1887

Abstract

A new actinobacterium strain, designated BMG 823, was isolated from a limestone sample collected in Tunisia. Its taxonomic position was scrutinized using a polyphasic approach. Colonies of strain BMG 823 were pink orange-coloured, regular and had a moist surface. Cells are Gram-stain-positive, catalase-negative and oxidase-negative. The strain grew at pH 5.5–9, 10–40 °C and in presence of up to 4 % NaCl (w/v). Chemotaxonomically, strain BMG 823 was characterized by cell-wall type III containing -diaminopimelic acid as diamino acid, glucose, ribose and rhamnose as whole-cell sugars, MK-9(H) as predominant menaquinone, and phosphatidylcholine, diphosphadidylglycerol, phosphatidethanolamine, phosphatidylcholine, phosphatidylinositol, unidentified glycolipid, unidentified aminophospholipids and unidentified glycophospholipid as major polar lipids. The fatty acid profile consisted of iso-C and iso-C 9. Phylogenetic trees based on 16S rRNA gene and genome sequences placed strain BMG 823 within the genus and separated it from all type strains of validly published species. Comparison of 16S rRNA gene sequence similarity, digital DNA–DNA hybridization and average nucleotide identity indicated that strain BMG 823 was most closely related to DSM 106127 and BMG 822 with pairwise values well below the species differentiation thresholds. The distinct phenotypic and genotypic features of strain BMG 823 (=DSM 46838=CECT 8881) within the genus warrant its recognition as the type strain for the new species for which we propose the name sp. nov.

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2022-06-23
2024-04-27
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References

  1. Ahrens R, Moll G. Ein neues knospendes Bakterium aus der Ostsee. Archiv Mikrobiol 1970; 70:243–265 [View Article]
    [Google Scholar]
  2. Sneath PHA, McGowan V, Skerman VBD. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980; 30:225–420 [View Article]
    [Google Scholar]
  3. Urzì C, Salamone P, Schumann P, Rohde M, Stackebrandt E. Blastococcus saxobsidens sp. nov., and emended descriptions of the genus Blastococcus Ahrens and Moll 1970 and Blastococcus aggregatus Ahrens and Moll 1970. Int J Syst Evol Microbiol 2004; 54:253–259 [View Article] [PubMed]
    [Google Scholar]
  4. Lee SD. Blastococcus jejuensis sp. nov., an actinomycete from beach sediment, and emended description of the genus Blastococcus Ahrens and Moll 1970. Int J Syst Evol Microbiol 2006; 56:2391–2396 [View Article] [PubMed]
    [Google Scholar]
  5. Hezbri K, Louati M, Nouioui I, Gtari M, Rohde M et al. Blastococcus capsensis sp. nov., isolated from an archaeological Roman pool and emended description of the genus Blastococcus, B. aggregatus, B. saxobsidens, B. jejuensis and B. endophyticus. Int J Syst Evol Microbiol 2016; 66:4864–4872 [View Article]
    [Google Scholar]
  6. Normand P. Geodermatophilaceae fam. nov., a formal description. Int J Syst Evol Microbiol 2006; 56:2277–2278 [View Article] [PubMed]
    [Google Scholar]
  7. Sen A, Daubin V, Abrouk D, Gifford I, Berry AM et al. Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders “Frankiales” and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. Int J Syst Evol Microbiol 2014; 64:3821–3832 [View Article]
    [Google Scholar]
  8. Luedemann GM. Geodermatophilus, a new genus of the Dermatophilaceae (Actinomycetales). J Bacteriol 1968; 96:1848–1858 [View Article] [PubMed]
    [Google Scholar]
  9. Huang J, Li J, Cao M, Liao S, Wang G. Cumulibacter manganitolerans gen. nov., sp. nov., isolated from sludge of a manganese mine. Int J Syst Evol Microbiol 2017; 67:2646–2652 [View Article]
    [Google Scholar]
  10. Montero-Calasanz MDC, Meier-Kolthoff JP, Zhang D-F, Yaramis A, Rohde M et al. Genome-scale data call for a taxonomic rearrangement of Geodermatophilaceae. Front Microbiol 2017; 8:2501 [View Article] [PubMed]
    [Google Scholar]
  11. Mevs U, Stackebrandt E, Schumann P, Gallikowski CA, Hirsch P. Modestobacter multiseptatus gen. nov., sp. nov., a budding actinomycete from soils of the Asgard Range (Transantarctic Mountains). Int J Syst Evol Microbiol 2000; 50 Pt 1:337–346 [View Article] [PubMed]
    [Google Scholar]
  12. Castro JF, Nouioui I, Sangal V, Choi S, Yang S-J et al. Blastococcus atacamensis sp. nov., a novel strain adapted to life in the Yungay core region of the Atacama Desert. Int J Syst Evol Microbiol 2018; 68:2712–2721 [View Article] [PubMed]
    [Google Scholar]
  13. Hezbri K, Nouioui I, Rohde M, Schumann P, Gtari M et al. Blastococcus colisei sp. nov, isolated from an archaeological amphitheatre. Antonie van Leeuwenhoek 2017; 110:339–346 [View Article] [PubMed]
    [Google Scholar]
  14. Yang Z-W, Asem MD, Li X, Li L-Y, Salam N et al. Blastococcus deserti sp. nov., isolated from a desert sample. Arch Microbiol 2019; 201:193–198 [View Article] [PubMed]
    [Google Scholar]
  15. Zhu W-Y, Zhang J-L, Qin Y-L, Xiong Z-J, Zhang D-F et al. Blastococcus endophyticus sp. nov., an actinobacterium isolated from Camptotheca acuminata. Int J Syst Evol Microbiol 2013; 63:3269–3273 [View Article] [PubMed]
    [Google Scholar]
  16. Lee DW, Lee H, Kwon B-O, Khim JS, Yim UH et al. Blastococcus litoris sp. nov., isolated from sea-tidal flat sediment. Int J Syst Evol Microbiol 2018; 68:3435–3440 [View Article] [PubMed]
    [Google Scholar]
  17. Hezbri K, Nouioui I, Rohde M, Spröer C, Schumann P et al. Blastococcus xanthinilyticus sp. nov., isolated from monument. Int J Syst Evol Microbiol 2018; 68:1177–1183 [View Article] [PubMed]
    [Google Scholar]
  18. Urzì C, Brusetti L, Salamone P, Sorlini C, Stackebrandt E et al. Biodiversity of Geodermatophilaceae isolated from altered stones and monuments in the Mediterranean basin. Environ Microbiol 2001; 3:471–479 [View Article] [PubMed]
    [Google Scholar]
  19. Gtari M, Essoussi I, Maaoui R, Sghaier H, Boujmil R et al. Contrasted resistance of stone-dwelling Geodermatophilaceae species to stresses known to give rise to reactive oxygen species. FEMS Microbiol Ecol 2012; 80:566–577 [View Article] [PubMed]
    [Google Scholar]
  20. Essoussi I, Ghodhbane-Gtari F, Amairi H, Sghaier H, Jaouani A et al. Esterase as an enzymatic signature of Geodermatophilaceae adaptability to Sahara desert stones and monuments. J Appl Microbiol 2010; 108:1723–1732 [View Article] [PubMed]
    [Google Scholar]
  21. Reasoner DJ, Blannon JC, Geldreich EE. Rapid seven-hour fecal coliform test. Appl Environ Microbiol 1979; 38:229–236 [View Article] [PubMed]
    [Google Scholar]
  22. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  23. Gregersen T. Rapid method for distinction of gram-negative from Gram-positive bacteria. European J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
    [Google Scholar]
  24. Shungu D, Valiant M, Tutlane V, Weinberg E, Weissberger B et al. GELRITE as an agar substitute in bacteriological media. Appl Environ Microbiol 1983; 46:840–845 [View Article] [PubMed]
    [Google Scholar]
  25. Gordon RE, SMITH MM. Proposed group of characters for the separation of Streptomyces and Nocardia. J Bacteriol 1955; 69:147–150 [View Article] [PubMed]
    [Google Scholar]
  26. Clarke SK. A simplified plate method for detecting gelatine-liquefying bacteria. J Clin Pathol 1953; 6:246–248 [View Article] [PubMed]
    [Google Scholar]
  27. Swan A. The use of a bile-aesculin medium and of Maxted’s technique of Lancefield grouping in the identification of enterococci (group D streptococci). J Clin Pathol 1954; 7:160–163 [View Article] [PubMed]
    [Google Scholar]
  28. Vaas LAI, Sikorski J, Hofner B, Fiebig A, Buddruhs N et al. opm: an R package for analysing OmniLog(R) phenotype microarray data. Bioinformatics 2013; 29:1823–1824 [View Article] [PubMed]
    [Google Scholar]
  29. Vaas LAI, Sikorski J, Michael V, Göker M, Klenk H-P. Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS One 2012; 7:e34846 [View Article] [PubMed]
    [Google Scholar]
  30. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
    [Google Scholar]
  31. 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]
  32. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 2006; 5:2359–2367 [View Article]
    [Google Scholar]
  33. 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]
  34. 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]
  35. 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]
  36. Kroppenstedt R, Goodfellow M. The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillispora and Thermomonospora. In The Prokaryotes vol 3 New York, NY, USA: Springer; 2006 pp 682–724
    [Google Scholar]
  37. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  38. Sasser Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
    [Google Scholar]
  39. Rainey FA, Ward-Rainey N, Kroppenstedt RM, Stackebrandt E. The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Bacteriol 1996; 46:1088–1092 [View Article] [PubMed]
    [Google Scholar]
  40. Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M et al. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol 2014; 12:e1001920 [View Article] [PubMed]
    [Google Scholar]
  41. Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D et al. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). Stand Genomic Sci 2015; 10:86 [View Article] [PubMed]
    [Google Scholar]
  42. Chen I-MA, Markowitz VM, Palaniappan K, Szeto E, Chu K et al. Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. BMC Genomics 2016; 17:307 [View Article] [PubMed]
    [Google Scholar]
  43. Chen I-MA, Markowitz VM, Chu K, Palaniappan K, Szeto E et al. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res 2017; 45:D507–D516 [View Article] [PubMed]
    [Google Scholar]
  44. 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]
    [Google Scholar]
  45. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  46. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
    [Google Scholar]
  47. Goloboff PA, Farris JS, Nixon KC. TNT, a free program for phylogenetic analysis. Cladistics 2008; 24:774–786 [View Article]
    [Google Scholar]
  48. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary?. J Comput Biol 2010; 17:337–354 [View Article] [PubMed]
    [Google Scholar]
  49. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), version 4.0 Sunderland: Sinauer Associates; 2002
    [Google Scholar]
  50. 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]
  51. 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] [PubMed]
    [Google Scholar]
  52. Lefort V, Desper R, Gascuel O. FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
    [Google Scholar]
  53. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  54. Yoon SH, Ha SM, 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]
  55. Yoon SH, Ha SM, 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]
  56. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
    [Google Scholar]
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