Description of sp. nov., harboring antibiotic- and toxic compound-resistant genes, isolated from poultry manure No Access

Abstract

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-YST696, harbouring antibiotic- and toxic compound-resistace genes, isolated from poultry manure in Taiwan. Cells of CC-YST696 were short rods, motile with polar flagella, catalase- and oxidase-positive. Optimal growth occurred at 30 °С, pH 9 and with 1 % NaCl. The results of phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by CC-YST696 associated with (97.9 % sequence identity), (97.3 %) and (97.2 %), and with lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 72.8–80.0 % (=17) compared within the type strains of species of of the genus . CC-YST696 contained C, C, Cω7 11-methyl and Cω6/ Cω7 as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, three unidentified glycolipids, two unidentified phospholipids and three unidentified lipids. The DNA G+C content was 62.2 mol% and the predominant quinone was ubiquinone Q-10. On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-YST696 is proposed to represent a novel species of the genus , for which the name sp. nov. (type strain CC-YST696=BCRC 81284=JCM 34167) is proposed.

Funding
This study was supported by the:
  • Ministry of Science and Technology, Taiwan (Award MOST 109-2634-F-005-002)
    • Principle Award Recipient: Chiu-ChungYoung
  • Ministry of Science and Technology, Taiwan (Award MOST 109-2634-F-005-002)
    • Principle Award Recipient: Chia-FangTsai
  • Ministry of Science and Technology, Taiwan (Award MOST 109-2634-F-005-002)
    • Principle Award Recipient: Shih-YaoLin
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004901
2021-07-21
2024-03-29
Loading full text...

Full text loading...

References

  1. Nakagawa Y, Sakane T, Yokota A. Transfer of “Pseudomonas riboflavina” (Foster 1944), a Gram-negative, motile rod with long-chain 3-hydroxy fatty acids, to Devosia riboflavina gen. nov., sp. nov., nom. rev. Int J Syst Bacteriol 1996; 46:16–22 [View Article] [PubMed]
    [Google Scholar]
  2. Ryu SH, Chung BS, Le NT, Jang HH, Yun P-Y et al. Devosia geojensis sp. nov., isolated from diesel-contaminated soil in Korea. Int J Syst Evol Microbiol 2008; 58:633–636
    [Google Scholar]
  3. Kumar M, Verma M, Lal R. Devosia chinhatensis sp. nov., isolated from a hexachlorocyclohexane (HCH) dump site in India. Int J Syst Evol Microbiol 2008; 58:861–865 [View Article] [PubMed]
    [Google Scholar]
  4. Zhang L, Song M, Chen X-L, Xu R-J, Chen K et al. Devosia honganensis sp. nov., isolated from the soil of a chemical factory. Antonie van Leeuwenhoek 2015; 108:1301–1307 [View Article] [PubMed]
    [Google Scholar]
  5. Galatis H, Martin K, Kämpfer P, Glaeser SP. Devosia epidermidihirudinis sp. nov. isolated from the surface of a medical leech. Antonie van Leeuwenhoek 2013; 103:1165–1171 [View Article] [PubMed]
    [Google Scholar]
  6. Mohd Nor MN, Sabaratnam V, GYA T. Devosia elaeis sp. nov., isolated from oil palm rhizospheric soil. Int J Syst Evol Microbiol 2017; 67:851–855 [View Article]
    [Google Scholar]
  7. Bautista VV, Monsalud RG, Yokota A. Devosia yakushimensis sp. nov., isolated from root nodules of Pueraria lobata (Willd.) Ohwi. Int J Syst Evol Microbiol 2010; 60:627–632 [View Article] [PubMed]
    [Google Scholar]
  8. Rivas R, Velázquez E, Willems A, Vizcaíno N, Subba-Rao NS et al. A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) druce. Appl Environ Microbiol 2002; 68:5217–5222 [View Article] [PubMed]
    [Google Scholar]
  9. Quan X-T, Siddiqi MZ, Liu Q-Z, Lee S-M, Im W-T. Devosia ginsengisoli sp. nov., isolated from ginseng cultivation soil. Int J Syst Evol Microbiol 2020; 70:1489–1495
    [Google Scholar]
  10. Zhang DC, Redzic M, Liu HC, Zhou YG, Schinner F et al. Devosia psychrophila sp. nov. and Devosia glacialis sp. nov., from alpine glacier cryoconite, and an emended description of the genus Devosia . Int J Syst Evol Microbiol 2012; 62:710–715 [View Article] [PubMed]
    [Google Scholar]
  11. Romanenko LA, Tanaka N, Svetashev VI. Devosia submarina sp. nov., isolated from deep-sea surface sediments. Int J Syst Evol Microbiol 2013; 63:3079–3085 [View Article] [PubMed]
    [Google Scholar]
  12. Jia YY, Sun C, Pan J, Zhang WY, Zhang X-Q et al. Devosia pacifica sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2014; 64:2637–2641 [View Article] [PubMed]
    [Google Scholar]
  13. Lin D, Huang Y, Chen Y, Zhu S, Yang J et al. Devosia indica sp. nov., isolated from surface seawater in the Indian Ocean. Int J Syst Evol Microbiol 2020; 70:340–345 [View Article] [PubMed]
    [Google Scholar]
  14. Liu Y, Du J, Zhang J, Lai Q, Shao Z et al. Devosia marina sp. nov., isolated from deep seawater of the South China Sea, and reclassification of Devosia subaequoris as a later heterotypic synonym of Devosia soli ; 20203062–3068
  15. Yoon J-H, Kang S-J, Park S, Oh T-K. Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia. Int J Syst Evol Microbiol 2007; 57:1310–1314 [View Article]
    [Google Scholar]
  16. 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]
  17. de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E et al. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852–1863 [View Article]
    [Google Scholar]
  18. Murray RGE, Doetsch RN, Robinow CF. Determination and cytological light microscopy. Gerhardt P, Murray R, Wood W, Krieg N. eds In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 32–34
    [Google Scholar]
  19. Lin SY, Liu YC, Hameed A, Hsu YH, Lai WA et al. Azospirillum fermentarium sp. nov., a nitrogen-fixing species isolated from a fermenter. Int J Syst Evol Microbiol 2013; 63:3762–3768 [View Article] [PubMed]
    [Google Scholar]
  20. Hameed A, Shahina M, Lin SY, Lai WA, Hsu YH et al. Aquibacter zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter . Int J Syst Evol Microbiol 2013; 64:138–145 [View Article] [PubMed]
    [Google Scholar]
  21. Zhou J, Fries MR, Sanford RA, Tiedje JM. Phylogenetic analysis of a new group of denitrifiers capable of anaerobic growth on toluene and description of Azoarcus tolulyticus sp. nov. Int J Syst Bacteriol 1995; 45:500–506 [View Article]
    [Google Scholar]
  22. Heiner CR, Hunkapiller LK, Chen SM, Glass JI, Chen EY. Sequencing multimegabase-template DNA using BigDye terminator chemistry. Genome Res 1998; 8:557–561 [View Article] [PubMed]
    [Google Scholar]
  23. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617
    [Google Scholar]
  24. 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]
  25. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994; 44:846–849
    [Google Scholar]
  26. 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]
  27. 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]
  28. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  29. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  30. Jukes TH, Cantor CR. Evolution of protein molecules. Munro HN. eds In Mammalian Protein Metabolism Vol 3 New York: Academic Press; 1969 pp 21–32
    [Google Scholar]
  31. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  32. 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] [PubMed]
    [Google Scholar]
  33. Meier-Kolthoff JP, Auch AF, Klenk HP, 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. 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]
  35. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994; 44:846–849
    [Google Scholar]
  36. 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]
  37. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
    [Google Scholar]
  38. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxyl acids. J Clin Microbiol 1982; 16:584–586 [View Article] [PubMed]
    [Google Scholar]
  39. Paisley R. MIS Whole Cell Fatty Acid Analysis by Gas Chromatography Training Manual Newark, DE: MIDI; 1996
    [Google Scholar]
  40. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. MIDI Inc: Newark, DE; 1990
    [Google Scholar]
  41. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322 [View Article] [PubMed]
    [Google Scholar]
  42. 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
    [Google Scholar]
  43. Collins MD. Isoprenoid quinone analysis in classification and identification. Goodfellow M, Minnikin D. eds In Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 267–287
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004901
Loading
/content/journal/ijsem/10.1099/ijsem.0.004901
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed