1887

Abstract

The taxonomic status of a strain, designated H13, isolated from a high altitude Atacama Desert soil, was established by using a polyphasic approach. The strain was found to have chemotaxonomic, cultural and morphological characteristics consistent with its classification within the genus and formed a well-supported clade in the phylogenomic tree together with the type strains of , and . Strain H13 was distinguished from its closest relatives by low average nucleotide identity (93.2–94.9 %) and DNA–DNA hybridization (52.5–62.4 %) values calculated from draft genome assemblies and by a range of phenotypic properties. On the basis of these results, it is proposed that the isolate be assigned to the genus as sp. nov. with isolate H13 (=CGMCC 4.7585=KCTC 49249) as the type strain.

Funding
This study was supported by the:
  • Wen-Jun Li , Natural Science Foundation of Guangdong Province , (Award 2016A030312003)
  • Nimaichand Salam , National Natural Science Foundation of China , (Award 31850410475)
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2020-04-22
2020-06-02
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References

  1. Meyer J. Nocardiopsis, a new genus of the order Actinomycetales . Int J Syst Bacteriol 1976; 26:487–493 [CrossRef]
    [Google Scholar]
  2. 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 [CrossRef]
    [Google Scholar]
  3. Goodfellow M, Order XV et al. Streptosporangiales ord. nov. In Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K et al. (editors) Bergey's Manual of Systematic Bacteriology, 2nd edition: The Actinobacteria Part A and B Springer; 2012 pp 1805–1806
    [Google Scholar]
  4. Hozzein WN, Trujillo ME et al. Nocardiopsis . In Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K et al. (editors) Bergey's Manual of Systematics Bacteriology 2nd Edition: The Actinobacteria, Part A and B Springer; 2012 pp 1891–1906
    [Google Scholar]
  5. Bennur T, Kumar AR, Zinjarde S, Javdekar V. Nocardiopsis species: Incidence, ecological roles and adaptations. Microbiol Res 2015; 174:33–47 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  6. Bouras N, Meklat A, Zitouni A, Mathieu F, Schumann P et al. Nocardiopsis algeriensis sp. nov., an alkalitolerant actinomycete isolated from Saharan soil. Antonie van Leeuwenhoek 2015; 107:313–320 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  7. Jiang C-L, L-H X. Actinomycete diversity in unusual habitats. In Jiang C-L, L-H Xu. (editors) Actinomycetes Research Yunnan: Yunnan University Press; 1993 pp 259–270
    [Google Scholar]
  8. Zitouni A, Boudjella H, Lamari L, Badji B, Mathieu F et al. Nocardiopsis and Saccharothrix genera in Saharan soils in Algeria: isolation, biological activities and partial characterization of antibiotics. Res Microbiol 2005; 156:984–993 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  9. Meklat A, Sabaou N, Zitouni A, Mathieu F, Lebrihi A. Isolation, taxonomy, and antagonistic properties of halophilic actinomycetes in Saharan soils of Algeria. Appl Environ Microbiol 2011; 77:6710–6714 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  10. Li W-J, Kroppenstedt RM, Wang D, Tang S-K, Lee J-C et al. Five novel species of the genus Nocardiopsis isolated from hypersaline soils and emended description of Nocardiopsis salina Li et al. 2004. Int J Syst Evol Microbiol 2006; 56:1089–1096 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  11. Hamedi J, Mohammadipanah F, Ventosa A. Systematic and biotechnological aspects of halophilic and halotolerant actinomycetes. Extremophiles 2013; 17:1–13 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  12. Bennur T, Ravi Kumar A, Zinjarde SS, Javdekar V. Nocardiopsis species: a potential source of bioactive compounds. J Appl Microbiol 2016; 120:1–16 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  13. Ajello L, Brown J, Macdonald E, Head E. Actinomycetoma caused by Nocardiopsis dassonvillei . Arch Dermatol 1987; 123:426 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  14. Mordarska H, Zakrzewska-Czerwiñska J, Paściak M, Szponar B, Rowiñski S, Rare RS. Rare, suppurative pulmonary infection caused by Nocardiopsis dassonvillei recognized by glycolipid markers. FEMS Immun Med Microbiol 1998; 21:47–55 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  15. Yassin AF, Rainey FA, Burghardt J, Gierth D, Ungerechts J et al. Description of Nocardiopsis synnemataformans sp. nov., elevation of Nocardiopsis alba subsp. prasina to Nocardiopsis prasina comb. nov., and designation of Nocardiopsis antarctica and Nocardiopsis alborubida as later subjective synonyms of Nocardiopsis dassonvillei . Int J Syst Bacteriol 1997; 47:983–988 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  16. Evtushenko LI, Taran VV, Akimov VN, Kroppenstedt RM, Tiedje JM et al. Nocardiopsis tropica sp. nov., Nocardiopsis trehalosi sp. nov., nom. rev. and Nocardiopsis dassonvillei subsp. albirubida subsp. nov., comb. nov. Int J Syst Evol Microbiol 2000; 50:73–81 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  17. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  18. Grund E, Kroppenstedt RM. Chemotaxonomy and numerical taxonomy of the genus Nocardiopsis Meyer 1976. Int J Syst Bacteriol 1990; 40:5–11 [CrossRef]
    [Google Scholar]
  19. Okoro CK, Brown R, Jones AL, Andrews BA, Asenjo JA et al. Diversity of culturable actinomycetes in hyper-arid soils of the Atacama desert, Chile. Antonie van Leeuwenhoek 2009; 95:121–133 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  20. Senechkin IV, Speksnijder AGCL, Semenov AM, van Bruggen AHC, van Overbeek LS. Isolation and partial characterization of bacterial strains on low organic carbon medium from soils fertilized with different organic amendments. Microb Ecol 2010; 60:829–839 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  21. Vickers JC, Williams ST. An assessment of plate inoculation procedures for the enumeration and isolation of soil streptomycetes. Microbios Lett 1987; 35:113–117
    [Google Scholar]
  22. Brocq-Rousseu D. Sur un Streptothrix. Rev Gen Bot 1904; 16:219–230
    [Google Scholar]
  23. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [CrossRef]
    [Google Scholar]
  24. Ming H, Yin Y-R, Li S, Nie G-X, Yu T-T et al. Thermus caliditerrae sp. nov., a novel thermophilic species isolated from a geothermal area. Int J Syst Evol Microbiol 2014; 64:650–656 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  25. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  26. Uchida K, Kudo T, Suzuki K-I, 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  27. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  28. Tamaoka J. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Met Enzymol 1986; 123:251–256 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  29. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-Layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188:221–233 [CrossRef]
    [Google Scholar]
  30. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [CrossRef]
    [Google Scholar]
  31. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [CrossRef]
    [Google Scholar]
  32. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids [database on the Internet]. http://www.microbialid.com/PDF/TechNote_101.pdf ; 2001
  33. Asem MD, Salam N, Zheng W, Liao L-H, Zhang X-T et al. Vitreimonas flagellata gen. nov., sp. nov., a novel member of the family Hyphomonadaceae isolated from an activated sludge sample. Int J Syst Evol Microbiol 2020 05 Mar 2020 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  34. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  35. Leifson E. Atlas of Bacterial Flagellation New York: Academic Press; 1960
    [Google Scholar]
  36. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  37. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  38. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: American Society of Microbiology; 2007 pp 330–393
    [Google Scholar]
  39. Li H-W, Zhi X-Y, Yao J-C, Zhou Y, Tang S-K et al. Comparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability. PLoS One 2013; 8:e61528 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  40. Harrison P, Strulo B. SPADES - a process algebra for discrete event simulation. J Logic Comput 2000; 10:3–42 [CrossRef]
    [Google Scholar]
  41. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  42. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 2010; 11:119 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  43. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  44. Potter SC, Luciani A, Eddy SR, Park Y, Lopez R et al. HMMER web server: 2018 update. Nucleic Acids Res 2018; 46:W200–W204 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  45. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016; 44:D286–D293 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  46. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  47. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  48. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  49. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MegaX: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  50. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  51. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  52. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  53. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  54. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  55. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  56. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  57. Letunic I, Bork P. Interactive tree of life (iTOL) V4: recent updates and new developments. Nucleic Acids Res 2019; 47:W256–W259 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  58. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  59. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  60. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Brenner DJ, Grimont PAD et al. Report of the ad hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [CrossRef]
    [Google Scholar]
  61. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  62. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  63. 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 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  64. Idris H. Actinobacterial Diversity in Atacama Desert Habitats as a Road Map to Biodiscovery UK; PhD thesis: Newcastle University; 2016
    [Google Scholar]
  65. Baltz RH. Gifted microbes for genome mining and natural product discovery. J Ind Microbiol Biotechnol 2017; 44:573–588 [CrossRef][PubMed][PubMed]
    [Google Scholar]
  66. Bull AT, Goodfellow M. Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 M of bioprospecting campaigns. Microbiology 2019; 165:1252–1264 [CrossRef][PubMed][PubMed]
    [Google Scholar]
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