1887

Abstract

A Gram-stain-negative, non-motile, and slightly halophilic alphaproteobacterium, designated strain EGI FJ00035, was isolated from enrichment sediment samples of a saline lake in Xinjiang Uygur Autonomous Region, PR China. The taxonomic position of the isolate was determined using the polyphasic taxonomic and phylogenomic analyses. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain EGI FJ00035 formed a distinct clade with ‘’ UJN715 and ‘’ lm93 with sequence similarities of 98.44 and 98.22 %, respectively, while sharing less than 96.7 % with other valid type strains. 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 FJ00035 occurred on marine agar 2216 at pH 7.0 and 30 °C. The major respiratory quinone was Q-10, while the major fatty acids (>5 %) were C cyclo ω8, summed feature 8 (C ω6 and/or C ω7), C, C, and iso-C. The detected polar lipids included diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, unidentified aminophospholipids, unidentified glycolipids, and an unidentified lipid. Based on its genome sequence, the G+C content of strain EGI FJ00035 was 63.2 mol%. The average nucleotide identity, average amino acid identity, and digital DNA–DNA hybridization values of strain EGI FJ00035 against related members of the genus were below the thresholds for delineation of a novel species. According our polyphasic taxonomic data, strain EGI FJ00035 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 FJ00035 (=KCTC 92251=CGMCC 1.19480).

Funding
This study was supported by the:
  • Xinjiang Uygur Autonomous Region regional coordinated innovation project (Award 2020E01047 and 2021E01018)
    • Principle Award Recipient: Wen-JunLi
  • National Science and Technology Fundamental Resources Investigation Program of China (Award 2021FY100900)
    • Principle Award Recipient: Bao-zhuFang
  • The Third Xinjiang Scientific Expedition Program (Award 2022xjkk1200)
    • Principle Award Recipient: Hong-chenJiang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006340
2024-04-15
2024-04-29
Loading full text...

Full text loading...

References

  1. Doronina NV, Kaparullina EN, Trotsenko YA, Nörtemann B, Bucheli-Witschel M et al. Chelativorans multitrophicus gen. nov., sp. nov. and Chelativorans oligotrophicus sp. nov., aerobic EDTA-degrading bacteria. Int J Syst Evol Microbiol 2010; 60:1044–1051 [View Article] [PubMed]
    [Google Scholar]
  2. Meng D, Liu Y-L, Gu P-F, Fan X-Y, Huang Z-S et al. Chelativorans alearense sp. nov., a novel bacterial species isolated from soil in Alear, China. Curr Microbiol 2021; 78:1656–1661 [View Article] [PubMed]
    [Google Scholar]
  3. Kämpfer P, Arun AB, Busse H-J, Zhang Z-L, Young C-C et al. Chelativorans intermedius sp. nov. and proposal to reclassify Thermovum composti as Chelativorans composti comb. nov. Int J Syst Evol Microbiol 2015; 65:1646–1652 [View Article] [PubMed]
    [Google Scholar]
  4. Meng D, Liu Y-L, Gu P-F, Fan X-Y, Huang Z-S et al. Chelativorans xinjiangense sp. nov., a novel bacterial species isolated from soil in Xinjiang, China. Arch Microbiol 2021; 203:693–699 [View Article] [PubMed]
    [Google Scholar]
  5. Liu Y, Beer LL, Whitman WB. Sulfur metabolism in archaea reveals novel processes. Environ Microbiol 2012; 14:2632–2644 [View Article] [PubMed]
    [Google Scholar]
  6. 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]
  7. 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]
  8. Gao L, Fang B-Z, Liu Y-H, Jiao J-Y, Li M-M et al. Comparative genomic analyses of Lutimaribacter degradans sp. nov. With the ability to PAHs-biodegradation and transformation. Int Bio 2023; 176:105505 [View Article]
    [Google Scholar]
  9. 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]
  10. 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]
  11. 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]
  12. Agarwala R, Barrett T, Beck J, Benson DA, Bollin C. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2018; 46:D8–D13 [View Article]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Kannan L, Wheeler WC. Maximum parsimony on phylogenetic networks. Algorithms Mol Biol 2012; 7:9 [View Article] [PubMed]
    [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. 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]
  19. Joshi NA, Fass JN. Sickle: a sliding-window, adaptive, quality-based trimming 365 tool for FastQ files (version 1.33); 2011 https://github.com/najoshi/sickle
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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] [PubMed]
    [Google Scholar]
  32. 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]
  33. 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]
  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] [PubMed]
    [Google Scholar]
  35. 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 Meth 1984; 2:233–241 [View Article]
    [Google Scholar]
  36. 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] [PubMed]
    [Google Scholar]
  37. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [Google Scholar]
  38. 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]
  39. 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] [PubMed]
    [Google Scholar]
  40. 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]
  41. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006340
Loading
/content/journal/ijsem/10.1099/ijsem.0.006340
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