Survivability of <i>Pantoea stewartii</i> subsp. <i>indologenes</i> in Crop Residue and Its Transmission Risk to Onions in the Poaceae– <i>Allium</i> Cropping System

<i>Pantoea stewartii</i> subsp. <i>indologenes</i> (<i>Psi</i>) isolates can cause disease in several Poaceae hosts, including millets and rice, and were recently known to cause foliar and bulb symptoms characteristic of center rot in onions. Cover crops such as millet and cash crops such as corn are commonly grown in the summer after onion harvest in Vidalia, Georgia, United States. However, the risk of pathogen transmission to onions in the cropping systems in which summer crops precede onion planting is largely understudied. We evaluated the survivability of <i>Psi</i> in corn and pearl millet residues and assessed its ability to colonize onions transplanted into the infested soil. Our microplot study showed that millet and corn residues support the transient survival of <i>Psi</i>. The presence of the pathogen in the soil also overlapped with the presence of onion transplants. However, despite planting onion seedlings in <i>Psi</i>-infested soil, no bacterial colonization was observed in their rhizosphere and foliar surfaces. Moreover, no visible symptoms of center rot were observed in onion foliage and bulbs, indicating a lesser risk of vertical transmission in the Poaceae-<i>Allium</i> cropping system. We further investigated genetic determinants for bacterial survival in millet residue and bare soil by creating deletion mutants of the genes responsible for exopolysaccharides, flagellar motility, quorum sensing, and pathogenicity in a <i>Psi</i> pathovar <i>cepacicola</i> strain PNA 14-12. All mutant strains persisted for at least 24 days in millet residue at high population levels, and colonies of all the strains remained detectable in bare soil until 44 days. Exopolysaccharide production played a minor role in <i>Psi</i> survival, whereas none of the other targeted genes contributed to bacterial persistence in millet residue or bare soil. Overall, our findings suggest that summer crop residues play an important role in the survival of <i>Psi</i> in fields under an onion-millet/corn cropping scheme; however, the risk of <i>Psi</i> transmission from millet or corn residue to onions appears minimal. Despite this observation, crop residues should be incorporated into the soil to facilitate decomposition before onion transplanting.