1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 10

Sphingobacterium haloxyli sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems in Kumtag desert Free

Abstract

A Gram-stain-negative, non-motile, aerobic, non-spore-forming, rod-shaped, bacterial strain, designated 5JN-11, was isolated from Haloxylonammodendron stems in Kumtag desert, Xinjiang province, China. Strain 5JN-11 grew at salinities of 0–6 % (w/v; optimum 0–2 %), a pH of 7.0–9.0 (pH 7.0–8.0) and temperatures of 20–42 °C (28–30 °C). Based on 16S rRNA gene sequences, the strain was designated a member of the genus Sphingobacterium and the phylogenetic analysis showed that strain 5JN-11 shared the highest similarity to Sphingobacterium gobiense H7, followed by Sphingobacterium chuzhouense DH-5 and Sphingobacterium arenae H-12. The unfinished draft genome of strain 5JN-11 was 4.69 Mb. The G+C content of strain 5JN-11 was 42.8 mol%. The average nucleotide identity to S. gobiense H7 was 90.5 %. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. On the basis of phenotypic, genotypic and phylogenetic evidence, strain 5JN-11 represents a novel species in the genus Sphingobacterium , for which the name Sphingobacterium haloxyli sp. nov. is proposed. The type strain is 5JN-11 (=ACCC 60072=KCTC 62457).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): endophytic bacterium , Haloxylon ammodendron , Kumtag desert , Sphingobacterium and Sphingobacterium haloxyli
© 2018 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002982
2018-08-29
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/10/3279.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002982&mimeType=html&fmt=ahah

References

  1. Yabuuchi E, Kaneko T, Yano I, Moss CW, Miyoshi N. Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting Gram-negative rods in CDC groups IIK-2 and IIb. Int J Syst Bacteriol 1983; 33:580–598 [View Article]
     [Google Scholar]
  2. Zhao P, Zhou Z, Chen M, Lin W, Zhang W et al. Sphingobacterium gobiense sp. nov., isolated from soil of the Gobi desert. Int J Syst Evol Microbiol 2014; 64:3931–3935 [View Article][PubMed]
     [Google Scholar]
  3. Jiang S, Chen M, Su S, Yang M, Li A et al. Sphingobacterium arenae sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol 2014; 64:248–253 [View Article][PubMed]
     [Google Scholar]
  4. Wang X, Zhang CF, Yu X, Hu G, Yang HX et al. Sphingobacterium chuzhouense sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2016; 66:4968–4974 [View Article][PubMed]
     [Google Scholar]
  5. Schmidt VS, Wenning M, Scherer S. Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment. Int J Syst Evol Microbiol 2012; 62:1506–1511 [View Article][PubMed]
     [Google Scholar]
  6. Lee DH, Hur JS, Kahng HY. Sphingobacterium cladoniae sp. nov., isolated from lichen, Cladonia sp., and emended description of Sphingobacterium siyangense. Int J Syst Evol Microbiol 2013; 63:755–760 [View Article][PubMed]
     [Google Scholar]
  7. Liu J, Yang LL, Xu CK, Xi JQ, Yang FX et al. Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco. Int J Syst Evol Microbiol 2012; 62:1809–1813 [View Article][PubMed]
     [Google Scholar]
  8. Yabe S, Aiba Y, Sakai Y, Hazaka M, Kawahara K et al. Sphingobacterium thermophilum sp. nov., of the phylum Bacteroidetes, isolated from compost. Int J Syst Evol Microbiol 2013; 63:1584–1588 [View Article][PubMed]
     [Google Scholar]
  9. Albert RA, Waas NE, Pavlons SC, Pearson JL, Ketelboeter L et al. Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 2013; 63:952–958 [View Article][PubMed]
     [Google Scholar]
  10. Sun LN, Zhang J, Chen Q, He J, Li SP. Sphingobacterium caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2013; 63:2260–2264 [View Article][PubMed]
     [Google Scholar]
  11. Zhang J, Zheng JW, Cho BC, Hwang CY, Fang C et al. Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge. Int J Syst Evol Microbiol 2012; 62:683–687 [View Article][PubMed]
     [Google Scholar]
  12. Holmes B, Owen RJ, Hollis DG. Flavobacterium spiritivorum, a new species isolated from human clinical specimens. Int J Syst Bacteriol 1982; 32:157–165 [View Article]
     [Google Scholar]
  13. Marques A, Pires C, Moreira H, Rangel A, Castro PML. Assessment of the plant growth promotion abilities of six bacterial isolates using Zea mays as indicator plant. Soil Biology and Biochemistry 2010; 42:1229–1235 [View Article]
     [Google Scholar]
  14. Ali A, Khalid R, Ali S, Akram Z, Hayat R. Characterization of plant growth promoting rhizobacteria isolated from chickpea (Cicer arietinum). Br Microbiol Res J 2015; 6:32–40 [View Article]
     [Google Scholar]
  15. Ahmed I, Ehsan M, Sin Y, Paek J, Khalid N et al. Sphingobacterium pakistanensis sp. nov., a novel plant growth promoting rhizobacteria isolated from rhizosphere of Vigna mungo. Antonie van Leeuwenhoek 2014; 105:325–333 [View Article][PubMed]
     [Google Scholar]
  16. Takeuchi M, Yokota A. Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum comb. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum. J Gen Appl Microbiol 1992; 38:465–482 [View Article]
     [Google Scholar]
  17. Long Y, Zhang J, Tian X, Wu S, Zhang Q et al. De novo assembly of the desert tree Haloxylon ammodendron (C. A. Mey.) based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. BMC Genomics 2014; 15:1111–1121 [View Article][PubMed]
     [Google Scholar]
  18. Liu L, Li L, Song Z, Wang S, Zhang J et al. Parapedobacter deserti sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems. Int J Syst Evol Microbiol 2017; 67:2148–2152 [View Article][PubMed]
     [Google Scholar]
  19. Dong XZ, Cai MY. Determination of biochemical properties. In Manual for the Systematic Identification of General Bacteria Beijing: Science Press; 2001
     [Google Scholar]
  20. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991
     [Google Scholar]
  21. 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]
  22. 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]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  24. 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]
  25. 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]
  26. 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]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  28. Li B, Yang X, Tan H, Ke B, He D et al. Vibrio parahaemolyticus O4:K8 forms a potential predominant clone in southern China as detected by whole-genome sequence analysis. Int J Food Microbiol 2017; 244:90–95 [View Article][PubMed]
     [Google Scholar]
  29. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015; 43:6761–6771 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–73 [View Article][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 [View Article]
     [Google Scholar]
  33. Collins MD. Isoprenoid quinone analysis in bacterial classification and identification. In Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 26–287
     [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  35. Wei W, Zhou Y, Wang X, Huang X, Lai R. Sphingobacterium anhuiense sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2008; 58:2098–2101 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002982
Loading
Sphingobacterium haloxyli sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems in Kumtag desert
Int J Syst Evol Microbiol 68, 3279 (2018); https://doi.org/10.1099/ijsem.0.002982
/content/journal/ijsem/10.1099/ijsem.0.002982
/content/journal/ijsem/10.1099/ijsem.0.002982
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