1887

Abstract

A novel bacterial strain, designated FGD1, was isolated from subtropical forest soil of the Nanling National Forest Park located in Guangdong Province, P.R. China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FGD1 was most closely related to DSM 25049 (98.8 %), followed by DSM 25411 (98.7 %), DSM 32207 (98.2 %), DSM 22890 (98.1 %) and other species of (<98 %). The draft genome sequence was 4.58 Mb in length with a G+C content of 65.1 mol%. The calculated average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain FGD1 and closely related type strains were 77.7‒79.6 % and 21.7–22.9 %, respectively. Major fatty acids were summed feature 8 (C ω and/or C ω), summed feature 3 (C ω and/or C ω), C 2-OH and C. The predominant respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Polar lipids were composed of sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, an unidentified phospholipid and lipid. The polyphasic taxonomic results indicated that strain FGD1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is FGD1 (=GDMCC 1.1761=KACC 21283).

Funding
This study was supported by the:
  • Guang-Da Feng , the Science and Technology Planning Projects of Guangdong Province , (Award 2018B030324001)
  • Guang-Da Feng , the Key Realm R&D Program of Guangdong Province , (Award 2018B020205001)
  • Honghui Zhu , the GDAS’ Special Project of Science and Technology Development , (Award 2020GDASYL-20200302002)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004115
2020-03-30
2020-06-03
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/4/2901.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004115&mimeType=html&fmt=ahah

References

  1. 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 [CrossRef]
    [Google Scholar]
  2. Kertesz MA, Kawasaki A. Hydrocarbon-degrading sphingomonads: Sphingomonas, Sphingobium, Novosphingobium, and Sphingopyxis . In Timmis KN. editor Handbook of Hydrocarbon and Lipid Microbiology Berlin, Heidelberg: Springer; 2010 pp 1693–1705
    [Google Scholar]
  3. Nagata Y, Kato H, Ohtsubo Y, Tsuda M. Lessons from the genomes of lindane-degrading sphingomonads. Environ Microbiol Rep 2019; 11:630–644 [CrossRef]
    [Google Scholar]
  4. Khara P, Roy M, Chakraborty J, Ghosal D, Dutta TK. Functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in Sphingobium sp. PNB. FEBS Open Bio 2014; 4:290–300 [CrossRef]
    [Google Scholar]
  5. Nagata Y, Kato H, Ohtsubo Y, Tsuda M. Mobile genetic elements involved in the evolution of bacteria that degrade recalcitrant xenobiotic compounds. In Nishida H, Oshima T. (editors) DNA Traffic in the Environment Singapore: Springer Singapore; 2019 pp 215–244
    [Google Scholar]
  6. Kontur WS, Bingman CA, Olmsted CN, Wassarman DR, Ulbrich A et al. Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin. J Biol Chem 2018; 293:4955–4968 [CrossRef]
    [Google Scholar]
  7. Lyu Y, Zheng W, Zheng T, Tian Y. Biodegradation of polycyclic aromatic hydrocarbons by Novosphingobium pentaromativorans US6-1. PLoS One 2014; 9:e101438 [CrossRef]
    [Google Scholar]
  8. 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 [CrossRef]
    [Google Scholar]
  9. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [CrossRef]
    [Google Scholar]
  10. Xian W-D, Li M-M, Salam N, Ding Y-P, Zhou E-M et al. Novosphingobium meiothermophilum sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2019; 69:1737–1743 [CrossRef]
    [Google Scholar]
  11. Feng G-D, Yang S-Z, Wang Y-H, Zhao G-Z, Deng M-R et al. Sphingomonas gimensis sp. nov., a novel Gram-negative bacterium isolated from abandoned lead-zinc ore mine. Antonie Van Leeuwenhoek 2014; 105:1091–1097 [CrossRef]
    [Google Scholar]
  12. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [CrossRef]
    [Google Scholar]
  13. 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 [CrossRef]
    [Google Scholar]
  14. 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 [CrossRef]
    [Google Scholar]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef]
    [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef]
    [Google Scholar]
  17. Rzhetsky A, Nei M. Theoretical Foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [CrossRef]
    [Google Scholar]
  18. 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 [CrossRef]
    [Google Scholar]
  19. 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 [CrossRef]
    [Google Scholar]
  20. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [CrossRef]
    [Google Scholar]
  21. 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 [CrossRef]
    [Google Scholar]
  22. 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 [CrossRef]
    [Google Scholar]
  23. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [CrossRef]
    [Google Scholar]
  24. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [CrossRef]
    [Google Scholar]
  25. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The seed and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [CrossRef]
    [Google Scholar]
  26. Kanehisa M, Sato Y. Kegg Mapper for inferring cellular functions from protein sequences. Protein Sci 2020; 29:28–35 [CrossRef]
    [Google Scholar]
  27. 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 [CrossRef]
    [Google Scholar]
  28. 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 [CrossRef]
    [Google Scholar]
  29. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [CrossRef]
    [Google Scholar]
  30. 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 [CrossRef]
    [Google Scholar]
  31. Sangwan N, Lata P, Dwivedi V, Singh A, Niharika N et al. Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels. PLoS One 2012; 7:12 [CrossRef]
    [Google Scholar]
  32. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [CrossRef]
    [Google Scholar]
  33. Tindall BJ, Sikorski J, Smibert RA, Krieg N. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Breznak TJ, Marzluf GA, Schmidt TM. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007 pp 330–393
    [Google Scholar]
  34. 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 [CrossRef]
    [Google Scholar]
  35. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101 Newark: MIDI Inc; 1990 pp 1–6
    [Google Scholar]
  36. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [CrossRef]
    [Google Scholar]
  37. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004115
Loading
/content/journal/ijsem/10.1099/ijsem.0.004115
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