1887

Abstract

A Gram-stain-negative, strictly aerobic, rod-shaped and non-motile bacterial strain, designated D-2Q-5-6, was isolated from a soil sample collected from the Arctic region. Strain D-2Q-5-6 was found to grow at 10–43 °C (optimum, 28 °C), at pH 6.0–9.0 (pH 7.0) and in 0–5 % (w/v) NaCl (0–1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain D-2Q-5-6 fell into the genus and shared less than 95.8 % identity with all type strains of recognized species of this genus. The major cellular fatty acids of strain D-2Q-5-6 were summed feature 8 (C 7 and/or C 6; 31.4 %), summed feature 3 (C 7 and/or C 6; 26.8 %) and C 2OH (11.7 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The predominant quinone was identified as Q10. The DNA G+C content of strain D-2Q-5-6 was 64.5 mol%. Based on the results of phylogenetic analysis and distinctive phenotypic characteristics, strain D-2Q-5-6 is concluded to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain of the species is D-2Q-5-6 (=MCCC 1A06070=KCTC 52311).

Funding
This study was supported by the:
  • The Science and Technology Plan Project of Guangdong Province (Award 2019B030316017)
    • Principle Award Recipient: Yang Liu
  • The Guangdong Province Science and Technology Innovation Strategy Special Fund (Award 2018B020205003)
    • Principle Award Recipient: Yang Liu
  • The GDAS' Project of Science and Technology Development (Award 2019GDASYL-0401002)
    • Principle Award Recipient: Yang Liu
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003943
2020-01-06
2021-10-15
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/3/1610.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003943&mimeType=html&fmt=ahah

References

  1. Jogler M, Chen H, Simon J, Rohde M, Busse H-J 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. Subhash Y, Sasikala C, Ramana CV. Sphingopyxis contaminans sp. nov., isolated from a contaminated Petri dish. Int J Syst Evol Microbiol 2014; 64:2238–2243 [View Article]
    [Google Scholar]
  8. 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]
  9. 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]
  10. 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]
  11. Kim H-S, Cha SH, Suk HY, Park N-H, Woo J-H. Complete genome sequence of Sphingorhabdus sp. YGSMI21, exhibiting high enantioselective epoxide hydrolase activity. Genome Announc 2018; 6: [View Article]
    [Google Scholar]
  12. Jeong HI, Jin HM, Jeon CO. Complete genome sequence of Sphingorhabdus sp. M41, a versatile hydrocarbon degrader, isolated from crude oil-contaminated costal sediment. J Biotechnol 2016; 227:41–42 [View Article]
    [Google Scholar]
  13. Lai Q, Liu Y, Yuan J, Du J, Wang L et al. Multilocus sequence analysis for assessment of phylogenetic diversity and biogeography in Thalassospira bacteria from diverse marine environments. PLoS One 2014; 9:e106353 [View Article]
    [Google Scholar]
  14. 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]
    [Google Scholar]
  15. Knyaz C, Stecher G, Li M, Kumar S, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549
    [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
    [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
    [Google Scholar]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  19. 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]
  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]
    [Google Scholar]
  21. 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]
    [Google Scholar]
  22. 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]
  23. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article]
    [Google Scholar]
  24. Siddaramappa S, Viswanathan V, Thiyagarajan S, Narjala A. Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales . Microb Genom 2018; 4: [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003943
Loading
/content/journal/ijsem/10.1099/ijsem.0.003943
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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