Transcriptomics and Lipidomics of the Environmental Strain Rhodococcus ruber Point out Consumption Pathways and Potential Metabolic Bottlenecks for Polyethylene Degradation

Abstract

Polyethylene (PE), one of the most prominent synthetic polymers used worldwide, is very poorly biodegradable in the natural environment. Consequently, PE represents by itself more than half of all plastic wastes. PE biodegradation is achieved through the combination of abiotic and biotic processes. Several microorganisms have been shown to grow on the surface of PE materials, among which are the species of the Rhodococcus genus, suggesting a potent ability of these microorganisms to use, at least partly, PE as a potent carbon source. However, most of them, if not all, fail to induce a clear-cut degradation of PE samples, showing that bottlenecks to reach optimal biodegradation clearly exist. To identify the pathways involved in PE consumption, we used in the present study a combination of RNA-sequencing and lipidomic strategies. We show that short-term exposure to various forms of PE, displaying different molecular weight distributions and oxidation levels, lead to an increase in the expression of 158 genes in a Rhodococcus representative, R. ruber. Interestingly, one of the most up-regulated pathways is related to alkane degradation and β-oxidation of fatty acids. This approach also allowed us to identify metabolic limiting steps, which could be fruitfully targeted for optimized PE consumption by R. ruber.

Microbial Ecotoxicology of Marine Plastic Debris: A Review on Colonization and Biodegradation by the “Plastisphere”

“…Interestingly, a recent study focused on soluble oxidized oligomers showed that 95% of these compounds were assimilated by a strain of Rhodococcus rhodochrous after 240 days of incubation (Eyheraguibel et al, 2017). The polymer is broken down into small oligomers of 600 Da incorporated in the cells by carriers belonging to the Major Facilitor Superfamily (MFS) or harboring ATP binding cassettes (ABC) (Gravouil et al, 2017). β-oxidation transforms oxidized carboxylic molecules (having an even number of carbon atoms) into acetyl coA or propionyl coA (if odd number of carbons).…”

“…Carboxylation of propionyl coA into succinyl coA is performed by propionyl-coA carboxylase. Gravouil et al (2017), propose identification of an overexpressed enzyme, when the bacteria find PE in the medium (Gravouil et al, 2017). Acetyl coA and succinyl coA enter the tricarboxylic acid (TCA) cycle (Figure 4).…”

“…Genetic evidence of PE biodegradation remains scarce in the literature, but preliminary work highlighted enzymes, transporters or genes that may be involved in this process (Gravouil et al, 2017). Alkane hydroxylase genes were found to play a central role in PE biodegradation for Pseudomonas sp.…”

Challenges with Verifying Microbial Degradation of Polyethylene

“…Several microorganisms have been shown to grow on the surface of PE materials, among which are the species of the genus Rhodococcus, suggesting a potent ability of these microorganisms to use, at least partly, PE as a carbon source (Table 2). However, most Rhodococcus species, if not all, fail to induce a clear-cut degradation of PE samples [82]. A number of recent papers have identified, isolated, and chararcterized PE degradation by marine bacteria [83,84], including Alcanivorax borkumensis [85].…”

Genome Sequencing and Comparative Transcriptomics Provide a Holistic View of 4-Nitrophenol Degradation and Concurrent Fatty Acid Catabolism by Rhodococcus sp. Strain BUPNP1

“…Oleaginous strains of Rhodococcus sp. tend to store intracellular carbon-rich lipid in nitrogen limiting conditions, for instance while degrading non-nitrogen containing hydrocarbons, such as phenol, polyethylene and anthracene (Yoneda et al, 2016; Goswami et al, 2017; Gravouil et al, 2017). As 4-NP degradation provides both carbon and nitrogen for growth, the absence of nitrogen limitation is likely responsible for the observed lipid deterioration in BUPNP1 growing on 4-NP.…”