Skip to main content
SpringerLink
Log in

Kribbella soli sp. nov., isolated from soil

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

Abstract

A novel actinobacterial strain, designated FMN22T, was isolated from soil and characterised using a polyphasic approach. Strain FMN22T showed high 16S rRNA gene sequence similarity to Kribbella karoonensis Q41T (99.3%), Kribbella shirazensis UTMC 693T (99.0%), Kribbella aluminosa HKI 0478T (98.9%) and Kribbella hippodromi S1.4T (98.6%). Phylogenetic analysis using the 16S rRNA and concatenated gene (gyrB, rpoB, relA, recA and atpD) sequences showed that strain FMN22T is closely related to the type strains of K. karoonensis DSM 17344T, K. shirazensis UTMC 693T, K. aluminosa HKI 0478T, K. hippodromi S1.4T, Kribbella jejuensis HD9T and Kribbella solani DSA1T. Based on concatenated gene genetic distances analysis, strain FMN22T is distinct from all Kribbella type strains. DNA–DNA hybridization experiments with closely related type strains, were found to be 59.2 ± 2.4, 54.8 ± 2.1, 16.4 ± 2.3 and 38.6 ± 2.5%, relatedness to K. karoonensis DSM 17344T, K. shirazensis DSM 45490T, K. aluminosa DSM 18824T and K. jejuensis DSM 17305T, respectively. The cell wall peptidoglycan contained ll-diaminopimelic acid, and whole cell sugars were glucose, mannose and ribose. The predominant menaquinone was MK-9(H4). The major phospholipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol. Major fatty acids are anteiso-C15:0 and iso-C16:0. These chemotaxonomic traits are in good agreement with those known for representatives of the genus Kribbella. A combination of DNA–DNA hybridization results and phenotypic properties demonstrated that strain FMN22T can be clearly distinguished from all close phylogenetic relatives. Therefore, strain FMN22T (=DSM 27132T = KCTC 29219T) is considered to be the type strain of a novel species of the genus Kribbella, for which the name Kribbella soli is proposed.

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

  • Carlsohn MR, Groth I, Spröer C, Schütze B, Saluz HP, Munder T, Stackebrandt E (2007) Kribbella aluminosa sp. nov., isolated from a medieval alum slate mine. Int J Syst Evol Microbiol 57:1943–1947

    Article  CAS  PubMed  Google Scholar 

  • Cashion P, Holder-Franklin MA, Mc Cully J, Franklin M (1977) A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81:461–466

    Article  CAS  PubMed  Google Scholar 

  • Chun J, Goodfellow M (1995) A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45:240–245

    Article  CAS  PubMed  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    Article  CAS  PubMed  Google Scholar 

  • Curtis SM, Meyers PR (2012) Multilocus sequence analysis of the actinobacterial genus Kribbella. Syst Appl Microbiol 35:441–446

    Article  CAS  PubMed  Google Scholar 

  • De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:143–153

    Article  PubMed  Google Scholar 

  • Euzéby JP (2012) Genus Kribbella. List of Prokaryotic Names with Standing in Nomenclature. http://www.bacterio.net/ijk/kribbella.html

  • Everest GJ, Meyers PR (2008) Kribbella hippodromi sp. nov., isolated from soil from a racecourse in South Africa. Int J Syst Evol Microbiol 58:443–446

    Article  CAS  PubMed  Google Scholar 

  • Everest GJ, Curtis SM, De Leo F, Urzì C, Meyers PR (2013) Kribbella albertanoniae sp. nov., isolated from a Roman catacomb, and emended description of the genus Kribbella. Int J Syst Evol Microbiol 63:3591–3596

    Article  CAS  PubMed  Google Scholar 

  • Everest GJ, Curtis SM, De Leo F, Urzì C, Meyers PR (2015) Description of Kribbella italica sp. nov., isolated from a Roman catacomb. Int J Syst Evol Microbiol 65:491–496

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogeny: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Gonzalez JM, Saiz-Jimenez C (2005) A simple fluorimetric method for the estimation of DNA–DNA relatedness between closely related microorganisms by thermal denaturation temperatures. Extremophiles 9:75–79

    Article  CAS  PubMed  Google Scholar 

  • Huss VAR, Festl H, Schleifer KH (1983) Studies on the spectrometric determination of DNA hybridisation from renaturation rates. Syst Appl Microbiol 4:184–192

    Article  CAS  PubMed  Google Scholar 

  • Jones KL (1949) Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 57:141–145

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol 3. Academic Press, New York, pp 21–132

    Chapter  Google Scholar 

  • Kaewkla O, Franco CMM (2016) Kribbella pittospori sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of an Australian native apricot tree, Pittosporum angustifolium. Int J Syst Evol Microbiol 66:2284–2290

    Article  PubMed  Google Scholar 

  • Kämpfer P, Kroppenstedt RM (1996) Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005

    Article  Google Scholar 

  • Kelly KL (1964) Inter-society color council-national bureau of standards color-name charts illustrated with centroid colors. US Government Printing Office, Washington, DC

    Google Scholar 

  • Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M, Na H, Park S-C, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  CAS  PubMed  Google Scholar 

  • Kirby BM, Le Roes M, Meyers PR (2006) Kribbella karoonensis sp. nov. and Kribbella swartbergensis sp. nov., isolated from soil from the Western Cape, South Africa. Int J Syst Evol Microbiol 56:1097–1101

    Article  CAS  PubMed  Google Scholar 

  • Kirby BM, Everest GJ, Meyers PR (2010) Phylogenetic analysis of the genus Kribbella based on the gyrB gene: proposal of a gyrB-sequence threshold for species delineation in the genus Kribbella. Antonie Van Leeuwenhoek 97:131–142

    Article  CAS  PubMed  Google Scholar 

  • Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32

    Article  Google Scholar 

  • Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger. J Liq Chromatogr 5:2359–2387

    Article  CAS  Google Scholar 

  • Kroppenstedt RM, Goodfellow M (2006) The Family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillispora and Thermomonospora. In: Dworkin M, Falkow S, Schleifer KH, Stackebrandt E (eds) The prokaryotes. Archaea and Bacteria: Firmicutes, Actinomycetes, vol 3, 3rd edn. Springer, New York, pp 682–724

    Google Scholar 

  • Lechevalier MP, Lechevalier HA (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443

    Article  CAS  Google Scholar 

  • Lee SD, Kang SO, Hah YC (2000) Hongia gen. nov., a new genus of the order Actinomycetales. Int J Syst Evol Microbiol 50:191–199

    Article  CAS  PubMed  Google Scholar 

  • Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal K, 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 

  • Mohammadipanah F, Hamedi J, Göker M, Fiebig A, Pukall R, Spröer C, Klenk H-P (2013) Kribbella shirazensis sp. nov., isolated from Iranian soil. Int J Syst Evol Microbiol 63:3369–3374

    Article  CAS  PubMed  Google Scholar 

  • Nash P, Krent MM (1991) Culture media. In: Ballows A, Hauser WJ, Herrmann KL, Isenberg HD, Shadomy HJ (eds) Manual of clinical microbiology, 3rd edn. American Society for Microbiology, Washington DC, pp 1268–1270

    Google Scholar 

  • Park YH, Yoon JH, Shin YK, Suzuki K, Kudo T, Seino A, Kim HJ, Lee JS, Lee ST (1999) Classification of ‘‘Nocardioides fulvus’’ IFO 14399 and Nocardioides sp. ATCC 39419 in Kribbella gen. nov., as Kribbella flavida sp. nov. and Kribbella sandramycini sp. nov. Int J Syst Bacteriol 49:743–752

    Article  CAS  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method. A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Article  Google Scholar 

  • Sohn K, Hong SG, Bae KS, Chun J et al (2003) Transfer of Hongia koreensis Lee et al. 2000 to the genus Kribbella Park et al. 1999 as Kribbella koreensis comb. nov. Int J Syst Evol Microbiol 53:1005–1007

    Article  CAS  PubMed  Google Scholar 

  • Song J, Kim BY, Hong SB, Cho HS, Sohn K, Chun J, Suh JW (2004) Kribbella solani sp. nov. and Kribbella jejuensis sp. nov., isolated from potato tuber and soil in Jeju. Korea. Int J Syst Evol Microbiol 54:1345–1348

    Article  CAS  PubMed  Google Scholar 

  • Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Waksman SA (1961) The actinomycetes, classification, identification and description of genera and species, vol 2. Williams & Wilkins, Baltimore

    Google Scholar 

  • Waksman SA (1967) The actinomycetes. A summary of current knowledge. Ronald Press, New York

    Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA, Sackin MJ (1983) Numerical classification of Streptomyces and related genera. J Gen Microbiol 129:1743–1813

    CAS  PubMed  Google Scholar 

  • Yoon JH, Park YH (2006) The genus Nocardioides. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes, vol 3. Springer, New York, pp 1099–1113

    Chapter  Google Scholar 

Download references

Acknowledgements

This research was supported by Ondokuz Mayis University (OMU), project no. PYO. FEN. 1904.09.009. We would like to thank Bettina Sträubler for excellent technical assistance.

Author information

Authors and Affiliations

  1. Department of Nursing, School of Health, Bilecik Seyh Edebali University, 11210, Bilecik, Turkey

    Fadime Ozdemir-Kocak

  2. Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139, Samsun, Turkey

    Hayrettin Saygin, Salih Saricaoglu, Nevzat Sahin & Kamil Isik

  3. Science Teaching Programme, Gazi Faculty of Education, Gazi University, 06500, Ankara, Turkey

    Demet Cetin

  4. Department of Biology, Faculty of ScienceAnadolu University, 26470, Eskisehir, Turkey

    Kiymet Guven

  5. Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrassse 7B, 38124, Brunswick, Germany

    Cathrin Spröer & Peter Schumann

  6. School of Biology, Newcastle University, Ridley Building, Newcastle upon Tyne, NE1 7RU, UK

    Hans-Peter Klenk

Authors
  1. Fadime Ozdemir-Kocak
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hayrettin Saygin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Salih Saricaoglu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Demet Cetin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kiymet Guven
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Cathrin Spröer
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Peter Schumann
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hans-Peter Klenk
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Nevzat Sahin
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Kamil Isik
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kamil Isik.

Additional information

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, gyrB, rpoB, relA, recA and atpD gene sequences of Kribbella soli FMN22T (=DSM 27132T = KCTC 29219T) are JN896613, KX348033, KX348034, KX348037, KX348036 and KX348035, respectively.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ozdemir-Kocak, F., Saygin, H., Saricaoglu, S. et al. Kribbella soli sp. nov., isolated from soil. Antonie van Leeuwenhoek 110, 641–649 (2017). https://doi.org/10.1007/s10482-017-0830-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-017-0830-x

Keywords

Search

Navigation