of dominant metabolic pathways across samples. Predicted MetaCyc pathways were largely associated with central carbon metabolism, amino acid biosynthesis, and energy production. At the same time, variation in predicted metabolic profiles was observed between samples. The ES sample showed higher relative representation of pathways related to chitin degradation, purine metabolism, and nitrifier denitrification, whereas the TL sample displayed higher relative representation of pathways associated with alternative TCA variants, glyoxylate metabolism, menaquinol biosynthesis, and aromatic compound degradation. Overall, this exploratory analysis suggests that substantial taxonomic variation may coexist with a relatively conserved predicted functional framework across contrasting eucalyptus plantation systems. These observations should be interpreted as hypothesis-generating and highlight the need for future studies incorporating replicated sampling and direct functional measurements.