Cover cropping reduces the negative effect of salinity on soil microbiomes

Introduction Soil salinization is a major abiotic stress that imposes high osmotic stress on plant growth, thereby limiting crop productivity. It also acts as an environmental filter for microbes, impacting associated ecosystem services and functions. Agricultural practices such as cover cropping can help mitigate the negative impacts of soil salinity. However, our knowledge of how cover cropping and salinity influence soil microbiome diversity and complexity is limited. Materials & Methods Using amplicon sequencing, metagenomics, and network analysis, we aimed to determine if cover cropping can be effective in maintaining microbiome complexity and functioning in salinity‐affected soils. We conducted a field study to determine the soil microbial properties over four locations with salinity (saline: SS, and nonsaline: NS) and cover cropping (cover‐cropped: CC, and no cover‐cropped: NC) treatments. We hypothesized that microbial diversity and complexity will be lower in saline as compared to nonsaline soils, and the reduction can be countered by inclusion of cover crops. Results Our results found a significant effect of salinity on the clustering of bacterial communities in soil. However, cover cropping increased bacterial and fungal alpha diversity. Cover cropping increased soil microbial network complexity under both saline and nonsaline conditions. Most of the keystone taxa were members of the order Thermomicrobiales, which are known to enhance stress tolerance in plants. Metagenomics revealed higher activities of genes related to transcription and folate metabolism in saline‐cover crop treatments. Conclusion Our results identify key microbial players under salinity stress and highlight the potential of using cover crops to mitigate the negative effect of salinity on soil microbiomes, which can facilitate sustainable productivity in saline agroecosystems.