1887

Abstract

A Gram-stain-negative, facultative anaerobic, non-motile and rod-shaped bacterial strain, designated LX32, was isolated from arsenic and cadmium contaminated farmland soil. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain LX32 was closely related to Phenylobacterium hankyongense HKS-05 (97.7 % sequence similarity), Phenylobacterium kunshanense CCTCC AB 2013085 (97.4 %) and Phenylobacterium deserti CCTCC AB 2016297 (97.1 %). The average nucleotide identity values of the whole genome sequences of LX32/P. hankyongense HKS-05, LX32/P. kunshanense CCTCC AB 2013085 and LX32/P. deserti CCTCC AB 2016297 were 79.8, 77.9 and 77.5 %, respectively. Its genome size was 4.02 Mb, comprising 3998 predicted genes with a DNA G+C content of 70.1 mol%. The major fatty acids were C15 : 0, C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The polar lipid profiles consisted of phosphatidylglycerol, aminophospholipid, seven glycolipids and two unidentified polar lipids. The predominantly respiratory quinone was ubiquinone-10. Based on polyphasic analyses, the isolate is considered to represent a novel species of the genus Phenylobacterium , for which the name Phenylobacterium soli sp. nov. is proposed. The type strain is LX32 (=KCTC 62522=CCTCC AB 2018055).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003325
2019-03-01
2019-09-20
Loading full text...

Full text loading...

References

  1. Lingens F, Blecher R, Blecher H, Blobel F, Eberspacher J et al. Phenylobacterium immobile gen. nov., sp. nov., a gram-negative bacterium that degrades the herbicide chloridazon. Int J Syst Bacteriol 1985;35:26–39 [CrossRef]
    [Google Scholar]
  2. Oh YS, Roh DH. Phenylobacterium muchangponense sp. nov., isolated from beach soil, and emended description of the genus Phenylobacterium. Int J Syst Evol Microbiol 2012;62:977–983 [CrossRef][PubMed]
    [Google Scholar]
  3. Khan IU, Hussain F, Habib N, Wadaan MAM, Ahmed I et al. Phenylobacterium deserti sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2017;67:4722–4727 [CrossRef][PubMed]
    [Google Scholar]
  4. Choi GM, Lee SY, Choi KD, Im WT. Phenylobacterium hankyongense sp. nov., isolated from ginseng field soil. Int J Syst Evol Microbiol 2018;68:125–130 [CrossRef][PubMed]
    [Google Scholar]
  5. Kanso S, Patel BK. Phenylobacterium lituiforme sp. nov., a moderately thermophilic bacterium from a subsurface aquifer, and emended description of the genus Phenylobacterium. Int J Syst Evol Microbiol 2004;54:2141–2146 [CrossRef][PubMed]
    [Google Scholar]
  6. Tiago I, Mendes V, Pires C, Morais PV, Verśsimo A. Phenylobacterium falsum sp. nov., an Alphaproteobacterium isolated from a nonsaline alkaline groundwater, and emended description of the genus Phenylobacterium. Syst Appl Microbiol 2005;28:295–302 [CrossRef][PubMed]
    [Google Scholar]
  7. Abraham WR, MacEdo AJ, Lünsdorf H, Fischer R, Pawelczyk S et al. Phylogeny by a polyphasic approach of the order Caulobacterales, proposal of Caulobacter mirabilis sp. nov., Phenylobacterium haematophilum sp. nov. and Phenylobacterium conjunctum sp. nov., and emendation of the genus Phenylobacterium. Int J Syst Evol Microbiol 2008;58:1939–1949 [CrossRef][PubMed]
    [Google Scholar]
  8. Aslam Z, Im WT, Ten LN, Lee ST. Phenylobacterium koreense sp. nov., isolated from South Korea. Int J Syst Evol Microbiol 2005;55:2001–2005 [CrossRef][PubMed]
    [Google Scholar]
  9. Chu C, Yuan C, Liu X, Yao L, Zhu J et al. Phenylobacterium kunshanense sp. nov., isolated from the sludge of a pesticide manufacturing factory. Int J Syst Evol Microbiol 2015;65:325–330 [CrossRef][PubMed]
    [Google Scholar]
  10. Weon HY, Kim BY, Kwon SW, Go SJ, Koo BS et al. Phenylobacterium composti sp. nov., isolated from cotton waste compost in Korea. Int J Syst Evol Microbiol 2008;58:2301–2304 [CrossRef][PubMed]
    [Google Scholar]
  11. Jo JH, Choi GM, Lee SY, Im WT. Phenylobacterium aquaticum sp. nov., isolated from the reservoir of a water purifier. Int J Syst Evol Microbiol 2016;66:3519–3523 [CrossRef][PubMed]
    [Google Scholar]
  12. Farh ME, Kim YJ, Singh P, Hoang VA, Yang DC. Phenylobacterium panacis sp. nov., isolated from the rhizosphere of rusty mountain ginseng. Int J Syst Evol Microbiol 2016;66:2691–2696 [CrossRef][PubMed]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Thompson JD. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef]
    [Google Scholar]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  19. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  21. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52:1049–1070
    [Google Scholar]
  22. Perry LB. Gliding motility in some non-spreading flexibacteria. J Appl Bacteriol 1973;36:227–232 [CrossRef][PubMed]
    [Google Scholar]
  23. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005;55:1149–1153 [CrossRef][PubMed]
    [Google Scholar]
  24. Cappuccino JG, Sherman N. Microbiology: A Laboratory Manual, 6th ed. Menlo Park, CA: Benjamin/Cummings; 2002
    [Google Scholar]
  25. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  26. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25:25–29 [CrossRef][PubMed]
    [Google Scholar]
  27. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007;35:W182–W185 [CrossRef][PubMed]
    [Google Scholar]
  28. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461–466 [CrossRef][PubMed]
    [Google Scholar]
  29. 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 [CrossRef][PubMed]
    [Google Scholar]
  30. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  31. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int J Syst Evol Microbiol 2014;64:316–324 [CrossRef][PubMed]
    [Google Scholar]
  32. 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 [CrossRef]
    [Google Scholar]
  33. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980;48:459–470 [CrossRef]
    [Google Scholar]
  34. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics (Society for Applied Bacteriology Technical Series)vol. 20 New York: Academic Press; 1985; pp.173–199
    [Google Scholar]
  35. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003325
Loading
/content/journal/ijsem/10.1099/ijsem.0.003325
Loading

Data & Media loading...

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