1887

Abstract

Two strains designated as c1 and c7, were isolated from the landfill leachate of a domestic waste treatment plant in Huizhou City, Guangdong Province, PR China. The cells of both strains were aerobic, rod-shaped, non-motile and formed yellow colonies on Reasoner’s 2A agar plates. Strain c1 grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 7.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Strain c7 grew at 10–42 °C (optimum, 30 °C), pH 4.5–10.5 (optimum, pH 6.0) and 0–2.0 % (w/v) NaCl (optimum, 0–0.5 %). Phylogenetic analyses revealed that strains c1 and c7 belong to the genus . The 16S rRNA gene sequence similarities of strains c1 and c7 to the type strains of species were 94.5–98.2 % and 94.3–99.1 %, respectively. The calculated pairwise average nucleotide identity values among strains c1, c7 and the reference strains were in the range of 75.2–85.9 % and the calculated pairwise average amino acid identity values among strains c1, c7 and reference strains were in the range of 72.0–88.3 %. Their major respiratory quinone was Q-10, and the major cellular fatty acids were C 7, C, C 7, C and C 2OH. The major polar lipids of strains c1 and c7 were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, unidentified lipids and unidentified phospholipid. Based on phenotypic, chemotaxonomic, phylogenetic and genomic results from this study, strains c1 and c7 should represent two independent novel species of , for which the names sp. nov. (type strain c1=GDMCC 1.2555=KCTC 82826) and sp. nov. (type strain c7=GDMCC 1.2556=KCTC 82827) are proposed. The gene function annotation results of strains c1 and c7 suggest that they could play an important role in the degradation of organic pollutants.

Funding
This study was supported by the:
  • GDAS’ Special Project of Science and Technology Development (Award 2022GDASZH-2022010105; 2021GDASYL-20210302001)
    • Principle Award Recipient: MeiyingXu
  • Hubei Technological Innovation Special Fund (Award 2018B020205003; 2019B110205003)
    • Principle Award Recipient: MeiyingXu
  • National Key Research and Development Program of China (Award 2021YFA0910300)
    • Principle Award Recipient: MeiyingXu
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005394
2022-05-27
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/72/5/ijsem005394.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005394&mimeType=html&fmt=ahah

References

  1. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold L-M et al. Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol 2020; 11:468 [View Article] [PubMed]
    [Google Scholar]
  2. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001; 51:1405–1417 [View Article] [PubMed]
    [Google Scholar]
  3. Kämpfer P, Busse H-J, Glaeser SP. Novosphingobium lubricantis sp. nov., isolated from a coolant lubricant emulsion. Int J Syst Evol Microbiol 2018; 68:1560–1564 [View Article] [PubMed]
    [Google Scholar]
  4. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  5. Zhou X-Y, Zhang L, Su X-J, Hang P, Hu B et al. Sphingomonas flavalba sp. nov., isolated from a procymidone-contaminated soil. Int J Syst Evol Microbiol 2019; 69:2936–2941 [View Article] [PubMed]
    [Google Scholar]
  6. Feng G-D, Chen W, Zhang J, Wang Y-H, Liu Y et al. Novosphingobium silvae sp. nov., isolated from subtropical forest soil. Int J Syst Evol Microbiol 2020; 70:2901–2906 [View Article] [PubMed]
    [Google Scholar]
  7. Geng Y, Zhang Y, Qin K, Liu J, Tian J et al. Sphingomonas paeninsulae sp. nov., isolated from soil sampled at Fildes Peninsula, Antarctica. Int J Syst Evol Microbiol 2019; 69:3702–3709 [View Article] [PubMed]
    [Google Scholar]
  8. Zhu D, Niu Y, Liu D, Wang G, Zheng S. Sphingomonas gilva sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2019; 69:3472–3477 [View Article] [PubMed]
    [Google Scholar]
  9. Sheu S-Y, Huang C-W, Chen J-C, Chen Z-H, Chen W-M. Novosphingobium arvoryzae sp. nov., isolated from a flooded rice field. Int J Syst Evol Microbiol 2018; 68:2151–2157 [View Article] [PubMed]
    [Google Scholar]
  10. Le VV, Ko S-R, Lee S-A, Jin L, Ahn C-Y et al. Novosphingobium aquimarinum sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2020; 70:5911–5917 [View Article]
    [Google Scholar]
  11. Qin D, Ma C, Lv M, Yu C-P. Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov., isolated from a wastewater treatment plant. Int J Syst Evol Microbiol 2020; 70:1822–1829 [View Article] [PubMed]
    [Google Scholar]
  12. Sheu S-Y, Yang C-C, Sheu D-S, Tsai J-M, Chen W-M. Sphingomonas lacunae sp. nov., isolated from a freshwater pond. Int J Syst Evol Microbiol 2020; 70:5899–5910 [View Article] [PubMed]
    [Google Scholar]
  13. Sheu S-Y, Chen Z-H, Chen W-M. Novosphingobium piscinae sp. nov., isolated from a fish culture pond. Int J Syst Evol Microbiol 2016; 66:1539–1545 [View Article] [PubMed]
    [Google Scholar]
  14. Lee Y, Jeon CO. Sphingobium paulinellae sp. nov. and Sphingobium algicola sp. nov., isolated from a freshwater green alga Paulinella chromatophora. Int J Syst Evol Microbiol 2017; 67:5165–5171 [View Article] [PubMed]
    [Google Scholar]
  15. Madhaiyan M, Alex THH, Cho H, Kim S-J, Weon H-Y et al. Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L. Int J Syst Evol Microbiol 2017; 67:5150–5158 [View Article] [PubMed]
    [Google Scholar]
  16. Gao S, Zhang Y, Jiang N, Luo L, Li QX et al. Novosphingobium fluoreni sp. nov., isolated from rice seeds. Int J Syst Evol Microbiol 2015; 65:1409–1414 [View Article] [PubMed]
    [Google Scholar]
  17. Kämpfer P, Martin K, McInroy JA, Glaeser SP. Proposal of Novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere. Int J Syst Evol Microbiol 2015; 65:195–200 [View Article] [PubMed]
    [Google Scholar]
  18. Kämpfer P, Martin K, McInroy JA, Glaeser SP. Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum. Int J Syst Evol Microbiol 2015; 65:2831–2837 [View Article] [PubMed]
    [Google Scholar]
  19. Fredrickson JK, Balkwill DL, Drake GR, Romine MF, Ringelberg DB et al. Aromatic-degrading Sphingomonas isolates from the deep subsurface. Appl Environ Microbiol 1995; 61:1917–1922 [View Article] [PubMed]
    [Google Scholar]
  20. Fujii K, Satomi M, Morita N, Motomura T, Tanaka T et al. Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int J Syst Evol Microbiol 2003; 53:47–52 [View Article] [PubMed]
    [Google Scholar]
  21. Wilkes H, Wittich R, Timmis KN, Fortnagel P, Francke W. Degradation of chlorinated dibenzofurans and dibenzo-p-dioxins by Sphingomonas sp. strain RW1. Appl Environ Microbiol 1996; 62:367–371 [View Article] [PubMed]
    [Google Scholar]
  22. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Sequencing Techniques in Bacterial Systematics New York, USA: Wiley; 1991 pp 115–175
    [Google Scholar]
  23. Lu H, Deng T, Cai Z, Liu F, Yang X et al. Janthinobacterium violaceinigrum sp. nov., Janthinobacterium aquaticum sp. nov. and Janthinobacterium rivuli sp. nov., isolated from a subtropical stream in China. Int J Syst Evol Microbiol 2020; 70:2719–2725 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic Local Alignment Search Tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  26. 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]
  27. Ninio J. The neutral theory of molecular evolution. FEBS Lett 1984; 170:210–211 [View Article]
    [Google Scholar]
  28. 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]
  29. 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]
  30. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  31. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  32. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
    [Google Scholar]
  33. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol 2017; 34:2115–2122 [View Article] [PubMed]
    [Google Scholar]
  34. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
    [Google Scholar]
  35. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  36. 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]
  37. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
    [Google Scholar]
  38. Zhu XF. Modern Experimental Technique of Microbiology Hangzhou, China: Zhejiang University Press; 2011, p. 39-41
    [Google Scholar]
  39. Chester FD. A Manual of Determinative Bacteriology Wentworth Press; 2016 pp 967–969
    [Google Scholar]
  40. Wu Y-H, Meng F-X, Xu L, Zhang X-Q, Wang C-S et al. Roseivivax pacificus sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2013; 63:4574–4579 [View Article] [PubMed]
    [Google Scholar]
  41. Kuykendall LD, Roy MA, O’neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  42. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. eds Methods in Phytobacteriology Budapest, Hungary: Akademiai Kaido; 1990 pp 199–204
    [Google Scholar]
  43. Tindall B. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202
    [Google Scholar]
  44. 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]
  45. Segura A, Hernández-Sánchez V, Marqués S, Molina L. Insights in the regulation of the degradation of PAHs in Novosphingobium sp. HR1a and utilization of this regulatory system as a tool for the detection of PAHs. Sci Total Environ 2017; 590–591:381–393 [View Article] [PubMed]
    [Google Scholar]
  46. Chen A, Huang Y. Acyl homoserine lactone based quorum sensing affects phenanthrene removal by Novosphingobium pentaromativorans US6-1 through altering cell surface properties. Int Biodeterior Biodegrad 2020; 147:104841 [View Article]
    [Google Scholar]
  47. Cui Z, Shao Z. Predominant strains of polycyclic aromatic hydrocarbon-degrading consortia from deep sea of the Middle Atlantic Ridge. Wei Sheng Wu Xue Bao 2009; 49:902–909 [PubMed]
    [Google Scholar]
  48. Luo YR, Kang SG, Kim S-J, Kim M-R, Li N et al. Genome sequence of benzo(a)pyrene-degrading bacterium Novosphingobium pentaromativorans US6-1. J Bacteriol 2012; 194:907 [View Article] [PubMed]
    [Google Scholar]
  49. Chen Y, Chai L, Tang C, Yang Z, Zheng Y et al. Kraft lignin biodegradation by Novosphingobium sp. B-7 and analysis of the degradation process. Bioresour Technol 2012; 123:682–685 [View Article] [PubMed]
    [Google Scholar]
  50. Li J, Peng L, Li J, Qiao Y. Divergent responses of functional gene expression to various nutrient conditions during microcystin-LR biodegradation by Novosphingobium sp. THN1 strain. Bioresour Technol 2014; 156:335–341 [View Article] [PubMed]
    [Google Scholar]
  51. Huang S, Xia F, Qian Y-M, Wei T, Jia C-X et al. Isolation and identification of a cembratriene-4,6-diol degradation and aroma producing strain from tobacco leaf. J Light Industry 2017; 32:73–80
    [Google Scholar]
  52. Yun SH, Choi C-W, Lee S-Y, Lee YG, Kwon J et al. Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1. PLoS One 2014; 9:e90812 [View Article] [PubMed]
    [Google Scholar]
  53. Sheu S-Y, Liu L-P, Chen W-M. Novosphingobium bradum sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2016; 66:5083–5090 [View Article] [PubMed]
    [Google Scholar]
  54. Liu Z-P, Wang B-J, Liu Y-H, Liu S-J. Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. Int J Syst Evol Microbiol 2005; 55:1229–1232 [View Article] [PubMed]
    [Google Scholar]
  55. Chaudhary DK, Dahal RH, Kim D-U, Kim J. Novosphingobium olei sp. nov., with the ability to degrade diesel oil, isolated from oil-contaminated soil and proposal to reclassify Novosphingobium stygium as a later heterotypic synonym of Novosphingobium aromaticivorans. Int J Syst Evol Microbiol 2021; 71:004628 [View Article] [PubMed]
    [Google Scholar]
  56. Krishnan R, Menon RR, Busse H-J, Tanaka N. Novosphingobium pokkalii sp nov, a novel rhizosphere-associated bacterium with plant beneficial properties isolated from saline-tolerant pokkali rice. Res Microbiol 2017; 168:113–121 [View Article] [PubMed]
    [Google Scholar]
  57. Yoo Y, Kim D, Lee H, Khim JS, Kim B et al. Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment. Int J Syst Evol Microbiol 2021; 71:004930 [View Article]
    [Google Scholar]
  58. Xie F, Quan S, Liu D, He W, Wang Y et al. Novosphingobium kunmingense sp. nov., isolated from a phosphate mine. Int J Syst Evol Microbiol 2014; 64:2324–2329 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005394
Loading
/content/journal/ijsem/10.1099/ijsem.0.005394
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