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Molecular approach for the rapid detection of Bacillus and Pseudomonas genera—dominant antagonistic groups—from diverse ecological niches using colony multiplex PCR

Abstract

Bacillus and Pseudomonas are the dominant groups of bacteria known for their antagonistic potential against many plant and animal pathogens. Presently, exploration of these genera with antagonistic property for disease management of aquaculture system is gaining more importance to overcome the use of antibiotics and related resistance issues. Rapid screening and identification of these genera from diverse bacterial populations by conventional methods is laborious, cost-intensive, and time-consuming. To overcome these limiting factors, in the present study, a colony multiplex PCR (cmPCR) method was developed and evaluated for the rapid detection of Bacillus and Pseudomonas. The technique amplifies the partial 16S rRNA gene of Bacillus and Pseudomonas with a product size of ~1,100 and ~375 bp, respectively, using single forward (BSF2) and two reverse primers (PAGSR and BK1R). Reliability of the cmPCR method was confirmed by screening 472 isolates obtained from ten different eco-stations, of which 133 isolates belonged to Bacillus and 32 to Pseudomonas. The cmPCR method also helped to identify six different Pseudomonas spp. and 14 different Bacillus spp. from environmental samples. Of the total 472 isolates studied, 46 showed antagonistic activity, among which 63 % were Bacillus and 17.4 % were Pseudomonas. Thus, the newly developed molecular approach provides a quick, sensitive, and potential screening tool to detect novel, antagonistically important Bacillus and Pseudomonas genera for their use in aquaculture. Further, it can also act as a taxonomic tool to understand the distribution of these genera from wide ecological niches and their exploitation for diverse biotechnological applications.

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Acknowledgments

The authors are thankful to the Indian Council of Agricultural Research (ICAR) for funding the study through the Application of Microorganisms in Agriculture and Allied Sectors (AMAAS project). We also express our sincere gratitude to the Director, Central Marine Fisheries Research Institute (CMFRI) for providing necessary facilities to carry out the research. The authors also thank Dr. Lijo John for his support and editorial input of this manuscript. All the authors have agreed to submit this manuscript to the “Journal of Industrial Microbiology and Biotechnology”.

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All authors declare that they have no conflicts of interest.

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Correspondence to K. K. Vijayan.

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Nair, A.V., Pradeep, M.A. & Vijayan, K.K. Molecular approach for the rapid detection of Bacillus and Pseudomonas genera—dominant antagonistic groups—from diverse ecological niches using colony multiplex PCR. J Ind Microbiol Biotechnol 41, 1085–1097 (2014). https://doi.org/10.1007/s10295-014-1441-4

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  • DOI: https://doi.org/10.1007/s10295-014-1441-4

Keywords

  • Bacillus
  • Bacterial identification
  • Colony multiplex PCR
  • Pseudomonas
  • Taxonomical tool