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Hymenobacter oligotrophus sp. nov., isolated from a contaminated agar plate

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A Correction to this article was published on 28 January 2020

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Abstract

A taxonomic study of a Gram-stain negative, rod-shaped, motile, asporogenous, catalase- and oxidase-positive bacterium, sh-6T, forming pink-red colonies, isolated from a contaminated R2A plate in the laboratory was performed. Its optimum growth temperature was determined to be 28 °C in the absence of NaCl on R2A plates. On the basis of 16S rRNA gene sequence analysis, strain sh-6T belongs to the genus Hymenobacter and is closely related to Hymenobacter deserti ZLB-3T (95.05%), Hymenobacter paludis KBP-30T (94.96%), Hymenobacter coalescens WW84T (94.04%), Hymenobacter gummosus ANT-18T (93.38%), Hymenobacter ocellatus Myx2105T (93.70%), Hymenobacter jeollabukensis 1-3-3-8T (93.48%) and Hymenobacter koreensis GYR3077T (93.21%). Comparison of the genome of strain sh-6T and that of H. gummosus ANT-18T gave digital DNA–DNA hybridization and Average Nucleotide Identity values of 20.6% and 78.4%, respectively. The respiratory isoprenoid quinone and polyamine component were identified as MK-7 and sym-homospermidine, respectively. The major cellular fatty acids identified as iso-C15:0, summed feature 4 (iso-C17:1 I/anteiso B), iso-C16:0, iso-C17:0 3-OH and iso-C17:0. The major polar lipid of strain sh-6T determined to be phosphatidylethanolamine. The DNA G+C content was determined to be 60.5 mol%. On the basis of the evidence presented in this study, a novel species of the genus Hymenobacter, Hymenobacter oligotrophus sp. nov., is proposed, with the type strain sh-6T (= CCTCC AB 2016064T = KCTC 62345T).

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Change history

  • 28 January 2020

    In the original publication, the deposit number of strain sh-6T was incorrectly published as ���CCTCC AB 2016064��� throughout the article.

References

  • Bowman JP (2000) Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50:1861–1868

    Article  CAS  PubMed  Google Scholar 

  • Buczolits S, Denner EB, Vybiral D, Wieser M, Kämpfer P, Busse HJ (2002) Classification of three airborne bacteria and proposal of Hymenobacter aerophilus sp. nov. Int J Syst Evol Microbiol 52:445–456

    Article  CAS  PubMed  Google Scholar 

  • Buczolits S, Denner EB, Kaempfer P, Busse HJ (2006) Proposal of Hymenobacter norwichensis sp nov., classification of ‘Taxeobacter ocellatus’, ‘Taxeobacter gelupurpurascens’ and ‘Taxeobacter chitinovorans’ as Hymenobacter ocellatus sp nov., Hymenobacter gelipurpurascens sp nov and Hymenobacter chitinivorans sp nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1998. Int J Syst Evol Microbiol 56:2071–2078

    Article  CAS  PubMed  Google Scholar 

  • Busse J, Auling G (1988) Polyamine pattern as a chemotaxonomic marker within the proteobacteria. Syst Appl Microbiol 11:1–8

    Article  CAS  Google Scholar 

  • Busse H-J, Bunka S, Hensel A, Lubitz W (1997) Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47:698–708

    Article  CAS  Google Scholar 

  • Chen WM, Chen ZH, Young CC, Sheu SY (2016) Hymenobacter paludis sp nov., isolated from a marsh. Int J Syst Evol Microbiol 66(3):1546–1553

    Article  CAS  PubMed  Google Scholar 

  • Chen WM, Chen WT, Young CC, Sheu SY (2017) Hymenobacter gummosus sp nov., isolated from a spring. Int J Syst Evol Microbiol 67(11):4728–4735

    Article  CAS  PubMed  Google Scholar 

  • Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10(6):563–569

    Article  CAS  PubMed  Google Scholar 

  • Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261

    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 

  • Collins MD, Hutson RA, Grant IR, Patterson MF (2000) Phylogenetic characterization of a novel radiation-resistant bacterium from irradiated pork: description of Hymenobacter actinosclerus sp nov. Int J Syst Evol Microbiol 50:731–734

    Article  PubMed  Google Scholar 

  • Doetsch RN (1981) Determinative methods of light microscopy. In: Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA et al (eds) Manual of methods for general bacteriology. American Society for Microbiology, Washington, DC, pp 21–33

    Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):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 

  • Han L, Wu SJ, Qin CY, Zhu YH, Lu ZQ, Xie B, Lv J (2014) Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter. Antonie Van Leeuwenhoek 105(5):971–978

    Article  CAS  PubMed  Google Scholar 

  • Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B, Gallikowski CA (1998) Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antarctic soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 21(3):374–383

    Article  CAS  PubMed  Google Scholar 

  • Kang JY, Chun J, Choi A, Moon SH, Cho JC, Jahng KY (2013) Hymenobacter koreensis sp. nov. and Hymenobacter saemangeumensis sp. nov., isolated from estuarine water. Int J Syst Evol Microbiol 63(Pt 12):4568–4573

    Article  CAS  PubMed  Google Scholar 

  • Kang JW, Baik KS, Im WT, Seong CN (2016) Hymenobacter coalescens sp nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 66(9):3546–3551

    Article  CAS  PubMed  Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, 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 

  • 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(Pt 2):346–351

    Article  CAS  PubMed  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(2):111–120

    Article  CAS  PubMed  Google Scholar 

  • Klassen JL, Foght JM (2008) Differences in carotenoid composition among Hymenobacter and related strains support a tree-like model of carotenoid evolution. Appl Environ Microbiol 74(7):2016–2022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kojima H, Watanabe M, Tokizawa R, Shinohara A, Fukui M (2016) Hymenobacter nivis sp nov., isolated from red snow in Antarctica. Int J Syst Evol Microbiol 66(11):4821–4825

    Article  CAS  PubMed  Google Scholar 

  • Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703

    Article  CAS  PubMed  Google Scholar 

  • Lin YC, Uemori K, de Briel DA, Arunpairojana V, Yokota A (2004) Zimmermannella helvola gen. Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae. Int J Syst Evol Microbiol 54:1669–1676

    Article  CAS  PubMed  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M (2013a) Genome sequence-based species delimitation with confidenceintervals and improved distance functions. BMC Bioinformatics 14:60

    Article  PubMed  PubMed Central  Google Scholar 

  • Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP (2013b) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195(6):413–418

    Article  CAS  PubMed  Google Scholar 

  • Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G (2008) Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24(24):2818–2824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Munoz R, Rosselló-Móra R, Amann R (2016) Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 39(5):281–296

    Article  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, 5th edn. American Society for Microbiology, Washington, DC, pp 1268–1270

    Google Scholar 

  • Qi J, Wang B, Hao BI (2004) Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol 58(1):1–11

    Article  CAS  PubMed  Google Scholar 

  • Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106(45):19126–19131

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roberts RJ, Carneiro MO, Schatz MC (2013) The advantages of SMRT sequencing. Genome Biol 14:405

    Article  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Tamaoka J, Katayama-Fujimura Y, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36

    Article  CAS  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(12):2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ten LN, Han YE, Park KI, Kang IK, Han JS, Jung HY (2018) Hymenobacter jeollabukensis sp. nov., isolated from soil. J Microbiol 56(7):500–506

    Article  CAS  PubMed  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(24):4876–4882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tindall BJ (1990) Lipid-composition of halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202

    Article  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, Truper 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 

  • Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Muller R, Wohlleben W, Breitling R, Takano E, Medema MH (2015) antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43:W237–W243

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    Article  CAS  PubMed  PubMed Central  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(5):1613–1617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Q, Liu C, Tang Y, Zhou G, Shen P, Fang C, Yokota A (2007) Hymenobacter xinjiangensis sp nov., a radiation-resistant bacterium isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 57:1752–1756

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Dai J, Tang Y, Luo X, Wang Y, An H, Fang C, Zhang C (2009) Hymenobacter deserti sp nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 59:77–82

    Article  CAS  PubMed  Google Scholar 

  • Zhang DC, Busse HJ, Liu HC, Zhou YG, Schinner F, Margesin R (2011) Hymenobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 61:859–863

    Article  CAS  PubMed  Google Scholar 

  • Zuo G, Hao B (2015) CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genom Proteom Bioinform 13:321–331

    Article  Google Scholar 

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Funding

This work was supported by the National Key R&D Program of China (2018YFC1406701), the R&D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People’s Republic of China (Grant No. NIMR-2017-8), the National Natural Science Foundation of China (Grant No. 31270538), and the Chinese Polar Scientific Strategy Research Fund IC201706.

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Authors and Affiliations

  1. China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, China

    Yingchao Geng, Yumin Zhang, Jin Tian, Jia Liu, Kun Qin, Yao Huang, Ziyan Wei & Fang Peng

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  1. Yingchao Geng
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  2. Yumin Zhang
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  3. Jin Tian
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  8. Fang Peng
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Contributions

YG performed the laboratory experiments, analysed the data, and drafted the manuscript. YZ contributed to the polyphasic taxonomy. JT contributed to the biochemical characterisation. KQ contributed to the fatty acids determination. JL contributed to strains activation and preservation. YH and ZW contributed to the morphological analyses. FP designed the experiments and supervised the manuscript.

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Correspondence to Fang Peng.

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Geng, Y., Zhang, Y., Tian, J. et al. Hymenobacter oligotrophus sp. nov., isolated from a contaminated agar plate. Antonie van Leeuwenhoek 112, 1533–1544 (2019). https://doi.org/10.1007/s10482-019-01279-3

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