1887

Abstract

A xanthan-degrading bacterium, strain AS7, was isolated from soil and its taxonomic position was determined using a polyphasic approach. Strain AS7 was a Gram-stain-variable, spore-forming, motile, aerobic, rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that strain AS7 belongs to the genus , sharing the highest level of sequence similarity with PALXIL04 (98.0 %). The cell-wall peptidoglycan contained -diaminopimelic acid. MK-7 was the dominant isoprenoid quinone and the major fatty acid was anteiso-C. Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. These chemotaxonomic characteristics were consistent with the isolate belonging to the genus . The G+C content of the genomic DNA was 51.0 mol% and the DNA–DNA hybridization value between strain AS7 and PALXIL04 was only 14.4±2.5 %. On the basis of phylogenetic analyses, phenotypic and chemotaxonomic characteristics, and DNA–DNA relatedness value, strain AS7 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is AS7 (=IBRC M 10987=LMG 29451).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002453
2018-01-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/1/76.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002453&mimeType=html&fmt=ahah

References

  1. García-Ochoa F, Santos VE, Casas JA, Gómez E. Xanthan gum: production, recovery, and properties. Biotechnol Adv 2000; 18:549–579 [View Article][PubMed]
    [Google Scholar]
  2. Nankai H, Hashimoto W, Miki H, Kawai S, Murata K. Microbial system for polysaccharide depolymerization: enzymatic route for xanthan depolymerization by Bacillus sp. strain GL1. Appl Environ Microbiol 1999; 65:2520–2526[PubMed]
    [Google Scholar]
  3. Priest FG. Genus I. Paenibacillus . In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey’s Manual of Systematic Bacteriology New York: Springer; 2009 pp. 269–295
    [Google Scholar]
  4. Rivas R, Mateos PF, Martínez-Molina E, Velázquez E. Paenibacillus phyllosphaerae sp. nov., a xylanolytic bacterium isolated from the phyllosphere of Phoenix dactylifera . Int J Syst Evol Microbiol 2005; 55:743–746 [View Article][PubMed]
    [Google Scholar]
  5. Ruijssenaars HJ, de Bont JA, Hartmans S. A pyruvated mannose-specific xanthan lyase involved in xanthan degradation by Paenibacillus alginolyticus XL-1. Appl Environ Microbiol 1999; 65:2446–2452[PubMed]
    [Google Scholar]
  6. Muchová M, Růzicka J, Julinová M, Dolezalová M, Houser J et al. Xanthan and gellan degradation by bacteria of activated sludge. Water Sci Technol 2009; 60:965–973 [View Article][PubMed]
    [Google Scholar]
  7. Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Antonie van Leeuwenhoek 1993; 64:253–260 [View Article]
    [Google Scholar]
  8. Ash C, Priest FG, Collins MD. Paenibacillus gen. nov. In validation of the publication of new names and new combinations previously effectively published outside the IJSB, List no. 51. Int J Syst Bacteriol 1994; 44:852–853 [Crossref]
    [Google Scholar]
  9. De Vos P, Ludwig W, Schleifer KH, Whitman WB. Family IV. Paenibacillaceae fam. nov. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey’s Manual of Systematic Bacteriology New York: Springer; 2009 p. 269
    [Google Scholar]
  10. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129 [Crossref]
    [Google Scholar]
  11. Logan NA, Berge O, Bishop AH, Busse HJ, de Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article][PubMed]
    [Google Scholar]
  12. Liu H, Huang C, Dong W, du Y, Bai X et al. Biodegradation of xanthan by newly isolated Cellulomonas sp. LX, releasing elicitor-active xantho-oligosaccharides-induced phytoalexin synthesis in soybean cotyledons. Process Biochem 2005; 40:3701–3706 [View Article]
    [Google Scholar]
  13. Hucker GJ, Conn HJ. Method of Gram staining. N Y State Agric Exp Stn Tech Bull 1923; 93:3–37
    [Google Scholar]
  14. Schaeffer AB, Fulton MD. A simplified method of staining endospores. Science 1933; 77:194 [View Article][PubMed]
    [Google Scholar]
  15. MacFaddin JF. Biochemical Tests for Identification of Medical Bacteria, 3rd ed. Philadelphia, PA: The Lippincott, Williams & Wilkins Co; 2000
    [Google Scholar]
  16. Son JS, Kang HU, Ghim SY. Paenibacillus dongdonensis sp. nov., isolated from rhizospheric soil of Elymus tsukushiensis . Int J Syst Evol Microbiol 2014; 64:2865–2870 [View Article][PubMed]
    [Google Scholar]
  17. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematic. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology Washington, DC: ASM Press; 2007 pp. 330–393
    [Google Scholar]
  18. Krieg N, Padgett JP. Phenotypic and physiological characterization methods. In Rainey F, Oren A. (editors) Methods in Microbiology, Taxonomy of Prokaryotes London: Academic Press, Elsevier; 2011 pp. 15–60 [Crossref]
    [Google Scholar]
  19. Simbert RM, Krieg NR. Phenotypic characterization. In Gerhard P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: ASM Press; 1994 pp. 607–655
    [Google Scholar]
  20. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
    [Google Scholar]
  21. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp. 115–175
    [Google Scholar]
  22. Chun J, Lee JH, Jung Y, Kim M, Kim S et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [View Article][PubMed]
    [Google Scholar]
  23. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  26. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526[PubMed]
    [Google Scholar]
  27. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  28. 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]
  29. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  30. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [View Article][PubMed]
    [Google Scholar]
  31. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983; 4:184–192 [View Article][PubMed]
    [Google Scholar]
  32. Cashion P, Holder-Franklin MA, Mccully J, Franklin M. A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 1977; 81:461–466 [View Article][PubMed]
    [Google Scholar]
  33. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [View Article]
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE, USA: Microbial ID Inc; 1990
    [Google Scholar]
  35. Collins MD. Isoprenoid quinone analysis in classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 267–287
    [Google Scholar]
  36. Wu C, Lu X, Qin M, Wang Y, Ruan J. The analysis of menaquinone compound in microbial cells by HPLC. Microbiology 1989; 16:176–178
    [Google Scholar]
  37. 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 Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  38. Stackebrandt E, Goebel BM. Taxonomic note: a place for dna-dna reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
  39. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [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. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  42. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  43. Kämpfer P, Rosselló-Mora R, Falsen E, Busse HJ, Tindall BJ. Cohnella thermotolerans gen. nov., sp. nov., and classification of 'Paenibacillus hongkongensis' as Cohnella hongkongensis sp. nov. Int J Syst Evol Microbiol 2006; 56:781–786 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002453
Loading
/content/journal/ijsem/10.1099/ijsem.0.002453
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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