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Title: In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes

Abstract

We investigated Bacteroidetes during spring algae blooms in the southern North Sea in 2010–2012 using a time series of 38 deeply sequenced metagenomes. Initial partitioning yielded 6455 bins, from which we extracted 3101 metagenome-assembled genomes (MAGs) including 1286 Bacteroidetes MAGs covering ~120 mostly uncultivated species. We identified 13 dominant, recurrent Bacteroidetes clades carrying a restricted set of conserved polysaccharide utilization loci (PULs) that likely mediate the bulk of bacteroidetal algal polysaccharide degradation. The majority of PULs were predicted to target the diatom storage polysaccharide laminarin, alpha-glucans, alpha-mannose-rich substrates, and sulfated xylans. Metaproteomics at 14 selected points in time revealed expression of SusC-like proteins from PULs targeting all of these substrates. Analyses of abundant key players and their PUL repertoires over time furthermore suggested that fewer and simpler polysaccharides dominated early bloom stages, and that more complex polysaccharides became available as blooms progressed.

Authors:
ORCiD logo [1];  [1];  [1];  [2]; ORCiD logo [3]; ORCiD logo [4];  [1];  [1]
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  1. Max Planck Inst. for Marine Microbiology, Bremen (Germany)
  2. USDOE Joint Genome Inst. (JGI), Walnut Creek, CA (United States)
  3. Univ. Greifswald (Germany)
  4. Univ. Greifswald (Germany); Inst. of Marine Biotechnology, Greifswald (Germany)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Inst. (JGI), Walnut Creek, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Max Planck Society; German Research Foundation (DFG)
OSTI Identifier:
1624027
Grant/Contract Number:  
AC02-05CH11231; AM 73/9-1; TE 813/2-1; BE 3869/4-1; SCHW 595/10-1
Resource Type:
Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 13; Journal Issue: 11; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Environmental Sciences & Ecology; Microbiology; Biodiversity; Metagenomics; Microbial Ecology; Proteomics

Citation Formats

Krüger, Karen, Chafee, Meghan, Francis, T. Ben, Glavina del Rio, Tijana, Becher, Dörte, Schweder, Thomas, Amann, Rudolf I., and Teeling, Hanno. In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes. United States: N. p., 2019. Web. https://doi.org/10.1038/s41396-019-0476-y.
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Krüger, Karen, Chafee, Meghan, Francis, T. Ben, Glavina del Rio, Tijana, Becher, Dörte, Schweder, Thomas, Amann, Rudolf I., & Teeling, Hanno. In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes. United States. https://doi.org/10.1038/s41396-019-0476-y
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Krüger, Karen, Chafee, Meghan, Francis, T. Ben, Glavina del Rio, Tijana, Becher, Dörte, Schweder, Thomas, Amann, Rudolf I., and Teeling, Hanno. Wed . "In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes". United States. https://doi.org/10.1038/s41396-019-0476-y. https://www.osti.gov/servlets/purl/1624027.
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@article{osti_1624027,
title = {In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes},
author = {Krüger, Karen and Chafee, Meghan and Francis, T. Ben and Glavina del Rio, Tijana and Becher, Dörte and Schweder, Thomas and Amann, Rudolf I. and Teeling, Hanno},
abstractNote = {We investigated Bacteroidetes during spring algae blooms in the southern North Sea in 2010–2012 using a time series of 38 deeply sequenced metagenomes. Initial partitioning yielded 6455 bins, from which we extracted 3101 metagenome-assembled genomes (MAGs) including 1286 Bacteroidetes MAGs covering ~120 mostly uncultivated species. We identified 13 dominant, recurrent Bacteroidetes clades carrying a restricted set of conserved polysaccharide utilization loci (PULs) that likely mediate the bulk of bacteroidetal algal polysaccharide degradation. The majority of PULs were predicted to target the diatom storage polysaccharide laminarin, alpha-glucans, alpha-mannose-rich substrates, and sulfated xylans. Metaproteomics at 14 selected points in time revealed expression of SusC-like proteins from PULs targeting all of these substrates. Analyses of abundant key players and their PUL repertoires over time furthermore suggested that fewer and simpler polysaccharides dominated early bloom stages, and that more complex polysaccharides became available as blooms progressed.},
doi = {10.1038/s41396-019-0476-y},
journal = {The ISME Journal},
number = 11,
volume = 13,
place = {United States},
year = {2019},
month = {7}
}
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Journal Article:
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https://doi.org/10.1038/s41396-019-0476-y
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Figures / Tables:

Fig. 1 Fig. 1: a Maximum-likelihood tree of Mash-clusters based on concatenated marker proteins according to the GTDB-Tk genome phylogeny. Only Mash-clusters (mc) were included that contained at least two MAGs ≥70% completeness, plus additional 29 singleton MAGs with ≥70% completeness, and ≤10% contamination. Mash-clusters reaching high abundances (>5 RPKM at onemore » time-point or 38 RPKM at all time-points combined) during the sampling period are highlighted together with their taxonomic affiliations. Scale bar: mean number of amino acid substitutions per site. Outgroup: Oceanithermus profundus. b Violin plots of MAG assembly size distributions within clades of abundant Mash-clusters (colored areas). Area width corresponds to MAG numbers. Solid lines represent median and deciles, and dashed lines represent quartiles« less
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