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Volume 72, Issue 1

sp. nov., isolated from saline lake sediment No Access

Abstract

A novel actinobacterium, designated strain CFH 90414, was isolated from sediment sampled at a saline lake in Yuncheng, Shanxi, PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of strain CFH 90414 were Gram-reaction-positive, aerobic and non-motile. Growth occured at 4−40 °C, pH 5.0−9.0 and in the presence of up to 0–3.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CFH 90414 was a member of the genus . The 16S rRNA gene sequence similarity analysis indicated that strain CFH 90414 was most closely related to JCM 14320 (98.07 %) and JCM 14321 (97.18 %). The whole genome of CFH 90414 was 3.64 Mb, and showed a G+C content of 71.5 mol%. The average nucleotide identity (ANI) values and digital DNA–DNA hybridization (dDDH) values between CFH 90414 and the other species of the genus were found to be low (ANI <78.99 % and dDDH <22.9 %). The whole-cell sugars were rhamnose, mannose, ribose, glucose and galactose. The isolate contained -2,4-diaminobutyric acid, -alanine, -glutamic acid and glycine in the cell-wall peptidoglycan. The predominant menaquinone was MK-12. The major cellular fatty acids were anteiso-C, anteiso-C and iso-C. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. On the basis of phenotypic, genotypic and phylogenetic data, strain CFH 90414 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CFH 90414 (=DSM 105966=KCTC 49062).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Agromyces agglutinans sp. nov. , polyphasic taxonomy and saline lake
Funding
This study was supported by the:
  • Doctor Scientific Research Fund of Xinxiang Medical University (Award XYBSKYZZ201625)
    • Principle Award Recipient: HongMing
  • Key Technologies R&D Program of Henan Province (Award 202102110107)
    • Principle Award Recipient: HongMing
© 2022 The Authors
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References

  1. Gledhill WE, Casida LE. Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia . Appl Microbiol 1969; 18:340–349 [View Article]
     [Google Scholar]
  2. Zgurskaya HI, Evtushenko LI, Akimov VN, Voyevoda HV, Dobrovolskaya TG et al. Emended description of the genus Agromyces and description of Agromyces cerinus subsp. cerinus sp. nov., subsp. nov., Agromyces cerinus subsp. nitratus sp. nov., subsp. nov., Agromyces fucosus subsp. fucosus sp. nov., subsp. nov., and Agromyces fucosus subsp. hippuratus sp. nov., subsp. nov. Int J Syst Bacteriol 1992; 42:635–641 [View Article]
     [Google Scholar]
  3. Takeuchi M, Hatano K. Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov. and Agromyces bracchium sp. nov., from the mangrove rhizosphere. Int J Syst Evol Microbiol 2001; 51:1529–1537 [View Article] [PubMed]
     [Google Scholar]
  4. Dorofeeva LV, Krausova VI, Evtushenko LI, Tiedje JM. Agromyces albus sp. nov., isolated from a plant (Androsace sp.). Int J Syst Evol Microbiol 2003; 53:1435–1438 [View Article] [PubMed]
     [Google Scholar]
  5. Rivas R, Trujillo ME, Mateos PF, Martínez-Molina E, Velázquez E. Agromyces ulmi sp. nov., a xylanolytic bacterium isolated from Ulmus nigra in Spain. Int J Syst Evol Microbiol 2004; 54:1987–1990 [View Article] [PubMed]
     [Google Scholar]
  6. Jurado V, Groth I, Gonzalez JM, Laiz L, Saiz-Jimenez C. Agromyces subbeticus sp. nov., isolated from a cave in southern Spain. Int J Syst Evol Microbiol 2005; 55:1897–1901 [View Article] [PubMed]
     [Google Scholar]
  7. Suzuki KI, Sasaki J, Uramoto M, Nakase T, Komagata K. Agromyces mediolanus sp. nov., nom. rev., comb. nov., a species for “Corynebacterium mediolanum” Mamoli 1939 and for some aniline-assimilating bacteria which contain 2,4-diaminobutyric acid in the cell wall peptidoglycan. Int J Syst Bacteriol 1996; 46:88–93 [View Article]
     [Google Scholar]
  8. Sasaki J, Chijimatsu M, Suzuki K. Taxonomic significance of 2,4-diaminobutyric acid isomers in the cell wall peptidoglycan of actinomycetes and reclassification of Clavibacter toxicus as Rathayibacter toxicus comb. nov. Int J Syst Bacteriol 1998; 48:403–410 [View Article] [PubMed]
     [Google Scholar]
  9. Li W-J, Zhang L-P, Xu P, Cui X-L, Xu L-H et al. Agromyces aurantiacus sp. nov., isolated from a Chinese primeval forest. Int J Syst Evol Microbiol 2003; 53:303–307 [View Article] [PubMed]
     [Google Scholar]
  10. 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 [View Article] [PubMed]
     [Google Scholar]
  11. Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article] [PubMed]
     [Google Scholar]
  12. 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]
  13. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  14. 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 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  19. Freel KC, Sarilar V, Neuvéglise C, Devillers H, Friedrich A et al. Genome sequence of the yeast Cyberlindnera fabianii (Hansenula fabianii). Genome Announc 2014; 2:e00638-14 [View Article] [PubMed]
     [Google Scholar]
  20. Delcher AL. Glimmer Release Notes Version 3.02 2006
     [Google Scholar]
  21. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [View Article] [PubMed]
     [Google Scholar]
  22. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article] [PubMed]
     [Google Scholar]
  23. 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] [PubMed]
     [Google Scholar]
  24. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  25. Waksman SA. The Actinomycetes. A summary of current knowledge New York: Ronald Press; 1967
     [Google Scholar]
  26. Atlas RM. Handbook of Microbiological Media Boca Raton, FL: CRC Press;1993;
     [Google Scholar]
  27. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  28. 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 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Leifson E. Atlas of bacterial flagellation. Q Rev Biol 1960; 242:
     [Google Scholar]
  31. Nie G-X, Ming H, Li S, Zhou E-M, Cheng J et al. Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2012; 62:2650–2656 [View Article] [PubMed]
     [Google Scholar]
  32. Gordon RE, Barnett DA, Handerhan JE, Pang C-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  33. Groth I, Rodriguez C, Schútze B, Schmitz P, Leistner E et al. Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. Int J Syst Evol Microbiol 2004; 54:2121–2129 [View Article]
     [Google Scholar]
  34. 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 [View Article]
     [Google Scholar]
  35. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL . In Williams ST, Sharpe ME, Holt JG. eds Bergey’s Manual of Systematic Bacteriology vol 4 Baltimore: Williams & Wilkins, Baltimore; 1989 pp 2452–2492
     [Google Scholar]
  36. Sasser M. MIDI Technical Note 101 Newark: Microbial ID, Inc; 1990
     [Google Scholar]
  37. 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]
  38. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatog 2006; 5:2359–2367 [View Article]
     [Google Scholar]
  39. 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]
  40. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  41. 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]
  42. 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]
     [Google Scholar]
  43. 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 [View Article]
     [Google Scholar]
  44. 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]
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Agromyces agglutinans sp. nov., isolated from saline lake sediment
Int J Syst Evol Microbiol 72, 005208 (2022); https://doi.org/10.1099/ijsem.0.005208
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