Novel Insights into Bioremediation of Petroleum-Polluted Environments and Bacterial Catabolic Pathways

Abstract

Oil-derived hydrocarbons (HCs) are major environmental pollutants due to their persistence and high toxicity for biological systems (Prince, 2010; Logeshwaran et al., 2018). The clean-up of HC-polluted sites is a critical challenge to restore the affected ecosystems (Fuentes et al., 2014). The most frequently used bioremediation strategies in HC-polluted environments are biostimulation and bioaugmentation. Biostimulation promotes native microbial metabolism by adding nutrients or biosurfactants, while bioaug-mentation consists of the inoculation of autochthonous or allochthonous microorganisms (Fuentes et al., 2014; Macaya et al., 2019a). For the optimal development of a biostimulation strategy, the nutritional requirements and the physicochemical properties of each impacted matrix should be studied (Hazen, 2010; Prince, 2010). Bioaugmentation is employed mainly in contaminated environments that possess a low number of HC-degrading microorganisms (Brusseau and Maier, 2004; Fuentes et al., 2014, 2016). Bacterial strains from soil and marine environments belonging to the genera Achromobacter, Acinetobacter, Alcaligenes, Alcanivorax, Arthrobacter, Bacillus, Brevibacterium, Burkholderia, Cycloclasticus, Marinobacter, Nocardia, Oleispira, Paraburkholderia, Pseudomonas, Rhodococcus, Roseobacter, and Sphingomonas with the capability to degrade HCs have been described (Logeshwaran et al., 2018; Unimke et al., 2018; Macaya et al., 2019a). In aliphatic and aromatic HC catabolism, key enzymes are required to activate the contaminants for further degradation. Different alkane hydroxylases are required to oxidize short-, medium-, and long-chain alkanes (Rojo, 2009; Gibu et al., 2019). Bacterial aromatic degradation involves two steps: the activation of the aromatic ring, and the subsequent cleavage reaction. Aerobic catabolic pathways initially modify the aromatic ring by mono- or dioxygenases, incorporating molecular oxygen to the HC (Seeger et al., 2001; Wang et al., 2017). Aerobic degradation of aromatic compounds is catalyzed by bacterial multicomponent monooxygenases (BMMs) and ring-hydroxylating dioxygenases (RHDs). The aromatic HCs are funneled through several peripheral catabolic pathways into diverse central pathways (Fuentes et al., 2014; El-Naas et al., 2014). Bacterial polycyclic aromatic hydrocarbon (PAH) degradation is mainly achieved by PAH-RHDs, which possess a low substrate specificity, enabling the oxidation of a wide spectrum of aromatic compounds (Notomista et al., 2003; Parales et al., 2008; Wang et al., 2017). In addition, hybrid aerobic pathways are involved in the bacterial degradation of aromatic compounds such as toluene and ethylbenzene (Ismail and Gescher, 2012; Grishin and Cygler, 2015). Anaerobic degradation of HCs has been less characterized than the aerobic catabolic routes. Anoxic activation of the aromatic ring or the aliphatic chain occurs mainly by addition of fumarate, carboxylation, or hydroxylation. In anaerobic pathways, HCs are commonly transformed into acetyl-CoA and CO2. In the absence of oxygen, HC degradation in bacteria is linked to the use of nitrate, iron, sulfate, and other compounds as electron acceptors (Kniemeyer et al., 2003; Fuchs et al., 2011; Meckenstock et al., 2016; Rabus et al., 2016; Boll and Estelmann, 2020). The microbial communities during petroleum pollution events and bioremediation have been studied to characterize their dynamics and understand the roles of main microbial members involved in HC biodegradation (Allen et al., 2007; Fuentes et al., 2016; Mahjoubi et al., 2018; Franzetti et al., 2020). The characterization of novel hydrocarbonoclastic microorganisms and the elucidation of their aliphatic and aromatic HC catabolic pathways are required to understand the complexities of the degradation of HCs and to establish novel bioremediation processes for specific polluted sites towards a more sustainable development. This chapter discusses the main bioremediation strategies for petroleum-polluted sites, and describes the key bacterial enzymes and catabolic pathways for the degradation of aliphatic and aromatic HCs.