Archives of Microbiology

, Volume 200, Issue 6, pp 939–943 | Cite as

Agromyces mangrovi sp. nov., a novel actinobacterium isolated from the rhizosphere of a mangrove

  • Moriyuki Hamada
  • Satomi Saitou
  • Tomohiko Tamura
Original Paper


A novel actinobacterium, designated HIr16-25T, was isolated from the rhizosphere soil of a mangrove growing on Iriomote Island in Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HIr16-25T fell within the cluster of the members of the genus Agromyces and the highest sequence similarity value was observed with Agromyces rhizospherae IFO 16236T (98.6%). Strain HIr16-25T possessed l-2,4-diaminobutyric acid as a diagnostic diamino acid of the peptidoglycan, and MK-12 and MK-11 as the predominant menaquinones. The major fatty acids were identified as iso-C16:0, anteiso-C15:0 and anteiso-C17:0 and the principal polar lipids were phosphatidylglycerol and one glycolipid. These chemotaxonomic features matched well those described for the members of the genus Agromyces. Meanwhile, the result of DNA–DNA hybridization and the presence of differential phenotypic characteristics between strain HIr16-25T and the type strain of A. rhizospherae indicated that strain HIr16-25T be classified as a novel species of the genus Agromyces. Therefore, we propose strain HIr16-25T to represent a novel species of the genus Agromyces, with the name Agromyces mangrovi sp. nov. The type strain is HIr16-25T (= NBRC 112812T = TBRC 7760T).


Actinobacteria Mangrove rhizosphere Agromyces Polyphasic taxonomy 



The authors thank Dr Satoshi Sekimoto and Ms Mayuko Sukisaki (NBRC) for supporting sample collection.

Supplementary material

203_2018_1504_MOESM1_ESM.pdf (246 kb)
Supplementary material 1 (PDF 246 KB)


  1. Akimov VN, Evtushenko LI (2012) Genus IV. Agromyces. In: Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki K, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 5, 2nd edn. Springer, New York, pp 862–876Google Scholar
  2. Corretto E, Antonielli L, Sessitsch A, Compant S, Gorfer M, Kuffner M, Brader G (2016) Agromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil. Int J Syst Evol Microbiol 66:3749–3754CrossRefPubMedGoogle Scholar
  3. Dittmer JC, Lester RL (1964) A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 5:126–127PubMedGoogle Scholar
  4. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229CrossRefGoogle Scholar
  5. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedGoogle Scholar
  6. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:738–791CrossRefGoogle Scholar
  7. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  8. Gledhill WE, Casida LE (1969) Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia. Appl Microbiol 18:340–349PubMedPubMedCentralGoogle Scholar
  9. Hamada M, Yamamura H, Komukai C, Tamura T, Suzuki K, Hayakawa M (2012) Luteimicrobium album sp. nov., a novel actinobacterium isolated from lichen collected in Japan, and emended description of the genus Luteimicrobium. J Antibiot 65:427–431CrossRefPubMedGoogle Scholar
  10. Hamada M, Shibata C, Tamura T, Nurkanto A, Ratnakomala S, Lisdiyanti P, Suzuki K (2016) Cellulosimicrobium marinum sp. nov., an actinobacterium isolated from sea sediment. Arch Microbiol 198:439–444CrossRefPubMedGoogle Scholar
  11. Jung SY, Lee SY, Oh TK, Yoon JH (2007) Agromyces allii sp. nov., isolated from the rhizosphere of Allium victorialis var. platyphyllum. Int J Syst Evol Microbiol 57:588–593CrossRefPubMedGoogle Scholar
  12. Minnikin DEM, Collins D, Goodfellow M (1975) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia related taxa. J Appl Bacteriol 47:87–95CrossRefGoogle Scholar
  13. Roselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria. Syst Appl Microbiol 110:455–456Google Scholar
  14. Saito H, Miura K (1963) Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 72:619–629CrossRefPubMedGoogle Scholar
  15. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  16. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc, NewarkGoogle Scholar
  17. Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477PubMedPubMedCentralGoogle Scholar
  18. Takeuchi M, Hatano K (2001) Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov. and Agromyces bracchium sp. nov., from the mangrove rhizosphere. Int J Syst Evol Microbiol 51:1529–1537CrossRefPubMedGoogle Scholar
  19. Tamaoka J, Komagata K (1984) Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128CrossRefGoogle Scholar
  20. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefPubMedPubMedCentralGoogle Scholar
  21. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefPubMedPubMedCentralGoogle Scholar
  22. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  23. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617CrossRefPubMedPubMedCentralGoogle Scholar
  24. Zgurskaya HI, Evtushenko LI, Akimov VN, Voyevoda HV, Dobrovol TG, Lysak LV, Kalakoutskii LV (1992) 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 Evol Microbiol 42:635–641Google Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Biological Resource CenterNational Institute of Technology and Evaluation (NBRC)KisarazuJapan

Personalised recommendations