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

<title>Abstract</title> Root channels formed by winter cover crop can enhance subsoil water and nutrient access for subsequent crops such as maize ( <italic>Zea mays</italic> L.) yet their fungal inhabitants remain poorly understood under drought. Here, we assessed drought-induced shifts in maize rhizosphere fungal communities within reused cover crop root channels across three contrasting soil types in northern Germany (Luvisol, Podzol and Phaeozem). Using a multi-omics approach combining ITS2 amplicon sequencing, quantitative PCR and metaproteomics, we linked community composition with functional responses. Drought consistently restructured fungal communities, with increased relative abundances of <italic>Ascomycota</italic> and <italic>Zoopagomycota</italic> and declines in <italic>Chytridiomycota</italic> and <italic>Mucoromycota</italic> . Taxa within the same subkingdom occupied complementary niches, indicating functional differentiation beyond higher-level taxonomy. At the protein level, drought responses were characterised either by enhanced antioxidant defence mechanisms including catalase–glutathione peroxidase systems, superoxide dismutase, fatty acid synthesis and the methionine cycle–transsulfuration pathway or by reduced carbon and nitrogen metabolic activity, suggesting energy conservation strategies. 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.