1887

Abstract

A Gram-staining-negative, aerobic, non-motile, capsule-forming and rod-shaped bacterium, designated JH-7, was isolated from sludge of a manganese mine. The 16S rRNA gene sequence of JH-7 showed highest similarities to those of Pseudaminobacter salicylatoxidans BN12 (97.4 %), Mesorhizobiumthiogangeticum SJT (97.0 %) and Pseudaminobacter defluvii THI 051 (96.5 %). Phylogenetic trees clustered JH-7 together with P. salicylatoxidans BN12 and P. defluvii THI 051. The DNA–DNA hybridization values between JH-7 and P. salicylatoxidans DSM 6986 and between JH-7 and M . thiogangeticum DSM 17097 were 34.8 and 20.1 %, respectively. The major fatty acids of JH-7 (>10 %) were C18 : 1ω7c, C19 : 0cyclo ω8c and C16 : 0. The genomic DNA G+C content was 61.6 mol%. The polyamines of JH-7 were sym-homospermidine (83 %) and putrescine (17 %), and the respiratory quinone was ubiquinone-10. The major polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and two unidentified lipids. Compared with the members of the genera Pseudaminobacter and Mesorhizobium , JH-7 showed some unique physiological and biochemical characters, such as being negative for H2S production, hydrolysis of Tween 40 and Tween 60, esterase lipase (C8) activity and assimilation of d-ribose and positive for acid production from d-galactose and assimilation of d-fructose. On the basis of the results of the polyphasic taxonomic analysis, JH-7 was considered to represent a novel species of the genus Pseudaminobacter , for which the name Pseudaminobacter manganicus sp. nov. is proposed. The type strain is JH-7 (=KCTC 52258=CCTCC AB 2016107).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001765
2017-05-30
2019-12-06
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/5/1589.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001765&mimeType=html&fmt=ahah

References

  1. Kämpfer P, Müller C, Mau M, Neef A, Auling G et al. Description of Pseudaminobacter gen. nov. with two new species, Pseudaminobacter salicylatoxidans sp. nov. and Pseudaminobacter defluvii sp. nov. Int J Syst Bacteriol 1999;49:887–897 [CrossRef][PubMed]
    [Google Scholar]
  2. Knösel DH. Genus IV. Phyllobacterium (ex Knösel 1962) nom. rev. (Phyllobacterium Knösel 1962, 96). In Krieg NR, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriologyvol. 1 Baltimore: Williams & Wilkins; 1984; pp.254–256
    [Google Scholar]
  3. Parte AC. LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014;42:D613–D616 [CrossRef][PubMed]
    [Google Scholar]
  4. Jarvis BDW, Pankhurst CE, Patel JJ. Rhizobium loti, a new species of legume root nodule bacteria. Int J Syst Bacteriol 1982;32:378–380 [CrossRef]
    [Google Scholar]
  5. Jarvis BDW, van Berkum P, Chen WX, Nour SM, Fernandez MP et al. Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to Mesorhizobium gen. nov. Int J Syst Bacteriol 1997;47:895–898 [CrossRef]
    [Google Scholar]
  6. Ghosh W, Roy P. Mesorhizobium thiogangeticum sp. nov., a novel sulfur-oxidizing chemolithoautotroph from rhizosphere soil of an Indian tropical leguminous plant. Int J Syst Evol Microbiol 2006;56:91–97 [CrossRef][PubMed]
    [Google Scholar]
  7. Nguyen TM, Pham VH, Kim J. Mesorhizobium soli sp. nov., a novel species isolated from the rhizosphere of Robinia pseudoacacia L. in South Korea by using a modified culture method. Antonie van Leeuwenhoek 2015;108:301–310 [CrossRef][PubMed]
    [Google Scholar]
  8. de Meyer SE, Tan HW, Heenan PB, Andrews M, Willems A. Mesorhizobium waimense sp. nov. isolated from Sophora longicarinata root nodules and Mesorhizobium cantuariense sp. nov. isolated from Sophora microphylla root nodules. Int J Syst Evol Microbiol 2015;65:3419–3426 [CrossRef][PubMed]
    [Google Scholar]
  9. Degefu T, Wolde-Meskel E, Liu B, Cleenwerck I, Willems A et al. Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees. Int J Syst Evol Microbiol 2013;63:1746–1753 [CrossRef][PubMed]
    [Google Scholar]
  10. Zhu YJ, Kun J, Chen YL, Wang SK, Sui XH et al. Mesorhizobium acaciae sp. nov., isolated from root nodules of Acacia melanoxylon R. Br. Int J Syst Evol Microbiol 2015;65:3558–3563 [CrossRef][PubMed]
    [Google Scholar]
  11. Choma A, Komaniecka I. Analysis of phospholipids and ornithine-containing lipids from Mesorhizobium spp. Syst Appl Microbiol 2002;25:326–331 [CrossRef][PubMed]
    [Google Scholar]
  12. Zheng WT, Li Y, Wang R, Sui XH, Zhang XX et al. Mesorhizobium qingshengii sp. nov., isolated from effective nodules of Astragalus sinicus. Int J Syst Evol Microbiol 2013;63:2002–2007 [CrossRef][PubMed]
    [Google Scholar]
  13. Sambrook J, Russell D. Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 2001
    [Google Scholar]
  14. Wilson KH, Blitchington RB, Greene RC. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol 1990;28:1942–1946[PubMed]
    [Google Scholar]
  15. Fan H, Su C, Wang Y, Yao J, Zhao K et al. Sedimentary arsenite-oxidizing and arsenate-reducing bacteria associated with high arsenic groundwater from Shanyin, Northwestern China. J Appl Microbiol 2008;105:529–539 [CrossRef][PubMed]
    [Google Scholar]
  16. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977;74:5463–5467 [CrossRef][PubMed]
    [Google Scholar]
  17. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  18. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  19. 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]
  20. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010;59:307–321 [CrossRef][PubMed]
    [Google Scholar]
  21. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  22. 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][PubMed]
    [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. Dussault HP. An improved technique for staining red halophilic bacteria. J Bacteriol 1955;70:484–485[PubMed]
    [Google Scholar]
  26. Xu D, Zheng S, Wang G, Wang L. Domibacillus antri sp. nov., isolated from the soil of a cave. Int J Syst Evol Microbiol 2016;66:2502–2508 [CrossRef]
    [Google Scholar]
  27. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
    [Google Scholar]
  28. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic Characterization and the Principles of Comparative Systematics. In Reddy CA. (editor) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.330–393
    [Google Scholar]
  29. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  31. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984;25:125–128 [CrossRef]
    [Google Scholar]
  32. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983;4:184–192 [CrossRef][PubMed]
    [Google Scholar]
  33. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proterobacteria. Syst Appl Microbiol 1988;11:1–8 [CrossRef]
    [Google Scholar]
  34. Schenkel E, Berlaimont V, Dubois J, Helson-Cambier M, Hanocq M. Improved high-performance liquid chromatographic method for the determination of polyamines as their benzoylated derivatives: application to P388 cancer cells. J Chromatogr B Biomed Appl 1995;668:189–197 [CrossRef][PubMed]
    [Google Scholar]
  35. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202 [CrossRef]
    [Google Scholar]
  36. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13:128–130 [CrossRef]
    [Google Scholar]
  37. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in BacterialSystematics (Society for Applied Bacteriology Technical Series No. 20) London: Academic Press; 1985; pp.173–199
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001765
Loading
/content/journal/ijsem/10.1099/ijsem.0.001765
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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