Project objectives:
Biodegradation of hydrocarbons is a complex process, and a vast amount of hydrocarbon-degradation capacity remains to be exploited in the bioremediation
of extensive areas of contaminated land throughout Europe and the world. DECAPAGE proposes to explore the microbial diversity of coastal microbial communities
for hydrocarbon compounds degradation. Emphasis will be largely on hydrocarbon degrading microbial consortia adapted to oxic/anoxic oscillations with
a special focus on anoxic metabolisms. This proposal has the ambition to characterize the chemical and microbiological aspects involved on hydrocarbons
biodegradation. It is based on innovative concepts and the use of the latest technologies. Their combination will allow the description of the dynamic adaptation
of bacterial communities to the presence of petroleum and how the oxygenation and redox oscillations affect their functioning. The DECAPAGE proposal seeks
to provide : (1) novel analytical approaches for the identification of hydroxylated metabolites of HC biodegradation and evaluation of the degradation of
high molecular weight petroleum fraction; (2) fingerprint of the evolution of metals complexes during biodegradation processes; (3) novel information
on the adaptation of bacterial communities to petroleum under oxygen and redox oscillations; (4) novel insights on the structure/function relationship
of HC-degrading bacterial communities; (5) novel genetic-information for biodegradation processes and hydrocarbon response; (6) novel insights on the
involvement of integrons in the adaptation of bacterial communities to petroleum; (7) Ultimately the newly developed tools, products and know-how will be
disseminated to the end-user community in collaboration with our partner cedre involved in oil spill cleanup management advertising. The overall objectives
of DECAPAGE are (1) Understand and predict hydrocarbon biodegradation rate and fate, and how they are influenced by oxygen and redox oscillations; (2) Characterise
the metabolites present in hydrocarbon-contaminated incubations (hydrocarbon-epimetabolome) in order to identify biomarkers and understand the flow
of carbon from hydrocarbons to CO2; (3) Understand and quantify the molecular genetic diversity of hydrocarbon-degrading microbes in contaminated microcosms
and identify the active prokaryote hydrocarbon-degrading microbes and their expressed genes; (4) Isolate novel hydrocarbon-degrading SRP; (5) Capture
and express novel genes involved in HC biodegradation, as well as genes involved in the whole-microbe response to hydrocarbons and determine the role of lateral
gene transfer in hydrocarbon-contaminated environments and identifyintegron-based genes (6) Develop, test and apply tools for molecular-biological
detection and quantification of hydrocarbon degrading microbes The expected results from DECAPAGE will provide a quantum leap in our fundamental understanding
of the ecology and genetic diversity of hydrocarbon-contaminated environments that will underpin and direct future bioremediation efforts. This knowledge
together with new tools to enhance (e.g. designed consortia with appropriate oxygenation regime), monitor (e.g. metabolites and molecular biological biomarkers)
bioremediation will be invaluable for numerous end-users including regulators, contaminated-land owners and remediation companies. The wider scientific
community will benefit additionally from protocols and concepts developed in DECAPAGE. Overall, we will transfer concepts and enhanced hydrocarbon-degradation
strategies to the end-user community via a symposium and advanced workshop, as well as raising awareness through diverse channels.
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Project
Summary:
Coastlines are subjected to a variety of pollution injuries from both sides, from the sea, predominantly by crude oil from shipping and offshore mining and
from the land, principally through agricultural practices, urban waste waters and industrial activities. Hydrocarbon compounds and crude oil derived products
are the most abundant pollutants. The damaging effects of such pollutants to the environment and human health coupled with new societal pressures make the
restoration of oil-contaminated areas an urgent priority. Although they are frequently found at unacceptably high concentrations, hydrocarbons are natural
compounds, and the collective catabolic diversity of microorganisms means that they can be biodegraded resulting in harmless products, thus making bioremediation
an attractive option. The in situ treatment methods, which are particularly useful in remote areas where waste management and/or disposal are an issue, are
applied to accelerate natural microbial processes that act on the oil. These methods include physical treatments such as mixing (also known as tilling or aeration),
chemical and biological treatments using respectively chemical agents to alter the physical or chemical properties of the oil and nutrient enhancement/bioremediation.
Indeed, studies have demonstrated hydrocarbon biodegradation capacities in coastal sediments (e.g. Duran and Goñi, 2010), but our understanding of the
particular microbes involved, their genetic and enzymatic capacities, their interactions, as well as their functioning in the changing redox conditions,
is largely unknown. Thus, DECAPAGE will focus on microbial communities inhabiting coastal sediments, developing and applying a suite of integrated cross-disciplinary
approaches to explore the hydrocarbon degradation capacities, understand the ecology of sediment ecosystems, particularly how the microbial communities
degrade and/or detoxify hydrocarbons and how they are affected by the redox oscillations and alternating oxygen supply. Recently, we showed that the effect
of petroleum on bacterial communities is enhanced by the presence of burrowing organisms (Stauffert et al, 2010). Indeed, the reworking activity deeply changes
the bacterial communities but the overall degradation efficiency is not affected highlighting the functional redundancy involved in hydrocarbons degradation.
These results rise up several important questions to understand the mechanisms underpinning the bacterial communities structuring: How microbial communities
respond, adapt and degrade petroleum compounds? How the fluctuations of environmental parameters, particularly oxygen oscillations, influence this process?
The DECAPAGE project aims precisely to answer these questions characterizing in depth these bacterial communities and comparing them with those resulting
from mechanical reworking that correspond to a mitigation strategy implemented during oil spills. A special interest will be made to the anoxic populations
that could be strongly affected by the oxygen oscillation. At the academic point of view, the expected results will allow to understand the adaptation mechanisms
driving the reorganization of bacterial communities in response to petroleum. This will help to determine the optimal oxygenation regimes for efficient
petroleum degradation, crucial information for the implementation of mitigation strategies.
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