Phylogeographic and functional assembly of population-level bacterial immunity

Bacterial pangenomes provide a shared reservoir of antiphage defenses, yet the ecological and functional constraints shaping this reservoir remain unclear. Here, we combine comparative genomics of 206 Xanthomonas oryzae pv. oryzae (Xoo) genomes with cross-infection assays of 50 strains against 36 phages and heterologous expression of 24 defense systems in a phage-sensitive Xoo chassis. The Xoo pan-defensome comprises a conserved core of 9 subtypes and a variable layer of 35 accessory and cloud subtypes structured by host phylogeography. Phages are more infectious on sympatric than allopatric hosts, consistent with local adaptation. Variable systems show stronger apparent activity than core systems, whereas resistance breadth is not predicted by defense system number. Co-expression of representative co-occurring and mutually exclusive system pairs reveals synergistic and antagonistic interactions underlying non-random repertoire assembly. Together, these findings extend the pan-immunity framework by showing that population-level immune reservoirs are shaped by both ecological structure and functional compatibility. In this study, the authors use comparative genomics and cross-infection assays to show a spatially and evolutionarily structured bacterial immune reservoir in which interactions among defense systems can reinforce or undermine phage resistance, refining the pan-immunity framework.