1887

Abstract

A novel e-waste-degrading strain, PE08, was isolated from contaminated soil collected from a paper mill yard in Lalkuan, Uttarakhand, India. Strain PE08 was Gram-stain-negative, rod-shaped, aerobic, oxidase-positive and catalase-positive. Optimum growth was observed at 30 °C (range, 5–40 °C), with 1–2 % NaCl (range, 0–3 %) and at pH 7 (range 6–11). The phylogeny based on 16S rRNA gene sequences delineated strain PE08 to the genus and showed highest sequence similarity to KF707 (98.70 %), followed by DSM 50071 (98.62 %) and DSM 21078 (97.93 %). The genome of strain PE08 was sequenced and had one scaffold of 6056953 bp, 99.84 % completeness and 182× coverage were obtained. The G+C content in the genome was 64.24 mol%. The DNA–DNA hybridization and average nucleotide identity values between strain PE08 and its closely related type strain, DSM 21078 were below 34.8 % and 87.96 %, respectively. The phylogenetic analysis based on whole-genome sequence and concatenated GyrB and RpoB proteins revealed that strain PE08 forms a district clade in the family . The predominant fatty acids were summed feature 8 (Cω7 and/or C ω6), summed feature 3 (Cω7 and/or Cω6), C and C. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The phenotypic, chemotaxonomic and genetic analysis, including overall genome relatedness index values, indicated that strain PE08 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is PE08 (=MCC 3792=KCTC 72454=CCUG 73691).

Funding
This study was supported by the:
  • , University Grants Commission (IN) , (Award 857/CSIR-UGC NET JUNE 2017)
  • , Department of Science and Technology, Ministry of Science and Technology, http://dx.doi.org/10.13039/501100001409, (Award SRG/2019/001818)
  • , Department of Biotechnology, Ministry of Science and Technology, http://dx.doi.org/10.13039/501100001407, (Award BT/COORD.II/01/03/2016)
  • , Science and Engineering Research Board, http://dx.doi.org/10.13039/501100001843, (Award SERB/EEQ/2016/000752)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004559
2020-11-11
2020-12-01
Loading full text...

Full text loading...

References

  1. Kodama K, Kimura N, Komagata K. Two new species of Pseudomonas: P. oryzihabitans isolated from rice paddy and clinical specimens and P. luteola isolated from clinical specimens. Int J Syst Bacteriol 1985; 35:467–474 [CrossRef]
    [Google Scholar]
  2. Dabboussi F, Hamze M, Singer E, Geoffroy V, Meyer JM et al. Pseudomonas mosselii sp. nov., a novel species isolated from clinical specimens. Int J Syst Evol Microbiol 2002; 52:363–376 [CrossRef][PubMed]
    [Google Scholar]
  3. Yumoto I, Yamazaki K, Hishinuma M, Nodasaka Y, Suemori A et al. Pseudomonas alcaliphila sp. nov., a novel facultatively psychrophilic alkaliphile isolated from seawater. Int J Syst Evol Microbiol 2001; 51:349–355 [CrossRef][PubMed]
    [Google Scholar]
  4. Madhaiyan M, Poonguzhali S, Saravanan VS, Selvapravin K, Duraipandiyan V et al. Pseudomonas sesami sp. nov., a plant growth-promoting Gammaproteobacteria isolated from the rhizosphere of Sesamum indicum L. Antonie van Leeuwenhoek 2017; 110:843–852 [CrossRef][PubMed]
    [Google Scholar]
  5. Raposo A, Pérez E, de Faria CT, Ferrús MA, Carrascosa C. Food spoilage by Pseudomonas spp. an overview. Food borne Pathog Antibiot Resist 201741–58
    [Google Scholar]
  6. Kimura N, Watanabe T, Suenaga H, Fujihara H, Futagami T et al. Pseudomonas furukawaii sp. nov., a polychlorinated biphenyl-degrading bacterium isolated from biphenyl-contaminated soil in Japan. Int J Syst Evol Microbiol 2018; 68:1429–1435 [CrossRef][PubMed]
    [Google Scholar]
  7. Samuel MS, Sivaramakrishna A, Mehta A. Bioremediation of p-Nitrophenol by Pseudomonas putida 1274 strain. J Environ Health Sci Eng 2014; 12:53 [CrossRef][PubMed]
    [Google Scholar]
  8. Raghuwanshi S, Agarwal T, Yadav A, Zaidi MGH, Shouche Y et al. Selection of Poly(R)-3-hydroxybutyric acid utilising bacteria by enrichment, optimisation and compatibility testing for consortia development. Chem Ecol 2016; 32:583–597 [CrossRef]
    [Google Scholar]
  9. Debbarma P, Zaidi MGH, Kumar S, Raghuwanshi S, Yadav A et al. Selection of potential bacterial strains to develop bacterial consortia for the remediation of e-waste and its in situ implications. Waste Manag 2018; 79:526–536 [CrossRef][PubMed]
    [Google Scholar]
  10. Skerman VBD, Sneath PHA, McGowan V. Approved Lists of bacterial names. Int J Syst Evol Microbiol 1980; 30:225–420 [CrossRef]
    [Google Scholar]
  11. Sasser M. “Tracking” a Strain Using the Sherlock Microbial Identification System (MIS). Tech Note 102:
    [Google Scholar]
  12. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [CrossRef][PubMed]
    [Google Scholar]
  13. Card GL. Metabolism of phosphatidylglycerol, phosphatidylethanolamine, and cardiolipin of Bacillus stearothermophilus. J Bacteriol 1973; 114:1125–1137 [CrossRef][PubMed]
    [Google Scholar]
  14. 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 [CrossRef]
    [Google Scholar]
  15. Brown J, Pirrung M, McCue LA. FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. Bioinformatics 2017; 33:3137–3139 [CrossRef][PubMed]
    [Google Scholar]
  16. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [CrossRef][PubMed]
    [Google Scholar]
  17. Zhao Y, Wu J, Yang J, Sun S, Xiao J et al. PGAP: pan-genomes analysis pipeline. Bioinformatics 2012; 28:416–418 [CrossRef][PubMed]
    [Google Scholar]
  18. 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 [CrossRef][PubMed]
    [Google Scholar]
  19. Edgar R. Usearch. Lawrence Berkeley National Lab (LBNL) CA, USA: Berkeley; 2010
    [Google Scholar]
  20. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  21. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [CrossRef][PubMed]
    [Google Scholar]
  22. Potter SC, Luciani A, Eddy SR, Park Y, Lopez R et al. HMMER web server: 2018 update. Nucleic Acids Res 2018; 46:W200–W204 [CrossRef][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 gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [CrossRef][PubMed]
    [Google Scholar]
  24. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  25. Auch AF, Klenk H-P, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [CrossRef][PubMed]
    [Google Scholar]
  26. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004559
Loading
/content/journal/ijsem/10.1099/ijsem.0.004559
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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