Wang, M. et al. The great Atlantic Sargassum belt. Science 365, 83–87 (2019).
Field, C. B. Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281, 237–240 (1998).
Krause-Jensen, D. & Duarte, C. M. Substantial role of macroalgae in marine carbon sequestration. Nat. Geosci. 9, 737–742 (2016).
Deniaud-Bouët, E. et al. Chemical and enzymatic fractionation of cell walls from Fucales: insights into the structure of the extracellular matrix of brown algae. Ann. Bot. 114, 1203–1216 (2014).
Trevathan-Tackett, S. M. et al. Comparison of marine macrophytes for their contributions to blue carbon sequestration. Ecology 96, 3043–3057 (2015).
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. 175, 395–408 (2017).
Arnosti, C. Microbial extracellular enzymes and the marine carbon cycle. Ann. Rev. Mar. Sci. 3, 401–425 (2011).
Kopplin, G. et al. Structural characterization of fucoidan from Laminaria hyperborea: assessment of coagulation and inflammatory properties and their structure–function relationship. ACS Appl. Bio. Mater. 1, 1880–1892 (2018).
Skriptsova, A. V., Shevchenko, N. M., Zvyagintseva, T. N. & Imbs, T. I. Monthly changes in the content and monosaccharide composition of fucoidan from Undaria pinnatifida (Laminariales, Phaeophyta). J. Appl. Phycol. 22, 79–86 (2010).
Cong, Q. et al. Structural characterization and effect on anti-angiogenic activity of a fucoidan from Sargassum fusiforme. Carbohydr. Polym. 136, 899–907 (2016).
Chevolot, L., Mulloy, B., Ratiskol, J., Foucault, A. & Colliec-Jouault, S. A disaccharide repeat unit is the major structure in fucoidans from two species of brown algae. Carbohydr. Res. 330, 529–535 (2001).
Bilan, M. I. et al. Further studies on the composition and structure of a fucoidan preparation from the brown alga Saccharina latissima. Carbohydr. Res. 345, 2038–2047 (2010).
Van Vliet, D. M. et al. Anaerobic degradation of sulfated polysaccharides by two novel Kiritimatiellales strains isolated from black sea sediment. Front. Microbiol. 10, 253 (2019).
Silchenko, A. et al. Hydrolysis of fucoidan by fucoidanase isolated from the marine bacterium, Formosa algae. Mar. Drugs 11, 2413–2430 (2013).
Barbeyron, T., L’Haridon, S., Michel, G. & Czjzek, M. Mariniflexile fucanivorans sp. nov., a marine member of the Flavobacteriaceae that degrades sulphated fucans from brown algae. Int. J. Syst. Evol. Microbiol. 58, 2107–2113 (2008).
Chen, F., Chang, Y., Dong, S. & Xue, C. Wenyingzhuangia fucanilytica sp. nov., a sulfated fucan utilizing bacterium isolated from shallow coastal seawater. Int. J. Syst. Evol. Microbiol. 66, 3270–3275 (2016).
Sakai, T., Ishizuka, K. & Kato, I. Isolation and characterization of a fucoidan-degrading marine bacterium. Mar. Biotechnol. 5, 409–416 (2003).
Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M. & Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, 490–495 (2014).
Hettle, A. G. et al. The molecular basis of polysaccharide sulfatase activity and a nomenclature for catalytic subsites in this class of enzyme. Structure 26, 747–758 (2018).
Barbeyron, T. et al. Matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity. PLoS ONE 11, e0164846 (2016).
Berteau, O., McCort, I., Goasdoué, N., Tissot, B. & Daniel, R. Characterization of a new α-l-fucosidase isolated from the marine mollusk Pecten maximus that catalyzes the hydrolysis of α-l-fucose from algal fucoidan (Ascophyllum nodosum). Glycobiology 12, 273–282 (2002).
Nagao, T. et al. Gene identification and characterization of fucoidan deacetylase for potential application to fucoidan degradation and diversification. J. Biosci. Bioeng. 124, 277–282 (2017).
Silchenko, A. S. et al. Fucoidan sulfatases from marine bacterium Wenyingzhuangia fucanilytica CZ1127T. Biomolecules 8, 98 (2018).
Vickers, C. et al. Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to α-l-fucosidases from GH29. J. Biol. Chem. 293, 18296–18308 (2018).
Colin, S. et al. Cloning and biochemical characterization of the fucanase FcnA: definition of a novel glycoside hydrolase family specific for sulfated fucans. Glycobiology 16, 1021–1032 (2006).
Schultz-Johansen, M. et al. Discovery and screening of novel metagenome-derived GH107 enzymes targeting sulfated fucans from brown algae. FEBS J. 285, 4281–4295 (2018).
Silchenko, A. S. et al. Expression and biochemical characterization and substrate specificity of the fucoidanase from Formosa algae. Glycobiology 27, 254–263 (2017).
Ndeh, D. et al. Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature 544, 65–70 (2017).
Reisky, L. et al. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Nat. Chem. Biol. 15, 803–812 (2019).
Wegner, C.-E. et al. Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula. Mar. Genom. 9, 51–61 (2013).
Thrash, J. C., Cho, J. C., Vergin, K. L., Morris, R. M. & Giovannoni, S. J. Genome sequence of Lentisphaera araneosa HTCC2155T, the type species of the order Lentisphaerales in the phylum Lentisphaerae. J. Bacteriol. 192, 2938–2939 (2010).
Almagro Armenteros, J. J. et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 37, 420–423 (2019).
Martens, E. C., Chiang, H. C. & Gordon, J. I. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4, 447–457 (2008).
Ficko-Blean, E. et al. Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria. Nat. Commun. 8, 1685 (2017).
Nishino, T., Nishioka, C., Ura, H. & Nagumo, T. Isolation and partial characterization of a novel amino sugar-containing fucan sulfate from commercial Fucus vesiculosus fucoidan. Carbohydr. Res. 255, 213–224 (1994).
Bilan, M. I., Grachev, A. A., Shashkov, A. S., Nifantiev, N. E. & Usov, A. I. Structure of a fucoidan from the brown seaweed Fucus serratus L. Carbohydr. Res. 341, 238–245 (2006).
Kappelmann, L. et al. Polysaccharide utilization loci of North Sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans. ISME J. 13, 76–91 (2019).
Corzett, C. H. et al. Evolution of a vegetarian vibrio: metabolic specialization of Vibrio breoganii to macroalgal substrates. J. Bacteriol. 200, e00020-18 (2018).
Labourel, A. et al. The mechanism by which arabinoxylanases can recognise highly decorated xylans. J. Biol. Chem. 291, 22149–22159 (2016).
Hehemann, J.-H. et al. Biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium Zobellia galactanivorans. J. Biol. Chem. 287, 30571–30584 (2012).
Katayama, T. et al. Molecular cloning and characterization of Bifidobacterium bifidum 1,2-α-l-fucosidase (AfcA), a novel inverting glycosidase (glycoside hydrolase family 95). J. Bacteriol. 186, 4885–4893 (2004).
Rogowski, A. et al. Glycan complexity dictates microbial resource allocation in the large intestine. Nat. Commun. 6, 7481 (2015).
Heinze, S. et al. Identification of endoxylanase XynE from Clostridium thermocellum as the first xylanase of glycoside hydrolase family GH141. Sci. Rep. 7, 11178 (2017).
Davies, G. J., Wilson, K. S. & Henrissat, B. Nomenclature for sugar-binding subsites in glycosyl hydrolases. Biochem. J. 321, 557–559 (1997).
Stam, M. R., Danchin, E. G. J., Rancurel, C., Coutinho, P. M. & Henrissat, B. Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins. Protein Eng. Des. Sel. 19, 555–562 (2006).
Mewis, K., Lenfant, N., Lombard, V. & Henrissat, B. Dividing the large glycoside hydrolase family 43 into subfamilies: a motivation for detailed enzyme characterization. Appl. Environ. Microbiol. 82, 1686–1692 (2016).
Viborg, A. H. et al. A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16). J. Biol. Chem. 294, 15973–15986 (2019).
Hobbs, J. K., Pluvinage, B., Robb, M., Smith, S. P. & Boraston, A. B. Two complementary α-fucosidases from Streptococcus pneumoniae promote complete degradation of host-derived carbohydrate antigens. J. Biol. Chem. 294, 12670–12682 (2019).
Biely, P., Benen, J., Heinrichová, K., Kester, H. C. M. & Visser, J. Inversion of configuration during hydrolysis of α-1,4-galacturonidic linkage by three Aspergillus polygalacturonases. FEBS Lett. 382, 249–255 (1996).
Tenkanen, M. & Siika-aho, M. An α-glucuronidase of Schizophyllum commune acting on polymeric xylan. J. Biotechnol. 78, 149–161 (2000).
McClure, R. et al. Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res. 41, e140 (2013).
Unfried, F. et al. Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms. ISME J. 12, 2894–2906 (2018).
Basan, M. et al. Overflow metabolism in Escherichia coli results from efficient proteome allocation. Nature 528, 99–104 (2015).
Shachrai, I., Zaslaver, A., Alon, U. & Dekel, E. Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. Mol. Cell 38, 758–767 (2010).
Axen, S. D., Erbilgin, O. & Kerfeld, C. A. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput. Biol. 10, e1003898 (2014).
He, S. et al. Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes. mSphere 2, e00277-17 (2017).
Erbilgin, O., McDonald, K. L. & Kerfeld, C. A. Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides. Appl. Environ. Microbiol. 80, 2193–2205 (2014).
Petit, E. et al. Involvement of a bacterial microcompartment in the metabolism of fucose and rhamnose by Clostridium phytofermentans. PLoS ONE 8, e54337 (2013).
Baldomà, L. & Aguilar, J. Metabolism of l-fucose and l-rhamnose in Escherichia coli: aerobic–anaerobic regulation of l-lactaldehyde dissimilation. J. Bacteriol. 170, 416–421 (1988).
Freitas, S. et al. Global distribution and diversity of marine verrucomicrobia. ISME J. 6, 1499–1505 (2012).
Needham, D. M. et al. Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling. ISME J. 12, 2417–2432 (2018).
Bachmann, J. et al. Environmental drivers of free-living vs. particle-attached bacterial community composition in the Mauritania upwelling system. Front. Microbiol. 9, 2836 (2018).
Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 12613590 (2015).
Kopf, A. et al. The ocean sampling day consortium. Gigascience 4, 27 (2015).
Desai, M. S. et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell 167, 1339–1353.e21 (2016).
Tegtmeier, D., Belitz, A., Radek, R., Heimerl, T. & Brune, A. Ereboglobus luteus gen. nov. sp. nov. from cockroach guts, and new insights into the oxygen relationship of the genera Opitutus and Didymococcus (Verrucomicrobia: Opitutaceae). Syst. Appl. Microbiol. 41, 101–112 (2018).
Mavromatis, K. et al. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24). Stand. Genomic Sci. 2, 290–299 (2010).
Kotak, M. et al. Complete genome sequence of the opitutaceae bacterium strain TAV5, a potential facultative methylotroph of the wood-feeding termite Reticulitermes flavipes. Genome Announc. 3, e00060–15 (2015).
Barbeyron, T. 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. 18, 4610–4627 (2016).
Hehemann, J.-H. et al. Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes. Nat. Commun. 7, 12860 (2016).
Razeq, F. M. et al. A novel acetyl xylan esterase enabling complete deacetylation of substituted xylans. Biotechnol. Biofuels 11, 74 (2018).
Zhou, J., Mopper, K., Passow, U. & Zhoul, J. The role of surface-active carbohydrates in the formation of transparent exopolymer of seawater particles by bubble adsorption. Limnology 43, 1860–1871 (2011).
Engel, A., Thoms, S., Riebesell, U., Rochelle-Newall, E. & Zondervan, I. Polysaccharide aggregation as a potential sink of marine dissolved organic carbon. Nature 428, 929–932 (2004).
Koch, H. et al. Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides. ISME J. 13, 92–103 (2019).
Enke, T. N., Leventhal, G. E., Metzger, M., Saavedra, J. T. & Cordero, O. X. Microscale ecology regulates particulate organic matter turnover in model marine microbial communities. Nat. Commun. 9, 2743 (2018).
Tibbles, B. J. & Rawlings, D. E. Characterization of nitrogen-fixing bacteria from a temperate saltmarsh lagoon, including isolates that produce ethane from acetylene. Microb. Ecol. 27, 65–80 (1994).
Diepenbroek, M. et al. in Informatik 2014 (eds Plödereder, E. et al.) 1711–1721 (Gesellschaft für Informatik, 2014).
Yilmaz, P. et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotechnol. 29, 415–420 (2011).
Harrison, P. W. et al. The European Nucleotide Archive in 2018. Nucleic Acids Res. 47, D84–D88 (2019).
Galperin, M. Y., Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43, D261–D269 (2015).
El-Gebali, S. et al. The Pfam protein families database in 2019. Nucleic Acids Res. 47, D427–D432 (2019).
Overbeek, R. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33, 5691–5702 (2005).
Darling, A. C. E. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394–1403 (2004).
Richter, M., Rosselló-Móra, R., Oliver Glöckner, F. & Peplies, J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32, 929–931 (2016).
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).
Zhang, H. et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46, W95–W101 (2018).
Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol. Biol. Evol. 33, 1635–1638 (2016).
Heinz, E. et al. The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PLoS Pathog. 8, e1002979 (2012).
Otto, A. et al. Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis. Nat. Commun. 1, 137 (2010).
Tyanova, S., Temu, T. & Cox, J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat. Protoc. 11, 2301–2319 (2016).
Shin, J. B. et al. Molecular architecture of the chick vestibular hair bundle. Nat. Neurosci. 16, 365–374 (2013).
Bo, T. H., Dysvik, B. & Jonassen, I. LSimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Res. 32, e34 (2004).
Kammers, K., Cole, R. N., Tiengwe, C. & Ruczinski, I. Detecting significant changes in protein abundance. EuPA Open Proteom. 7, 11–19 (2015).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Anders, S., Pyl, P. T. & Huber, W. HTSeq-A python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2009).
Ritchie, M. E. et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 43, e47 (2015).
Dubois, M., Gilles, K. A., Hamilton, J. K., Rebers, P. A. & Smith, F. Colorimetric method for determination of sugars and related substances. Anal. Chem. 28, 350–356 (1956).
Engel, A. & Händel, N. A novel protocol for determining the concentration and composition of sugars in particulate and in high molecular weight dissolved organic matter (HMW-DOM) in seawater. Mar. Chem. 127, 180–191 (2011).
Sogin, E. M., Puskás, E., Dubilier, N. & Liebeke, M. Marine metabolomics: a method for nontargeted measurement of metabolites in seawater by gas chromatography–mass spectrometry. mSystems 4, e00638-19 (2019).
Pruesse, E., Peplies, J. & Glöckner, F. O. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823–1829 (2012).
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, 590–596 (2013).
Steinegger, M., Mirdita, M. & Söding, J. Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold. Nat. Methods 16, 603–606 (2019).
Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).
Silberfeld, T. et al. A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): investigating the evolutionary nature of the ‘brown algal crown radiation’. Mol. Phylogenet. Evol. 56, 659–674 (2010).
Nagaoka, M. et al. Structural study of fucoidan from Cladosiphon okamuranus TOKIDA. Glycoconj. J. 16, 19–26 (1999).
Hemmingson, J. A., Falshaw, R., Furneaux, R. H. & Thompson, K. Structure and antiviral activity of the galactofucan sulfates extracted from Undaria pinnatifida (Phaeophyta). J. Appl. Phycol. 18, 185–193 (2006).
Nishino, T., Nagumo, T., Kiyohara, H. & Yamada, H. Structural characterization of a new anticoagulant fucan sulfate from the brown seaweed Ecklonia kurome. Carbohydr. Res. 211, 77–90 (1991).
Source: Ecology - nature.com
