Protocol | Published:

Biological and chemical strategies for exploring inter- and intra-kingdom communication mediated via bacterial volatile signals

Nature Protocols volume 12, pages 13591377 (2017) | Download Citation

Abstract

Airborne chemical signals emitted by bacteria influence the behavior of other bacteria and plants. We present an overview of in vitro methods for evaluating bacterial and plant responses to bacterial volatile compounds (BVCs). Three types of equipment have been used to physically separate the bacterial test strains from either other bacterial strains or plants (in our laboratory we use either Arabidopsis or tobacco plant seedlings): a Petri dish containing two compartments (BI Petri dish); two Petri dishes connected with tubing; and a microtiter-based assay. The optimized procedure for the BI Petri dish system is described in this protocol and can be widely used for elucidation of potential function in interactions between diverse microbes and those plant and chemical volatiles emitted by bacteria that are most likely to mediate bacterial or plant responses to BVCs. We also describe a procedure for metabolome-based BVC profiling via dynamic (i.e., continuous airflow) or static headspace sampling using solid-phase microextraction (SPME). Using both these procedures, bacteria–bacteria communications and bacteria–plant interactions mediated by BVCs can be rapidly investigated (within 1–4 weeks).

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Acknowledgements

This research was supported by grants from the BioNano Health-Guard Research Center, funded by the Ministry of Science, ICT and Future Planning of Korea as a Global Frontier Project (Grant H-GUARD_2013M3A6B2078953); the Woo Jang-Choon Project (PJ01093904) of the Rural Development Administration (RDA); and KRIBB Initiative Program South Korea to C.-M.R. B.A. and J.-M.G. are supported by grant no.: ANR-10-LABX-62-IBEID (Investissement d'Avenir Program) and by Fondation pour la Recherche Médicale grant Equipe FRM DEQ20140329508. M.A.F. acknowledges funding received from the Alexander von Humboldt Foundation, Germany, and Cairo University Research Grant no. 31.

Author information

Author notes

    • Yong-Soon Park

    Present address: Institute of Environment Biosystem, Department of Biological Sciences, Chungnam National University, Daejeon, South Korea.

Affiliations

  1. Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt.

    • Mohamed A Farag
  2. Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, South Korea.

    • Geun Cheol Song
    • , Yong-Soon Park
    • , Soohyun Lee
    •  & Choong-Min Ryu
  3. Genetics of Biofilms Unit, Department of Microbiology, Institut Pasteur, Paris, France.

    • Bianca Audrain
    •  & Jean-Marc Ghigo
  4. Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA.

    • Joseph W Kloepper
  5. Department of Biosystems and Bioengineering, University of Science and Technology, Daejeon, South Korea.

    • Choong-Min Ryu

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Contributions

C.-M.R. and M.A.F. designed the experiments; M.A.F., G.C.S., S.L., B.A. and J.-M.G. performed the experiments; and M.A.F., C.-M.R., Y.-S.P., J.-M.G., B.A. and J.W.K. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Choong-Min Ryu.

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  1. 1.

    Supplementary Figure 1

    Chromatographic profiles of volatiles released from (a) B. subtilis PGPR strain GBO3 and (b) uninoculated medium.

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https://doi.org/10.1038/nprot.2017.023

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