1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 12

sp. nov., isolated from wheat leaf tissue No Access

Abstract

A bacterium, designated strain ZK17L-C2, was isolated from the leaf tissues of wheat () collected in Chengdu, Sichuan Province, PR China. It is aerobic, non-motile, Gram-negative, rod-shaped and red-to-pink in colour. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZK17L-C2 belonged to the genus and was most closely related to KCTC 12533 (98.68 %) and 9PBR-2 (98.19 %). Digital DNA–DNA hybridization (dDDH) values between strain ZK17L-C2 and these two type strains were 26.6 and 26.5 %, and average nucleotide identity (ANI) values were 84.9 and 84.8 %, respectively; these values are lower than the proposed and generally accepted species boundaries for dDDH and ANI. The genomic DNA G+C content of strain ZK17L-C2 was 59.4 mol%. It can grow at pH 5.5–7.5 and 15–30 °C, which is different from the closely related type strains. The major fatty acids of strain ZK17L-C2 were iso-C, C and C. Overall, the results from biochemical, chemical taxonomy and phylogenetic analyses indicate that strain ZK17L-C2 (=CGMCC 1.19373=KCTC 92184 ) represents a new species of the genus , for which the name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Hymenobacter endophyticus , UV resistant and wheat
Funding
This study was supported by the:
  • Hebei Normal University of Science and Technology (Award 2023YB007)
    • Principle Award Recipient: YumeiDai
  • Applied Basic Research Program of Sichuan Province (Award 2021YJ0291)
    • Principle Award Recipient: YumeiDai
  • Major Research Plan (Award 41877042)
    • Principle Award Recipient: YumeiDai
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006197
2023-12-07
2024-05-08
Loading full text...

Full text loading...

References

  1. Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B et al. Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 1998; 21:374–383 [View Article] [PubMed]
     [Google Scholar]
  2. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  3. Park Y, Chang Y, Kim MK. Hymenobacter armeniacus sp. nov. and Hymenobacter montanus sp. nov., two radiation-resistant bacteria from soil. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  4. Dahal RH, Chaudhary DK, Kim DU, Kim J. Hymenobacter polaris sp. nov., a psychrotolerant bacterium isolated from an Arctic station. Int J Syst Evol Microbiol 2020; 70:4890–4896 [View Article] [PubMed]
     [Google Scholar]
  5. Kim MC, Kim CM, Kang OC, Zhang Y, Liu Z et al. Hymenobacter rutilus sp. nov., isolated from marine sediment in the Arctic. Int J Syst Evol Microbiol 2017; 67:856–861 [View Article] [PubMed]
     [Google Scholar]
  6. Chen Y, Zhu L, Bai P, Cui S, Xin Y et al. Hymenobacter terricola sp. nov., isolated from Antarctic soil. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  7. Kim MC, Kim CM, Kang OC, Zhang Y, Liu Z et al. Hymenobacter rutilus sp. nov., isolated from marine sediment in the Arctic. Int J Syst Evol Microbiol 2017; 67:856–861 [View Article]
     [Google Scholar]
  8. Roldán DM, Kyrpides N, Woyke T, Shapiro N, Whitman WB et al. Hymenobacter artigasi sp. nov., isolated from air sampling in maritime Antarctica. Int J Syst Evol Microbiol 2020; 70:4935–4941 [View Article] [PubMed]
     [Google Scholar]
  9. Kojima H, Watanabe M, Tokizawa R, Shinohara A, Fukui M. Hymenobacter nivis sp. nov., isolated from red snow in Antarctica. Int J Syst Evol Microbiol 2016; 66:4821–4825 [View Article]
     [Google Scholar]
  10. Roldán DM, Kyrpides N, Woyke T, Shapiro N, Whitman WB et al. Hymenobacter caeli sp. nov., an airborne bacterium isolated from King George Island, Antarctica. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  11. Sedláček I, Pantůček R, Zeman M, Holochová P, Šedo O et al. Hymenobacter terrestris sp. nov. and Hymenobacter lapidiphilus sp. nov., isolated from regoliths in Antarctica. Int J Syst Evol Microbiol 2020; 70:6364–6372 [View Article] [PubMed]
     [Google Scholar]
  12. Jiang F, Danzeng W, Zhang Y, Zhang Y, Jiang L et al. Hymenobacter rubripertinctus sp. nov., isolated from Antarctic tundra soil. Int J Syst Evol Microbiol 2018; 68:663–668 [View Article] [PubMed]
     [Google Scholar]
  13. Feng G-D, Zhang J, Zhang X-J, Wang S-N, Xiong X et al. Hymenobacter metallilatus sp. nov., isolated from abandoned lead–zinc ore. Int J Syst Evol Microbiol 2019; 69:2142–2146 [View Article]
     [Google Scholar]
  14. Feng GD, Zhang J, Chen W, Wang SN. Isolated from abandoned lead-zinc mine. Int J Syst Evol Microbiol 2020; 70:4867–4873 [View Article] [PubMed]
     [Google Scholar]
  15. Sun J, Xing M, Wang W, Dai F, Liu J et al. Hymenobacter profundi sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2018; 68:947–950 [View Article] [PubMed]
     [Google Scholar]
  16. Chang X, Zheng J, Jiang F, Liu P, Kan W et al. Hymenobacter arcticus sp. nov., isolated from glacial till. Int J Syst Evol Microbiol 2014; 64:2113–2118 [View Article] [PubMed]
     [Google Scholar]
  17. Liu K, Liu Y, Wang N, Gu Z, Shen L et al. Hymenobacter glacieicola sp. nov., isolated from glacier ice. Int J Syst Evol Microbiol 2016; 66:3793–3798 [View Article] [PubMed]
     [Google Scholar]
  18. Gu Z, Liu Y, Xu B, Wang N, Jiao N et al. Hymenobacter frigidus sp. nov., isolated from a glacier ice core. Int J Syst Evol Microbiol 2017; 67:4121–4125 [View Article] [PubMed]
     [Google Scholar]
  19. Zhang Q, Liu C, Tang Y, Zhou G, Shen P et al. Hymenobacter xinjiangensis sp. nov., a radiation-resistant bacterium isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 2007; 57:1752–1756 [View Article] [PubMed]
     [Google Scholar]
  20. Zhang L, Dai J, Tang Y, Luo X, Wang Y et al. Hymenobacter deserti sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 2009; 59:77–82 [View Article] [PubMed]
     [Google Scholar]
  21. Cha I, Kang H, Kim H, Bae S, Joh K. Hymenobacter ginkgonis sp. nov., isolated from bark of Ginkgo biloba. Int J Syst Evol Microbiol 2020; 70:4760–4766 [View Article] [PubMed]
     [Google Scholar]
  22. Chhetri G, Kim J, Kim I, Kim H, Seo T. Hymenobacter setariae sp. nov., isolated from the ubiquitous weedy grass Setaria viridis. Int J Syst Evol Microbiol 2020; 70:3724–3730 [View Article] [PubMed]
     [Google Scholar]
  23. Park Y, Noh H-J, Hwang CY, Shin SC, Hong SG et al. Hymenobacter siberiensis sp. nov., isolated from a marine sediment of the East Siberian Sea and Hymenobacter psoromatis sp. nov., isolated from an Antarctic lichen. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  24. Dai Y, Yang F, Zhang L, Xu Z, Fan X et al. Wheat-associated microbiota and their correlation with stripe rust reaction. J Appl Microbiol 2020; 128:544–555 [View Article] [PubMed]
     [Google Scholar]
  25. Zhang L-L, Gan L-Z, Xu Z-B, Yang F, Li Y et al. Pedobacter chitinilyticus sp. nov., a chitin-degrading bacterium isolated from wheat leaf tissue. Int J Syst Evol Microbiol 2018; 68:3713–3719 [View Article] [PubMed]
     [Google Scholar]
  26. Itoh T, Hibi T, Fujii Y, Sugimoto I, Fujiwara A et al. Cooperative degradation of chitin by extracellular and cell surface-expressed chitinases from Paenibacillus sp. strain FPU-7. Appl Environ Microbiol 2013; 79:7482–7490 [View Article] [PubMed]
     [Google Scholar]
  27. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991 pp 115–175
     [Google Scholar]
  28. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  29. Jeon Y-S, Lee K, Park S-C, Kim B-S, Cho Y-J et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article] [PubMed]
     [Google Scholar]
  30. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  31. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  32. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  33. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  34. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  35. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
     [Google Scholar]
  36. Wu L, Ma J. The Global Catalogue of Microorganisms (GCM) 10K type strain sequencing project: providing services to taxonomists for standard genome sequencing and annotation. Int J Syst Evol Microbiol 2019; 69:895–898 [View Article] [PubMed]
     [Google Scholar]
  37. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  38. Liu Y, Schröder J, Schmidt B. Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics 2013; 29:308–315 [View Article] [PubMed]
     [Google Scholar]
  39. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article] [PubMed]
     [Google Scholar]
  40. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  41. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article] [PubMed]
     [Google Scholar]
  42. Kajitani R, Toshimoto K, Noguchi H, Toyoda A, Ogura Y et al. Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. Genome Res 2014; 24:1384–1395 [View Article] [PubMed]
     [Google Scholar]
  43. Chen I-MA, Chu K, Palaniappan K, Ratner A, Huang J et al. The IMG/M data management and analysis system v.7: content updates and new features. Nucleic Acids Res 2023; 51:D723–D732 [View Article]
     [Google Scholar]
  44. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  45. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  46. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, NR K. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 611–651
     [Google Scholar]
  47. Maeng S, Kim MK, Subramani G. Hymenobacter jejuensis sp. nov., a UV radiation-tolerant bacterium isolated from Jeju Island. Antonie van Leeuwenhoek 2020; 113:553–561 [View Article] [PubMed]
     [Google Scholar]
  48. Dai J, Wang Y, Zhang L, Tang Y, Luo X et al. Hymenobacter tibetensis sp. nov., a UV-resistant bacterium isolated from Qinghai-Tibet plateau. Syst Appl Microbiol 2009; 32:543–548 [View Article] [PubMed]
     [Google Scholar]
  49. Jang JH, Maeng SH, Jung HY, Kim MK, Subramani G. Hymenobacter radiodurans sp. nov., isolated from soil in the Republic of Korea. Arch Microbiol 2021; 203:655–661 [View Article] [PubMed]
     [Google Scholar]
  50. Damdintogtokh T, Cha IT. Radiation-resistant species isolated from soil in South Korea. Curr Microbiol 2021; 78:3334–3341
     [Google Scholar]
  51. Srinivasan S, Lee J-J, Park KR, Park S-H, Jung H-Y et al. Hymenobacter terrae sp. nov., a bacterium isolated from soil. Curr Microbiol 2015; 70:643–650 [View Article] [PubMed]
     [Google Scholar]
  52. Sasser M. Technical Note 101: Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI Inc; 1990
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006197
Loading
Hymenobacter endophyticus sp. nov., isolated from wheat leaf tissue
Int J Syst Evol Microbiol 73, 006197 (2023); https://doi.org/10.1099/ijsem.0.006197
/content/journal/ijsem/10.1099/ijsem.0.006197
/content/journal/ijsem/10.1099/ijsem.0.006197
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error