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Link to original content: https://pubmed.ncbi.nlm.nih.gov/25478683/
Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom - PubMed Skip to main page content
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. 2015 Jun;9(6):1410-22.
doi: 10.1038/ismej.2014.225. Epub 2014 Dec 5.

Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom

Peng Xing  1 , Richard L Hahnke  2 , Frank Unfried  3 , Stephanie Markert  4 , Sixing Huang  2 , Tristan Barbeyron  5 , Jens Harder  2 , Dörte Becher  6 , Thomas Schweder  7 , Frank Oliver Glöckner  8 , Rudolf I Amann  2 , Hanno Teeling  2
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Niches of two polysaccharide-degrading Polaribacter isolates from the North Sea during a spring diatom bloom

Peng Xing et al. ISME J. 2015 Jun.

Abstract

Members of the flavobacterial genus Polaribacter thrive in response to North Sea spring phytoplankton blooms. We analyzed two respective Polaribacter species by whole genome sequencing, comparative genomics, substrate tests and proteomics. Both can degrade algal polysaccharides but occupy distinct niches. The liquid culture isolate Polaribacter sp. strain Hel1_33_49 has a 3.0-Mbp genome with an overall peptidase:CAZyme ratio of 1.37, four putative polysaccharide utilization loci (PULs) and features proteorhodopsin, whereas the agar plate isolate Polaribacter sp. strain Hel1_85 has a 3.9-Mbp genome with an even peptidase:CAZyme ratio, eight PULs, a mannitol dehydrogenase for decomposing algal mannitol-capped polysaccharides but no proteorhodopsin. Unlike other sequenced Polaribacter species, both isolates have larger sulfatase-rich PULs, supporting earlier assumptions that Polaribacter take part in the decomposition of sulfated polysaccharides. Both strains grow on algal laminarin and the sulfated polysaccharide chondroitin sulfate. For strain Hel1_33_49, we identified by proteomics (i) a laminarin-induced PUL, (ii) chondroitin sulfate-induced CAZymes and (iii) a chondroitin-induced operon that likely enables chondroitin sulfate recognition. These and other data suggest that strain Hel1_33_49 is a planktonic flavobacterium feeding on proteins and a small subset of algal polysaccharides, while the more versatile strain Hel1_85 can decompose a broader spectrum of polysaccharides and likely associates with algae.

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Figures

Figure 1
Figure 1
Maximum likelihood tree based on Polaribacter spp. 16S rRNA gene sequences. Strains Hel1_33_49 and Hel1_85 are depicted in bold. Bootstrap values are based on 1000 sub-samplings. Polaribacter species with sequenced genomes are marked by an asterisk (*). Outgroup: Tenacibaculum spp. Bar: 0.05 substitutions per nucleotide position.
Figure 2
Figure 2
Laminarin-induced locus of Polaribacter sp. Hel1_33_49: (a) Differential expression of the genes in laminarin- vs mannose-supplied cells. Ordinate: NSAFs; abscissa: position in the Hel1_33_49 genome (large contig; Supplementary Figure S4D). (b) Gene arrangement of the locus as well as similar loci in other Flavobacteriaceae, including Polaribacter sp. Hel1_85 (see Supplementary Figure S5B); numbers indicate GH families (nc=not classified); species that have been shown to use laminarin in cultivation experiments are marked by an asterisk (*); species where laminarin usage is supported by proteomics are marked by a hash (#).
Figure 3
Figure 3
Synteny between a PUL in Polaribacter sp. strain Hel1_33_49 (Supplementary Figure S4C) and a partial PUL on fosmid S3_860 from the Atlantic Ocean identified by Gómez-Pereira et al. (2012). Cho, Man and Lam indicate proteins that were only detected in chondroitin sulfate-, mannose- and laminarin-supplied cells, respectively. Numbers above genes represent gene locus tags; numbers in genes represent CAZyme family affiliations. The asterisk (*) indicates a possible sequencing error mimicking a gene fusion.
Figure 4
Figure 4
Chondroitin sulfate-induced locus in Polaribacter sp. Hel1_33_49. (a) Differential expression with chondroitin sulfate and laminarin vs mannose. Ordinate: NSAFs; abscissa: position in the Hel1_33_49 genome (large contig). (b) Gene arrangement of the locus as well as similar loci in other Flavobacteriaceae.
Figure 5
Figure 5
Comparison of 27 Flavobacteriaceae genomes based on automated annotations (Supplementary Table S3): (a) Interdependency of the number of degradative CAZymes and the number of CAZyme families (trend line: logarithmic regression). Genomes are represented by circles with radii proportional to genome sizes. Relative proportions of CAZymes vs peptidases are shown for each genome. (b) Densities of CAZymes with degradation functions and peptidases vs genome size (trend lines: second-order polynominal regressions).
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