New Insights into the Biodegradation of Organic Contaminants in Subsurface Ecosystems: Approaches and Achievements of the Multiomics Era

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Background

Contamination of the subsurface ecosystems with organic compounds originating from the petrochemical, pharmaceutical and agricultural industries is a persistent and growing problem globally. Due to the world’s population growth, more and more complex organic molecules are released to the environment, threatening pristine drinking water reservoirs or soil health.

Although much is known about the microorganisms and metabolic pathways taking part in the biodegradation of the most prevalent petroleum hydrocarbons e.g. alkanes and aromatic hydrocarbons, old industrial or military-originated subsurface contaminations still present a major challenge to the researchers. Therefore, the application of cutting edge molecular ecological methods is important to better understand the environmental fate of these contaminants in different subsurface environments. Moreover, contaminants of emerging concern (CEC), such as pharmaceuticals, personal or household care products; 1,4-dioxane and poly- and perfluoroalkyl substances (PFASs), or agrochemicals such as atrazine and its alternatives (e.g. terbuthylazine) also present an important focus of research, since molecular mechanisms of their biotransformation remain elusive, underscoring the importance of a more in-depth research to uncover the fundamentals and regulatory factors. Furthermore, identifying novel microorganisms involved in the biodegradation of organic compounds begins to get more attention as several recent studies have demonstrated that rare microbial species may play an important role in biodegradation of conventional organic pollutants.

Despite the enormous amount of data on organic contaminant degrading microbial communities and strains provided by genomic and metagenomic studies, there are still several questions that remain unanswered due to the limitations of using these techniques alone. Recent advancements of “omic” technologies and applications, such as the development of genome-resolved metagenomics, made it possible to reveal the metabolic potentials of the uncultivated majority of microbes. Coupling this method with cultivation independent approaches such as stable isotope probing (SIP) and/or magnetic-nanoparticle mediated isolation (MMI) can open the door to gain a deeper insight into the diversity and function of contaminant degrading bacteria. It is possible to study the degradation of contaminants with a low assimilation rate, or to identify microbial subpopulations playing role in the degradation but having remained hidden so far due to their low growth rate. For instance, such studies have already revealed (i) the role of Rhodoferax-related bacteria in the degradation of sulfolane, (ii) PAH (polycyclic aromatic hydrocarbons)-degraders in chronically polluted seawater, (iii) anaerobic hydrocarbon-degrading capability of members of the candidate phylum 'Atribacteria', and (iv) bacteria degrading toluene microaerobically in polluted aquifer.

Overall, this Research Topic intends to cover up-to-date research on the biodegradation of organic subsurface (soil, groundwater, sediment) contaminants, applying multiomics approaches alone or in the combination with other molecular ecological methods.

The Research Topic editors won’t accept descriptive manuscripts, which report only on the diversity of microbial communities of contaminated environments. Besides papers describing original research, we encourage the submission of reviews and mini-reviews as well.

Specifically, this Research Topic welcomes contributions focusing on the following areas:

• Multiomics analysis of subsurface microbial communities taking part in the biodegradation of organic contaminants.
• Identification and characterization of novel microorganisms which play direct role in the degradation of subsurface organic contaminants under environmental or laboratory conditions.
• Enrichment studies aiming to reveal subsurface originated microbial communities taking part in the degradation of the subsurface organic contaminants.
• Genomic and transcriptomic analysis of organic contaminant degrading bacterial strains to uncover degradation pathways of subsurface xenobiotic compounds.
• Genomic adaptation mechanisms of subsurface microorganisms for organic contaminant degradation.
• Innovation in bioremediation strategies applicable to mitigate subsurface pollutants.

Keywords: biodegradation, organic contaminants, subsurface contamination, metagenomics, genome-resolved metagenomics, multiomics approaches

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