1887

Abstract

During a phylogenetic analysis of and its closely related genera in the family , we found that the genus and the species might not be properly assigned in the taxonomy. Phylogenetic, phenotypic and chemotaxonomic characterizations clearly showed that the genus should be reclassified into two genera (Clade I and Clade II), for which the original genus name, , is proposed to be retained only for Clade I, and a new genus named as gen. nov. is proposed for Clade II with four new combinations: comb. nov., comb. nov., comb. nov. and comb. nov. Moreover, should represent a novel genus in the family , for which the name gen. nov. is proposed, with a combination of comb. nov. The study provides a new insight into the taxonomy of closely related genera in the family .

Funding
This study was supported by the:
  • the GDAS' Special Project of Science and Technology Development (Award 2020GDASYL-20200302002)
    • Principle Award Recipient: Hong-Hui Zhu
  • the Science and Technology Programs of Guangdong Province (Award 2019B030316009)
    • Principle Award Recipient: Guang-Da Feng
  • the Key Realm R&D Program of GuangDong Province (Award 2018B020205001)
    • Principle Award Recipient: Guang-Da Feng
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2020-02-03
2024-10-11
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References

  1. Stolz A. Degradative plasmids from sphingomonads. FEMS Microbiol Lett 2014; 350:9–19 [View Article]
    [Google Scholar]
  2. Stolz A. Molecular characteristics of xenobiotic-degrading sphingomonads. Appl Microbiol Biotechnol 2009; 81:793–811 [View Article]
    [Google Scholar]
  3. Yan X, Gu T, Yi Z, Huang J, Liu X et al. Comparative genomic analysis of isoproturon-mineralizing sphingomonads reveals the isoproturon catabolic mechanism. Environ Microbiol 2016; 18:4888–4906 [View Article]
    [Google Scholar]
  4. Gatheru Waigi M, Sun K, Gao Y. Sphingomonads in microbe-assisted phytoremediation: tackling soil pollution. Trends Biotechnol 2017; 35:883–899 [View Article]
    [Google Scholar]
  5. Huang Y, Feng H, Lu H, Zeng Y. Novel 16S rDNA primers revealed the diversity and habitats-related community structure of sphingomonads in 10 different niches. Antonie van Leeuwenhoek 2017; 110:877–889 [View Article]
    [Google Scholar]
  6. Aylward FO, McDonald BR, Adams SM, Valenzuela A, Schmidt RA et al. Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities. Appl Environ Microbiol 2013; 79:3724–3733 [View Article]
    [Google Scholar]
  7. 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]
  8. 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]
    [Google Scholar]
  9. 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 2002:1485–1496
    [Google Scholar]
  10. Maruyama T, Park H-D, Ozawa K, Tanaka Y, Sumino T et al. Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int J Syst Evol Microbiol 2006; 56:85–89 [View Article]
    [Google Scholar]
  11. Kämpfer P, Arun AB, Young CC, Busse HJ, Kassmannhuber J et al. Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring. Int J Syst Evol Microbiol 2012; 62:1326–1330 [View Article]
    [Google Scholar]
  12. Kim M, Kang O, Zhang Y, Ren L, Chang X et al. Sphingoaurantiacus polygranulatus gen. nov., sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of the genera Sandarakinorhabdus, Polymorphobacter and Rhizorhabdus and the species Sandarakinorhabdus limnophila, Rhizorhabdus argentea and Sphingomonas wittichii . Int J Syst Evol Microbiol 2016; 66:91–100 [View Article]
    [Google Scholar]
  13. Francis IM, Jochimsen KN, De Vos P, van Bruggen AH. Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. Int J Syst Evol Microbiol 2014; 64:1340–1350 [View Article]
    [Google Scholar]
  14. Uchida H, Hamana K, Miyazaki M, Yoshida T, Nogi Y et al. Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm. Int J Syst Evol Microbiol 2012; 62:2224–2228 [View Article]
    [Google Scholar]
  15. Jogler M, Chen H, Simon J, Rohde M, Busse HJ et al. Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov. Int J Syst Evol Microbiol 2013; 63:1342–1349 [View Article]
    [Google Scholar]
  16. Tan Y, Wang Y, Wang D, Wang G, Zheng S. Sphingoaurantiacus capsulatus sp. nov., isolated from mountain soil, and emended description of the genus Sphingoaurantiacus . Int J Syst Evol Microbiol 2016; 66:4930–4935 [View Article]
    [Google Scholar]
  17. 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]
    [Google Scholar]
  18. Hamana K, Sakamoto A, Tachiyanagi S, Terauchi E. Polyamine profiles of some members of the gamma subclass of the class Proteobacteria: polyamine analysis of twelve recently described genera. Microbiol Cult Coll 2003; 19:4901–4903
    [Google Scholar]
  19. Chen W-M, Li Y-S, Sheu S-Y. Sphingomonas piscinae sp. nov., isolated from a fish pond. Int J Syst Evol Microbiol 2016; 66:5301–5308 [View Article]
    [Google Scholar]
  20. Lee Y, Jeon CO. Sphingomonas frigidaeris sp. nov., isolated from an air conditioning system. Int J Syst Evol Microbiol 2017; 67:3907–3912 [View Article]
    [Google Scholar]
  21. Kim JH, Kim SH, Kim KH, Lee PC. Sphingomonas lacus sp. nov., an astaxanthin-dideoxyglycoside-producing species isolated from soil near a pond. Int J Syst Evol Microbiol 2015; 65:2824–2830 [View Article]
    [Google Scholar]
  22. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article]
    [Google Scholar]
  23. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci U S A 1978; 75:4801–4805 [View Article]
    [Google Scholar]
  24. Eren AM, Esen Özcan C, Quince C, Vineis JH, Morrison HG et al. Anvi'o: an advanced analysis and visualization platform for 'omics data. PeerJ 2015; 3:e1319 [View Article]
    [Google Scholar]
  25. 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]
    [Google Scholar]
  26. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
    [Google Scholar]
  27. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article]
    [Google Scholar]
  28. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM et al. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007 pp 330–393
    [Google Scholar]
  29. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322 [View Article]
    [Google Scholar]
  30. García-Romero I, Pérez-Pulido AJ, González-Flores YE, Reyes-Ramírez F, Santero E et al. Genomic analysis of the nitrate-respiring Sphingopyxis granuli (formerly Sphingomonas macrogoltabida) strain TFA. BMC Genomics 2016; 17:93 [View Article]
    [Google Scholar]
  31. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393–2411 [View Article]
    [Google Scholar]
  32. Baek M-G, Shin S-K, Yi H. Sphingorhabdus lutea sp. nov., isolated from sea water. Int J Syst Evol Microbiol 2019; 69:3593–3598 [View Article]
    [Google Scholar]
  33. Kim B-S, Lim YW, Chun J. Sphingopyxis marina sp. nov. and Sphingopyxis litoris sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2008; 58:2415–2419 [View Article]
    [Google Scholar]
  34. Yoon J-H, Oh T-K. Sphingopyxis flavimaris sp. nov., isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005; 55:369–373 [View Article]
    [Google Scholar]
  35. Romanenko LA, Tanaka N, Svetashev VI, Mikhailov VV. Sphingorhabdus pacificus sp. nov., isolated from sandy sediments of the Sea of Japan seashore. Arch Microbiol 2015; 197:147–153 [View Article]
    [Google Scholar]
  36. Yoon J-H, Lee C-H, Yeo S-H, Oh T-K. Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2005; 55:1223–1227 [View Article]
    [Google Scholar]
  37. Yang S-Z, Xiong X, Feng G-D, Li H-P, Zhu H-H. Reclassification of Sphingopyxis contaminans as Sphingorhabdus contaminans comb. nov. and emended description of the genus Sphingorhabdus . Int J Syst Evol Microbiol 2017; 67:4328–4331 [View Article]
    [Google Scholar]
  38. Park J-M, Park S, Jung Y-T, Kim H, Lee J-S et al. Sphingorhabdus arenilitoris sp. nov., isolated from a coastal sand, and reclassification of Sphingopyxis rigui as Sphingorhabdus rigui comb. nov. and Sphingopyxis wooponensis as Sphingorhabdus wooponensis comb. nov. Int J Syst Evol Microbiol 2014; 64:2551–2557 [View Article]
    [Google Scholar]
  39. Yang S-Z, Xiong X, Feng G-D, Li H-P, Zhu H-H. Reclassification of Sphingopyxis contaminans as Sphingorhabdus contaminans comb. nov. and emended description of the genus Sphingorhabdus . Int J Syst Evol Microbiol 2017; 67:4328–4331 [View Article]
    [Google Scholar]
  40. Chen H, Piao A-L, Tan X, Nogi Y, Yeo J et al. Sphingorhabdus buctiana sp. nov., isolated from fresh water, and reclassification of Sphingopyxis contaminans as Sphingorhabdus contaminans comb. nov. Antonie Van Leeuwenhoek 2018; 111:323–331 [View Article]
    [Google Scholar]
  41. Baik KS, Choe HN, Park SC, Hwang YM, Kim EM et al. Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., isolated from wetland freshwater, and emended description of the genus Sphingopyxis . Int J Syst Evol Microbiol 2013; 63:1297–1303 [View Article]
    [Google Scholar]
  42. Jung G-Y, Nam I-H, Han Y-S, Ahn JS, Rhee S-K et al. Sphingorhabdus pulchriflava sp. nov., isolated from a river. Int J Syst Evol Microbiol 2019; 69:2644–2650 [View Article]
    [Google Scholar]
  43. Jeong SE, Kim KH, Baek K, Jeon CO. Parasphingopyxis algicola sp. nov., isolated from a marine red alga Asparagopsis taxiformis and emended description of the genus Parasphingopyxis Uchida et al. 2012. Int J Syst Evol Microbiol 2017; 67:3877–3881 [View Article]
    [Google Scholar]
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