100‐year‐old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii

Abstract

SummaryThe first representative of the phylum Planctomycetes, Planctomyces bekefii, was described nearly one century ago. This morphologically conspicuous freshwater bacterium is a rare example of as‐yet‐uncultivated prokaryotes with validly published names and unknown identity. We report the results of molecular identification of this elusive bacterium, which was detected in a eutrophic boreal lake in Northern Russia. By using high‐performance cell sorting, P. bekefii‐like cell rosettes were selectively enriched from lake water. The retrieved 16S rRNA gene sequence was nearly identical to those in dozens of metagenomes assembled from freshwater lakes during cyanobacterial blooms and was phylogenetically placed within a large group of environmental sequences originating from various freshwater habitats worldwide. In contrast, 16S rRNA gene sequence similarity to all currently described members of the order Planctomycetales was only 83%–92%. The metagenome assembled for P. bekefii reached 43% genome coverage and showed the potential for degradation of peptides, pectins, and sulfated polysaccharides. Tracing the seasonal dynamics of P. bekefii by Illumina paired‐end sequencing of 16S rRNA gene fragments and by fluorescence in situ hybridization revealed that these bacteria only transiently surpass the detection limit, with a characteristic population peak of up to 104 cells ml−1 following cyanobacterial blooms.

Thalassoglobus polymorphus sp. nov., a novel Planctomycete isolated close to a public beach of Mallorca Island

“…Phylogenetic analyses The 16S rRNA gene-based phylogenetic analysis of strain Mal48 T was computed along with sequences of all described planctomycetal species (assessed in January 2020), including recently published isolates (Kohn et al 2016(Kohn et al , 2020aKulichevskaya et al 2015;Boersma et al 2019;Kallscheuer et al 2019a;Dedysh et al 2020). SINA was used to perform the 16S rRNA gene sequence alignment (Pruesse et al 2012).…”

Rosistilla oblonga gen. nov., sp. nov. and Rosistilla carotiformis sp. nov., isolated from biotic or abiotic surfaces in Northern Germany, Mallorca, Spain and California, USA

“…16S rRNA gene sequence-based phylogeny was computed for strains Poly24 T , CA51 T and Mal33 and the type strains of all described planctomycetal species (as of May 2020), including recently published strains (Boersma et al 2019;Dedysh et al 2020a;Dedysh et al 2020b;Kallscheuer et al 2019a;Kallscheuer et al 2020a;Kallscheuer et al 2020b;Kallscheuer et al 2019c;Kallscheuer et al 2019d;Kohn et al 2020;Kumar et al 2020;Peeters et al 2020;Rensink et al 2020). An alignment of 16S rRNA gene sequences was made with SINA (Pruesse et al 2012).…”

Caulifigura coniformis gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from a red biofilm sampled in a hydrothermal area

“…16S rRNA gene sequence-based phylogeny was computed for strain Pan44 T , the type strains of all described planctomycetal species (assessed in January 2020) including all isolates recently published and described (Boersma et al 2019;Dedysh et al 2019aDedysh et al , 2019bKallscheuer et al 2019aKallscheuer et al , 2019cKallscheuer et al , 2020aKohn et al 2020;Peeters et al 2020;Rensink et al 2020). The 16S rRNA gene sequences were aligned with SINA (Pruesse et al 2012) and the phylogenetic inference was calculated with RAxML (Stamatakis 2014) with a maximum likelihood approach with 1000 bootstraps, nucleotide substitution model GTR, gamma distributed rate variation and estimation of proportion of invariable sites (GTRGAMMAI option).…”