1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 5

sp. nov., isolated from farmland soil Free

Abstract

A Gram-stain-negative, rod-shaped bacterium, strain H23, was isolated from farmland soil sampled in Enshi City, Hubei Province, PR China. The isolate grew optimally at 28–32 °C, pH 8.0 and with 0.5 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, strain H23 belonged to the genus with the highest degree of 16S rRNA gene sequence similarity to Y4 (97.41 %). The DNA G+C content was 65.88 mol%. The average nucleotide identity and the Genome-to-Genome Distance Calculator results also showed low relatedness (below 95 and 70 %, respectively) between strain H23 and type strains in the genus . Ubiquinone-8 was the predominant quinone. The major fatty acids were iso-C, iso-C, iso-C and iso-C ω9. Polar lipids were dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unidentified phospholipids. Low digital DNA–DNA hybridization values, as well as physiological and biochemical differences, such as no casein hydrolysis, being catalase-negative, and tesing positive for cystine arylamidase, α-chymotrypsin and -acetyl-β-glucosaminidase, could distinguish strain H23 from its closely related species. Strain H23 is considered to represent a novel species in the genus , for which the name sp. nov. is proposed, with strain H23 (=CCTCC AB 2019255=KCTC 72593) as the type strain.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): farmland soil , Luteimonas gilva and novel bacterium
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award No. 31970095)
    • Principle Award Recipient: Mingshun Li
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004197
2020-05-05
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/5/3462.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004197&mimeType=html&fmt=ahah

References

  1. Finkmann W, Altendorf K, Stackebrandt E, Lipski A. Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. Int J Syst Evol Microbiol 2000; 50 Pt 1:273–282 [View Article][PubMed][PubMed]
     [Google Scholar]
  2. Baik KS, Park SC, Kim MS, Kim EM, Park C et al. Luteimonas marina sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2008; 58:2904–2908 [View Article][PubMed][PubMed]
     [Google Scholar]
  3. Chou J-H, Cho N-T, Arun AB, Young C-C, Chen W-M. Luteimonas aquatica sp. nov., isolated from fresh water from Southern Taiwan. Int J Syst Evol Microbiol 2008; 58:2051–2055 [View Article][PubMed][PubMed]
     [Google Scholar]
  4. Wu G, Liu Y, Li Q, Du H, You J et al. Luteimonas huabeiensis sp. nov., isolated from stratum water. Int J Syst Evol Microbiol 2013; 63:3352–3357 [View Article][PubMed][PubMed]
     [Google Scholar]
  5. Ten LN, Jung H-M, Im W-T, Yoo S-A, Oh H-M et al. Lysobacter panaciterrae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2009; 59:958–963 [View Article][PubMed][PubMed]
     [Google Scholar]
  6. Zhang D-C, Liu H-C, Xin Y-H, Zhou Y-G, Schinner F et al. Luteimonas terricola sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 2010; 60:1581–1584 [View Article][PubMed][PubMed]
     [Google Scholar]
  7. Rani P, Mukherjee U, Verma H, Kamra K, Lal R. Luteimonas tolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2016; 66:1851–1856 [View Article][PubMed][PubMed]
     [Google Scholar]
  8. Romanenko LA, Tanaka N, Svetashev VI, Kurilenko VV, Mikhailov VV. Luteimonas vadosa sp. nov., isolated from seashore sediment. Int J Syst Evol Microbiol 2013; 63:1261–1266 [View Article][PubMed][PubMed]
     [Google Scholar]
  9. Roh SW, Kim K-H, Nam Y-D, Chang H-W, Kim M-S et al. Luteimonas aestuarii sp. nov., isolated from tidal flat sediment. J Microbiol 2008; 46:525–529 [View Article][PubMed][PubMed]
     [Google Scholar]
  10. Fan X, Yu T, Li Z, Zhang X-H. Luteimonas abyssi sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2014; 64:668–674 [View Article][PubMed][PubMed]
     [Google Scholar]
  11. Young C-C, Kämpfer P, Chen W-M, Yen W-S, Arun AB et al. Luteimonas composti sp. nov., a moderately thermophilic bacterium isolated from food waste. Int J Syst Evol Microbiol 2007; 57:741–744 [View Article][PubMed][PubMed]
     [Google Scholar]
  12. Ngo HTT, Yin CS. Luteimonas terrae sp. nov., isolated from rhizosphere soil of Radix ophiopogonis. Int J Syst Evol Microbiol 2016; 66:1920–1925 [View Article][PubMed][PubMed]
     [Google Scholar]
  13. Cheng J, Zhang M-Y, Wang W-X, Manikprabhu D, Salam N et al. Luteimonas notoginsengisoli sp. nov., isolated from rhizosphere. Int J Syst Evol Microbiol 2016; 66:946–950 [View Article][PubMed][PubMed]
     [Google Scholar]
  14. Zhao G-Y, Shao F, Zhang M, Zhang X-J, Wang J-Y, Dai MX et al. Luteimonas rhizosphaerae sp. nov., isolated from the rhizosphere of Triticum aestivum L. Int J Syst Evol Microbiol 2018; 68:1197–1203 [View Article][PubMed][PubMed]
     [Google Scholar]
  15. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed][PubMed]
     [Google Scholar]
  16. Kim O-S, Cho Y-J, Lee K, Yoon S-H, 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][PubMed]
     [Google Scholar]
  17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed][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 [View Article][PubMed][PubMed]
     [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed][PubMed]
     [Google Scholar]
  20. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed][PubMed]
     [Google Scholar]
  21. 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][PubMed]
     [Google Scholar]
  22. 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][PubMed]
     [Google Scholar]
  23. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed][PubMed]
     [Google Scholar]
  24. Claus D. A standardized gram staining procedure. World J Microbiol Biotechnol 1992; 8:451–452 [View Article][PubMed][PubMed]
     [Google Scholar]
  25. Smibert RM, Krieg NR. Phenotypic characterization. in methods for general and molecular bacteriology. American Society for Microbiology 1994607–654
     [Google Scholar]
  26. Chung YC, Kobayashi T, Kanai H, Akiba T, Kudo T. Purification and properties of extracellular amylase from the hyperthermophilic archaeon Thermococcus profundus DT5432. Appl Environ Microbiol 1995; 61:1502–1506 [View Article][PubMed][PubMed]
     [Google Scholar]
  27. 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]
  28. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  29. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  30. 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 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004197
Loading
Luteimonas gilva sp. nov., isolated from farmland soil
Int J Syst Evol Microbiol 70, 3462 (2020); https://doi.org/10.1099/ijsem.0.004197
/content/journal/ijsem/10.1099/ijsem.0.004197
/content/journal/ijsem/10.1099/ijsem.0.004197
Loading

Data & Media loading...

Supplements

Supplementary material 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