Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Mucilaginibacter aquariorum sp. nov., Isolated from Fresh Water

  • Ve Van Le (Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • So-Ra Ko (Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Mingyeong Kang (Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Hee-Mock Oh (Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Chi-Yong Ahn (Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB))
  • Received : 2022.08.12
  • Accepted : 2022.10.25
  • Published : 2022.12.28
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Abstract

A Gram-stain-negative, rod-shaped bacterial strain, JC4T, was isolated from a freshwater sample and determined the taxonomic position. Initial identification based on 16S rRNA gene sequences revealed that strain JC4T is affiliated to the genus Mucilaginibacter with a sequence similarity of 97.97% to Mucilaginibacter rigui WPCB133T. The average nucleotide identity and digital DNA-DNA hybridization values between strain JC4T and Mucilaginibacter species were estimated below 80.92% and 23.9%, respectively. Strain JC4T contained summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and iso-C15:0 as predominant cellular fatty acids. The dominant polar lipids were identified as phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, and two unidentified lipids. The respiratory quinone was MK-7. The genomic DNA G+C content of strain JC4T was determined to be 42.44%. The above polyphasic evidences support that strain JC4T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter aquariorum sp. nov. is proposed. The type strain is JC4T (= KCTC 92230T = LMG 32715T).

Keywords

Acknowledgement

We thank Professor Aharon Oren for his expert advice concerning the species epithet and Latin etymology.

References

  1. Pankratov TA, Tindall BJ, Liesack W, Dedysh SN. 2007. Mucilaginibacter paludis gen. nov., sp. nov. and Mucilaginibacter gracilis sp. nov., pectin-, xylan- and laminarin-degrading members of the family Sphingobacteriaceae from acidic Sphagnum peat bog. Int. J. Syst. Evol. Microbiol. 57: 2349-2354. https://doi.org/10.1099/ijs.0.65100-0
  2. Lee SA, Le VV, Ko SR, Lee N, Oh HM, Ahn CY. 2021. Mucilaginibacter inviolabilis sp. nov., isolated from the phycosphere of Haematococcus lacustris NIES 144 culture. Int. J. Syst. Evol. Microbiol. 71: 004668. doi: 10.1099/ijsem.0.004668.
  3. Kang H, Kim H, Bae S, Joh K. 2021. Mucilaginibacter aquatilis sp. nov., Mucilaginibacter arboris sp. nov., and Mucilaginibacter ginkgonis sp. nov., novel bacteria isolated from freshwater and tree bark. Int. J. Syst. Evol. Microbiol. 71: 004755.
  4. Yoon JH, Kang SJ, Park S, Oh TK. 2012. Mucilaginibacter litoreus sp. nov., isolated from marine sand. Int. J. Syst. Evol. Microbiol. 62: 2822-2827. https://doi.org/10.1099/ijs.0.034900-0
  5. Kim JH, Kang SJ, Jung YT, Oh TK, Yoon JH. 2012. Mucilaginibacter lutimaris sp. nov., isolated from a tidal flat sediment. Int. J. Syst. Evol. Microbiol. 62: 515-519. https://doi.org/10.1099/ijs.0.030213-0
  6. Choi L, Zhao X, Song Y, Wu M, Wang G, Li M. 2020. Mucilaginibacter hurinus sp. nov., isolated from briquette warehouse soil. Arch. Microbiol. 202: 127-134. https://doi.org/10.1007/s00203-019-01720-1
  7. Li YP, You LX, Yang XJ, Yu YS, Zhang HT, Yang B, et al. 2022. Extrapolymeric substances (EPS) in Mucilaginibacter rubeus P2 displayed efficient metal(loid) bio-adsorption and production was induced by copper and zinc. Chemosphere 291: 132712.
  8. Fan X, Tang J, Nie L, Huang J, Wang G. 2018. High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30T 06. Stand. Genomic Sci. 13: 34.
  9. Smith DL, Smith DL. 2022. Mucilaginibacter sp. K improves growth and induces salt tolerance in nonhost plants via multilevel mechanisms. Front. Plant Sci. 13: 938697.
  10. Wang ZY, Wang RX, Zhou JS, Cheng JF, Li YH. 2020. An assessment of the genomics, comparative genomics and cellulose degradation potential of Mucilaginibacter polytrichastri strain RG4-7. Bioresour. Technol. 297: 122389.
  11. Lin L, Yang H, Xu X. 2022. Effects of water pollution on human health and disease heterogeneity: a review. Front. Environ. Sci. 10: 880246.
  12. Yin H, Niu J, Ren Y, Cong J, Zhang X, Fan F, et al. 2015. An integrated insight into the response of sedimentary microbial communities to heavy metal contamination. Sci. Rep. 5: 14266.
  13. Le VV, Ko SR, Kang M, Oh HM, Ahn CY. 2022. Hymenobacter cyanobacteriorum sp. nov., isolated from a freshwater reservoir during the cyanobacterial bloom period. Arch. Microbiol. 204: 369.
  14. Baik KS, Park SC, Kim EM, Lim CH, Seong CN. 2010. Mucilaginibacter rigui sp. nov., isolated from wetland freshwater, and emended description of the genus Mucilaginibacter. Int. J. Syst. Evol. Microbiol. 60: 134-139. https://doi.org/10.1099/ijs.0.011130-0
  15. Ten LN, Jeon NY, Li W, Cho YJ, Kim MK, Lee SY, et al. 2019. Mucilaginibacter terrigena sp. nov., a novel member of the family Sphingobacteriaceae. Curr. Microbiol. 76: 1152-1160. https://doi.org/10.1007/s00284-019-01748-y
  16. Ko SR, Le VV, Jin L, Lee SA, Ahn CY, Oh HM. 2021. Mariniflexile maritimum sp. nov., isolated from seawater of the South Sea in the Republic of Korea. Int. J. Syst. Evol. Microbiol. 71: 004925.
  17. 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
  18. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
  19. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376. https://doi.org/10.1007/BF01734359
  20. 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
  21. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35: 1547-1549. https://doi.org/10.1093/molbev/msy096
  22. Kimura M. 1983. The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  23. Le VV, Ko S-R, Lee S-A, Jin L, Blom J, Ahn C-Y, et al. 2021. Cochlodiniinecator piscidefendens gen. nov., sp. nov., an algicidal bacterium against the ichthyotoxic dinoflagellate Cochlodinium polykrikoides. Int. J. Syst. Evol. Microbiol. 71: 005124.
  24. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
  25. Simao FA, Waterhouse RM, Ioannidis P, Kriventseva E V, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31: 3210-3212. https://doi.org/10.1093/bioinformatics/btv351
  26. Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R, Butler RM, et al. 2020. The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res. 48: D606-D612.
  27. Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J. 2012. PGAP: pan-genomes analysis pipeline. Bioinformatics 28: 416-418. https://doi.org/10.1093/bioinformatics/btr655
  28. Cantalapiedra CP, Her andez-Plaza A, Letunic I, Bork P, Huerta-Cepas J. 2021. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38: 5825-5829. https://doi.org/10.1093/molbev/msab293
  29. 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
  30. Yoon SH, Ha S min, 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
  31. 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.
  32. 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.
  33. 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 DC, USA.
  34. Bauer AW, Kirby WM, Sherris JC, Turck M. 1966. Antibiotic susceptibility testing by a standardized single disk method. Am. J. Clin. Pathol. 45: 493-496. https://doi.org/10.1093/ajcp/45.4_ts.493
  35. Sasser M. 1990. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  36. 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
  37. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. 2007. Phenotypic characterization and the principles of comparative systematics, pp. 330-393. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR (eds), Methods for General and Molecular Bacteriology, 3rd Ed. American Society for Microbiology, Washington DC, USA.
  38. Kates M. 1972. Techniques of Lipidology: Isolation, Analysis and Identification of Lipids. Amsterdam: North-Holland Pub. Co.
  39. 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
  40. Tamaoka J. 1986. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol. 123: 251-256.
  41. 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
  42. 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
  43. Barbosa J, Caetano T, Mendo S. 2015. Class I and class II lanthipeptides produced by Bacillus spp. J. Nat. Prod. 78: 2850-2866. https://doi.org/10.1021/np500424y
  44. Oldfield E, Lin FY. 2012. Terpene biosynthesis: modularity rules. Angew. Chemie - Int. Ed. 51: 1124-1137. https://doi.org/10.1002/anie.201103110
  45. Ay H. 2020. Nonomuraea terrae sp. nov., isolated from arid soil. Arch. Microbiol. 202: 2197-2205. https://doi.org/10.1007/s00203-020-01941-9
  46. Le VV, Ko SR, Lee SA, Kang M, Oh HM, Ahn CY. 2022. Caenimonas aquaedulcis sp. nov., isolated from freshwater of Daechung Reservoir during Microcystis bloom. J. Microbiol. Biotechnol. 32: 575-581. https://doi.org/10.4014/jmb.2201.01023
  47. 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.
  48. Nouioui I, Potter G, Jando M, Goodfellow M. 2022. Nocardia noduli sp. nov., a novel actinobacterium with biotechnological potential. Arch. Microbiol. 204: 260.
  49. Yamada Y, Kuzuyama T, Komatsu M, Shin-ya K, Omura S, Cane DE, et al. 2015. Terpene synthases are widely distributed in bacteria. Proc. Natl. Acad. Sci. USA 112: 857-862. https://doi.org/10.1073/pnas.1422108112
  50. 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.
  51. Keto-Timonen R, Hietala N, Palonen E, Hakakorpi A, Lindstrom M, Korkeala H. 2016. Cold shock proteins: a minireview with special emphasis on Csp-family of enteropathogenic Yersinia. Front. Microbiol. 7: 1151.
  52. Kim M, Oh HS, Park SC, Chun J. 2014. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Microbiol. 64: 346-351. https://doi.org/10.1099/ijs.0.059774-0
  53. 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
  54. Richter M, Rossell-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