Microbial community dynamics in rotational cropping: seasonality versus crop-specific effects

Debora Casagrande Pierantoni¹Angela Conti²Laura Corte²Giacomo Tosti³Paolo Benincasa³GIANLUIGI CARDINALI^2*Marcello Guiducci³

• ¹Universita degli Studi di Perugia, Perugia, Italy
• ²Universita degli Studi di Perugia Dipartimento di Scienze Farmaceutiche, Perugia, Italy
• ³Universita degli Studi di Perugia Dipartimento di Scienze Agrarie Alimentari e Ambientali, Perugia, Italy

Soil microbial communities are central to soil health and plant productivity, yet their responses to crop rotation and seasonal changes remain incompletely understood. This study examines how different crop species and their growth stages influence the diversity, composition, and functional characteristics of soil microbiota in a long-term rotation system. By integrating high-throughput DNA sequencing with soil chemical and spectroscopic analyses, we assessed microbial community dynamics across three key seasonal time points. Our results indicate that while crops and their growth stages can influence microbial community structure, these effects are generally modest and variable. In contrast, seasonal factors and soil physicochemical properties, especially electrical conductivity, exerted stronger and more consistent effects on microbial beta diversity. Despite shifts in taxonomic composition, a core microbiome dominated by Acidobacteriota and Bacillus was consistently present across crops and seasons. Functional predictions pointed to a seasonal peak in nitrification potential during warmer months, suggesting an environmental rather than crop-driven control of this process. Together, these findings highlight the resilience of the soil microbiome in rotational systems and underscore the importance of seasonal and abiotic drivers. Understanding these dynamics can help refine agricultural practices aimed at sustaining microbial function and long-term soil health.