Comparative metaproteomics to assess environmental changes: The combined effects of oil, sunlight and dispersant on marine microbial communities

Unraveling the complex structure and functioning of microbial communities is essential to accurately predict the impact of perturbations and/or environmental changes. From all molecular tools available today to resolve the dynamics of microbial communities, metaproteomics stands out, allowing the establishment of phenotype-genotype linkages. Comparative metaproteomics aims at investigating protein expression from complex microbial communities and provides direct evidence of physiological and metabolic regulations. Despite its rapid development, this technology has faced many technical challenges that hampered its potential power. The first objective of this study is to provide a step-by-step guideline of the marine metaproteomics workflow. Our recent advances made on marine metaproteomics from water sampling and protein isolation to database searching and protein annotation will be presented.

Using the Deepwater Horizon (DWH) spill as a case study, we performed comparative metaproteomics to decipher the impact of oil spill on marine microbial communities. This is the first time that a robust metaproteomic workflow is used to assess the combined effect of oil, dispersant (Corexit) and solar radiation on the functioning of marine microbial communities. Surface water sampled in the Gulf of Mexico was incubated with amendments of crude oil, and/ or dispersant, with or without UV radiation, leading to 8 mesocosms. Microbial communities (< 0.2 µm) were analyzed at T0 and Tf, both in terms of the community structure and functioning using shotgun gel-free metaproteomics. The resulting metaproteomes provided different outcomes for each condition in terms of (i) total protein numbers, (ii) taxonomic structures, and (iii) protein functions. Our study demonstrates that the combination of solar radiation and dispersant alter the functioning of microbial communities exposed to oil. To what extent marine bacteria are impacted by contaminants, how this influences their population structure and functioning, and impinges on species interactions are presented and discussed in this study.