Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Agromyces silvae sp. nov., Rathayibacter soli sp. nov., and Nocardioides terrisoli sp. nov., Isolated from Soil

  • Hyosun Lee (Department of Biological Science, College of Science and Engineering, Sangji University) ;
  • Dhiraj Kumar Chaudhary (Department of Microbiology, Pukyong National University) ;
  • Dong-Uk Kim (Department of Biological Science, College of Science and Engineering, Sangji University)
  • Received : 2024.04.03
  • Accepted : 2024.05.10
  • Published : 2024.07.28
Download PDF
⟨ Previous Next ⟩

Abstract

Three Gram-stain-positive, aerobic, rod-shaped, and non-motile bacteria, labelled as W11T, SW19T, and YR1T, were isolated from soil, and performed their polyphasic taxonomic investigation. The phylogenetic and 16S rRNA gene sequence analysis showed that strains W11T, SW19T, and YR1T belonged to the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Strain W11T was closely affiliated with Agromyces cavernae SYSU K20354T (98.1%), strain SW19T showed the closest affiliation with Rathayibacter rubneri ZW T2_19T (97.0%), and strain YR1T was most closely related to Nocardioides marmorisolisilvae KIS18-7T (98.0%). The genome sizes of strains W11T, SW19T, and YR1T were 4,181,720 bp, 4,740,677 bp, and 4,228,226 bp, respectively, with DNA G+C contents of 70.5%, 64.2%, and 69.7%, respectively. Average nucleotide identity and digital DNA-DNA hybridization values of W11T, SW19T, and YR1T with their respective reference species were <79.6% and <23.6%, respectively. The predominant cellular fatty acids detected in strain W11T were anteiso-C15:0, iso-C16:0, and anteiso-C17:0. In strain SW19T, they were summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω 9c), anteiso-C17:0, and anteiso-C15:0. Strain YR1T exhibited C18:1ω 9c, C18:0 10-methyl, TBSA, and anteiso-C15:0 as its major cellular fatty acids. Overall, the polyphasic taxonomic comparisons indicated that strains W11T, SW19T, and YR1T represent novel species within the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Accordingly, we propose the names Agromyces silvae sp. nov., with the type strain W11T (=KCTC 49818T =NBRC 115999T), Rathayibacter soli sp. nov., with the type strain SW19T (=KCTC 49860T =NBRC 116108T), and Nocardioides terrisoli sp. nov., with the type strain YR1T (=KCTC 49863T =NBRC 116165T).

Keywords

Acknowledgement

This work was supported by a grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR202203112).

References

  1. Gledhill WE, Casida Jr L. 1969. Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia. Appl. Microbiol. 18: 340-349. https://doi.org/10.1128/am.18.3.340-349.1969
  2. Zgurskaya H, Evtushenko L, Akimov V, Kalakoutskii L. 1993. Rathayibacter gen. nov., including the species Rathayibacter rathayi comb. nov., Rathayibacter tritici comb. nov., Rathayibacter iranicus comb. nov., and six strains from annual grasses. Int. J. Syst. Evol. Microbiol. 43: 143-149.
  3. Prauser H. 1976. Nocardioides, a new genus of the order Actinomycetales. Int. J. Syst. Evol. Microbiol. 26: 58-65.
  4. Lee JC, Whang KS. 2020. Agromyces humi sp. nov., actinobacterium isolated from farm soil. Int. J. Syst. Evol. Microbiol. 70: 5032-5039. https://doi.org/10.1099/ijsem.0.004376
  5. Fang BZ, Gao L, Jiao JY, Zhang ZT, Li MM, Mohamad OAA, et al. 2022. 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.
  6. Heo J, Hamada M, Tamura T, Saito S, Lee SD, Kim JS, et al. 2020. Agromyces protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis. Int. J. Syst. Evol. Microbiol. 70: 1259-1265. https://doi.org/10.1099/ijsem.0.003908
  7. Yi Bf, Xia Tt, Niu Mm, Zhao Zy, Su Qy, Ming H, et al. 2022. Agromyces agglutinans sp. nov., isolated from saline lake sediment. Int. J. Syst. Evol. Microbiol. 72: 005208.
  8. Park EJ, Kim MS, Jung MJ, Roh SW, Chang HW, Shin KS, et al. 2010. Agromyces atrinae sp. nov., isolated from fermented seafood. Int. J. Syst. Evol. Microbiol. 60: 1056-1059. https://doi.org/10.1099/ijs.0.012294-0
  9. Chen Z, Guan Y, Wang J, Li J. 2016. Agromyces binzhouensis sp. nov., an actinobacterium isolated from a coastal wetland of the Yellow River Delta. Int. J. Syst. Evol. Microbiol. 66: 2278-2283. https://doi.org/10.1099/ijsem.0.001022
  10. Yoon JH, Kim IG, Kang KH, Oh TK, Park YH. 2004. Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea. Int. J. Syst. Evol. Microbiol. 54: 71-75. https://doi.org/10.1099/ijs.0.02585-0
  11. Jiang ZK, Pan Z, Li FN, Li XJ, Liu SW, Tuo L, et al. 2017. Marmoricola endophyticus sp. nov., an endophytic actinobacterium isolated from Thespesia populnea. Int. J. Syst. Evol. Microbiol. 67: 4379-4384. https://doi.org/10.1099/ijsem.0.002297
  12. Li FN, Jiang ZK, Liu SW, Tuo L, Lee SMY, Sun CH. 2019. Marmoricola mangrovicus sp. nov., an endophytic actinobacterium isolated from Kandelia candel. Int. J. Syst. Evol. Microbiol. 69: 1343-1349. https://doi.org/10.1099/ijsem.0.003326
  13. Stoll DA, Grimmler C, Hetzer B, Kulling SE, Huch M. 2023. Rathayibacter rubneri sp. nov. isolated from Allium cepa var. Rijnsburger, an onion landrace. Int. J. Syst. Evol. Microbiol. 73: 005811.
  14. Suzuki KI, Sasaki J, Uramoto M, Nakase T, Komagata K. 1996. 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. Evol. Microbiol. 46: 88-93.
  15. Chaudhary DK, Kim J. 2017. Sphingomonas olei sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil. Int. J. Syst. Evol. Microbiol. 67: 2731-2738. https://doi.org/10.1099/ijsem.0.002010
  16. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ. 2008. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl. Environ. Microbiol. 74: 2461-2470. https://doi.org/10.1128/AEM.02272-07
  17. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, et al. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67: 1613-1617. https://doi.org/10.1099/ijsem.0.001755
  18. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35: 1547.
  19. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376. https://doi.org/10.1007/BF01734359
  20. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
  21. Fitch WM. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Biol. 20: 406-416. https://doi.org/10.1093/sysbio/20.4.406
  22. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791. https://doi.org/10.2307/2408678
  23. Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16: 111-120. https://doi.org/10.1007/BF01731581
  24. Lee I, Chalita M, Ha SM, Na SI, Yoon SH, Chun J. 2017. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int. J. Syst. Evol. Microbiol. 67: 2053-2057. https://doi.org/10.1099/ijsem.0.001872
  25. Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7: 203-214. https://doi.org/10.1089/10665270050081478
  26. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44: 6614-6624. https://doi.org/10.1093/nar/gkw569
  27. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
  28. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, et al. 2016. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44: D286-D293. https://doi.org/10.1093/nar/gkv1248
  29. Sun J, Lu F, Luo Y, Bie L, Xu L, Wang Y. 2023. OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res. 51: W397-W403. https://doi.org/10.1093/nar/gkad313
  30. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60.
  31. Yoon SH, Ha Sm, Lim J, Kwon S, Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110: 1281-1286. https://doi.org/10.1007/s10482-017-0844-4
  32. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F, Alanjary M, et al. 2023. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res. 51: W46-W50.
  33. Meier-Kolthoff JP, Goker M. 2019. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat. Commun. 10: 2182.
  34. Lee H, Chaudhary DK, Lim OB, Lee KE, Cha IT, Chi WJ, et al. 2023. Paenibacillus caseinilyticus sp. nov., isolated forest soil. Int. J. Syst. Evol. Microbiol. 73: 006171.
  35. Smibert RM, Krieg NR. 1994. Phenotypic characterization. In Gerhardt, P., Murray, R. G. E., Wood, W. A., and Krieg, N. R. (eds.), Methods for general and molecular bacteriology, pp. 607-654. ASM Press, Washington D.C., USA.
  36. Sasser M. 1990. Bacterial identification by gas chromatographic analysis of fatty acid methyl esters (GC-FAME) (MIDI Technical Note 101. Newark, DE: MIDI Inc.
  37. Staneck JL, Roberts GD. 1974. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl. Microbiol. 28: 226-231. https://doi.org/10.1128/am.28.2.226-231.1974
  38. Collins MD, Jones D. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol. Rev. 45: 316-354. https://doi.org/10.1128/mr.45.2.316-354.1981
  39. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, et al. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2: 233-241. https://doi.org/10.1016/0167-7012(84)90018-6
  40. Komagata K, Suzuki KI. 1988. 4 Lipid and cell-wall analysis in bacterial systematics. Method Microbiol. 19: 161-207. https://doi.org/10.1016/S0580-9517(08)70410-0
  41. Stackebrandt E. 2006. Taxonomic parameters revisited: tarnished gold standards. Microbiol. Today 33: 152-155.
  42. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, et al. 2008. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst. Appl. Microbiol. 31: 241-250. https://doi.org/10.1016/j.syapm.2008.07.001
  43. Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-19131. https://doi.org/10.1073/pnas.0906412106
  44. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, et al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Evol. Microbiol. 37: 463-464.  https://doi.org/10.1099/00207713-37-4-463