Community dynamics and metagenomic analyses reveal Bacteroidota's role in widespread enzymatic Fucus vesiculosus cell wall degradation

[1]  M. Blümel,et al.  Metabolomics and Microbiomics Insights into Differential Surface Fouling of Three Macroalgal Species of Fucus (Fucales, Phaeophyceae) That Co-Exist in the German Baltic Sea , 2023, Marine Drugs.

[2]  F. M. Hassan,et al.  Cultivation of blue green algae (Arthrospira platensis Gomont, 1892) in wastewater for biodiesel production. , 2023, Chemosphere.

[3]  Thomas L. Madden,et al.  Database resources of the National Center for Biotechnology Information in 2023 , 2022, Nucleic Acids Res..

[4]  Silvio C. E. Tosatto,et al.  InterPro in 2022 , 2022, Nucleic Acids Res..

[5]  M. Hoebeke,et al.  SulfAtlas, the sulfatase database: state of the art and new developments , 2022, Nucleic Acids Res..

[6]  D. Hanelt,et al.  Microalgae and Bacteria Interaction—Evidence for Division of Diligence in the Alga Microbiota , 2022, Microbiology spectrum.

[7]  A. Boraston,et al.  Sulfatases: Critical Enzymes for Algal Polysaccharide Processing , 2022, Frontiers in Plant Science.

[8]  Zhong Hu,et al.  Insights into Algal Polysaccharides: A Review of Their Structure, Depolymerases, and Metabolic Pathways. , 2022, Journal of agricultural and food chemistry.

[9]  Konstantinos D. Tsirigos,et al.  SignalP 6.0 predicts all five types of signal peptides using protein language models , 2022, Nature Biotechnology.

[10]  B. Henrissat,et al.  The carbohydrate-active enzyme database: functions and literature , 2021, Nucleic Acids Res..

[11]  J. C. Carvalho,et al.  Advances in microalgal cell wall polysaccharides: a review focused on structure, production, and biological application , 2021, Critical reviews in biotechnology.

[12]  R. Amann,et al.  Selfish bacteria are active throughout the water column of the ocean , 2021, bioRxiv.

[13]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[14]  V. Eijsink,et al.  Polysaccharide degradation by the Bacteroidetes - mechanisms and nomenclature. , 2021, Environmental microbiology reports.

[15]  Hanna Koch,et al.  Sweet spheres: Succession and CAZyme expression of marine bacterial communities colonising a mix of alginate and pectin particles. , 2021, Environmental microbiology.

[16]  H. Drost,et al.  Sensitive protein alignments at tree-of-life scale using DIAMOND , 2021, Nature Methods.

[17]  R. Daniel,et al.  Pseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle. , 2020, Systematic and applied microbiology.

[18]  Anders F. Andersson,et al.  Deltaproteobacteria and Spirochaetes-Like Bacteria Are Abundant Putative Mercury Methylators in Oxygen-Deficient Water and Marine Particles in the Baltic Sea , 2020, Frontiers in Microbiology.

[19]  Manuel Liebeke,et al.  Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan , 2020, Nature Microbiology.

[20]  S. Gorb,et al.  Mapping the Surface Microbiome and Metabolome of Brown Seaweed Fucus vesiculosus by Amplicon Sequencing, Integrated Metabolomics and Imaging Techniques , 2019, Scientific Reports.

[21]  I-Min A. Chen,et al.  Genomes OnLine database (GOLD) v.7: updates and new features , 2018, Nucleic Acids Res..

[22]  M. A. Glaring,et al.  Discovery and screening of novel metagenome‐derived GH107 enzymes targeting sulfated fucans from brown algae , 2018, The FEBS journal.

[23]  A. Kalinovsky,et al.  Fucoidan Sulfatases from Marine Bacterium Wenyingzhuangia fucanilytica CZ1127T , 2018, Biomolecules.

[24]  E. Benešová,et al.  Active site complementation and hexameric arrangement in the GH family 29; a structure–function study of &agr;-L-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus , 2018, Glycobiology.

[25]  Janine N Copp,et al.  Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. , 2018, Biochemistry.

[26]  U. Azimov,et al.  Algae biofuel: Current status and future applications , 2018, Renewable and Sustainable Energy Reviews.

[27]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[28]  Konrad U. Förstner,et al.  Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches , 2017, Front. Microbiol..

[29]  P. Biller,et al.  The seasonal variation of fucoidan within three species of brown macroalgae , 2017 .

[30]  Anders F. Andersson,et al.  Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea , 2016, Front. Microbiol..

[31]  M. Hoebeke,et al.  Matching the Diversity of Sulfated Biomolecules: Creation of a Classification Database for Sulfatases Reflecting Their Substrate Specificity , 2016, PloS one.

[32]  Steven Salzberg,et al.  Bracken: Estimating species abundance in metagenomics data , 2016, bioRxiv.

[33]  M. H. Foley,et al.  The Sus operon: a model system for starch uptake by the human gut Bacteroidetes , 2016, Cellular and Molecular Life Sciences.

[34]  L. Airoldi,et al.  Diversity and Temporal Dynamics of the Epiphytic Bacterial Communities Associated with the Canopy-Forming Seaweed Cystoseira compressa (Esper) Gerloff and Nizamuddin , 2016, Front. Microbiol..

[35]  S. Künzel,et al.  Restructuring of Epibacterial Communities on Fucus vesiculosus forma mytili in Response to Elevated pCO2 and Increased Temperature Levels , 2016, Front. Microbiol..

[36]  R. Daniel,et al.  Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans. , 2015, Environmental microbiology.

[37]  Savita Kaul,et al.  Algae based biorefinery - how to make sense? , 2015 .

[38]  J. VanderGheynst,et al.  Elevated CO2 concentration impacts cell wall polysaccharide composition of green microalgae of the genus Chlorella , 2015, Letters in applied microbiology.

[39]  Shunsuke Takahashi,et al.  Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing , 2014, PloS one.

[40]  M. Wahl,et al.  Salinity affects compositional traits of epibacterial communities on the brown macroalga Fucus vesiculosus. , 2014, FEMS microbiology ecology.

[41]  Derrick E. Wood,et al.  Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.

[42]  S. Acinas,et al.  Spatial and temporal variability among marine Bacteroidetes populations in the NW Mediterranean Sea. , 2014, Systematic and applied microbiology.

[43]  Bernd Wemheuer,et al.  Metagenome Survey of a Multispecies and Alga-Associated Biofilm Revealed Key Elements of Bacterial-Algal Interactions in Photobioreactors , 2013, Applied and Environmental Microbiology.

[44]  S. Eddy,et al.  Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions , 2013, Nucleic acids research.

[45]  M. Wahl,et al.  Temperature-driven shifts in the epibiotic bacterial community composition of the brown macroalga Fucus vesiculosus , 2013, MicrobiologyOpen.

[46]  J. Holm‐Nielsen,et al.  Influence of different pre-treatment routes on the anaerobic digestion of a filamentous algae , 2013 .

[47]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[48]  Bernard Henrissat,et al.  Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts , 2011, PLoS biology.

[49]  Il-Hwan Seo,et al.  Review: Application of computational fluid dynamics for modeling and designing photobioreactors for microalgae production: A review , 2011 .

[50]  Susan Løvstad Holdt,et al.  Bioactive compounds in seaweed: functional food applications and legislation , 2011, Journal of Applied Phycology.

[51]  William A. Walters,et al.  Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample , 2010, Proceedings of the National Academy of Sciences.

[52]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[53]  Chun-Hung Lin,et al.  Structural basis of alpha-fucosidase inhibition by iminocyclitols with K(i) values in the micro- to picomolar range. , 2010, Angewandte Chemie.

[54]  P. Qian,et al.  Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies , 2009, PloS one.

[55]  G. Michel,et al.  Mariniflexile fucanivorans sp. nov., a marine member of the Flavobacteriaceae that degrades sulphated fucans from brown algae. , 2008, International journal of systematic and evolutionary microbiology.

[56]  Bo Li,et al.  Fucoidan: Structure and Bioactivity , 2008, Molecules.

[57]  A. Cardoso,et al.  Relationships between bacterial diversity and environmental variables in a tropical marine environment, Rio de Janeiro. , 2007, Environmental microbiology.

[58]  S. Turgeon,et al.  Characterization of polysaccharides extracted from brown seaweeds , 2007 .

[59]  F. Studier,et al.  Protein production by auto-induction in high density shaking cultures. , 2005, Protein expression and purification.

[60]  M. Bilan,et al.  A highly regular fraction of a fucoidan from the brown seaweed Fucus distichus L. , 2004, Carbohydrate research.

[61]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[62]  R. Sinsabaugh,et al.  Metabolic and structural response of hyporheic microbial communities to variations in supply of dissolved organic matter , 2003 .

[63]  Xiaomin Zhang,et al.  GRAZING AND GROWTH OF THE MIXOTROPHIC CHRYSOMONAD POTERIOOCHROMONAS MALHAMENSIS (CHRYSOPHYCEAE) FEEDING ON ALGAE , 2001 .

[64]  Abigail A. Salyers,et al.  Characterization of Four Outer Membrane Proteins Involved in Binding Starch to the Cell Surface ofBacteroides thetaiotaomicron , 2000, Journal of bacteriology.

[65]  M. Lürling,et al.  Grazer-induced defenses in Scenedesmus (Chlorococcales; Chlorophyceae): coenobium and spine formation , 1999 .

[66]  G. Macfarlane,et al.  Formation of glycoprotein degrading enzymes by Bacteroides fragilis. , 1991, FEMS microbiology letters.

[67]  L. Duchesne,et al.  Cellulose and the Evolution of Plant LifeThe physical and biological properties of cellulose have made it the most abundant molecule in the biosphere , 1989 .

[68]  W. Black The seasonal variation in the combined L‐fucose content of the common British Laminariaceae and fucaceae , 1954 .

[69]  OUP accepted manuscript , 2022, Nucleic Acids Research.

[70]  Colm P. O'Donnell,et al.  Extraction, structure and biofunctional activities of laminarin from brown algae , 2015 .

[71]  S. Nandini,et al.  The efficacy of Scenedesmus morphology as a defense mechanism against grazing by selected species of rotifers and cladocerans , 2005, Aquatic Ecology.

[72]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[73]  N. Schiller,et al.  ALGINATE LYASE: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications. , 2000, Annual review of microbiology.

[74]  M. Mccully,et al.  Histological studies on the genus Fucus. V. An autoradiographic and electron microscopic study of the early stages of regeneration , 1971 .