Tissue-specific experimental evolution reveals adaptive trade-offs in the plant vascular pathogen Clavibacter michiganensis

The plant pathogenic bacterium Clavibacter michiganensis (Cm) is a systemic vascular pathogen that colonizes both xylem vessels and the intracellular apoplast during different stages of infection. To identify traits and loci associated with adaptation to these distinct host microenvironments, we conducted tissue-specific experimental evolution. Twenty independent Cm lineages were repeatedly passaged in either tomato stems or leaves to promote adaptation to vascular or apoplastic lifestyles, respectively. After fifteen passages, adapted clones were characterized for virulence and virulence-related traits. These characterizations demonstrated clear differential associations of virulence-associated traits with the adapted tissue. The majority of vascular-adapted clones displayed enhanced surface attachment, reduced cellulase activity, reduced exopolysaccharide (EPS) production, and attenuated virulence on tomato compared to the parent clone. In contrast, apoplast-adapted clones displayed reduced biofilm formation and enhanced EPS production and retained their virulence on tomato. Whole-genome sequencing of all adapted clones revealed candidate loci linked to tissue adaptation. Six of ten vascular-adapted clones carried two independent mutations in CMM_1284, a putative HipB/XRE-type transcriptional regulator. A CMM_1284 marker exchange mutant displayed phenotypes similar to vascular-adapted clones, suggesting a role for this regulator in vascular colonization. Together, these findings highlight the role of phenotypic plasticity in tissue adaptation of plant pathogens, showing that tissue-specific adaptation involves modulation of surface attachment, EPS production, and cell wall-degrading enzymes and suggest a trade-off between vascular persistence, supported by strong surface attachment, and systemic virulence, which depends on bacterial dispersal and migration.