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2017-06-06 - Colloque/Présentation - poster - Anglais - 1 page(s)

Beraud Mélanie , Giambarresi Giuseppe , Wattiez Ruddy , Gillan David , "SWATH-MS increases coverage in metaproteomics: Application to a Zn-stressed marine synthetic community." in BAGECO 14, Aberdeen, Ecosse, 2017

  • Codes CREF : Biochimie (DI3112), Biologie moléculaire (DI3111), Biologie (DI3100), Microbiologie et protistologie [bacteriol.,virolog.,mycolog.] (DI3130), Ecologie (DI3123)
  • Unités de recherche UMONS : Protéomie et Microbiologie (S828)
  • Instituts UMONS : Institut des Biosciences (Biosciences)
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Abstract(s) :

(Anglais) SWATH-MS increases coverage in metaproteomics: Application to a Zn-stressed marine synthetic community. Beraud Mélanie, Giuseppe Giambarresi, Ruddy Wattiez and David C. Gillan Introduction Microbial communities in nature are often complex and may feature hundreds of species. In vitro synthetic microbial ecosystems may therefore be designed in order to reduce complexity. These synthetic microbial consortia, composed of only a few cultivated species, are of growing interest in microbial ecology because they offer a powerful approach whereby biological questions can be addressed in a well-defined framework. However, when synthetic microbial ecosystems are studied by metaproteomics and that equitability is low, rare species are not visible. This is a problem as rare species may have important functions in the community. Objectives The aim of the present research was to show that the SWATH-MS metaproteomic approach may be used to gain insight in the activity of rare bacterial species in a synthetic community. Methods Nine different bacterial species were cultivated separately then mixed in identical proportions. The mixed community was then grown in a simulated marine environment that was stressed by Zn at 0.5 mM. After 28-days, the structure of the synthetic community was determined by quantitative PCR (Q-PCR). Metaproteomics, using a classical data-dependent LC-MS/MS approach was used. The recently developed SWATH approach (sequential window acquisition of all theoretical mass spectra) was used in parallel. Results After 28 days, Q-PCR indicated that the synthetic community was composed of abundant (Pseudomonas putida and Shewanella baltica) and rarer species (Cupriavidus metallidurans, Escherichia coli, Methylibium petroleiphilum). P. putida was so abundant (ca. 90% of the community) that the classical metaproteomic approach failed (only P. putida was visible). However, using the SWATH approach, the detection of rarer species became possible. For instance, proteins combating oxidative stress damages were visible and could be quantified. Conclusion This work describes the first use of SWATH-MS in a synthetic marine community with promising results. Contrary to the classical metaproteomic approach, we were able to visualize a part of the proteome in rarer species and analyze their response to environmental metallic stressors.