Polynucleobacter paneuropaeus sp. nov., characterized by six strains isolated from freshwater lakes located along a 3000 km north–south cross-section across Europe

Abstract

Six Polynucleobacter (Burkholderiaceae, Betaproteobacteria) strains isolated from different freshwater lakes located across Europe were taxonomically investigated. Phylogenetic analyses based on 16S rRNA gene sequences assigns all six strains to the cryptic species complex PnecC within the genus Polynucleobacter. Analyses of partial glutamine synthetase (glnA) genes suggests that all six strains belong to the species-like taxon designated F15 in previous papers. Comparative genome analyses reveal that the six strains form a genomically coherent group characterized by whole-genome average nucleotide identity (gANI) values of > 98% but separated by gANI values of < 88% from the type strains and representatives of the 16 previously described Polynucleobacter species. In phylogenetic analyses based on nucleotide sequences of 319 orthologous genes, the six strains represent a monophyletic cluster that is clearly separated from all other described species. Genome sizes of the six strains range from 1.61 to 1.83 Mbp, which is smaller than genome sizes of the majority of type strains representing previously described Polynucleobacter species. By contrast, G+C content of the DNA of the strains is well in the range of 44.8-46.6 mol% previously found for other type strains of species affiliated with the subgroup PnecC. Variation among the six strains representing the new species is evident in a number of traits. These include gene content differences, for instance regarding a gene cluster encoding anoxygenic photosynthesis, as well as phenotypic traits. We propose to name the new species represented by the six strains P. paneuropaeus sp. nov. and designate strain MG-25-Pas1-D2T (=DSM 103454T =CIP 111323T) as the type strain.

Continental-Scale Gene Flow Prevents Allopatric Divergence of Pelagic Freshwater Bacteria

“…1 ). Twenty-four strains were obtained previously by using the acclimatization method, which provides a slow transition from the low environmental substrate concentrations to the high concentration of standard microbial media ( Hahn et al 2004 ), without employing strategies for species-specific targeted isolation ( Hoetzinger et al 2019 ). For further isolation, we focused on the geographic regions defined by isolation sites of these initial 24 strains.…”

“…Genomic DNA of strains was extracted as described previously ( Hahn et al 2017 ). Apart from six previously published genomes ( Hoetzinger et al 2019 ), which were sequenced and assembled by a hybrid approach (Roche GS FLX and Illumina), genomes were sequenced by an Illumina MiSeq (paired-end, 300 bp) or an Illumina HiSeq instrument (paired-end, 150 bp) by Eurofins Genomics, Ebersberg, Germany. Reads which passed the Illumina chastity filter (average Phred score of 34.1 with 86.9% of all reads with Phred >Q30) were assembled using SPAdes v.3.10 ( Bankevich et al 2012 ) in the mismatch careful mode (including read error correction) with six k-mer lengths (21, 33, 55, 77, 99, and 127).…”

“…Here, we investigated Polynucleobacter paneuropaeus , a species of pelagic freshwater bacteria previously described on the basis of six strains, isolated from lakes and ponds located along a 3,400 km cross-section across Europe ( Hoetzinger et al 2019 ). Mainly by targeted isolation from habitats of the same geographic range, we increased the total number of strains affiliated to this species to 120.…”

Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients

“…Further, C_77 exhibited exceptionally broad ecological preferences, specifically in latitudinal distribution, conductivity, and pH (Figure 4). While a pan-European distribution was determined for Polynucleobacter paneuropeaus (Hoetzinger et al, 2019) that has a matching 16S rRNA gene sequence with C_77, the covered conductivity and pH ranges of C_77 likely exceed the niche this species might be adapted to. Six strains of P. paneuropeaus were isolated from habitats with conductivities and pH values ranging from 15-55 µS cm −1 and 4.6-7.5, respectively (Hoetzinger et al, 2019), which cover only a small part of the environmental range C_77 occured in.…”

“…While a pan-European distribution was determined for Polynucleobacter paneuropeaus (Hoetzinger et al, 2019) that has a matching 16S rRNA gene sequence with C_77, the covered conductivity and pH ranges of C_77 likely exceed the niche this species might be adapted to. Six strains of P. paneuropeaus were isolated from habitats with conductivities and pH values ranging from 15-55 µS cm −1 and 4.6-7.5, respectively (Hoetzinger et al, 2019), which cover only a small part of the environmental range C_77 occured in. The type strain of Polynucleobacter hirudinilacicola, also comprised in the OTU C_77, was isolated from a pond with relatively high conductivity (353 µS cm −1 ) and a pH of 8.0 (Hahn et al, 2018).…”