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Volume 72, Issue 8

sp. nov., a novel member of the genus isolated from a karstic cave in Shaoguan No Access

Abstract

A novel actinobacterial strain, designated SYSU K20354, was isolated from a soil sample collected from a karst cave in Shaoguan city, Guangdong province, southern China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and non-motile. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU K20354 was most closely related to JCM 14319, and shared the highest sequence identity of 98.3 % based on NCBI database. In addition, 2,4-diaminobutyric acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were galactose, glucose, mannose and ribose. The major isoprenoid quinone was MK-12, while the major fatty acids (>10 %) were isoC, anteisoC and anteisoC. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, three unknown glycolipids, three unknown phospholipids and two unknown lipids. The draft genome size of strain SYSU K20354 was 3.96 Mbp with G+C content of 69.7 mol%. Furthermore, the average nucleotide identity and digital DNA–DNA hybridization values between strain SYSU K20354 and JCM 14319 were 90.3 and 55.6 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K20354 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SYSU K20354 (=KCTC 49499= CGMCC 4.7691).

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Keyword(s): Agromyces cavernae sp. nov. , karst cave and polyphasic taxonomy
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2022-08-24
2024-05-20
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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. Akimov VN, Evtushenko LI, Genus IV. Agromyces. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki K et al. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol 5 New York: Springer; 2012 pp 862–876
     [Google Scholar]
  4. Hamada M, Shibata C, Tamura T, Suzuki K. Agromyces marinus sp. nov., a novel actinobacterium isolated from sea sediment. J Antibiot (Tokyo) 2014; 67:703–706 [View Article] [PubMed]
     [Google Scholar]
  5. Jurado V, Groth I, Gonzalez JM, Laiz L, Schuetze B et al. Agromyces italicus sp. In Nov., Agromyces Humatus Sp. Nov. and Agromyces Lapidis Sp. Nov., Isolated from Roman Catacombs. Int J Syst Evol Microbiol 2005b vol 55 pp 871–875 [View Article]
     [Google Scholar]
  6. Suzuki K, 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]
  7. 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]
  8. Jurado V, Groth I, Gonzalez JM, Laiz L, Saiz-Jimenez C. Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov. Int J Syst Evol Microbiol 2005; 55:153–157 [View Article] [PubMed]
     [Google Scholar]
  9. Yoon JH, Schumann P, Kang SJ, Park S, Oh TK. Agromyces terreus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2008; 58:1308–1312 [View Article] [PubMed]
     [Google Scholar]
  10. Zhang D-C, Schumann P, Liu H-C, Xin Y-H, Zhou Y-G et al. Agromyces bauzanensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2010; 60:2341–2345 [View Article] [PubMed]
     [Google Scholar]
  11. Thawai C, Tanasupawat S, Suwanborirux K, Kudo T. Agromyces tropicus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61:605–609 [View Article] [PubMed]
     [Google Scholar]
  12. Chen J, Chen H-M, Zhang Y-Q, Wei Y-Z, Li Q-P et al. Agromyces flavus sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 2011; 61:1705–1709 [View Article] [PubMed]
     [Google Scholar]
  13. Lee M, Ten LN, Woo SG, Park J. Agromyces soli sp. nov., isolated from farm soil. Int J Syst Evol Microbiol 2011; 61:1286–1292 [View Article] [PubMed]
     [Google Scholar]
  14. Dastager SG, Qiang ZL, Damare S, Tang SK, Li WJ. Agromyces indicus sp. nov., isolated from mangroves sediment in Chorao Island, Goa, India. Antonie van Leeuwenhoek 2012; 102:345–352 [View Article] [PubMed]
     [Google Scholar]
  15. Hamada M, Shibata C, Ishida Y, Tamura T, Yamamura H et al. Agromyces iriomotensis sp. nov. and Agromyces subtropicus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:833–838 [View Article] [PubMed]
     [Google Scholar]
  16. Hamada M, Shibata C, Tamura T, Suzuki K. Agromyces marinus sp. nov., a novel actinobacterium isolated from sea sediment. J Antibiot 2014; 67:703–706 [View Article]
     [Google Scholar]
  17. 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]
  18. Jung SY, Lee SY, Oh TK, Yoon JH. Agromyces allii sp. nov., isolated from the rhizosphere of Allium victorialis var. platyphyllum. Int J Syst Evol Microbiol 2007; 57:588–593 [View Article]
     [Google Scholar]
  19. Sun T, Cao P, Sun K, Li C, Jiang M et al. Agromyces tardus sp. nov., an actinobacterium isolated from the rhizosphere soil of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2019; 69:3268–3275 [View Article]
     [Google Scholar]
  20. Wang R, Ye Y, Huang Y, Nie Y, Han S et al. Agromyces kandeliae sp. nov., isolated from rhizosphere soil of Kandelia candel in a mangrove. Int J Syst Evol Microbiol 2020; 70:5861–5867 [View Article]
     [Google Scholar]
  21. Heo J, Hamada M, Tamura T, Saito S, Lee SD et al. Agromyces protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis. Int J Syst Evol Microbiol 2020; 70:1259–1265 [View Article]
     [Google Scholar]
  22. Lee SA, Heo J, Kim MA, Tamura T, Saitou S et al. Protaetiibacter larvae sp. nov. and agromyces intestinalis sp. nov., isolated from the gut of larvae of protaetia brevitarsis seulensis, reclassification of lysinimonas yzui as pseudolysinimonas yzui comb. nov. and emended description of the genus pseudolysinimonas. Int J Syst Evol Microbiol 2021; 71:4669
     [Google Scholar]
  23. 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]
  24. 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]
  25. Park E-J, Kim M-S, Jung M-J, Roh SW, Chang H-W et al. Agromyces atrinae sp. nov., isolated from fermented seafood. Int J Syst Evol Microbiol 2010; 60:1056–1059 [View Article] [PubMed]
     [Google Scholar]
  26. Cheeptham N. Cave microbiomes: A novel resource for drug discoveryMicrobiomes: A Novel Resource for Drug Discovery. In Advances and Challenges in Studying Cave Microbial Diversity Cave Microbiomes: A Novel Resource for Drug Discovery New York: Springer; 2013 pp 1–34 [View Article]
     [Google Scholar]
  27. Fang B-Z, Salam N, Han M-X, Jiao J-Y, Cheng J et al. Insights on the effects of heat pretreatment, pH, and calcium salts on isolation of rare Actinobacteria from karstic caves. Front Microbiol 2017; 8:1535 [View Article]
     [Google Scholar]
  28. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 1987; 65:501–509 [View Article]
     [Google Scholar]
  29. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7 [View Article] [PubMed]
     [Google Scholar]
  30. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  31. Atlas RM. Handbook of Microbiological Media. Edited by L. C. Parks Boca Raton, FL: CRC Press; 1993
     [Google Scholar]
  32. Waksman SA. The actinomycetes. A summary of current knowledge New York: Ronald Press; 1967
     [Google Scholar]
  33. Kelly KL. Inter-Society Color Council-National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors Washington: US Government Printing Office; 1964
     [Google Scholar]
  34. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article]
     [Google Scholar]
  35. 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]
  36. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Williams ST, Sharpe and J. G. Holt ME. eds In Bergey’s Manual of Systematic Bacteriology vol 4 Baltimore: Williams and Willkins; 1989 pp 2453–2492
     [Google Scholar]
  37. Athalye M, Goodfellow M, Lacey J, White RP. Numerical classification of actinomadura and ocardiopsis. Int J Syst Bacteriol 1985; 35:86–98 [View Article]
     [Google Scholar]
  38. Pridham TG, Gottlieb D. The utilization of carbon compounds by some actinomycetales as an aid for species determination. J Bacteriol 1948; 56:107–114 [View Article]
     [Google Scholar]
  39. Nie GX, Ming H, Li S, Zhou EM, Cheng J et al. Amycolatopsis dongchuanensis sp. nov., a novel actinobacterium isolated from dry-hot valley in Yunnan, south-west China. Int J Syst Evol Microbiol 2012; 62:2650–2656
     [Google Scholar]
  40. Fang B-Z, Han M-X, Jiao J-Y, Xie Y-G, Zhang X-T et al. Streptomyces cavernae sp. nov., a novel actinobacterium isolated from a karst cave sediment sample. Int J Syst Evol Microbiol 2020; 70:120–125 [View Article]
     [Google Scholar]
  41. 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]
     [Google Scholar]
  42. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic Local Alignment Search Tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
     [Google Scholar]
  43. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  44. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  45. 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]
  46. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  47. 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]
  48. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  49. Harrison P. SPAdes – a process algebra for discrete event simulation. J Logic Comput 2000; 10:3–42 [View Article]
     [Google Scholar]
  50. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  51. Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods 2015; 12:59–60 [View Article] [PubMed]
     [Google Scholar]
  52. Yin Y, Mao X, Yang J, Chen X, Mao F et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2012; 40:W445–51 [View Article] [PubMed]
     [Google Scholar]
  53. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [View Article] [PubMed]
     [Google Scholar]
  54. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [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 [View Article] [PubMed]
     [Google Scholar]
  56. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  57. Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44:W242–5 [View Article]
     [Google Scholar]
  58. 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]
  59. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article]
     [Google Scholar]
  60. Sasser M. Technical note 101: Identification of bacteria by gas chromatography of cellular fatty acids. MIDI; 1990
  61. 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]
  62. 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]
  63. 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]
  64. 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]
     [Google Scholar]
  65. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI 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]
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Agromyces cavernae sp. nov., a novel member of the genus Agromyces isolated from a karstic cave in Shaoguan
Int J Syst Evol Microbiol 72, 005503 (2022); https://doi.org/10.1099/ijsem.0.005503
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