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. We used a
faster evolving protein-encoding marker to reveal ecological patterns
hidden within a single OTU defined by >99% 16S rRNA
sequence similarity. The studied taxon, subcluster PnecC of the genus
Polynucleobacter, represents a ubiquitous group of planktonic
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 3400 km (42°N to 71°N) and a pH gradient of 4.2 to
8.6. Besides 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. A
unexpected pattern was the almost complete compositional separation of
Polynucleobacter communities of Ca-rich and
Ca-poor habitats, which strongly resembled the
vicariance of plant species on silicate and limestone soils. The
presented new cultivation-independent approach 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.
Functional similarity of attached and free-living bacteria during freshwater phytoplankton blooms