1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 67, Issue 8

sp. nov. and sp. nov., two novel species within the group isolated from forest soil Free

Abstract

Within the frame of a biotechnological screening, we isolated two strains from forest soil. 16S rRNA gene sequence analysis indicated that strain CCOS 864 shared 99.8 % similarity with HYS, while strain CCOS 865 shared 99.0 % similarity with DSM 291 and lower similarity with other group type strains. Based on multilocus sequence analysis, the two strains were genotypically distinct from each other, each forming a separate clade. Strains CCOS 864 and CCOS 865 were Gram-stain-negative, motile and rod-shaped, growing at a temperature range of 4–37 °C. Strain CCOS 864 could be phenotypically distinguished from group species by the combination of gelatinase-positive reaction and positive growth on -acetyl--glucosamine, -hydroxyphenylacetic acid and inosine but lack of fluorescein production on King’s B medium, while strain CCOS 865 could be distinguished from group species by the combination of positive growth with saccharic acid and negative growth with -hydroxyphenylacetic acid and -pyroglutamic acid. The major polar lipid for both strains was phosphatidylethanolamine; the major quinone was ubiquinone Q-9. DNA–DNA hybridization and average nucleotide identities confirmed the novel species status for the two strains. The DNA G+C contents of CCOS 864 and CCOS 865 were 62.1 and 63.8 mol%, respectively. The phenotypic, phylogenetic and DNA–DNA relatedness data support the suggestion that CCOS 864 and CCOS 865 represent two novel species. The names sp. nov. (type strain CCOS 864=LMG 29327) and sp. nov. (type strain CCOS 865=LMG 29328) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): biotechnological application , Pseudomonas and screening
© 2017 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002035
2017-08-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/8/2853.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002035&mimeType=html&fmt=ahah

References

  1. Palleroni NJ. Pseudomonas. In Brenner DJ, Krieg NR, Staley JT. (editors) Bergey's Manual of Systematic Bacteriology, 2nd ed. vol. 2 New York: Springer; 2005 pp. 323–379
     [Google Scholar]
  2. Moore ERB, Mau M, Arnscheidt A, Böttger EC, Hutson RA et al. The determination and comparison of the 16S rRNA gene sequences of species of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships. Syst Appl Microbiol 1996; 19:478–492 [View Article]
     [Google Scholar]
  3. Yamamoto S, Kasai H, Arnold DL, Jackson RW, Vivian A et al. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 2000; 146:2385–2394 [View Article][PubMed]
     [Google Scholar]
  4. Mulet M, Gomila M, Scotta C, Sánchez D, Lalucat J et al. Concordance between whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry and multilocus sequence analysis approaches in species discrimination within the genus Pseudomonas. Syst Appl Microbiol 2012; 35:455–464 [View Article][PubMed]
     [Google Scholar]
  5. Gomila M, Peña A, Mulet M, Lalucat J, García-Valdés E. Phylogenomics and systematics in Pseudomonas. Front Microbiol 2015; 6:214 [View Article][PubMed]
     [Google Scholar]
  6. Flury P, Aellen N, Ruffner B, Péchy-Tarr M, Fataar S et al. Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. ISME J 2016; 10:2527–2542 [View Article][PubMed]
     [Google Scholar]
  7. Yonezuka K, Shimodaira J, Tabata M, Ohji S, Hosoyama A et al. Phylogenetic analysis reveals the taxonomically diverse distribution of the Pseudomonas putida group. J Gen Appl Microbiol 2017; 63:1–10 [View Article][PubMed]
     [Google Scholar]
  8. Stanier RY, Palleroni NJ, Doudoroff M. The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 1966; 43:159–271 [View Article][PubMed]
     [Google Scholar]
  9. King EO, Ward MK, Raney DE. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 1954; 44:301–307[PubMed]
     [Google Scholar]
  10. Goldenberger D, Perschil I, Ritzler M, Altwegg M. A simple "universal" DNA extraction procedure using SDS and proteinase K is compatible with direct PCR amplification. PCR Methods Appl 1995; 4:368–370 [View Article][PubMed]
     [Google Scholar]
  11. 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 [View Article][PubMed]
     [Google Scholar]
  12. Edgar R, Friedman N, Molshanski-Mor S, Qimron U. Reversing bacterial resistance to antibiotics by phage-mediated delivery of dominant sensitive genes. Appl Environ Microbiol 2012; 78:744–751 [View Article][PubMed]
     [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
     [Google Scholar]
  14. Gao J, Xie G, Peng F, Xie Z. Pseudomonas donghuensis sp. nov., exhibiting high-yields of siderophore. Antonie van Leeuwenhoek 2015; 107:83–94 [View Article]
     [Google Scholar]
  15. Salerno A, Delétoile A, Lefevre M, Ciznar I, Krovacek K et al. Recombining population structure of Plesiomonas shigelloides (Enterobacteriaceae) revealed by multilocus sequence typing. J Bacteriol 2007; 189:7808–7818 [View Article][PubMed]
     [Google Scholar]
  16. Süβmuth R, Eberspächer J, Haag R, Springer W. Biochemisch-Mikrobiologisches Praktikum Stuttgart, Germany: Georg Thieme Verlag; 1987
     [Google Scholar]
  17. Murthy N, Bleakley B. Simplified method of preparing collodial chitin used for screening of chitinase-producing microorganisms. Internet J Microbiol 2012; 10:1–5
     [Google Scholar]
  18. Tang YW, Ellis NM, Hopkins MK, Smith DH, Dodge DE et al. Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. J Clin Microbiol 1998; 36:3674–3679[PubMed]
     [Google Scholar]
  19. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note #101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  20. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
     [Google Scholar]
  21. 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]
  22. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  23. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007 pp. 330–393
     [Google Scholar]
  24. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
     [Google Scholar]
  25. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
     [Google Scholar]
  26. Smits THM, Pothier JF, Ruinelli M, Blom J, Frasson D et al. Complete genome sequence of the cyanogenic phosphate-solubilizing Pseudomonas sp. strain CCOS 191, a close relative of Pseudomonas mosselii. Genome Announc 2015; 3:e00616-1500616615 [View Article][PubMed]
     [Google Scholar]
  27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  28. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  29. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article][PubMed]
     [Google Scholar]
  30. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
     [Google Scholar]
  31. Lang K, Zierow J, Buehler K, Schmid A. Metabolic engineering of Pseudomonas sp. strain VLB120 as platform biocatalyst for the production of isobutyric acid and other secondary metabolites. Microb Cell Fact 2014; 13:2 [View Article][PubMed]
     [Google Scholar]
  32. Verhoef S, Wierckx N, Westerhof RGM, de Winde JH, Ruijssenaars HJ. Bioproduction of p-hydroxystyrene from glucose by the solvent-tolerant bacterium Pseudomonas putida S12 in a two-phase water-decanol fermentation. Appl Environ Microbiol 2009; 75:931–936 [View Article][PubMed]
     [Google Scholar]
  33. Zinn M, Durner R, Zinn H, Ren Q, Egli T et al. Growth and accumulation dynamics of poly(3-hydroxyalkanoate) (PHA) in Pseudomonas putida GPo1 cultivated in continuous culture under transient feed conditions. Biotechnol J 2011; 6:1240–1252 [View Article][PubMed]
     [Google Scholar]
  34. Witholt B, Kessler B. Perspectives of medium chain length poly(hydroxyalkanoates), a versatile set of bacterial bioplastics. Curr Opin Biotechnol 1999; 10:279–285 [View Article][PubMed]
     [Google Scholar]
  35. Ren Q, Ruth K, Thöny-Meyer L, Zinn M. Enatiomerically pure hydroxycarboxylic acids: current approaches and future perspectives. Appl Microbiol Biotechnol 2010; 87:41–52 [View Article][PubMed]
     [Google Scholar]
  36. Zinn M, Witholt B, Egli T. Occurrence, synthesis and medical application of bacterial polyhydroxyalkanoate. Adv Drug Deliv Rev 2001; 53:5–21 [View Article][PubMed]
     [Google Scholar]
  37. Mulet M, Gomila M, Lemaitre B, Lalucat J, García-Valdés E. Taxonomic characterisation of Pseudomonas strain L48 and formal proposal of Pseudomonas entomophila sp. nov. Syst Appl Microbiol 2012; 35:145–149 [View Article][PubMed]
     [Google Scholar]
  38. Pungrasmi W, Lee HS, Yokota A, Ohta A. Pseudomonas japonica sp. nov., a novel species that assimilates straight chain alkylphenols. J Gen Appl Microbiol 2008; 54:61–69 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002035
Loading
Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidholzensis sp. nov., two novel species within the Pseudomonas putida group isolated from forest soil
Int J Syst Evol Microbiol 67, 2853 (2017); https://doi.org/10.1099/ijsem.0.002035
/content/journal/ijsem/10.1099/ijsem.0.002035
/content/journal/ijsem/10.1099/ijsem.0.002035
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error