Isolation, Identification, and Plant Growth-Promoting Mechanisms of Strain BN5, with a Focus on Exogenously Trp-Independent IAA Biosynthesis, and Its Impact on Cucumber Cultivation

Highlights

• First systematic report of Niallia taxi BN5 with plant growth-promoting (PGP) activity, filling the Niallia PGP mechanism gap (previously studied for bioremediation/antibacterial functions).

• Multi-omics (genome/transcriptome/qPCR) show BN5 has a complete trp operon for constitutive IAA biosynthesis (17.64 μg/mL); tryptophan regulates trp/motility genes.

• BN5 enhances cucumber growth (height +24.29%, stem +11.23%), yield (+17.55%) and quality (vitamin C +17.2%, soluble sugar +37.41%) in pot/greenhouse trials.

• BN5 reshapes rhizosphere microbiomes (enriches Bacillus/Pseudomonas) and elevates soil enzymes, providing a microbial resource for sustainable agriculture.

Abstract

The genus Niallia was recently separated as a taxonomic group from Bacillus based on conserved signature insertions and deletions in the genome. Unlike its role in bioremediation, its function in plant growth promotion has not attracted widespread attention. This study identifies Niallia taxi BN5, focusing on the role of tryptophan in IAA synthesis and regulation, as well as the effects of cucumber. The study employed pot and greenhouse experiments to evaluate the impacts of BN5 on cucumber growth, yield, and quality. Genome analysis explored the tryptophan-regulated IAA biosynthesis pathway, with transcriptome and qPCR examining expression of IAA-related, tryptophan synthesis, and motility genes. It also evaluated impacts on rhizosphere microbial communities and soil enzyme activities. BN5 significantly enhanced cucumber growth (height: +24.29%, stem diameter: +11.23%), yield (+17.55%), and quality (vitamin C: +17.2% soluble sugar: +37.41%, all p<0.05). It increased soil enzyme activities (urease by +52.12%, dehydrogenase by +44.70%, p<0.05) and reshaped the microbial structure. Owing to its possession of a complete tryptophan synthase operon (trpE-D-G-C-F-B-A), strain BN5 is able to produce IAA at a concentration of 17.64 μg/mL via a tryptophan-dependent biosynthetic pathway, with no reliance on exogenous tryptophan. Exogenous tryptophan downregulated the trp cluster but upregulated motility genes (mcp and fliC, p<0.05), indicating adaptive regulation of IAA precursors. This study clarifies the plant growth-promoting mechanisms of Niallia spp., focusing on tryptophan-mediated regulation of IAA biosynthesis that is independent of exogenous tryptophan. It lays a foundation for efficient microbial fertilizers, highlighting BN5′s potential in sustainable agriculture.

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