Ren Minglei, Hu Ang, Zhang Lu, Yao Xiaolong, Zhao Zhonghua, Kimirei Ismael Aaron, Wang Jianjun
Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
Tanzania Fisheries Research Institute-Headquarter, Dar Es Salaam P.O. Box 9750, Tanzania.
Water Res. 2024 Nov 15;266:122393. doi: 10.1016/j.watres.2024.122393. Epub 2024 Sep 3.
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.
微生物氨基酸组成（AA）反映了细胞和分子调控的适应性策略，例如嗜碱菌中酸性氨基酸（包括谷氨酸和天冬氨酸）的比例较高。微生物的氨基酸含量如何与其pH适应性相关，特别是在自然环境中，这一点仍未得到充分研究。在这里，我们利用宏基因组学研究了东非湖泊39份水和沉积物样本中的原核生物群落及其基因的氨基酸组成，这些样本的pH值范围从7.2到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，这表明它们在湖泊中有不同的栖息地偏好。微生物群落在碱性湖泊中的酸性蛋白质组比中性湖泊中的更高。物种的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的氨基酸组成。比较基因组分析进一步表明，与中性条件下的微生物相比，嗜碱微生物含有更多具有较高酸性氨基酸的功能基因。这些特征包括编码不同类型阳离子跨膜转运蛋白、反向转运蛋白和相容性溶质转运蛋白的基因，它们参与高pH条件下的细胞质pH稳态和渗透胁迫防御。我们的研究结果为原核生物氨基酸组成与其栖息地偏好之间的紧密关系提供了实地证据，并强调氨基酸优化是环境适应的策略。
