Drought initiates counter-mitigative responses from microbes residing in cover crop root channels

The rising frequency of droughts presents a substantial risk to agricultural output. A promising technique to augment agricultural resilience to drought is by using root channels of winter cover crops, which can promote access to subsoil water and nutrients for succeeding cash crops such as maize (Zea mays L.). However, the effect of drought on bacterial and fungal communities residing in these root canals has not been documented properly. This study examined drought-induced alterations in maize rhizosphere bacterial and fungal communities and their functional adaptations within cover crop root channels across three soil types in northern Germany (Luvisol, Podzol, and Phaeozem) with the help of a multi-omics approach (16S rRNA and ITS2 gene amplicon sequencing, qPCR, and metaproteomics). Our findings indicate a preference for bacterial K-strategists in drought conditions, signifying a transition towards stress-tolerant populations. The fungal community distribution highlights a complementary distribution of niches among phyla within the same subkingdoms. Metaproteomics analyses indicated that drought-stressed aerobic taxa within Pseudomonadota and Verrucomicrobiota upregulated the glyoxylate cycle, likely improving carbon and energy conservation, and implemented antioxidant defences (catalase, glutathione peroxidase, superoxide dismutase and methionine cycle, transsulfuration pathway), which was also reciprocated by fungal communities of Ascomycota and Basidiomycota. These drought-mitigating measures were particularly evident in root channels created by Brassicaceae and Poaceae cover crops in Luvisol and Podzol soils. These findings illustrate the functional adaptability of rhizosphere bacterial communities in reused root channels as a response to drought, emphasising the potential to utilise microbiome-mediated resilience in agricultural methods.