100‐year‐old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii
Summary The 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 resul...
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Published in | Environmental microbiology Vol. 22; no. 1; pp. 198 - 211 |
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Main Authors | , , , , , , , , |
Format | Journal Article |
Language | English |
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Hoboken, USA
John Wiley & Sons, Inc
01.01.2020
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Abstract | Summary
The 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. |
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AbstractList | The 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. The 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 10 4 cells ml −1 following cyanobacterial blooms. The 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 10 cells ml following cyanobacterial blooms. Summary The 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. |
Author | Kulichevskaya, Irina S. Ivanova, Anastasia A. Philippov, Dmitriy A. Meier‐Kolthoff, Jan P. Huang, Sixing Henke, Petra Göker, Markus Dedysh, Svetlana N. Overmann, Jörg |
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BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31637799$$D View this record in MEDLINE/PubMed |
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The first representative of the phylum Planctomycetes, Planctomyces bekefii, was described nearly one century ago. This morphologically conspicuous... The first representative of the phylum Planctomycetes, Planctomyces bekefii, was described nearly one century ago. This morphologically conspicuous freshwater... The first representative of the phylum Planctomycetes , Planctomyces bekefii , was described nearly one century ago. This morphologically conspicuous... |
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SubjectTerms | Aquatic habitats Bacteria Biodegradation Biogeography Blooms Eutrophic lakes Eutrophication Fluorescence Fluorescence in situ hybridization Freshwater Freshwater environments Freshwater lakes Gene sequencing Genomes Hybridization Identification Inland water environment Nucleotide sequence Pectin Peptides Phylogeny Polysaccharides Prokaryotes rRNA 16S Saccharides Seasonal variations Sequencing |
Title | 100‐year‐old enigma solved: identification, genomic characterization and biogeography of the yet uncultured Planctomyces bekefii |
URI | https://onlinelibrary.wiley.com/doi/abs/10.1111%2F1462-2920.14838 https://www.ncbi.nlm.nih.gov/pubmed/31637799 https://www.proquest.com/docview/2331711010 https://search.proquest.com/docview/2307739523 |
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