Amplicon sequencing of soybean associated soil communities following inoculation with rhizobia

This mesocosm experiment investigated the impact of inoculating soybean with rhizobia on soil microbiomes sampled from two different fields on a single UK farm. One soil had no history of previous soybean cultivation/ inoculation and the other had soybean grown and inoculated with a commercial inoculant (containing B. japonicum SEMIA 5079 and B. diazoefficiens SEMIA 5080) in the season prior. An experiment was designed with each soil (no-soya and soya) split into 4 inoculation treatments: a control mock-inoculated treatment, a control supplemented with Nitrogen fertiliser, a Bradyrhizobium diazoefficiens inoculant and a Sinorhizobium fredii inoculant treatment each with 5 replicates. Starting microbiome samples of each bulk soil were taken on the day of planting (T0). Soil microbiomes from pots were repeatedly sampled at 2 days post treatment (seedling emergence - VE), 22 dpt (vegetative growth stages V2 -V3), 63 dpt (pod formation R3- R5) and 84 dpt (green pod fill R6), when plants were harvested. Soil samples were snap frozen in liquid nitrogen before storing at -80 degrees C, DNA was extracted from 500 mg of soil. Seven plant root nodules were excised from roots at harvest, sterilised, crushed and 100 microlitre extract taken and stored at -80 degrees C until DNA extractions. Amplicons were generated for 16S rRNA (Caporaso et al ., 2012) and rpoB (alphaproteobacteria - Wardell G. Thesis 2024) for soil DNA and rpoB for nodule DNA.