1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 2

Three novel species isolated by using polyaspartic acid as a water-retaining agent for the enrichment No Access

Abstract

Three novel actinomycete strains, designated TRM66264-DLM, TRM88002 and TRM88003, were isolated by using polyaspartic acid as a water-retaining agent for the enrichment . The 16S rRNA gene sequence and phylogenetic analyses of three strains indicated that they belonged to the genus . The phylogenetically closest strains of TRM66264-DLM, TRM88002 and TRM88003 were LIPI11-2-Ac043 (98.4 %), A4029 (98.0 %) and IFO15555 (98.1 %), respectively. The major polar lipids of strains TRM66264-DLM and TRM88002 were phosphatidylethanolamine and disphosphatidylglycerol, while strain TRM88003 only had phosphatidylethanolamine. The predominant menaquinones of strain TRM66264-DLM were identified as MK-9(H) and MK-9 (H). Strains TRM88002 and TRM88003 had MK-9(H). The cell-wall peptidoglycan of three strains contained -diaminopimelic acid. The whole-cell sugars of strain TRM66264-DLM were identified as arabinose, glucose, galactose and xylose. Strains TRM88002 and TRM88003 mainly had arabinose and glucose. The DNA G+C content of strains TRM66264-DLM, TRM88002 and TRM88003 were 70.48, 70.46 and 70.64 mol%, respectively. Genotypic and phenotypic analysis confirmed that all three strains sre new members of the genus . Therefore, it is proposed that strains TRM66264-DLM, TRM88002 and TRM88003 represent three novel species of the genus , for which the names sp. nov. (type strain TRM66264-DLM=CCTCC AA 2021015=LMG 32389), sp. nov. (type strain TRM88002=CCTCC AA 2021036=LMG 32621) and sp. nov. (type strain TRM88003=CCTCC AA 2021037 =LMG 32622) are proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Actinoplanes aksuensis sp. nov. , Actinoplanes hotanensis sp. nov. , Actinoplanes polyasparticus sp. nov. , polyaspartic acid and polyphasic taxonomy
Funding
This study was supported by the:
  • Microbial Resources Utilization Innovation Team in Key Field of Xinjiang Production and Construction Corps (Award 2017CB014)
    • Principle Award Recipient: Chuan-XingWan
  • Instituto Nacional de Ciência e Tecnologia Centro de Estudos das Adaptações da Biota Aquática da Amazônia (Award 2021BB007)
    • Principle Award Recipient: Chuan-XingWan
  • National Natural Science Foundation (Award 32060023)
    • Principle Award Recipient: Chuan-XingWan
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005705
2023-02-07
2024-05-14
Loading full text...

Full text loading...

References

  1. Yushchuk O, Homoniuk V, Ostash B, Marinelli F, Fedorenko V. Genetic insights into the mechanism of teicoplanin self-resistance in Actinoplanes teichomyceticus. J Antibiot 2020; 73:255–259 [View Article]
     [Google Scholar]
  2. Yushchuk O, Homoniuk V, Datsiuk Y, Ostash B, Marinelli F et al. Development of a gene expression system for the uncommon actinomycete Actinoplanes rectilineatus NRRL B-16090. J Appl Genet 2020; 61:141–149 [View Article] [PubMed]
     [Google Scholar]
  3. Aretz W, Meiwes J, Seibert G, Vobis G, Wink J. Friulimicins: novel lipopeptide antibiotics with peptidoglycan synthesis inhibiting activity from Actinoplanes friuliensis sp. nov. I. Taxonomic studies of the producing microorganism and fermentation. J Antibiot 2000; 53:807–815 [View Article]
     [Google Scholar]
  4. Couch JN. Actinoplanes, a new genus of the actinomycetales. J Elisha Mitchell Sci Soc 1950; 66:87–92
     [Google Scholar]
  5. Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E. The Prokaryotes New York, NY: Gamma Subclass .[M]; 2006 [View Article]
     [Google Scholar]
  6. Saeng-in P, Kanchanasin P, Yuki M, Kudo T, Ohkuma M et al. Actinoplanes lichenicola sp. nov. and Actinoplanes ovalisporus sp. nov., isolated from lichen in Thailand. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  7. Zhang Y, Zhang J, Fan L, Pang H, Xin Y et al. Actinoplanes atraurantiacus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2012; 62:2533–2537 [View Article] [PubMed]
     [Google Scholar]
  8. Beretta G. Actinoplanes italicus, a new red-pigmented species. Int J Syst Bacteriol 1973; 23:37–42 [View Article]
     [Google Scholar]
  9. Sazak A, Sahin N, Camas M. Actinoplanes abujensis sp. nov., isolated from Nigerian arid soil. Int J Syst Evol Microbiol 2012; 62:960–965 [View Article]
     [Google Scholar]
  10. Nurkanto A, Lisdiyanti P, Hamada M, Ratnakomala S, Shibata C et al. Actinoplanes bogoriensis sp. nov., a novel actinomycete isolated from leaf litter. J Antibiot 2016; 69:26–30 [View Article]
     [Google Scholar]
  11. Nurkanto A, Lisdiyanti P, Hamada M, Ratnakomala S, Shibata C et al. Actinoplanes tropicalis sp. nov. and Actinoplanes cibodasensis sp. nov., isolated from leaf litter. Int J Syst Evol Microbiol 2015; 65:3824–3829 [View Article]
     [Google Scholar]
  12. Goodfellow M, Stanton LJ, Simpson KE, Minnikin DE. Numerical and chemical classification of Actinoplanes and some related actinomycetes. J Gen Microbiol 1990; 136:19–36 [View Article]
     [Google Scholar]
  13. Qu Z, Bao X-D, Xie Q-Y, Zhao Y-X, Yan B et al. Actinoplanes sediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2018; 68:71–75 [View Article] [PubMed]
     [Google Scholar]
  14. Shen Y, Liu C, Wang X, Zhao J, Jia F et al. Actinoplanes hulinensis sp. nov., a novel actinomycete isolated from soybean root (Glycine max (L.) Merr). Antonie Van Leeuwenhoek 2013; 103:293–298 [View Article] [PubMed]
     [Google Scholar]
  15. Fl A, Zhang Y, Adil M et al. Antibiotic discovery: combining isolation chip (ichip) technology and co-culture technique. J Appl Microbiol Biotechnol 20181–9
     [Google Scholar]
  16. Mazza P, Monciardini P, Cavaletti L, Sosio M, Donadio S. Diversity of Actinoplanes and related genera isolated from an Italian soil. Microb Ecol 2003; 45:362–372 [View Article]
     [Google Scholar]
  17. Hayakawa M, Tamura T, Iino H, Nonomura H. Pollen-baiting and drying method for the highly selective isolation of Actinoplanes spp. from soil. J Ferment and Bioeng 1991; 72:433–438 [View Article]
     [Google Scholar]
  18. Hayakawa M, Tamura T, Iino H. Application of a method incorporating differential centrifugation for selective isolation of motile actinomycetes in soil and plant litter. Antonie van Leeuwenhoek 2000; 78:171–185 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. 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]
  21. 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]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [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. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  25. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article]
     [Google Scholar]
  26. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
     [Google Scholar]
  27. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article]
     [Google Scholar]
  28. 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] [PubMed]
     [Google Scholar]
  29. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  30. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [View Article]
     [Google Scholar]
  31. Waksman SA. The Actinomycetes Vol. II. In Classification, Identification and Descriptions of Genera and Species Baltimore, MD: Williams & Wilkins Company; 1961
     [Google Scholar]
  32. Kelly KL. Inter-society color council: National Bureau of standards color name charts illustrated with centroid colors Washington, DC: US Government Printing Offifice; 1964
     [Google Scholar]
  33. Cao P, Li C, Tan K, Liu C, Xu X et al. Characterization, phylogenetic analyses, and pathogenicity of Enterobacter cloacae on rice seedlings in heilongjiang province, China. Plant Dis 2020; 104:1601–1609 [View Article]
     [Google Scholar]
  34. Zhao J, Han L, Yu M, Cao P, Li D et al. Characterization of Streptomyces sporangiiformans sp. nov., a novel soil actinomycete with antibacterial activity against Ralstonia solanacearum. Microorganisms 2019; 7:7–360 [View Article]
     [Google Scholar]
  35. 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]
  36. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicus gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 1993; 43:805–812 [View Article]
     [Google Scholar]
  37. Goodfellow M, Alderson G, Lacey J. Numerical taxonomy of Actinomadura and related actinomycetes. J Gen Microbiol 1979; 112:95–111 [View Article] [PubMed]
     [Google Scholar]
  38. 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]
  39. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
     [Google Scholar]
  40. Mikami H, Ishida Y. Post-column fluorometric detection of reducing sugars in high performance liquid chromatography using arginine. Bunseki Kagaku 1983; 32:E207–E210 [View Article]
     [Google Scholar]
  41. 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]
  42. Kroppenstedt RM, Goodfellow M. The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillospora and Thermomonospora. In Dworkin M, Falkow S, Schleifer KH, Stackebrandt E. eds The Prokaryotes. Archaea and Bacteria: Firmicutes, Actinomycetes, Vol 3, 3rd. edn New York: Springer; 2006 pp 682–724
     [Google Scholar]
  43. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  44. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990:199–202
     [Google Scholar]
  45. Wu C, Lu X, Qin M et al. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology 1989; 16:176–178
     [Google Scholar]
  46. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Usfcc Newsl 1990
     [Google Scholar]
  47. 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]
  48. 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 Bacteriol 1987; 37:463–464 [View Article]
     [Google Scholar]
  49. Awakawa T, Fujita N, Hayakawa M, Ohnishi Y, Horinouchi S. Characterization of the biosynthesis gene cluster for alkyl-O-dihydrogeranyl-methoxyhydroquinones in Actinoplanes missouriensis. Chembiochem 2011; 12:439–448 [View Article] [PubMed]
     [Google Scholar]
  50. Li NC, Zhang JY, Hu CM et al. Study on inhibitory effect of allelopathic substances on the attachment of lichen spores. Environ Sci Technol 2021; 44(S1):26–34
     [Google Scholar]
  51. Garrity GM, Heimbuch BK, Gagliardi M. Isolation of zoosporogenous actinomycetes from desert soils. J Ind Microbiol Biotechnol 1996; 17:260–267 [View Article]
     [Google Scholar]
  52. Li WJ, Zhang ZZ, Jiang CL. Selective isolation of several major rare actinomycetes. Foreign Medicine 2002; 01:18–22
     [Google Scholar]
  53. Makkar NS, Cross T. Actinoplanetes in soil and on plant litter from freshwater habitats. J Appl Microbiol 2010; 52:209–218 [View Article]
     [Google Scholar]
  54. Rabeh SA, Azab EA, Aly MM. Studies on bacterioplankton and inhibitory strains of aquatic actinomycetes in Lake Bardawil, Egypt. World J Microbiol Biotechnol 2007; 23:167–176 [View Article]
     [Google Scholar]
  55. Mazza P, Monciardini P, Cavaletti L, Sosio M, Donadio S. Diversity of Actinoplanes and related genera isolated from an Italian soil. Microb Ecol 2003; 45:362–372 [View Article]
     [Google Scholar]
  56. Yamamura H, Shimizu A, Nakagawa Y, Hamada M, Otoguro M et al. Actinoplanes rishiriensis sp. nov., a novel motile actinomycete isolated by rehydration and centrifugation method. J Antibiot 2012; 65:249–253 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005705
Loading
Three novel Actinoplanes species isolated by using polyaspartic acid as a water-retaining agent for the enrichment in situ
Int J Syst Evol Microbiol 73, 005705 (2023); https://doi.org/10.1099/ijsem.0.005705
/content/journal/ijsem/10.1099/ijsem.0.005705
/content/journal/ijsem/10.1099/ijsem.0.005705
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