1887

Abstract

A benzene, - and -xylene-degrading Gram-stain-negative, aerobic, yellow-pigmented bacterium, designated as D2P1, was isolated from a -xylene-degrading enrichment culture. Phylogenetic analyses based on 16S rRNA genes showed that D2P1 shares a distinct phyletic lineage within the genus and shows highest 16S rRNA gene sequence similarity to NBRC 102512 (99.2 %) and NBRC 102513 (98.3 %). The draft genome sequence of D2P1 is 5.63 Mb long and the genomic DNA G+C content is 65.5 %. Orthologous average nucleotide identity (OrthoANI) and digital DNA–DNA hybridization (dDDH) analyses confirmed low genomic relatedness to its closest relatives (OrthoANI <86 %; dDDH <30 %). D2P1 contains ubiquinone 8 (Q-8) as the only respiratory quinone and phospholipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol as major polar lipids. The main whole-cell fatty acids of D2P1 are summed feature 3 (C 7/C 6), C and summed feature 8 (C 7/C 6). The polyphasic taxonomic results indicated that strain D2P1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is D2P1 (=LMG 31780=NCAIM B 02655).

Funding
This study was supported by the:
  • Tempus Public Foundation (HU) (Award Stipendium Hungaricum Scholarship Programme)
    • Principle Award Recipient: SinchanBanerjee
  • Ministry of Innovation and Technology of Hungary (Award TKP2020-IKA-12)
    • Principle Award Recipient: NotApplicable
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2021-03-10
2021-10-17
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References

  1. Willems A, Busse J, Goor M, Pot B, Falsen E. Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (formerly Pseudomonas flava), Hydrogenophaga palleronii (formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (formerly Pseudomonas pseudoflava). Int J Syst Bacteriol 1989; 39:319–333
    [Google Scholar]
  2. Chung BS, Ryu SH, Park M, Jeon Y, Chung YR et al. Hydrogenophaga caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2007; 57:1126–1130 [View Article][PubMed]
    [Google Scholar]
  3. Lin SY, Hameed A, Wen CZ, Hsu Y-H, Liu YC et al. Hydrogenophaga aquatica sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2017; 67:3716–3721 [View Article][PubMed]
    [Google Scholar]
  4. Du J, Yang J-E, Singh H, Akter S, Won K et al. Hydrogenophaga luteola sp. nov. isolated from reed pond water. Antonie van Leeuwenhoek 2015; 108:695–701 [View Article]
    [Google Scholar]
  5. Baek C, Kim E, Shin S-K, Choi S, Yi H. Hydrogenophaga crassostreae sp. nov., isolated from a Pacific oyster. Int J Syst Evol Microbiol 2017; 67:4045–4049 [View Article][PubMed]
    [Google Scholar]
  6. Choi G, Lee SY, Kim SY, Wee J-H, Im W-T. Hydrogenophaga borbori sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2020; 70:555–561 [View Article][PubMed]
    [Google Scholar]
  7. Yoon JH, Kang SJ, Ryu SH, Jeon CO, Oh T-K. Hydrogenophaga bisanensis sp. nov., isolated from wastewater of a textile dye works. Int J Syst Evol Microbiol 2008; 58:393–397 [View Article][PubMed]
    [Google Scholar]
  8. Contzen M, Moore ERB, Blümel S, Stolz A, Kämpfer P. Hydrogenophaga intermedia sp. nov., a 4-aminobenzenesulfonate degrading organism. Syst Appl Microbiol 2000; 23:487–493 [View Article][PubMed]
    [Google Scholar]
  9. Kampfer P, Schulze R, Jäckel U, Malik KA, Amann R et al. Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2005; 55:341–344 [View Article][PubMed]
    [Google Scholar]
  10. Yang D, Cha S, Choi J, Seo T. Hydrogenophaga soli sp. nov., isolated from rice field soil. Int J Syst Evol Microbiol 2017; 67:4200–4204 [View Article][PubMed]
    [Google Scholar]
  11. Mantri S, Chinthalagiri MR, Gundlapally SR. Description of Hydrogenophaga laconesensis sp. nov. isolated from tube well water. Arch Microbiol 2016; 198:637–644 [View Article][PubMed]
    [Google Scholar]
  12. Fahy A, Ball AS, Lethbridge G, Timmis KN, McGenity TJ. Isolation of alkali-tolerant benzene-degrading bacteria from a contaminated aquifer. Lett Appl Microbiol 2008; 47:60–66 [View Article][PubMed]
    [Google Scholar]
  13. Táncsics A, Farkas M, Szoboszlay S, Szabó I, Kukolya J et al. One-year monitoring of meta-cleavage dioxygenase gene expression and microbial community dynamics reveals the relevance of subfamily I.2.C extradiol dioxygenases in hypoxic, BTEX-contaminated groundwater. Syst Appl Microbiol 2013; 36:339–350 [View Article][PubMed]
    [Google Scholar]
  14. Révész F, Farkas M, Kriszt B, Szoboszlay S, Benedek T et al. Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: enrichment, isolation and whole-genome analysis. Environ Sci Pollut Res Int 2020; 27:31130–31142 [View Article][PubMed]
    [Google Scholar]
  15. Claus D. A standardized Gram staining procedure. World J Microbiol Biotechnol 1992; 8:451–452 [View Article][PubMed]
    [Google Scholar]
  16. Ohad I, Danon D, Hestrin S. The use of shadow-casting technique for measurement of the width of elongated particles. J Cell Biol 1963; 17:321–326 [View Article][PubMed]
    [Google Scholar]
  17. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Cambridge: Cambridge University Press; 2004
    [Google Scholar]
  18. Farkas M, Táncsics A, Kriszt B, Benedek T, Tóth EM et al. Zoogloea oleivorans sp. nov., a floc-forming, petroleum hydrocarbon-degrading bacterium isolated from biofilm. Int J Syst Evol Microbiol 2015; 65:274–279 [View Article][PubMed]
    [Google Scholar]
  19. Spring S, Jäckel U, Wagner M, Kämpfer P. Ottowia thiooxydans gen. nov., sp. nov., a novel facultatively anaerobic, N2O-producing bacterium isolated from activated sludge, and transfer of Aquaspirillum gracile to Hylemonella gracilis gen. nov., comb. nov. Int J Syst Evol Microbiol 2004; 54:99–106 [View Article][PubMed]
    [Google Scholar]
  20. Yoon K-S, Tsukada N, Sakai Y, Ishii M, Igarashi Y et al. Isolation and characterization of a new facultatively autotrophic hydrogen-oxidizing Betaproteobacterium, Hydrogenophaga sp. AH-24. FEMS Microbiol Lett 2008; 278:94–100 [View Article][PubMed]
    [Google Scholar]
  21. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
  22. Soergel DAW, Dey N, Knight R, Brenner SE. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J 2012; 6:1440–1444 [View Article][PubMed]
    [Google Scholar]
  23. Yoon SH, 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]
  24. 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]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  26. 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]
  27. 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]
  28. Borsodi AK, Aszalos JM, Bihari P, Nagy I, Schumann P et al. Anaerobacillus alkaliphilus sp. nov., a novel alkaliphilic and moderately halophilic bacterium. Int J Syst Evol Microbiol 2019; 69:631–637 [View Article][PubMed]
    [Google Scholar]
  29. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
    [Google Scholar]
  30. 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]
  31. Lee I, Ouk Kim Y, Park S-C, 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. Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S et al. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 2006; 34:53–65 [View Article][PubMed]
    [Google Scholar]
  33. Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L et al. MicroScope: a platform for microbial genome annotation and comparative genomics. Database 2009; 2009:bap021 [View Article][PubMed]
    [Google Scholar]
  34. Caspi R, Altman T, Billington R, Dreher K, Foerster H et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome databases. Nucleic Acids Res 2014; 42:D459–D471 [View Article][PubMed]
    [Google Scholar]
  35. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000; 28:27–30 [View Article][PubMed]
    [Google Scholar]
  36. UniProt Consortium Bateman A. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 2019; 47:D506–D515 [View Article][PubMed]
    [Google Scholar]
  37. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI. Report of the ad hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Evol Microbiol 1987; 37:463–464
    [Google Scholar]
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