1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 8

sp. nov., an alkalitolerant species isolated from Chilean Altiplano soil, and emended description of (Krasil'nikov et al. 1965) Pridham 1970 Free

Abstract

A polyphasic approach was used for evaluating the taxonomic status of strain HST21 isolated from Salar de Huasco in the Atacama Desert. The results of 16S rRNA gene and multilocus sequence phylogenetic analyses assigned strain HST21 to the genus with DSM 41800and DSM 40150 as its nearest neighbours. Digital DNA–DNA hydridization (dDDH) and average nucleotide identity (ANI) values between the genome sequences of strain HST21 and DSM 41800 (35.6 and 88.2 %) and DSM 40105 (47.2 and 88.8 %) were below the thresholds of 70  and 95–96 % for prokaryotic conspecific assignation. Phenotypic, chemotaxonomic and genetic results distinguished strain HST21 from its closest neighbours. Strain HST21 is characterized by the presence of -diaminopimelic acid in its peptidoglycan layer; glucose and ribose as whole cell sugars; diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, glycophospholipids, unknown lipids and phospholipids as polar lipids; and -C (21.6 %) and -C (20.5 %) as major fatty acids (>15 %). Based on these results, strain HST21 merits recognition as a novel species, for which the name sp. nov. is proposed. The type strain is HST21 DSM 107267=CECT 9647. While analysing the phylogenies of strain HST21, DSM 40420 and DSM 40431 were found to have 100 % 16S rRNA gene sequence similarity with digital DNA–DNA hydridization (dDDH) and average nucleotide identity (ANI) values of 95.3 and 99.4 %, respectively. Therefore, is considered as a later heterotypic synonym of and, consequently, we emend the description of .

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Actinobacteria , Atacama Desert , genome sequence and taxonomy
© 2019 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003525
2019-08-01
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/8/2498.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003525&mimeType=html&fmt=ahah

References

  1. Waksman SA, Henrici AT. The Nomenclature and Classification of the Actinomycetes. J Bacteriol 1943; 46:4[PubMed]
     [Google Scholar]
  2. Watve MG, Tickoo R, Jog MM, Bhole BD. How many antibiotics are produced by the genus Streptomyces?. Arch Microbiol 2001; 176:386–390 [View Article][PubMed]
     [Google Scholar]
  3. Angert ER. Alternatives to binary fission in bacteria. Nat Rev Microbiol 2005; 3:214–224 [View Article][PubMed]
     [Google Scholar]
  4. Kämpfer P. Genus I. Streptomyces . In Whitman W, Goodfellow M, Kämpfer P, Busse H-J, Trujillo M et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 5 New York: Springer; 2012 pp. 1455–1767
     [Google Scholar]
  5. Kroppenstedt R. Fatty acid and menaquinon analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Elsevier Science & Technology Books; 1985 pp. 173–199
     [Google Scholar]
  6. Cortés-Albayay C, Silber J, Imhoff JF, Asenjo JA, Andrews B et al. The polyextreme ecosystem, salar de huasco at the chilean altiplano of the atacama desert houses diverse Streptomyces spp. with promising pharmaceutical potentials. Diversity 2019; 11:69 [View Article]
     [Google Scholar]
  7. Gause GF, Preobrazhenskaya TP, Sveshnikova MA, Terekhova LP, Maximova TS et al. A guide for the determination of actinomycetes. Genera Streptomyces, Streptoverticillium, and Chainia Moscow: URSS, Nauka; 1983
     [Google Scholar]
  8. Kudrina ES. In Gauze G, Preobrazhenskaya TP, Kudrina ES. (editors) Problems of Classification of Actinomycetes-Antagonists Moscow: Publishing house of medical literature, Medgiz; 1957 pp. 1–398
     [Google Scholar]
  9. Pridham TG, Hesseltine CW, Benedict RG. A guide for the classification of streptomycetes according to selected groups; placement of strains in morphological sections. Appl Microbiol 1958; 6:52–79[PubMed]
     [Google Scholar]
  10. Krasil'nikov NA, Korenyako AI, Nikitina NI. Actinomycetes of the yellow group. In Krasil'nikov NA. (editor) Biology of selected groups of Actinomycetes (in Russian) Moscow: Publishing Firm Nauka; 1965 pp. 1–372
     [Google Scholar]
  11. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  12. Vaas LA, Sikorski J, Michael V, Göker M, Klenk HP. Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS One 2012; 7:e34846 [View Article][PubMed]
     [Google Scholar]
  13. Vaas LA, 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]
  14. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
     [Google Scholar]
  15. 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]
  16. 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]
  17. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  18. Cortés-Albayay C, Dorador C, Schumann P, Andrews B A et al. Streptomyces huasconensis sp. nov., an haloalkalitolerant actinobacteria isolated from a high altitude saline wetland at the Chilean Altiplano. Int J Syst Evol Microbiol 2019:
     [Google Scholar]
  19. 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[PubMed]
     [Google Scholar]
  20. 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]
  21. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. 1990
     [Google Scholar]
  22. 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]
  23. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083T), the type strain (U5/41T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2 [View Article][PubMed]
     [Google Scholar]
  24. 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]
  25. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
     [Google Scholar]
  26. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  27. 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]
  28. Goloboff PA, Farris JS, Nixon KC. TNT, a free program for phylogenetic analysis. Cladistics 2008; 24:774–786 [View Article]
     [Google Scholar]
  29. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  30. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  31. Pattengale ND, Alipour M, Bininda-Emonds OR, Moret BM, Stamatakis A. How many bootstrap replicates are necessary?. J Comput Biol 2010; 17:337–354 [View Article][PubMed]
     [Google Scholar]
  32. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods, Version 4.0. Sunderland: Sinauer Associates; 2002
     [Google Scholar]
  33. Tamura T, Hayakawa M, Hatano K. A new genus of the order Actinomycetales, Cryptosporangium gen. nov., with descriptions of Cryptosporangium arvum sp. nov. and Cryptosporangium japonicum sp. nov. Int J Syst Bacteriol 1998; 48 Pt 3:995–1005 [View Article][PubMed]
     [Google Scholar]
  34. Labeda DP, Dunlap CA, Rong X, Huang Y, Doroghazi JR et al. Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis. Antonie van Leeuwenhoek 2017; 110:563–583 [View Article][PubMed]
     [Google Scholar]
  35. Busarakam K, Bull AT, Girard G, Labeda DP, van Wezel GP et al. Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees. Antonie van Leeuwenhoek 2014; 105:849–861 [View Article][PubMed]
     [Google Scholar]
  36. Idris H, Labeda DP, Nouioui I, Castro JF, del Carmen Montero-Calasanz M et al. Streptomyces aridus sp. nov., isolated from a high altitude Atacama Desert soil and emended description of Streptomyces noboritoensis Isono et al. 1957. Antonie van Leeuwenhoek 2017; 110:705–717 [View Article][PubMed]
     [Google Scholar]
  37. Labeda DP. Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS Culture Collection (NRRL) using multi-locus sequence analysis. Antonie van Leeuwenhoek 2016; 109:349–356 [View Article][PubMed]
     [Google Scholar]
  38. 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]
  39. Le Roes-Hill M, Rohland J, Meyers PR, Cowan DA, Burton SG et al. Streptomyces hypolithicus sp. nov., isolated from an Antarctic hypolith community. Int J Syst Evol Microbiol 2009; 59:2032–2035 [View Article][PubMed]
     [Google Scholar]
  40. 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; 9:9 [View Article][PubMed]
     [Google Scholar]
  41. Rong X, Huang Y. Multi-locus sequence analysis. Taking prokaryotic systematics to the next level. Methods Microbiol 2014; 41:221–251
     [Google Scholar]
  42. Rong X, Huang Y. Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol 2012; 35:7–18 [View Article][PubMed]
     [Google Scholar]
  43. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
     [Google Scholar]
  44. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article][PubMed]
     [Google Scholar]
  45. 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]
  46. Lee I, Ouk Kim Y, 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]
  47. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR 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]
  48. 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][PubMed]
     [Google Scholar]
  49. 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]
  50. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003525
Loading
Streptomyces altiplanensis sp. nov., an alkalitolerant species isolated from Chilean Altiplano soil, and emended description of Streptomyces chryseus (Krasil'nikov et al. 1965) Pridham 1970
Int J Syst Evol Microbiol 69, 2498 (2019); https://doi.org/10.1099/ijsem.0.003525
/content/journal/ijsem/10.1099/ijsem.0.003525
/content/journal/ijsem/10.1099/ijsem.0.003525
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

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