1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 9

sp. nov., isolated from abandoned arsenic-contaminated farmland soil Free

Abstract

A Gram-stain-negative, aerobic, rod-shaped, non-motile, pink-pigmented bacterium, designated NL, was isolated from arsenic-contaminated farmland soil. Strain NL showed the highest 16S rRNA gene sequence similarities with those of 1-3-3-8 (98.9 %), ANT-18 (97.5 %), KBP-30 (97.4 %), Myx2105 (97.1 %) and WW84 (96.4 %). The values of genomic orthoANI and dDDH between strain NL and KCTC 52741 was 90.5 and 41.2 %, respectively, and those between strain NL and KCTC 52166 was 84.4 and 28.4 %, respectively. Strain NL exhibited DNA–DNA hybridisation values of 41.3 and 44.1 % with KCTC 32237 and DSM 11117, respectively. Strain NL had major fatty acids (>10 %) of summed feature 4 (iso-C I and/or anteiso-C B), iso-C and anteiso-C and the predominant polyamine of homospermidine. The only respiratory quinone was menaquinone-7. The polar lipids were phosphatidylethanolamine, phospholipid, three unidentified lipids and two amino lipids. Strain NL had a genome size of 6.04 Mb and the average G+C content of 65.6 %. Compared to the other spp., strain NL is different in polar lipid profile (without aminophospholipid) and leucine arylamidase activity. Based on the data of the polyphasic analysis, it is considered that strain NL represented a novel species of genus , for which the name sp. nov. is proposed. The type strain is NL (=KCTC 62521=CCTCC AB 2018028).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Cytophagaceae and Hymenobacter edaphi
© 2019 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003578
2019-09-01
2023-03-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/9/2921.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003578&mimeType=html&fmt=ahah

References

  1. Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B et al. Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 1998; 21:374–383 [View Article][PubMed]
     [Google Scholar]
  2. Buczolits S, Denner EB, Kämpfer P, Busse HJ. Proposal of Hymenobacter norwichensis sp. nov., classification of 'Taxeobacter ocellatus', 'Taxeobacter gelupurpurascens' and 'Taxeobacter chitinovorans' as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999. Int J Syst Evol Microbiol 2006; 56:2071–2078 [View Article][PubMed]
     [Google Scholar]
  3. Han L, Wu SJ, Qin CY, Zhu YH, Lu ZQ et al. Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter . Antonie van Leeuwenhoek 2014; 105:971–978 [View Article][PubMed]
     [Google Scholar]
  4. Jiang F, Danzeng W, Zhang Y, Zhang Y, Jiang L et al. Hymenobacter rubripertinctus sp. nov., isolated from Antarctic tundra soil. Int J Syst Evol Microbiol 2018; 68:663–668 [View Article][PubMed]
     [Google Scholar]
  5. Sheu SY, Hsieh TY, Kwon SW, Chen WM. Hymenobacter rivuli sp. nov., isolated from a freshwater creek. Int J Syst Evol Microbiol 2018; 68:1220–1226 [View Article][PubMed]
     [Google Scholar]
  6. Liu K, Liu Y, Wang N, Gu Z, Shen L et al. Hymenobacter glacieicola sp. nov., isolated from glacier ice. Int J Syst Evol Microbiol 2016; 66:3793–3798 [View Article][PubMed]
     [Google Scholar]
  7. Subhash Y, Sasikala C, Ramana C. Hymenobacter roseus sp. nov., isolated from sand. Int J Syst Evol Microbiol 2014; 64:4129–4133 [View Article][PubMed]
     [Google Scholar]
  8. Fan X, Wang Q, Zheng S, Shi K, Wang G. Hymenobacter monticola sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2016; 66:812–816 [View Article][PubMed]
     [Google Scholar]
  9. Zhu HZ, Yang L, Muhadesi JB, Wang BJ, Liu SJ. Hymenobacter cavernae sp. nov., isolated from a karst cave. Int J Syst Evol Microbiol 2017; 67:4825–4829 [View Article][PubMed]
     [Google Scholar]
  10. Kim MC, Kim CM, Kang OC, Zhang Y, Liu Z et al. Hymenobacter rutilus sp. nov., isolated from marine sediment in the Arctic. Int J Syst Evol Microbiol 2017; 67:856–861 [View Article][PubMed]
     [Google Scholar]
  11. Lee JJ, Park SJ, Lee YH, Lee SY, Ten LN et al. Hymenobacter aquaticus sp. nov., a radiation-resistant bacterium isolated from a river. Int J Syst Evol Microbiol 2017; 67:1206–1211 [View Article][PubMed]
     [Google Scholar]
  12. Xu JL, Liu QM, Yu HS, Jin FX, Lee ST et al. Hymenobacter daecheongensis sp. nov., isolated from stream sediment. Int J Syst Evol Microbiol 2009; 59:1183–1187 [View Article][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 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  15. 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]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  17. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  19. 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 [View Article][PubMed]
     [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  21. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
     [Google Scholar]
  22. 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]
  23. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 2015; 16:157 [View Article][PubMed]
     [Google Scholar]
  24. 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 [View Article][PubMed]
     [Google Scholar]
  25. 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]
  26. 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 [View Article][PubMed]
     [Google Scholar]
  27. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
     [Google Scholar]
  28. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  29. Hugh R, Leifson E. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 1953; 66:24–26[PubMed]
     [Google Scholar]
  30. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
     [Google Scholar]
  31. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI Technical Note 101, MIDI Inc; 1990
     [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 [View Article]
     [Google Scholar]
  33. Shah HN, Collins MD. Fatty acid and isoprenoid quinone composition in the classification of Bacteroides melaninogenicus and related taxa. J Appl Bacteriol 1980; 48:75–87[PubMed]
     [Google Scholar]
  34. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 1988; 11:1–8 [View Article]
     [Google Scholar]
  35. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997; 47:698–708 [View Article]
     [Google Scholar]
  36. Chen WM, Chen WT, Young CC, Sheu SY. Hymenobacter gummosus sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2017; 67:4728–4735 [View Article][PubMed]
     [Google Scholar]
  37. Ten LN, Han YE, Park KI, Kang IK, Han JS et al. Hymenobacter jeollabukensis sp. nov., isolated from soil. J Microbiol 2018; 56:500–506 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003578
Loading
Hymenobacter edaphi sp. nov., isolated from abandoned arsenic-contaminated farmland soil
Int J Syst Evol Microbiol 69, 2921 (2019); https://doi.org/10.1099/ijsem.0.003578
/content/journal/ijsem/10.1099/ijsem.0.003578
/content/journal/ijsem/10.1099/ijsem.0.003578
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited this month 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