Bacteria have highly flexible pangenomes, which are thought to facilitate evolutionary responses to environmental change, but the impacts of environmental stress on pangenome evolution remain unclear. Using a landscape pangenomics approach, I demonstrate that environmental stress leads to consistent, continuous reduction in genome content along four environmental stress gradients (acidity, aridity, heat, salinity) in naturally occurring populations of Bradyrhizobium diazoefficiens (widespread soil-dwelling plant mutualists). Using gene-level network and duplication functional traits to predict accessory gene distributions across environments, genes predicted to be superfluous are more likely lost in high stress, while genes with multi-functional roles are more likely retained. Genes with higher probabilities of being lost with stress contain significantly higher proportions of codons under strong purifying and positive selection. Gene loss is widespread across the entire genome, with high gene-retention hotspots in close spatial proximity to core genes, suggesting Bradyrhizobium has evolved to cluster essential-function genes (accessory genes with multifunctional roles and core genes) in discrete genomic regions, which may stabilise viability during genomic decay. In conclusion, pangenome evolution through genome streamlining are important evolutionary responses to environmental change. This raises questions about impacts of genome streamlining on the adaptive capacity of bacterial populations facing rapid environmental change.

细菌具有高度灵活的泛基因组，这被认为可以促进对环境变化的进化反应，但环境压力对泛基因组进化的影响仍不清楚。使用景观泛基因组学方法，我证明了环境压力导致自然发生的重氮慢生根瘤菌种群中基因组含量沿着四个环境压力梯度（酸度、干旱度、热度、盐度）一致、持续减少（广泛的土壤栖息植物互惠生）。使用基因级网络和重复功能特征来预测跨环境的辅助基因分布，被预测为多余的基因更有可能在高压力下丢失，而具有多功能作用的基因更有可能保留。在强纯化和正选择下，具有较高压力丢失概率的基因包含显着较高比例的密码子。基因丢失在整个基因组中普遍存在，在靠近核心基因的空间上具有高基因保留热点，表明慢生根瘤菌已经进化到在离散的基因组区域中聚集必需功能基因（具有多功能作用的辅助基因和核心基因），这可以在基因组衰变期间稳定生存能力。总之，通过基因组精简的泛基因组进化是对环境变化的重要进化反应。这引发了关于基因组精简对面临快速环境变化的细菌种群适应能力的影响的问题。