Transcriptome Analysis of Environmental Pseudomonas Isolates Reveals Mechanisms of Biodegradation of Naphthenic Acid Fraction Compounds (NAFCs) in Oil Sands Tailings

Abstract

Naphthenic acid fraction compounds (NAFCs) are highly recalcitrant constituents of oil sands tailings. Although some microorganisms in the tailings can individually and synergistically metabolize NAFCs, the biochemical mechanisms that underpin these processes are hitherto unknown. To this end, we isolated two microorganisms, Pseudomonas protegens and Pseudomonas putida, from oils sands tailings and analyzed their transcriptomes to shed light on the metabolic processes employed by them to degrade and detoxify NAFCs. We identified 1048, 521 and 1434 genes that are upregulated in P. protegens, P. putida and a 1:1 co-culture of the strains, respectively. We subsequently enumerated the biochemical activities of enriched genes and gene products to reveal the identities of the enzymes that are associated with NAFC degradation. Separately, we analyzed the NAFCs that are degraded by the two pseudomonads and their 1:1 co-culture and determined the composition of the molecules using mass spectrometry. We then compared these molecular formulas to those of the cognate substrates of the enriched enzymes to chart the metabolic network and understand the mechanisms of degradation that are employed by the microbial cultures. Not only does the consortium behave differently than the pure cultures, but our analysis also revealed the mechanisms responsible for accelerated rate of degradation of NAFCs by the co-culture. Our findings provide new directions for engineering or evolving microorganisms and their consortia for degrading NAFCs more stably and aggressively.

Microbial degradation of naphthenic acids using constructed wetland treatment systems: metabolic and genomic insights for improved bioremediation of process-affected water

“…A few studies have reported that mixed indigenous microbial communities, rather than a single taxon, are more likely to promote the degradation of recalcitrant compounds due to complementary degradation steps or consumption of intermediate products in syntrophic relationships (communal metabolic efforts). For instance, mixed bacterial communities have been shown to degrade model NAs more rapidly than pure cultures (Demeter et al 2014 ), and Pseudomonas co-cultures degraded a higher quantity of NAs in OSPW than was observed in pure cultures (Chegounian et al 2021 ). Similarly, co-cultures of algae and microorganisms in inocula from an end pit lake degraded cyclohexaneacetic acid while the pure algal cultures or pure end pit lake inoculum did not (Yu et al 2019 ).…”