Advertisement

Amnibacterium setariae sp. nov., an endophytic actinobacterium isolated from dried foxtail

  • Inhyup Kim
  • Geeta Chhetri
  • Jiyoun Kim
  • Taegun SeoEmail author
Original Paper
  • 27 Downloads

Abstract

A Gram-stain positive, short rod-shaped, aerobic, motile by means of gliding, yellow-pigmented actinobacterium, designated strain DD4aT, was isolated from dry yellow foxtail. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DD4aT is closely related to Amnibacterium soli MB78T (98.4% similarity), Amnibacterium kyonggiense KSL51201-037T (98.2%) and Amnibacterium endophyticum 1T4Z-3T (97.43%). Strain DD4aT forms yellow colonies on R2A agar medium. The peptidoglycan was found to contains diaminopimelic acid (which is a diagnostic cell wall diamino acid), alanine, glutamic acid and lysine. The polar lipids diphosphatidylglycerol, phosphatidylglycerol, six unidentified glycolipids and an unidentified polar lipid were found to be present in strain DD4aT. The major cellular fatty acids anteiso-C15:0 (42.9%) and iso-C16:0 (34.6%) were found in strain DD4aT. The predominant respiratory quinones were found to be MK-11 and MK-12. The DNA G+C content of strain DD4aT is 73.9 mol%. DNA–DNA relatedness of strain DD4aT with A. soli MB78T, A. kyonggiense KSL51201-037T, and A. endophyticum 1T4Z-3T were 53.3% (± 1.1%), 47.0% (± 0.5%), and 47.9% (± 0.9%), respectively. The digital DNA–DNA hybridisation and average nucleotide identity values between strain DD4aT and A. kyonggiense KSL51201-037T were determined to be 26.1% and 82.7%. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, DD4aT represents a novel member of the genus Amnibacterium, for which the name Amnibacterium setariae sp. nov., is proposed. The type strain of Amnibacterium setariae is DD4aT (= KACC 19817T = JCM 32878T).

Keywords

Amnibacterium Gliding motility Setaria Gram-stain positive 

Notes

Author contributions

IK isolated the bacterium, designed the study, performed the phenotypic and biochemical characterization, wrote the original draft; GC and JK helped the analysis of taxonomic data; TS designed and supervised the study, edited the original draft.

Funding

This research was supported by a National Research Foundation of Korea (NRF) Grant by the Korean Government (MIST) (NRF-2017R1A2B4009448).

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

10482_2019_1302_MOESM1_ESM.docx (8.8 mb)
Supplementary material 1 (DOCX 8973 kb)

References

  1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefPubMedPubMedCentralGoogle Scholar
  2. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75.  https://doi.org/10.1186/1471-2164-9-75 CrossRefGoogle Scholar
  3. Bernardet JF, Nakagawa Y, Holmes B, Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070Google Scholar
  4. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T et al (2019) AntiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:81–87.  https://doi.org/10.1093/nar/gkz310 CrossRefGoogle Scholar
  5. Buck JD (1982) Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993PubMedPubMedCentralGoogle Scholar
  6. Chhetri G, Yang D, Choi J et al (2018) Edaphorhabdus rosea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea. Antonie van Leeuwenhoek 111:2385–2392CrossRefPubMedGoogle Scholar
  7. Chhetri G, Kim J, Kim I et al (2019) Runella soli sp. nov., isolated from garden soil. Antonie van Leeuwenhoek 112:1245–1252CrossRefPubMedGoogle Scholar
  8. Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354PubMedPubMedCentralGoogle Scholar
  9. De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142CrossRefPubMedGoogle Scholar
  10. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  11. Gillis M, Ley JD, Cleene MD (1970) The determination of molecular weight of bacterial genome DNA from renaturation rates. Eur J Biochem 12:143–153CrossRefPubMedGoogle Scholar
  12. Hall T (1997) BioEdit. Biological sequence alignment editor for Win 95/98/NT/2 K/XP. Carlsbad, CA: Ibis TherapeuticsGoogle Scholar
  13. Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by highperformance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469CrossRefGoogle Scholar
  14. Jin L, Lee HG, Kim HS, Ahn CY, Oh HM (2013) Amnibacterium soli sp. nov., an actinobacterium isolated from grass soil. Int J Syst Evol Microbiol 63:4750–4753CrossRefPubMedGoogle Scholar
  15. Kim SJ, Lee SS (2011) Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae. Int J Syst Evol Microbiol 61:155–159CrossRefPubMedGoogle Scholar
  16. Kim I, Choi J, Chhetri G et al (2019) Lysobacter helvus sp. nov. and Lysobacter xanthus sp. nov., isolated from Soil in South Korea. Antonie van Leeuwenhoek 112:1253–1262CrossRefPubMedGoogle Scholar
  17. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefGoogle Scholar
  18. Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–205CrossRefGoogle Scholar
  19. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis Version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefPubMedPubMedCentralGoogle Scholar
  20. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE (1988) Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 38:358–361Google Scholar
  21. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948CrossRefGoogle Scholar
  22. Li FN, Tuo L, Lee SM, Jin T, Liao S, Li W, Yan X, Sun CH (2018) Amnibacterium endophyticum sp. nov., an endophytic actinobacterium isolated from Aegiceras corniculatum. Int J Syst Evol Microbiol 68:1327–1332CrossRefPubMedGoogle Scholar
  23. Loveland-Curtze J, Miteva VI, Brenchley JE, Vanya IM, Jean EB (2011) Evaluation of a new fluorimetric DNA–DNA hybridization method. Can J Microbiol 57:250–255CrossRefPubMedGoogle Scholar
  24. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18.  https://doi.org/10.1186/2047-217X-1-18 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Rosselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: timely move towards a database-driven systematics of archaea and bacteria. Syst Appl Microbiol 40:121–122CrossRefPubMedGoogle Scholar
  26. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  27. Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477PubMedPubMedCentralGoogle Scholar
  28. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44:846–849CrossRefGoogle Scholar
  29. Tuo L, Yan XR, Li FN, Yang C, An MB, Sun CH (2018) Amnibacterium flavum sp. nov., a novel endophytic actinobacterium isolated from bark of Nerium indicum Mill. Int J Syst Evol Microbiol 69:285–290CrossRefPubMedGoogle Scholar
  30. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, International Committee on Systematic Bacteriology et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464CrossRefGoogle Scholar
  31. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H (2017a) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617CrossRefPubMedPubMedCentralGoogle Scholar
  32. Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286CrossRefPubMedGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Inhyup Kim
    • 1
  • Geeta Chhetri
    • 1
  • Jiyoun Kim
    • 1
  • Taegun Seo
    • 1
    Email author
  1. 1.Department of Life ScienceDongguk University-SeoulGoyangSouth Korea

Personalised recommendations