Cover Crop Root Channels Promote Bacterial Adaptation to Drought in the Maize Rhizosphere

Increasing drought frequency poses a significant threat to agricultural productivity. A promising strategy to enhance crop resilience against drought is the utilisation of root channels left by winter cover crops, which can improve access to subsoil water and nutrients for subsequent cash crops like maize (Zea mays L.). The impact of drought on bacterial communities inhabiting these root channels remains largely unknown. Here, we investigated drought-induced shifts in maize rhizosphere bacterial communities and their functional adaptation in cover crop root channels across three soil types in northern Germany (Luvisol, Podzol, and Phaeozem) using a multi-omics approach (16S rRNA gene amplicon sequencing, qPCR, and metaproteomics). Our results reveal a preference towards bacterial K-strategists under drought conditions, indicating a shift towards stress-tolerant populations. Under drought stress, the relative abundances of Acidobacteriota, Actinomycetota, Planctomycetota, and Pseudomonadota increased, while Chloroflexota, Methylomirabilota, Ca. Patescibacteria, and Verrucomicrobiota declined. Metaproteomics analyses revealed that drought-stressed aerobic taxa among the Pseudomonadota and Verrucomicrobiota upregulated the glyoxylate cycle, potentially enhancing carbon and energy conservation, and increased antioxidant defences (catalase–glutathione peroxidase and methionine cycle–transsulfuration pathway). These drought-mitigating strategies were especially pronounced in root channels formed by Brassicaceae and Poaceae cover crops in the Luvisol and Podzol soils. These findings demonstrate the functional plasticity of rhizosphere bacterial communities in reused root channels in response to drought, highlighting the potential to leverage microbiome-mediated resilience for agricultural practices.