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Dyadobacter luteus sp. nov., isolated from rose rhizosphere soil

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Abstract

A novel Gram-negative, aerobic, rod-shaped bacterium, RS19T, was isolated from rose rhizosphere soil. The strain was psychrophilic and showed good growth over a temperature range of 1–37 ℃. Colonies on TSB agar were circular, smooth, mucoid, convex with clear edges and yellow. Phylogenetic analysis based on 16S rRNA gene sequences characterized RS19T in the genus Dyadobacter and showed that strain RS19T was most closely related to Dyadobacter psychrophilus CGMCC 1.8951T (97.4%) and Dyadobacter alkalitolerans CGMCC 1.8973T (97.1%). The average nucleotide identity values to the closest related species type strains were less than 84.0%. The DNA G + C content was 43.1 mol%, and the predominant respiratory menaquinone was MK-7. The major fatty acids were summed features 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0, C16:1ω5c and iso-C17:0 3-OH. Based on genotypic, phenotypic and chemotaxonomic data, strain RS19T is different from closely related species of the genus Dyadobacter. RS19T represents a novel species within the genus Dyadobacter, for which the name Dyadobacter luteus sp. nov. is proposed. The type strain is RS19T (= CGMCC 1.13719T = ACCC 60381T = JCM 32940T).

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Abbreviations

NCBI:

National Center for Biotechnology Information database

NJ:

Neighbor joining

ML:

Maximum-likelihood

ME:

Minimum evolution

ORFs:

Open-reading frames

ANI:

Average nucleotide identities

TSB:

Tryptic soy broth

TSA:

Tripticase soy agar

PE:

Phosphatidylethanolamine

PL:

Unidentified phospholipid

AL:

Aminolipids

L:

Unidentified lipids

MK-7:

Menaquinone-7

References

  • Baik KS, Kim MS, Kim EM, Kim HR, Seong CM (2007) Dyadobacter koreensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 57:1227–1231

    Article  CAS  Google Scholar 

  • Chaturvedi P, Reddy GSN, Shivaji S (2005) Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India. Int J Syst Evol Microbiol 55:2113–2117

    Article  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  CAS  Google Scholar 

  • Chen L, Jiang F, Xiao M, Dai J, Kan W, Fang C, Peng F (2012) Dyadobacter arcticus sp. nov., isolated from high Arctic soil on the Svalbard Archipelago, Norway. Int J Syst Evol Microbiol 63:1616–1620

    Article  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  CAS  Google Scholar 

  • Coil D, Jospin G, Darling AE (2015) A5-miseq: An updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31:587–589

    Article  CAS  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  Google Scholar 

  • Dahal RH, Kim J (2018) Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov., two novel members of the family Cytophagaceae isolated from forest soil. Arch Microbiol 7:1067–1074

    Article  Google Scholar 

  • Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679

    Article  CAS  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  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91

    Article  CAS  Google Scholar 

  • Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    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  CAS  Google Scholar 

  • Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12

    Article  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  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Meier-Kolthoff JP, Klenk HP, Göker M (2014) Taxonomic use of DNA G + C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356

    Article  CAS  Google Scholar 

  • Miller RA, Beno SM, Kent DJ, Carroll ML, Martin NH, Boor KJ, Kovac J (2016) Bacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments. Int J Syst Evol Microbiol 66:4744–4753

    Article  CAS  Google Scholar 

  • Minnikin DE, Patel PV, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of nocardia and related bacteria. Int J Syst Bacteriol 27:104–117

    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 soil 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  CAS  Google Scholar 

  • Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 106:19126–19131

    Article  CAS  Google Scholar 

  • Sasser M (2001) Identification of bacteria by gas chromatography of cellular fatty acids. Tech Note 101:1–6

    Google Scholar 

  • Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863–864

    Article  CAS  Google Scholar 

  • Shen L, Liu Y, Yao T, Wang N, Xu B, Jiao N, Liu H, Zhou Y, Liu X, Wang Y (2013) Dyadobacter tibetensis sp. nov., isolated from glacial ice core. Int J Syst Evol Microbiol 63:3636–3639

    Article  CAS  Google Scholar 

  • Song Z, Song Y, Yu Y, Choi L, Wang G, Li M (2019) Dyadobacter luticola sp. nov., isolated from a sewage sediment sample. Int J Syst Evol Microbiol 69:465–469

    Article  CAS  Google Scholar 

  • Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci 101:11030–11035

    Article  CAS  Google Scholar 

  • Tang Y, Dai J, Zhang L, Mo Z, Wang Y, Li Y, Ji S, Fang C, Zheng C (2009) Dyadobacter alkalitolerans sp. nov., isolated from desert sand. Int J Syst Evol Microbiol 59:60–64

    Article  CAS  Google Scholar 

  • 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 25:4876–4882

    Article  CAS  Google Scholar 

  • Tian M, Zhang RG, Han L, Zhao XM, Lv J (2015) Dyadobacter sediminis sp. nov., isolated from a subterranean sediment sample. Int J Syst Evol Microbiol 65:827–832

    Article  CAS  Google Scholar 

  • Wang L, Chen L, Ling O, Li C, 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  CAS  Google Scholar 

  • Xie C-H, Yokota A (2003) Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 49:345–349

    Article  CAS  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  CAS  Google Scholar 

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Acknowledgements

We would like to thank Prof. Aharon Oren for very valuable help in naming the organism. We thank Yu Luo for the help with acquisition of the SEM images of the strain.

Funding

This work was supported by the Fundamental Research Funds for the Central Non-profit Research Institution of the Chinese Academy of Forestry (CAFYBB2017MA020, CAFYBB2017MA017) and National Natural Science Foundation of China (31700548, 31700571).

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Authors and Affiliations

  1. Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, 102300, People’s Republic of China

    Lin Chen, Xu Gao, Qinghua Ma, Huihui Liu, Xinghong Wang & Yan Xu

  2. Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People’s Republic of China

    Yunpeng Liu

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  1. Lin Chen
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  2. Xu Gao
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  3. Qinghua Ma
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Correspondence to Yunpeng Liu.

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Communicated by Erko Stackebrandt.

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The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene and genome of Dyadobacter luteus sp. nov. strain RS19T are MH558673 and QNUL00000000. The digital protologue database (DPD) Taxon Number of strain RS19T is TA01031.

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Chen, L., Gao, X., Ma, Q. et al. Dyadobacter luteus sp. nov., isolated from rose rhizosphere soil. Arch Microbiol 202, 191–196 (2020). https://doi.org/10.1007/s00203-019-01738-5

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  • DOI: https://doi.org/10.1007/s00203-019-01738-5

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