New Hydrocarbon Degradation Pathways in the Microbial Metagenome from Brazilian Petroleum Reservoirs

Abstract

Current knowledge of the microbial diversity and metabolic pathways involved in hydrocarbon degradation in petroleum reservoirs is still limited, mostly due to the difficulty in recovering the complex community from such an extreme environment. Metagenomics is a valuable tool to investigate the genetic and functional diversity of previously uncultured microorganisms in natural environments. Using a function-driven metagenomic approach, we investigated the metabolic abilities of microbial communities in oil reservoirs. Here, we describe novel functional metabolic pathways involved in the biodegradation of aromatic compounds in a metagenomic library obtained from an oil reservoir. Although many of the deduced proteins shared homology with known enzymes of different well-described aerobic and anaerobic catabolic pathways, the metagenomic fragments did not contain the complete clusters known to be involved in hydrocarbon degradation. Instead, the metagenomic fragments comprised genes belonging to different pathways, showing novel gene arrangements. These results reinforce the potential of the metagenomic approach for the identification and elucidation of new genes and pathways in poorly studied environments and contribute to a broader perspective on the hydrocarbon degradation processes in petroleum reservoirs.

Deep-Sea Biofilms, Historic Shipwreck Preservation and the Deepwater Horizon Spill

“…Mason et al (2014) demonstrated that alcohol dehydrogenase, including butanol dehydrogenase genes, were frequently observed in a Colwellia phylotype enriched during the spill. Alcohol dehydrogenases are enzymes that are crucial for the degradation of hydrocarbon compounds, and their elevation at Anona and U-166 may imply that biodegradation of residual oil compounds was still occurring at these contaminated sites (Sierra-García et al, 2014).…”

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

“…Metagenomic, metatranscriptomic, metaproteomic, and metabolomic analyses of complex communities are allowing for a deeper understanding of how microbial communities interact with each other, the environment and the organisms around them (Villas-Boas and Bruheim, 2007; Bell et al, 2014; Kaul et al, 2016). It is easy to envision implementing metagenomic tools in the field of PHC remediation in order to: pre-assess the biodegradative capacity of an environment, monitor in situ biodegradation performance, assist with the selection of inoculants, identify new biodegradative pathways, and eventually to guide efforts in synthetic biology to develop new enzymatic activities (Baek et al, 2007; Yergeau et al, 2012; Uhlik et al, 2013; Dellagnezze et al, 2014; Sierra-Garcia et al, 2014). Having said this, there are still that need to be faced as the technologies mature and, for more information, the reader is referred to the following reviews (Desai et al, 2010; Hazen et al, 2013; Techtmann and Hazen, 2016).…”

Microbial Genes Involved in the Aromatic Compound Degradation Deciphered Through Metagenomics Analysis of Industrial Wastewater.

“…The abundance of functional genes in different stage revealed that the microbial community were metabolized by diverse type of benzoate-containing compounds [27]. The pervious study revealed that the pathways of benzoate degradation in bacteria occurs either through anaerobic or aerobic processes and with the mechanism of degradation via CoA ligation or via hydroxylation [29]. The third hybrid pathway for benzoate degradation occurs by introducing oxygen to activate the aromatic ring for cleavage, this pathway was previously identi ed as catabolism of benzoate and mineralization of aromatic compounds by [30] [31].…”

“…The third hybrid pathway for benzoate degradation occurs by introducing oxygen to activate the aromatic ring for cleavage, this pathway was previously identi ed as catabolism of benzoate and mineralization of aromatic compounds by [30] [31]. The utilization of this pathway as a degradation of xenobiotics may help for microorganism to survive in less or uctuating oxygen concentration in waste water e uent [29]. The different species of Rhodopseudomonas, Pseudomonas, and Acinetobacter are reported by many researchers as the potential for degradation of benzoate, phenol, and PAH family compounds group of compounds.…”