1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 7

sp. nov., isolated from the surface of an Antarctic brown macroalga Free

Abstract

Two moderately psychrophilic actinobacterial strains, designated AU-G6 and AU-A3.2, isolated from the surface of an Antarctic macroalga, (Bory) Skottsberg, was taxonomically characterized based on a polyphasic investigation. The two strains had nearly identical 16S rRNA gene sequences and formed a distinct phyletic line within the genus of the family . They were phylogenetically close to JCM 14717, JCM 14545 and DSM 45510, with 16S rRNA gene sequence similarities of 97.77, 97.20 and 97.19 %, respectively. Phylogenomic analysis based on the whole genome data supported that strain AU-G6 was distantly related to the species. The isolates shared a range of phenotypic markers typical of members of the genus , but also had a range of cultural, physiological and biochemical characteristics that separated them from related species. The isolates showed growth only in media supplemented with salt, indicating their marine origin. The cell wall of the isolates contained -diaminopimelic acid, and arabinose and galactose were detected as diagnostic sugars (type IV). The main menaquinone was MK-9(H). The main polar lipids were phosphatidylethanolamine, hydroxy-phosphotidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol (type II). The fatty acid type was 3c. The combined genotypic and phenotypic data indicated that the two isolates represent a novel species of the genus . The name proposed for this species is sp. nov., with type strain AU-G6 (=CGMCC 4.7351=NBRC 112404).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Amycolatopsis , Amycolatopsis antarctica sp. nov. , Antarctic , marine macroalga and polyphasic taxonomy
© 2018 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002844
2018-07-01
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/7/2348.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002844&mimeType=html&fmt=ahah

References

  1. Goecke F, Thiel V, Wiese J, Labes A, Imhoff JF. Algae as an important environment for bacteria–phylogenetic relationships among new bacterial species isolated from algae. Phycologia 2013; 52:14–24 [View Article]
     [Google Scholar]
  2. Hollants J, Leliaert F, de Clerck O, Willems A. What we can learn from sushi: a review on seaweed-bacterial associations. FEMS Microbiol Ecol 2013; 83:1–16 [View Article][PubMed]
     [Google Scholar]
  3. Lechevalier MP, Lechevalier HA. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443
     [Google Scholar]
  4. Warwick S, Bowen T, McVeigh H, Embley TM. A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia. Int J Syst Bacteriol 1994; 44:293–299 [View Article][PubMed]
     [Google Scholar]
  5. Labeda DP, Goodfellow M, Chun J, Zhi XY, Li WJ. Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae Embley et al. 1989 emend. Zhi et al. 2009. Int J Syst Evol Microbiol 2011; 61:1259–1264 [View Article][PubMed]
     [Google Scholar]
  6. Labeda DP, Goodfellow M. Family I. Pseudonocardiaceae Embley, Smida and Stackebrandt 1989, 205VP emend. Labeda, Goodfellow, Chun, Zhi and Li 2010. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki K et al. (editors) Bergey's Manual of Systematic Bacteriology New York: Springer; 2012 pp. 1302–1445
     [Google Scholar]
  7. Kim SB, Goodfellow M. Reclassification of Amycolatopsis rugosa Lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov. Int J Syst Bacteriol 1999; 49:507–512 [View Article][PubMed]
     [Google Scholar]
  8. Tan GY, Ward AC, Goodfellow M. Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Syst Appl Microbiol 2006; 29:557–569 [View Article][PubMed]
     [Google Scholar]
  9. Chun J, Kim SB, Oh YK, Seong CN, Lee DH et al. Amycolatopsis thermoflava sp. nov., a novel soil actinomycete from Hainan Island, China. Int J Syst Bacteriol 1999; 49:1369–1373 [View Article][PubMed]
     [Google Scholar]
  10. Saintpierre-Bonaccio D, Amir H, Pineau R, Tan GY, Goodfellow M. Amycolatopsis plumensis sp. nov., a novel bioactive actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil. Int J Syst Evol Microbiol 2005; 55:2057–2061 [View Article][PubMed]
     [Google Scholar]
  11. Lee SD. Amycolatopsis jejuensis sp. nov. and Amycolatopsis halotolerans sp. nov., novel actinomycetes isolated from a natural cave. Int J Syst Evol Microbiol 2006; 56:549–553 [View Article][PubMed]
     [Google Scholar]
  12. Lee SD, Kinkel LL, Samac DA. Amycolatopsis minnesotensis sp. nov., isolated from a prairie soil. Int J Syst Evol Microbiol 2006; 56:265–269 [View Article][PubMed]
     [Google Scholar]
  13. Klykleung N, Tanasupawat S, Pittayakhajonwut P, Ohkuma M, Kudo T. Amycolatopsis stemonae sp. nov., isolated from a Thai medicinal plant. Int J Syst Evol Microbiol 2015; 65:3894–3899 [View Article][PubMed]
     [Google Scholar]
  14. Miao Q, Qin S, Bian GK, Yuan B, Xing K et al. Amycolatopsis endophytica sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L. Antonie van Leeuwenhoek 2011; 100:333–339 [View Article][PubMed]
     [Google Scholar]
  15. Xing K, Liu W, Zhang YJ, Bian GK, Zhang WD et al. Amycolatopsis jiangsuensis sp. nov., a novel endophytic actinomycete isolated from a coastal plant in Jiangsu, China. Antonie van Leeuwenhoek 2013; 103:433–439 [View Article][PubMed]
     [Google Scholar]
  16. Bian J, Li Y, Wang J, Song FH, Liu M et al. Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment. Int J Syst Evol Microbiol 2009; 59:477–481 [View Article][PubMed]
     [Google Scholar]
  17. Zhang G, Wang L, Li J, Zhou Y. Amycolatopsis albispora sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2016; 66:3860–3864 [View Article][PubMed]
     [Google Scholar]
  18. Leiva S, Alvarado P, Huang Y, Wang J, Garrido I. Diversity of pigmented Gram-positive bacteria associated with marine macroalgae from Antarctica. FEMS Microbiol Lett 2015; 362:fnv206 [View Article][PubMed]
     [Google Scholar]
  19. 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]
  20. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  21. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5:113 [View Article][PubMed]
     [Google Scholar]
  22. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  23. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 1978; 75:4801–4805 [View Article][PubMed]
     [Google Scholar]
  24. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article][PubMed]
     [Google Scholar]
  25. Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007; 56:564–577 [View Article][PubMed]
     [Google Scholar]
  26. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  27. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416
     [Google Scholar]
  28. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376[PubMed]
     [Google Scholar]
  29. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article][PubMed]
     [Google Scholar]
  30. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. (editor) Mammalian Protein Metabolism New York: Academic Press; 1969 pp. 21–132
     [Google Scholar]
  31. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  32. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340
     [Google Scholar]
  33. Kelly KL. Inter-Society Color Council – National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  34. Hucker GJ. A new modification and application of the gram stain. J Bacteriol 1921; 6:395–397[PubMed]
     [Google Scholar]
  35. Gregersen T. Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biot 1978; 5:123–127
     [Google Scholar]
  36. Kuester E, Williams ST. Production of hydrogen sulfide by streptomycetes and methods for its detection. Appl Microbiol 1964; 12:46–52[PubMed]
     [Google Scholar]
  37. Frazier NC. A method for the detection of changes in gelatin due to bacteria. J Infect Dis 1926; 39:302–309
     [Google Scholar]
  38. Hsu SC, Lockwood JL. Powdered chitin agar as a selective medium for enumeration of actinomycetes in water and soil. Appl Microbiol 1975; 29:422–426[PubMed]
     [Google Scholar]
  39. Gordon RE, Barnett DA, Handerhan JE, Pang CH. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63
     [Google Scholar]
  40. 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][PubMed]
     [Google Scholar]
  41. Kämpfer P, Kroppenstedt RM, Dott W. A numerical classification of the genera Streptomyces and Streptoverticillium using miniaturized physiological tests. J Gen Microbiol 1991; 137:1831–1891
     [Google Scholar]
  42. Groth I, Tan GY, González JM, Laiz L, Carlsohn MR et al. Amycolatopsis nigrescens sp. nov., an actinomycete isolated from a Roman catacomb. Int J Syst Evol Microbiol 2007; 57:513–519 [View Article][PubMed]
     [Google Scholar]
  43. Camas M, Sahin N, Sazak A, Spröer C, Klenk HP. Amycolatopsis magusensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2013; 63:1254–1260 [View Article][PubMed]
     [Google Scholar]
  44. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
     [Google Scholar]
  45. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322
     [Google Scholar]
  46. Tang SK, Wang Y, Chen Y, Lou K, Cao LL et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol 2009; 59:2025–2031 [View Article][PubMed]
     [Google Scholar]
  47. 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
     [Google Scholar]
  48. 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]
  49. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367
     [Google Scholar]
  50. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  51. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005
     [Google Scholar]
  52. Uchida K, Aida K. An improved method for the glycolate test for simple identification of the acyl type of bacterial cell walls. J Gen Appl Microbiol 1984; 30:131–134
     [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][PubMed]
     [Google Scholar]
  54. Marmur J. A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 1961; 3:208–218
     [Google Scholar]
  55. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
     [Google Scholar]
  56. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article][PubMed]
     [Google Scholar]
  57. 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]
  58. Wu M, Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol 2008; 9:R151 [View Article][PubMed]
     [Google Scholar]
  59. Gonzalez JM, Saiz-Jimenez C. A simple fluorimetric method for the estimation of DNA–DNA relatedness between closely related microorganisms by thermal denaturation temperatures. Extremophiles 2005; 9:75–79 [View Article][PubMed]
     [Google Scholar]
  60. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
     [Google Scholar]
  61. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  62. 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]
  63. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  64. Lechevalier MP, Prauser H, Labeda DP, Ruan J-S. Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Bacteriol 1986; 36:29–37
     [Google Scholar]
  65. Yassin AF, Haggenei B, Budzikiewicz H, Schaal KP. Fatty-acid and polar lipid-composition of the genus Amycolatopsis - application of fast-atom-bombardment mass-spectrometry to structure-analysis of underivatized phospholipids. Int J Syst Bacteriol 1993; 43:414–420
     [Google Scholar]
  66. Lechevalier MP, Bièvre CD, Lechevalier HA. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 1977; 5:249–260
     [Google Scholar]
  67. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics (SAB Technical Series no 20) London: Academic Press; 1985 pp. 173–199
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002844
Loading
Amycolatopsis antarctica sp. nov., isolated from the surface of an Antarctic brown macroalga
Int J Syst Evol Microbiol 68, 2348 (2018); https://doi.org/10.1099/ijsem.0.002844
/content/journal/ijsem/10.1099/ijsem.0.002844
/content/journal/ijsem/10.1099/ijsem.0.002844
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