1887

Abstract

Two bacterial strains, designated as SYSU D00720 and SYSU D00722, were isolated from a desert sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped, oxidase-positive and catalase-negative. Colonies were circular, opaque, convex, smooth, orange on Reasoner’s 2A (R2A) agar. The isolates were found to grow at 4–45 °C (optimum, 28–30 °C), at pH 6.0–7.0 (optimum, 7.0) and with 0–1.5 % (w/v) NaCl (optimum, 0%). Growth was observed on R2A agar, Luria–Bertani agar and nutrient agar, but not on trypticase soy agar. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified aminolipids, one unidentified glycolipid, one unidentified aminoglycolipid, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified lipids. The main fatty acids (>10%) were C 6, summed feature 8 (C 7 and/or C 6) and C. The major respiratory quinone was ubiquinone-10 and the major polyamine was -homospermidine. The genomic DNA G+C content was 66.0 mol%. Strains SYSU D00720 and SYSU D00722 were nearly identical with a 16S rRNA gene sequence similarity of 99.6 %, and 100.0 % average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values. Phylogenetic analyses clearly demonstrated that these two strains belonged to the same species of the genus , and had highest sequence similarity to KCTC 23642 (97.3 %). The ANI, AAI and dDDH values of strains SYSU D00720 and SYSU D00722 to KCTC 23642 were both 73.2, 69.9 and 19.2 %, respectively. Based on phylogenetic, phenotypic and chemotaxonomic distinctiveness, strains SYSU D00720 and SYSU D00722 represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SYSU D00720 (=MCCC 1K05154=NBRC 115061).

Funding
This study was supported by the:
  • Natural Science Foundation of Guangdong Province, China (Award 2016A030312003)
    • Principle Award Recipient: Wen-JunLi
  • Xinjiang Uygur Autonomous Region regional coordinated innovation project (Award 2021E01018)
    • Principle Award Recipient: Wen-JunLi
  • National Natural Science Foundation of China (Award 32061143043)
    • Principle Award Recipient: Wen-JunLi
  • National Natural Science Foundation of China (Award 32000005)
    • Principle Award Recipient: LeiDong
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005195
2022-01-21
2024-11-02
Loading full text...

Full text loading...

References

  1. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas . Microbiol Immunol 1990; 34:99–119 [View Article]
    [Google Scholar]
  2. Takeuchi M, Kawai F, Shimada Y, Yokota A. Taxonomic study of polyethylene glycol-utilizing bacteria: emended description of the genus Sphingomonas and new descriptions of Sphingomonas macrogoltabidus sp. nov., Sphingomonas sanguis sp. nov. and Sphingomonas terrae sp. nov. Syst Appl Microbiol 1993; 16:227–238 [View Article]
    [Google Scholar]
  3. 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]
  4. Yabuuchi E, Kosako Y, Naka T, Suzuki S, Yano I. Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas . Microbiol Immunol 1985339–349
    [Google Scholar]
  5. Yabuuchi E, Kosako Y, Fujiwara N, Naka T, Matsunaga I et al. Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola . Int J Syst Evol Microbiol 2002; 52:1485–1496 [View Article] [PubMed]
    [Google Scholar]
  6. Busse H-J, Denner EBM, Buczolits S, Salkinoja-Salonen M, Bennasar A et al. Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas . Int J Syst Evol Microbiol 2003; 53:1253–1260 [View Article] [PubMed]
    [Google Scholar]
  7. Chen H, Jogler M, Rohde M, Klenk H-P, Busse H-J et al. Reclassification and emended description of Caulobacter leidyi as Sphingomonas leidyi comb. nov., and emendation of the genus Sphingomonas . Int J Syst Evol Microbiol 2012; 62:2835–2843 [View Article] [PubMed]
    [Google Scholar]
  8. Feng G-D, Yang S-Z, Xiong X, Li H-P, Zhu H-H. Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead-zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica. Int J Syst Evol Microbiol 2017; 67:2160–2165 [View Article] [PubMed]
    [Google Scholar]
  9. Maeng S, Liu Q-. Z, Park Y, Bai J, Im W-T. Sphingomonas panacisoli sp. nov., bacterium isolated from soil in South Korea. Int J Syst Evol Microbiol 2019; 71:004675 [View Article] [PubMed]
    [Google Scholar]
  10. Kang M, Chhetri G, Kim J, Kim I, Seo T. Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand. Int J Syst Evol Microbiol 2021; 71:4896 [View Article]
    [Google Scholar]
  11. Madhaiyan M, Saravanan VS, Wirth JS, Alex THH, Kim S-J et al. Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov., endophytically associated phyllosphere bacteria isolated from economically important crop plants. Antonie Van Leeuwenhoek 2020; 113:1617–1632 [View Article] [PubMed]
    [Google Scholar]
  12. Menon RR, Kumari S, Kumar P, Verma A, Krishnamurthi S et al. Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis. Syst Appl Microbiol 2019; 42:334–342 [View Article] [PubMed]
    [Google Scholar]
  13. Zhang D-F, Cui X-W, Zhao Z, Zhang A-H, Huang J-K et al. Sphingomonas hominis sp. nov., isolated from hair of a 21-year-old girl. Antonie van Leeuwenhoek 2020; 113:1523–1530 [View Article] [PubMed]
    [Google Scholar]
  14. Heidler von Heilborn D, Reinmüller J, Hölzl G, Meier-Kolthoff JP, Woehle C et al. Sphingomonas aliaeris sp. nov., a new species isolated from pork steak packed under modified atmosphere. Int J Syst Evol Microbiol 2021; 71:4973 [View Article] [PubMed]
    [Google Scholar]
  15. Li S, Shi L, Lian W-H, Lin Z-L, Lu C-Y et al. Arenibaculum pallidiluteum gen. nov., sp. nov., a novel bacterium in the family Azospirillaceae, isolated from desert soil, and reclassification of Skermanella xinjiangensis to a new genus Deserticella as Deserticella xinjiangensis comb. nov., and transfer of the genera Indioceanicola and Oleisolibacter from the family Rhodospirillaceae to the family Azospirillaceae . Int J Syst Evol Microbiol 2021; 71:004874
    [Google Scholar]
  16. Li S, Dong L, Lian W-H, Lin Z-L, Lu C-Y et al. Exploring untapped potential of Streptomyces spp. in Gurbantunggut Desert by use of highly selective culture strategy. Sci Total Environ 2021; 790:148235 [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. 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]
  19. 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]
  20. 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]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  22. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  23. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article] [PubMed]
    [Google Scholar]
  24. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  27. Lee JH, Kim DI, Kang JW, Seong CN. Sphingomonas lutea sp. nov., isolated from freshwater of an artificial reservoir. Int J Syst Evol Microbiol 2016; 66:5493–5499 [View Article] [PubMed]
    [Google Scholar]
  28. Harrison PG, Strulo B. SPADES - a process algebra for discrete event simulation. J Log Comput 2000; 10:3–42 [View Article]
    [Google Scholar]
  29. 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]
  30. An D-S, Liu Q-M, Lee H-G, Jung M-S, Kim S-C et al. Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov. Int J Syst Evol Microbiol 2013; 63:496–501 [View Article]
    [Google Scholar]
  31. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. 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 [View Article] [PubMed]
    [Google Scholar]
  34. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
  35. Lowe TM, Chan PP. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016; 44:W54–7 [View Article] [PubMed]
    [Google Scholar]
  36. Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 2013; 29:2933–2935 [View Article] [PubMed]
    [Google Scholar]
  37. 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; 11:1–11 [View Article] [PubMed]
    [Google Scholar]
  38. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:D277–80 [View Article] [PubMed]
    [Google Scholar]
  39. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000; 28:33–36 [View Article] [PubMed]
    [Google Scholar]
  40. Deng Y-Y, Li J-Q, Wu S-F, Zhu Y-P, Chen Y-W et al. Integrated nr database in protein annotation system and its localization. Comput Eng 2006; 32:71–72
    [Google Scholar]
  41. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 2016; 44:D279–D285 [View Article]
    [Google Scholar]
  42. Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 2000; 28:45–48 [View Article] [PubMed]
    [Google Scholar]
  43. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 2017; 45:D566–D573 [View Article] [PubMed]
    [Google Scholar]
  44. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 2009; 37:D233–8 [View Article] [PubMed]
    [Google Scholar]
  45. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
    [Google Scholar]
  46. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol 2017; 35:725–731 [View Article] [PubMed]
    [Google Scholar]
  47. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033–1034 [View Article] [PubMed]
    [Google Scholar]
  48. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article] [PubMed]
    [Google Scholar]
  49. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
    [Google Scholar]
  50. 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]
  51. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
    [Google Scholar]
  52. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes 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 [View Article]
    [Google Scholar]
  53. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
    [Google Scholar]
  54. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  55. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
    [Google Scholar]
  56. 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]
  57. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
    [Google Scholar]
  58. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the proteobacteria. Syst Appl Microbiol 1988; 11:1–8 [View Article]
    [Google Scholar]
  59. Busse HJ, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997; 47:698–708 [View Article]
    [Google Scholar]
  60. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
    [Google Scholar]
  61. 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]
/content/journal/ijsem/10.1099/ijsem.0.005195
Loading
/content/journal/ijsem/10.1099/ijsem.0.005195
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