Journal ArticleDOI
Candidatus Prosiliicoccus vernus, a spring phytoplankton bloom associated member of the Flavobacteriaceae.
TLDR
Metabolic reconstruction indicates this highly abundant species most likely degrades proteins and the polysaccharide laminarin, and for the most abundant and well characterised of the three species the name Candidatus Prosiliicoccus vernus.About:
This article is published in Systematic and Applied Microbiology.The article was published on 2019-01-01. It has received 27 citations till now. The article focuses on the topics: Candidatus & Algal bloom.read more
Citations
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Journal ArticleDOI
In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes.
Karen Krüger,Meghan Chafee,T. Ben Francis,Tijana Glavina del Rio,Dörte Becher,Thomas Schweder,Rudolf Amann,Hanno Teeling +7 more
TL;DR: 13 dominant, recurrent Bacteroidetes clades carrying a restricted set of conserved polysaccharide utilization loci (PULs) that likely mediate the bulk of bacteroidetal algal poly Saccharide degradation are identified.
Journal ArticleDOI
Marine Proteobacteria metabolize glycolate via the β-hydroxyaspartate cycle
Lennart Schada von Borzyskowski,Francesca Severi,Karen Krüger,Lucas Hermann,Alexandre Gilardet,Felix Sippel,Bianca Pommerenke,Peter Claus,Niña Socorro Cortina,Timo Glatter,Stefan Zauner,Jan Zarzycki,Bernhard M. Fuchs,Erhard Bremer,Uwe G. Maier,Rudolf Amann,Tobias J. Erb,Tobias J. Erb +17 more
TL;DR: Marine Proteobacteria use the β-hydroxyaspartate cycle to assimilate glycolate, which is secreted by algae on a petagram scale, providing evidence of a previously undescribed trophic interaction between autotrophic phytoplankton and heterotrophic bacterioplankon.
Journal ArticleDOI
Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms
TL;DR: The hypothesis that sympatric Polaribacter clades occupy distinct glycan niches during North Sea spring algal blooms is supported, and polysaccharide utilization capabilities contribute to niche differentiation of Polaribacteria spp.
Journal ArticleDOI
Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms.
Luis H. Orellana,T. Ben Francis,Marcela Ferraro,Jan-Hendrik Hehemann,Bernhard M. Fuchs,Rudolf Amann +5 more
TL;DR: In this paper, genomic and proteomic data indicate that small, coccoid, free-living Verrucomicrobiota specialise in fucose and rhamnose consumption during spring algal blooms in the North Sea.
Journal ArticleDOI
Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota.
Luis H. Orellana,T. Ben Francis,Karen Krüger,Hanno Teeling,Marie-Caroline Müller,Bernhard M. Fuchs,Konstantinos T. Konstantinidis,Rudolf Amann +7 more
TL;DR: Based on multiple lines of evidence, this work proposes distinct niche adaptations of MGIIa and MGIIb Euryarchaeota populations that are characteristic of summer and winter conditions in the coastal North Sea.
References
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Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
TL;DR: This work presents some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees.
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast,Elmar Pruesse,Pelin Yilmaz,Jan Gerken,Timmy Schweer,Pablo Yarza,Jörg Peplies,Frank Oliver Glöckner +7 more
TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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Prokka: Rapid Prokaryotic Genome Annotation
TL;DR: Prokka is introduced, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer, and produces standards-compliant output files for further analysis or viewing in genome browsers.
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Prodigal: prokaryotic gene recognition and translation initiation site identification
Doug Hyatt,Doug Hyatt,Gwo Liang Chen,Philip F. LoCascio,Miriam Land,Frank W. Larimer,Frank W. Larimer,Loren Hauser +7 more
TL;DR: This work developed a new gene prediction algorithm called Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm), which achieved good results compared to existing methods, and it is believed it will be a valuable asset to automated microbial annotation pipelines.