Continuous Cropping Chinese Chive Alters Rhizosphere Metabolites and Microbial Communities

Abstract

Continuous cropping obstacles severely constrain Chinese chive (Allium tuberosum) production, yet the integrated mechanisms involving soil properties, microbial communities, and rhizosphere metabolites remain unclear. We hypothesized that long-term monoculture induces soil degradation and shifts rhizosphere microbiomes via accumulated putative allelochemicals, with a critical tipping point. Rhizosphere soils from 1-to-5-year continuous cropping fields were analyzed using high-throughput sequencing, non-targeted metabolomics, and physicochemical assays. Results showed significant salinization and nutrient depletion after three years, along with a slight decrease in soil pH. Enzyme activities (sucrase, urease, alkaline phosphatase, and catalase) first rose then fell. Bacterial richness declined sharply after four years, with beneficial genera (such as Devosia) decreasing and pathogenic genera (such as Thelonectria) enriched. Metabolomics identified 1175 metabolites, primarily enriched in linoleic acid and α-linolenic acid pathways. Oxidized fatty acids accumulated significantly and correlated positively with pathogen abundance and negatively with beneficial bacteria. We conclude that continuous chive cropping exceeding three years is associated with soil degradation via putative allelochemical accumulation and pathogen enrichment. We recommend crop rotation after three years, offering a theoretical basis for sustainable chive production.