Microbial amino acid composition (AA) reflects adaptive strategies of cellular and molecular regulations such as a high proportion of acidic AAs, including glutamic and aspartic acids in alkaliphiles. It remains understudied how microbial AA content is linked to their pH adaptation especially in natural environments. Here we examined prokaryotic communities and their AA composition of genes with metagenomics for 39 water and sediments of East African lakes along a gradient of pH spanning from 7.2 to 10.1. We found that Shannon diversity declined with the increasing pH and that species abundance were either positively or negatively associated with pH, indicating their distinct habitat preference in lakes. Microbial communities showed higher acidic proteomes in alkaline than neutral lakes. Species acidic proteomes were also positively correlated with their pH preference, which was consistent across major bacterial lineages. These results suggest selective pressure associated with high pH likely shape microbial amino acid composition both at the species and community levels. Comparative genome analyses further revealed that alkaliphilic microbes contained more functional genes with higher acidic AAs when compared to those in neutral conditions. These traits included genes encoding diverse classes of cation transmembrane transporters, antiporters, and compatible solute transporters, which are involved in cytoplasmic pH homeostasis and osmotic stress defense under high pH conditions. Our results provide the field evidence for the strong relationship between prokaryotic AA composition and their habitat preference and highlight amino acid optimization as strategies for environmental adaptation.

中文翻译：

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酸性蛋白质组与非洲湖泊中的微生物碱性偏好有关


微生物氨基酸组成 （AA） 反映了细胞和分子调节的适应性策略，例如高比例的酸性 AA，包括嗜碱性物质中的谷氨酸和天冬氨酸。微生物 AA 含量如何与其 pH 适应相关联，尤其是在自然环境中，仍未得到充分研究。在这里，我们用宏基因组学检查了东非湖泊的 39 个水和沉积物的原核群落及其基因的 AA 组成，其 pH 梯度范围为 7.2 至 10.1。我们发现香农多样性随着 pH 值的升高而下降，物种丰度与 pH 值呈正相关或负相关，表明它们在湖泊中独特的栖息地偏好。微生物群落在碱性湖泊中表现出比中性湖泊更高的酸性蛋白质组。物种酸性蛋白质组也与其 pH 偏好呈正相关，这在主要细菌谱系中是一致的。这些结果表明，与高 pH 值相关的选择压力可能在物种和群落水平上塑造微生物氨基酸组成。比较基因组分析进一步显示，与中性条件下的微生物相比，亲碱微生物包含更多的功能性基因和更高的酸性 AAs。这些性状包括编码不同类别的阳离子跨膜转运蛋白、反向转运蛋白和相容溶质转运蛋白的基因，它们参与高 pH 条件下的细胞质 pH 稳态和渗透应激防御。我们的结果为原核生物 AA 组成与其栖息地偏好之间的密切关系提供了现场证据，并强调了氨基酸优化作为环境适应策略。