Microhabitat Primarily Structures Bacterial Communities, While Management History Shapes Functional Potential in Tomato-Associated Soils

Intensive horticultural management modifies soil physicochemical conditions, yet its effects on microbial community assembly and functional organization remain poorly resolved. This study examined bulk soil (BS) and rhizosphere soil (Rh) bacterial communities associated with tomato plants grown in two contrasting commercial horticultural establishments: a long-term intensive monoculture (>10 years; MC) and a recently established system (FC). Total bacterial abundance and community structure were characterized using qPCR and 16S rRNA gene amplicon sequencing, respectively; the abundance and diversity of functional plant-growth-promoting (PGP) genes—nifH, phoD, and acdS—were assessed by qPCR and DGGE profiling. The MC system, associated with increased salinity, nutrient accumulation, and organic matter content, supported higher bacterial abundance, whereas the FC system showed a higher relative abundance of PGP genes. Amplicon sequencing revealed significant differentiation between BS and Rh, identifying microhabitat in tomato-associated soil as the primary driver of taxonomic structure, while site effects were weaker. In contrast, DGGE profiling supported differences in functional gene composition between management systems, whereas predicted pathway profiles inferred from 16S data were comparatively similar across samples. Overall, these results indicate that horticultural intensification is associated with shifts in predicted functional potential that are not paralleled by major changes in taxonomic structure.