1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 3

sp. nov., a novel species originating from lake sediment Free

Abstract

An aerobic, Gram-stain-negative, non-spore-forming and rod-shaped bacterial strain, designated N8, was isolated from the interfacial sediment of Taihu Lake in PR China. The strain formed white to blue colonies on R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain N8 represented a member of the genus and was most closely related to A1-9 (97.97 %). The average nucleotide identity and digital DNA–DNAhybridization values between strain N8 and A1-9 based on their whole genomes were 78.8 and 21.7 %, respectively. Q-10 was the main predominant ubiquinone. The major fatty acids were summed feature 8 (Cω7 and/or Cω6), C and C. The G+C content of the genomic DNA was 66.1 mol%. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid, two unidentified glycolipids and two unidentified lipids. Based on its physiological, biochemical and chemotaxonomic characteristics, strain N8 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is N8=(KACC 21307=MCCC 1K04036).

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): Gemmobacter caeruleus , polyphasic identification , sediment and Taihu Lake
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31370147)
    • Principle Award Recipient: Jian-Hang Qu
  • Key Scientific Research Project of Colleges and Universities in Henan Province (Award 20A180009)
    • Principle Award Recipient: Jian-Hang Qu
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004007
2020-01-30
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/3/1987.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004007&mimeType=html&fmt=ahah

References

  1. Rothe B, Fischer A, Hirsch P, Sittig M, Stackebrandt E. The phylogenetic position of the budding bacteria Blastobacter aggregatus and Gemmobacter aquatilis gen., nov. sp. nov. Arch Microbiol 1987; 147:92–99 [View Article]
     [Google Scholar]
  2. Chen W-M, Cho N-T, Huang W-C, Young C-C, Sheu S-Y. Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis . Int J Syst Evol Microbiol 2013; 63:470–478 [View Article]
     [Google Scholar]
  3. Liu Y, Xu C-J, Jiang J-T, Liu Y-H, Song X-F et al. Catellibacterium aquatile sp. nov., isolated from fresh water, and emended description of the genus Catellibacterium Tanaka et al. 2004. Int J Syst Evol Microbiol 2010; 60:2027–2031 [View Article]
     [Google Scholar]
  4. Sheu S-Y, Sheu D-S, Sheu F-S, Chen W-M. Gemmobacter tilapiae sp. nov., a poly-β-hydroxybutyrate-accumulating bacterium isolated from a freshwater pond. Int J Syst Evol Microbiol 2013; 63:1550–1556 [View Article]
     [Google Scholar]
  5. Sheu S-Y, Shiau Y-W, Wei Y-T, Chen W-M. Gemmobacter lanyuensis sp. nov., isolated from a freshwater spring. Int J Syst Evol Microbiol 2013; 63:4039–4045 [View Article]
     [Google Scholar]
  6. Kang JY, Kim MJ, Chun J, Son KP, Jahng KY et al. Gemmobacter straminiformis sp. nov., isolated from an artificial fountain. Int J Syst Evol Microbiol 2017; 67:5019–5025 [View Article]
     [Google Scholar]
  7. Tanaka Y, Hanada S, Manome A, Tsuchida T, Kurane R et al. Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth. Int J Syst Evol Microbiol 2004; 54:955–959 [View Article]
     [Google Scholar]
  8. Zheng J-W, Chen Y-G, Zhang J, Ni Y-Y, Li W-J et al. Description of Catellibacterium caeni sp. nov., reclassification of Rhodobacter changlensis Anil Kumar et al. 2007 as Catellibacterium changlense comb. nov. and emended description of the genus Catellibacterium . Int J Syst Evol Microbiol 2011; 61:1921–1926 [View Article]
     [Google Scholar]
  9. Zhang J, Chen S-A, Zheng J-W, Cai S, Hang B-J et al. Catellibacterium nanjingense sp. nov., a propanil-degrading bacterium isolated from activated sludge, and emended description of the genus Catellibacterium . Int J Syst Evol Microbiol 2012; 62:495–499 [View Article]
     [Google Scholar]
  10. Liu J-J, Zhang X-Q, Chi F-T, Pan J, Sun C et al. Gemmobacter megaterium sp. nov., isolated from coastal planktonic seaweeds. Int J Syst Evol Microbiol 2014; 64:66–71 [View Article]
     [Google Scholar]
  11. Kämpfer P, Jerzak L, Wilharm G, Golke J, Busse H-J et al. Gemmobacter intermedius sp. nov., isolated from a white stork (Ciconia ciconia). Int J Syst Evol Microbiol 2015; 65:778–783 [View Article]
     [Google Scholar]
  12. Yoo Y, Lee DW, Lee H, Kwon B-O, Khim JS et al. Gemmobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2019; 69:1676–1681 [View Article]
     [Google Scholar]
  13. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7 [View Article]
     [Google Scholar]
  14. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45:240–245 [View Article]
     [Google Scholar]
  15. Qu J-H, Fu Y-H, Li X-D, Li H-F, Tian H-L. Brevundimonas lutea sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2019; 69:1417–1422 [View Article]
     [Google Scholar]
  16. McGinnis S, Madden TL. Blast: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 2004; 32:W20–W25 [View Article]
     [Google Scholar]
  17. 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]
     [Google Scholar]
  18. 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]
     [Google Scholar]
  19. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  20. 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]
  21. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  23. Pospiech A, Neumann B. A versatile quick-prep of genomic DNA from gram-positive bacteria. Trends Genet 1995; 11:217–218 [View Article]
     [Google Scholar]
  24. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article]
     [Google Scholar]
  25. 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]
  26. Boetzer M, Pirovano W. Toward almost closed genomes with GapFiller. Genome Biol 2012; 13:R56 [View Article]
     [Google Scholar]
  27. Massouras A, Hens K, Gubelmann C, Uplekar S, Decouttere F et al. Primer-initiated sequence synthesis to detect and assemble structural variants. Nat Methods 2010; 7:485–486 [View Article]
     [Google Scholar]
  28. 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]
     [Google Scholar]
  29. 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]
     [Google Scholar]
  30. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  31. Qu J-H, Ma W-W, Li H-F, Wang X-F, Lu B-B et al. Altererythrobacter amylolyticus sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2019; 69:1231–1236 [View Article]
     [Google Scholar]
  32. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article]
     [Google Scholar]
  33. Shieh WY, Chen AL, Chiu HH. Vibrio aerogenes sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production. Int J Syst Evol Microbiol 2000; 50:321–329 [View Article]
     [Google Scholar]
  34. Cowan ST, Feltham RKA, Barrow GI, Steel KJ. Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge, New York: Cambridge University Press; 1993
     [Google Scholar]
  35. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation); 2001
     [Google Scholar]
  36. Tindall BJ, Sikorski J, Smibert RA, Krieg NR, Reddy CA et al. Phenotypic Characterization and the Principles of Comparative Systematics Washington, DC: American Society for Microbiology Press; 2017
     [Google Scholar]
  37. Qu J-H, Zhang L-J, Fu Y-H, Li H-F. Rufibacter sediminis sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 2019; 69:662–666 [View Article]
     [Google Scholar]
  38. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [View Article]
     [Google Scholar]
  39. Komagata K, Suzuki KI. 4 lipid and cell-wall analysis in bacterial Systematics. Methods Microbiol 1988; 19:161–207
     [Google Scholar]
  40. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004007
Loading
Gemmobacter caeruleus sp. nov., a novel species originating from lake sediment
Int J Syst Evol Microbiol 70, 1987 (2020); https://doi.org/10.1099/ijsem.0.004007
/content/journal/ijsem/10.1099/ijsem.0.004007
/content/journal/ijsem/10.1099/ijsem.0.004007
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