Crop rotation-driven changes in secondary metabolites of potato rhizosphere soil exert stronger regulation on soil microbial community

Abstract

Introduction Crop rotation promotes ecological effects and production by regulating belowground processes, particularly the shaping of the rhizosphere soil microbiome. Rhizosphere metabolites are a key driver of belowground processes and play a crucial role in shaping soil microbial community composition. However, the rhizosphere metabolites of different potato rotations have rarely been reported, and the regulation of key metabolites on the rhizosphere soil microbiome remains unclear. Methods This study measured agronomic traits of potatoes, collected potato rhizosphere soils from three crop rotations, including potato monoculture (P-P), maize ( Zea mays )-potato rotation (M-P), cowpea ( Vigna unguiculata )-potato rotation (V-P), to determine rhizosphere soil metabolites and analyze defense metabolites, and assess the soil bacterial and fungal diversity and community composition. Results Compared to monoculture, the potato rotations had positive effects on growth and yield. Potato rotations had more primary metabolites, such as amino acids and carbohydrates and conjugates, but significantly reduced secondary metabolites with defensive functions in rhizosphere soils including phenols and other benzene derivatives, flavonoids, alkaloids and other N-containing compounds, and terpenoids. Potato rotation systems supported higher diversity of bacteria and fungi and enriched beneficial bacteria such as biocontrol, nitrogen fixation, C degradation, denitrification, and pollutant degradation bacteria, while suppressing pathogenic fungi in the rhizosphere soils. Rhizosphere soil metabolites strongly correlated with the microbial community composition. The secondary metabolites, which are predominantly alkaloids, terpenoids, and flavonoids, exerted a dominant regulatory effect on the composition of soil microbial community. Discussion These results demonstrate the important regulation of rhizosphere metabolites on soil microbial community composition, deepening our understanding of the benefits of crop rotation via the belowground effect.

Key findings

• ▸Potato monoculture (P-P), maize-potato (M-P), and cowpea-potato (V-P) rotations induce distinct profiles of rhizosphere defense metabolites.
• ▸These rotation-driven changes in secondary metabolites exert a significant regulatory effect on the composition and diversity of soil bacterial and fungal communities.
• ▸The regulation by rhizosphere metabolites is identified as a key mechanism underlying the ecological benefits of crop rotation in potato production.

Keywords

Identifiers

DOI

10.3389/fmicb.2026.1768797

Journal

Frontiers in Microbiology

Year

2026