Soil Microbial Community Responses to Cover Crops and Microbial Inoculants in Different Farming Systems

This study investigates the effects of cover cropping (fallow vs. cover crop) and microbial grain inoculation; Control, arbuscular mycorrhizal fungi (AMF), and combination of AMF and bacteria on soil microbial communities and maize yield across conventional, organic, and transitional farming systems. Soil samples were collected at two time points: before inoculation (before cover crop termination) and after inoculation (before maize harvest). Microbial community composition was analyzed using MiSeq Illumina amplicon sequencing of bacterial (16S rRNA) and fungal (18S rRNA) DNA. Sequencing data were processed using Cutadapt, fastp, VSEARCH, and QIIME2, with taxonomic classification based on the SILVA database. Farming systems were the dominant factor shaping microbial diversity, with organic systems exhibiting the highest diversity. Microbial inoculation enhanced maize yield in high-fertility conventional fields, while cover crops improved yield in organic and transitional systems. This dataset provides insights into the context-dependent effects of microbial inoculants and cover cropping, supporting targeted approaches for sustainable agriculture.