1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 4

sp. nov., isolated from root nodules of in a lead–zinc mine Free

Abstract

A novel endophytic bacterium, designated strain HZ10, was isolated from root nodules of growing in a lead–zinc mine in Mianxian County, Shaanxi Province, China. The bacterium was Gram-stain-negative, aerobic, motile, slightly curved- and rod-shaped, methyl red-negative, catalase-positive, and did not produce HS. Strain HZ10 grew at 4–45 °C (optimum, 25–30 °C), pH 5–9 (optimum, pH 7–8) and 0–1 % (w/v) NaCl. The major fatty acids were identified as C, summed feature 8 (Cω7 and/or Cω6) and summed feature 3 (Cω7 and/or Cω6), and the quinone type was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of the genomic DNA was 64.9 mol% based on the whole genome sequence. According to the 16S rRNA gene sequence analysis, the closest phylogenetic relative to strain HZ10 is CPW301 (98.72 % sequence identity). Genome relatedness of the type strains CPW301, Z67 and IEH 4430, was quantified by using the average nucleotide identity (86.9–88.0 %) and a genome-to-genome distance analysis (26.6 %–29.3 %), with both strongly supporting the notion that strain HZ10 belongs to the genus as a novel species. Based on the results from phylogenetic, chemotaxonomic and physiological analyses, strain HZ10 represents a novel species, for which the name sp. nov. is proposed. The type strain is HZ10 (=JCM 31754=CCTCC AB 2014352).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene sequence , Herbaspirillum robiniae , Locust root nodule and Polyphasic taxonomy
© 2018 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002666
2018-04-01
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/4/1300.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002666&mimeType=html&fmt=ahah

References

  1. Im WT, Bae HS, Yokota A, Lee ST. Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium. Int J Syst Evol Microbiol 2004; 54:851–855 [View Article][PubMed]
     [Google Scholar]
  2. Baldani J, Baldani V, Seldin L, Döbereiner J. Characterization of Herbaspirillum seropedicae gen. nov., sp. nov., a root-associated nitrogen-fixing bacterium. Int J Syst Evol Micr 1986; 36:86–93
     [Google Scholar]
  3. Dobritsa AP, Reddy MC, Samadpour M. Reclassification of Herbaspirillum putei as a later heterotypic synonym of Herbaspirillum huttiense, with the description of H. huttiense subsp. huttiense subsp. nov. and H. huttiense subsp. putei subsp. nov., comb. nov., and description of Herbaspirillum aquaticum sp. nov. Int J Syst Evol Microbiol 2010; 60:1418–1426 [View Article][PubMed]
     [Google Scholar]
  4. Valverde A, Velázquez E, Gutiérrez C, Cervantes E, Ventosa A et al. Herbaspirillum lusitanum sp. nov., a novel nitrogen-fixing bacterium associated with root nodules of Phaseolus vulgaris . Int J Syst Evol Microbiol 2003; 53:1979–1983 [View Article][PubMed]
     [Google Scholar]
  5. Jung SY, Lee MH, Oh TK, Yoon JH. Herbaspirillum rhizosphaerae sp. nov., isolated from rhizosphere soil of Allium victorialis var. platyphyllum . Int J Syst Evol Microbiol 2007; 57:2284–2288 [View Article][PubMed]
     [Google Scholar]
  6. Dobereiner J, Bergersen FJ. Forage grasses and grain crops. Methods for Evaluating Biological Nitrogen Fixation Chichester: Wiley; 1980 pp. 535–555
     [Google Scholar]
  7. Baldani J, Pot B, Kirchhof G, Falsen E, Baldani V et al. Emended description of Herbaspirillum; inccusion of [Pseudomonas] rubrisubalbicans, a mild plant pathogen, as Herbaspirillum rubrisubalbicans comb. Nov.; and classification of a Group of Clinical Isolates (EF Group 1) as Herbaspirillum species 3. Int J Syst Evol Micr 1996; 46:802–810
     [Google Scholar]
  8. Lin SY, Hameed A, Arun AB, Liu YC, Hsu YH et al. Description of Noviherbaspirillum malthae gen. nov., sp. nov., isolated from an oil-contaminated soil, and proposal to reclassify Herbaspirillum soli, Herbaspirillum aurantiacum, Herbaspirillum canariense and Herbaspirillum psychrotolerans as Noviherbaspirillum soli comb. nov., Noviherbaspirillum aurantiacum comb. nov., Noviherbaspirillum canariense comb. nov. and Noviherbaspirillum psychrotolerans comb. nov. based on polyphasic analysis. Int J Syst Evol Microbiol 2013; 63:4100–4107 [View Article][PubMed]
     [Google Scholar]
  9. Chaudhary DK, Kim J. Noviherbaspirillum agri sp. nov., isolated from reclaimed grassland soil, and reclassification of Herbaspirillum massiliense (Lagier et al., 2014) as Noviherbaspirillum massiliense comb. nov. Int J Syst Evol Microbiol 2017; 67:1508–1515 [View Article][PubMed]
     [Google Scholar]
  10. Kirchhof G, Eckert B, Stoffels M, Baldani JI, Reis VM et al. Herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in C4-fibre plants. Int J Syst Evol Microbiol 2001; 51:157–168 [View Article][PubMed]
     [Google Scholar]
  11. Ding L. Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov . Int J Syst Evol Microbio 2004; 54:2223–2230 [View Article]
     [Google Scholar]
  12. Rothballer M, Schmid M, Klein I, Gattinger A, Grundmann S et al. Herbaspirillum hiltneri sp. nov., isolated from surface-sterilized wheat roots. Int J Syst Evol Microbiol 2006; 56:1341–1348 [View Article][PubMed]
     [Google Scholar]
  13. Kamicker BJ, Brill WJ. Identification of Bradyrhizobium japonicum nodule isolates from Wisconsin soybean farms. Appl Environ Microbiol 1986; 51:487–492[PubMed]
     [Google Scholar]
  14. Vincent JM. A Manual for the Practical Study of the Root-Nodule Bacteria Oxford: Blackwell Scientific Publications; 1970
     [Google Scholar]
  15. Dong X, Cai M. Determination of biochemical properties. Manual for the Systematic Identification of General Bacteria Beijing: Science Press; 2001 pp. 370–398
     [Google Scholar]
  16. Skerman VBD. A guide to the identification of the genera of bacteria. J Clin Pathol 1960; 53:796
     [Google Scholar]
  17. Cappuccino JG, Sherman N. Microbiology: A Laboratory Manual Menlo Park, CA: The Benjamin/Cummings Publishing Co; 1996 pp. 129–182
     [Google Scholar]
  18. Smibert R. Phenotypic characterization. In: Methods for general and molecular bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
     [Google Scholar]
  19. Tan ZY, Wang ET, Peng GX, Zhu ME, Martínez-Romero E et al. Characterization of bacteria isolated from wild legumes in the north-western regions of China. Int J Syst Bacteriol 1999; 49:1457–1469 [View Article][PubMed]
     [Google Scholar]
  20. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [Crossref]
     [Google Scholar]
  21. Komagata K, Susuki K. Lipid and cell-wall systematics in bacterial systematics. Method Microbiol 1987; 19:161–207 [Crossref]
     [Google Scholar]
  22. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Meth 1984; 2:233–241 [Crossref]
     [Google Scholar]
  23. Lin SY, Hameed A, Arun AB, Liu YC, Hsu YH et al. Description of Noviherbaspirillum malthae gen. nov., sp. nov., isolated from an oil-contaminated soil, and proposal to reclassify Herbaspirillum soli, Herbaspirillum aurantiacum, Herbaspirillum canariense and Herbaspirillum psychrotolerans as Noviherbaspirillum soli comb. nov., Noviherbaspirillum aurantiacum comb. nov., Noviherbaspirillum canariense comb. nov. and Noviherbaspirillum psychrotolerans comb. nov. based on polyphasic analysis. Int J Syst Evol Microbiol 2013; 63:4100 [View Article][PubMed]
     [Google Scholar]
  24. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Evol Micr 1995; 45:240–245
     [Google Scholar]
  25. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci USA 1978; 75:4801–4805[PubMed] [Crossref]
     [Google Scholar]
  26. Willems A, Collins MD. Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences. Int J Syst Bacteriol 1993; 43:305–313 [View Article][PubMed]
     [Google Scholar]
  27. Yanagi M, Yamasato K. Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer. FEMS Microbiol Lett 1993; 107:115–120[PubMed] [Crossref]
     [Google Scholar]
  28. Yoon SH, Ha SM, 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]
  29. 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[PubMed] [Crossref]
     [Google Scholar]
  30. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article][PubMed]
     [Google Scholar]
  31. 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[PubMed] [Crossref]
     [Google Scholar]
  32. Tavare S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on Mathematics in the Life Sciences 1986 pp. 17
     [Google Scholar]
  33. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  34. Young J, Stacey G. Phylogenetic classification of nitrogen-fixing organisms. Biological Nitrogen Fixation 1992 pp. 43–86
     [Google Scholar]
  35. Stoltzfus J, So R, Malarvithi P, Ladha J, de Bruijn F. Isolation of endophytic bacteria from rice and assessment of their potential for supplying rice with biologically fixed nitrogen. Plant Soil 1997; 194:25–36 [Crossref]
     [Google Scholar]
  36. Poly F, Monrozier LJ, Bally R. Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res Microbiol 2001; 152:95–103[PubMed] [Crossref]
     [Google Scholar]
  37. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
     [Google Scholar]
  38. Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618[PubMed] [Crossref]
     [Google Scholar]
  39. 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]
  40. 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]
  41. Wayne L. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464 [Crossref]
     [Google Scholar]
  42. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002666
Loading
Herbaspirillum robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia in a lead–zinc mine
Int J Syst Evol Microbiol 68, 1300 (2018); https://doi.org/10.1099/ijsem.0.002666
/content/journal/ijsem/10.1099/ijsem.0.002666
/content/journal/ijsem/10.1099/ijsem.0.002666
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