1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 1

sp. nov., isolated from downstream sediment sample of the river Ganges, Kanpur, India Free

Abstract

A Gram-stain-negative, non-endospore-producing, short-rod strain, KNDSS-Mac4, was isolated from a downstream sediment sample of the river Ganges, Kanpur, India and studied by using the polyphasic taxonomic approach. 16S rRNA gene sequence analysis uncovered that the strain had similarity to species of the genus and formed a distinct phylogenetic cluster with KACC16524. However, KNDSS-Mac4 showed closest phylogenetic affiliation to DSM 14742 with 16S rRNA gene sequence similarity of 98.7 % followed by DSM 14743 (98.6 %), (98.2 %), KACC16524 (98.2 %), ATCC 55363 (98.2 %) and DSM 12266 (98.0 %). The digital DNA–DNA hybridization and average nucleotide identity values between strain KNDSS-Mac4 and the two most closely related taxa, DSM 14742 and DSM 14743, were 26.0, 26.7 and 84.0, 84.3 % respectively. Major lipids present were phosphatidylglycerol, three unknown aminophospholipids, phosphatidylmethylethanolamine, two unidentified lipids and Q-8 as the only ubiquonone. The major cellular fatty acids present were C ω6/Cω7 and C. The DNA G+C content of strain KNDSS-Mac4 was 65.9 %. Based on data from phenotypic tests and the genotypic differences of strain KNDSS-Mac4 from its closest phylogenetic relatives, it is evident that this isolate should be regarded as a new species. It is proposed that strain KNDSS-Mac4 should be classified in the genus as a novel species, sp. nov. The type strain is KNDSS-Mac4 (=KCTC 52820=VTCC-B-910017).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , dDDH , fatty acid methyl esters and Thauera
© 2018 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002508
2018-01-01
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/1/341.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002508&mimeType=html&fmt=ahah

References

  1. Macy JM, Rech S, Auling G, Dorsch M, Stackebrandt E et al. Thauera selenatis gen. nov., sp. nov., a member of the beta subclass of Proteobacteria with a novel type of anaerobic respiration. Int J Syst Bacteriol 1993; 43:135–142 [View Article][PubMed]
     [Google Scholar]
  2. Mechichi T, Stackebrandt E, Gad'on N, Fuchs G. Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylacetica sp. nov., Thauera aminoaromaticasp. nov., and Azoarcus buckelii sp. nov. Arch Microbiol 2002; 178:26–35 [View Article][PubMed]
     [Google Scholar]
  3. Anders HJ, Kaetzke A, Kämpfer P, Ludwig W, Fuchs G. Taxonomic position of aromatic-degrading denitrifying pseudomonad strains K 172 and KB 740 and their description as new members of the genera Thauera, as Thauera aromatica sp. nov., and Azoarcus, as Azoarcus evansii sp. nov., respectively, members of the beta subclass of the Proteobacteria. Int J Syst Bacteriol 1995; 45:327–333 [View Article][PubMed]
     [Google Scholar]
  4. Dubbels BL, Sayavedra-Soto LA, Bottomley PJ, Arp DJ. Thauera butanivorans sp. nov., a C2-C9 alkane-oxidizing bacterium previously referred to as 'Pseudomonas butanovora'. Int J Syst Evol Microbiol 2009; 59:1576–1578 [View Article][PubMed]
     [Google Scholar]
  5. Song B, Palleroni NJ, Kerkhof LJ, Häggblom MM. Characterization of halobenzoate-degrading, denitrifying Azoarcus and Thauera isolates and description of Thauera chlorobenzoica sp. nov. Int J Syst Evol Microbiol 2001; 51:589–602 [View Article][PubMed]
     [Google Scholar]
  6. Yang GQ, Zhang J, Kwon SW, Zhou SG, Han LC et al. Thauera humireducens sp. nov., a humus-reducing bacterium isolated from a microbial fuel cell. Int J Syst Evol Microbiol 2013; 63:873–878 [View Article][PubMed]
     [Google Scholar]
  7. Foss S, Harder J. Thauera linaloolentis sp. nov. and Thauera terpenica sp. nov., isolated on oxygen-containing monoterpenes (linalool, menthol, and eucalyptol) nitrate. Syst Appl Microbiol 1998; 21:365–373 [View Article][PubMed]
     [Google Scholar]
  8. Scholten E, Lukow T, Auling G, Kroppenstedt RM, Rainey FA et al. Thauera mechernichensis sp. nov., an aerobic denitrifier from a leachate treatment plant. Int J Syst Bacteriol 1999; 49:1045–1051 [View Article][PubMed]
     [Google Scholar]
  9. Dhanjal S, Ruckmani A, Cameotra SS, Pukall R, Klenk HP et al. Yaniella fodinae sp. nov., isolated from a coal mine. Int J Syst Evol Microbiol 2011; 61:535–539 [View Article][PubMed]
     [Google Scholar]
  10. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
     [Google Scholar]
  11. Cowan ST, Steel KJ. Manual for the identification of Medical Bacteria London: Cambridge University Press; 1965
     [Google Scholar]
  12. 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]
  13. Lanyi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67
     [Google Scholar]
  14. Smith NR, Gordon RE, Clark FE. Aerobic Spore Forming Bacteria Washington, DC: Agriculture Monograph No. 16, United States Department of Agriculture; 1952
     [Google Scholar]
  15. Pandey KK, Mayilraj S, Chakrabarti T. Pseudomonas indica sp. nov., a novel butane-utilizing species. Int J Syst Evol Microbiol 2002; 52:1559–1567 [View Article][PubMed]
     [Google Scholar]
  16. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  17. Saha P, Mondal AK, Mayilraj S, Krishnamurthi S, Bhattacharya A et al. Paenibacillus assamensis sp. nov., a novel bacterium isolated from a warm spring in Assam, India. Int J Syst Evol Microbiol 2005; 55:2577–2581 [View Article][PubMed]
     [Google Scholar]
  18. 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]
  19. Komagata K, Suzuki K. Lipid and cell wall analysis in bacterial systematics. In Booth C, Bergan T, Bennett PM, Brown AJP, Colwell RR et al. (editors) Methods in Microbiology St. Louis, MO, USA: Academic Press; 1987 p. 99
     [Google Scholar]
  20. Mayilraj S, Saha P, Suresh K, Saini HS. Ornithinimicrobium kibberense sp. nov., isolated from the Indian Himalayas. Int J Syst Evol Microbiol 2006; 56:1657–1661 [View Article][PubMed]
     [Google Scholar]
  21. 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 [View Article][PubMed]
     [Google Scholar]
  22. 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]
  23. Kumar RM, Kaur G, Kumar N, Kumar A, Singh NK et al. Taxonomic description and genome sequence of Salinicoccus sediminis sp. nov., a halotolerant bacterium isolated from marine sediment. Int J Syst Evol Microbiol 2015; 65:3794–3799 [View Article][PubMed]
     [Google Scholar]
  24. 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]
  25. 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]
  26. Heider J, Fuchs G. Genus XI. Thauera Macy, Rech, Auling, Dorsch, Stackebrandt and Sly 1993, 139VP emend. Song, Young and Palleroni 1998, 893. Bergey's Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Inc., in association with Bergey's Manual Trust; 2015 pp. 1–11
     [Google Scholar]
  27. 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 Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  28. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  29. 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 [View Article][PubMed]
     [Google Scholar]
  30. Pal D, Mathan Kumar R, Kaur N, Kumar N, Kaur G et al. Bacillus maritimus sp. nov., a novel member of the genus Bacillus isolated from marine sediment. Int J Syst Evol Microbiol 2017; 67:60–66 [View Article][PubMed]
     [Google Scholar]
  31. Jia X, Jia B, Kim KH, Jeon CO. Algoriphagus aestuariicola sp. nov., isolated from estuary sediment. Int J Syst Evol Microbiol 2017; 67:914–919 [View Article][PubMed]
     [Google Scholar]
  32. Mohd Nor MN, Sabaratnam V, Tan GYA. Devosia elaeis sp. nov., isolated from oil palm rhizospheric soil. Int J Syst Evol Microbiol 2017; 67:851–855 [View Article][PubMed]
     [Google Scholar]
  33. Kumar RM, Kaur G, Kumar A, Bala M, Singh NK et al. Taxonomic description and genome sequence of Bacillus campisalis sp. nov., a member of the genus Bacillus isolated from a solar saltern. Int J Syst Evol Microbiol 2015; 65:3235–3240 [View Article][PubMed]
     [Google Scholar]
  34. Meier-Kolthoff JP, Klenk HP, 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 [View Article][PubMed]
     [Google Scholar]
  35. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526[PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002508
Loading
Thauera propionica sp. nov., isolated from downstream sediment sample of the river Ganges, Kanpur, India
Int J Syst Evol Microbiol 68, 341 (2018); https://doi.org/10.1099/ijsem.0.002508
/content/journal/ijsem/10.1099/ijsem.0.002508
/content/journal/ijsem/10.1099/ijsem.0.002508
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited 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