Comparative genomic insights into the genus Pantoea: genetic determinants of ecological lifestyle diversity and plant growth–promoting potential

TL;DR

This study explores the genetic diversity of Pantoea bacteria to understand their roles in promoting plant growth and causing disease.

Contribution

The study identifies genetic markers distinguishing beneficial and pathogenic traits in Pantoea through comparative genomics.

Findings

Plant growth-promoting genes like those for phosphate solubilization are widely conserved in Pantoea.

Intrinsic antibiotic resistance mechanisms involve efflux pumps and β-lactamases across the genus.

Genetic markers like hrp/hrc and ibeB distinguish pathogenic from beneficial strains.

Abstract

Pantoea is a genus of Gram-negative bacteria isolated from diverse environments. Over time, it has drawn considerable attention for its potential to promote plant growth. However, its biotechnological application is complicated by high genomic plasticity, which underlies both its beneficial traits and its ability to cause disease in a wide range of plants, as well as occasional opportunistic infections in humans, raising biosafety concerns. In this study, we conducted a comparative genomic analysis of all publicly available Pantoea genomes. Our goals were to refine taxonomic classifications and to identify genes linked to biotechnological potential, virulence, and antibiotic resistance, thereby clarifying lifestyle strategies within the genus. We found that plant growth-promoting genes are widely conserved, particularly those involved in phosphate solubilization, phytohormone biosynthesis, and siderophore production. In contrast, traits such as nitrogen fixation and ACC deaminase activity were restricted to specific species. The resistome analysis revealed intrinsic resistance mechanisms conserved across the genus, primarily involving diverse efflux pump families and β-lactamases conferring resistance to cephalosporins. In parallel, the pan-GWAS highlighted lifestyle-defining genetic markers, including the hrp/hrc genes encoding type III secretion system components, pepM (phosphoenolpyruvate mutase) associated with the production of a phytotoxin, and ibeB, an invasin linked to clinical infections. Together, our findings underscore both the biotechnological potential of Pantoea and the importance of genetic markers for distinguishing beneficial from pathogenic lifestyles, supporting the safe application of selected strains in biotechnology.

The online version contains supplementary material available at 10.1007/s11274-025-04780-2.

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