1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 8

Description of gen. nov., sp. nov., and gen. nov., comb. nov. via reclassification of the genus Free

Abstract

Strain MEBiC09520, which was isolated from a tidal sediment in Incheon, Korea, is a pale yellow, rod-shaped bacterium, cells of which are 0.4–0.5 µm in width and 1.5–2 µm in length. Strain MEBiC09520 shared 95.17 and 92.57% 16S rRNA gene sequence similarity with and , respectively. It grew optimally at pH 6.0, at 55 °C and with 2.5–3.5% (w/v) NaCl. Its polar lipid components included phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), an unidentified phospholipid (PL), three unidentified aminolipids (ALs) and two unidentified lipids (L). The fatty acids C, C cyclo ω8, C 2-OH and summed feature 8 (Cω7 and/or Cω6) were predominantly present in its cell wall. Strain MEBiC09520 was thermophilic, while and were mesophilic. Although showed no nitrate reduction activity, MEBiC09520 and showed a positive reaction. These strains differed in carbohydrate utilization. In particular, was able to thrive on various carbohydrate substrates as compared to the other strains. The average nucleotide identity value was 69.92% between strain MEBiC09520 and ZYL, 70.38% between ZYL and HTCJW17, and 72.83% between strain MEBiC09520 and HTCJW17. Considering these differences, strain MEBiC09520 (=KCCM 43320=MCCC 1K03920) is suggested to represent and novel species of a new genus, gen. nov., sp. nov., and should be reclassified as gen. nov., comb. nov.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Emcibacteraceae , reclassification , thermophilic and tidal sediments
Funding
This study was supported by the:
  • Ministry of Ocean and Fisheries, Korea (Award 20170431)
    • Principle Award Recipient: Kae Kyoung Kwon
  • Korea Institute of Ocean Science and Technology (Award PE99822)
    • Principle Award Recipient: Kae Kyoung Kwon
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004334
2020-07-22
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/8/4691.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004334&mimeType=html&fmt=ahah

References

  1. Iino T, Ohkuma M, Kamagata Y, Amachi S. Iodidimonas muriae gen. nov., sp. nov., an aerobic iodide-oxidizing bacterium isolated from brine of a natural gas and iodine recovery facility, and proposals of Iodidimonadaceae fam. nov., Iodidimonadales ord. nov., Emcibacteraceae fam. nov. and Emcibacterales ord. nov. Int J Syst Evol Microbiol 2016; 66:5016–5022 [View Article][PubMed]
     [Google Scholar]
  2. Liu X, Li G, Lai Q, Sun F, Du Y et al. Emcibacter nanhaiensis gen. nov. sp. nov., isolated from sediment of the South China Sea. Antonie van Leeuwenhoek 2015; 107:893–900 [View Article][PubMed]
     [Google Scholar]
  3. Zhao Z, Shen X, Chen W, Yu X-Y, Fu G-Y et al. Emcibacter congregatus sp. nov., isolated from sediment cultured in situ. Int J Syst Evol Microbiol 2018; 68:2846–2850 [View Article][PubMed]
     [Google Scholar]
  4. Alain K, Harder J, Widdel F, Zengler K. Anaerobic utilization of toluene by marine alpha- and Gammaproteobacteria reducing nitrate. Microbiology 2012; 158:2946–2957 [View Article][PubMed]
     [Google Scholar]
  5. Shaw AK, Halpern AL, Beeson K, Tran B, Venter JC et al. It's all relative: ranking the diversity of aquatic bacterial communities. Environ Microbiol 2008; 10:2200–2210 [View Article][PubMed]
     [Google Scholar]
  6. Gao B, Shang X, Li L, Di W, Zeng R. Phylogenetically diverse, acetaldehyde-degrading bacterial community in the deep sea water of the West Pacific Ocean. Acta Oceanologica Sinica 2018; 37:54–64 [View Article]
     [Google Scholar]
  7. Verna C, Ramette A, Wiklund H, Dahlgren TG, Glover AG et al. High symbiont diversity in the bone-eating worm Osedax mucofloris from shallow whale-falls in the North Atlantic. Environ Microbiol 2010; 12:2355–2370 [View Article]
     [Google Scholar]
  8. Dishaw LJ, Flores-Torres J, Lax S, Gemayel K, Leigh B et al. The gut of geographically disparate Ciona intestinalis harbors a core microbiota. PLoS One 2014; 9:e93386 [View Article][PubMed]
     [Google Scholar]
  9. Santelli CM, Orcutt BN, Banning E, Bach W, Moyer CL et al. Abundance and diversity of microbial life in ocean crust. Nature 2008; 453:653–656 [View Article][PubMed]
     [Google Scholar]
  10. Barco RA, Hoffman CL, Ramírez GA, Toner BM, Edwards KJ et al. In-situ incubation of iron-sulfur mineral reveals a diverse chemolithoautotrophic community and a new biogeochemical role for Thiomicrospira . Environ Microbiol 2017; 19:1322–1337 [View Article]
     [Google Scholar]
  11. Sylvan JB, Toner BM, Edwards KJ. Life and death of deep-sea vents: bacterial diversity and ecosystem succession on inactive hydrothermal sulfides. mBio 2012; 3:e00279–00211 [View Article][PubMed]
     [Google Scholar]
  12. Li J, Su L, Wang F, Yang J, Gu L et al. Elucidating the biomineralization of low-temperature hydrothermal precipitates with varying Fe, Si contents: Indication from ultrastructure and microbiological analyses. Deep Sea Res Part I: Oceanographic Research Papers ; 2019; 103208
  13. Maeda R, Nagashima H, Widada J, Iwata K, Omori T. Novel marine carbazole-degrading bacteria. FEMS Microbiol Lett 2009; 292:203–209 [View Article][PubMed]
     [Google Scholar]
  14. Darjany LE, Whitcraft CR, Dillon JG. Lignocellulose-responsive bacteria in a southern California salt marsh identified by stable isotope probing. Front Microbiol 2014; 5:263 [View Article][PubMed]
     [Google Scholar]
  15. Meier DV, Pjevac P, Bach W, Markert S, Schweder T et al. Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses. Environ Microbiol 2019; 21:682–701 [View Article]
     [Google Scholar]
  16. Britschgi TB, Giovannoni SJ. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing. Appl Environ Microbiol 1991; 57:1707–1713 [View Article][PubMed]
     [Google Scholar]
  17. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
     [Google Scholar]
  18. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  19. 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]
  20. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Protein Metabolism 3 New York: Academic Press; 1969 pp 21–132
     [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  23. 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][PubMed]
     [Google Scholar]
  24. 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][PubMed]
     [Google Scholar]
  25. 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 [View Article][PubMed]
     [Google Scholar]
  26. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575580 [View Article][PubMed]
     [Google Scholar]
  27. ZoBell CE. Studies on marine bacteria I. The cultural requirements of heterotrophic aerobes. J Mar Res 1941; 4:41–75
     [Google Scholar]
  28. Bae SS, Kwon KK, Yang SH, Lee H-S, Kim S-J et al. Flagellimonas eckloniae gen. nov., sp. nov., a mesophilic marine bacterium of the family Flavobacteriaceae, isolated from the rhizosphere of Ecklonia kurome . Int J Syst Evol Microbiol 2007; 57:1050–1054 [View Article][PubMed]
     [Google Scholar]
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note #101. 1990
     [Google Scholar]
  30. Yang S-H, Seo H-S, Oh H-M, Kim S-J, Lee J-H et al. Brumimicrobium mesophilum sp. nov., isolated from a tidal flat sediment, and emended descriptions of the genus Brumimicrobium and Brumimicrobium glaciale. Int J Syst Evol Microbiol 2013; 63:1105–1110 [View Article][PubMed]
     [Google Scholar]
  31. 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 [View Article]
     [Google Scholar]
  32. Lalitha M. Manual on antimicrobial susceptibility testing. Performance standards for antimicrobial testing: Twelfth Informational Supplement; 2004; 56238454–456
  33. Yoon S-H, Ha S-M, 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]
  34. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
     [Google Scholar]
  35. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004334
Loading
Description of Luteithermobacter gelatinilyticus gen. nov., sp. nov., and Paremcibacter congregatus gen. nov., comb. nov. via reclassification of the genus Emcibacter
Int J Syst Evol Microbiol 70, 4691 (2020); https://doi.org/10.1099/ijsem.0.004334
/content/journal/ijsem/10.1099/ijsem.0.004334
/content/journal/ijsem/10.1099/ijsem.0.004334
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