1887

Abstract

A pink-pigmented, Gram-stain-positive, aerobic, coccoid-shaped bacterial strain, designated as S5-TSA-19, was isolated from an explosives contaminated site in Panchkula, Haryana, India. The 16S rRNA gene sequencing analysis indicated that the strain is a member of the family with the highest sequence similarity to XN13 (96.1 %), followed by S1 (95.6 %), DSM 23997 (95.6 %), ISL-41 (95.6 %), M8 (95.5 %), LCB217 (95.5 %) and DSM 17275 (95.5 %). Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences (based on a conserved set of 400 proteins) retrieved the strain in a distinct branch indicating a separate lineage within the family . Strain S5-TSA-19 had a distinctive chemotaxonomic pattern comprising A4α type peptidoglycan based on -Lys--Asp, iso-C as the major fatty acid, absence of phosphatidylethanolamine as a major lipid and MK-7 and MK-6 as the major menaquinones, differentiating it from the genera and , thus supporting the findings of molecular phylogeny. Further, strain S5-TSA-19 was able to biotransform hexahydro-1,3,5,-trinitro-1,2,5-triazine (RDX) into nitrite derivatives under aerobic conditions in 2–4 days, whereas the closest reference strains did not possess this property. On the basis of polyphasic taxonomic characterization and a phylogenomics approach, strain S5-TSA-19 is proposed as the type strain of a novel species in a novel genus for which the name gen. nov., sp. nov. is proposed (=JCM 31737=KCTC 33871=MTCC 12608).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003541
2019-08-01
2019-10-21
Loading full text...

Full text loading...

References

  1. Krasil’nikov NA. Opredelitelv bakterii i Actinomicetov. Akedemii Nauk SSSR, Moscow 1949;328
    [Google Scholar]
  2. Rosenberg E, Delong EF, Lory S, Stackebrandt E, Thompson F et al. The family Planococcaceae. The Prokaryotes- Firmicutes and Tenericutes, 4th ed. 2014; pp.303–351
    [Google Scholar]
  3. Yoon JH, Weiss N, Kang KH, Oh TK, Park YH. Planococcus maritimus sp. nov., isolated from sea water of a tidal flat in Korea. Int J Syst Evol Microbiol 2003;53:2013–2017 [CrossRef][PubMed]
    [Google Scholar]
  4. Yoon JH, Kang SS, Lee KC, Lee ES, Kho YH et al. Planomicrobium koreense gen. nov., sp. nov., a bacterium isolated from the Korean traditional fermented seafood jeotgal, and transfer of Planococcus okeanokoites (Nakagawa et al. 1996) and Planococcus mcmeekinii (Junge et al. 1998) to the genus Planomicrobium. Int J Syst Evol Microbiol 2001;51:1511–1520 [CrossRef][PubMed]
    [Google Scholar]
  5. Siddikee MA, Chauhan PS, Anandham R, Han GH, Sa T. Isolation, characterization, and use for plant growth promotion under salt stress, of ACC deaminase-producing halotolerant bacteria derived from coastal soil. J Microbiol Biotechnol 2010;20:1577–1584[PubMed]
    [Google Scholar]
  6. Manorama R, Pindi PK, Reddy GS, Shivaji S. Bhargavaea cecembensis gen. nov., sp. nov., isolated from the Chagos-Laccadive ridge system in the Indian Ocean. Int J Syst Evol Microbiol 2009;59:2618–2623 [CrossRef][PubMed]
    [Google Scholar]
  7. Liu R, Yu Z, Zhang H, Yang M, Shi B et al. Diversity of bacteria and mycobacteria in biofims of two urban drinking water distribution systems. Can J Microbiology 2012;58:261–270
    [Google Scholar]
  8. Wan C, Du M, Lee DJ, Yang X, Ma W et al. Electrokinetic remediation and microbial community shift of β-cyclodextrin-dissolved petroleum hydrocarbon-contaminated soil. Appl Microbiol Biotechnol 2011;89:2019–2025 [CrossRef][PubMed]
    [Google Scholar]
  9. Labuzek S, Hupert-Kocurek KT, Shurnik M. Isolation and characterization of new Planococcus sp. strain able for aromatic hydrocarbon degradation. Acta Microbiol 2003;94:889–895
    [Google Scholar]
  10. Achal V, Pan X, Fu Q, Zhang D. Biomineralization based remediation of As(III) contaminated soil by Sporosarcina ginsengisoli. J Hazard Mater 2012;201–202:178–184 [CrossRef][PubMed]
    [Google Scholar]
  11. Bafana A. Mercury resistance in Sporosarcina sp. G3. Biometals 2011;24:301–309 [CrossRef][PubMed]
    [Google Scholar]
  12. Khan MI, Lee J, Park J. Microbial degradation and toxicity of hexahydro-1,3,5-trinitro-1,3,5-triazine. J Microbiol Biotechnol 2012;22:1311–1323 [CrossRef][PubMed]
    [Google Scholar]
  13. Migula W. Über ein neues system der bakterien. Arb Bakteriol Inst Karlsruhe 1894;1:235–238
    [Google Scholar]
  14. Bohacek J, Kocur M, Martinec T. DNA base composition and taxonomy of some micrococci. J Gen Microbiol 1967;46:369–376 [CrossRef]
    [Google Scholar]
  15. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  16. Shivaji S, Ray MK, Saisree L, Jagannadham MV, Seshu KG. Sphingobacterium antarcticus sp. nov. a psychrotrophic bacterium from the soils of Schirmacher Oasis. Antarctica. Int J Syst Bacteriol 1992;42:102–106
    [Google Scholar]
  17. Lanyi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987;19:1–67
    [Google Scholar]
  18. Verma A, Ojha AK, Dastager SG, Natarajan R, Mayilraj S et al. Domibacillus mangrovi sp. nov. and Domibacillus epiphyticus sp. nov., isolated from marine habitats of the central west coast of India. Int J Syst Evol Microbiol 2017;67:3063–3070 [CrossRef][PubMed]
    [Google Scholar]
  19. Krishnamurthi S, Bhattacharya A, Mayilraj S, Saha P, Schumann P et al. Description of Paenisporosarcina quisquiliarum gen. nov., sp. nov., and reclassification of Sporosarcina macmurdoensis Reddy et al. 2003 as Paenisporosarcina macmurdoensis comb. nov. Int J Syst Evol Microbiol 2009;59:1364–1370 [CrossRef][PubMed]
    [Google Scholar]
  20. Yoon SH, Ha SM, 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]
  21. 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]
  22. Verma A, Ojha AK, Pal Y, Kumari P, Schumann P et al. An investigation into the taxonomy of “Bacillus aminovorans” and its reclassification to the genus Domibacillus as Domibacillus aminovorans sp. nov. Sys Appl Microbiol 2017;40:458–467
    [Google Scholar]
  23. Segata N, Börnigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 2013;4:2304 [CrossRef][PubMed]
    [Google Scholar]
  24. Hyatt D, Chen GL, 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]
  25. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other tree. Nucleic Acids Re 2016;44:242–249
    [Google Scholar]
  26. 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 Research 2013;42:206–214
    [Google Scholar]
  27. 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][PubMed]
    [Google Scholar]
  28. Stothard P, Wishart DS. Circular genome visualization and exploration using CGView. Bioinformatics 2005;21:537–539 [CrossRef][PubMed]
    [Google Scholar]
  29. Wang Y, Coleman-Derr D, Chen G, Gu YQ. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Res 2015;43:W78–W84 [CrossRef][PubMed]
    [Google Scholar]
  30. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res 2017;45:535–542 [CrossRef][PubMed]
    [Google Scholar]
  31. 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]
  32. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987;19:161–207
    [Google Scholar]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI, Inc; 2001
    [Google Scholar]
  34. Schumann P. Peptidoglycan structure. Methods Microbiol 2011;38:101–129
    [Google Scholar]
  35. Griess P. Bemerkungen zu der abhandlung der H.H. Weselsky und Benedikt “Ueber einige azoverbindungen”. Ber Deutsch Chem Ges 1879;12:426–428
    [Google Scholar]
  36. Gan L, Zhang H, Tian J, Li X, Long X et al. Planococcus salinus sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil. Int J Syst Evol Microbiol 2018;68:589–595 [CrossRef][PubMed]
    [Google Scholar]
  37. See-Too WS, Ee R, Madhaiyan M, Kwon SW, Tan JY et al. Planococcus versutus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017;67:944–950 [CrossRef][PubMed]
    [Google Scholar]
  38. Wang X, Wang Z, Zhao X, Huang X, Zhou Y et al. Planococcus ruber sp. nov., isolated from a polluted farmland soil sample. Int J Syst Evol Microbiol 2017;67:2549–2554 [CrossRef][PubMed]
    [Google Scholar]
  39. Nakagawa Y, Sakane T, Yokota A. Emendation of the genus Planococcus and transfer of Flavobacterium okeanokoites Zobell and Upham 1944 to the genus Planococcus as Planococcus okeanokoites comb. nov. Int J Syst Bacteriol 1996;46:866–870 [CrossRef][PubMed]
    [Google Scholar]
  40. Vos PD, Garrity GM, Jones D, Krieg NR, Ludwig W et al. Bergey’s Manual of Systematic Bacteriology, 2nd ed.vol. 3 2009; pp.349–385
    [Google Scholar]
  41. Verma P, Pandey PK, Gupta AK, Seong CN, Park SC et al. Reclassification of Bacillus beijingensis Qiu et al. 2009 and Bacillus ginsengi Qiu et al. 2009 as Bhargavaea beijingensis comb. nov. and Bhargavaea ginsengi comb. nov. and emended description of the genus Bhargavaea. Int J Syst Evol Microbiol 2012;62:2495–2504 [CrossRef][PubMed]
    [Google Scholar]
  42. 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]
  43. Kim M, Oh HS, Park SC, 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][PubMed]
    [Google Scholar]
  44. Coleman NV, Nelson DR, Duxbury T. Aerobic biodegradation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) as a nitrogen source by a Rhodococcus sp., strain DN22. Soil Biol Biochem 1998;30:1159–1167 [CrossRef]
    [Google Scholar]
  45. Fournier D, Halasz A, Spain J, Fiurasek P, Hawari J. Determination of key metabolites during biodegradation of hexahydro-1,3,5-trinitro-1,3,5-triazine with Rhodococcus sp. strain DN22. Appl Environ Microbiol 2002;68:166–172 [CrossRef][PubMed]
    [Google Scholar]
  46. Seth-Smith HM, Rosser SJ, Basran A, Travis ER, Dabbs ER et al. Cloning sequencing and characterization of the gene cluster from Rhodococcus rhodochrous. Appl Environ Microbiol 2002;68:4764–4771
    [Google Scholar]
  47. Bhushan B, Trott S, Spain JC, Halasz A, Paquet L et al. Biotransformation of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by a rabbit liver cytochrome P450: insight into the mechanism of RDX biodegradation by Rhodococcus sp. strain DN22. Appl Environ Microbiol 2003;69:1347–1351 [CrossRef][PubMed]
    [Google Scholar]
  48. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  49. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  50. 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[PubMed]
    [Google Scholar]
  51. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992;8:275–282[PubMed]
    [Google Scholar]
  52. Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol 1992;9:678–687 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003541
Loading
/content/journal/ijsem/10.1099/ijsem.0.003541
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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