Community dynamics and metagenomic analyses reveal Bacteroidota's role in widespread enzymatic Fucus vesiculosus cell wall degradation
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P. Pérez-García | I. Krohn | Y. Schneider | Wolfgang R. Streit | Jascha F H Macdonald | Patrick Blümke | Daniela Indenbirken | Jeanette H Andersen
[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 .