Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics’era

Abstract

Coastal marine sediments, where important biological processes take place, supply essential ecosystem services. By their location, such ecosystems are particularly exposed to human activities as evidenced by the recent Deepwater Horizon disaster. This catastrophe revealed the importance to better understand the microbial processes involved on hydrocarbon degradation in marine sediments raising strong interests of the scientific community. During the last decade, several studies have shown the key role played by microorganisms in determining the fate of hydrocarbons in oil-polluted sediments but only few have taken into consideration the whole sediment’s complexity. Marine coastal sediment ecosystems are characterized by remarkable heterogeneity, owning high biodiversity and are subjected to fluctuations in environmental conditions, especially to important oxygen oscillations due to tides. Thus, for understanding the fate of hydrocarbons in such environments, it is crucial to study microbial activities, taking into account sediment characteristics, physical-chemical factors (electron acceptors, temperature), nutrients, co-metabolites availability as well as sediment’s reworking due to bioturbation activities. Key information could be collected from in situ studies, which provide an overview of microbial processes, but it is difficult to integrate all parameters involved. Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity. To overcome these lacks, strategies have been developed, by creating experiments as close as possible to environmental conditions, for studying natural microbial communities subjected to oil pollution. We present here a review of these approaches, their results and limitation, as well as the promising future of applying “omics” approaches to characterize in-depth microbial communities and metabolic networks involved in hydrocarbon degradation. In addition, we present the main conclusions of our studies in this field.

Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment

“…Although PAH microbial degradation mechanisms are well known, the ecology of microbial communities facing the presence of PAHs in marine environments requires further elucidation due to the myriad of factors that can contribute to and/or affect microbial community structure in different polluted environments (Cravo-Laureau and Duran 2014; Duran et al. 2015c).…”

“…2012; Cravo-Laureau and Duran 2014; McGenity 2014; Acosta-González and Marqués 2016). Here we focus mainly on the most recent oil spill, the Deepwater Horizon oil spill, which largely increased the input of PAHs in the Gulf of Mexico (Reddy et al.…”

Input of organic matter enhances degradation of weathered diesel fuel in sub-tropical sediments

“…The effectiveness of hydrocarbon removal (degradation) in sediments by microbial bioremediation processes depends on several environmental factors, including temperature, soil moisture, nutrient availability, and pH (Alexander, 1999;Horel and Schiewer, 2009;Sutton et al, 2013). The presence of naturally occurring microbial communities capable of metabolizing hydrocarbons as a carbon and/or energy source will also be an essential factor for hydrocarbon mineralization (Cravo-Laureau and Duran, 2014;Kostka et al, 2011).…”

Changes of benthic bacteria and meiofauna assemblages during bio-treatments of anthracene-contaminated sediments from Bizerta lagoon (Tunisia)

“…In a previous study, we demonstrated that biological top-down control by meiofauna was more effective in shaping bacterial community structure than the selective pressure exerted by a PAH cocktail (Louati et al 2013b). The benthic meiofauna strongly influence microbial structure (Stauffert et al 2013;Cravo-Laureau and Duran 2014), particularly functional groups such as sulfatereducing (Stauffert et al 2014a) and denitrifying (Stauffert et al 2014b) microorganisms.…”

“…The meiofauna/microorganisms interactions, including trophic and non-trophic interactions (De Mesel et al 2003Moens et al 2005), play a major role in the overall carbon fluxes (Meysman et al 2005;Van Oevelen et al 2006) and organic matter mineralization (Aller and Aller 1992;Alkemade et al 1992). We recently demonstrated that the benthic meiofauna influenced the prokaryotic hydrocarbon-degrading community structure and composition without affecting the overall hydrocarbon-degradation capacity (Stauffert et al 2013;2014;Cravo-Laureau and Duran 2014). The presence of pollutants such as hydrocarbon compounds may disrupt the balance of sediments ecosystem, affecting particularly microbial and meiofaunal communities (Louati et al 2013a, b).…”