Duarte C, Middelburg JJ, Caraco N. Major role of marine vegetation on the oceanic carbon cycle. Biogeosciences. 2005;2:1–8.
Google Scholar
Kloareg B, Quatrano RS. Structure of the cell walls of marine algae and ecophysiological functions of the matrix polysaccharides. Ocean Mar Biol Annu Rev. 1988;26:259–315.
Fletcher HR, Biller P, Ross AB, Adams JMM. The seasonal variation of fucoidan within three species of brown macroalgae. Algal Res. 2017;22:79–86.
Google Scholar
Deniaud-Bouët E, Hardouin K, Potin P, Kloareg B, Hervé C. A review about brown algal cell walls and fucose-containing sulfated polysaccharides: Cell wall context, biomedical properties and key research challenges. Carbohydr Polym. 2017;175:395–408.
Google Scholar
Haug A, Larsen B, Smidsrød O. Uronic acid sequence in alginate from different sources. Carbohydr Res. 1974;32:217–225.
Google Scholar
Bruhn A, Janicek T, Manns D, Nielsen MM, Balsby TJS, Meyer AS, et al. Crude fucoidan content in two North Atlantic kelp species, Saccharina latissima and Laminaria digitata—seasonal variation and impact of environmental factors. J Appl Phycol. 2017;29:3121–3137.
Google Scholar
Ponce NMA, Stortz CA. A comprehensive and comparative analysis of the fucoidan compositional data across the Phaeophyceae. Front Plant Sci. 2020;11:556312.
Google Scholar
Fleurence J. The enzymatic degradation of algal cell walls: A useful approach for improving protein accessibility? J Appl Phycol. 1999;11:313–314.
Google Scholar
Verhaeghe EF, Fraysse A, Guerquin-Kern JL, Wu TD, Devès G, Mioskowski C, et al. Microchemical imaging of iodine distribution in the brown alga Laminaria digitata suggests a new mechanism for its accumulation. J Biol Inorg Chem. 2008;13:257–269.
Google Scholar
Schiener P, Black KD, Stanley MS, Green DH. The seasonal variation in the chemical composition of the kelp species Laminaria digitata, Laminaria hyperborea, Saccharina latissima and Alaria esculenta. J Appl Phycol. 2015;27:363–373.
Google Scholar
Deniaud-Bouët E, Kervarec N, Michel G, Tonon T, Kloareg B, Hervé C. Chemical and enzymatic fractionation of cell walls from Fucales: Insights into the structure of the extracellular matrix of brown algae. Ann Bot. 2014;114:1203–1216.
Google Scholar
Michel G, Tonon T, Scornet D, Cock JM, Kloareg B. Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: Insights into the origin and evolution of storage carbohydrates in Eukaryotes. N. Phytol. 2010;188:67–81.
Google Scholar
Mann K. Ecology of coastal waters—A systems approach, Berkeley: University of California Press; 1982.
Egan S, Harder T, Burke C, Steinberg P, Kjelleberg S, Thomas T. The seaweed holobiont: Understanding seaweed-bacteria interactions. FEMS Microbiol Rev. 2013;37:462–476.
Google Scholar
Kirchman DL. The ecology of Cytophaga–Flavobacteria in aquatic environments. FEMS Microbiol Ecol. 2002;39:91–100.
Google Scholar
Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G. Environmental and gut Bacteroidetes: The food connection. Front Microbiol. 2011;2:93.
Google Scholar
Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A, Bennke CM, et al. Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science. 2012;336:608–611.
Google Scholar
Wietz M, Wemheuer B, Simon H, Giebel HA, Seibt MA, Daniel R, et al. Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans. Environ Microbiol. 2015;17:3822–3831.
Google Scholar
Arnosti C, Wietz M, Brinkhoff T, Hehemann J-H, Probant D, Zeugner L, et al. The biogeochemistry of marine polysaccharides: sources, inventories, and bacterial drivers of the carbohydrate cycle. Ann Rev Mar Sci. 2020;13:9.1–9.28.
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:490–495.
Google Scholar
Barbeyron T, Brillet-Guéguen L, Carré W, Carrière C, Caron C, Czjzek M, et al. Matching the diversity of sulfated biomolecules: Creation of a classification database for sulfatases reflecting their substrate specificity. PLoS One. 2016;11:1–33.
Google Scholar
Tang K, Lin Y, Han Y, Jiao N. Characterization of potential polysaccharide utilization systems in the marine Bacteroidetes Gramella flava JLT2011 using a multi-omics approach. Front Microbiol. 2017;8:220.
Google Scholar
Zhu Y, Chen P, Bao Y, Men Y, Zeng Y, Yang J, et al. Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation. Sci Rep. 2016;6:38248.
Google Scholar
Thomas F, Bordron P, Eveillard D, Michel G. Gene expression analysis of Zobellia galactanivorans during the degradation of algal polysaccharides reveals both substrate-specific and shared transcriptome-wide responses. Front Microbiol. 2017;8:1808.
Google Scholar
Ficko-Blean E, Préchoux A, Thomas F, Rochat T, Larocque R, Zhu Y, et al. Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria. Nat Commun. 2017;8:1685.
Google Scholar
Koch H, Dürwald A, Schweder T, Noriega-Ortega B, Vidal-Melgosa S, Hehemann JH, et al. Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. ISME J. 2019;13:92–103.
Google Scholar
Bunse C, Koch H, Breider S, Simon M, Wietz M. Sweet spheres: succession and CAZyme expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Environ Microbiol. 2021;23:3130–3148.
Google Scholar
Hehemann JH, Arevalo P, Datta MS, Yu X, Corzett CH, Henschel A, et al. Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes. Nat Commun. 2016;7:12860.
Google Scholar
Gralka M, Szabo R, Stocker R, Cordero OX. Trophic interactions and the drivers of microbial community assembly. Curr Biol. 2020;30:R1176–R1188.
Google Scholar
Jiménez DJ, Dini-Andreote F, DeAngelis KM, Singer SW, Salles JF, van Elsas JD. Ecological insights into the dynamics of plant biomass-degrading microbial consortia. Trends Microbiol. 2017;25:788–796.
Google Scholar
Kang S, Kim JK. Reuse of red seaweed waste by a novel bacterium, Bacillus sp. SYR4 isolated from a sandbar. World J Microbiol Biotechnol. 2015;31:209–217.
Google Scholar
Jonnadula R, Verma P, Shouche YS, Ghadi SC. Characterization of Microbulbifer strain CMC-5, a new biochemical variant of Microbulbifer elongatus type strain DSM6810T isolated from decomposing seaweeds. Curr Microbiol. 2009;59:600–607.
Google Scholar
Martin M, Barbeyron T, Martin R, Portetelle D, Michel G, Vandenbol M. The cultivable surface microbiota of the brown alga Ascophyllum nodosum is enriched in macroalgal-polysaccharide-degrading bacteria. Front Microbiol. 2015;6:1487.
Google Scholar
Dogs M, Wemheuer B, Wolter L, Bergen N, Daniel R, Simon M, et al. Rhodobacteraceae on the marine brown alga Fucus spiralis are abundant and show physiological adaptation to an epiphytic lifestyle. Syst Appl Microbiol. 2017;40:370–382.
Google Scholar
Brunet M, le Duff N, Fuchs B, Amann R, Barbeyron T, Thomas F. Specific detection and quantification of the marine flavobacterial genus Zobellia on macroalgae using novel qPCR and CARD-FISH assays. Syst Appl Microbiol. 2021;44:126269.
Google Scholar
Barbeyron T, L’Haridon S, Corre E, Kloareg B, Potin P. Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of [Cytophaga] uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Zobellia uliginosa gen. nov., comb. nov. Int J Syst Evol Microbiol. 2001;51:985–997.
Google Scholar
Barbeyron T, Thiébaud M, Le Duff N, Martin M, Corre E, Tanguy G, et al. Zobellia roscoffensis sp. nov. and Zobellia nedashkovskayae sp. nov., two flavobacteria from the epiphytic microbiota of the brown alga Ascophyllum nodosum, and emended description of the genus Zobellia. Int J Syst Evol Microbiol. 2021;71:004913.
Nedashkovskaya OI, Suzuki M, Vancanneyt M, Cleenwerck I, Lysenko AM, Mikhailov VV, et al. Zobellia amurskyensis sp. nov., Zobellia laminariae sp. nov. and Zobellia russellii sp. nov., novel marine bacteria of the family Flavobacteriaceae. Int J Syst Evol Microbiol. 2004;54:1643–1648.
Google Scholar
Nedashkovskaya O, Otstavnykh N, Zhukova N, Guzev K, Chausova V, Tekutyeva L, et al. Zobellia barbeyronii sp. nov., a new member of the family Flavobacteriaceae, isolated from seaweed, and emended description of the species Z. amurskyensis, Z. laminariae, Z. russellii and Z. uliginosa. Diversity. 2021;13:520.
Google Scholar
Chernysheva N, Bystritskaya E, Stenkova A, Golovkin I. Comparative genomics and CAZyme genome repertoires of marine Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T. Mar Drugs. 2019;17:661.
Google Scholar
Chernysheva N, Bystritskaya E, Likhatskaya G, Nedashkovskaya O, Isaeva M. Genome-wide analysis of PL7 alginate lyases in the genus Zobellia. Molecules. 2021;26:2387.
Google Scholar
Barbeyron T, Thomas F, Barbe V, Teeling H, Schenowitz C, Dossat C, et al. Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: Example of the model algae-associated bacterium Zobellia galactanivorans DsijT. Environ Microbiol. 2016;18:4610–4627.
Google Scholar
Potin P, Sanseau A, Le Gall Y, Rochas C, Kloareg B. Purification and characterization of a new k‐carrageenase from a marine Cytophaga‐like bacterium. Eur J Biochem. 1991;201:241–247.
Google Scholar
Lami R, Grimaud R, Sanchez-Brosseau S, Six C, Thomas F, West NJ, et al. Marine bacterial models for experimental biology. In: Boutet A, Schierwater B, editors. Handbook of Marine Model Organisms in Experimental Biology. London: Taylor & Francis Ltd; 2021.
Dudek M, Dieudonné A, Jouanneau D, Rochat T, Michel G, Sarels B, et al. Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT. Nucleic Acids Res. 2020;48:7786–7800.
Google Scholar
Thomas F, Lundqvist LCE, Jam M, Jeudy A, Barbeyron T, Sandström C, et al. Comparative characterization of two marine alginate lyases from Zobellia galactanivorans reveals distinct modes of action and exquisite adaptation to their natural substrate. J Biol Chem. 2013;288:23021–23037.
Google Scholar
Thomas F, Barbeyron T, Tonon T, Génicot S, Czjzek M, Michel G. 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. Environ Microbiol. 2012;14:2379–94.
Google Scholar
Jam M, Flament D, Allouch J, Potin P, Thion L, Kloareg B, et al. The endo-β-agarases AgaA and AgaB from the marine bacterium Zobellia galactanivorans: Two paralogue enzymes with different molecular organizations and catalytic behaviours. Biochem J. 2005;385:703–713.
Google Scholar
Hehemann JH, Correc G, Thomas F, Bernard T, Barbeyron T, Jam M, et al. Biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium Zobellia galactanivorans. J Biol Chem. 2012;287:30571–30584.
Google Scholar
Labourel A, Jam M, Jeudy A, Hehemann JH, Czjzek M, Michel G. The β-glucanase ZgLamA from Zobellia galactanivorans evolved a bent active site adapted for efficient degradation of algal laminarin. J Biol Chem. 2014;289:2027–2042.
Google Scholar
Labourel A, Jam M, Legentil L, Sylla B, Hehemann JH, Ferrières V, et al. Structural and biochemical characterization of the laminarinase ZgLamCGH16 from Zobellia galactanivorans suggests preferred recognition of branched laminarin. Acta Crystallogr. 2015;D71:173–184.
Dorival J, Ruppert S, Gunnoo M, Orłowski A, Chapelais-Baron M, Dabin J, et al. The laterally-acquired GH5 ZgEngAGH5_4 from the marine bacterium Zobellia galactanivorans is dedicated to hemicellulose hydrolysis. Biochem J. 2018;475:3609–3628.
Google Scholar
Groisillier A, Labourel A, Michel G, Tonon T. The mannitol utilization system of the marine bacterium Zobellia galactanivorans. Appl Environ Microbiol. 2015;81:1799–1812.
Google Scholar
Fournier JB, Rebuffet E, Delage L, Grijol R, Meslet-Cladière L, Rzonca J, et al. The vanadium iodoperoxidase from the marine Flavobacteriaceae species Zobellia galactanivorans reveals novel molecular and evolutionary features of halide specificity in the vanadium haloperoxidase enzyme family. Appl Environ Microbiol. 2014;80:7561–7573.
Google Scholar
Grigorian E, Groisillier A, Thomas F, Leblanc C, Delage L. Functional characterization of a L-2-haloacid dehalogenase from Zobellia galactanivorans DsijT suggests a role in haloacetic acid catabolism and a wide distribution in marine environments. Front Microbiol. 2021;12:725997.
Google Scholar
Zhu Y, Thomas F, Larocque R, Li N, Duffieux D, Cladière L, et al. Genetic analyses unravel the crucial role of a horizontally acquired alginate lyase for brown algal biomass degradation by Zobellia galactanivorans. Environ Microbiol. 2017;19:2164–2181.
Google Scholar
Zablackis E, Perez J. A partially pyruvated carrageenan from hawaiian Grateloupia filicina (Cryptonemiales, Rhodophyta). Bot Mar. 1990;33:273–276.
Google Scholar
Filisetti-Cozzi T, Carpita N. Measurement of uronic acids without interference from neutral sugars. Anal Biochem. 1991;197:15162.
Google Scholar
Blumenkrantz N, Asboe-Hansen G. New method for quantitative determination of uronic acids. Anal Biochem. 1973;54:484–489.
Google Scholar
Cumashi A, Ushakova NA, Preobrazhenskaya ME, D’Incecco A, Piccoli A, Totani L, et al. A comparative study of the anti-inflammatory, anticoagulant, antiangiogenic, and antiadhesive activities of nine different fucoidans from brown seaweeds. Glycobiology. 2007;17:541–552.
Google Scholar
Jung SY, Oh TK, Yoon JH. Tenacibaculum aestuarii sp. nov., isolated from a tidal flat sediment in Korea. Int J Syst Evol Microbiol. 2006;56:1577–1581.
Google Scholar
ZoBell C. Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J Mar Res. 1941;4:75.
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.
Google Scholar
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417–419.
Google Scholar
Vallenet D, Calteau A, Dubois M, Amours P, Bazin A, Beuvin M, et al. MicroScope: An integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. Nucleic Acids Res. 2020;48:D579–D589.
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–359.
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–2079.
Google Scholar
Thomas F, Barbeyron T, Michel G. Evaluation of reference genes for real-time quantitative PCR in the marine flavobacterium Zobellia galactanivorans. J Microbiol Methods. 2011;84:61–6.
Google Scholar
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–26.
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:1–21.
Google Scholar
R Core Team. R: A language and environment for statistical computing. 2018. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
Lex A, Gehlenborg N, Strobelt H. UpSet: Visualization of intersecting sets. IEEE Trans Vis Comput Graph. 2014;20:1983–1992.
Google Scholar
Krassowski M. krassowski/complex-upset. 2020. https://doi.org/10.5281/zenodo.3700590.
Murtagh F, Legendre P. Ward’s hierarchical clustering method: clustering criterion and agglomerative algorithm. J Classif. 2014;31:274–295.
Google Scholar
Wickham H Use R! ggplot2: Elegant graphics for data analysis. 2nd ed. London: Springer; 2016.
Kidby DK, Davidson DJ. Ferricyanide estimation of sugars in the nanomole range. Anal Biochem. 1973;55:321–325.
Google Scholar
Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, et al. DbCAN2: A meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2018;46:W95–W101.
Google Scholar
Chen X, Hu Y, Yang B, Gong X, Zhang N, Niu L, et al. Structure of lpg0406, a carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response from Legionella pneumophila. Protein Sci. 2015;24:2070–2075.
Google Scholar
Enke TN, Datta MS, Schwartzman J, Cermak N, Schmitz D, Barrere J, et al. Modular assembly of polysaccharide-degrading marine microbial communities. Curr Biol. 2019;29:1528–1535.e6.
Google Scholar
Pollak S, Gralka M, Sato Y, Schwartzman J, Lu L, Cordero OX. Public good exploitation in natural bacterioplankton communities. Sci Adv. 2021;7:eabi4717.
Pontrelli S, Szabo R, Pollak S, Schwartzman J, Ledezma D, Cordero OX, et al. Metabolic cross-feeding structures the assembly of polysaccharide degrading communities. Sci Adv. 2022;8:eabk3076.
Holdt SL, Kraan S. Bioactive compounds in seaweed: Functional food applications and legislation. J Appl Phycol. 2011;23:543–597.
Google Scholar
Kawamura-Konishi Y, Watanabe N, Saito M, Nakajima N, Sakaki T, Katayama T, et al. Isolation of a new phlorotannin, a potent inhibitor of carbohydrate-hydrolyzing enzymes, from the brown alga Sargassum patens. J Agric Food Chem. 2012;60:5565–5570.
Google Scholar
Garbary DJ, Brown NE, MacDonell HJ, Toxopeux J. Ascophyllum and its symbionts — A complex symbiotic community on North Atlantic shores. Algal and Cyanobacteria Symbioses. 2017:547–572.
Pluvinage B, Grondin JM, Amundsen C, Klassen L, Moote PE, Xiao Y, et al. Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont. Nat Commun. 2018;9:1043.
Google Scholar
Reintjes G, Arnosti C, Fuchs BM, Amann R. An alternative polysaccharide uptake mechanism of marine bacteria. ISME J. 2017;11:1640–1650.
Google Scholar
Hollants J, Leliaert F, de Clerck O, Willems A. What we can learn from sushi: A review on seaweed-bacterial associations. FEMS Microbiol Ecol. 2013;83:1–16.
Google Scholar
Thomas F, Le Duff N, Wu TD, Cébron A, Uroz S, Riera P, et al. Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria. ISME J. 2021;15:3062–3075.
Google Scholar
Datta MS, Sliwerska E, Gore J, Polz MF, Cordero OX. Microbial interactions lead to rapid micro-scale successions on model marine particles. Nat Commun. 2016;7:11965.
Google Scholar
Enke TN, Leventhal GE, Metzger M, Saavedra JT, Cordero OX. Microscale ecology regulates particulate organic matter turnover in model marine microbial communities. Nat Commun. 2018;9:2743.
Google Scholar
Sichert A, Cordero OX. Polysaccharide-bacteria Interactions from the lens of evolutionary ecology. Front Microbiol. 2021;12:705082.
Google Scholar
Sichert A, Corzett CH, Schechter M, Unfried F, Markert S, Becher D, et al. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol. 2020;5:1026–1039.
Google Scholar
Reisky L, Préchoux A, Zühlke MK, Bäumgen M, Robb CS, Gerlach N, et al. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Nat Chem Biol. 2019;15:803–812.
Google Scholar
Mabeau S, Kloareg B, Joseleau J-P. Fractionation and analysis of fucans from brown algae. Phytochemistry. 1990;29:2441–2445.
Google Scholar
Küpper FC, Kloareg B, Guern J, Potin P. Oligoguluronates elicit an oxidative burst in the brown algal kelp Laminaria digitata. Plant Physiol. 2001;125:278–291.
Google Scholar
Küpper FC, Müller DG, Peters AF, Kloareg B, Potin P. Oligoalginate recognition and oxidative burst play a key role in natural and induced resistance of sporophytes of Laminariales. J Chem Ecol. 2002;28:2057–2081.
Google Scholar
Leonard S, Hommais F, Nasser W, Reverchon S. Plant–phytopathogen interactions: bacterial responses to environmental and plant stimuli. Environ Microbiol. 2017;19:1689–1716.
Google Scholar
Sato K, Naito M, Yukitake H, Hirakawa H, Shoji M, McBride MJ, et al. A protein secretion system linked to bacteroidete gliding motility and pathogenesis. PNAS. 2010;107:276–281.
Google Scholar
Eckroat TJ, Greguske C, Hunnicutt DW. The type 9 secretion system is required for Flavobacterium johnsoniae biofilm formation. Front Microbiol. 2021;12:660887.
Google Scholar
Xie S, Tan Y, Song W, Zhang W, Qi Q, Lu X. N-glycosylation of a cargo protein C-terminal domain recognized by the type IX secretion system in Cytophaga hutchinsonii affects protein secretion and localization. Appl Environ Microbiol. 2022;88:e0160621.
Google Scholar
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