1887

Abstract

A Gram-stain-positive, facultative aerobic, oxidase-negative, catalase-positive, non-sporulating, and non-motile bacterium, which degraded benzophenone-3, was isolated from stream sediment collected in the Republic of Korea and designated as strain S2-17. Cells of this strain were rod-shaped during the early growth phase but became coccoid after the late exponential growth phase. Bacterial growth was observed at 15–37 °C (optimum, 25–30 °C) and pH 6.0–9.5 (optimum, pH 7.5–8.5) and in the presence of 0–9.0 % (w/v) NaCl (optimum, 0–1.0 %). Menaquinone-8 (H) was the sole isoprenoid quinone, and C, C 8, summed feature 3 (comprising C 7/C 6) and C 9 were the major fatty acids. The cell wall of strain S2-17 contained -diaminopimelic acid, and arabinose, galactose and mycolic acid were found in whole-cell hydrolysates, suggesting a chemotype IV cell wall. The G+C content of the genome was 65.6 mol%. Phylogenetic analyses revealed that strain S2-17 formed a phyletic lineage within the genus and was most closely related to DSM 44719 (99.2 % 16S rRNA gene sequence similarity). Average nucleotide identity and digital DNA–DNA hybridization values between strain S2-17 and DSM 44719 were 82.6 and 26.5 %, respectively, indicating differences between the species. Based on its phenotypic, chemotaxonomic and molecular features, strain S2-17 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is S2-17 (=KACC 19281=JCM 32046).

Funding
This study was supported by the:
  • Nakdonggang National Institute of Biological Resources (Award NNIBR202202107)
    • Principle Award Recipient: HyunMi Jin
  • Chung-Ang University
    • Principle Award Recipient: WoonheeBaek
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005433
2022-06-15
2022-06-25
Loading full text...

Full text loading...

References

  1. Zopf W. Über ausscheidung von fettfarbstoffen (lipochromen) seitens gewisser spaltpilze. Ber Dtsch Bot Ges 1891; 9:22–28
    [Google Scholar]
  2. Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021; 71:005056 [View Article]
    [Google Scholar]
  3. Jones AL, Goodfellow M. Genus IV. Rhodococcus (Zopf 1891) emend. Goodfellow, Alderson and Chun 1998a. In Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K. et al. eds Bergey’s Manual of Systematic Bacteriology, 2nd Edn, Vol. 5, The Actinobacteria, Part A New York: Springer; 2012 pp 437–464
    [Google Scholar]
  4. Zhang D, Su Z, Li L, Tang W. Rhodococcus spongiicola sp. nov. and Rhodococcus xishaensis sp. nov., from marine sponges. Int J Syst Evol Microbiol 2021; 71:004863 [View Article]
    [Google Scholar]
  5. Lee SD, Kim IS, Kim YJ, Joung Y. Rhodococcus cavernicola sp. nov., isolated from a cave, and Rhodococcus degradans is a later heterosynonym of Rhodococcus qingshengii. Int J Syst Evol Microbiol 2020; 70:4409–4415 [View Article]
    [Google Scholar]
  6. Kämpfer P, Dott W, Martin K, Glaeser SP. Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov. Int J Syst Evol Microbiol 2014; 64:755–761 [View Article] [PubMed]
    [Google Scholar]
  7. Li Y, Kawamura Y, Fujiwara N, Naka T, Liu H et al. Rothia aeria sp. nov., Rhodococcus baikonurensis sp. nov. and Arthrobacter russicus sp. nov., isolated from air in the Russian space laboratory Mir. Int J Syst Evol Microbiol 2004; 54:827–835 [View Article]
    [Google Scholar]
  8. Ramaprasad EVV, Mahidhara G, Sasikala C, Ramana CV. Rhodococcus electrodiphilus sp. nov., a marine electro active actinobacterium isolated from coral reef. Int J Syst Evol Microbiol 2018; 68:2644–2649 [View Article] [PubMed]
    [Google Scholar]
  9. Chaudhary DK, Kim J. Rhodococcus olei sp. nov., with the ability to degrade petroleum oil, isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:1749–1756 [View Article] [PubMed]
    [Google Scholar]
  10. Goodfellow M, Jones AL, Maldonado LA, Salanitro J. Rhodococcus aetherivorans sp. nov., a new species that contains methyl t-butyl ether-degrading actinomycetes. Syst Appl Microbiol 2004; 27:61–65 [View Article] [PubMed]
    [Google Scholar]
  11. Kim D, Choi KY, Yoo M, Zylstra GJ, Kim E. Biotechnological potential of Rhodococcus biodegradative pathways. J Microbiol Biotechnol 2018; 28:1037–1051 [View Article] [PubMed]
    [Google Scholar]
  12. Martínková L, Uhnáková B, Pátek M, Nesvera J, Kren V. Biodegradation potential of the genus Rhodococcus. Environ Int 2009; 35:162–177 [View Article] [PubMed]
    [Google Scholar]
  13. Cappelletti M, Presentato A, Piacenza E, Firrincieli A, Turner RJ et al. Biotechnology of Rhodococcus for the production of valuable compounds. Appl Microbiol Biotechnol 2020; 104:8567–8594 [View Article] [PubMed]
    [Google Scholar]
  14. Vázquez-Boland JA, Meijer WG. The pathogenic actinobacterium Rhodococcus equi: what’s in a name?. Mol Microbiol 2019; 112:1–15 [View Article] [PubMed]
    [Google Scholar]
  15. Dhaouadi S, Mougou AH, Rhouma A. The plant pathogen Rhodococcus fascians. History, disease symptomatology, host range, pathogenesis and plant–pathogen interaction. Ann Appl Biol 2020; 177:4–15 [View Article]
    [Google Scholar]
  16. Stanier RY, Palleroni NJ, Doudoroff M. The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 1966; 43:159–271 [View Article] [PubMed]
    [Google Scholar]
  17. Baek JH, Kim KH, Lee Y, Jeong SE, Jin HM et al. Elucidating the biodegradation pathway and catabolic genes of benzophenone-3 in Rhodococcus sp. S2-17. Environ Pollut 2022; 299:118890 [View Article] [PubMed]
    [Google Scholar]
  18. Kim KR, Kim KH, Khan SA, Kim HM, Han DM et al. Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil. J Microbiol 2021; 59:709–718
    [Google Scholar]
  19. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  20. Nawrocki EP, Eddy SR. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 2007; 3:e56 [View Article] [PubMed]
    [Google Scholar]
  21. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  22. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  23. Kim J, Na S-I, Kim D, Chun J. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609–615 [View Article] [PubMed]
    [Google Scholar]
  24. Lee I, Ouk Kim Y, Park S-C, 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]
  25. 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]
  26. 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]
  27. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  28. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–5 [View Article] [PubMed]
    [Google Scholar]
  29. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
    [Google Scholar]
  30. Lee Y, Lee Y, Jeon CO. Biodegradation of naphthalene, BTEX, and aliphatic hydrocarbons by Paraburkholderia aromaticivorans BN5 isolated from petroleum-contaminated soil. Sci Rep 2019; 9:1–13 [View Article] [PubMed]
    [Google Scholar]
  31. Abbasian F, Lockington R, Mallavarapu M, Naidu R. A comprehensive review of aliphatic hydrocarbon biodegradation by bacteria. Appl Biochem Biotechnol 2015; 176:670–699 [View Article] [PubMed]
    [Google Scholar]
  32. Varjani SJ, Gnansounou E, Pandey A. Comprehensive review on toxicity of persistent organic pollutants from petroleum refinery waste and their degradation by microorganisms. Chemosphere 2017; 188:280–291 [View Article] [PubMed]
    [Google Scholar]
  33. Gomori G. Preparation of buffers for use in enzyme studies. In Colowick SP, Kaplan NO. eds Method in Enzymology New York: Academic Press; 1955 pp 138–146
    [Google Scholar]
  34. Bernardet J-F, Nakagawa Y, Holmes B. 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]
  35. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67
    [Google Scholar]
  36. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  37. Takeuchi M, Hatano K, Sedlácek I, Pácová Z. Rhodococcus jostii sp. nov., isolated from a medieval grave. Int J Syst Evol Microbiol 2002; 52:409–413 [View Article] [PubMed]
    [Google Scholar]
  38. Yoon JH, Cho YG, Kang SS, Kim SB, Lee ST et al. Rhodococcus koreensis sp. nov., a 2,4-dinitrophenol-degrading bacterium. Int J Syst Evol Microbiol 2000; 50 Pt 3:1193–1201 [View Article] [PubMed]
    [Google Scholar]
  39. Helmke E, Weyland H. Rhodococcus marinonascens sp. nov., an actinomycete from the sea. Int J Syst Bacteriol 1984; 34:127–138 [View Article]
    [Google Scholar]
  40. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  41. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  42. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer J. eds Actinomycete Taxonomy (Special Publication No.6) Arlington, VA: Society for Industrial Microbiology; 1980 pp 227–291
    [Google Scholar]
  43. 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]
  44. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromat A 1980; 188:221–233 [View Article]
    [Google Scholar]
  45. Uchida K, Kudo T, Suzuki KI, Nakase T. A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 1999; 45:49–56 [View Article] [PubMed]
    [Google Scholar]
  46. Goodfellow M. Genus Rhodococcus Zopf 1891, 28AL. In Sneath PHA, Mair NS, ME S, Holt JG. eds Bergey’s Manual of Systematic Bacteriology vol 2 Baltimore: Williams & Wilkins; 1986 pp 1472–1481
    [Google Scholar]
  47. Lechevalier MP, Lechevalier HA. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005433
Loading
/content/journal/ijsem/10.1099/ijsem.0.005433
Loading

Data & Media loading...

Supplements

Supplementary material 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