1887

Abstract

A Gram-stain positive, aerobic, irregularly rod-shaped, non-spore-forming bacterium, designated as BN130099, was isolated from farmland soil sampled in Goesan-gun, Chungbuk, Republic of Korea. Phylogenetic analysis of its 16S rRNA gene sequence showed that the strain is closely related to KACC 19192 with 98.11 % similarity. The DNA G+C content of strain BN130099 was 68.84 mol% (draft genome sequence). The genome sequence of BN130099 displayed key enzymes involved in bioremediation of organic pollutants and biosynthetic clusters of saquayamycin. The strain contained -2,6-diaminopimelic acid in the cell-wall peptidoglycan and MK-8(H) as the major respiratory quinone. The predominant fatty acid was iso-C. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. The results of physiological and biochemical characterization allowed the phenotypic differentiation of strain BN130099 from KACC 19192. The strain represents a novel species of the genus , for which we propose the name sp. nov. The type strain is BN130099 (=KCTC 49079=CCTCC AB 2018135).

Funding
This study was supported by the:
  • National Institute of Fisheries Science (Award R2021026)
    • Principle Award Recipient: Dong-GyunKim
  • Ministry of Science and ICT of the Korea Government (Award NRF-2013M3A9A5076601)
    • Principle Award Recipient: Chang-JinKim
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004928
2022-02-14
2024-03-29
Loading full text...

Full text loading...

References

  1. Prauser H. Nocardioides, a new genus of the order Actinomycetales. Int J Syst Evol Microbiol 1976; 26:58–65
    [Google Scholar]
  2. Yoon JH, Park YH. The genus Nocardioides. In The Prokaryotes: Volume 3: Archaea Bacteria: Firmicutes, Actinomycetes New York: Springer; 2006 pp 1099–1113
    [Google Scholar]
  3. Tuo L, Dong YP, Habden X, Liu JM, Guo L. Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil. Int J Syst Evol Microbiol 2015; 65:1604–1610 [View Article] [PubMed]
    [Google Scholar]
  4. Han JH, Kim TS, Joung Y, Kim MN, Shin KS et al. Nocardioides endophyticus sp. nov. and Nocardioides conyzicola sp. nov., isolated from herbaceous plant roots. Int J Syst Evol Microbiol 2013; 63:4730–4734
    [Google Scholar]
  5. Lin SY, Wen CZ, Hameed A, Liu YC, Hsu YH et al. Nocardioides echinoideorum sp. nov., isolated from sea urchins (Tripneustes gratilla). Int J Syst Evol Microbiol 2015; 65:1953–1958
    [Google Scholar]
  6. Zhang H-X, Wang K, Xu Z-X, Chen G-J, Du Z-J. Nocardioides gilvus sp. nov., isolated from namtso lake. Antonie van Leeuwenhoek 2016; 109:1367–1374
    [Google Scholar]
  7. Dastager SG, Lee JC, Ju Y-J, Park DJ, Kim CJ. Nocardioides halotolerans sp. nov., isolated from soil on Bigeum Island, Korea. Syst Appl Microbiol 2008; 31:24–29 [View Article]
    [Google Scholar]
  8. Lee SD, Lee DW. Nocardioides rubroscoriae sp. nov., isolated from volcanic ash. Antonie van Leeuwenhoek 2014; 105:1017–1023 [View Article] [PubMed]
    [Google Scholar]
  9. Lee S, Lee W, Chung HM, Park S. Nocardioides suum sp. nov. isolated from the air environment in an indoor pig farm. J Microbiol 2017; 55:417–420 [View Article] [PubMed]
    [Google Scholar]
  10. Zhang DC, Schumann P, Redzic M, Zhou YG, Liu HC. Nocardioides alpinus sp. nov., a psychrophilic actinomycete isolated from alpine glacier cryoconite. Int J Syst Evol Microbiol 2012; 62:445–450 [View Article] [PubMed]
    [Google Scholar]
  11. Kubota M, Kawahara K, Sekiya K, Uchida T, Hattori Y et al. Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments. Syst Appl Microbiol 2005; 28:165–174 [View Article] [PubMed]
    [Google Scholar]
  12. Sayavedra‐Soto LA, Hamamura N, Liu CW, Kimbrel JA, Chang JH. The membrane‐associated monooxygenase in the butane‐oxidizing Gram‐positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family. Environ Microbiol Rep 2011; 3:390–396 [View Article] [PubMed]
    [Google Scholar]
  13. Arora PK, Srivastava A, Singh VP. Bacterial degradation of nitrophenols and their derivatives. J Hazard Mater 2014; 266:42–59 [View Article] [PubMed]
    [Google Scholar]
  14. Rhee SK, Lee ST, Lee KY, Chung JC. Degradation of pyridine by Nocardioides sp. strain OS4 isolated from the oxic zone of a spent shale column. Can J Microbiol 1997; 43:205–209 [View Article]
    [Google Scholar]
  15. Inoue K, Habe H, Yamane H, Nojiri H. Characterization of novel carbazole catabolism genes from gram-positive carbazole degrader Nocardioides aromaticivorans IC177. Appl Environ Microbiol 2006; 72:3321–3329 [View Article] [PubMed]
    [Google Scholar]
  16. Miyauchi K, Sukda P, Nishida T, Ito E, Matsumoto Y. Isolation of dibenzofuran-degrading bacterium, Nocardioides sp. DF412, and characterization of its dibenzofuran degradation genes. J Biosci Bioeng 2008; 105:628–635 [View Article] [PubMed]
    [Google Scholar]
  17. Iwabuchi T, Harayama S. Biochemical and genetic characterization of trans-2’-carboxybenzalpyruvate hydratase-aldolase from a phenanthrene-degrading Nocardioides strain. J Bacteriol 1998; 180:945–949 [View Article] [PubMed]
    [Google Scholar]
  18. Takagi K, Iwasaki A, Kamei I, Satsuma K, Yoshioka Y et al. Aerobic mineralization of hexachlorobenzene by newly isolated pentachloronitrobenzene-degrading Nocardioides sp. strain PD653. Appl Environ Microbiol 2009; 75:4452–4458 [View Article]
    [Google Scholar]
  19. Liu J, Ma G, Chen T, Hou Y, Yang S. Nicotine-degrading microorganisms and their potential applications. Appl Microbiol Biotechnol 2015; 99:3775–3785 [View Article] [PubMed]
    [Google Scholar]
  20. King GM, Weber CF. Distribution, diversity and ecology of aerobic CO-oxidizing bacteria. Nat Rev Microbiol 2007; 5:107–118 [View Article] [PubMed]
    [Google Scholar]
  21. Dastager SG, Lee JC, Ju Y-J, Park DJ, Kim CJ. Nocardioides koreensis sp. nov., Nocardioides bigeumensis sp. nov. and Nocardioides agariphilus sp. nov., isolated from soil from Bigeum Island, Korea. Int J Syst Evol Microbiol 2008; 58:2292–2296 [View Article]
    [Google Scholar]
  22. Dastager SG, Lee JC, Ju Y-J, Park DJ, Kim CJ. Nocardioides dilutes sp. nov. isolated from soil in Bigeum Island, Korea. Curr Microbiol 2008; 56:569–573 [View Article]
    [Google Scholar]
  23. Dastager SG, Lee JC, Ju Y-J, Park DJ, Kim CJ. Nocardioides islandiensis sp. nov., isolated from soil in Bigeum Island Korea. Antonie Van Leeuwenhoek 2008; 93:401–406 [View Article]
    [Google Scholar]
  24. Dastager SG, Lee JC, Pandey A, Kim CJ. Nocardioides mesophilus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2010; 60:2288–2292 [View Article] [PubMed]
    [Google Scholar]
  25. Dastager SG, Lee J-C, Ju Y-J, Park D-J, Kim C-J. Nocardioides sediminis sp. nov., isolated from a sediment sample. Int J Syst Evol Microbiol 2009; 59:280–284 [View Article] [PubMed]
    [Google Scholar]
  26. Dastager SG, Lee J-C, Ju Y-J, Park D-J, Kim C-J. Nocardioides tritolerans sp. nov., isolated from soil in bigeum island, korea. J Microbiol Biotechnol 2008; 18:1203–1206 [PubMed]
    [Google Scholar]
  27. 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]
  28. 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]
    [Google Scholar]
  29. Lee I, Kim YO, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  30. Yan ZF, Lin P, Li C-T, Kook M, Yi T-H. Nocardioides pelophilus sp. nov., isolated from freshwater mud. Int J Syst Evol Microbiol 2018; 68:1942–1948 [View Article] [PubMed]
    [Google Scholar]
  31. Lu L, Cao M, Wang D, Yuan K, Zhuang W. Nocardioides immobilis sp. nov., isolated from iron mine soil. Int J Syst Evol Microbiol 2017; 67:5230–5234 [View Article] [PubMed]
    [Google Scholar]
  32. Li C, Shi K, Zhang Y, Wang G. Nocardioides silvaticus sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2018; 69:68–73 [View Article] [PubMed]
    [Google Scholar]
  33. Cho CH, Lee JS, DS A, Whon TW, Kim SG. Nocardioides panacisoli sp. nov., isolated from the soil of a ginseng field. Int J Syst Evol Microbiol 2010; 60:387–392 [View Article] [PubMed]
    [Google Scholar]
  34. Khan IU, Hussain F, Habib N, Xiao M, Ahmed I. Nocardioides thalensis sp. nov., isolated from a desert. Int J Syst Evol Microbiol 2017; 67:2848–2852 [View Article] [PubMed]
    [Google Scholar]
  35. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P. 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]
  36. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  37. Ishiyama D, Vujaklija D, Davies J. Novel pathway of salicylate degradation by Streptomyces sp. strain WA46. Appl Environ Microbiol 2004; 70:1297–1306 [View Article] [PubMed]
    [Google Scholar]
  38. Shen X, Liu S. Key enzymes of the protocatechuate branch of the β-ketoadipate pathway for aromatic degradation in Corynebacterium glutamicum. Sci China Life Sci 2005; 48:241–249
    [Google Scholar]
  39. Gunsch CK, Cheng Q, Kinney KA, Szaniszlo PJ, Whitman CP. Identification of a homogentisate-1, 2-dioxygenase gene in the fungus Exophiala lecanii-corni: analysis and implications. Appl Microbiol Biotechnol 2005; 68:405–411 [View Article] [PubMed]
    [Google Scholar]
  40. Fuchs G, Boll M, Heider J. Microbial degradation of aromatic compounds—from one strategy to four. Nat Rev Microbiol 2011; 9:803–816 [View Article] [PubMed]
    [Google Scholar]
  41. Rojo F. Degradation of alkanes by bacteria. Environ Microbiol 2009; 11:2477–2490 [View Article] [PubMed]
    [Google Scholar]
  42. Gao B, Ellis HR. Altered mechanism of the alkanesulfonate FMN reductase with the monooxygenase enzyme. Biochem Biophys Res Commun 2005; 331:1137–1145 [View Article] [PubMed]
    [Google Scholar]
  43. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
    [Google Scholar]
  44. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
    [Google Scholar]
  45. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
    [Google Scholar]
  46. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
    [Google Scholar]
  47. 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 Meth 1984; 2:233–241 [View Article]
    [Google Scholar]
  48. Wang Y, Jiang Y. Chemotaxonomy of Actinobacteria. Dhanasekaran D, Jiang Y. eds In Actinobacteria - Basics and Biotechnological Applications InTech Press; 2016 pp 113–139
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004928
Loading
/content/journal/ijsem/10.1099/ijsem.0.004928
Loading

Data & Media loading...

Supplements

Supplementary material 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