The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome transitions, resulting in species-level separation between aquatic biomes.

中文翻译：

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水生细菌的大规模系统基因组学揭示了适应盐度的分子机制

环境障碍的跨越带来了重大的适应性挑战。淡水-海洋过渡的稀有性将细菌群落分开，但这些与半咸水对应物的关系仍然难以捉摸，促进跨生物群落过渡的分子适应性也是如此。我们对淡水、半咸水和海洋质量过滤宏基因组组装的基因组进行了大规模系统发育分析 (11,248)。平均核苷酸同一性分析表明，细菌物种很少存在于多个生物群落中。相比之下，不同的咸水盆地共存有许多物种，但它们的种内种群结构显示出明显的地理分离迹象。我们进一步确定了最近的跨生物群落转变，这些转变是罕见的、古老的，并且最常见于咸水生物群落。转变伴随着氨基酸组成的系统变化和推断的蛋白质组的等电点分布，这些变化经过数百万年的进化，以及特定基因功能的收敛性增益或损失。因此，需要蛋白质组重组和基因含量特定变化的适应性挑战限制了跨生物群落的转变，导致水生生物群落之间的物种水平分离。