Systemic trade-offs between core and accessory genomes govern stress adaptation in <i>Rhodococcus erythropolis</i>

ABSTRACT The genus Rhodococcus is a premier biotechnological chassis for organic pollutant bioremediation and natural product biosynthesis, yet the systemic genetic basis of its stress resilience remains poorly defined. Here, we elucidate adaptive strategies in Rhodococcus erythropolis by integrating pangenomics with multi-omics and phenotypic analyses. We refined R. erythropolis taxonomy using average nucleotide identity across 671 genomes and constructed a high-quality pangenome that exhibits an open architecture, with continuous expansion of the accessory cloud genome via horizontal gene transfer to enable environmental adaptation. Using R. erythropolis strain XP as a representative model, we confirmed broad physiological robustness, including tolerance to multiple heavy metals [Ni(II), Zn(II), Pb(II), Cu(II), and Cr(VI); minimum inhibitory concentrations, 2–7 mM], wide pH ranges (5–11), and high salinity (1.5 M NaCl). Integration of comparative transcriptomics with weighted gene co-expression network analysis revealed the transcriptional basis of this resilience. A key growth-regulatory module (ME1), dominated by evolutionarily conserved core genes (68.8%), including essential cell division components, was identified. Under severe stress, this core module is strongly downregulated, coinciding with stress-induced filamentation. These results expose a fundamental evolutionary trade-off: repression of vertical propagation via core functions enables preferential deployment of accessory cloud genes that confer resistance. Collectively, this study links pangenome plasticity to physiological trade-offs and provides a conceptual framework for optimizing R. erythropolis in industrial applications. IMPORTANCE Microorganisms must continually balance rapid growth with survival under stress, yet the genomic architecture underlying this trade-off remains unclear. By analyzing 671 genomes to refine the taxonomy of the biotechnologically important bacterium Rhodococcus erythropolis and integrating multi-omics data, we demonstrate that this physiological balance is mirrored by an evolutionary division of labor. The conserved core genome predominantly governs growth, whereas the horizontally acquired accessory cloud genome drives stress resistance. Under severe stress, the bacterium downregulates core cell division machinery to prioritize resources for activating its accessory defense repertoire. This work establishes a direct link between pangenome evolution and cellular fitness, offering theoretical guidance for engineering robust microbial chassis.