Skip to main content
SpringerLink
Log in

Description of Fimbriimonas ginsengisoli gen. nov., sp. nov. within the Fimbriimonadia class nov., of the phylum Armatimonadetes

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

Strain Gsoil 348T was isolated from a ginseng field soil sample by selecting micro-colonies from one-fifth strength modified R2A agar medium after a long incubation period. 16S rRNA gene sequence analysis indicated that the strain is related to members of the phylum Armatimonadetes (formerly called candidate phylum OP10). Strain Gsoil 348T is mesophilic, strictly aerobic, non-motile and rod-shaped. It only grows in low nutrient media. The major respiratory quinones are menaquinones MK-11 and MK-10, and the main fatty acids are iso-C15:0, iso-C17:0, C16:0 and C16:1 ω11c. The G+C content is 61.4 mol%. The 16S rRNA gene sequences in public databases belonging to the phylum Armatimonadetes were clustered here into 6 groups. Five of these groups constituted a coherent cluster distinct from the sequences of other phyla in phylogenetic trees that were constructed using multiple-outgroup sequences from 49 different phyla. On the basis of polyphasic taxonomic analyses, it is proposed that strain Gsoil 348T (= KACC 14959T = JCM 17079T) should be placed in Fimbriimonas ginsengisoli gen. nov., sp. nov., as the cultured representative of the Fimbriimonadia class. nov., corresponding with Group 4 of the phylum Armatimonadetes.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • An DS, Lee HG, Im WT, Liu OM, Lee ST (2007) Segetibacter koreensis gen. nov., sp nov., a novel member of the phylum Bacteroidetes, isolated from the soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 57:1828–1833

    Article  PubMed  CAS  Google Scholar 

  • Atlas RM (1993) Handbook of microbiological media. CRC Press, Boca Raton

  • Buck JD (1982) Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993

    PubMed  CAS  Google Scholar 

  • Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM (2005) The ribosomal database project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33:D294–D296

    Article  PubMed  CAS  Google Scholar 

  • Connon SA, Giovannoni SJ (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68:3878–3885

    Article  PubMed  CAS  Google Scholar 

  • Cruz-Martinez K, Suttle KB, Brodie EL, Power ME, Andersen GL, Banfield JF (2009) Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J 3:738–744

    Article  PubMed  CAS  Google Scholar 

  • Dalevi D, Hugenholtz P, Blackall LL (2001) A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data. Int J Syst Evol Microbiol 51:385–391

    PubMed  CAS  Google Scholar 

  • Geissinger O, Herlemann DPR, Morschel E, Maier UG, Brune A (2009) The Ultramicrobacterium “Elusimicrobium minutum” gen. nov., sp nov., the first cultivated representative of the termite group 1 phylum. Appl Environ Microbiol 75:2831–2840

    Article  PubMed  CAS  Google Scholar 

  • Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685

    Article  PubMed  CAS  Google Scholar 

  • Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469

    Article  CAS  Google Scholar 

  • Hugenholtz P, Goebel BM, Pace NR (1998a) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774

    PubMed  CAS  Google Scholar 

  • Hugenholtz P, Pitulle C, Hershberger KL, Pace NR (1998b) Novel division level bacterial diversity in a yellowstone hot spring. J Bacteriol 180:366–376

    PubMed  CAS  Google Scholar 

  • Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 69:7210–7215

    Article  PubMed  CAS  Google Scholar 

  • Jumas-Bilak E, Roudiere L, Marchandin H (2009) Description of ‘Synergistetes’ phyl. nov and emended description of the phylum ‘Deferribacteres’ and of the family Syntrophomonadaceae, phylum ‘Firmicutes’. Int J Syst Evol Microbiol 59:1028–1035

    Article  PubMed  CAS  Google Scholar 

  • Kim MK, Im WT, Ohta H, Lee M, Lee ST (2005) Sphingopyxis granuli sp. nov., a beta-glucosidase-producing bacterium in the family Sphingomonadaceae in alpha-4 subclass of the Proteobacteria. J Microbiol 43:152–157

    PubMed  CAS  Google Scholar 

  • Komagata K, Suzuki K (1987) Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207

    Article  CAS  Google Scholar 

  • Lee M, Ten LN, Lee HW, Oh HW, Im WT, Lee ST (2008) Sphingopyxis ginsengisoli sp nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 58:2342–2347

    Article  PubMed  CAS  Google Scholar 

  • Lee KCY, Dunfield PF, Morgan XC, Crowe MA, Houghton KM, Vyssotski M, Ryan JLJ, Lagutin K, McDonald IR, Stott MB (2011) Chthonomonas calidirosea gen. nov., sp nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10. Int J Syst Evol Microbiol 61:2482–2490

    Article  PubMed  CAS  Google Scholar 

  • Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  • Minnikin DE, Odonnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  • Moore DD, Dowhan D (1995) Preparation and analysis of DNA. In: Ausubel FW, Brent R, Kingston RE et al (eds) Current protocols in molecular biology. Wiley, New York, pp 2–11

    Google Scholar 

  • Mori K, Yamaguchi K, Sakiyama Y, Urabe T, Suzuki K (2009) Caldisericum exile gen. nov., sp nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov and Caldisericia classis nov. Int J Syst Evol Microbiol 59:2894–2898

    Article  PubMed  CAS  Google Scholar 

  • Pace NR (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 73:565–576

    Article  PubMed  CAS  Google Scholar 

  • Portillo MC, Gonzalez JM (2009) Members of the candidate division OP10 are spread in a variety of environments. World J Microbiol Biotechnol 25:347–353

    Article  CAS  Google Scholar 

  • Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig WG, Peplies J, Glockner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196

    Article  PubMed  CAS  Google Scholar 

  • Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394

    Article  PubMed  CAS  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc, Newark

  • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541

    Article  PubMed  CAS  Google Scholar 

  • Stott MB, Crowe MA, Mountain BW, Smirnova AV, Hou SB, Alam M, Dunfield PF (2008) Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol 10:2030–2041

    Article  PubMed  CAS  Google Scholar 

  • Tamaki H, Tanaka Y, Matsuzawa H, Muramatsu M, Meng XY, Hanada S, Mori K, Kamagata Y (2011) Armatimonas rosea gen. nov., sp nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. Int J Syst Evol Microbiol 61:1442–1447

    Article  PubMed  Google Scholar 

  • Ten LN, Im WT, Kim MK, Kang MS, Lee ST (2004) Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 56:375–382

    Article  PubMed  CAS  Google Scholar 

  • Tschech A, Pfennig N (1984) Growth yield increase linked to caffeate reduction in Acetobacterium woodii. Arch Microbiol 137:163–167

    Article  CAS  Google Scholar 

  • Widdel F, Bak F (1992) Gram-negative mesophilic sulfate reducing bacteria. In: Balows A, Truper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes. Springer, New York

  • Widdel F, Kohring G, Mayer F (1983) Studies in dissimilatory sulfate-reducing bacteria that decompose fatty acids III. Characterization of the filamentous gliding Desulfonema limicola gen. nov., sp. nov. and Desulfonema magnum sp. nov. Arch Microbiol 134:286–294

    Article  CAS  Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271

    PubMed  CAS  Google Scholar 

  • Yoon MH, Im WT (2007) Flavisolibacter ginsengiterrae gen. nov., sp nov and Flavisolibacter ginsengisoli sp nov., isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 57:1834–1839

    Article  PubMed  CAS  Google Scholar 

  • Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, Nakamura K (2003) Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol 53:1155–1163

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the Global Frontier Intelligent Biosystem Design and Synthesis Center Program, Ministry of Science and Technology and by the project on survey and excavation of Korean indigenous species of the National Institute of Biological Resources (NIBR) under the Ministry of Environment, Korea. We thank Jean Euzéby for his comments on specific etymology and nomenclature.

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea

    Wan-Taek Im & Sung-Taik Lee

  2. Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, People’s Republic of China

    Zi-Ye Hu, Han Meng & Zhe-Xue Quan

  3. Department of Microbiology, Pukyong National University, Pusan, 608-737, Korea

    Kyoung-Ho Kim

  4. Department of Microbiology, Chungbuk National University, Cheongju, 361-763, Korea

    Sung-Keun Rhee

Authors
  1. Wan-Taek Im
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zi-Ye Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kyoung-Ho Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sung-Keun Rhee
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Han Meng
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sung-Taik Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Zhe-Xue Quan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zhe-Xue Quan.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 968 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Im, WT., Hu, ZY., Kim, KH. et al. Description of Fimbriimonas ginsengisoli gen. nov., sp. nov. within the Fimbriimonadia class nov., of the phylum Armatimonadetes . Antonie van Leeuwenhoek 102, 307–317 (2012). https://doi.org/10.1007/s10482-012-9739-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-012-9739-6

Keywords

Search

Navigation