1887

Abstract

A novel Gram-stain-negative, strictly aerobic, rod-shaped, brick red-pigmented bacterium, designated R-22-1 c-1, was isolated from water from Baiyang Lake, Hebei Province, PR China. The strain was able to grow at 20–30 °C (optimum, 30 °C) and pH 6–7 (optimum, pH 6) in Reasoner’s 2A medium. 16S rRNA gene sequence and phylogenetic analyses of R-22-1 c-1 revealed closest relationships to MCC P1 (97.8 %), H-1 (97.9 %) and MDT1-10-3 (97.0 %), with other species of the genus showing less than 97.0 % sequence similarity. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids and three unidentified lipids. The major cellular fatty acids were iso-C, C 6, C 6, anteiso-C, summed feature 3 (iso-C 2-OH and/or C 7 and/or C 6) and summed feature 4 (iso-CI and/or anteiso-CB). The respiratory quinone was MK-7. The draft genome of R-22-1 c-1 was 5.6 Mbp in size, with a G+C content of 50.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization relatedness values between strain R-22-1 c-1 and related type strains were MCC P1 (77.2 and 21.8 %), H-1 (81.6 and 21.4 %) and 1351 (78.5 and 22.9 %). Based on these phylogenetic, chemotaxonomic and genotypic results, strain R-22-1 c-1 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain is R-22-1 c-1 (=CGMCC 1.13570=KCTC 62781).

Funding
This study was supported by the:
  • yunzhen yang , Beijing Municipal Science & Technology Commission , (Award No. Z161100000116042)
  • yunzhen yang , National Natural Science Foudation of China , (Award No. 31872632)
  • yunzhen yang , Science and Technology Basic Resources Investigation Project , (Award No. 2017FY100300)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004500
2020-10-05
2020-11-25
Loading full text...

Full text loading...

References

  1. Abaydulla G, Luo X, Shi J, Peng F, Liu M et al. Rufibacter tibetensis gen. nov., sp. nov., a novel member of the family Cytophagaceae isolated from soil. Antonie van Leeuwenhoek 2012; 101:725–731 [CrossRef]
    [Google Scholar]
  2. Liang ST, Jiang S. The historical examination of the harnessing and development of the water resources in baiyangdian lake. Journal of Hebei University 2017; 3:110–116
    [Google Scholar]
  3. Xu Y, Xu X, Lan R, Xiong Y, Ye C et al. An O island 172 encoded RNA helicase regulates the motility of Escherichia coli O157:H7. PLoS One 2013; 8:e64211 [CrossRef]
    [Google Scholar]
  4. Gordon RE, Barnett DA, Handerhan JE, Pang CH. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [CrossRef]
    [Google Scholar]
  5. Felföldi T, Mentes A, Schumann P, Kéki Z, Máthé I et al. Rufibacter quisquiliarum sp. nov., a new member of the phylum Bacteroidetes isolated from a bioreactor treating landfill leachate. Int J Syst Evol Microbiol 2016; 66:5150–5154 [CrossRef]
    [Google Scholar]
  6. Liu Q, Liu HC, Zhang JL, Zhou YG, Xin YH. Rufibacter glacialis sp. nov., a psychrotolerant bacterium isolated from glacier soil. Int J Syst Evol Microbiol 2016; 66:315–318 [CrossRef]
    [Google Scholar]
  7. Kamekura M. Lipids of extreme halophiles. The Biology of Halophilic Bacteria 1993 pp 135–161
    [Google Scholar]
  8. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. Methods for General and Molecular Microbiology 2007 pp 330–393
    [Google Scholar]
  9. Collins MD. Isoprenoid quinone analysis in classification and identification. Chemical Methods in Bacterial Systematics 1985 pp 267–287
    [Google Scholar]
  10. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 20062359–2367
    [Google Scholar]
  11. YT H, Zhou PJ, Zhou YG, Liu ZH, Liu SJ. Saccharothrix xinjiangensis sp. nov., a pyrene-degrading actinomycete isolated from Tianchi lake, Xinjiang, China. Int J Syst Evol Microbiol 2004; 54:2091–2094
    [Google Scholar]
  12. Boontosaeng T, Nimrat S, Vuthiphandchai V. Pigments production of bacteria isolated from dried seafood and capability to inhibit microbial pathogens. IOSR J Environ Sci Toxicol Food Technol 2016; 10:30–34
    [Google Scholar]
  13. Hou Q, Bai X, Li W, Gao X, Zhang F et al. Design of primers for evaluation of lactic acid bacteria populations in complex biological samples. Front Microbiol 2045; 2018:9
    [Google Scholar]
  14. 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]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425
    [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef]
    [Google Scholar]
  17. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [CrossRef]
    [Google Scholar]
  18. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [CrossRef]
    [Google Scholar]
  19. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [CrossRef]
    [Google Scholar]
  20. 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 [CrossRef]
    [Google Scholar]
  21. 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 [CrossRef]
    [Google Scholar]
  22. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [CrossRef]
    [Google Scholar]
  23. Chovancová E, Kosinski J, Bujnicki JM, Damborský J et al. Phylogenetic analysis of haloalkane dehalogenases. Proteins 2007; 67:305–316 [CrossRef]
    [Google Scholar]
  24. Massara TM, Malamis S, Guisasola A, Baeza JA, Noutsopoulos C et al. A review on nitrous oxide (N2O) emissions during biological nutrient removal from municipal wastewater and sludge reject water. Sci Total Environ 2017; 596-597:106–123 [CrossRef][PubMed]
    [Google Scholar]
  25. Gao QS, Jiao LX, Yang L, Tian ZQ, Yang SW et al. Occurrence and ecological risk assessment of typical persistent organic pollutants in Baiyangdian lake. Huan Jing Ke Xue 2018; 39:1616–1627
    [Google Scholar]
  26. Polkade AV, Ramana VV, Joshi A, Pardesi L, Shouche YS. Rufibacter immobilis sp. nov., isolated from a high-altitude saline lake. Int J Syst Evol Microbiol 2015; 65:1592–1597 [CrossRef]
    [Google Scholar]
  27. JH Q, Zhang LJ, YH F, HF L. Rufibacter sediminis sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 2019; 69:662–666
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004500
Loading
/content/journal/ijsem/10.1099/ijsem.0.004500
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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