Data from: Ecological genomics of mutualism decline in nitrogen-fixing bacteria

Anthropogenic changes can influence mutualism evolution; however, the genomic regions underpinning mutualism that are most affected by environmental change are generally unknown, even in well-studied model mutualisms like the interaction between legumes and their nitrogen (N)-fixing rhizobia. Such genomic information can shed light on the agents and targets of selection maintaining cooperation in nature. We recently demonstrated that N-fertilization has caused an evolutionary decline in mutualistic partner quality in the rhizobia that form symbiosis with clover. Here population genomic analyses of N-fertilized versus control rhizobium populations indicate that evolutionary differentiation at a key symbiosis gene region on the symbiotic plasmid (pSym) contributes to partner quality decline. Moreover patterns of genetic variation at selected loci were consistent with recent positive selection within N-fertilized environments, suggesting that N-rich environments might select for less-beneficial rhizobia. By studying the molecular population genomics of a natural bacterial population within a long-term ecological field experiment, we find that: 1) the N environment is indeed a potent selective force mediating mutualism evolution in this symbiosis, 2) natural variation in rhizobium partner quality is mediated in part by key symbiosis genes on the symbiotic plasmid, and 3) differentiation at selected genes occurred in the context of otherwise recombining genomes, resembling eukaryotic models of adaptation.

人为活动变化可影响互利共生演化（mutualism evolution）；然而，即便在豆科植物与其固氮根瘤菌（nitrogen-fixing rhizobia）这类被充分研究的典型互利共生体系中，受环境变化影响最显著的、支撑互利共生的基因组区域通常仍未明确。此类基因组信息可阐明自然界中维持合作关系的选择作用因子与作用靶点。我们近期研究证实，氮素施肥导致了与三叶草形成共生关系的根瘤菌的互利共生伙伴品质发生进化衰退。本研究通过对施加氮素施肥与对照组的根瘤菌种群开展种群基因组分析，发现共生质粒（symbiotic plasmid, pSym）上关键共生基因区域的进化分化是导致伙伴品质衰退的原因之一。此外，受选择位点的遗传变异模式与氮素施肥环境下近期发生的正选择（positive selection）特征相符，表明富氮环境可能会选择出互利性更低的根瘤菌菌株。本研究依托长期野外生态实验，通过对自然细菌种群开展分子种群基因组学研究，得到以下结论：1）氮素环境确实是介导该共生体系互利共生演化的强选择压力；2）根瘤菌伙伴品质的自然变异部分由共生质粒上的关键共生基因所介导；3）即便在基因组广泛重组的背景下，受选择基因仍可发生分化，这一现象与真核生物的适应性演化模型相符。