1887

Abstract

A rod-shaped and Gram-stain-negative bacterial strain, 1B, was isolated from an air sample collected at King George Island, maritime Antarctica. Strain 1B is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth of strain 1B is observed at 0–20 °C (optimum, 10 °C), pH 6.0–8.0 (optimum, pH 8.0) and in the presence of 0–1.0% NaCl (optimum, 0.5 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences places strain 1B within the genus and shows the highest similarity to VUG-A42aa (97.5 %). The predominant menaquinone of strain 1B is MK-7 and the major fatty acids (>10 %) comprise summed feature 3 (C 7 and/or C 6; 32.5 %), iso-C (17.6 %) and anteiso C (12.3 %). The polar lipid profile consists of the major compounds phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids and one unidentified phospholipid. The DNA G+C content based on the draft genome sequence is 61.2 mol%. Based on the data from the current polyphasic study, 1B represents a novel species of the genus , for which the name sp. nov. is suggested. The type strain is 1B (=CCM 8970=CGMCC 1.16843).

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2020-08-03
2024-03-29
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References

  1. Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B et al. Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 1998; 21:374–383 [View Article][PubMed]
    [Google Scholar]
  2. Munoz R, Rosselló-Móra R, Amann R. Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016; 39:281–296 [View Article][PubMed]
    [Google Scholar]
  3. Buczolits S, Denner EBM, Kämpfer P, Busse HJ. Proposal of Hymenobacter norwichensis sp. nov., classification of ‘Taxeobacter ocellatus’, ‘Taxeobacter gelupurpurascens’ and ‘Taxeobacter chitinovorans’as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivor . Int J Syst Evol Microbiol 2006; 56:2071–2078
    [Google Scholar]
  4. Reddy GS. Phylogenetic Analyses of the Genus Hymenobacter and Description of Siccationidurans gen. nov., and Parahymenobacter gen. nov. J Phylogen Evol Biol 2013; 01:1–9 [View Article]
    [Google Scholar]
  5. Han L, Wu S-J, Qin C-Y, Zhu Y-H, Lu Z-Q et al. Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter . Antonie Van Leeuwenhoek 2014; 105:971–978 [View Article][PubMed]
    [Google Scholar]
  6. Buczolits S, Busse H-J. Hymenobacter. In Whitman WB. editor Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Inc., in association with Bergey’s Manual Trust; 2015 pp 1–11
    [Google Scholar]
  7. Zhang G, Niu F, Busse H-J, Ma X, Liu W et al. Hymenobacter psychrotolerans sp. nov., isolated from the Qinghai--Tibet Plateau permafrost region. Int J Syst Evol Microbiol 2008; 58:1215–1220 [View Article][PubMed]
    [Google Scholar]
  8. Sedláček I, Králová S, Kýrová K, Mašlaňová I, Busse H-J et al. Red-pink pigmented Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov., isolated from ROCKs in Antarctica. Int J Syst Evol Microbiol 2017; 67:1975–1983 [View Article][PubMed]
    [Google Scholar]
  9. Sedláček I, Pantůček R, Holochová P, Králová S, Staňková E et al. Hymenobacter humicola sp. nov., isolated from soils in Antarctica. Int J Syst Evol Microbiol 2019; 69:2755–2761 [View Article][PubMed]
    [Google Scholar]
  10. Klassen JL, Foght JM. Characterization of Hymenobacter isolates from Victoria Upper Glacier, Antarctica reveals five new species and substantial non-vertical evolution within this genus. Extremophiles 2011; 15:45–57 [View Article][PubMed]
    [Google Scholar]
  11. Kojima H, Watanabe M, Tokizawa R, Shinohara A, Fukui M. Hymenobacter nivis sp. nov., isolated from red snow in Antarctica. Int J Syst Evol Microbiol 2016; 66:4821–4825 [View Article][PubMed]
    [Google Scholar]
  12. Machin EV, Asem MD, Salam N, Iriarte A, Langleib M et al. Nesterenkonia natronophila sp. nov., an alkaliphilic actinobacterium isolated from a soda lake, and emended description of the genus Nesterenkonia . Int J Syst Evol Microbiol 2019; 69:1960–1966 [View Article][PubMed]
    [Google Scholar]
  13. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
    [Google Scholar]
  14. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  16. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  17. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  18. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
    [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  20. Bennett S. Solexa Ltd. pharmacogenomics; 2004; 5433–438
  21. Bushnell B. BB tools software package. URL http://bbtools.jgi.doe.gov .
  22. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  23. 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; 25:1043–1055 [View Article][PubMed]
    [Google Scholar]
  24. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41:D590–D596 [View Article][PubMed]
    [Google Scholar]
  25. Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D et al. The standard operating procedure of the DOE-JGI microbial genome annotation pipeline (MGAP v.4). Stand Genomic Sci 2015; 10:4–9 [View Article]
    [Google Scholar]
  26. Chen I-MA, Chu K, Palaniappan K, Pillay M, Ratner A et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res 2019; 47:D666–D677 [View Article][PubMed]
    [Google Scholar]
  27. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  28. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  29. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490–10 [View Article][PubMed]
    [Google Scholar]
  30. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL et al. KBase: the United States department of energy systems biology knowledgebase. Nat Biotechnol 2018; 36:566–569 [View Article][PubMed]
    [Google Scholar]
  31. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 101, MIDI Tech Note. 1990 pp 1–6
    [Google Scholar]
  32. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988; 11:1–8 [View Article]
    [Google Scholar]
  33. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Evol Microbiol 1997; 47:698–708 [View Article]
    [Google Scholar]
  34. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  35. Tindall BJ. A Comparative Study of the Lipid Composition of Halobacterium saccharovorum from Various Sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  36. Altenburgera P, Kämpferb P, Makristathisc A, Lubitza W, Bussea H-J. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996; 47:39–52 [View Article]
    [Google Scholar]
  37. Stolz A, Busse H-J, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576 [View Article][PubMed]
    [Google Scholar]
  38. Ten LN, Lim SJ, Kim B-O, Kang I-K, Jung H-Y. Hymenobacter segetis sp. nov., isolated from soil. Arch Microbiol 2018; 200:1167–1175 [View Article][PubMed]
    [Google Scholar]
  39. Gu Z, Liu Y, Xu B, Wang N, Jiao N et al. Hymenobacter frigidus sp. nov., isolated from a glacier ice core. Int J Syst Evol Microbiol 2017; 67:4121–4125 [View Article][PubMed]
    [Google Scholar]
  40. Buczolits S, Denner EBM, Vybiral D, Wieser M, Kämpfer P et al. Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp. nov. Int J Syst Evol Microbiol 2002; 52:445–456 [View Article][PubMed]
    [Google Scholar]
  41. Zhang D-C, Busse H-J, Liu H-C, Zhou Y-G, Schinner F et al. Hymenobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 2011; 61:859–863 [View Article][PubMed]
    [Google Scholar]
  42. Sedláček I, Pantůček R, Králová S, Mašlaňová I, Holochová P et al. Hymenobacter amundsenii sp. nov. resistant to ultraviolet radiation, isolated from regoliths in Antarctica. Syst Appl Microbiol 2019; 42:284–290 [View Article][PubMed]
    [Google Scholar]
  43. Bernardet J-F, Nakagawa Y, Holmes B. 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 [View Article][PubMed]
    [Google Scholar]
  44. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for Identification of Medical Bacteria Cambridge: Cambridge University Press; 2003
    [Google Scholar]
  45. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM; 2014 pp 330–393
    [Google Scholar]
  46. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
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