[P008] Poster

1:00 PM - 1:50 PM JST(4:00 AM - 4:50 AM UTC)

[P04-524] Crop rotation and appropriate fertilization promote the robustness of soil microbiomes

○Motomu Matsui¹ (1. Institute for Chemical Research, Kyoto University (Japan))

Keywords:

Crop rotation,agricultural field,soil microbiome,bioinformatics,trait-based approach

Crop rotation is widely recognized to enhance agricultural sustainability by suppressing pests and maintaining soil fertility, yet its mechanistic basis remains poorly resolved, particularly with respect to the role of microbial communities. Here, we investigate the dynamics and functional consequences of microbiomes in a long-term crop rotation field using an integrated framework that combines time-resolved metagenomics with soil physicochemical analyses. Conceptualizing the field as a “post-Koch ecosystem”—a complex biological system that includes uncultivable and previously unobservable microorganisms—we capture ecosystem-wide interactions across multiple domains of life.
Our analyses reveal that both microbial community structure and ecosystem-level metabolic potential are highly responsive to fertilization regimes and environmental fluctuations. We detect signatures of phage–host interactions and dynamic microbial fluxes across the rhizosphere boundary, indicating tightly coupled ecological processes. Remarkably, following severe perturbations such as chloropicrin fumigation, microbial communities exhibit rapid and reproducible recovery, with the rate and resilience of restoration strongly modulated by fertilization conditions. This provides the first quantitative evidence linking management practices to microbiome resilience in agricultural systems.
Furthermore, we demonstrate that sustained crop rotation combined with appropriate fertilization enhances soil organic matter, thereby reinforcing beneficial plant–microbe interactions. By applying Bac2Feature, a computational framework for inferring phenotypic traits from 16S rRNA data, we uncover a strikingly stable “morphological composition” of the microbial community, suggesting the existence of higher-order constraints governing community assembly.
Together, our findings establish a quantitative link between agricultural practices, microbiome dynamics, and ecosystem function, highlighting microbial communities as central determinants of resilience and productivity in crop rotation systems.