The effect of crop-rotation systems in regenerative agricultural environments on the rhizosphere microbiome of dry-land winter wheat

Regenerative agriculture is a multi-faceted approach that aims at transitioning farmers from conventional to sustainable management practices, by increasing biodiversity, functional redundancy, and nutrient cycling efficiency in the soil. This study investigated the effects of three crop rotation systems, wheat after wheat, wheat after medicago, and wheat after canola on the soil fungal and bacterial communities, in a regenerative agriculture system, in the Western Cape, South Africa, following a record-breaking drought (2015–2019). Utilising 16S rRNA and ITS targeted amplicon sequences, soil-geochemical properties, and qPCR analyses, it was found that crop rotations had little significant effect on the alpha-diversity between different crop-rotation systems. Medicago and wheat had the most similar communities, with canola diverging from the other rotation systems. Host driven selection was prevalent the rhizosphere microbiome during the wheat growth period, across treatments and farms. After senescence, the microbiome composition transitioned from the wheat-selected communities towards communities consisting of saprotrophs and yeasts. qPCR analyses of nitrogen-associated genes revealed that genes for nitrification (amoA) and denitrification (nirK) increased during fertilizer application events, whereas genes associated with nitrogen fixation (nifH), denitrification (nirS), and nitrification (nxrB) increased throughout the season. Genera associated with drought and halotolerance were enriched in all samples.