West Annie G, Boey Jian Sheng, Tee Hwee Sze, Handley Kim M
School of Biological Sciences, University of Auckland, Auckland 1010, Auckland, New Zealand.
Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom.
ISME Commun. 2025 Jul 16;5(1):ycaf122. doi: 10.1093/ismeco/ycaf122. eCollection 2025 Jan.
Salinity imposes a major barrier to microbial dispersal and colonization due to the requirement for osmoadaptations to maintain cell turgor and protein stability. Estuaries may facilitate infrequent evolutionary transitions between freshwater and marine habitats, which are characterized by differences in both salinity and resource availability. Here we illustrate niche differentiation of the Luna-1 subcluster sister lineages within an estuarine system: freshwater-adapted and saltwater-adapted . Comparative genomic and transcriptomic analyses highlighted key differences in osmoregulation, photoheterotrophy, and nutrient acquisition. Both genera are differentiated by mechanisms for osmoregulation, phosphate and iron uptake, and carbohydrate utilization, and by their rhodopsin preference (actinorhodopsin or heliorhodopsin). To clarify which traits are habitat versus lineage specific, we investigated the global distribution of Luna-1 subcluster taxa. The two constituent genera are both more commonly known from freshwater sources, although there are reports of isolated from saltwater. Results here confirm that is almost exclusively freshwater-derived. instead comprises distinct clades of predominantly freshwater- or saltwater-derived taxa, with approximately half of representing slight halophiles from brackish and marine waters. Consistent with observations from the estuary, traits associated with osmoregulation and photoheterotrophy (rhodopsin preference and carbohydrate utilization) differentiated saltwater and freshwater members of the global dataset (both and ), and are therefore likely to be habitat rather than lineage-specific traits. Together, findings demonstrate various genomic characteristics enabling habitat-based niche differentiation between and within lineages of the Luna-1 subcluster, providing insights into microbial adaptation across salinity gradients.
由于需要进行渗透适应以维持细胞膨压和蛋白质稳定性，盐度对微生物的扩散和定殖构成了主要障碍。河口可能促进淡水和海洋栖息地之间不频繁的进化转变，这两种栖息地的特点是盐度和资源可用性都存在差异。在这里，我们阐述了河口系统中Luna-1亚群姐妹谱系的生态位分化：适应淡水的和适应盐水的。比较基因组学和转录组学分析突出了渗透调节、光能异养和养分获取方面的关键差异。这两个属在渗透调节机制、磷酸盐和铁的摄取以及碳水化合物利用方面存在差异，并且在视紫红质偏好（肌动视紫红质或嗜盐视紫红质）方面也有所不同。为了阐明哪些特征是特定于栖息地还是特定于谱系的，我们研究了Luna-1亚群分类单元的全球分布。这两个组成属在淡水源中更为常见，尽管有从盐水中分离出的报道。这里的结果证实，几乎完全源自淡水。相反，包含主要源自淡水或盐水的分类单元的不同进化枝，其中约一半的代表来自微咸水和海水的轻度嗜盐菌。与河口的观察结果一致，与渗透调节和光能异养相关的特征（视紫红质偏好和碳水化合物利用）区分了全球数据集中适应盐水和淡水的成员（和），因此可能是特定于栖息地而非特定于谱系的特征。总之，研究结果表明了各种基因组特征，这些特征能够使Luna-1亚群谱系之间和谱系内部基于栖息地的生态位分化，为跨盐度梯度的微生物适应提供了见解。
