Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 74, Issue 5

sp. nov. and sp. nov., isolated from a pond No Access

Abstract

Two Gram-negative bacteria, designated as strains LF1 and HM2-2, were isolated from an artificial pond in a honey farm at Hoengseong-gun, Gangwon-do, Republic of Korea. The 16S rRNA sequence analysis results revealed that strain LF1 belonged to the genus and had the highest sequence similarity to GH41-7 (99.0 %), CJ29 (98.9 %), and SYSU H10001 (98.2 %). Its growth occurred at 20–37 °C, at pH 5.0–12.0, and in the presence of 0–2% NaCl. The major fatty acids were iso-C, iso-C, and summed feature 9 (iso-C 9 and/or C 10-methyl). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The DNA G+C content was 67.5 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain LF1 and species of the genus were 79.1–84.4% and 22.0–27.5 %, respectively. The 16S rRNA sequence analysis results revealed that strain HM2-2 belonged to the genus and was most closely related to II-D5 (98.9 %), JUR4 (98.4%), and II-B4 (98.4 %). Its growth occurred at 10–35 °C, at pH 5.0–11.0, and in the presence of 0–2% NaCl. The major fatty acids were C and summed feature 3 (C 7/C 6). The major polar lipid was phosphatidylethanolamine. The DNA G+C content was 59.9 mol%. The ANI and dDDH values between strain HM2-2 and its closely related strains were 75.1–83.0% and 20.4–26.4 %, respectively. Phenotypic, genomic, and phylogenetic data revealed that strains LF1 and HM2-2 represent novel species in the genera and , for which the names sp. nov. and sp. nov. are proposed, respectively. The type strain of is LF1 (=KACC 23251=TBRC 17648), and that of is HM2-2 (=KACC 23250=TBRC 17649).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Limnohabitans , Lysobacter , novel species and phylogenetic tree
Funding
This study was supported by the:
  • National Research Foundation of Korea (Award 2022R1F1A1070108)
    • Principle Award Recipient: TaegunSeo
  • National Institute of Biological Resources (Award NIBR202304204)
    • Principle Award Recipient: TaegunSeo
© 2024 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006400
2024-05-28
2025-04-25
Loading full text...

Full text loading...

References

  1. Christensen P, Cook FD. Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 1978; 28:367–393 [View Article]
     [Google Scholar]
  2. Park JH, Kim R, Aslam Z, Jeon CO, Chung YR. Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter. Int J Syst Evol Microbiol 2008; 58:387–392 [View Article] [PubMed]
     [Google Scholar]
  3. Mao S, Li S, Guo B, Mu W, Hou X et al. Lysobacter selenitireducens sp. nov., isolated from river sediment. Int J Syst Evol Microbiol 2022; 72:005550 [View Article] [PubMed]
     [Google Scholar]
  4. Liu Z, Jiang P, Niu G, Wang W, Li J. Lysobacter antarcticus sp. nov., an SUF-system-containing bacterium from Antarctic coastal sediment. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  5. Zhao Y, Jiang T, Xu H, Xu G, Qian G et al. Characterization of Lysobacter spp. strains and their potential use as biocontrol agents against pear anthracnose. Microbiol Res 2021; 242:126624 [View Article] [PubMed]
     [Google Scholar]
  6. Palumbo JD, Yuen GY, Jochum CC, Tatum K, Kobayashi DY. Mutagenesis of beta-1,3-glucanase genes in Lysobacter enzymogenes strain C3 results in reduced biological control activity toward bipolaris leaf spot of tall fescue and pythium damping-off of sugar beet. Phytopathology 2005; 95:701–707 [View Article] [PubMed]
     [Google Scholar]
  7. Zhao Y, Qian G, Ye Y, Wright S, Chen H et al. Heterocyclic aromatic N -oxidation in the biosynthesis of phenazine antibiotics from Lysobacter antibioticus. Org Lett 2016; 18:2495–2498 [View Article]
     [Google Scholar]
  8. Laborda P, Zhao Y, Ling J, Hou R, Liu F. Production of antifungal p-aminobenzoic acid in Lysobacter antibioticus OH13. J Agric Food Chem 2018; 66:630–636 [View Article] [PubMed]
     [Google Scholar]
  9. Folman LB, De Klein MJEM, Postma J, van Veen JA. Production of antifungal compounds by Lysobacter enzymogenes isolate 3.1T8 under different conditions in relation to its efficacy as a biocontrol agent of Pythium aphanidermatum in cucumber. Biological Control 2004; 31:145–154 [View Article]
     [Google Scholar]
  10. Jochum CC, Osborne LE, Yuen GY. Fusarium head blight biological control with Lysobacter enzymogenes strain C3. Biological Control 2006; 39:336–344 [View Article]
     [Google Scholar]
  11. Hahn MW, Kasalický V, Jezbera J, Brandt U, Jezberová J et al. Limnohabitans curvus gen. nov., sp. nov., a planktonic bacterium isolated from a freshwater lake. Int J Syst Evol Microbiol 2010; 60:1358–1365 [View Article] [PubMed]
     [Google Scholar]
  12. Chhetri G, Kim J, Kim I, Kang M, Seo T. Limnohabitans radicicola sp. nov., a slow-growing bacterium isolated from rhizosphere of rice plant and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 2021; 71:004957 [View Article] [PubMed]
     [Google Scholar]
  13. Hahn MW, Kasalický V, Jezbera J, Brandt U, Šimek K. Limnohabitans australis sp. nov., isolated from a freshwater pond, and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 2010; 60:2946–2950 [View Article]
     [Google Scholar]
  14. Kasalický V, Jezbera J, Šimek K, Hahn MW. Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 2010; 60:2710–2714 [View Article] [PubMed]
     [Google Scholar]
  15. Nuy JK, Hoetzinger M, Hahn MW, Beisser D, Boenigk J. Ecological differentiation in two major freshwater bacterial taxa along environmental gradients. Front Microbiol 2020; 11:154 [View Article] [PubMed]
     [Google Scholar]
  16. Props R, Denef VJ. Temperature and nutrient levels correspond with lineage-specific microdiversification in the ubiquitous and abundant freshwater genus Limnohabitans. Appl Environ Microbiol 2020; 86:1–17 [View Article] [PubMed]
     [Google Scholar]
  17. Chen X, Ye Q, Du J, Zhang J. Bacterial and archaeal assemblages from two size fractions in submarine groundwater near an industrial zone. Water 2019; 11:1261 [View Article]
     [Google Scholar]
  18. So Y, Chhetri G, Kim I, Kang M, Kim J et al. Halomonas antri sp. nov., a carotenoid-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  19. Kang M, Chhetri G, Kim J, Kim I, So Y et al. Tumebacillus amylolyticus sp. nov., isolated from garden soil in Korea. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  20. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article] [PubMed]
     [Google Scholar]
  21. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article] [PubMed]
     [Google Scholar]
  22. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  23. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  28. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  29. Kang M, Chhetri G, Kim J, Kim I, Seo T. Pontibacter cellulosilyticus sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  30. 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]
  31. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  32. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  33. 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]
  34. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
     [Google Scholar]
  35. He YW, Cao XQ, Poplawsky AR. Chemical structure, biological roles, biosynthesis and regulation of the yellow xanthomonadin pigments in the phytopathogenic genus Xanthomonas. Mol Plant Microbe Interact 2020; 33:705–714 [View Article] [PubMed]
     [Google Scholar]
  36. Kim JC, Yoon JW, Kim CH, Park MS, Cho SH. Repression of flagella motility in enterohemorrhagic Escherichia coli O157:H7 by mucin components. Biochem Biophys Res Commun 2012; 423:789–792 [View Article] [PubMed]
     [Google Scholar]
  37. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  38. 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]
  39. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL et al. KBase: The United States Department of Energy systems biology knowledgebase. Nat Biotechnol 2018; 36:566–569 [View Article] [PubMed]
     [Google Scholar]
  40. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [View Article] [PubMed]
     [Google Scholar]
  41. Na S-I, Kim YO, Yoon S-H, Ha S, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
     [Google Scholar]
  42. 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]
  43. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article]
     [Google Scholar]
  44. Kim I, Seo T. Pseudarthrobacter humi sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2023; 73:005671 [View Article] [PubMed]
     [Google Scholar]
  45. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article] [PubMed]
     [Google Scholar]
  46. Kim I, Chhetri G, Kim J, So Y, Seo T. Quadrisphaera setariae sp. nov., polyphosphate-accumulating bacterium occurring as tetrad or aggregate cocci and isolated from Setaria viridis. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  47. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4347–4354 [View Article] [PubMed]
     [Google Scholar]
  48. Smibert RM, Kreig NR. Phenotypic characterization. In Gerhardt P, Murray R, W W, Kreig N. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  49. Kim S-J, Ahn J-H, Weon H-Y, Hong S-B, Seok S-J et al. Parasegetibacter terrae sp. nov., isolated from paddy soil and emended description of the genus Parasegetibacter. Int J Syst Evol Microbiol 2015; 65:113–116 [View Article]
     [Google Scholar]
  50. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the xlassification of nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
     [Google Scholar]
  51. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
  52. Singh H, Won K, Du J, Yang J-E, Akter S et al. Lysobacter agri sp. nov., a bacterium isolated from soil. Antonie van Leeuwenhoek 2015; 108:553–561 [View Article] [PubMed]
     [Google Scholar]
  53. Weon H-Y, Kim B-Y, Kim M-K, Yoo S-H, Kwon S-W et al. Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol 2007; 57:548–551 [View Article]
     [Google Scholar]
  54. Choi JH, Seok JH, Cha JH, Cha CJ. Lysobacter panacisoli sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 2014; 64:2193–2197 [View Article] [PubMed]
     [Google Scholar]
  55. Fang B-Z, Xie Y-G, Zhou X-K, Zhang X-T, Liu L et al. Lysobacter prati sp. nov., isolated from a plateau meadow sample. Antonie van Leeuwenhoek 2020; 113:763–772 [View Article] [PubMed]
     [Google Scholar]
  56. Srinivasan S, Kim MK, Sathiyaraj G, Kim H-B, Kim Y-J et al. Lysobacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010; 60:1543–1547 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006400
Loading
Lysobacter stagni sp. nov. and Limnohabitans lacus sp. nov., isolated from a pond
Int J Syst Evol Microbiol 74, 006400 (2024); https://doi.org/10.1099/ijsem.0.006400
/content/journal/ijsem/10.1099/ijsem.0.006400
/content/journal/ijsem/10.1099/ijsem.0.006400
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