Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Comparative Genome analysis of the Genus Curvibacter and the Description of Curvibacter microcysteis sp. nov. and Curvibacter cyanobacteriorum sp. nov., Isolated from Fresh Water during the Cyanobacterial Bloom Period

  • Ve Van Le (Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology) ;
  • So-Ra Ko (Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology) ;
  • Mingyeong Kang (Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology) ;
  • Seonah Jeong (Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology) ;
  • Hee-Mock Oh (Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology) ;
  • Chi-Yong Ahn (Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology)
  • Received : 2023.06.08
  • Accepted : 2023.08.15
  • Published : 2023.11.28
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Abstract

The three Gram-negative, catalase- and oxidase-positive bacterial strains RS43T, HBC28, and HBC61T, were isolated from fresh water and subjected to a polyphasic study. Comparison of 16S rRNA gene sequence initially indicated that strains RS43T, HBC28, and HBC61T were closely related to species of genus Curvibacter and shared the highest sequence similarity of 98.14%, 98.21%, and 98.76%, respectively, with Curvibacter gracilis 7-1T. Phylogenetic analysis based on genome sequences placed all strains within the genus Curvibacter. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the three strains and related type strains supported their recognition as two novel genospecies in the genus Curvibacter. Comparative genomic analysis revealed that the genus possessed an open pangenome. Based on KEGG BlastKOALA analyses, Curvibacter species have the potential to metabolize benzoate, phenylacetate, catechol, and salicylate, indicating their potential use in the elimination of these compounds from the water systems. The results of polyphasic characterization indicated that strain RS43T and HBC61T represent two novel species, for which the name Curvibacter microcysteis sp. nov. (type strain RS43T =KCTC 92793T=LMG 32714T) and Curvibacter cyanobacteriorum sp. nov. (type strain HBC61T =KCTC 92794T=LMG 32713T) are proposed.

Keywords

Acknowledgement

This research was supported by Korea Environment Industry & Technology Institute (KEITI) through Aquatic Ecosystem Conservation Research Program (2022003050004) and the National Research Foundation of Korea (2023R1A2C1003308) and the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM5252322).

References

  1. Ding L, Yokota A. 2004. Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov. . Int. J. Syst. Evol. Microbiol. 54: 2223-2230. https://doi.org/10.1099/ijs.0.02975-0
  2. Parte AC, Carbasse JS, Meier-Kolthoff JP, Reimer LC, Goker M. 2020. List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int. J. Syst. Evol. Microbiol. 70: 5607-5612. https://doi.org/10.1099/ijsem.0.004332
  3. Ding L, Yokota A. 2010. Curvibacter fontana sp. nov., a microaerobic bacteria isolated from well water. J. Gen. Appl. Microbiol. 56: 267-271. https://doi.org/10.2323/jgam.56.267
  4. Leifson E. 1962. The bacterial flora of distilled and stored water. III. New species of the genera Corynebacterium, Flavobacterium, Spirillum and Pseudomonas. Int. Bull. Bacteriol. Nomencl. Taxon. 12: 161-170. https://doi.org/10.1099/0096266X-12-4-161
  5. Bullerjahn GS, Post AF. 2014. Physiology and molecular biology of aquatic cyanobacteria. Front. Microbiol. 5: 359.
  6. Huisman J, Codd GA, Paerl HW, Ibelings BW, Verspagen JMH, Visser PM. 2018. Cyanobacterial blooms. Nat. Rev. Microbiol. 16: 471-483. https://doi.org/10.1038/s41579-018-0040-1
  7. Le VV, Ko SR, Kang M, Lee SA, Oh HM, Ahn CY. 2022. Panacibacter microcysteis sp. nov., isolated from a eutrophic reservoir during the Microcystis bloom period. Arch. Microbiol. 204: 291.
  8. Weisburg WG, Barns SM, Pelletier 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
  9. Baker GC, Smith JJ, Cowan DA. 2003. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 55: 541-555. https://doi.org/10.1016/j.mimet.2003.08.009
  10. Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, Elshahed MS. 2009. Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl. Environ. Microbiol. 75: 5227-5236. https://doi.org/10.1128/AEM.00592-09
  11. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, et al. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67: 1613-1617. https://doi.org/10.1099/ijsem.0.001755
  12. Kanehisa M, Sato Y, Morishima K. 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428: 726-731. https://doi.org/10.1016/j.jmb.2015.11.006
  13. Dieckmann MA, Beyvers S, Nkouamedjo-Fankep RC, Hanel PHG, Jelonek L, Blom J, et al. 2021. EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure. Nucleic Acids Res. 49: W185-W192. https://doi.org/10.1093/nar/gkab341
  14. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, et al. 2019. AntiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47: W81-W87. https://doi.org/10.1093/nar/gkz310
  15. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376. https://doi.org/10.1007/BF01734359
  16. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
  17. Nei M, Kumar S, Takahashi K. 1998. The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc. Natl. Acad. Sci. USA 95: 12390-12397. https://doi.org/10.1073/pnas.95.21.12390
  18. Tamura K, Stecher G, Kumar S. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38: 3022-3027. https://doi.org/10.1093/molbev/msab120
  19. Kimura M. 1983. The Neutral Theory of Molecular Evolution. Cambride: Cambridge University Press.
  20. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60.
  21. Meier-Kolthoff JP, Goker M. 2019. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat. Commun. 10: 2182.
  22. Skerman VBD. 1967. A Guide to the Identification of the Genera of Bacteria. 2nd edition. The Williams & Wilkins Co.
  23. Smibert RM, Krieg NR. 1994. Phenotypic characterization, pp 607-654, In Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds.), Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington.
  24. Sasser M. 1990. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  25. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. 2007. Phenotypic characterization and the principles of comparative systematic, pp. 330-393. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR (eds.), Methods for General and Molecular Bacteriology. Washington, DC: American Society for Microbiology.
  26. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, et al. 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
  27. Oren A, Duker S, Ritter S. 1996. The polar lipid composition of Walsby's square bacterium. FEMS Microbiol. Lett. 138: 135-140. https://doi.org/10.1111/j.1574-6968.1996.tb08146.x
  28. Kates M. 1972. Techniques of Lipidology: Isolation, Analysis and Identification of Lipids. Amsterdam: North-Holland Pub. Co.
  29. Tamaoka J. 1986. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol. 123: 251-256. https://doi.org/10.1016/S0076-6879(86)23028-1
  30. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, 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
  31. Luo C, Rodriguez-R LM, Konstantinidis KT. 2014. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res. 42: e73.
  32. Qin QL, Xie B Bin, Zhang XY, Chen XL, Zhou BC, Zhou J, et al. 2014. A proposed genus boundary for the prokaryotes based on genomic insights. J. Bacteriol. 196: 2210-2215. https://doi.org/10.1128/JB.01688-14
  33. Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-19131. https://doi.org/10.1073/pnas.0906412106
  34. Auch AF, von Jan M, Klenk HP, Goker M. 2010. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand. Genomic Sci. 2: 117-134. https://doi.org/10.4056/sigs.531120
  35. Rouli L, Merhej V, Fournier PE, Raoult D. 2015. The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect. 7: 72-85. https://doi.org/10.1016/j.nmni.2015.06.005
  36. Park SC, Lee K, Kim YO, Won S, Chun J. 2019. Large-scale genomics reveals the genetic characteristics of seven species and importance of phylogenetic distance for estimating pan-genome size. Front. Microbiol. 10: 834.
  37. Tettelin H, Riley D, Cattuto C, Medini D. 2008. Comparative genomics: the bacterial pan-genome. Curr. Opin. Microbiol. 11: 472-477. https://doi.org/10.1016/j.mib.2008.09.006
  38. Osbourn A. 2010. Secondary metabolic gene clusters: evolutionary toolkits for chemical innovation. Trends Genet. 26: 449-457. https://doi.org/10.1016/j.tig.2010.07.001
  39. Oldfield E, Lin FY. 2012. Terpene biosynthesis: modularity rules. Angew. Chem. - Int. Ed. 51: 1124-1137. https://doi.org/10.1002/anie.201103110
  40. Robinson SL, Christenson JK, Wackett LP. 2019. Biosynthesis and chemical diversity of β-lactone natural products. Nat. Prod. Rep. 36: 458-475. https://doi.org/10.1039/C8NP00052B
  41. Agrawal S, Acharya D, Adholeya A, Barrow CJ, Deshmukh SK. 2017. Nonribosomal peptides from marine microbes and their antimicrobial and anticancer potential. Front. Pharmacol. 8: 828.
  42. Croft MT, Lawrence AD, Raux-Deery E, Warren MJ, Smith AG. 2005. Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature 438: 90-93. https://doi.org/10.1038/nature04056
  43. Kim M, Lee J, Yang D, Park HY, Park W. 2020. Seasonal dynamics of the bacterial communities associated with cyanobacterial blooms in the Han River. Environ. Pollut. 266: 115198.
  44. Valderrama JA, Durante-Rodriguez G, Blazquez B, Garcia JL, Carmona M, Diaz E. 2012. Bacterial degradation of benzoate: crossregulation between aerobic and anaerobic pathways. J. Biol. Chem. 287: 10494-10508. https://doi.org/10.1074/jbc.M111.309005
  45. Seo J-S, Keum Y-S, Li Q. 2009. Bacterial degradation of aromatic compounds. Int. J. Environ. Res. Public Health 6: 278-309. https://doi.org/10.3390/ijerph6010278
  46. Krieg NR. 1984. Genus Aquaspirillum. Hylemon, Wells, Krieg and Jannasch 1973, 361AL, In Krieg NR, Holt JG (eds.), Bergey's Manual of Systematic Bacteriology. Baltimore: Williams & Wilkins.