Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria

Warming the phycosphere: Differential effect of temperature on the use of diatom‐derived carbon by two copiotrophic bacterial taxa

(2020) Nestor Arandia‐Gorostidi et al.   ENVIRONMENTAL MICROBIOLOGY

Response of bacterial communities from Kongsfjorden (Svalbard, Arctic Ocean) to macroalgal polysaccharide amendments

(2020) Anand Jain et al.   MARINE ENVIRONMENTAL RESEARCH

The Biogeochemistry of Marine Polysaccharides: Sources, Inventories, and Bacterial Drivers of the Carbohydrate Cycle

(2020) C. Arnosti et al.   Annual Review of Marine Science

Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT

(2020) Magda Dudek et al.   NUCLEIC ACIDS RESEARCH

The dynamics and stoichiometry of dissolved organic carbon release by kelp

(2020) Brooke L. Weigel et al.   ECOLOGY

Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription

(2020) Benjamin Pontiller et al.   Frontiers in Microbiology

Adaptations of Alteromonas sp. 76-1 to Polysaccharide Degradation: A CAZyme Plasmid for Ulvan Degradation and Two Alginolytic Systems

(2019) Hanna Koch et al.   Frontiers in Microbiology

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil

(2019) François Thomas et al.   ISME Journal

Coupling between taxonomic and functional diversity in protistan coastal communities

(2019) Pierre Ramond et al.   ENVIRONMENTAL MICROBIOLOGY

Peptide-based functional annotation of carbohydrate-active enzymes by conserved unique peptide patterns (CUPP)

(2019) Kristian Barrett et al.   Biotechnology for Biofuels

Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities

(2019) Tim N. Enke et al.   CURRENT BIOLOGY

Kelp beds and their local effects on seawater chemistry, productivity, and microbial communities

(2019) Catherine A. Pfister et al.   ECOLOGY

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

(2019) Karen Krüger et al.   ISME Journal

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Evaluation of a new primer combination to minimize plastid contamination in 16S rDNA metabarcoding analyses of alga‐associated bacterial communities

(2019) François Thomas et al.   Environmental Microbiology Reports

Structural and biochemical characterization of a multidomain alginate lyase reveals a novel role of CBM32 in CAZymes

(2018) Qianqian Lyu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

(2018) Nicholas D. Youngblut et al.   PLoS One

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

(2018) Nicholas D. Youngblut et al.   Frontiers in Microbiology

Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017

(2018) Koo Nagasawa et al.   Frontiers in Microbiology

Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides

(2018) Hanna Koch et al.   ISME Journal

Cloning, expression and characterization of an endo-acting bifunctional alginate lyase of marine bacteria Wenyingzhuangia fucanilytica

(2018) Xiaojie Pei et al.   PROTEIN EXPRESSION AND PURIFICATION

Community structural differences shape microbial responses to high molecular weight organic matter

(2018) John Paul Balmonte et al.   ENVIRONMENTAL MICROBIOLOGY

Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation

(2018) Greta Reintjes et al.   ISME Journal

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9T to Adapt to Macroalgal Niches

(2018) Angélique Gobet et al.   Frontiers in Microbiology

Calculation of Single Cell Assimilation Rates From SIP-NanoSIMS-Derived Isotope Ratios: A Comprehensive Approach

(2018) Hryhoriy Stryhanyuk et al.   Frontiers in Microbiology

Genetic analyses unravel the crucial role of a horizontally acquired alginate lyase for brown algal biomass degradation by Z obellia galactanivorans

(2017) Yongtao Zhu et al.   ENVIRONMENTAL MICROBIOLOGY

Sustainable harvesting of wild seaweed resources

(2017) Michéal Mac Monagail et al.   EUROPEAN JOURNAL OF PHYCOLOGY

Algal polysaccharide utilisation by saprotrophic planktonic marine fungi

(2017) Michael Cunliffe et al.   Fungal Ecology

An alternative polysaccharide uptake mechanism of marine bacteria

(2017) Greta Reintjes et al.   ISME Journal

Polysaccharide Utilization Loci: Fueling Microbial Communities

(2017) Julie M. Grondin et al.   JOURNAL OF BACTERIOLOGY

Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses

(2017) François Thomas et al.   Frontiers in Microbiology

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans DsijT

(2016) Tristan Barbeyron et al.   ENVIRONMENTAL MICROBIOLOGY

Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain

(2016) Maximilian Mitulla et al.   ENVIRONMENTAL MICROBIOLOGY

Marinomonas blandensis sp. nov., a novel marine gammaproteobacterium

(2016)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean

(2016) William D Orsi et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Deciphering ocean carbon in a changing world

(2016) Mary Ann Moran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Validation of the metabolic pathway of the alginate-derived monomer in Saccharophagus degradans 2-40 T by gas chromatography–mass spectrometry

(2016) Do Hyoung Kim et al.   PROCESS BIOCHEMISTRY

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

(2016) Jan-Hendrik Hehemann et al.   Nature Communications

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

(2016) Hanno Teeling et al.   eLife

Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

(2016) Charles Pepe-Ranney et al.   Frontiers in Microbiology

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Novel Alginate Lyase (Aly5) from a Polysaccharide-Degrading Marine Bacterium, Flammeovirga sp. Strain MY04: Effects of Module Truncation on Biochemical Characteristics, Alginate Degradation Patterns, and Oligosaccharide-Yielding Properties

(2015) Wenjun Han et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Defluviitalea phaphyphila sp. nov., a Novel Thermophilic Bacterium That Degrades Brown Algae

(2015) Shi-Qi Ji et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Temporal fluctuation in the abundance of alginate-degrading bacteria in the gut of abalone Haliotis gigantea over 1 year

(2015) Reiji Tanaka et al.   AQUACULTURE RESEARCH

Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans

(2015) Matthias Wietz et al.   ENVIRONMENTAL MICROBIOLOGY

The hidden seasonality of the rare biosphere in coastal marine bacterioplankton

(2015) Laura Alonso-Sáez et al.   ENVIRONMENTAL MICROBIOLOGY

The Cultivable Surface Microbiota of the Brown Alga Ascophyllum nodosum is Enriched in Macroalgal-Polysaccharide-Degrading Bacteria

(2015) Marjolaine Martin et al.   Frontiers in Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Peng Xing et al.   ISME Journal

Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii’ KT0803

(2014) Antje Kabisch et al.   ISME Journal

Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach

(2014) Dagmar Woebken et al.   ISME Journal

Biochemical and antiviral activities of enzymatic hydrolysates from different invasive French seaweeds

(2013) K. Hardouin et al.   JOURNAL OF APPLIED PHYCOLOGY

Comparative Characterization of Two Marine Alginate Lyases fromZobellia galactanivoransReveals Distinct Modes of Action and Exquisite Adaptation to Their Natural Substrate

(2013) François Thomas et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Characterization of the first alginolytic operons in a marine bacterium: from their emergence in marine Flavobacteriia to their independent transfers to marine Proteobacteria and human gut Bacteroides

(2012) François Thomas et al.   ENVIRONMENTAL MICROBIOLOGY

Free-living and particle-associated prokaryote metabolism in giant kelp forests: Implications for carbon flux in a sub-Antarctic coastal area

(2012) Mathilde Schapira et al.   ESTUARINE COASTAL AND SHELF SCIENCE

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

HISH–SIMS analysis of bacterial uptake of algal-derived carbon in the Río de la Plata estuary

(2012) Cecilia Alonso et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade

(2012) J. Grote et al.   mBio

Cloning and Characterization of a Novel Oligoalginate Lyase from a Newly Isolated Bacterium Sphingomonas sp. MJ-3

(2011) Hwan Hee Park et al.   MARINE BIOTECHNOLOGY

Dissolved Organic Matter in the Ocean: A Controversy Stimulates New Insights

(2011) Dennis Hansell et al.   OCEANOGRAPHY

Assembling the Marine Metagenome, One Cell at a Time

(2009) Tanja Woyke et al.   PLoS One

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS