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Volume 72, Issue 10

sp. nov., a home for novel actinobacteria isolated from stable foams on activated sludge wastewater treatment plants No Access

Abstract

The taxonomic status of two strains, designated BEN371 and CON9, isolated from stable foams on activated sludge plants was the subject of a polyphasic study which also included the type strains of species and three authenticated strains recovered from such foams. Phylogenetic analyses of 16S rRNA gene sequences showed that these isolates formed a compact cluster suggesting a well-supported lineage together with a second branch containing the strains. A phylogenomic tree based on sequences of 92 core genes extracted from whole genome sequences of the isolates, the strains and type strains confirmed the assignment of the isolates and the strains to separate but closely associated lineages. Average nucleotide index (ANI) and digital DNA–DNA hybridisation (dDDH) similarities showed that BEN371 and CON9 belonged to the same species and had chemotaxonomic and morphological features consistent with their assignment to the genus . The isolates and the strains were distinguished using a range of phenotypic features and by low ANI and dDDH values of 84.2 and 27.0 %, respectively. These data supplemented with associated genome characteristics show that BEN371 and CON9 represent a novel species of the genus . The name proposed for members of this taxon is sp. nov. with isolate CON9 (=DSM 43602=JCM 35249) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): foam , Gordonia , pseudamarae , sludge and water treatment
Funding
This study was supported by the:
  • La Trobe Institute for Molecular Science, La Trobe University
    • Principle Award Recipient: SeviourRobert J.
  • Ministerio de Ciencia, Innovación y Universidades (Award PGC2018-096185-B-I00)
    • Principle Award Recipient: TrujilloMartha E.
© 2022 The Authors
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2022-10-18
2024-05-05
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References

  1. Goodfellow M, Kumar Y, Maldonado LA. Gordonia. Bergey’s Man Syst Archaea Bact 2015; 69:1–29 [View Article]
     [Google Scholar]
  2. 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]
     [Google Scholar]
  3. Tsukamura M. Differentiation of the “Mycobacterium” rhodochrous-group from Nocardiae by beta-galactosidase activity. J Gen Microbiol 1974; 80:553–555 [View Article]
     [Google Scholar]
  4. Goodfellow M, Alderson G. The actinomycete-genus Rhodococcus: a home for the “rhodochrous” complex. J Gen Microbiol 1977; 100:99–122 [View Article]
     [Google Scholar]
  5. Stackebrandt E, Smida J, Collins MD. Evidence of phylogenetic heterogeneity within the genus Rhodococcus: revival of the genus Gordona (Tsukamura). J Gen Appl Microbiol 1988; 34:341–348 [View Article]
     [Google Scholar]
  6. Tsukamura M. Numerical analysis of the taxonomy of Nocardiae and Rhodococci. Microbiol Immunol 1982; 26:1101–1119 [View Article] [PubMed]
     [Google Scholar]
  7. Lechevalier MP, Lechevalier HA. Nocardia amarae sp. nov., an actinomycete common in foaming activated sludge. Int J Syst Bacteriol 1974; 24:278–288 [View Article]
     [Google Scholar]
  8. Klatte S, Rainey FA, Kroppenstedt RM. Transfer of Rhodococcus aichiensis Tsukamura 1982 and Nocardia amarae Lechevalier and Lechevalier 1974 to the genus Gordona as Gordona aichiensis comb. nov. and Gordona amarae comb. nov. Int J Syst Bacteriol 1994; 44:769–773 [View Article]
     [Google Scholar]
  9. Lechevalier H, Lechevalier M, Wyszkowski P, Mariat F. Actinomycetes Found in sewage-treatment plants of the activated sludge type. In Arai T. eds Actinomycetes: He Boundary Microorganisms Tokyo & Singapore: Toppan; 1976 pp 227–247
     [Google Scholar]
  10. Stackebrandt E, Rainey FA, Ward-rainey NL. Proposal for a new hierarchic classification ystem, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
     [Google Scholar]
  11. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:2007 [View Article]
     [Google Scholar]
  12. Kämpfer P, Andersson MA, Rainey FA, Kroppenstedt RM, Salkinoja-Salonen M. Williamsia muralis gen. nov., sp. nov., isolated from the indoor environment of a children’s day care centre. Int J Syst Bacteriol 1999; 49 Pt 2:681–687 [View Article]
     [Google Scholar]
  13. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with tanding in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article]
     [Google Scholar]
  14. Zhang G, Huang Y, Yang J, Lai X-H, Jin D et al. Gordonia jinghuaiqii sp. nov. and Gordonia zhaorongruii sp. nov., isolated from Tibetan Plateau wildlife. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  15. Janke A. Allgemeine technische Mikrobiologie. In Steinkopf T. eds 1. I. Teil: Die Mikroorganismen Dresden & Leipzig: 1924
     [Google Scholar]
  16. Goodfellow M, Jones AL. Corynebacteriales ord. nov. Bergey’s Man Syst Archaea Bact 2015; 1–14: [View Article]
     [Google Scholar]
  17. Arenskötter M, Bröker D, Steinbüchel A. Biology of the metabolically diverse genus Gordonia. Appl Environ Microbiol 2004; 70:3195–3204 [View Article]
     [Google Scholar]
  18. 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]
  19. Sowani H, Kulkarni M, Zinjarde S. An insight into the ecology, diversity and adaptations of Gordonia species. Crit Rev Microbiol 2018; 44:393–413 [View Article] [PubMed]
     [Google Scholar]
  20. Elfalah HWA, Ahmad A, Usup G. Anti-microbial properties of secondary metabolites of arine Gordonia tearrae Extract. JAS 2013; 5:94–101 [View Article]
     [Google Scholar]
  21. Kim YS, Roh SG, Kim SB. Gordonia insulae sp. nov., isolated from an island soil. Int J Syst Evol Microbiol 2020; 70:2079–2083 [View Article] [PubMed]
     [Google Scholar]
  22. Xie Y, Zhou S, Xu Y, Wu W, Xia W et al. Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan. Int J Syst Evol Microbiol 2020; 70:4537–4543 [View Article] [PubMed]
     [Google Scholar]
  23. Raghuram A. Gordonia catheter-related bacteremia and native valve endocarditis treated with ceftriaxone and oral ciprofloxacin- a case report and review of the Literature. INID 2015; 1:1–3 [View Article]
     [Google Scholar]
  24. Sowani H, Kulkarni M, Zinjarde S, Javdekar V. Gordonia and relatedgenera as opportunistic human pathogens causing infections ofskin, soft tissues, and bones. In Clinical Microbiology: Diagnosis, Treatments and Prophylaxis of Infections Academic Press; 2017 pp 105–121 [View Article]
     [Google Scholar]
  25. Tamura T, Saito S, Hamada M, Kang Y, Hoshino Y et al. Gordonia crocea sp.nov. Int J Syst Evol Microbiol 2020; 70:3718–3723 [View Article]
     [Google Scholar]
  26. Batinovic S, Rose JJA, Ratcliffe J, Seviour RJ, Petrovski S. Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams. Nat Microbiol 2021; 6:703–711 [View Article]
     [Google Scholar]
  27. Gupta RS, Lo B, Son J. Phylogenomics and comparative genomic studies robustly support division of the genus Mycobacterium into an emended genus Mycobacterium and four novel genera. Front Microbiol 2018; 9:67 [View Article]
     [Google Scholar]
  28. Männle D, McKinnie SMK, Mantri SS, Steinke K, Lu Z et al. Comparative genomics and Metabolomics in the genus Nocardia. mSystems 2020; 5:e00125-20 [View Article]
     [Google Scholar]
  29. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The clustalx windows interface: flexible strategies for multiple sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acid Res 1997; 22:4673–4680 [View Article]
     [Google Scholar]
  30. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article] [PubMed]
     [Google Scholar]
  33. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article]
     [Google Scholar]
  34. 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]
     [Google Scholar]
  35. 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 2022; 50:D801–D807 [View Article]
     [Google Scholar]
  36. Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 2016; 32:2847–2849 [View Article]
     [Google Scholar]
  37. Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O. PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data. PLoS One 2013; 8:e77302 [View Article]
     [Google Scholar]
  38. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
     [Google Scholar]
  39. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  40. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
     [Google Scholar]
  41. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [View Article]
     [Google Scholar]
  42. Gordon RE, Mihm JM. Identification of Nocardia caviae (Erikson) nov. comb.. Ann NY Acad Sci 1962; 98:628–636 [View Article]
     [Google Scholar]
  43. MacFaddin JF. Media for Isolation-cultivation-identification-maintenance of Medical Bacteria Baltimore, MD: Williams & Wilkins; 1985
     [Google Scholar]
  44. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article]
     [Google Scholar]
  45. Christensen WB. Urea decomposition as a means of differentiating proteus and paracolon cultures from each other and from Salmonella and Shigella Types 1. J Bacteriol 1946; 52:461–466 [View Article]
     [Google Scholar]
  46. Sierra G. A simple method for the detection of lipolytic activity of micro-organisms and some observations on the influence of the contact between cells and fatty substrates. Antonie van Leeuwenhoek 1957; 23:15–22 [View Article]
     [Google Scholar]
  47. Ferreira L, Sánchez-Juanes F, García-Fraile P, Rivas R, Mateos PF et al. MALDI-TOF mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family Rhizobiaceae. PLoS One 2011; 6:e20223 [View Article]
     [Google Scholar]
  48. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article]
     [Google Scholar]
  49. Minnikin DE, Abdolrahimzadeh H, Baddiley J. The occurrence of phosphatidylethanolamine and glycosyl diglycerides in thermophilic bacilli. J Gen Microbiol 1974; 83:415–418 [View Article]
     [Google Scholar]
  50. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982; 16:584–586 [View Article]
     [Google Scholar]
  51. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  52. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Technical Note, MIDI Inc 1990; 101:
     [Google Scholar]
  53. 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]
     [Google Scholar]
  54. Suriyachadkun C, Ngaemthao W, Pujchakarn T, Chunhametha S. Gordonia asplenii sp. nov., isolated from humic soil on bird’s nest fern (Asplenium nidus L.). Int J Syst Evol Microbiol 2019; 71: [View Article]
     [Google Scholar]
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Gordonia pseudamarae sp. nov., a home for novel actinobacteria isolated from stable foams on activated sludge wastewater treatment plants
Int J Syst Evol Microbiol 72, 005547 (2022); https://doi.org/10.1099/ijsem.0.005547
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