Abstract
The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.
Highlights
Various hydrocarbon (HC) compounds, derived from crude oil (n-alkanes; other aliphatics; mono, di- and polyaromatic compounds; heterocyclic aromatics), are the most abundant hazardous organic wastes which are mostly released during the extraction processes, drilling of wells, transportation and unsuitable storage of oil, even in the immediate vicinity of filling stations (Lim et al, 2016; Bacosa et al, 2018; Xu et al, 2018)
The multi-omics era provides a multitude of opportunities for the examination of individual microbes, microbial communities, their metabolism and interactions
Genomics and metagenomics characterize the metabolic potential of the microorganisms; we can identify new microbes in a community and elucidate new pathways and genes which are responsible for hydrocarbon biodegradation
Summary
Various hydrocarbon (HC) compounds, derived from crude oil (n-alkanes; other aliphatics; mono-, di- and polyaromatic compounds; heterocyclic aromatics), are the most abundant hazardous organic wastes which are mostly released during the extraction processes, drilling of wells, transportation and unsuitable storage of oil, even in the immediate vicinity of filling stations (Lim et al, 2016; Bacosa et al, 2018; Xu et al, 2018). Several recent review articles have summarized the microorganisms and metabolic pathways involved in the anaerobic hydrocarbon biodegradation. The current knowledge about anaerobic hydrocarbon-degrading microorganisms, metabolic pathways, microbial interactions in the multi-omics era is overviewed. Ralf Rabus and colleagues elucidated the catabolic network of Aromatoleum aromaticum EbN1 during aromatics biodegradation applying more than 50 growth conditions They identified 20 new proteins participating in the peripheral pathway of anaerobic aromatics mineralization and tested the effect of environmental conditions such as carbon limitation or solvent toxicity on the proteome of A. aromaticum EbN1 (Rabus et al, 2014). Buccitelli and Selbach argue in their recent review that integrated transcriptomics and proteomics should become a common integrated approach and quantifying protein and mRNA levels (which are the result of synthesis and degradation) would provide a complete picture on gene expression dynamics (Buccitelli and Selbach, 2020). We discuss further examples and techniques in the following chapters
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