1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 11

sp. nov., a tellurite- and selenite-resistant bacterium isolated from the sediment of an acid mine drainage stream No Access

Abstract

A polyphasic taxonomic study was carried out on strain TSed Te1, isolated from sediment of a stream contaminated with acid drainage from a coal mine. The bacterium forms pink-pigmented colonies and has a rod–coccus growth cycle, which also includes some coryneform arrangements. This bacterium is capable of growing in the presence of up to 750 μg ml tellurite and 5000 μg ml selenite, reducing each to elemental form. Nearly complete 16S rRNA gene sequence analysis associated the strain with , with 99.5 and 99.3 % similarity to and , respectively. Computation of the average nucleotide identity and digital DNA–DNA hybridization comparisons with the closest phylogenetic neighbour of TSed Te1 revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The dominant fatty acids were C, C, C and tuberculostearic acid. The DNA G+C content was 67.6 mol%. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside, while MK-9(H) was the only menaquinone found. Mycolic acids of C–C were present. Whole-cell hydrolysates contained -diaminopimelic acid along with arabinose and galactose as the major cell-wall sugars. On the basis of the results obtained in this study, the bacterium was assigned to the genus and represents a new species with the name sp. nov. The type strain is TSed Te1 (=NRRL B-65678=DSM 114093).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): acid mine drainage , Gordonia , Gordonia metallireducens , metal(loid) oxyanion , metal(loid) resistance , selenite and tellurite
Funding
This study was supported by the:
  • Slippery Rock University Department of Biology
    • Principle Award Recipient: NotApplicable
  • Slippery Rock University Student Research Grant
    • Principle Award Recipient: DavidGrimm
  • Slippery Rock University Faculty Student Research Grant
    • Principle Award Recipient: ChrisMaltman
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006176
2023-11-22
2024-05-08
Loading full text...

Full text loading...

References

  1. Tsukamura M. Proposal of a new genus, Gordona, for slightly acid-fast organisms occurring in sputa of patients with pulmonary disease and in soil. J Gen Microbiol 1971; 68:15–26 [View Article] [PubMed]
     [Google Scholar]
  2. Goodfellow M, Alderson G, Chun J. Rhodococcal systematics: problems and developments. Antonie van Leeuwenhoek 1998; 74:1–12 [View Article] [PubMed]
     [Google Scholar]
  3. Stackebrandt E, Rainey FA, Ward-rainey NL. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
     [Google Scholar]
  4. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  5. Goodfellow M. The family Nocardiaceae. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. eds The Prokaryotes Berlin, Heidelberg: Springer; [View Article]
     [Google Scholar]
  6. Arenskötter M, Bröker D, Steinbüchel A. Biology of the metabolically diverse genus Gordonia. Appl Environ Microbiol 2004; 70:3195–3204 [View Article] [PubMed]
     [Google Scholar]
  7. Lemmer H, Kroppensted RM. Chemotaxonomy and physiology of some actinomycetes isolated from scumming activated sludge. Syst Appl Microbiol 1984; 5:124–135 [View Article]
     [Google Scholar]
  8. Bendinger B, Rainey FA, Kroppenstedt RM, Moormann M, Klatte S. Gordona hydrophobica sp. nov., isolated from biofilters for waste gas treatment. Int J Syst Evol Microbiol 1995; 45:544–548 [View Article]
     [Google Scholar]
  9. Klatte S, Kroppenstedt RM, Schumann P, Altendorf K, Rainey FA. Gordona hirsuta sp. nov. Int J Syst Bacteriol 1996; 46:876–880 [View Article] [PubMed]
     [Google Scholar]
  10. Kummer C, Schumann P, Stackebrandt E. Gordonia alkanivorans sp. nov., isolated from tar-contaminated soil. Int J Syst Bacteriol 1999; 49:1513–1522 [View Article] [PubMed]
     [Google Scholar]
  11. Chatterjee S, Dutta TK. Metabolism of butyl benzyl phthalate by Gordonia sp. strain MTCC 4818. Biochem Biophys Res Comm 2003; 309:36–43 [View Article] [PubMed]
     [Google Scholar]
  12. Linos A, Berekaa MM, Steinbüchel A, Kim KK, Sproer C et al. Gordonia westfalica sp. nov., a novel rubber-degrading actinomycete. Int J Syst Evol Microbiol 2002; 52:1133–1139 [View Article] [PubMed]
     [Google Scholar]
  13. Yoon JH, Lee JJ, Kang SS, Takeuchi M, Shin YK et al. Gordonia nitida sp. nov., a bacterium that degrades 3-ethylpyridine and 3-methylpyridine. Int J Syst Evol Microbiol 2000; 50:1203–1210 [View Article] [PubMed]
     [Google Scholar]
  14. Zhang H, Lin Z, Liu B, Wang G, Weng L et al. Bioremediation of di-(2-ethylhexyl) phthalate contaminated red soil by Gordonia terrae RL-JC02: Characterization, metabolic pathway and kinetics. Sci Total Environ 2020; 733:139138 [View Article] [PubMed]
     [Google Scholar]
  15. Jung CM, Carr M, Blakeney GA, Indest KJ. Enhanced plasmid-mediated bioaugmentation of RDX-contaminated matrices in column studies using donor strain Gordonia sp. KTR9. J Ind Microbiol Biotechnol 2019; 46:1273–1281 [View Article] [PubMed]
     [Google Scholar]
  16. Kong X, Jin D, Tai X, Yu H, Duan G et al. Bioremediation of dibutyl phthalate in a simulated agricultural ecosystem by Gordonia sp. strain QH-11 and the microbial ecological effects in soil. Sci Total Environ 2019; 667:691–700 [View Article] [PubMed]
     [Google Scholar]
  17. Gurbanov R, Tunçer S, Mingu S, Severcan F, Gozen AG. Methylation, sugar puckering and Z-form status of DNA from a heavy metal-acclimated freshwater Gordonia sp. J Photochem Photobiol B Biol 2019; 198:111580 [View Article]
     [Google Scholar]
  18. Bröker D, Arenskötter M, Legatzki A, Nies DH, Steinbüchel A. Characterization of the 101-kilobase-pair megaplasmid pKB1, isolated from the rubber-degrading bacterium Gordonia westfalica Kb1. J Bacteriol 2004; 186:212–225 [View Article] [PubMed]
     [Google Scholar]
  19. Nahurira R, Wang J, Yan Y, Jia Y, Fan S et al. In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2. AMB Express 2019; 9:1–13 [View Article] [PubMed]
     [Google Scholar]
  20. Wang X, Jin D, Zhou L, Wu L, An W et al. Draft genome sequence of Gordonia alkanivorans strain CGMCC6845, a halotolerant hydrocarbon-degrading bacterium. Genome Announc 2014; 2:e01274-13 [View Article] [PubMed]
     [Google Scholar]
  21. Vivod R, Oetermann S, Hiessl S, Gutsche S, Remmers N et al. Oligo(cis-1,4-isoprene) aldehyde-oxidizing dehydrogenases of the rubber-degrading bacterium Gordonia polyisoprenivorans VH2. Appl Microbiol Biotechnol 2017; 101:7945–7960 [View Article] [PubMed]
     [Google Scholar]
  22. Drzyzga O. The strengths and weaknesses of Gordonia: a review of an emerging genus with increasing biotechnological potential. Crit Rev Microbiol 2012; 38:300–316 [View Article] [PubMed]
     [Google Scholar]
  23. Denholm C, Johnson D, Taylor W, Shearer R, Danehy T et al. Case study: “The Jennings System” - over a decade of successful passive treatment. Proc Amer Soc Mining Reclaim 2010; 2010:154–169 [View Article]
     [Google Scholar]
  24. Yurkov VV, Van Gemerden H. Abundance and salt tolerance of obligately aerobic, phototrophic bacteria in a marine microbial mat. Neth J Sea Res 1993; 31:57–62 [View Article]
     [Google Scholar]
  25. Jordan EO, Caldwell ME, Reiter D. Bacterial motility. J Bacteriol 1934; 27:165–174 [View Article] [PubMed]
     [Google Scholar]
  26. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [PubMed]
     [Google Scholar]
  27. Holt JG, Krieg NR, Sneath PHA. Bergey’s Manual of Determinative Bacterology Baltimore, MD: Williams and Wilkins Co; 1994
     [Google Scholar]
  28. Sasser M. Technical Note 101: Identification of bacteria by gas chromatography of cellular fatty acids; 2001 https://gcms.cz/labrulez-bucket-strapi-h3hsga3/paper/MIS_Technote_101.pdf
  29. 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]
  30. Minnikin DE, Alshamaony L, Goodfellow M. Differentiation of Mycobacterium, Nocardia, and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. J Gen Microbiol 1975; 88:200–204 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976; 72:248–254 [View Article] [PubMed]
     [Google Scholar]
  33. Chen WP, Kuo TT. A simple and rapid method for the preparation of Gram-negative bacterial genomic DNA. Nucleic Acids Res 1993; 21:2260 [View Article] [PubMed]
     [Google Scholar]
  34. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  35. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:1–10 [View Article] [PubMed]
     [Google Scholar]
  36. Yoon S-H, Ha S-M, 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]
  37. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2021; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  38. Brandão PF, Maldonado LA, Ward AC, Bull AT, Goodfellow M. Gordonia namibiensis sp. nov., a novel nitrile metabolising actinomycete recovered from an African sand. Syst Appl Microbiol 2001; 24:510–515 [View Article] [PubMed]
     [Google Scholar]
  39. 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]
  40. de Menezes CBA, Afonso RS, de Souza WR, Parma M, de Melo IS et al. Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp. Antonie van Leeuwenhoek 2016; 109:297–303 [View Article] [PubMed]
     [Google Scholar]
  41. Goodfellow M, Kumar Y, Maldonado L. Gordonia. In Goodfellow M, Kampfer P, Busse HJ, Trujillo M, Suzuki K. eds Bergey’s Manual of Systematics of Archaea and Bacteria, 2nd. edn vol 5 John Wiley & Sons; 2012 pp 419–434
     [Google Scholar]
  42. Yurkov V, Jappe J, Vermeglio A. Tellurite resistance and reduction by obligately aerobic photosynthetic bacteria. Appl Environ Microbiol 1996; 62:4195–4198 [View Article] [PubMed]
     [Google Scholar]
  43. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Evol Microbiol 1977; 27:104–117 [View Article]
     [Google Scholar]
  44. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Evol Syst Microbiol 1970; 20:435–443 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006176
Loading
Gordonia metallireducens sp. nov., a tellurite- and selenite-resistant bacterium isolated from the sediment of an acid mine drainage stream
Int J Syst Evol Microbiol 73, 006176 (2023); https://doi.org/10.1099/ijsem.0.006176
/content/journal/ijsem/10.1099/ijsem.0.006176
/content/journal/ijsem/10.1099/ijsem.0.006176
Loading

Data & Media loading...

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