Chlorpyrifos-Mineralizing Endophyte Klebsiella pneumoniae Strain HSTU-BF3R2 (Sequence Type ST10063), Without Acquired Resistance or Canonical Hypervirulence Loci, Enhances Tomato Plant Growth with 70% Less Urea

Klebsiella pneumoniae includes clinically important opportunistic pathogens and has also been recovered from plant tissues, yet plant-derived isolates are usually judged by genus rather than by genome. We characterised HSTU-BF3R2, an endophyte of surface-sterilised brinjal roots from Dinajpur, Bangladesh, and evaluated it in tomato. The 5,318,912 bp draft assembly (67 contigs; 57.40% G+C; 4996 coding sequences) is K. pneumoniae sensu stricto (98.96% average nucleotide identity to the type strain) and was assigned the new sequence type ST10063 by the Institut Pasteur BIGSdb curators, distinguished by a single-nucleotide variant in tonB. No acquired resistance gene or canonical hypervirulence locus was detected, whereas 50 complete reference genomes carried 0–33 acquired genes, and a putative IncFIB plasmid reconstruction lacked detected conjugation machinery and contained metal- and heat-stress-associated determinants. Candidate annotations were checked by reciprocal BLASTp, and potentially missed genes were searched by tBLASTn. Nutrient acquisition dominates the verified repertoire and includes an annotated pqqA–F/gcd route potentially associated with gluconate-mediated phosphate solubilisation together with a 14-gene phosphonate uptake and C–P lyase complement, whereas the nitrogenase (nif) cluster, canonical auxin biosynthesis, ACC deaminase and the chemotaxis and flagellar genes are absent: no canonical nitrogen-fixation machinery was detected. In a three-treatment field trial, inoculation with 70% less urea and no scheduled sprays increased shoot length by 63.3% and fruit number 3.54-fold over fully fertilised, conventionally sprayed controls, and raised fruit number 22.8-fold over a matched uninoculated low-input control that differed only in the inoculum. Rhizosphere soil of inoculated plants held 1.25–1.66-fold more total N, available P, exchangeable K and available S, and leaves showed higher phenylalanine ammonia-lyase (2.71-fold), peroxidase (2.25-fold) and total phenolics (2.35-fold) but 87% less proline; treatment explained 96.2% of the combined soil–leaf variation (PERMANOVA, p = 0.008). Strain-resolved genomic analysis is informative, but not sufficient by itself, for assessing plant-derived Klebsiella isolates.