TWO DISTINCT LINEAGES OF PANTOEA ANANATIS ARE DIVERGENT IN TOXIN PRODUCTION POTENTIAL AND HOST SPECIALIZATION

Abstract

Pantoea ananatis has recently emerged as a causal agent of Pantoea leaf blight of rice in the United States, raising concerns about its potential impact on rice production. Despite increasing reports of the disease, the mechanisms underlying host specialization and virulence within this pathosystem remain poorly understood. Here, comparative genomics and in-planta assays are combined to investigate population structure and virulence determinants among rice-associated P. ananatis strains. Average nucleotide identity analysis of P. ananatis genomes resolved two distinct lineages with contrasting host associations. One lineage, composed of strains recovered exclusively from rice, lacked the HiVir operon responsible for synthesis of the phosphonate toxin pantaphos. A second, more broadly distributed lineage included P. ananatis isolated from diverse hosts, including rice, and many contained the HiVir operon. HiVir-mediated pantaphos production drove necrotic symptom development in rice but was not required for bacterial replication within rice tissue. Accordingly, strains lacking HiVir, including those from the rice-associated lineage and targeted mutants, exhibited reduced necrosis while achieving bacterial population sizes comparable to wild-type generalist strains during infection of rice. Conversely, host-range experiments showed that rice-associated strains exhibited reduced colonization in onion tissue relative to generalist strains, consistent with evolutionary specialization to rice. Comparative pangenome analysis supported the evolutionary separation of these lineages and identified hundreds of lineage-specific genes, in-tact secretion systems, and secondary metabolite biosynthetic gene clusters that may underpin host associations. These findings demonstrate that P. ananatis populations associated with rice comprise distinct evolutionary lineages with differing genomic features and virulence strategies and reveal a decoupling between symptom development and bacterial proliferation during infection of rice.