1887

Abstract

A rod-shaped, yellow-pigmented, Gram-stain-negative, non-motile and aerobic bacterium, designated 7-3A, was isolated from soil from King George Island, maritime Antarctica, and subjected to a polyphasic taxonomic study. Growth occurred at 4–37 °C (optimum, 20°C) and at pH 5.0–9.0 (optimum, pH 7.0–8.0). Tolerance to NaCl was up to 4 % (w/v) with optimum growth in the absence of NaCl. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 7-3A represented a member of the family . Strain 7-3A showed the highest sequence similarities with HMD 1043 (96.65 %), NCTC 13525 (96.53 %), DSM 23145 (96.27 %), LMG 24720 (96.13 %) and DSM 17048 (96.06 %). A whole genome-level comparison of 7-3A with DSM 17048, LMG 24720, DSM 23145, and DSM 21579 revealed average nucleotide identity (ANI) values of 79.03, 82.25, 78.12, and 74.42 %, respectively. The major respiratory isoprenoid quinone was identified as MK-6 and a few ubiquinones Q-10 were identified. In addition, flexirubin-type pigments were absent. The polar lipid profile of 7-3A was found to contain one phosphatidylethanolamine, six unidentified aminolipids (AL) and two unidentified lipids (L). The G+C content of the genomic DNA was determined to be 34.54 mol%. The main fatty acids were iso-C, summed feature 9 (comprising iso-Cω9 and/or C 10-methyl), anteiso-C, iso-C and summed feature 3 (comprising Cω7 and/or Cω6). On the basis of the evidence presented in this study, a novel species of the genus , sp. nov., is proposed, with the type strain 7-3A (=CCTCC AB 2016141= KCTC 52492). Emended descriptions of , , and are also given.

Funding
This study was supported by the:
  • the Chinese Polar Scientific Strategy Research Fund (Award IC201706)
    • Principle Award Recipient: FangPeng
  • the National Natural Science Foundation of China (Award Grant No. 42076230)
    • Principle Award Recipient: FangPeng
  • the R&D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People’s Republic of China (Award Grant No. NIMR-2020-8)
    • Principle Award Recipient: FangPeng
  • the National Key R&D Program of China (Award 2018YFC1406701)
    • Principle Award Recipient: FangPeng
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004740
2021-03-16
2022-01-19
Loading full text...

Full text loading...

References

  1. Kim MK, Im W-T, Shin YK, Lim JH, Kim S-H et al. Kaistella koreensis gen. nov., sp. nov., a novel member of the Chryseobacterium–Bergeyella–Riemerella branch. Int J Syst Evol Microbiol 2004; 54:2319–2324 [View Article][PubMed]
    [Google Scholar]
  2. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432–4450 [View Article][PubMed]
    [Google Scholar]
  3. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–147
    [Google Scholar]
  4. 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 [View Article][PubMed]
    [Google Scholar]
  5. 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]
  6. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  7. 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]
  8. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  9. 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]
  10. 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]
  11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  12. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
  13. Joung Y, Joh K. Chryseobacterium yonginense sp. nov., isolated from a mesotrophic artificial lake. Int J Syst Evol Microbiol 2011; 61:1413–1417 [View Article][PubMed]
    [Google Scholar]
  14. Kämpfer P, Fallschissel K, Avendaño-Herrera R. Chryseobacterium chaponense sp. nov., isolated from farmed Atlantic salmon (Salmo salar). Int J Syst Evol Microbiol 2011; 61:497–501 [View Article][PubMed]
    [Google Scholar]
  15. Yi H, Yoon HI, Chun J. Sejongia antarctica gen. nov., sp. nov. and Sejongia jeonii sp. nov., isolated from the Antarctic. Int J Syst Evol Microbiol 2005; 55:409–416 [View Article][PubMed]
    [Google Scholar]
  16. Kämpfer P, Lodders N, Vaneechoutte M, Wauters G. Transfer of Sejongia antarctica, Sejongia jeonii and Sejongia marina to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov., Chryseobacterium jeonii comb. nov. and Chryseobacterium marinum comb. nov. Int J Syst Evol Microbiol 2009; 59:2238–2240 [View Article][PubMed]
    [Google Scholar]
  17. Pires C, Carvalho MF, De Marco P, Magan N, Castro PML. Chryseobacterium palustre sp. nov. and Chryseobacterium humi sp. nov., isolated from industrially contaminated sediments. Int J Syst Evol Microbiol 2010; 60:402–407 [View Article][PubMed]
    [Google Scholar]
  18. Holmes B, Steigerwalt AG, Nicholson AC. DNA–DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov. Int J Syst Evol Microbiol 2013; 63:4639–4662 [View Article][PubMed]
    [Google Scholar]
  19. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA. (editors) Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981 pp 21–33
    [Google Scholar]
  20. 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 Pt 5:1861–1868 [View Article][PubMed]
    [Google Scholar]
  21. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article][PubMed]
    [Google Scholar]
  22. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria London: Cambridge University Press; 1965
    [Google Scholar]
  23. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070
    [Google Scholar]
  24. 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][PubMed]
    [Google Scholar]
  25. Senol Cali D, Kim JS, Ghose S, Alkan C, Mutlu O. Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. Brief Bioinform 2019; 20:1542–1559 [View Article][PubMed]
    [Google Scholar]
  26. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  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][PubMed]
    [Google Scholar]
  29. 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][PubMed]
    [Google Scholar]
  30. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article][PubMed]
    [Google Scholar]
  31. Zuo G, Hao B. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 2015; 13:321–331 [View Article][PubMed]
    [Google Scholar]
  32. 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]
  33. Mario JM. Role of chlorine in stratospheric chemistry. Pure Appl Chem 1996; 68:1749–1756
    [Google Scholar]
  34. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article]
    [Google Scholar]
  35. Xie C-H, Yokota A. Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003; 49:345–349 [View Article][PubMed]
    [Google Scholar]
  36. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  37. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004740
Loading
/content/journal/ijsem/10.1099/ijsem.0.004740
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