Draft genome sequence of Lysinibacillus capsici NAVL5D with potential for plant growth promotion.

Abstract

The use of plant growth-promoting (PGP) bacteria is an emerging strategy for sustainable agriculture, offering alternatives to chemical fertilisers and pesticides. Here, we report the draft genome sequence and functional characterization of Lysinibacillus capsici NAVL5D isolated from the leaf of ready-to-eat lettuce plant grown in South Africa. The genome generated using the Illumina NovaSeq 6000 had a size of 4,631,824 bp, with 22 contigs and a G + C content of 37.3%. In vitro tests demonstrated the strain's potential for plant growth promotion through nitrogen fixation, phosphate solubilization, indole-3-acetic acid (IAA) production, hydrogen cyanide (HCN) synthesis, and siderophore production. Genome analysis revealed key subsystems underpinning these traits such as auxin biosynthesis, nitrogen, phosphorus, and potassium metabolism, as well as putative PGP genes supporting these growth-promoting traits. In addition, five biocontrol secondary metabolites were predicted in the genome including terpenes and cyclic-lactone-autoinducers. However, eight minimal pathogenicity-related genes and six antibiotic resistance genes were also identified, including vanW, vanT, vanY, qacJ, msr(G), and FosBx1. Antibiotic susceptibility testing confirmed resistance to beta-lactams. Evidence of phage with could mediate horizontal gene transfer was observed in the genome. In vivo seed germination assays further demonstrated the strain's ability to promote plant growth, confirming its functional potential beyond in vitro observations. While L. capsici NAVL5D shows promise for sustainable agriculture applications, its potential warrant further investigation to ensure its safe use as a plant growth-promoting agent.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04488-y.