Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 73, Issue 3

sp. nov., a novel marine actinobacterium isolated from seawater in the upper gulf of Thailand No Access

Abstract

An actinobacterium strain, SW21, was isolated from seawater collected in the upper Gulf of Thailand. Cells were Gram-stain-positive, aerobic and rod-shaped. Growth was observed from 15 to 37 °C and at pH 6–8. Maximum NaCl for growth was 14 % (w/v). -Diaminopimelic acid, arabinose, galactose, glucose, rhamnose and ribose were detected in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside were detected as the phospholipids in the cells. The major menaquinones were MK-9(H) and MK-7(H). The major cellular fatty acids were C, C 9, C and C10-methyl (TBSA). The 16S rRNA gene sequence data supported the assignment of strain SW21 to the genus and showed that KCTC 49383 (98.7 %) was the closest relative. Moreover, the average nucleotide identity- (85.5 %) and digital DNA–DNA hybridization (30.7 %) values between strain SW21 and its closest neighbour were below the threshold values for delineation of a novel species. The combination of genotypic and phenotypic data indicated that strain SW21 is representative of novel species of the genus . The name sp. nov. is proposed for strain SW21. The type strain is SW21 (=TBRC 15691=NBRC 115558).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , actinomycete , Gordonia , Gulf of Thailand and whole-genome sequence analysis
Funding
This study was supported by the:
  • The School of Science, King Mongkut’s Institute of Technology Ladkrabang (Award CW-1-2564-M-001)
    • Principle Award Recipient: RawiratPansomsuay
  • The National Science, Research and Innovation Fund (NSRF) (Award RE-KRIS/FF65/23)
    • Principle Award Recipient: ChittiThawai
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005804
2023-03-24
2025-03-19
Loading full text...

Full text loading...

References

  1. 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] [PubMed]
     [Google Scholar]
  2. Goodfellow M, Kumar Y, Maldonado LA. Genus Gordonia. In Kampfer P, Busse H-J, Trujillo ME, Suzuki K-I. eds Bergey’s Manual of Systematic BacteriologyThe Actinobacteria vol 2 Springer: New York; 2012 pp 419–435
     [Google Scholar]
  3. 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]
  4. Riesco R, Rose JJA, Batinovic S, Petrovski S, Sánchez-Juanes F et al. Gordonia pseudamarae sp. nov., a home for novel actinobacteria isolated from stable foams on activated sludge wastewater treatment plants. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  5. Tamura T, Saito S, Hamada M, Kang Y, Hoshino Y et al. Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant. Int J Syst Evol Microbiol 2020; 70:3718–3723 [View Article]
     [Google Scholar]
  6. Muangham S, Lipun K, Thamchaipenet A, Matsumoto A, Duangmal K. Gordonia oryzae sp. nov., isolated from rice plant stems (Oryza sativa L.). Int J Syst Evol Microbiol 2019; 69:1621–1627 [View Article] [PubMed]
     [Google Scholar]
  7. 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]
  8. Sangkanu S, Suriyachadkun C, Phongpaichit S. Gordonia sediminis sp. nov., an actinomycete isolated from mangrove sediment. Int J Syst Evol Microbiol 2019; 69:1814–1820 [View Article] [PubMed]
     [Google Scholar]
  9. de Menezes CBA, Afonso RS, de Souza WR, Parma M, de Melo IS et al. Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp. Antonie van Leeuwenhoek 2016; 109:297–303 [View Article]
     [Google Scholar]
  10. Selim MSM, Abdelhamid SA, Mohamed SS. Secondary metabolites and biodiversity of actinomycetes. J Genet Eng Biotechnol 2021; 19:72 [View Article]
     [Google Scholar]
  11. Buangrab K, Sutthacheep M, Yeemin T, Harunari E, Igarashi Y et al. Streptomyces corallincola and Kineosporia corallincola sp. nov., two new coral-derived marine actinobacteria. Int J Syst Evol Microbiol 2022; 72:005249 [View Article] [PubMed]
     [Google Scholar]
  12. Phongsopitanun W, Suwanborirux K, Tanasupawat S. Identification and antimicrobial activity of Streptomyces strains from Thai mangrove sediment. Thai J Pharm Sci 2014; 38:49–56
     [Google Scholar]
  13. Manivasagan P, Kang K-H, Sivakumar K, Li-Chan ECY, Oh H-M et al. Marine actinobacteria: an important source of bioactive natural products. Environ Toxicol Pharmacol 2014; 38:172–188 [View Article] [PubMed]
     [Google Scholar]
  14. Harunari E, Doyo H, Phongsopitanun W, Tanasupawat S, Sutthacheep M et al. 1-(6-Methylsalicyloyl)glycerol from stony coral-derived Micromonospora sp. J Antibiot 2022; 75:005788 [View Article]
     [Google Scholar]
  15. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  16. Zhang J, Zhang L. Improvement of an isolation medium for actinomycetes. MAS 2011; 5:124–127 [View Article]
     [Google Scholar]
  17. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  18. Tamaoka J. Determination of DNA base composition. In Goodfellow M, O’Donnell AG. eds Chemical Methods in Prokaryotic Systematics Chichester: John Wiley and Sons; 1994 pp 463–470
     [Google Scholar]
  19. Nakajima Y, Kitpreechavanich V, Suzuki K, Kudo T. Microbispora corallina sp. nov., a new species of the genus Microbispora isolated from Thai soil. Int J Syst Bacteriol 1999; 49 Pt 4:1761–1767 [View Article] [PubMed]
     [Google Scholar]
  20. 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 [View Article] [PubMed]
     [Google Scholar]
  21. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  22. 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]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  24. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  25. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
     [Google Scholar]
  26. 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]
     [Google Scholar]
  27. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
     [Google Scholar]
  28. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  29. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  30. 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]
  31. Kim M, Oh H-S, Park S-C, 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]
  32. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article]
     [Google Scholar]
  33. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:9–75 [View Article] [PubMed]
     [Google Scholar]
  34. 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:D206–14 [View Article]
     [Google Scholar]
  35. 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 [View Article] [PubMed]
     [Google Scholar]
  36. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
     [Google Scholar]
  37. 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]
  38. 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 [View Article] [PubMed]
     [Google Scholar]
  39. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
     [Google Scholar]
  40. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article]
     [Google Scholar]
  41. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
     [Google Scholar]
  42. 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]
  43. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article] [PubMed]
     [Google Scholar]
  44. Pohl P, Saparov SM, Borgnia MJ, Agre P. Highly selective water channel activity measured by voltage clamp: analysis of planar lipid bilayers reconstituted with purified AqpZ. Proc Natl Acad Sci 2001; 98:9624–9629 [View Article]
     [Google Scholar]
  45. Smits SHJ, Höing M, Lecher J, Jebbar M, Schmitt L et al. The compatible-solute-binding protein OpuAC from Bacillus subtilis: ligand binding, site-directed mutagenesis, and crystallographic studies. J Bacteriol 2008; 190:5663–5671 [View Article] [PubMed]
     [Google Scholar]
  46. Liu M, Liu H, Shi M, Jiang M, Li L et al. Microbial production of ectoine and hydroxyectoine as high-value chemicals. Microb Cell Fact 2021; 20:76 [View Article] [PubMed]
     [Google Scholar]
  47. Graf R, Anzali S, Buenger J, Pfluecker F, Driller H. The multifunctional role of ectoine as a natural cell protectant. Clin Dermatol 2008; 26:326–333 [View Article] [PubMed]
     [Google Scholar]
  48. Sakagami H, Ishihara M, Hoshino Y, Ishikawa J, Mikami Y et al. Cytotoxicity of nocobactins NA-a, NA-b and their ferric complexes assessed by semiempirical molecular orbital method. In Vivo 2005; 19:277–282 [PubMed]
     [Google Scholar]
  49. Itoh T, Kudo T, Parenti F, Seino A. Amended description of the genus Kineosporia, based on chemotaxonomic and morphological studies. Int J Syst Bacteriol 1989; 39:168–173 [View Article]
     [Google Scholar]
  50. Waksman SA. The Actinomycetes Baltimore: Williams and Wilkins; 1961
     [Google Scholar]
  51. Kelly KL. Inter-Society Color Council–National Bureau of Standard Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  52. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  53. Arai T. Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes Japan; 1975 pp 1–131
     [Google Scholar]
  54. Williams ST, Cross T. Actinomycetes. In Booth C. eds Methods in Microbiology vol 4 London: Academic Press; 1971 pp 295–334
     [Google Scholar]
  55. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  56. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  57. 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 [View Article]
     [Google Scholar]
  58. 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]
  59. 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 [View Article]
     [Google Scholar]
  60. 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]
  61. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
     [Google Scholar]
  62. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark: Microbial ID, Inc; 1990
     [Google Scholar]
  63. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  64. Reimer LC, Sardà Carbasse J, Koblitz J, Ebeling C, Podstawka A et al. BacDive in 2022: the knowledge base for standardized bacterial and archaeal data. Nucleic Acids Res 2022; 50:D741–D746 [View Article]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005804
Loading
Gordonia aquimaris sp. nov., a novel marine actinobacterium isolated from seawater in the upper gulf of Thailand
Int J Syst Evol Microbiol 73, 005804 (2023); https://doi.org/10.1099/ijsem.0.005804
/content/journal/ijsem/10.1099/ijsem.0.005804
/content/journal/ijsem/10.1099/ijsem.0.005804
Loading

Data & Media loading...

Supplements

Supplementary material 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