Abstract
Three Gram-stain-negative, aerobic, circular, convex, red-colored and rod-shaped bacterial strains, designated BT439T, BT662T and BT683T were obtained from soil collected in South Korea. The phylogenetic analysis based on 16S rRNA gene sequences of the strains revealed a distinct lineage within the genus Hymenobacter. The complete genome sequence of strains BT439T, BT662T and BT683T is 5,542,738 bp, 5,964,541 bp, and 5,192,601 bp size, respectively. All three strains were found to have MK-7 as the major respiratory quinone. The major polar lipids of strains BT439T and BT662T were identified as phosphatidylethanolamine, aminophospholipids and amino lipids. Strain BT683T contained phosphatidylethanolamine. The major cellular fatty acids of strain BT439T were iso-C15:0, summed feature 3 (C16:1 ω6c/C16:1 ω7c) and anteiso-C15:0; strain BT662T possessed iso-C15:0 and summed feature 3 (C16:1 ω6c/C16:1 ω7c); strain BT683T were summed feature 3 (C16:1 ω6c/C16:1 ω7c), C16:1 ω5c, iso-C15:0 and anteiso-C15:0. Based on the polyphasic analysis, strains BT439T, BT662T and BT683T can be suggested as three novel bacterial species within the genus Hymenobacter and the proposed names are Hymenobacter properus sp. nov., Hymenobacter ruricola sp. nov. and Hymenobacter jeongseonensis sp. nov., respectively. The type strain of Hymenobacter properus is BT439T (= KCTC 72900T = NBRC 114849T), Hymenobacter ruricola is BT662T (= KACC 21966T = NBRC 114855T) and the type strain of Hymenobacter jeongseonensis is BT683T (= KACC 22013T = NBRC xxxxxT).
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10482-021-01583-x/MediaObjects/10482_2021_1583_Fig1_HTML.png)
Similar content being viewed by others
References
Buczolits SE, Denner BM, Kämpfer 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 HymenobacterHirsch et al. 1999. Int J Syst Evol Microbiol 56:2189–2192. https://doi.org/10.1099/ijs.0.64371-0
Cappuccino JG, Sherman N (2002) Microbiology-A laboratory manual, 6th edn. Pearson Education, Inc. Benjamin Cummings, California
Cha I, Kang H, Kim H, Bae S, Joh K (2020) Hymenobacter ginkgonis sp. nov., isolated from bark of Ginkgo biloba. Int J Syst Evol Microbiol 70:4760–4766. https://doi.org/10.1099/ijsem.0.004343
Chhetri G, Kim J, Kim I, Kim H, Seo T (2020) Hymenobacter setariae sp. nov., isolated from the ubiquitous weedy grass Setaria viridis. Int J Syst Evol Microbiol 70:3724–3730. https://doi.org/10.1099/ijsem.0.004226
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516
Dahal RH, Chaudhary DK, Kim DU, Kim J (2020) Hymenobacter polaris sp. nov., a psychrotolerant bacterium isolated from an Arctic station. Int J Syst Evol Microbiol 70:4890–4896. https://doi.org/10.1099/ijsem.0.004356
Fan X, Wang Q, Zheng S, Shi K, Wang G (2016) Hymenobacter monticola sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 66:812–816. https://doi.org/10.1099/ijsem.0.000792
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Felsenstein J (1985) Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Feng GD, Zhang J, Chen W, Wang SN, Zhu H (2020) Hymenobacter fodinae sp. nov. and Hymenobacter metallicola sp. nov., isolated from abandoned lead-zinc mine. Int J Syst Evol Microbiol 70:4867–4873. https://doi.org/10.1099/ijsem.0.004313
Feng GD, Zhang J, Zhang XJ, Wang SN, **ong X, Zhang YL, Huang HR, Zhu HH (2019) Hymenobacter metallilatus sp. nov., isolated from abandoned lead-zinc ore. Int J Syst Evol Microbiol 269:2142–2146. https://doi.org/10.1099/ijsem.0.003450
Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416. https://doi.org/10.2307/2412116
Han L, Wu SJ, Qin CY, Zhu YH, Lu ZQ, **e 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 105:971–978. https://doi.org/10.1007/s10482-014-0155-y
Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469. https://doi.org/10.2323/jgam.42.457
Jeon YS, Lee K, Park SC, Kim BS, Cho YJ, Ha SM, Chun J (2014) EzEditor: a versatile sequence alignment editor for both rRNA-and protein-coding genes. Int J Syst Evol Microbiol 64:689–691. https://doi.org/10.1099/ijs.0.059360-0
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 63:4568–4573. https://doi.org/10.1099/ijs.0.051870-0
Kim KH, Im WT, Lee ST (2008) Hymenobacter soli sp. nov., isolated from grass soil. Int J Syst Evol Microbiol 58:941–945. https://doi.org/10.1099/ijs.0.64447-0
Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
Komagata K, Suzuki K (1987) 4 Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207. https://doi.org/10.1016/S0580-9517(08)70410-0
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549. https://doi.org/10.1093/molbev/msy096
Lee JJ, Kang MS, Joo ES, Jung HY, Kim MK (2016) Hymenobacter sedentarius sp. nov., isolated from a soil. J Microbiol 54:283–289. https://doi.org/10.1007/s12275-016-5386-3
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60
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. https://doi.org/10.1016/0167-7012(84)90018-6
Munoz R, Rossello MR, Amann R (2017) Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 39:281–296. https://doi.org/10.1016/j.syapm.2016.04.004
Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131
Roldan DM, Kyrpides N, Woyke T, Shapiro N, Whitman WB, Kralova S, Sedlacek I, Busse HJ, Menes RJ (2020) Hymenobacter artigasi sp. nov., isolated from air sampling in maritime Antarctica. Int J Syst Evol Microbiol 70:4935–4941. https://doi.org/10.1099/ijsem.0.004362
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc, Newark
Sedlacek I, Pantucek R, Kralova S, Maslanova I, Holochova P, Stankova E, Vrbovska V, Svec P, Busse HJ (2019) Hymenobacter amundsenii sp. nov. resistant to ultraviolet radiation, isolated from regoliths in Antarctica. Syst Appl Microbiol 42:284–290. https://doi.org/10.1016/j.syapm.2018.12.004
Srinivasan S, Joo ES, Lee JJ, Kim MK (2015) Hymenobacter humi sp. nov., a bacterium isolated from soil. Antonie Van Leeuwenhoek 107:1411–1419. https://doi.org/10.1007/s10482-015-0436-0
Tatusova T, DiCuccio M, Badretdin A et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569
Wang C, Liu BT, Zhang R, Liu CL, Du ZJ (2020) Hymenobacter sediminis sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 70:1895–1902. https://doi.org/10.1099/ijsem.0.003990
Weisburg WG, Barns SM, Pellerier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703. https://doi.org/10.1128/jb.173.2.697-703.1991
Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4
Acknowledgements
This work was supported by a research Grant from Seoul Women’s University (2021) and by a Grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR202002203). We are grateful to Dr. Aharon Oren (The Hebrew University of Jerusalem, Israel) for hel** with the etymology.
Author information
Authors and Affiliations
Contributions
All authors contributed equally to this manuscript.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that there are no conflict of interest.
Ethical approval
This article does not contain any studies with human participants or animals.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
The 16S rRNA gene sequences of the strains BT439T, BT662T and BT683T were deposited in GenBank/EMBL/DDBJ under the accession numbers are MT804607, MT795743 and MT795747, respectively. The draft genome sequences of the strains BT439T, BT662T and BT683T are available at the following accessions JADQDQ000000000, JADQDM000000000 and JADQDP000000000, respectively.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Bang, M., Srinivasan, S. & Sathiyaraj, G. Hymenobacter properus sp. nov., Hymenobacter ruricola sp. nov., and Hymenobacter jeongseonensis sp. nov., three new species isolated from mountain and beach soil in South Korea. Antonie van Leeuwenhoek 114, 1131–1139 (2021). https://doi.org/10.1007/s10482-021-01583-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10482-021-01583-x