Changes in the potato rhizosphere microbiota richness and diversity occur in a growth stage-dependent manner.

Plant root and soil-associated microbiomes are influenced by niches, including bulk and rhizosphere soil. In this work, we collected bulk and rhizosphere soil samples at four potato developmental stages (leaf growth, flowering, tuber elongation and harvest) to identify whether rhizosphere microbiota are structured in a growth stage-dependent manner. The bacterial and fungal microbiota showed significant temporal differences in the rhizosphere and bulk soil. Rhizobacteria were most diverse at the tuber elongation stage, and dominant ASVs identified as Sphingomonas, Rhodanobacter, Sphingobium, Hyphomicrobium, and Solirubrobacter spp. In contrast, rhizosphere fungal diversity peaked at flowering stage, with Lecanicillium spp. being prominent. Furthermore, the abundance of saprophytic fungal genera, including Colletotrichum and Fusarium, and Alternaria, sharply increased at harvest stage, likely contributing to plant residue decomposition. Indicator taxa analysis highlighted the dominance of these genera at harvest. Network analysis revealed increased microbial complexity during the later growth stage, with 721 edges compared to 521 edges in the early growth stage. This increase included positive correlations between bacteria and negative correlations between bacteria and fungi. These changes suggest that microbial interactions become more interconnected and complex as potato plants mature. Our findings highlight the potential role of saprophytic fungi in shaping microbial dynamics during the later growth stage in rhizosphere soil.