1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 2

sp. nov., isolated from a freshwater river Free

Abstract

An isolate, designated TTM-7, recovered from a freshwater river in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain TTM-7 is affiliated with species in the genus . Strain TTM-7 was most closely related to NJ-8 with a 98.2 % 16S rRNA gene sequence similarity, followed by H32-4 (97.4 %) and SS2-56 (96.3 %). Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed orange colonies. Optimal growth occurred at 25 °C, pH 7 and 0 % NaCl. The major fatty acids of strain TTM-7 were iso-C, summed feature 3 (comprising Cωc/Cω and/or iso-C 2-OH) and iso-C G. The predominant hydroxy fatty acid was iso-C 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, two unidentified aminoglycolipids, five unidentified aminophospholipids and one unidentified lipid. The major isoprenoid quinone was MK-7. Genomic DNA G+C content of strain TTM-7 was 40.6 mol%. Strain TTM-7 showed 83.6 % average nucleotide identity and 16.0 % digital DNA–DNA hybridization identity with NJ-8. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TTM-7 should be classified in a novel species of the genus , for which the name sp. nov. is proposed. The type strain is TTM-7 (=BCRC 81159=LMG 30926=KCTC 62870).

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): Chitinophagaceae , Chitinophagales , Chitinophagia and Lacibacter luteus sp. nov.
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003926
2019-12-18
2023-12-03
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/2/1404.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003926&mimeType=html&fmt=ahah

References

  1. Qu JH, Yuan HL, Yang JS, Li HF, Chen N et al. Lacibacter cauensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from sediment of a eutrophic lake. Int J Syst Evol Microbiol 2009; 59:1153–1157 [View Article]
     [Google Scholar]
  2. Jin L, Shin SY, Lee HG, Ahn CY, Oh HM et al. Lacibacter daechungensis sp. nov., isolated from deep freshwater of a reservoir. Int J Syst Evol Microbiol 2013; 63:4519–4523 [View Article]
     [Google Scholar]
  3. Han JH, Baek K, Lee MH. Lacibacter nakdongensis sp. nov., isolated from river sediment. Int J Syst Evol Microbiol 2017; 67:352–356 [View Article]
     [Google Scholar]
  4. 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]
  5. Anzai Y, Kudo Y, Oyaizu H. The phylogeny of the genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 1997; 47:249–251 [View Article]
     [Google Scholar]
  6. Chen WM, Laevens S, Lee TM, Coenye T, De Vos P et al. Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 2001; 51:1729–1735 [View Article]
     [Google Scholar]
  7. 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]
     [Google Scholar]
  8. Nawrocki EP, Eddy SR. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 2007; 3:e56 [View Article]
     [Google Scholar]
  9. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  10. 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]
     [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  13. Kluge AG, Farris JS. Quantitative Phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
     [Google Scholar]
  14. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983
     [Google Scholar]
  15. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article]
     [Google Scholar]
  16. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
     [Google Scholar]
  17. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016; 32:3047–3048 [View Article]
     [Google Scholar]
  18. 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]
     [Google Scholar]
  19. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
     [Google Scholar]
  20. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
     [Google Scholar]
  21. 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]
     [Google Scholar]
  22. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  23. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
     [Google Scholar]
  24. 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]
     [Google Scholar]
  25. 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]
     [Google Scholar]
  26. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article]
     [Google Scholar]
  27. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  28. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
     [Google Scholar]
  29. Beveridge TJ, Lawrence JR, Murray RGE. Sampling and staining for light microscopy. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp 19–33
     [Google Scholar]
  30. Pitt A, Schmidt J, Koll U, Hahn MW. Aquirufa antheringensis gen. nov., sp. nov. and Aquirufa nivalisilvae sp. nov., representing a new genus of widespread freshwater bacteria. Int J Syst Evol Microbiol 2019; 69:2739–2749 [View Article]
     [Google Scholar]
  31. Schlegel HG, Lafferty R, Krauss I. The isolation of mutants not accumulating poly-?-hydroxybutyric acid. Archiv. Mikrobiol. 1970; 71:283–294 [View Article]
     [Google Scholar]
  32. Spiekermann P, Rehm BHA, Kalscheuer R, Baumeister D, Steinbüchel A. A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch Microbiol 1999; 171:73–80 [View Article]
     [Google Scholar]
  33. Reichenbach H. The order Cytophagales . In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH. (editors) The Prokaryotes, a Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd ed. New York, NY: Springer; 1992 pp 3631–3675
     [Google Scholar]
  34. Schmidt K, Connor A, Britton G. Analysis of pigments: carotenoids and related polyenes. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994 pp 403–461
     [Google Scholar]
  35. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp 309–329
     [Google Scholar]
  36. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp 330–393
     [Google Scholar]
  37. Wen CM, Tseng CS, Cheng CY, Li YK, Purification LYK. Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 2002; 35:213–219 [View Article]
     [Google Scholar]
  38. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50:1861–1868 [View Article]
     [Google Scholar]
  39. Chang SC, Wang JT, Vandamme P, Hwang JH, Chang PS et al. Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst Appl Microbiol 2004; 27:43–49 [View Article]
     [Google Scholar]
  40. Nokhal TH, Schlegel HG. Taxonomic study of Paracoccus denitrificans . Int J Syst Bacteriol 1983; 33:26–37 [View Article]
     [Google Scholar]
  41. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  42. Embley TM, Wait R. Structural lipids of eubacteria. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994 pp 121–161
     [Google Scholar]
  43. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. (editors) Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994 pp 265–309
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003926
Loading
Lacibacter luteus sp. nov., isolated from a freshwater river
Int J Syst Evol Microbiol 70, 1404 (2020); https://doi.org/10.1099/ijsem.0.003926
/content/journal/ijsem/10.1099/ijsem.0.003926
/content/journal/ijsem/10.1099/ijsem.0.003926
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