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Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov., two novel members of the family Cytophagaceae isolated from forest soil

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Abstract

Two strains of bacteria designated strains S-53T and A27T were isolated from forest soil and subjected to polyphasic characterization. Cells were aerobic, Gram-staining-negative, catalase- and oxidase- positive, non-motile, non-spore-forming, rod-shaped, and yellow-pigmented. Flexirubin-type pigments were present. Both strains were positive for PNPG, hydrolysed casein, and tyrosine. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strains S-53T and A27T formed a lineage within the family Cytophagaceae that were distinct from various members of the genus Dyadobacter (98.9–93.2% sequence similarity). Closest member for strain S-53T was Dyadobacter jejuensis AM1R11T (95.7%) and for A27T Dyadobacter endophyticus 65T (98.9%). The predominant respiratory quinone was MK-7 for both strains. The major polar lipid for both strains was phosphatidylethanolamine. The major cellular fatty acids for both strains were summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0, C16:1ω5c, and C16:0. The DNA G+C content of strains ranges from 46.5 to 48.7 mol%. On the basis of phenotypic, genotypic, chemotaxonomic, and phylogenetic analysis, both strains S-53T and A27T represent a novel member in the genus Dyadobacter, for which the name Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov. are proposed, respectively. The type strain of D. flavus is S-53T (= KEMB 9005-541T = KACC 19149T = NBRC 112681T) and type strain of D. terricola is A27T (= KEMB 9005-524T = KACC 19147T = NBRC 112680T).

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References

  • Breznak JA, Costilow RN (2007) Physicochemical factors in growth. In: Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR (eds) Methods for general and molecular bacteriology, 3rd edn. American Society for Microbiology, Washington, D.C., pp 309–329

    Google Scholar 

  • Card GL (1973) Metabolism of phosphatidylglycerol, phosphatidylethanolamide and cardiolipin of Bacillus stearothermophilus. J Bacteriol 114:1125–1137

    PubMed  PubMed Central  CAS  Google Scholar 

  • Chelius MK, Triplett EW (2000) Dyadobacter fermentans gen. nov., sp. nov., a novel Gram-negative bacterium isolated from surface-sterilized Zea mays stems. Int J Syst Evol Microbiol 50:751–758

    Article  PubMed  CAS  Google Scholar 

  • Chen L, Jiang F, Xiao M, Dai J, Kan W, Fang C, Peng F (2013) Dyadobacter articus sp. nov., isolated from Arctic soil. Int J Syst Evol Microbiol 63:1616–1620

    Article  PubMed  CAS  Google Scholar 

  • Chun J, Kang JY, Joung Y, Kim H, Joh K, Jahng KY (2013) Dyadobacter jejuensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 63:1788–1792

    Article  PubMed  CAS  Google Scholar 

  • Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354

    PubMed  PubMed Central  CAS  Google Scholar 

  • Dahal RH, Kim J (2017) Microvirga soli sp. nov., a novel alphaproteobacterium from soil. Int J Syst Evol Microbiol 67:127–132

    Article  PubMed  Google Scholar 

  • Doetsch RN (1981) Determinative methods of light microscopy. In: Gerhardt P (ed) Manual of methods for general bacteriology. American Society for Microbiology, Washington, DC, pp 21–33

    Google Scholar 

  • Dong Z, Guo X, Zhang X, Qiu F, Sun L, Gong H, Zhang F (2007) Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China. Int J Syst Evol Microbiol 57:862–865

    Article  PubMed  CAS  Google Scholar 

  • Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric DNA–DNA hybridization in microdilution wells as an alternative to member filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 39:224–229

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, Olsen GJ (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA gene. Appl Environ Microbiol 74:2461–2470

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Yuan M, Yang MM, Sun JG (2016) Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 66:4022–4026

    Article  PubMed  CAS  Google Scholar 

  • Hall TA (1999) BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  PubMed  CAS  Google Scholar 

  • Komagata K, Suzuki K (1987) Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 19:161–203

    Article  CAS  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  PubMed  CAS  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007)) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  PubMed  CAS  Google Scholar 

  • Lee M, Woo SG, Park J, Yoo SA (2010) Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil. Int J Syst Evol Microbiol 60:2577–2582

    Article  PubMed  CAS  Google Scholar 

  • Liu QM, Im WT, Lee M, Yang DC, Lee ST (2006) Dyadobacter ginsengisoli sp. nov., isolated from soil of ginseng field. Int J Syst Evol Microbiol 56:1939–1944

    Article  PubMed  CAS  Google Scholar 

  • Ludwig W, Euzéby J, Whitman WB (2011) Taxonomic outlines of the phyla Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. In: Whitman W Bergey’s manual of systematic bacteriology, vol 4, 2nd edn. The Williams & Wilkins Co., Baltimore, pp 21–24

    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 Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  • Minnikin DE, O’Donnell 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 

  • Reddy GSN, Garcia-Pichel F (2005) Dyadobacter crusticola sp. nov., from biological crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000. Int J Syst Evol Microbiol 55:1295–1299

    Article  PubMed  CAS  Google Scholar 

  • Reichenbach H (1992) The order Cytophagales. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The Prokaryotes, vol 4, 2nd edn. Springer, New York, pp 3631–3675

    Chapter  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

  • Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for General and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  • 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 44:846–849

    Article  CAS  Google Scholar 

  • Stanier RY (1940) Studies on the Cytophagas. J Bacteriol 40:619–635

    PubMed  PubMed Central  CAS  Google Scholar 

  • Wang L, Chen L, Ling Q, Li CC, Tao Y, Wang M (2015) Dyadobacter jiangsuensis sp. nov., a methyl red degrading bacterium isolated from a dye-manufacturing factory. Int J Syst Evol Microbiol 65:1138–1143

    Article  PubMed  CAS  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 systematic. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Wilson K 1997) Preparation of genomic DNA from bacteria. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K(eds) Current protocols in molecular biology. Wiley, New York, pp 2.4.1–2.4.5

    Google Scholar 

  • 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 67:1613–1617

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang DC, Liu HC, Xin YH, Zhou YG, Schinner F, Margesin R (2010) Dyadobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 60:1640–1643

    Article  PubMed  CAS  Google Scholar 

Download references

Funding

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2016R1D1A1A09916982).

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Authors and Affiliations

  1. Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do, 16227, South Korea

    Ram Hari Dahal & Jaisoo Kim

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  1. Ram Hari Dahal
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  2. Jaisoo Kim
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Correspondence to Jaisoo Kim.

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The authors declare that there are no conflicts of interest regarding the publication of this manuscript.

Ethical statement

This study does not describe any experimental work related to human.

Additional information

Communicated by Erko Stackebrandt.

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains S-53T and A27T are KY117465 and KY117482, respectively. The Digital Protologue database Taxon Number for strains S-53T and A27T is TA00416 and TA00417, respectively.

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Dahal, R.H., Kim, J. Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov., two novel members of the family Cytophagaceae isolated from forest soil. Arch Microbiol 200, 1067–1074 (2018). https://doi.org/10.1007/s00203-018-1521-3

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  • DOI: https://doi.org/10.1007/s00203-018-1521-3

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