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

Cravo-Laureau C, Duran R - Front Microbiol (2014)

Bottom Line: Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity.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.

View Article: PubMed Central - PubMed

Affiliation: Equipe Environnement et Microbiologie UMR IPREM 5254, Université de Pau et des Pays de l'Adour Pau, France.

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.

No MeSH data available.


Related in: MedlinePlus

Understanding microbial processes involved on hydrocarbon degradation in marine coastal sediments. The general scheme from scientific questions to microbial processes is presented together with the comparison of experimental approaches developed at different environmental complexity.
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Figure 2: Understanding microbial processes involved on hydrocarbon degradation in marine coastal sediments. The general scheme from scientific questions to microbial processes is presented together with the comparison of experimental approaches developed at different environmental complexity.

Mentions: We reviewed here recent approaches implemented in order to assess microbial processes involved on hydrocarbon degradation in marine coastal sediments. Microbiologists have developed several approaches, including more or less sophisticated experimental systems and in situ studies to answer the scientific questions regarding the microbial mechanisms that take place in response to oil and hydrocarbon contaminations. Figure 2 summarize the main advantage and limitations for the approach considered in addressing the scientific questions. Experimental ecology using experimental systems mimicking as close as possible the environmental conditions combine the advantages of lab controlled systems with the possibility of extrapolation to the real situation found in complex ecosystems. Such approaches offer the opportunity to conduct experiments in replicates, crucial advantage for robust statistical analyses as highlighted by Prosser (2010). The advent of next generation sequencing technologies combined with high-throughput methods assessing functionality (proteomics and metabolomics) has allowed the development of systems biology, a holistic approach to understand complex biological systems. However, because the sediments’ ecology in coastal areas is extremely complex, analysis using system biology tools at different environmental scales would be useful to elucidate microbial hydrocarbon degradation processes.


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

Cravo-Laureau C, Duran R - Front Microbiol (2014)

Understanding microbial processes involved on hydrocarbon degradation in marine coastal sediments. The general scheme from scientific questions to microbial processes is presented together with the comparison of experimental approaches developed at different environmental complexity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3921567&req=5

Figure 2: Understanding microbial processes involved on hydrocarbon degradation in marine coastal sediments. The general scheme from scientific questions to microbial processes is presented together with the comparison of experimental approaches developed at different environmental complexity.
Mentions: We reviewed here recent approaches implemented in order to assess microbial processes involved on hydrocarbon degradation in marine coastal sediments. Microbiologists have developed several approaches, including more or less sophisticated experimental systems and in situ studies to answer the scientific questions regarding the microbial mechanisms that take place in response to oil and hydrocarbon contaminations. Figure 2 summarize the main advantage and limitations for the approach considered in addressing the scientific questions. Experimental ecology using experimental systems mimicking as close as possible the environmental conditions combine the advantages of lab controlled systems with the possibility of extrapolation to the real situation found in complex ecosystems. Such approaches offer the opportunity to conduct experiments in replicates, crucial advantage for robust statistical analyses as highlighted by Prosser (2010). The advent of next generation sequencing technologies combined with high-throughput methods assessing functionality (proteomics and metabolomics) has allowed the development of systems biology, a holistic approach to understand complex biological systems. However, because the sediments’ ecology in coastal areas is extremely complex, analysis using system biology tools at different environmental scales would be useful to elucidate microbial hydrocarbon degradation processes.

Bottom Line: Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity.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.

View Article: PubMed Central - PubMed

Affiliation: Equipe Environnement et Microbiologie UMR IPREM 5254, Université de Pau et des Pays de l'Adour Pau, France.

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.

No MeSH data available.


Related in: MedlinePlus