Tracking Root Colonization Dynamics Using WISH-Tagged Rhizobacteria in Arabidopsis thaliana

Abstract

Global agricultural production must increase by up to 70% by 2050 to meet the demands of a growing population (1). Sustainable agriculture, harnessing the power of naturally occurring plant-associated microbes, offers a promising way to improve agricultural productivity. Optimizing the performance of beneficial microbes will require a deeper understanding of how these bacteria colonize roots and interact with the plant immune system. Traditional tools for microbial tracking such as 16S rRNA sequencing, fluorescence markers, or antibiotic resistance are often limited by resolution, bias, and poor compatibility with soil environments (17-19). This study applies Wild-Type Isogenic Standardized Hybrid (WISH) tagging, a novel microbial barcoding technique developed by Daniel et al. (2024), to track and quantify root colonization dynamics with (20). In this study, WISH tags were inserted into the following bacterial strains: Pseudomonas simiae WCS417, Dyella japonica MF79 wildtype, and its mutant, a knockout of the immunosuppressive subtilase A (IssA) gene. Sequencing of WISH-tagged populations revealed a competitive advantage of the ΔIssA mutant over the wild-type, indicating that immune suppression traits may incur fitness trade-offs. Overall, this work demonstrates the power of WISH-tagging for high-resolution analysis of plant–microbe interactions and underscores its potential as a tool for future microbiome engineering and sustainable agricultural innovation.