1887

Abstract

Four Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacteria (R-46770, R-48165, R-50232 and R-50233) were isolated from intertidal sediment and water of the Westerschelde estuary between 2006 and 2012. Analysis of their 16S rRNA gene sequences revealed that the four strains form a separate cluster between validly described type strains of the genus . DNA–DNA reassociation values of two representative strains (i.e. R-48165 and R-50232) of the new group with type strains of species ranged from 18.7 to 56.6 %. A comparative genome analysis of the two strains and the type strains confirmed average nucleotide identity values from 75.6 to 94.4 %. The G+C contents of the genomic DNA of strains R-48165 and R-50232 were 37.80 and 37.83 mol%, respectively. The predominant cellular fatty acids of the four novel strains were summed feature 3 (i.e. Cω7 and/or iso-C 2-OH), iso-C, iso-C G and iso-C 3-OH. The four new -like strains grew with 0.5–12 % (w/v) NaCl, at pH 5.5–9.0 and displayed optimum growth between 20 and 30 °C. Based on the results of phenotypic, genomic, phylogenetic and chemotaxonomic analyses, the four new strains represent a novel species of the genus for which the name sp. nov. is proposed. The type strain is LMG 30908 (=R-48165=CECT 9775=DSM 107866). Genome analysis of type strains of the genus revealed a large number of glycosyl hydrolases, peptidases and carboxyl esterases per Mb, whereas the number of transporters per Mb was low compared to other bacteria. This confirmed the environmental role of species as (bio)polymer degraders, with a specialization on degrading proteins and high molecular weight compounds. Additionally, the presence of a large number of genes involved in gliding motility and surface adhesion, and large numbers of glycosyl transferases per Mb confirmed the importance of these features for species.

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/content/journal/ijsem/10.1099/ijsem.0.003959
2020-01-10
2020-01-27
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References

  1. Nedashkovskaya OI, Vancanneyt M, Dawyndt P, Engelbeen K, Vandemeulebroecke K et al. Reclassification of [Cytophaga] marinoflava Reichenbach 1989 as Leeuwenhoekiella marinoflava gen. nov., comb. nov. and description of Leeuwenhoekiella aequorea sp. nov. Int J Syst Evol Microbiol 2005;55:1033–1038 [CrossRef]
    [Google Scholar]
  2. Nedashkovskaya OI, Kukhlevskiy AD, Zhukova NV, Kim SB. Flavimarina pacifica gen. nov., sp. nov., a new marine bacterium of the family Flavobacteriaceae, and emended descriptions of the genus Leeuwenhoekiella, Leeuwenhoekiella Aequorea and Leeuwenhoekiella marinoflava. Antonie Van Leeuwenhoek 2014;106:421–429 [CrossRef]
    [Google Scholar]
  3. Liu Q, Li J, Wei B, Zhang X, Zhang L et al. Leeuwenhoekiella nanhaiensis sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2016;66:1352–1357 [CrossRef]
    [Google Scholar]
  4. Nedashkovskaya OI, Vancanneyt M, Kim SB, Zhukova NV, Han JH et al. Leeuwenhoekiella palythoae sp. nov., a new member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2009;59:3074–3077 [CrossRef]
    [Google Scholar]
  5. Pinhassi J, Bowman JP, Nedashkovskaya OI, Lekunberri I, Gomez-Consarnau L et al. Leeuwenhoekiella blandensis sp. nov., a genome-sequenced marine member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2006;56:1489–1493 [CrossRef]
    [Google Scholar]
  6. Si O-J, Kim S-J, Jung M-Y, Choi S-B, Kim J-G et al. Leeuwenhoekiella polynyae sp. nov., isolated from a polynya in Western Antarctica. Int J Syst Evol Microbiol 2015;65:1694–1699 [CrossRef]
    [Google Scholar]
  7. Brinkmeyer R, Knittel K, Jürgens J, Weyland H, Amann R et al. Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Appl Environ Microbiol 2003;69:6610–6619 [CrossRef]
    [Google Scholar]
  8. Bennke CM, Krüger K, Kappelmann L, Huang S, Gobet A et al. Polysaccharide utilisation loci of Bacteroidetes from two contrasting open ocean sites in the North Atlantic. Environ Microbiol 2016;18:4456–4470 [CrossRef]
    [Google Scholar]
  9. Gómez-Pereira PR, Schüler M, Fuchs BM, Bennke C, Teeling H et al. Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean. Environ Microbiol 2012;14:52–66 [CrossRef]
    [Google Scholar]
  10. Eilers H, Pernthaler J, Glöckner FO, Amann R. Culturability and in situ abundance of pelagic bacteria from the North sea. Appl Environ Microbiol 2000;66:3044–3051 [CrossRef]
    [Google Scholar]
  11. Morris JJ, Kirkegaard R, Szul MJ, Johnson ZI, Zinser ER. Facilitation of robust growth of Prochlorococcus colonies and dilute liquid cultures by "helper" heterotrophic bacteria. Appl Environ Microbiol 2008;74:4530–4534 [CrossRef]
    [Google Scholar]
  12. Du H, Jiao N, Hu Y, Zeng Y. Diversity and distribution of pigmented heterotrophic bacteria in marine environments. FEMS Microbiol Ecol 2006;57:92–105 [CrossRef]
    [Google Scholar]
  13. Gómez-Pereira PR, Fuchs BM, Alonso C, Oliver MJ, van Beusekom JEE et al. Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean. ISME J 2010;4:472–487 [CrossRef]
    [Google Scholar]
  14. Bidle KD, Lee S, Marchant DR, Falkowski PG. Fossil genes and microbes in the oldest ice on earth. Proc Natl Acad Sci U S A 2007;104:13455–13460 [CrossRef]
    [Google Scholar]
  15. Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K et al. Ocean plankton. structure and function of the global ocean microbiome. Science 2015;348:1261359 [CrossRef]
    [Google Scholar]
  16. Choi S-B, Kim J-G, Jung M-Y, Kim S-J, Min U-G et al. Cultivation and biochemical characterization of heterotrophic bacteria associated with phytoplankton Bloom in the Amundsen sea polynya, Antarctica. Deep Sea Research Part II: Topical Studies in Oceanography 2016;123:126–134 [CrossRef]
    [Google Scholar]
  17. Wieme AD, Spitaels F, Aerts M, De Bruyne K, Van Landschoot A et al. Effects of growth medium on matrix-assisted laser desorption–Ionization time of flight mass spectra: a case study of acetic acid bacteria. Appl Environ Microbiol 2014;80:1528–1538 [CrossRef]
    [Google Scholar]
  18. Niemann S, Pühler A, Tichy HV, Simon R, Selbitschka W. Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population. J Appl Microbiol 1997;82:477–484 [CrossRef]
    [Google Scholar]
  19. Tahon G, Willems A. Isolation and characterization of aerobic anoxygenic phototrophs from exposed soils from the Sør Rondane Mountains, East Antarctica. Syst Appl Microbiol 2017;40:357–369 [CrossRef]
    [Google Scholar]
  20. Tahon G, Tytgat B, Lebbe L, Carlier A, Willems A. Abditibacterium utsteinense sp. nov., the first cultivated member of candidate phylum FBP, isolated from ice-free Antarctic soil samples. Syst Appl Microbiol 2018;41:279–290 [CrossRef]
    [Google Scholar]
  21. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 2014;30:2114–2120 [CrossRef]
    [Google Scholar]
  22. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013;29:1072–1075 [CrossRef]
    [Google Scholar]
  23. Markowitz VM, Mavromatis K, Ivanova NN, Chen I-MA, Chu K et al. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009;25:2271–2278 [CrossRef]
    [Google Scholar]
  24. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75 [CrossRef]
    [Google Scholar]
  25. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016;44:W16–W21 [CrossRef]
    [Google Scholar]
  26. Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 2018;46:W246–W251 [CrossRef]
    [Google Scholar]
  27. 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–D495 [CrossRef]
    [Google Scholar]
  28. Rawlings ND, Waller M, Barrett AJ, Bateman A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 2014;42:D503–D509 [CrossRef]
    [Google Scholar]
  29. Elbourne LDH, Tetu SG, Hassan KA, Paulsen IT. TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. Nucleic Acids Res 2017;45:D320–D324 [CrossRef]
    [Google Scholar]
  30. Barbeyron T, Brillet-Guéguen L, Carré W, Carrière C, Caron C et al. Matching the diversity of sulfated biomolecules: creation of a classification database for sulfatases reflecting their substrate specificity. PLoS One 2016;11:e0164846 [CrossRef]
    [Google Scholar]
  31. Chen I-MA, Markowitz VM, Chu K, Palaniappan K, Szeto E et al. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res 2017;45:D507–D516 [CrossRef]
    [Google Scholar]
  32. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60 [CrossRef]
    [Google Scholar]
  33. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 2015;16:157 [CrossRef]
    [Google Scholar]
  34. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017;45:D535–D542 [CrossRef]
    [Google Scholar]
  35. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef]
    [Google Scholar]
  36. Ankenbrand MJ, Keller A. bcgTree: automatized phylogenetic tree building from bacterial core genomes. Genome 2016;59:783–791 [CrossRef]
    [Google Scholar]
  37. 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–W245 [CrossRef]
    [Google Scholar]
  38. Mergaert J, Verdonck L, Kersters K. Transfer of Erwinia ananas (synonym, Erwinia uredovora) and Erwinia stewartii to the Genus Pantoea emend. as Pantoea ananas (Serrano 1928) comb. nov. and Pantoea stewartii (Smith 1898) comb. nov., Respectively, and Description of Pantoea stewartii subsp. indologenes subsp. nov. Int J Syst Bacteriol 1993;43:162–173 [CrossRef]
    [Google Scholar]
  39. Henriques M, Silva A, Rocha J.Extraction and quantification of pigments from a marine microalga: a simple and reproducible method In Méndez-Vilas A. editor Communicating Current Research and Educational Topics and Trends in Applied Microbiology (Communicating Current Research and Educational Topics and Trends in Applied Microbiology Spain: FORMATEX; 2007
    [Google Scholar]
  40. Mohammadi M, Burbank L, Roper MC. Biological role of pigment production for the bacterial phytopathogen Pantoea stewartii subsp. stewartii. Appl Environ Microbiol 2012;78:6859–6865 [CrossRef]
    [Google Scholar]
  41. Srinivasan S, Joo ES, Lee J-J, Kim MK. Hymenobacter humi sp. nov., a bacterium isolated from soil. Antonie Van Leeuwenhoek 2015;107:1411–1419 [CrossRef]
    [Google Scholar]
  42. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980;8:87–91 [CrossRef]
    [Google Scholar]
  43. MacFaddin JF. Biochemical Tests for Identification of Medical Bacteria, 2nd ed. Baltimore (Md.: Williams & Wilkins Co; 1980
    [Google Scholar]
  44. Bernardet J-F, Nakagawa Y, Holmes B.Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52:1049–1070 [CrossRef]
    [Google Scholar]
  45. Jovel J, Patterson J, Wang W, Hotte N, O'Keefe S et al. Characterization of the gut microbiome using 16S or shotgun Metagenomics. Front Microbiol 2016;7:459 [CrossRef]
    [Google Scholar]
  46. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987;37:463–464 [CrossRef]
    [Google Scholar]
  47. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef]
    [Google Scholar]
  48. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461–466 [CrossRef]
    [Google Scholar]
  49. Zeng Z, Fu Y, Guo D, Wu Y, Ajayi OE et al. Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host. BMC Genomics 2018;19:688 [CrossRef]
    [Google Scholar]
  50. Marmur J, Doty P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 1962;5:109–118 [CrossRef]
    [Google Scholar]
  51. Suttle CA. Viruses in the sea. Nature 2005;437:356–361 [CrossRef]
    [Google Scholar]
  52. Fuhrman JA. Marine viruses and their biogeochemical and ecological effects. Nature 1999;399:541–548 [CrossRef]
    [Google Scholar]
  53. Marraffini LA, Sontheimer EJ. Crispr interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 2010;11:181–190 [CrossRef]
    [Google Scholar]
  54. Xiao R, Zheng Y. Overview of microalgal extracellular polymeric substances (Eps) and their applications. Biotechnol Adv 2016;34:1225–1244 [CrossRef]
    [Google Scholar]
  55. Brunnegård J, Grandel S, Ståhl H, Tengberg A, Hall POJ. Nitrogen cycling in deep-sea sediments of the porcupine abyssal plain, Ne Atlantic. Progress in Oceanography 2004;63:159–181 [CrossRef]
    [Google Scholar]
  56. Yang J-Y, Wang P, Li C-Y, Dong S, Song X-Y et al. Characterization of a New M13 Metallopeptidase from Deep-Sea Shewanella sp. E525-6 and Mechanistic Insight into Its Catalysis. Front Microbiol 2015;6:1498 [CrossRef]
    [Google Scholar]
  57. Helbert W. Marine polysaccharide sulfatases. Front Mar Sci 2017;4: [CrossRef]
    [Google Scholar]
  58. 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;281:36269–36279 [CrossRef]
    [Google Scholar]
  59. Grondin JM, Tamura K, Déjean G, Abbott DW, Brumer H. Polysaccharide utilization loci: Fueling microbial communities. J Bacteriol 2017;199:e00860–00816 [CrossRef]
    [Google Scholar]
  60. Kappelmann L, Krüger K, Hehemann J-H, Harder J, Markert S et al. Polysaccharide utilization loci of North sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans. Isme J 2019;13:76–91 [CrossRef]
    [Google Scholar]
  61. Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG et al. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J 2013;7:1026–1037 [CrossRef]
    [Google Scholar]
  62. Cregut M, Piutti S, Slezack-Deschaumes S, Benizri E. Compartmentalization and regulation of arylsulfatase activities in Streptomyces sp., Microbacterium sp. and Rhodococcus sp. soil isolates in response to inorganic sulfate limitation. Microbiol Res 2013;168:12–21 [CrossRef]
    [Google Scholar]
  63. Sekimoto K, Inomata S, Tanimoto H, Fushimi A, Fujitani Y et al. Characterization of nitromethane emission from automotive exhaust. Atmos Environ 2013;81:523–531 [CrossRef]
    [Google Scholar]
  64. Patey MD, Rijkenberg MJA, Statham PJ, Stinchcombe MC, Achterberg EP et al. Determination of nitrate and phosphate in seawater at nanomolar concentrations. TrAC Trends in Analytical Chemistry 2008;27:169–182 [CrossRef]
    [Google Scholar]
  65. Kamykowski D. Estimating upper Ocean phosphate concentrations using ARGO float temperature profiles. Deep Sea Research Part I: Oceanographic Research Papers 2008;55:1580–1589 [CrossRef]
    [Google Scholar]
  66. Santos-Beneit F. The PHO regulon: a huge regulatory network in bacteria. Front Microbiol 2015;6:402 [CrossRef]
    [Google Scholar]
  67. Martín JF, Rodríguez-García A, Liras P. The master regulator PhoP coordinates phosphate and nitrogen metabolism, respiration, cell differentiation and antibiotic biosynthesis: comparison in Streptomyces coelicolor and Streptomyces avermitilis. J Antibiot 2017;70:534–541 [CrossRef]
    [Google Scholar]
  68. Hulett FM.The Pho regulon Bacillus Subtilis and Its Closest Relatives American Society of Microbiology; 2002
    [Google Scholar]
  69. Zakem EJ, Follows MJ. A theoretical basis for a nanomolar critical oxygen concentration. Limnol Oceanogr 2017;62:795–805 [CrossRef]
    [Google Scholar]
  70. Burchard RP, Sorongon ML. A gliding bacterium strain inhibits adhesion and motility of another gliding bacterium strain in a marine biofilm. Appl Environ Microbiol 1998;64:4079–4083
    [Google Scholar]
  71. Jarrell KF, McBride MJ. The surprisingly diverse ways that prokaryotes move. Nat Rev Microbiol 2008;6:466–476 [CrossRef]
    [Google Scholar]
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