Skip to content
1887

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

Volume 71, Issue 10

sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water Free

Abstract

A Gram-stain-negative, rod-shaped, non-motile, red-pink bacterium designated SD6 was isolated from coastal marine water at Sadong Beach, Ulleung Island, South Korea. Cells of SD6 grew at 10–42 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 6.0–7.0) and at 0–8.0 % (w/v) NaCl (optimum, 0–3 %). Moreover, 16S rRNA gene sequence analysis indicated that strain SD6 was a member of the genus , sharing similarities to XAAS-1 (98.0 %), 9-2 (97.3 %), X14-1 (97.2 %) and HYL7-26 (96.8 %). The predominant fatty acids of strain SD6 were identified as iso-C and summed feature 4 (comprising anteiso-C B and/or iso-C I) and the sole respiratory quinone was identified as MK-7 (menaquinone 7). Major polar lipids included phosphatidylethanolamine, one unidentified phosphoglycolipid, two unidentified glycolipids and one unidentified lipid. The average nucleotide identity and DNA–DNA hybridization values of strain SD6 with its closely related strains were 72.8–79.8 % and 19.2–22.6 %, respectively. The genomic DNA G+C content was 45.4 mol%. In accordance with the results of phenotypic, chemotaxonomic and phylogenetic data, strain SD6 represents a novel species of the genus r, for which the name sp. nov. is proposed. The type strain is SD6 (=KACC 21543=NBRC 114313=JCM 31022).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): carboxymethyl cellulose , carotenoids , coastal surface seawater , Hymenobacteraceae , Pontibacter and Pontibacter cellulosilyticus
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005058
2021-10-25
2025-12-05

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/10/ijsem005058.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005058&mimeType=html&fmt=ahah

References

  1. Munoz R, Rosselló-Móra R, Amann R. Revised phylogeny of bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016; 39:281–296S0723-2020(16)30018-2 [View Article] [PubMed]
     [Google Scholar]
  2. Nedashkovskaya OI, Kim SB, Suzuki M, Shevchenko LS, Lee MS et al. Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum ‘Bacteriodetes’, and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovshaya et al. 2003. Int J Syst Evol Microbiol 2005; 55:2583–2588 [View Article] [PubMed]
     [Google Scholar]
  3. Chhetri G, Kim J, Kim I, Kim MK, Seo T. Pontibacter chitinilyticus sp. nov., a novel chitin-hydrolysing bacterium isolated from soil. Antonie van Leeuwenhoek 2019; 112:1011–1018 [View Article] [PubMed]
     [Google Scholar]
  4. Chhetri G, Kim J, Kim H, Kim I, Seo T. Pontibacter oryzae sp. nov., a carotenoid-producing species isolated from a rice paddy field. Antonie van Leeuwenhoek 2019; 112:1705–1713 [View Article] [PubMed]
     [Google Scholar]
  5. Liu Z-W, Zhang J, Yu Y, Li H-R, Du Z-J. Pontibacter arcticus sp. nov., isolated from rhizosphere soil of Saxifraga oppositifolia. Int J Syst Evol Microbiol 2019; 69:3609–3615 [View Article] [PubMed]
     [Google Scholar]
  6. Dai J, Xu M, Peng F, Jiang F, Chen X et al. Pontibacter soli sp. nov., isolated from the soil of a Populus rhizosphere in Xinjiang, China. Antonie van Leeuwenhoek 2014; 105:65–72 [View Article] [PubMed]
     [Google Scholar]
  7. Osman G, Zhang T, Lou K, Gao Y, Chang W et al. Pontibacter aydingkolensis sp. nov., isolated from soil of a salt lake. Int J Syst Evol Microbiol 2016; 66:5523–5528 [View Article] [PubMed]
     [Google Scholar]
  8. Zhang L, Zhang Q, Luo X, Tang Y, Dai J et al. Pontibacter korlensis sp. nov., isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 2008; 58:1210–1214 [View Article] [PubMed]
     [Google Scholar]
  9. Subhash Y, Sasikala C, Ramana CV. Pontibacter ruber sp. nov. and Pontibacter deserti sp. nov., isolated from the desert. Int J Syst Evol Microbiol 2014; 64:1006–1011 [View Article] [PubMed]
     [Google Scholar]
  10. Singh P, Kumari R, Nayyar N, Lal R. Pontibacter aurantiacus sp. nov. isolated from hexachlorocyclohexane (HCH) contaminated soil. Int J Syst Evol Microbiol 2017; 67:1400–1407 [View Article] [PubMed]
     [Google Scholar]
  11. Kim DI, Lee JH, Kang JW, Ka J-O, Seong CN. Pontibacter rugosus sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016; 66:4389–4394 [View Article] [PubMed]
     [Google Scholar]
  12. Wu Y-H, Zhou P, Jian S-L, Liu Z-S, Wang C-S et al. Pontibacter amylolyticus sp. nov., isolated from a deep-sea sediment hydrothermal vent field. Int J Syst Evol Microbiol 2016; 66:1760–1767 [View Article] [PubMed]
     [Google Scholar]
  13. Dai J, Dai W, Qiu C, Yang Z, Zhang Y. Unraveling adaptation of Pontibacter korlensis to radiation and infertility in desert through complete genome and comparative transcriptomic analysis. Sci Rep 2015; 5:10929 [View Article] [PubMed]
     [Google Scholar]
  14. Bomble YJ, Lin C-. Y, Amore A, Wei H, Holwerda EK et al. Lignocellulose deconstruction in the biosphere. Curr Opin Chem Biol 2017; 41:61–70 [View Article] [PubMed]
     [Google Scholar]
  15. Ghosh D, Jana BB, Lahiri S, Bhakta J, Bhattacharjee A. Assessing the cellulase enzyme heterogeneity of bacterial strains and their feedback to cattle manure degradation in a greenhouse model of in vivo pond ecosystem. Environ Monit Assess 2018; 190:452 [View Article] [PubMed]
     [Google Scholar]
  16. Oke MA, Annuar MSM, Simarani K. Mixed lignocellulosic biomass degradation and utilization for bacterial cellulase production. Waste Biomass Valor 2017; 8:893–903 [View Article]
     [Google Scholar]
  17. Yoon SH, Ha SM, 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]
  18. 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]
  19. 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]
  20. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettian PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  21. 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]
  22. Guidon 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]
  23. 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]
  24. 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]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  26. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  29. Blin K, Shaw S, Steinke K, Villebro R, Ziemart N. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article] [PubMed]
     [Google Scholar]
  30. Yoon SH, Ha SM, 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]
  31. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  32. Na SI, Kim YO, Yoon SH, Ha SM, 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] [PubMed]
     [Google Scholar]
  33. Wang ZY, Wang RX, Zhou JS, Cheng JF, Li YH. An assessment of the genomics, comparative genomics and cellulose degradation potential of mucilaginibacter polytrichastri strain RG4-7. Bioresour Technol 2020; 297:122389 [View Article]
     [Google Scholar]
  34. Liang M-H, Zhu J, Jiang J-G. Carotenoids biosynthesis and cleavage related genes from bacteria to plants. Crit Rev Food Sci Nutr 2018; 58:2314–2333 [View Article] [PubMed]
     [Google Scholar]
  35. 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]
  36. Kim J, Chhetri G, Kim I, Lee B, Jang W et al. Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil. Int J Syst Evol Microbiol 2020; 70:2449–2456 [View Article] [PubMed]
     [Google Scholar]
  37. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. Proposed minimal standards for describing new taxa of the family Flavobactericeae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article]
     [Google Scholar]
  38. Buck JD. Nonstaining (KOH) method for determination of Gram reactions in marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article] [PubMed]
     [Google Scholar]
  39. Schaeffer AB, Fulton MD. A simplified method of staining endospores. Science 1933; 77:194 [View Article] [PubMed]
     [Google Scholar]
  40. Smibert RM, Kreig NR. Phenotypic characterization. Gerhardt P, Murray RGE, Wood WA, Kreig NR. eds In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  41. 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]
  42. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316–354 [View Article] [PubMed]
     [Google Scholar]
  43. Komagata K, Suzuki KI. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207 [View Article]
     [Google Scholar]
  44. 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]
  45. Kim I, Chhetri G, Kim J, Kang M, Seo T. Lewinella aurantiaca sp. nov., a carotenoid pigment-producing bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:6180–6187 [View Article] [PubMed]
     [Google Scholar]
  46. Nedashkovskaya OI, Kim SB, Genus XIV et al. Pontibacter Nedashkovskaya. Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ. eds In Bergey’s Manual of Systematic Bacteriology Springer; 2010 pp 410–412
     [Google Scholar]
  47. Kuhad RC, Gupta R, Singh A. Microbial enzyme: Applications in industry and in bioremediation. Enzyme Res 2011 [View Article]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005058
Loading
Pontibacter cellulosilyticus sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water
Int J Syst Evol Microbiol 71, 005058 (2021); https://doi.org/10.1099/ijsem.0.005058
/content/journal/ijsem/10.1099/ijsem.0.005058
/content/journal/ijsem/10.1099/ijsem.0.005058
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