Novel Verrucomicrobiota strains associated with plant root tissue enhances plant growth and suppresses bacterial wilt in tomato.

Rhizosphere microbes interact with plant roots, playing a crucial role in promoting plantgrowth and alleviating both biotic and abiotic stresses. Our previous study identified putativekeystone taxa associated with bacterial wilt (BW) resistance in tomato plants. Among thesetaxa, bacteria in phylum Verrucomicrobiota remain poorly characterized due to challenges inlaboratory cultivation. Here, we aimed to isolate novel Verrucomicrobiota strains fromtomato rhizosphere soil using various carbon and antibiotic-enriched culture media combinedwith microbiota analysis. Microbiota analysis revealed the carbon-source dependentmicrobial community structure in the enrichment cultures. Verrucomicrobiota strains were themost abundant in the cultures enriched with grounded plant roots and antibiotics. A total of27 novel bacteria, including two Verrucomicrobiota strains (V1 and V2), were isolated fromdifferent enrichment cultures. In-planta plant growth promotion (PGP) assay, strain V2demonstrated a higher plant fresh weight than strain V1. Disease severity assessment showedthat V1 was more effective in controlling BW than V2. This suggested that plant-associatedVerrucomicrobiota members are involved in plant-beneficial interaction in the rhizosphere.Our study presents a novel strategy for isolating previously uncultivated Verrucomicrobiotastrains from the tomato rhizosphere using carbon and antibiotic-enriched cultures.