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Volume 73, Issue 12

sp. nov., isolated from the rhizosphere soil of H. Open Access

Abstract

A novel Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated pc2-12, was isolated from the rhizosphere soil of the herb collected from arid areas of Tibet. The strain grew most vigorously with 1 % (w/v) NaCl, at pH 7.0 and at 25 °C. According to the results of 16S rRNA gene sequence analysis, pc2-12 was closely related to the members of the genus , with highest levels of sequence similarity to 687B-08 (98.42 %), 701B-08 (98.11 %) and DSM 18017 (97.98 %). The average nucleotide identity values between pc2-12 and 687B-08, 701B-08 and DSM 18017 were 79.71, 79.49 and 79.26 %, respectively. The DNA–DNA hybridisation values between pc2-12 and . 687B-08, 701B-08 and DSM 18017 were 23.30, 23.00 and 22.90 %, respectively. The draft genome sequence of pc2-12 was 4.64 Mb long, with DNA G+C content of 37.0 mol%. The fatty acids contained in the cells of pc2-12 were mainly composed of iso-C, iso-C 3-OH and summed feature 3 (Cω6 and/or Cω7). The main polar lipid was phosphatidylethanolamine. MK-6 was the sole respiratory quinone. On the basis of the results of analysis of all the data described, pc2-12 is considered to represent a novel species of the genus , for which the name sp. nov., is proposed. The type strain is pc2-12 (=GDMCC 1.3256= JCM 35712).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , Chryseobacterium , genome and polyphasic taxonomy
Funding
This study was supported by the:
  • Central Public-interest Scientific Institution Basal Research Fund (Award No. Y2022GH18)
    • Principle Award Recipient: ZhiyongRuan
  • Fundamental Research Funds for Central Non-profit Scientific Institution (Award 1610132020009)
    • Principle Award Recipient: ZhiyongRuan
  • Agricultural Resources and Environment Discipline Construction Project (Award 533320003)
    • Principle Award Recipient: YanWang
  • National Natural Science Foundation of China (Award NSFC 3211101206)
    • Principle Award Recipient: ZhiyongRuan
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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References

  1. Vandamme P, Bernardet JF, Segers P, Kersters K, Holmes B. NOTES: new perspectives in the classification of the Flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Bacteriol 1994; 44:827–831 [View Article]
     [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. Kong D, Wang Y, Li Q, Zhou Y, Jiang X et al. Chryseobacterium subflavum sp. nov., isolated from soil. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  4. Chen XY, Zhao R, Chen ZL, Liu L, Li XD et al. Chryseobacterium polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Chryseobacterium. Antonie van Leeuwenhoek 2015; 107:403–410 [View Article] [PubMed]
     [Google Scholar]
  5. Kämpfer P, McInroy JA, Glaeser SP. Chryseobacterium zeae sp. nov., Chryseobacterium arachidis sp. nov., and Chryseobacterium geocarposphaerae sp. nov. isolated from the rhizosphere environment. Antonie van Leeuwenhoek 2014; 105:491–500 [View Article] [PubMed]
     [Google Scholar]
  6. Zamora L, Fernández-Garayzábal JF, Palacios MA, Sánchez-Porro C, Svensson-Stadler LA et al. Chryseobacterium oncorhynchi sp. nov., isolated from rainbow trout (Oncorhynchus mykiss). Syst Appl Microbiol 2012; 35:24–29 [View Article] [PubMed]
     [Google Scholar]
  7. Loveland-Curtze J, Miteva V, Brenchley J. Novel ultramicrobacterial isolates from a deep Greenland ice core represent a proposed new species, Chryseobacterium greenlandense sp. nov. Extremophiles 2010; 14:61–69 [View Article]
     [Google Scholar]
  8. Kutsuna R, Mashima I, Miyoshi-Akiyama T, Muramatsu Y, Tomida J et al. Chryseobacterium lecithinasegens sp. nov., a siderophore-producing bacterium isolated from soil at the bottom of a pond. Int J Syst Evol Microbiol 2021; 71:5135 [View Article] [PubMed]
     [Google Scholar]
  9. Kämpfer P, Trček J, Skok B, Šorgo A, Glaeser SP. Chryseobacterium limigenitum sp. nov., isolated from dehydrated sludge. Antonie van Leeuwenhoek 2015; 107:1633–1638 [View Article] [PubMed]
     [Google Scholar]
  10. Kangale LJ, Raoult D, Ghigo E, Fournier P-E. Chryseobacterium schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea. Sci Rep 2021; 11:11002 [View Article] [PubMed]
     [Google Scholar]
  11. Saticioglu IB, Duman M, Altun S. Genome analysis and antimicrobial resistance characteristics of Chryseobacterium aquaticum isolated from farmed salmonids. Aquaculture 2021; 535:736364 [View Article]
     [Google Scholar]
  12. Hantsis-Zacharov E, Senderovich Y, Halpern M. Chryseobacterium bovis sp. nov., isolated from raw cow’s milk. Int J Syst Evol Microbiol 2008; 58:1024–1028 [View Article] [PubMed]
     [Google Scholar]
  13. Etesami H, Maheshwari DK. Use of plant growth promoting rhizobacteria (PGPRs) with multiple plant growth promoting traits in stress agriculture: Action mechanisms and future prospects. Ecotoxicol Environ Saf 2018; 156:225–246 [View Article] [PubMed]
     [Google Scholar]
  14. Radzki W, Gutierrez Mañero FJ, Algar E, Lucas García JA, García-Villaraco A et al. Bacterial siderophores efficiently provide iron to iron-starved tomato plants in hydroponics culture. Antonie van Leeuwenhoek 2013; 104:321–330 [View Article] [PubMed]
     [Google Scholar]
  15. Montero-Calasanz MDC, Goker M, Rohde M, Sproer C, Schumann P et al. Chryseobacterium oleae sp. nov. An efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium. Syst Appl Microbiol 2014; 37:342–350 [View Article] [PubMed]
     [Google Scholar]
  16. Yao X-H, Zhang D-Y, Zu Y-G, Fu Y, Luo M et al. Free radical scavenging capability, antioxidant activity and chemical constituents of Pyrola incarnata Fisch. leaves. Ind Crops Prod 2013; 49:247–255 [View Article]
     [Google Scholar]
  17. Etesami H, Alikhani HA, Hosseini HM. Indole-3-acetic acid and 1-aminocyclopropane-1-carboxylate deaminase: bacterial traits required in rhizosphere, rhizoplane and/or endophytic competence by beneficial bacteria. In Bacterial Metabolites in Sustainable Agroecosystem 2015 pp 183–258 [View Article]
     [Google Scholar]
  18. Tanatorn C, Kannika D. Actinomycetospora soli sp. nov., isolated from the rhizosphere soil of Averrhoa carambola L. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  19. Alexander DB, Zuberer DA. Use of chrome azurol S reagents to evaluate siderophore production by rhizosphere bacteria. Biol Fert Soils 1991; 12:39–45 [View Article]
     [Google Scholar]
  20. Glickmann E, Dessaux Y. A critical examination of the specificity of the Salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Environ Microbiol 1995; 61:793–796 [View Article] [PubMed]
     [Google Scholar]
  21. Gordon SA, Weber RP. Colorimetric estimation of indole acetic acid.. Plant Physiol 1951; 26:192–195 [View Article] [PubMed]
     [Google Scholar]
  22. Vazquez P, Holguin G, Puente ME, Lopez-Cortes A, Bashan Y. Phosphate-solubilizing microorganisms associated with the rhizosphere of mangroves in a semiarid coastal lagoon. Biol Fertil Soils 2000; 30:460–468 [View Article]
     [Google Scholar]
  23. Jha PN, Kumar A. Endophytic colonization of Typha australis by a plant growth-promoting bacterium Klebsiella oxytoca strain GR-3. J Appl Microbiol 2007; 103:1311–1320 [View Article] [PubMed]
     [Google Scholar]
  24. Ghavami N, Alikhani HA, Pourbabaei AA, Besharati H. Effects of two new siderophore-producing rhizobacteria on growth and iron content of maize and canola plants. J Plant Nutr 2017; 40:736–746 [View Article]
     [Google Scholar]
  25. Adnan M, Shah Z, Fahad S, Arif M, Alam M et al. Phosphate-solubilizing bacteria nullify the antagonistic effect of soil calcification on bioavailability of phosphorus in alkaline soils. Sci Rep 2017; 7:16131 [View Article] [PubMed]
     [Google Scholar]
  26. Cai M, Wang L, Cai H, Li Y, Wang Y-N et al. Salinarimonas ramus sp. nov. and Tessaracoccus oleiagri sp. nov., isolated from a crude oil-contaminated saline soil. Int J Syst Evol Microbiol 2011; 61:1767–1775 [View Article] [PubMed]
     [Google Scholar]
  27. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article]
     [Google Scholar]
  28. Pandey KK, Mayilraj S, Chakrabarti T. Pseudomonas indica sp. nov., a novel butane-utilizing species. Int J Syst Evol Microbiol 2002; 52:1559–1567 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  31. Miya M, Nishida M. Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol Phylogenet Evol 2000; 17:437–455 [View Article] [PubMed]
     [Google Scholar]
  32. 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]
  33. Zamora L, Vela AI, Palacios MA, Sánchez-Porro C, Svensson-Stadler LA et al. Chryseobacterium viscerum sp. nov., isolated from diseased fish. Int J Syst Evol Microbiol 2012; 62:2934–2940 [View Article] [PubMed]
     [Google Scholar]
  34. Herzog P, Winkler I, Wolking D, Kämpfer P, Lipski A. Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants. Int J Syst Evol Microbiol 2008; 58:26–33 [View Article] [PubMed]
     [Google Scholar]
  35. Sun C, Fu G-Y, Zhang C-Y, Hu J, Xu L et al. Isolation and complete genome sequence of Algibacter alginolytica sp. nov., a novel seaweed-degrading Bacteroidetes bacterium with diverse putative polysaccharide utilization loci. Appl Environ Microbiol 2016; 82:2975–2987 [View Article] [PubMed]
     [Google Scholar]
  36. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article] [PubMed]
     [Google Scholar]
  37. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  38. 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]
  39. 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]
  40. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  41. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  42. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  43. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  44. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on systematic Bacteriology. Report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Bacteriol 1987; 37:463–464 [View Article]
     [Google Scholar]
  45. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article] [PubMed]
     [Google Scholar]
  46. Hofmann M, Heine T, Schulz V, Hofmann S, Tischler D. Draft genomes and initial characterization of siderophore producing pseudomonads isolated from mine dump and mine drainage. Biotechnology Reports 2020; 25:e00403 [View Article]
     [Google Scholar]
  47. Duca DR, Glick BR. Indole-3-acetic acid biosynthesis and its regulation in plant-associated bacteria. Appl Microbiol Biotechnol 2020; 104:8607–8619 [View Article] [PubMed]
     [Google Scholar]
  48. Jin M, Zhao Q, Zhou Z, Zhu L, Zhang Z et al. Draft genome sequence of a potential organic phosphorus-degrading bacterium Brevibacterium frigoritolerans GD44, iolated from radioactive soil in Xinjiang, China. Curr Microbiol 2020; 77:2896–2903 [View Article]
     [Google Scholar]
  49. Siles JA, Starke R, Martinovic T, Parente Fernandes ML, Orgiazzi A et al. Distribution of phosphorus cycling genes across land uses and microbial taxonomic groups based on metagenome and genome mining. Soil Biol Biochem 2022; 174:108826 [View Article]
     [Google Scholar]
  50. Ruan Z, Wang Y, Song J, Jiang S, Wang H et al. Kurthia huakuii sp. nov., isolated from biogas slurry, and emended description of the genus Kurthia. Int J Syst Evol Microbiol 2014; 64:518–521 [View Article] [PubMed]
     [Google Scholar]
  51. Stokes EJ. A guide to the identification of the genera of bacteria. J Clin Pathol 1968; 61:209–210 [View Article]
     [Google Scholar]
  52. Chen Y-G, Cui X-L, Pukall R, Li H-M, Yang Y-L et al. Salinicoccus kunmingensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-west China. Int J Syst Evol Microbiol 2007; 57:2327–2332 [View Article] [PubMed]
     [Google Scholar]
  53. Wang X, Li Y, Xue C-X, Li B, Zhou S et al. Photobacterium chitinilyticum sp. nov., a marine bacterium isolated from seawater at the bottom of the East China Sea. Int J Syst Evol Microbiol 2019; 69:1477–1483 [View Article]
     [Google Scholar]
  54. Smibert RM, Krieg NR. Phenotypic characterization. In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  55. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark,DE: MIDI inc; 1990
     [Google Scholar]
  56. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  57. Xu X-W, Huo Y-Y, Wang C-S, Oren A, Cui H-L et al. Pelagibacterium halotolerans gen. nov., sp. nov. and Pelagibacterium luteolum sp. nov., novel members of the family Hyphomicrobiaceae. Int J Syst Evol Microbiol 2011; 61:1817–1822 [View Article] [PubMed]
     [Google Scholar]
  58. Kates M. Technique of Lipidology: Isolation, Analysis and Identification of Lipids 1986
     [Google Scholar]
  59. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
     [Google Scholar]
  60. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge JT, Breznak JA, Marzluf GA, Schmidt TM. eds Methods for General and Molecular Microbiology, 3rd. edn Washington, DC: American Society for Microbiology; 2007 pp 330–393
     [Google Scholar]
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Chryseobacterium pyrolae sp. nov., isolated from the rhizosphere soil of Pyrola calliantha H.
Int J Syst Evol Microbiol 73, 006068 (2023); https://doi.org/10.1099/ijsem.0.006068
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