Fungal response to drought in the maize rhizosphere after reusing cover crop root channels

Abstract Root channels formed by winter cover crop can enhance subsoil water and nutrient access for subsequent crops such as maize (Zea mays L.). Structure and function of fungal communities in these habitats remain poorly understood, especially under drought. We conducted a field experiment across three different soil types in northern Germany (Luvisol, Podzol and Phaeozem) planted with different cover crop mixtures containing Brassicaceae, Fabaceae and Poaceae, followed by maize cultivation under contrasting water regimes (drought vs. rainfall-fed). Drought-induced shifts in maize rhizosphere fungal communities and their functional responses within reused cover crop root channels were assessed using a multi-omics approach combining ITS2 amplicon sequencing, quantitative PCR and metaproteomics. Drought consistently restructured fungal communities, with relative abundances of Ascomycota and Zoopagomycota increasing and that of Chytridiomycota and Mucoromycota decreasing, alongside soil- and depth-specific shifts in fungal trophic modes, with pronounced subsoil responses. Metaproteomics revealed that drought responses were either via enhanced antioxidant defence mechanisms or by reduced levels of carbon and nitrogen metabolism-associated proteins, suggesting energy conservation strategies. Further, drought-stimulated upregulation of fungal cellulose- and hemicellulose-degrading and redox-active enzymes may have enhanced soluble sugar release and redox balancing, supporting osmotic homeostasis and metabolic flexibility under water limitation. These responses were strongly influenced by soil types, being most pronounced in the drought-prone Podzol and Luvisol and markedly buffered in the water-retentive Phaeozem. Together, our results demonstrate substantial structural and functional plasticity of rhizosphere fungal communities in reused root channels under water limitation, highlighting their potential role in microbiome-mediated drought resilience in agroecosystems.