Peat-vermiculite alters microbiota composition towards increased soil fertility and crop productivity

Harnessing soil microbiomes is a major demand for development of sustainable and productive agriculture. Here we aimed to assess the impact of two different types of organic material amendments in combination with chemical fertilizer on the plant-soil microbiota in maize farming and its link to soil fertility and crop productivity. Soils and roots were collected from a long-term wheat-maize rotation system involving three experimental treatments: chemical fertilizer (CF); chemical fertilizer plus seasonal application of manure (OM); and chemical fertilizer plus one-time application of peat and vermiculite (PV). Crop residues were returned in all three treatments each season. Bacterial 16S rRNA gene and fungal ITS sequencing were conducted to elucidate the treatment-specific response of the microbiota in bulk soil, rhizosphere soil, and root compartment. Relative to CF and OM treatments, PV amendment led to significant increases in soil organic carbon (SOC) content, aboveground plant biomass, and grain yield over the five-year field study. The PV-induced changes in microbial composition involved the greatest treatment-specific “effect size” on indicator ASVs (amplicon sequence variants) in bulk and rhizosphere soils. The number of interactions was more than doubled in the PV co-occurrence network relative to those in the CF and OM co-occurrence networks. Potential beneficial microbes, such as Glomeromycota (arbuscular mycorrhiza), Basidiomycota, and various members of the Actinobacteria and Burkholderiales, were most enriched in the root compartment of the PV treatment. Peat-vermiculite enhanced microbiota-driven soil fertility and crop productivity, thereby providing new insights into plant-soil-microbiota interactions that can be harnessed for smart farming.