Microbial Ecogenomics: Elucidation of key community structures and functions in bioremediation processes in situ

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Background

Microorganisms are a boundless source of biochemistry and metabolic potential, but their infamous interactions with humans (e.g., pathogens and disease) overshadow some of their most beneficial capabilities (e.g., nutrient cycling or beneficial associations with higher organisms). One of the well-recognized but understudied features at the community-function level is the ability to detoxify contaminants in the environment. The identification of predominant populations and biomarkers to evaluate biogeochemical capacity of a given system is crucial for the evaluation and prediction of remedial strategies in the field. Populations within the community respond differently to disturbances, and it is the cumulative effect of multiple populations, directly or indirectly connected, that facilitates the net movement of energy and nutrients through an ecosystem. For many years, bioremediation research was delineated in terms of the contaminant, organic or inorganic, due to the kind of microorganisms and functions selected. This separation is now finding common ground due to advances in microbial ecology knowledge and analytical technologies available (omics) that constitutes an exciting common bridge that joins the different interdisciplinary expertise observed in the bioremediation field. Molecular microbial ecology approaches, namely the emphasis on the meta-omic content, as well as population distributions at different levels of resolution, have inspired the application of these techniques in model ecosystems, allowing high-throughput characterization of microorganisms in situ, as well as under environmentally-relevant conditions, to gain insight into physiological responses (i.e., structure-function relationships). However, the ultimate challenge is to elucidate environmentally-relevant community structures and the possible associations with detected functions in order to attempt translational research development for applications in environmental microbiology, thus guiding and improving the decision-making process for different types of field sites and contaminants. The focus of the Research Topic we are presenting here is to document cutting-edge contributions on the application of eco-genomics to explore, understand and foresee a more precise and better manipulation and prediction of the microbial communities present at or applied to contaminated field sites, constituting an enriching forum where the latest outstanding advances in microbial bioremediation research will be disseminated. We encourage researchers in the field to communicate and integrate recent state-of-the-art microbial ecogenomics breakthroughs related to bioremediation of organic and/or inorganic contaminants.

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