Salinibacter ruber strain:M1 | isolate:Salinibacter ruber M1 Genome sequencing and assembly. Salinibacter ruber strain:M1 | isolate:Salinibacter ruber M1

The halophilic bacterium Salinibacter ruber is an abundant and ecologically important member of halophilic communities worldwide. Given its broad distribution and high intraspecific genetic diversity, S. ruber is considered one of the main models for ecological and evolutionary studies of bacterial adaptation to hypersaline environments. However, current insights on the genomic diversity of this species is limited to the comparison of the genomes of two co-isolated strains. Here, we present a comparative genomic analysis of eight S. ruber strains isolated at two different time points in each of two different Mediterranean solar salterns. Our results show an open pangenome with contrasting evolutionary patterns in the core and accessory genomes. We found that the core genome is shaped by extensive homologous recombination (HR), which results in limited sequence variation within population clusters. In contrast, the accessory genome is modulated by Horizontal Gene Transfer (HGT), with genomic islands and plasmids acting as gateways to the rest of the genome. In addition, both types of genetic exchange are modulated by Restriction and modification (RM) or CRISPR-Cas systems. Finally, genes differentially impacted by such processes reveal functional processes relevant for environmental interactions and adaptation to extremophylic conditions. Altogether, our results provide support for scenarios that conciliate both the “Neutral” and the “Kill the Winner” models of bacterial evolution.

嗜盐细菌（halophilic bacterium）红嗜盐杆菌（Salinibacter ruber）是全球嗜盐群落中丰度可观且生态学意义重大的类群。鉴于其分布范围广泛、种内遗传多样性（intraspecific genetic diversity）极高，红嗜盐杆菌被视作研究细菌适应高盐环境（hypersaline environments）的生态学与进化学过程的核心模型之一。然而，当前学界对该物种基因组多样性的认知仅局限于两株共分离菌株的基因组比较分析。本研究针对从两处不同的地中海太阳能盐场（Mediterranean solar salterns）、每个盐场各于两个不同时间点分离得到的8株红嗜盐杆菌菌株，开展了比较基因组分析（comparative genomic analysis）。研究结果表明，该物种的泛基因组呈开放状态，核心基因组（core genome）与附属基因组（accessory genome）展现出截然相反的进化模式。我们发现，核心基因组受到广泛的同源重组（homologous recombination, HR）塑造，致使种群簇内的序列变异十分有限。与之相对，附属基因组则受水平基因转移（Horizontal Gene Transfer, HGT）调控，基因组岛（genomic islands）与质粒（plasmids）充当了基因向基因组其他区域转移的门户。此外，限制修饰系统（Restriction and modification, RM）与CRISPR-Cas系统（CRISPR-Cas systems）可对这两类遗传交换过程进行调控。受此类过程差异化影响的基因，其功能均与环境互作及极端环境适应（extremophylic conditions）相关。综上，本研究结果为调和细菌进化的“中性模型”与“胜者为王（Kill the Winner）”模型提供了实证支撑。