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Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms

  • 1.

    Laine RA. A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05×10(12) structures for a reducing hexasaccharide – the isomer-barrier to development of single-method saccharide sequencing or synthesis systems. Glycobiology. 1994;4:759–67.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 2.

    Varki A. Biological roles of glycans. Glycobiology. 2017;27:3–49.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 3.

    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;336:608–11.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 4.

    Myklestad SM. Release of extracellular products by phytoplankton with special emphasis on polysaccharides. Sci Total Environ. 1995;165:155–64.

    CAS 
    Article 

    Google Scholar 

  • 5.

    Field CB, Behrenfeld MJ, Randerson JT, Falkowski P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science. 1998;281:237–40.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 6.

    Wetz MS, Wheeler PA. Release of dissolved organic matter by coastal diatoms. Limnol Oceanogr. 2007;52:798–807.

    CAS 
    Article 

    Google Scholar 

  • 7.

    Reintjes G, Fuchs BM, Scharfe M, Wiltshire KH, Amann R, Arnosti C. Short-term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom. Environ Microbiol. 2020;22:1884–900.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 8.

    Vidal-Melgosa S, Sichert A, Francis TB, Bartosik D, Niggemann J, Wichels A, et al. Diatom fucan polysaccharide precipitates carbon during algal blooms. Nat Commun. 2021;12:1150.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 9.

    Becker S, Tebben J, Coffinet S, Wiltshire K, Iversen MH, Harder T, et al. Laminarin is a major molecule in the marine carbon cycle. P Natl Acad Sci USA. 2020;117:6599–607.

    CAS 
    Article 

    Google Scholar 

  • 10.

    Engel A, Thoms S, Riebesell U, Rochelle-Newall E, Zondervan I. Polysaccharide aggregation as a potential sink of marine dissolved organic carbon. Nature. 2004;428:929–32.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 11.

    Aluwihare LI, Repeta DJ, Chen RF. A major biopolymeric component to dissolved organic carbon in surface sea water. Nature. 1997;387:166–9.

    CAS 
    Article 

    Google Scholar 

  • 12.

    Hedges JI, Baldock JA, Gelinas Y, Lee C, Peterson M, Wakeham SG. Evidence for non-selective preservation of organic matter in sinking marine particles. Nature. 2001;409:801–4.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 13.

    Meador TB, Aluwihare LI. Production of dissolved organic carbon enriched in deoxy sugars representing an additional sink for biological C drawdown in the Amazon River plume. Glob Biogeochem Cycles. 2014;28:1149–61.

    CAS 
    Article 

    Google Scholar 

  • 14.

    Teeling H, Fuchs BM, Bennke CM, Krüger K, Chafee M, Kappelmann L, et al. Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms. Elife. 2016;5:e11888.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 15.

    Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, et al. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol. 2020;5:1026–39.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 16.

    Martinez-Garcia M, Brazel DM, Swan BK, Arnosti C, Chain PS, Reitenga KG, et al. Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PLoS ONE. 2012;7:e35314.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 17.

    Cardman Z, Arnosti C, Durbin A, Ziervogel K, Cox C, Steen AD, et al. Verrucomicrobia are candidates for polysaccharide-degrading bacterioplankton in an arctic fjord of Svalbard. Appl Environ Microbiol. 2014;80:3749–56.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 18.

    Spring S, Bunk B, Sproer C, Schumann P, Rohde M, Tindall BJ, et al. Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum. ISME J. 2016;10:2801–16.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 19.

    Cabello-Yeves PJ, Ghai R, Mehrshad M, Picazo A, Camacho A, Rodriguez-Valera F. Reconstruction of diverse verrucomicrobial genomes from metagenome datasets of freshwater reservoirs. Front Microbiol. 2017;8:2131.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 20.

    He S, Stevens SL, Chan L-K, Bertilsson S, del Rio TG, Tringe SG, et al. Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes. mSphere. 2017;2:e00277–17.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 21.

    Tran P, Ramachandran A, Khawasik O, Beisner BE, Rautio M, Huot Y, et al. Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered Lakes. Environ Microbiol. 2018;20:2568–84.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 22.

    Sizikov S, Burgsdorf I, Handley KM, Lahyani M, Haber M, Steindler L. Characterization of sponge‐associated Verrucomicrobia: microcompartment‐based sugar utilization and enhanced toxin–antitoxin modules as features of host‐associated Opitutales. Environ Microbiol. 2020;22:4669–88.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 23.

    Chafee M, Fernàndez-Guerra A, Buttigieg PL, Gerdts G, Eren AM, Teeling H, et al. Recurrent patterns of microdiversity in a temperate coastal marine environment. ISME J. 2018;12:237–52.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 24.

    Francis TB, Kruger K, Fuchs BM, Teeling H, Amann RI. Candidatus Prosiliicoccus vernus, a spring phytoplankton bloom associated member of the Flavobacteriaceae. Syst Appl Microbiol. 2019;42:41–53.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 25.

    Kruger K, Chafee M, Ben Francis T, Glavina Del Rio T, Becher D, Schweder T, et al. In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes. ISME J. 2019;13:2800–16.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 26.

    Francis TB, Bartosik D, Sura T, Sichert A, Hehemann JH, Markert S, et al. Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom. ISME J. 2021;15:2336–50.

    CAS 
    Article 

    Google Scholar 

  • 27.

    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 28.

    Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, et al. Binning metagenomic contigs by coverage and composition. Nat Methods. 2014;11:1144–6.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 29.

    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 30.

    Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 2015;43:6761–71.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 31.

    Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 32.

    Smoot ME, Ono K, Ruscheinski J, Wang P-L, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2010;27:431–2.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 33.

    Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;36:1925–7.

    PubMed Central 

    Google Scholar 

  • 34.

    Eren AM, Esen OC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 35.

    Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 36.

    Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 37.

    Orellana LH, Ben Francis T, Kruger K, Teeling H, Muller MC, Fuchs BM, et al. Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota. ISME J. 2019;13:3024–36.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 38.

    Orellana LH, Rodriguez RL, Konstantinidis KT. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores. Nucleic Acids Res. 2017;45:e14.

    PubMed 
    PubMed Central 

    Google Scholar 

  • 39.

    Rodriguez RL, Tsementzi D, Luo C, Konstantinidis KT. Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences. Environ Microbiol. 2020;22:3394–412.

    Article 
    CAS 

    Google Scholar 

  • 40.

    Delmont TO, Quince C, Shaiber A, Esen OC, Lee ST, Rappe MS, et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018;3:804–13.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 41.

    Sievers F, Higgins DG. Clustal Omega for making accurate alignments of many protein sequences. Protein Sci. 2018;27:135–45.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 42.

    Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 2010;5:e9490.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 43.

    Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44:W242–5. W1

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 44.

    Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6. Database issue

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 45.

    Pruesse E, Peplies J, Glockner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012;28:1823–9.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 46.

    Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–3.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 47.

    Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 2016;44:D286–93. D1

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 48.

    Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, et al. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 2007;35:D260–4. Database issue

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 49.

    El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2019;47:D427–D32. D1

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 50.

    Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res. 2018;46:D624–D32. D1

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 51.

    Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinforma. 2009;10:421.

    Article 
    CAS 

    Google Scholar 

  • 52.

    Saier MH Jr, Reddy VS, Tsu BV, Ahmed MS, Li C, Moreno-Hagelsieb G. The Transporter Classification Database (TCDB): recent advances. Nucleic Acids Res. 2016;44:D372–9. D1

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 53.

    Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 2014;42:D490–5. Database issue

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 54.

    Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7:e1002195.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 55.

    Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012;40:W445–51. Web Server issue

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 56.

    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. W1

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 57.

    Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30:1236–40.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 58.

    Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16:157.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 59.

    Thiele S, Fuchs B, Amann R. Identification of microorganisms using the ribosomal RNA approach and fluorescence in situ hybridization. In: Wilderer PA, editor. Treatise on Water Science. Elsevier Science; Oxford, United Kingdom; 2011. p. 171–89.

  • 60.

    Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 61.

    Zverlov VV, Hertel C, Bronnenmeier K, Hroch A, Kellermann J, Schwarz WH. The thermostable alpha-L-rhamnosidase RamA of Clostridium stercorarium: biochemical characterization and primary structure of a bacterial alpha-L-rhamnoside hydrolase, a new type of inverting glycoside hydrolase. Mol Microbiol. 2000;35:173–9.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 62.

    Miyata T, Kashige N, Satho T, Yamaguchi T, Aso Y, Miake F. Cloning, sequence analysis, and expression of the gene encoding Sphingomonas paucimobilis FP2001 alpha-L -rhamnosidase. Curr Microbiol. 2005;51:105–9.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 63.

    Ndeh D, Rogowski A, Cartmell A, Luis AS, Basle A, Gray J, et al. Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Nature. 2017;544:65–70.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 64.

    Li B, Lu F, Wei X, Zhao R. Fucoidan: structure and bioactivity. Molecules. 2008;13:1671–95.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 65.

    Ale MT, Mikkelsen JD, Meyer AS. Important determinants for fucoidan bioactivity: a critical review of structure-function relations and extraction methods for fucose-containing sulfated polysaccharides from brown seaweeds. Mar Drugs. 2011;9:2106–30.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 66.

    Katayama T, Sakuma A, Kimura T, Makimura Y, Hiratake J, Sakata K, et al. Molecular cloning and characterization of Bifidobacterium bifidum 1,2-alpha-L-fucosidase (AfcA), a novel inverting glycosidase (glycoside hydrolase family 95). J Bacteriol. 2004;186:4885–93.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 67.

    Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R. Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum. J Biol Chem. 2007;282:18497–509.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 68.

    Anderson KL, Salyers AA. Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes. J Bacteriol. 1989;171:3192–8.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 69.

    Bjursell MK, Martens EC, Gordon JI. Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J Biol Chem. 2006;281:36269–79.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 70.

    Grondin JM, Tamura K, Dejean G, Abbott DW, Brumer H. Polysaccharide Utilization Loci: fueling microbial communities. J Bacteriol. 2017;199:e00860–16.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 71.

    Barbeyron T, Brillet-Gueguen L, Carre W, Carriere 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:e0164846.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 72.

    Silchenko AS, Rasin AB, Zueva AO, Kusaykin MI, Zvyagintseva TN, Kalinovsky AI, et al. Fucoidan sulfatases from marine bacterium Wenyingzhuangia fucanilytica CZ1127(T). Biomolecules. 2018;8:98.

    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 73.

    Reisky L, Prechoux A, Zuhlke MK, Baumgen M, Robb CS, Gerlach N, et al. A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Nat Chem Biol. 2019;15:803–12.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 74.

    Hettle AG, Vickers C, Robb CS, Liu F, Withers SG, Hehemann JH, et al. The molecular basis of polysaccharide sulfatase activity and a nomenclature for catalytic subsites in this class of enzyme. Structure. 2018;26:747–58.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 75.

    Erbilgin O, McDonald KL, Kerfeld CA. Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides. Appl Environ Microbiol. 2014;80:2193–205.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 76.

    Axen SD, Erbilgin O, Kerfeld CA. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput Biol. 2014;10:e1003898.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • 77.

    Sutter M, Melnicki MR, Schulz F, Woyke T, Kerfeld CA. A catalog of the diversity and ubiquity of bacterial microcompartments. Nat Commun. 2021;12:3809.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 78.

    Engel A, Goldthwait S, Passow U, Alldredge A. Temporal decoupling of carbon and nitrogen dynamics in a mesocosm diatom bloom. Limnol Oceanogr. 2002;47:753–61.

    CAS 
    Article 

    Google Scholar 

  • 79.

    Yew WS, Fedorov AA, Fedorov EV, Rakus JF, Pierce RW, Almo SC, et al. Evolution of enzymatic activities in the enolase superfamily: L-fuconate dehydratase from Xanthomonas campestris. Biochemistry. 2006;45:14582–97.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 80.

    Arredondo-Alonso S, Willems RJ, van Schaik W, Schurch AC. On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data. Micro Genom. 2017;3:e000128.

    Google Scholar 

  • 81.

    Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kampfer P, et al. Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol. 2020;5:987–94.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 82.

    Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 83.

    Konstantinidis KT, Rossello-Mora R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J. 2017;11:2399–406.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 84.

    Alejandre-Colomo C, Harder J, Fuchs BM, Rossello-Mora R, Amann R. High-throughput cultivation of heterotrophic bacteria during a spring phytoplankton bloom in the North Sea. Syst Appl Microbiol. 2020;43:126066.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 


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