Skip to main content
SpringerLink
Log in

Saccharopolyspora hattusasensis sp. nov., isolated from soil

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

Abstract

A Saccharopolyspora strain, designated CR3506T, isolated from a soil sample collected from Sungurlu, Corum, Turkey, was examinated using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence analysis showed that the strain is closely related to the type strains of Saccharopolyspora spinosa NRRL 18395T (99.1%), Saccharopolyspora phatthalungensis NRRL B-24798T (98.4%) and Saccharopolyspora shandongensis 88T (98.1%); low levels of DNA–DNA relatedness were found between the isolate and S. spinosa and S. phatthalungensis (<50%). Strain CR3506T was found to have chemotaxonomic and phylogenetic properties consistent with its classification in the genus Saccharopolyspora. The strain contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained arabinose and galactose. The polar lipids were identified as phosphatidylmethylethanolamine, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinones (>10%) were MK-9(H4) and MK-8(H4). Major fatty acids were (>10%) iso-C16:0, C15:03OH, C18:0 and iso-C15:0. Further, the morphological, physiological and biochemical characteristics of strain CR3506T are distinct from S. spinosa and other species of the genus Saccharopolyspora with which this strain has high 16S rRNA gene sequence similarity (98.0–98.5%). Strain CR3506T has antimicrobial activity against Bacillus subtilis NRRL B-209, Citrobacter freundi NRRL B-2643 and Staphylococcus aureus ATCC 29213. Consequently, it is proposed that strain CR3506T represents a novel Saccharopolyspora species for which the name Saccharopolyspora hattusasensis sp. nov. is proposed. The type strain is CR3506T (=KCTC 29104T = DSM 45715T).

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

Similar content being viewed by others

References

  • Cheng J, Zhang YG, Chen W, Li L, Zhang DF, Wang HF, Lu XH, Duan YQ, Li WJ (2013) Saccharopolyspora cavernae sp. nov., a novel actinomycete isolated from the Swallow Cave in Yunnan, south-west China. Antonie Van Leeuwenhoek 104(5):837–843

    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 

  • 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 

  • Duangmal K, Mingma R, Thamchaipenet A, Matsumoto A, Takahashi Y (2010) Saccharopolyspora phatthalungensis sp. nov., isolated from rhizosphere soil of Hevea brasiliensis. Int J Syst Evol Microbiol 60(8):1904–1908

    Article  CAS  PubMed  Google Scholar 

  • Embley TM, Wait R, Dobson G, Goodfellow M (1987) Fatty acid composition in the classification of Saccharopolyspora hirsuta. FEMS Microbiol Lett 41:131–135

    Article  CAS  Google Scholar 

  • Embley TM, Smida J, Stackebrandt E (1988) The phylogeny of mycolate-less wall chemotype IV actinomycetes and description of Pseudonocardiaceae fam. nov. Syst Appl Microbiol 11:44–52

    Article  CAS  Google Scholar 

  • Fabre B, Velours J, Etienne G, Legendre F, Tiraby G (1993) CL307-24, a new antibiotic complex from Saccharopolyspora aurantiaca sp. nov. II. Physico-chemical and biological properties. J Antibiot 46(9):1421–1427

    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  PubMed  Google Scholar 

  • Goodfellow M, Lacey J, Athalye M, Embley TM, Bowen T (1989) Saccharopolyspora gregorii and Saccharopolyspora hordei: two new actinomycete species from fodder. J Gen Microbiol 135:2125–2139

    CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Jiang Y, Wei X, Chen X, Jiang Y, Xue Q, Lai H, Jiang C (2016) Saccharopolyspora griseoalba sp. nov., a novel actinomycete isolated from the Dead Sea. Antonie Van Leeuwenhoek 109(12):1635–1641

    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 

  • 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 HJ, White-Phillip JA, Ogasawara Y, Shin N, Isiorho EA, Liu HW (2010) Biosynthesis of spinosyn in Saccharopolyspora spinosa: synthesis of permethylated rhamnose and characterization of the functions of SpnH, SpnI, and SpnK. J Am Chem Soc 132:2901–2903

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    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 

  • Korn-Wendisch F, Kempf A, Grund E, Kroppenstedt RM, Kutzner HJ (1989) Transfer of Faenia rectivirgula (Kurup and Agre 1983) to the genus Saccharopolyspora as Saccharopolyspora rectivirgula comb. nov. and emended genus description of Saccharopolyspora. Int J Syst Bacteriol 39:430–441

    Article  Google Scholar 

  • Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger. J Liquid 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

    Chapter  Google Scholar 

  • Lacey J, Goodfellow M (1975) A novel actinomycete from sugarcane bagasse: saccharopolyspora hirsuta gen. et sp. nov. J Gen Microbiol 88:75–85

    Article  CAS  PubMed  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 

  • Lu Z, Liu Z, Wang L, Zhang Y, Qi W, Goodfellow M (2001) Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp. nov., novel actinomycetes from soil. Int J Syst Evol Microbiol 51:319–325

    Article  CAS  PubMed  Google Scholar 

  • Lv L-L, Zhang Y-F, Xia Z-F, Zhang J-J, Zhang L-L (2014) Saccharopolyspora halotolerans sp. nov., a halophilic actinomycete isolated from a hypersaline lake. Int J Syst Evol Microbiol 64:3532–3537

    Article  PubMed  Google Scholar 

  • Mandel M, Marmur J (1968) Use of ultraviolet absorbance-temperature profiles for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B:195

    Article  Google Scholar 

  • Marmur J (1961) A procedure for the isolation of desoxyribonucleic acid from microorganisms. J Mol Biol 3:208

    Article  CAS  Google Scholar 

  • Mertz FP, Yao RC (1990) Saccharopolyspora spinosa sp. nov. isolated from soil collected in a sugar mill rum still. Int J Syst Bacteriol 40(1):34–39

    Article  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 

  • Nash P, Krent MM (1991) Culture media. In: Balows 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 

  • 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, DE

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

    Article  Google Scholar 

  • Stackebrandt E, Rainey FA, Ward-Rainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491

    Article  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 

  • Sun M, Ou J, Li W, Lu C (2017) Quinoline and naphthalene derivatives from Saccharopolyspora sp. YIM M13568. J Antibiot 70:320–322

    Article  CAS  PubMed  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 

  • Tan GYA, Ward AC, Goodfellow M (2006) Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Syst Appl Microbiol 29:557–569

    Article  CAS  PubMed  Google Scholar 

  • Tittsler RP, Sandholzer LA (1936) The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 31:575–580

    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 

  • Warwick S, Bowen T, McVeigh H, Embley TM (1994) A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia. Int J Syst Bacteriol 44:293–299

    Article  CAS  PubMed  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 

  • Wu H, Liu B, Pan S (2016) Saccharopolyspora subtropica sp. nov., a thermophilic actinomycete isolated from soil of a sugar cane field. Int J Syst Evol Microbiol 66(5):1990–1995

    Article  CAS  PubMed  Google Scholar 

  • Yassin AF (2009) Saccharopolyspora rosea sp. nov., isolated from a patient with bronchial carcinoma. Int J Syst Evol Microbiol 59:1148–1152

    Article  CAS  PubMed  Google Scholar 

  • Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y, Seo H, Chun J (2016) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol. doi:10.1099/ijsem.0.001755

    Google Scholar 

  • Yuan L-J, Zhang Y-Q, Guan Y, Wei Y-Z, Li Q-P, Yu L-Y, Li W-J, Zhang Y-Q (2008) Saccharopolyspora antimicrobica sp. nov., an actinomycete from soil. Int J Syst Evol Microbiol 58:1180–1185

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Wu D, Zhang J, Liu Z, Song F (2008) Saccharopolyspora shandongensis sp. nov., isolated from wheat-field soil. Int J Syst Evol Microbiol 58(5):1094–1099

    Article  CAS  PubMed  Google Scholar 

  • Zhang YJ, Zhang WD, Qin S, Bian GK, Xing K, Li YF, Cao CL, Jiang JH (2013) Saccharopolyspora dendranthemae sp. nov. a halotolerant endophytic actinomycete isolated from a coastal salt marsh plant in Jiangsu, China. Antonie Van Leeuwenhoek 103(6):1369–1376

    Article  CAS  PubMed  Google Scholar 

  • Zhi XY, Li WJ, Stackebrandt E (2009) An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59:589–608

    Article  CAS  PubMed  Google Scholar 

  • Zhou ZH, Liu ZH, Qian YD, Kim SB, Goodfellow M (1998) Saccharopolyspora spinosporotrichia sp. nov., a novel actinomycete from soil. Int J Syst Bacteriol 48:53–58

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

This research was supported by Ondokuz Mayis University (OMU), Project No. PYO. FEN. 1901.12.014 and Ondokuz Mayis University (OMU), Project No. PYO. FEN. 1901.09.003.

Author information

Authors and Affiliations

  1. Department of Bioengineering, Faculty of Engineering and Architecture, Sinop University, 57000, Sinop, Turkey

    Aysel Veyisoglu

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

    Hayrettin Saygin & Nevzat Sahin

  3. Department of Medical Documentation and Secretary, Osmancık Omer Derindere Vocational Higher School, Hitit University, 19500, Corum, Turkey

    Demet Tatar

  4. Department of Molecular Biology and Genetics, Faculty of Sciences, Karadeniz Technical University, 61080, Trabzon, Turkey

    Kadriye Inan Bektas

Authors
  1. Aysel Veyisoglu
    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. Demet Tatar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kadriye Inan Bektas
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Nevzat Sahin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nevzat Sahin.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

The GenBank accession number for the 16S rRNA gene sequence of Saccharopolyspora hattusasensis CR3506T (=KCTC 29104T = DSM 45715T) is JN989298.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Fig. S1

Scanning electron micrograph of strain CR3506T grown on ISP 3 agar at 30 °C for 21 days. Bar, 1 µm (JPEG 144 kb)

Supplementary Fig. S2

Two-dimensional TLC of polar lipids from strain CR3506T. For detection of polar lipids, molybdophosphoric acid (DPG, diphosphatidylglycerol; PME, phosphatidylmethylethanolamine; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PC, phosphatidylcholine; PI, phosphatidylinositol; 6PL, six unidentified polar lipids) was applied. (JPEG 63 kb)

Supplementary Fig. S3

Maximum-likelihood tree based on almost complete 16S rRNA gene sequences showing the position of strain CR3506T with the Saccharopolyspora gene tree. Numbers at the nodes indicate levels of bootstrap support (%), only values ≥50 % are shown. Bar, 0.01 substitutions per nucleotide position. Supplementary Fig. S4. Maximum-parsimony tree based on almost complete 16S rRNA gene sequences showing the position of strain CR3506T with the Saccharopolyspora gene tree. Numbers at the nodes indicate levels of bootstrap support (%), only values ≥50 % are shown (DOC 396 kb)

Supplementary Table S1

Cellular fatty acid profiles of strain CR3506T and the type strains of related species (DOC 54 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Veyisoglu, A., Saygin, H., Tatar, D. et al. Saccharopolyspora hattusasensis sp. nov., isolated from soil. Antonie van Leeuwenhoek 110, 1719–1727 (2017). https://doi.org/10.1007/s10482-017-0921-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-017-0921-8

Keywords

Search

Navigation