Contrasting Rhizosphere Bacterial and Fungal Responses to Saline-Alkali Stress Reveal Spiromastix and Scytalidium as Yield-Linked Environmental Biomarkers for Sustainable Millet Management

Abstract Soil salinization threatens over 800 million hectares of agricultural land globally, yet its effects on the rhizosphere microbiomes of stress-tolerant cereal crops remain poorly understood. We profiled bacterial and fungal communities (16S rRNA and ITS amplicon sequencing) of four foxtail millet ( Setaria italica L.) cultivars grown in paired saline-alkali and non-saline fields (n = 24). Saline-alkali stress significantly reduced bacterial diversity and richness and reduced fungal richness without altering fungal diversity. Soil habitat was the dominant factor structuring both bacterial (R = 0.634, p = 0.001) and fungal (R = 0.25, p = 0.004) communities, with salinity-related factors explaining 47.79% of bacterial and 22.75% of fungal community variance, substantially exceeding host genotype effects. Co-occurrence network analysis revealed contrasting microbial adaptive strategies: bacterial networks became larger, denser and more modular under stress (edges: 649-1,921), whereas fungal networks lost overall connectivity but retained modular hub structure, with arbuscular mycorrhizal fungi (e.g., Rhizophagus ) acting as key connectors. LEfSe identified 275 bacterial and 114 fungal genera differentiating saline from control habitats, including nitrogen-cycling taxa and AMF/pathogen complexes. Critically, correlating 23 key fungal genera with 13 agronomic traits under salinity (n = 12) and applying Benjamini-Hochberg FDR correction across 299 tests revealed a robust bifurcated pattern: Spiromastix abundance was positively associated with multiple yield traits (e.g., plot grain weight, r = 0.819, q = 0.041), whereas Scytalidium was negatively correlated with grain yield (r = -0.831, q = 0.041). These FDR-robust fungal genera provide testable microbial targets for sustainable foxtail millet production on saline-alkali lands, serving as potential ecological indicators for soil health management in salinity-affected agricultural ecosystems.