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Community structures and comparison of nosZ and 16S rRNA genes from culturable denitrifying bacteria

  • Cumhur AvşarEmail author
  • E. Sümer Aras
Original Article

Abstract

The objectives of this study were (i) to isolate and characterize of cultivable denitrifying bacteria using classic microbiological and molecular methods, (ii) to compare of 16S rRNA and nosZ genes as molecular markers, (iii) to determine bacterial community structure and diversity in soil samples using single-strand conformation polymorphism (SSCP) analysis. In this study, 49 bacterial isolates were cultivated and phylogenetic analyses grouped them into two phyla: Proteobacteria (37 species) and Firmicutes (12 species). Our study showed that the nosZ functional gen could be used to identify denitrifying bacteria abundance in environment but could not be used to identify pure bacterial cultures. In addition, the bacterial community structure showed significant differences among the various soil types. Phylogenetic analysis of community structure indicated that 51 clones could be divided into 2 phylotypes. Uncultured bacteria (80.4%) and Gammaproteobacteria (19.6%) were the dominant components of the soil bacterial community. For 16S rRNA, PCR products of 49 bacteria were obtained with 27F-1492R primer pairs. For nosZ, PCR products were obtained with primers 1F-1R (259 bp), 2F-2R (267 bp), and F-1622R (453 bp) of 39 bacteria that the single nosZ band provided on the agarose gel. The bacterial 16S rRNA gene clone library was dominated by Gammaproteobacteria and Bacilli. The nosZ clone sequences did not represent the bacteria from which they were obtained but were found to be closer to the environmental clones. Our study showed that the nosZ functional gene could be used to identify denitrification abundance in environment but could not be used to identify pure bacterial cultures. It was also found that the nosZ sequences showed uncultured denitrifier species.

Notes

Authors’ contributions

CA and ESA made a contribution to designing the study. CA was responsible for completing the experiments and data analysis. CA and ESA made a contribution to writing the manuscript. All authors read and approved the final manuscript.

Funding information

This research has been supported by Ankara University Scientific Research Project Coordination Unit. Project Number: 17L0430004, 2017-2018.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

12223_2019_754_MOESM1_ESM.docx (55 kb)
ESM 1 (DOCX 55 kb)

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Copyright information

© Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2019

Authors and Affiliations

  1. 1.Department of Biology, Faculty of Arts and SciencesSinop UniversitySinopTurkey
  2. 2.Department of Biology, Faculty of ScienceAnkara UniversityAnkaraTurkey

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