1887

Abstract

A Gram-stain-negative, non-motile, slightly halophilic and non-endospore-forming alphaproteobacterium, designated strain EGI L200073, was isolated from saline lake sediment sampled in Xinjiang Uygur Autonomous Region, China. The taxonomic position of the isolate was determined using the polyphasic taxonomic analysis and phylogenomic analysis. Phylogenetic analysis based on 16S rRNA gene sequence similarities indicated that strain EGI L200073 formed a distinct clade with DSM 14827 and shared sequence identity of 98.56 %. The novel isolate could be distinguished from other species of the genus by its distinct phenotypic, physiological and genotypic characteristics. Optimal growth of strain EGI L200073 occurred on marine agar 2216 at pH 8.0 and 30 °C. The major respiratory quinone was Q-10, while the major fatty acids (>10%) were summed feature 8 (C 6 and/or C 7) and C. The detected polar lipids included diphosphatidylglycerol, phosphatidylcholine and phosphatidylglycerol. Based on the genome sequence of strain EGI L200073, the G+C content of the novel isolate was 65.7 mol%. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values of strain EGI L200073 against related members in the genus were below the cut-off points proposed for delineation of a novel species. According our polyphasic taxonomic data, strain EGI L200073 represents a new species of the genus , for which the name sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L200073 (=KCTC 92045=CGMCC 1.19242).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005473
2022-08-08
2024-10-12
Loading full text...

Full text loading...

References

  1. Davis DH, Doudoroff M, Stanier RY, Mandel M. Proposal to reject the genus Hydrogenomonas: Taxonomic implications. Int J Syst Bacteriol 1969; 19:375–390 [View Article]
    [Google Scholar]
  2. Ludwig W, Mittenhuber G, Friedrich CG. Transfer of Thiosphaera pantotropha to Paracoccus denitrificans. Int J Syst Bacteriol 1993; 43:363–367 [View Article]
    [Google Scholar]
  3. Katayama Y, Hiraishi A, Kuraishi H. Paracoccus thiocyanatus sp. nov., a new species of thiocyanate-utilizing facultative chemolithotroph, and transfer of Thiobacillus versutus to the genus Paracoccus as Paracoccus versutus comb. nov. with emendation of the genus. Microbiology 1995; 141 (Pt 6):1469–1477 [View Article]
    [Google Scholar]
  4. Liu Z-P, Wang B-J, Liu X-Y, Dai X, Liu Y-H et al. Paracoccus halophilus sp. nov., isolated from marine sediment of the South China Sea, China, and emended description of genus Paracoccus Davis 1969. Int J Syst Evol Microbiol 2008; 58:257–261 [View Article] [PubMed]
    [Google Scholar]
  5. Lyu L, Zhi B, Lai Q, Shao Z, Yu Z. Paracoccus xiamenensis sp. nov., isolated from seawater on the Xiamen. Int J Syst Evol Microbiol 2020; 70:4285–4290 [View Article] [PubMed]
    [Google Scholar]
  6. Van Spanning RJ, Stouthamer AH, Baker SC, Van Verseveld HW et al. Paracoccus. In Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P. eds In Bergey’s Manual of Systematics of Archaea and Bacteria 2015
    [Google Scholar]
  7. Zhang G, Jiao K, Xie F, Pei S, Jiang L. Paracoccus subflavus sp. nov., isolated from Pacific Ocean sediment. Int J Syst Evol Microbiol 2019; 69:1472–1476 [View Article] [PubMed]
    [Google Scholar]
  8. Rainey FA, Kelly DP, Stackebrandt E, Burghardt J, Hiraishi A et al. A re-evaluation of the taxonomy of Paracoccus denitrificans and A proposal for the combination Paracoccus pantotrophus comb. nov. Int J Syst Bacteriol 1999; 49 Pt 2:645–651 [View Article] [PubMed]
    [Google Scholar]
  9. Meng X-L, Ming H, Huang J-R, Zhang L-Y, Cheng L-J et al. Paracoccus halotolerans sp. nov., isolated from a salt lake. Int J Syst Evol Microbiol 2019; 69:523–528 [View Article] [PubMed]
    [Google Scholar]
  10. Li J, Lu S, Jin D, Yang J, Lai X-H et al. Paracoccus liaowanqingii sp. nov., isolated from Tibetan antelope (Pantholops hodgsonii). Int J Syst Evol Microbiol 2020; 70:744–750 [View Article] [PubMed]
    [Google Scholar]
  11. Uemoto H, Saiki H. Nitrogen removal by tubular gel containing Nitrosomonas europaea and Paracoccus denitrificans. Appl Environ Microbiol 1996; 62:4224–4228 [View Article] [PubMed]
    [Google Scholar]
  12. Liu Y, Beer LL, Whitman WB. Sulfur metabolism in archaea reveals novel processes. Environ Microbiol 2012; 14:2632–2644 [View Article] [PubMed]
    [Google Scholar]
  13. Guan TW, Lin YJ, Ou MY, Chen KB. Isolation and diversity of sediment bacteria in the hypersaline aiding lake, China. PLoS One 2020; 15:e0236006 [View Article] [PubMed]
    [Google Scholar]
  14. Zhang L, Shen T, Cheng Y, Zhao T, Li L et al. Temporal and spatial variations in the bacterial community composition in Lake Bosten, a large, brackish lake in China. Sci Rep 2020; 10:304 [View Article] [PubMed]
    [Google Scholar]
  15. Darabpour E, Roayaei Ardakani M, Motamedi H, Taghi Ronagh M. Isolation of a potent antibiotic producer bacterium, especially against MRSA, from northern region of the Persian Gulf. Bosn J Basic Med Sci 2012; 12:108–121 [View Article] [PubMed]
    [Google Scholar]
  16. Fang B-Z, Han M-X, Jiao J-Y, Xie Y-G, Zhang X-T et al. Streptomyces cavernae sp. nov., a novel actinobacterium isolated from a karst cave sediment sample. Int J Syst Evol Microbiol 2020; 70:120–125 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. NCBI Resource Coordinators Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2018; 46:D8–D13 [View Article]
    [Google Scholar]
  19. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
    [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] [PubMed]
    [Google Scholar]
  21. Kannan L, Wheeler WC. Maximum parsimony on phylogenetic networks. Algorithms Mol Biol 2012; 7:9 [View Article] [PubMed]
    [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  23. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  24. Efron B, Halloran E, Holmes S. Bootstrap confidence levels for phylogenetic trees. Proc Natl Acad Sci U S A 1996; 93:7085–7090 [View Article] [PubMed]
    [Google Scholar]
  25. Fass JN. Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files. Version 1.33). [Software]. Available at: 2011 https://github.com/najoshi /sickle
  26. 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] [PubMed]
    [Google Scholar]
  27. Galperin MY, Kristensen DM, Makarova KS, Wolf YI, Koonin EV. Microbial genome analysis: the COG approach. Brief Bioinform 2019; 20:1063–1070 [View Article] [PubMed]
    [Google Scholar]
  28. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 2016; 44:D457–62 [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. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  31. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:2007 [View Article] [PubMed]
    [Google Scholar]
  32. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
    [Google Scholar]
  33. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  34. Sali W, Patoli D, Pais de Barros J-P, Labbé J, Deckert V et al. Polysaccharide chain length of lipopolysaccharides from salmonella minnesota Is a determinant of aggregate stability, plasma residence time and proinflammatory propensity in vivo. Front Microbiol 2019; 10:1774 [View Article] [PubMed]
    [Google Scholar]
  35. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article] [PubMed]
    [Google Scholar]
  36. Jacobs JM, Pesce C, Lefeuvre P, Koebnik R. Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas. Front Plant Sci 2015; 6:431 [View Article] [PubMed]
    [Google Scholar]
  37. Liu Z-T, Jiao J-Y, Liu L, Li M-M, Ming Y-Z et al. Rhabdothermincola sediminis gen. nov., sp. nov., a new actinobacterium isolated from hot spring sediment, and emended description of the family Iamiaceae. Int J Syst Evol Microbiol 2019; 71: [View Article]
    [Google Scholar]
  38. Fang B-Z, Xie Y-G, Zhou X-K, Zhang X-T, Liu L et al. Lysobacter prati sp. nov., isolated from a plateau meadow sample. Antonie Van Leeuwenhoek 2020; 113:763–772 [View Article] [PubMed]
    [Google Scholar]
  39. Pridham TG, Gottlieb D. The utilization of carbon compounds by some actinomycetales as an aid for species determination. J Bacteriol 1948; 56:107–114 [View Article] [PubMed]
    [Google Scholar]
  40. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
    [Google Scholar]
  41. 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]
  42. Groth I, Schumann P, Rainey FA, Martin K, Schuetze B et al. Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol 1997; 47:1129–1133 [View Article]
    [Google Scholar]
  43. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded Ion exchanger as stationary phases. J Liq Chromatogr 2006; 5:2359–2367 [View Article]
    [Google Scholar]
  44. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric Acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  45. Yin L-Z, Liu Z-T, Li J-L, Wang P-D, Dong L et al. Agilicoccus flavus gen. nov., sp. nov., a novel member of the family Dermatophilaceae isolated from the Pearl River. Int J Syst Evol Microbiol 2021; 71: [View Article]
    [Google Scholar]
  46. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
  47. Kim M, Oh H-S, Park S-C, 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 [View Article] [PubMed]
    [Google Scholar]
  48. 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]
  49. Pukall R, Laroche M, Kroppenstedt RM, Schumann P, Stackebrandt E et al. Paracoccus seriniphilus sp. nov., an L-serine-dehydratase-producing coccus isolated from the marine bryozoan Bugula plumosa. Int J Syst Evol Microbiol 2003; 53:443–447 [View Article] [PubMed]
    [Google Scholar]
  50. Kim BY, Weon HY, Yoo SH, Kwon SW, Cho YH et al. Paracoccus homiensis sp. nov., isolated from a sea-sand sample. Int J Syst Evol Microbiol 2006; 56:2387–2390 [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005473
Loading
/content/journal/ijsem/10.1099/ijsem.0.005473
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