sp. nov., isolated from mineral peloid Free

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
2024-03-29
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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 [View Article][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 [View Article]
    [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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article]
    [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 323–328Edited 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 [View Article][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 [View Article][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 [View Article][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 [View Article]
    [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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 493–521Edited 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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][PubMed]
    [Google Scholar]
  31. Tindall B. J. 1990a; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [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 [View Article]
    [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 [View Article]
    [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 [View Article]
    [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 [View Article][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 [View Article][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 [View Article][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 [View Article][PubMed]
    [Google Scholar]
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