Soil freeze-thaw cycles (FTCs) are common in temperate agricultural ecosystems during the non-growing season and are progressively influenced by climate change. The impact of these cycles on soil microbial communities, crucial for ecosystem functioning, varies under different agricultural management practices. Here, we investigated the dynamic changes in soil microbial communities in a Mollisol during seasonal FTCs and examined the effects of stover mulching and nitrogen fertilization. We revealed distinct responses between bacterial and fungal communities. The dominant bacterial phyla reacted differently to FTCs: for example, Proteobacteria responded opportunistically, Actinobacteria, Acidobacteria, Choroflexi and Gemmatimonadetes responded sensitively, and Saccharibacteria exhibited a tolerance response. In contrast, the fungal community composition remained relatively stable during FTCs, except for a decline in Glomeromycota. Certain bacterial OTUs acted as sensitive indicators of FTCs, forming keystone modules in the network that are closely linked to soil carbon, nitrogen content and potential functions. Additionally, neither stover mulching nor nitrogen fertilization significantly influenced microbial richness, diversity and potential functions. However, over time, more indicator species specific to these agricultural practices began to emerge within the networks and gradually occupied the central positions. Furthermore, our findings suggest that farming practices, by introducing keystone microbes and changing interspecies interactions (even without changing microbial richness and diversity), can enhance microbial community stability against FTC disturbances. Specifically, higher nitrogen input with stover removal promotes fungal stability during soil freezing, while lower nitrogen levels increase bacterial stability during soil thawing. Considering the fungal tolerance to FTCs, we recommend reducing nitrogen input for manipulating bacterial interactions, thereby enhancing overall microbial resilience to seasonal FTCs. In summary, our research reveals that microbial responses to seasonal FTCs are reshaped through land management to support ecosystem functions under environmental stress amid climate change.

Introduction The phenomenon in which the damage of plant diseases is suppressed by continuous cropping is defined as suppressiveness and the development of suppressive soils and key beneficial microorganisms have been identified through various previous studies. However, no studies have been conducted on microbial communities related to disease occurrence before the initial occurrence of diseases in crop monoculture.Methods We aimed to investigate the ecological modifications of pathogen population density in soil, disease occurrence rate, and microbiota community shifting during ginseng monoculture to better understand the tripartite social relationships in the monoculture system. To achieve the study's objectives, a long-term monoculture of ginseng was established. The microbial diversity and community structure were analyzed using high-throughput sequencing, and the pathogen population density and disease occurrence rate were determined using qPCR and observation.Results and discussion The results showed that the initial rhizosphere bacterial community of ginseng had already collapsed before the development of the root rot disease. The study also identified the crucial role of soil-borne pathogens in causing disease and the loss of initial keystone taxa populations in the early stages of monoculture. Our study revealed a novel aspect of soil microbiota dynamics during ginseng monoculture, with seven distinct microbes (Beijerinckiaceae, Comamonadaceae, Devosiaceae, Rhizobiaceae, Sphingobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae) participating in soil nitrogen metabolism as an 'initial community' that regulates root rot disease through nutritional competition. The findings contribute to ecological research on disease-suppressiveness soil, disease management, and sustainable agriculture.