Latent Dirichlet Allocation reveals tomato root-associated bacterial interactions responding to hairy root disease

Abstract

Hairy root disease (HRD), caused by rhizogenic Agrobacterium strains, is a significant disease threat to modern hydroponic greenhouses, which can result in up to 15% loss in yield. Our prior research has suggested increased alpha diversity after infection in hydroponic tomato root-associated microbiota. However, a more detailed investigation of how root-associated microbial components (MCs; clusters of weighted bacterial features) respond to disease and the underlying mechanisms remains lacking. To address this gap, we applied Latent Dirichlet Allocation (LDA) to analyze MCs from 12 Belgian commercial hydroponic tomato greenhouses. Using high-throughput amplicon sequencing of the 16S rRNA locus, three locations along each greenhouse irrigation system (beginning, middle, and end) were sampled at 5 time points throughout the 2018 growing season.