1887

Abstract

Strain P1297 was isolated in the frame of a project aimed on the psychrotolerant microbiota occurring in water sources. The strain initially identified as a tentative species of the genus was rod-shaped, Gram-stain-negative, facultatively anaerobic and oxidase-positive. Subsequently, 16S rRNA gene sequence analysis placed strain P1297 within the class and showed TRO-001DR8 as the closest phylogenetic relative with 99.28 % 16S rRNA gene sequence similarity. Digital DDH and average nucleotide identity (ANI) were determined to evaluate the genomic relationship between strain P1297 and CCM 7607. Digital DDH estimation (31.3 ± 2.46 %) as well as ANI (85.6001 %; reciprocal value 85.3277 %) proved the dissimilarity of strain P1297. Further investigation using phenotyping, automated ribotyping, whole-cell protein profiling and PCR-fingerprinting methods showed a distinct taxonomic position of strain P1297 among hitherto described species of the genus . DNA–DNA hybridization experiments revealed low binding values between strain P1297 and CCM 7607 (57 ± 3 %) and CCM 7935 (41 ± 5 %). The DNA G+C content of strain P1297 was 60.3 mol%. The predominant fatty acids were Cω7/ iso-C 2-OH (47.0 %), C (24.5 %) and Cω7 (10.6 %), and the quinone system contained predominantly ubiquinone Q-8. The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids and one unidentified aminophospholipid. Obtained results of genotypic and chemotaxonomic methods clearly proved that strain P1297 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is P1297 ( = CCM 7557 = LMG 28989 = CCUG 67440).

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2016-02-01
2019-10-18
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References

  1. Adav S. S. , Lee D.-J. , Lai J.-Y. . ( 2010;). Potential cause of aerobic granular sludge breakdown at high organic loading rates. Appl Microbiol Biotechnol 85: 1601–1610 [CrossRef] [PubMed].
    [Google Scholar]
  2. Altenburger P. , Kämpfer P. , Makristathis A. , Lubitz W. , Busse H.-J. . ( 1996;). Classification of bacteria isolated from a medieval wall painting. J Biotechnol 47: 39–52 [CrossRef].
    [Google Scholar]
  3. Altschul S. F. , Madden T. L. , Schäffer A. A. , Zhang J. , Zhang Z. , Miller W. , Lipman D. J. . ( 1997;). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402 [CrossRef] [PubMed].
    [Google Scholar]
  4. Aravena-Román M. , Beaz-Hidalgo R. , Inglis T. J. J , Riley T. V. , Martínez-Murcia A. J. , Chang B. J. , Figueras M. J. . ( 2013;). Aeromonas australiensis sp. nov., isolated from irrigation water. Int J Syst Evol Microbiol 63: 2270–2276 [CrossRef] [PubMed].
    [Google Scholar]
  5. Auch A. F. , Klenk H.-P. , Göker M. . ( 2010a;). Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2: 142–148 [CrossRef] [PubMed].
    [Google Scholar]
  6. Auch A. F. , von Jan M. , Klenk H.-P. , Göker M. . ( 2010b;). Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2: 117–134 [CrossRef] [PubMed].
    [Google Scholar]
  7. Caravieri F. A. , Ferreira A. J. , Ferreira A. , Clivati D. , de Miranda V. F. O , Araújo W. L. . ( 2014;). Bacterial community associated with traps of the carnivorous plants Utricularia hydrocarpa and Genlisea filiformis . Aquat Bot 116: 8–12 [CrossRef].
    [Google Scholar]
  8. Christian R. R. , Capone D. G. . ( 2002;). Overview of issues in aquatic microbial ecology. . In Manual of Environmental Microbiology , 2nd edition., pp. 323–328. Edited by Hurst C. J. , Crawford R. L. , Knudsen G. R. , McInerney M. J. , Stetzenbach L. D. . Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  9. Chung A. P. , Tiago I. , Nobre M. F. , Veríssimo A. , Morais P. V. . ( 2013;). Glaciimonas singularis sp. nov., isolated from a uranium mine wastewater treatment plant. Int J Syst Evol Microbiol 63: 2344–2350 [CrossRef] [PubMed].
    [Google Scholar]
  10. Coenye T. , Falsen E. , Vancanneyt M. , Hoste B. , Govan J. R. W , Kersters K. , Vandamme P. . ( 1999;). Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov. Int J Syst Bacteriol 49: 405–413 [CrossRef] [PubMed].
    [Google Scholar]
  11. De Ley J. , Cattoir H. , Reynaerts A. . ( 1970;). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12: 133–142 [CrossRef] [PubMed].
    [Google Scholar]
  12. Euzéby J. P. . ( 1997;). List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol 47: 590–592 [CrossRef].
    [Google Scholar]
  13. Gray S. M. , Akob D. M. , Green S. J. , Kostka J. E. . ( 2012;). The bacterial composition within the Sarracenia purpurea model system: local scale differences and the relationship with the other members of the food web. PLoS One 7: e50969 [CrossRef] [PubMed].
    [Google Scholar]
  14. Hughes M. S. , James G. , Ball N. , Scally M. , Malik R. , Wigney D. I. , Martin P. , Chen S. , Mitchell D. , Love D. N. . ( 2000;). Identification by 16S rRNA gene analyses of a potential novel mycobacterial species as an etiological agent of canine leproid granuloma syndrome. J Clin Microbiol 38: 953–959 [PubMed].
    [Google Scholar]
  15. Huss V. A. R , Festl H. , Schleifer K. H. . ( 1983;). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4: 184–192 [CrossRef] [PubMed].
    [Google Scholar]
  16. Kim O. S. , Cho Y. J. , Lee K. , Yoon S. H. , Kim M. , Na H. , Park S. C. , Jeon Y. S. , Lee J. H. , Yi H. , Won S. , Chun J. . ( 2012;). Introducing EzTaxon: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62: 716–721.[CrossRef]
    [Google Scholar]
  17. Kim B. S. , Seo J. R. , Park D. H. . ( 2013;). Variation and characterization of bacterial communities contaminating two saunas operated at 64 °C and 76 °C. J Bacteriol Virol 43: 195–203.[CrossRef]
    [Google Scholar]
  18. Kosina M. , Barták M. , Mašlanˇová I. , Pascutti A. V. , Šedo O. , Lexa M. , Sedláček I. . ( 2013;). Pseudomonas prosekii sp. nov., a novel psychrotrophic bacterium from Antarctica. Curr Microbiol 67: 637–646 [CrossRef] [PubMed].
    [Google Scholar]
  19. Lau H.-T. , Faryna J. , Triplett E. W. . ( 2006;). Aquitalea magnusonii gen. nov., sp. nov., a novel Gram-negative bacterium isolated from a humic lake. Int J Syst Evol Microbiol 56: 867–871 [CrossRef] [PubMed].
    [Google Scholar]
  20. Lee C. M. , Weon H.-Y. , Kim Y.-J. , Son J.-A. , Yoon S.-H. , Koo B.-S. , Kwon S.-W. . ( 2009;). Aquitalea denitrificans sp. nov., isolated from a Korean wetland. Int J Syst Evol Microbiol 59: 1045–1048 [CrossRef] [PubMed].
    [Google Scholar]
  21. Meier-Kolthoff J. P. , Auch A. F. , Klenk H.-P. , Göker M. . ( 2013;). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60 [CrossRef] [PubMed].
    [Google Scholar]
  22. Pot B. , Vandamme P. , Kersters K. . ( 1994;). Analysis of electrophoretic whole-organism protein fingerprints. . In Modern Microbiological methods: Chemical Methods in Prokaryotic Systematics, pp. 493–521. Edited by Goodfellow M. , O'Donnell A. G. . Chichester: Wiley;.
    [Google Scholar]
  23. Roth T. , Foley J. , Worth J. , Piovia-Scott J. , Pope K. , Lawler S. . ( 2013;). Bacterial flora on Cascades frogs in the Klamath mountains of California. Comp Immunol Microbiol Infect Dis 36: 591–598 [CrossRef] [PubMed].
    [Google Scholar]
  24. Saitou N. , Nei M. . ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425 [PubMed].
    [Google Scholar]
  25. Sasser M. . ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc;.
    [Google Scholar]
  26. Stolz A. , Busse H.-J. , Kämpfer P. . ( 2007;). Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 57: 572–576 [CrossRef] [PubMed].
    [Google Scholar]
  27. Švec P. , Pantu˚ček R. , Petráš P. , Sedláček I. , Nováková D. . ( 2010a;). Identification of Staphylococcus spp. using (GTG)5-PCR fingerprinting. Syst Appl Microbiol 33: 451–456 [CrossRef] [PubMed].
    [Google Scholar]
  28. Švec P. , Kukletová M. , Sedlácˇek I. . ( 2010b;). Comparative evaluation of automated ribotyping and RAPD-PCR for typing of Lactobacillus spp. occurring in dental caries. Anton Leeuw 98: 85–92 [CrossRef] [PubMed].
    [Google Scholar]
  29. Švec P. , Vandamme P. , Bryndová H. , Holochová P. , Kosina M. , Masˇlanˇová I. , Sedlácˇek I. . ( 2012;). Enterococcus plantarum sp. nov., isolated from plants. Int J Syst Evol Microbiol 62: 1499–1505 [CrossRef] [PubMed].
    [Google Scholar]
  30. Tamura K. , Dudley J. , Nei M. , Kumar S. . ( 2007;). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24: 1596–1599 [CrossRef] [PubMed].
    [Google Scholar]
  31. Tindall B. J. . ( 1990a;). Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66: 199–202 [CrossRef].
    [Google Scholar]
  32. Tindall B. J. . ( 1990b;). A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13: 128–130 [CrossRef].
    [Google Scholar]
  33. Turki Y. , Mehri I. , Cherif H. , Hassen A. , Ouzari H. . ( 2013;). Effect of biological treatment and ultraviolet (UV)-C radiation disinfection process on wastewater bacterial community as assessed by denaturing gradient gel electrophoresis (DGGE) fingerprints. Afr J Microbiol Res 7: 4927–4933 [CrossRef].
    [Google Scholar]
  34. Versalovic J. , Schneider M. , de Brulin F. J. , Lupski J. R. . ( 1994;). Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 5: 25–40.
    [Google Scholar]
  35. Vlková E. , Killer J. , Kmet V. , Rada V. , Musilová Š. , Bunešová V. , Hovorková P. , Božík M. , Salmonová H. , Rajchard J. . ( 2015;). Identification of microbiota associated with Pectinatella magnifica in South Bohemia. Biologia 70: 365–371 [CrossRef].
    [Google Scholar]
  36. Weber K. A. , Hedrick D. B. , Peacock A. D. , Thrash J. C. , White D. C. , Achenbach L. A. , Coates J. D. . ( 2009;). Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002. Appl Microbiol Biotechnol 83: 555–565 [CrossRef] [PubMed].
    [Google Scholar]
  37. Woo H. L. , Hazen T. C. , Simmons B. A. , DeAngelis K. M. . ( 2014;). Enzyme activities of aerobic lignocellulolytic bacteria isolated from wet tropical forest soils. Syst Appl Microbiol 37: 60–67 [CrossRef] [PubMed].
    [Google Scholar]
  38. Yoon J.-H. , Lee S.-Y. , Jung Y.-T. , Lee J.-S. , Lee K.-C. . ( 2013;). Litorisediminicola beolgyonensis gen. nov., sp. nov., isolated from a coastal sediment. Int J Syst Evol Microbiol 63: 2025–2031 [CrossRef] [PubMed].
    [Google Scholar]
  39. Zhang Z. , Schwartz S. , Wagner L. , Miller W. . ( 2000;). A greedy algorithm for aligning DNA sequences. J Comput Biol 7: 203–214 [CrossRef] [PubMed].
    [Google Scholar]
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