Dissecting the Herbicidal Mechanism of Microbial Natural Product Lydicamycins Using a Deep Learning-Based Nonlinear Regression Model

The plant microbiome significantly influences plant-microbe interactions, but the mechanisms are often complex and nonlinear. Here we show the nonlinear regulatory effects of <i>Streptomyces ginsengnesis</i> G7 on <i>Arabidopsis thaliana</i> growth. We focused on lydicamycin, a molecule from this bacterium that interferes with auxin polar transport. Using a deep learning approach with a feedforward neural network, we integrated multiomics data to elucidate the mechanism of lydicamycin on plant growth and development. We also examined the impact of flavonol metabolites, particularly isorhamnetin from <i>A. thaliana</i>, on the PIN protein family's role in auxin transport. Our findings indicate that lydicamycin regulates auxin transport by inducing flavonol overaccumulation in <i>A. thaliana</i>, affecting plant development. This study identifies potential molecular targets for crop enhancement and improved agricultural productivity.