Abstract
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, 600species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3,400km (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.
Highlights
Prokaryotes are the most numerous organisms on earth
We evaluated if 16S rRNA based amplicon sequence variant (ASV) of Polynucleobacter bacteria possess a predictive power regarding environmental preferences of ASVs
Amplicon sequencing of the priB gene provided an unprecedented insight into the diversity of Polynucleobacter bacteria and structuring of their local communities by environmental factors
Summary
Prokaryotes are the most numerous organisms on earth. Our current knowledge on diversity of prokaryotes and composition of prokaryotic communities is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Despite being frequently stated in publications, and independent of the applied sequence similarity threshold used for OTU demarcation, the established OTUs do not represent species-like taxa. Due to all these limitations, prokaryotic communities remained at the species level black boxes. A few alternative markers and primers have been developed for profiling the composition and structure of bacterial communities with higher resolution than that provided by the 16S rRNA gene (Hill et al, 2002; Ogier et al, 2019; Sánchez et al, 2014) Such approaches have to deal with the trade-off of either relying on strongly degenerated primers ensuring a taxonomically broad match of the primers (Hill et al, 2002; Ogier et al, 2019), or using less degenerated primers, which only match to genes of much more narrow taxonomic groups (Sánchez et al, 2014)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
