1887

Abstract

A Gram-negative, moderately halophilic and facultatively aerobic bacterium, designated strain GTF13, was isolated from a sea tidal flat. Cells were curved rods and motile by a single polar flagellum showing catalase and oxidase activities. Growth was observed at 20–37 °C, pH 5.0–8.5 and 1.0–6.0 % (w/v) NaCl. Strain GTF13 contained C summed feature 3 (comprising C ω6/C ω7), summed feature 8 (comprising C ω6c/C ω7) and C 3-OH as major fatty acids and ubiquinone-9 and ubiquinone-8 as major quinones. Phosphatidylethanolamine and two unidentified phospholipids were detected as major polar lipids. The G+C content of the genomic DNA was 59.8 mol%. Strain GTF13 was most closely related to SA1, CL-33 and FR1439, belonging to different families or orders of the class , with less than 92.0 % 16S rRNA gene sequence similarities. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GTF13 formed a phylogenetic lineage with the family , but the genome-based phylogenomic tree showed that strain GTF13 formed a distinct phylogenetic lineage within the order . The very low 16S rRNA gene sequence similarities and distinct phylogenetic relationships, together with distinct phenotypic and chemotaxonomic properties, served to differentiate strain GTF13 from phylogenetically closely related families. Here, strain GTF13 is proposed as a novel genus and species, for which the name gen. nov., sp. nov. is proposed, within a new family fam. nov. of the order . The type strain is GTF13 (=KACC 19788=JCM 32043).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003976
2020-02-11
2020-05-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/4/2239.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003976&mimeType=html&fmt=ahah

References

  1. Garrity GM, Bell JA, Lilburn TI. Oceanospirillales ord. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd edn. New York: Springer; 2005270
    [Google Scholar]
  2. Golyshin PN, Chernikova TN, Abraham WR, Lünsdorf H, Timmis KN et al. Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. Int J Syst Evol Microbiol 2002; 52:901–911
    [Google Scholar]
  3. Labrenz M, Lawson PA, Tindall BJ, Collins MD, Hirsch P. Saccharospirillum Impatiens gen. nov., sp. nov., a novel gamma-proteobacterium isolated from hypersaline Ekho lake (East Antarctica). Int J Syst Evol Microbiol 2003; 53:653–660 [CrossRef]
    [Google Scholar]
  4. Garrity GM, Bell JA, Lilburn TI, Family I. Oceanospirillaceae fam. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd edn. New York: Springer; 2005271
    [Google Scholar]
  5. Golyshin PN, Harayama S, Timmis KN, Yakimov MM, Family II. Alcanivoraceae fam. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) In Bergey’s Manual of Systematic Bacteriology, 2nd edn, vol. 2, part B, p. 270. Edited by New York: Springer; 2005
    [Google Scholar]
  6. Garrity GM, Bell JA, Lilburn TI. Hahellaceae fam. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd edn. New York: Springer; 2005270
    [Google Scholar]
  7. Kim H, Choo Y-J, Cho J-C, fam L. Litoricolaceae fam. nov., to include Litoricola lipolytica gen. nov., sp. nov., a marine bacterium belonging to the order Oceanospirillales . Int J Syst Evol Microbiol 2007; 57:1793–1798 [CrossRef]
    [Google Scholar]
  8. Franzmann PD, Wehmeyer U, Stackebrandt E. Halomonadaceae fam. nov., a new family of the class Proteobacteria to accommodate the genera Halomonas and Deleya . Syst Appl Microbiol 1988; 11:16–19 [CrossRef]
    [Google Scholar]
  9. Wang G, He H, Chen C, Tang M, Li T et al. Aliikangiella marina gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122, and proposal of Kangiellaceae fam. nov. in the order Oceanospirillales . Int J Syst Evol Microbiol 2015; 65:4488–4494 [CrossRef]
    [Google Scholar]
  10. Bartz J-O, Blom J, Busse H-J, Mvie JB, Hardt M et al. Parendozoicomonas haliclonae gen. nov. sp. nov. isolated from a marine sponge of the genus Haliclona and description of the family Endozoicomonadaceae fam. nov. comprising the genera Endozoicomonas, Parendozoicomonas, and Kistimonas . Syst Appl Microbiol 2018; 41:73–84 [CrossRef]
    [Google Scholar]
  11. Krishnan R, Lang E, Midha S, Patil PB, Rameshkumar N. Isolation and characterization of a novel 1-aminocyclopropane-1-carboxylate (ACC) deaminase producing plant growth promoting marine Gammaproteobacteria from crops grown in brackish environments. Proposal for Pokkaliibacter plantistimulans gen. nov., sp. nov., Balneatrichaceae fam. nov. in the order Oceanospirillales and an emended description of the genus Balneatrix . Syst Appl Microbiol 2018; 41:570–580 [CrossRef]
    [Google Scholar]
  12. Wang Y, Yu M, Liu Y, Yang X, Zhang X-H. Bacterioplanoides pacificum gen. nov., sp. nov., isolated from seawater of South Pacific Gyre. Int J Syst Evol Microbiol 2016; 66:5010–5015 [CrossRef]
    [Google Scholar]
  13. Feng T, Kim KH, Chun BH, Jeon CO. Amylibacter lutimaris sp. nov., isolated from sea-tidal flat sediment. Int J Syst Evol Microbiol 2018; 68:2088–2092 [CrossRef]
    [Google Scholar]
  14. Lee Y, Lee B, Lee K, Jeon CO. Solimonas fluminis sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2018; 68:2755–2759 [CrossRef]
    [Google Scholar]
  15. Yoon S-H, Ha S-M, 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 [CrossRef]
    [Google Scholar]
  16. Ludwig W et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [CrossRef]
    [Google Scholar]
  17. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73:5261–5267 [CrossRef]
    [Google Scholar]
  18. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef]
    [Google Scholar]
  19. Sambrook J, Fritsch EF, Maniatis T. Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory; 1989
    [Google Scholar]
  20. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [CrossRef]
    [Google Scholar]
  21. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [CrossRef]
    [Google Scholar]
  22. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [CrossRef]
    [Google Scholar]
  23. Gomori G. Preparation of buffers for use in enzyme studies. Methods Enzymol 1955; 1:138–146
    [Google Scholar]
  24. Kodaka H, Armfield AY, Lombard GL, Dowell VR. Practical procedure for demonstrating bacterial flagella. J Clin Microbiol 1982; 16:948–952 [CrossRef]
    [Google Scholar]
  25. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. editor Methods for general and molecular bacteriology Washington, DC: American Society for Microbiology; 1994607–654
    [Google Scholar]
  26. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1988; 19:1–67
    [Google Scholar]
  27. Choi A, Lee K, Oh H-M, Feng J, Cho J-C et al. Litoricola marina sp. nov. Int J Syst Evol Microbiol 2010; 60:1303–1306 [CrossRef]
    [Google Scholar]
  28. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [CrossRef]
    [Google Scholar]
  29. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  30. 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 [CrossRef]
    [Google Scholar]
  31. Kurahashi M, Yokota A. Endozoicomonas elysicola gen. nov., sp. nov., a gamma-proteobacterium isolated from the sea slug Elysia ornata. Syst Appl Microbiol 2007; 30:202–206 [CrossRef]
    [Google Scholar]
  32. Sheu S-Y, Lin K-R, Hsu M-yuan, Sheu D-S, Tang S-L et al. Endozoicomonas acroporae sp. nov., isolated from Acropora coral . Int J Syst Evol Microbiol 2017; 67:3791–3797 [CrossRef]
    [Google Scholar]
  33. Appolinario LR, Tschoeke DA, Rua CPJ, Venas T, Campeão ME et al. Description of Endozoicomonas arenosclerae sp. nov. using a genomic taxonomy approach. Antonie Van Leeuwenhoek 2016; 109:431–438 [CrossRef]
    [Google Scholar]
  34. Schreiber L, Kjeldsen KU, Obst M, Funch P, Schramm A. Description of Endozoicomonas ascidiicola sp. nov., isolated from Scandinavian ascidians. Syst Appl Microbiol 2016; 39:313–318 [CrossRef]
    [Google Scholar]
  35. Hyun D-W, Shin N-R, Kim M-S, Oh SJ, Kim PS et al. Endozoicomonas atrinae sp. nov., isolated from the intestine of a comb pen shell Atrina pectinata . Int J Syst Evol Microbiol 2014; 64:2312–2318 [CrossRef]
    [Google Scholar]
  36. Pike RE, Haltli B, Kerr RG. Description of Endozoicomonas euniceicola sp. nov. and Endozoicomonas gorgoniicola sp. nov., bacteria isolated from the octocorals Eunicea fusca and Plexaura sp., and an emended description of the genus Endozoicomonas . Int J Syst Evol Microbiol 2013; 63:4294–4302 [CrossRef]
    [Google Scholar]
  37. Yang CS, Chen MH, Arun AB, Chen CA, Wang JT et al. Endozoicomonas montiporae sp. nov., isolated from the encrusting pore coral Montipora aequituberculata . Int J Syst Evol Microbiol 2010; 60:1158–1162 [CrossRef]
    [Google Scholar]
  38. Nishijima M, Adachi K, Katsuta A, Shizuri Y, Yamasato K. Endozoicomonas numazuensis sp. nov., a gammaproteobacterium isolated from marine sponges, and emended description of the genus Endozoicomonas Kurahashi and Yokota 2007. Int J Syst Evol Microbiol 2013; 63:709–714 [CrossRef]
    [Google Scholar]
  39. Choi EJ, Kwon HC, Sohn YC, Yang HO. Kistimonas asteriae gen. nov., sp. nov., a gammaproteobacterium isolated from Asterias amurensis . Int J Syst Evol Microbiol 2010; 60:938–943 [CrossRef]
    [Google Scholar]
  40. Ellis JC, Thomas MS, Lawson PA, Patel NB, Faircloth W et al. Kistimonas alittae sp. nov., a gammaproteobacterium isolated from the marine annelid Alitta succinea . Int J Syst Evol Microbiol 2019; 69:235–240 [CrossRef]
    [Google Scholar]
  41. Lee J, Shin N-R, Lee H-W, Roh SW, Kim M-S et al. Kistimonas scapharcae sp. nov., isolated from a dead ark clam (Scapharca broughtonii), and emended description of the genus Kistimonas . Int J Syst Evol Microbiol 2012; 62:2865–2869 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003976
Loading
/content/journal/ijsem/10.1099/ijsem.0.003976
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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