Variation in genomic islands contribute to genome plasticity in Cupriavidus metallidurans

Different Cupriavidus metallidurans strains isolated from metal-contaminated and other anthropogenic environments were genotypically and phenotypically compared with C. metallidurans type strain CH34. The latter is well-studied for its resistance to a wide range of metals, which is carried for a substantial part by its two megaplasmids pMOL28 and pMOL30. Comparative genomic hybridization (CGH) indicated that the extensive arsenal of determinants involved in metal resistance was well conserved among the different C. metallidurans strains. Contrary, the mobile genetic elements identified in type strain CH34 were not present in all strains but clearly showed a pattern, although, not directly related to a particular biotope nor location (geographical). One group of strains carried almost all mobile genetic elements, while these were much less abundant in the second group. This occurrence was also reflected in their ability to degrade toluene and grow autotrophically on hydrogen gas and carbon dioxide, which are two traits linked to separate genomic islands of the Tn4371-family. In addition, the clear pattern of genomic islands distribution allowed to identify new putative genomic islands on chromosome 1 and 2 of C. metallidurans CH34. Metal resistance determinants are shared by all C. metallidurans strains and their occurrence is apparently irrespective of the strain's isolation type and place. Cupriavidus metallidurans strains do display substantial differences in the diversity and size of their mobile gene pool, which may be extensive in some (including the type strain) while marginal in others. Comparative genome hybridization experiments. Comparing genomic DNA samples of different strains with a common reference strain (CH34).

从金属污染环境及其他人为活动干扰环境中分离得到的多株耐金属贪铜菌（Cupriavidus metallidurans），与该菌的模式菌株CH34进行了基因型与表型的比较分析。该模式菌株因对多种金属具备抗性而被广泛研究，其金属抗性的主要部分由其携带的两个大型质粒pMOL28和pMOL30所介导。
比较基因组杂交（Comparative Genomic Hybridization, CGH）结果显示，金属抗性相关的丰富抗性决定因子在所有耐金属贪铜菌菌株中均高度保守。与之相反，模式菌株CH34中鉴定出的移动遗传元件（mobile genetic elements）并非在所有菌株中均存在，但呈现出明确的分布模式——尽管该模式与特定生境或地理位置并无直接关联。其中一类菌株几乎携带全部移动遗传元件，而另一类菌株中这些元件的丰度则显著较低。
这种分布特征也体现在菌株的两项性状上：降解甲苯的能力，以及以氢气与二氧化碳为底物进行自养生长的能力，这两项性状均与Tn4371家族的独立基因组岛（genomic islands）相关。此外，清晰的基因组岛分布模式帮助研究人员在耐金属贪铜菌CH34的1号与2号染色体上鉴定出了新的潜在基因组岛。
所有耐金属贪铜菌菌株均共享金属抗性决定因子，这些因子的存在与否显然与菌株的分离来源及分离地点无关。耐金属贪铜菌菌株在移动基因库的多样性与规模上存在显著差异：部分菌株（包括模式菌株）的移动基因库规模庞大，而另一部分菌株则相对有限。
本研究采用比较基因组杂交实验方法：将不同菌株的基因组DNA样本与统一参考菌株CH34进行比对分析。