Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. The faster evolving protein-encoding gene priB was used to reveal ecological patterns hidden within a single operational taxonomic unit (OTU) defined by >99% 16S rRNA sequence similarity. The studied subcluster PnecC of the genus Polynucleobacter represents a ubiquitous group of abundant freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3,400 km (42°N to 71°N) and a pH gradient of 4.2 to 8.6. In addition to the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. An unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca²⁺-rich and Ca²⁺-poor habitats. This compositional pattern strongly resembled the vicariance of plant species on silicate and limestone soils. The new cultivation-independent approach presented opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria.

中文翻译：

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打开下一代黑匣子：在单个细菌 >99% 16S rRNA 操作分类单元中发现了数百种类物种的生态趋势

目前关于自由生活细菌的环境分布和分类群丰富度的知识主要基于使用 16S rRNA 基因测序方法进行的独立培养调查。然而，16S rRNA 基因在进化上相当保守，导致该标记提供的分类和生态分辨率有限。进化速度更快的蛋白质编码基因 priB 用于揭示隐藏在单个操作分类单元 (OTU) 中的生态模式，该单元由 >99% 16S rRNA 序列相似性定义。研究的多核杆菌属的亚群 PnecC代表无处不在的丰富的淡水细菌群，具有世界性的分布，淡水系统的多样性调查经常发现这种细菌。基于基因组分类法和大量的基因组序列，可以建立一个序列相似性阈值来描述类物种的分类群。总共在分布在三个地区的 99 个淡水栖息地中检测到 600 种类似物种的类群，这些地区代表纬度范围为 3,400 公里（北纬 42 度至 71 度），pH 梯度为 4.2 至 8.6。除了出乎意料的高丰富度外，增加的分类分辨率揭示了多核杆菌的结构群落由几个宏观生态趋势，以前仅在系统发育上更广泛的细菌群中得到证明。一个意想不到的模式是在富含Ca ²⁺和缺乏Ca ^{2+ 的}栖息地的多核杆菌群落的组成上几乎完全分离。这种组成模式非常类似于硅酸盐和石灰石土壤上植物物种的变异性。提出的新的不依赖培养的方法为令人难以置信的、以前看不见的多样性打开了一扇窗户，并使调查能够更深入地了解环境条件如何塑造细菌群落并推动自由生活细菌的进化。