Culturing oil sands microbes as mixed species communities enhances ex situ model naphthenic acid degradation

How to deal with xenobiotic compounds through environment friendly approach?

Every year, a huge amount of lethal compounds, such as synthetic dyes, pesticides, pharmaceuticals, hydrocarbons, etc. are mass produced worldwide, which negatively affect soil, air, and water quality. At present, pesticides are used very frequently to meet the requirements of modernized agriculture. The Food and Agriculture Organization of the United Nations (FAO) estimates that food production will increase by 80% by 2050 to keep up with the growing population, consequently pesticides will continue to play a role in agriculture. However, improper handling of these highly persistent chemicals leads to pollution of the environment and accumulation in food chain. These effects necessitate the development of technologies to eliminate or degrade these pollutants. Degradation of these compounds by physical and chemical processes is expensive and usually results in secondary compounds with higher toxicity. The biological strategies proposed for the degradation of these compounds are both cost-effective and eco-friendly. Microbes play an imperative role in the degradation of xenobiotic compounds that have toxic effects on the environment. This review on the fate of xenobiotic compounds in the environment presents cutting-edge insights and novel contributions in different fields. Microbial community dynamics in water bodies, genetic modification for enhanced pesticide degradation and the use of fungi for pharmaceutical removal, white-rot fungi's versatile ligninolytic enzymes and biodegradation potential are highlighted. Here we emphasize the factors influencing bioremediation, such as microbial interactions and carbon catabolism repression, along with a nuanced view of challenges and limitations. Overall, this review provides a comprehensive perspective on the bioremediation strategies.

Low adsorption affinity of athabasca oil sands naphthenic acid fraction compounds to a peat-mineral mixture

Much of the toxicity in oil sands process-affected water in Athabasca oil sands tailings has been attributed to naphthenic acids (NAs) and associated naphthenic acid fraction compounds (NAFCs). Previous work has characterized the environmental behaviour and fate of these compounds, particularly in the context of constructed treatment wetlands. There is evidence that wetlands can attenuate NAFCs in natural and engineered contexts, but relative contributions of chemical, biotic, and physical adsorption with sequestration require deconvolution. In this work, the objective was to evaluate the extent to which prospective wetland substrate material may adsorb NAFCs using a peat-mineral mix (PMM) sourced from the Athabasca Oil Sands Region (AOSR). The PMM and NAFCs were first mixed and then equilibrated across a range of NAFC concentrations (5-500 mg/L) with moderate ionic strength and hardness (∼200 ppm combined Ca2+ and Mg2+) that approximate wetland water chemistry. Under these experimental conditions, low sorption of NAFCs to PMM was observed, where sorbed concentrations of NAFCs were approximately zero mg/kg at equilibrium. When NAFCs and PMM were mixed and equilibrated together at environmentally relevant concentrations, formula diversity increased more than could be explained by combining constituent spectra. The TOC present in this PMM was largely cellulose-derived, with low levels of thermally recalcitrant carbon (e.g., lignin, black carbon). The apparent enhancement of the concentration and diversity of components in PMM/NAFCs mixtures are likely related to aqueous solubility of some PMM-derived organic materials, as post-hoc combination of dissolved components from PMM and NAFCs cannot replicate enhanced complexity observed when the two components are agitated and equilibrated together.

Selenite bioreduction by a consortium of halophilic/halotolerant bacteria and/or yeasts in saline media

Selenium oxyanions are released into environments by natural and anthropogenic activities and are present in agricultural and glass manufacturing wastewater in several locations worldwide. Excessive amounts of this metalloid have adverse effects on the health of living organisms. Halophilic and halotolerant microorganisms were selected for selenium oxyanions remediation due to presence of significant amount of salt in selenium-containing wastewater. Effects of aeration, carbon sources, competitive electron acceptors, and reductase inhibitors were investigated on SeO₃^2- bio-removal. Additionally, NO₃^--containing wastewater were exploited to investigate SeO₃^2- remediation in synthetic agricultural effluents. The results showed that the SeO₃^2- removal extent is maximum in aerobic conditions with succinate as a carbon source. SO₄^2- and PO₄^3- do not significantly interfere with SeO₃^2- reduction, while WO₄^2- and TeO₃^2- decrease the SeO₃^2- removal percentage (up to 35 and 37%, respectively). Furthermore, NO₃^- had an adverse effect on SeO₃^2- biotransformation by our consortia. All consortia reduced SeO₃^2- in synthetic agricultural wastewaters with a 45-53% removal within 120 h. This study suggests that consortia of halophilic/halotolerant bacteria and yeasts could be applied to treat SeO₃^2--contaminated drainage water. In addition, sulphates, and phosphates do not interfere with selenite bioreduction by these consortia, which makes them suitable candidates for the bioremediation of selenium-containing wastewater.

Use of Microbial Consortia in Bioremediation of Metalloid Polluted Environments

Metalloids are released into the environment due to the erosion of the rocks or anthropogenic activities, causing problems for human health in different world regions. Meanwhile, microorganisms with different mechanisms to tolerate and detoxify metalloid contaminants have an essential role in reducing risks. In this review, we first define metalloids and bioremediation methods and examine the ecology and biodiversity of microorganisms in areas contaminated with these metalloids. Then we studied the genes and proteins involved in the tolerance, transport, uptake, and reduction of these metalloids. Most of these studies focused on a single metalloid and co-contamination of multiple pollutants were poorly discussed in the literature. Furthermore, microbial communication within consortia was rarely explored. Finally, we summarized the microbial relationships between microorganisms in consortia and biofilms to remove one or more contaminants. Therefore, this review article contains valuable information about microbial consortia and their mechanisms in the bioremediation of metalloids.

Unraveling the complex regulatory networks in biofilm formation in bacteria and relevance of biofilms in environmental remediation

Biofilms are assemblages of bacteria embedded within a matrix of extracellular polymeric substances (EPS) attached to a substratum. The process of biofilm formation is a complex phenomenon regulated by the intracellular and intercellular signaling systems. Various secondary messenger molecules such as cyclic dimeric guanosine 3',5'-monophosphate (c-di-GMP), cyclic adenosine 3',5'-monophosphate (cAMP), and cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP) are involved in complex signaling networks to regulate biofilm development in several bacteria. Moreover, the cell to cell communication system known as Quorum Sensing (QS) also regulates biofilm formation via diverse mechanisms in various bacterial species. Bacteria often switch to the biofilm lifestyle in the presence of toxic pollutants to improve their survivability. Bacteria within a biofilm possess several advantages with regard to the degradation of harmful pollutants, such as increased protection within the biofilm to resist the toxic pollutants, synthesis of extracellular polymeric substances (EPS) that helps in the sequestration of pollutants, elevated catabolic gene expression within the biofilm microenvironment, higher cell density possessing a large pool of genetic resources, adhesion ability to a wide range of substrata, and metabolic heterogeneity. Therefore, a comprehensive account of the various factors regulating biofilm development would provide valuable insights to modulate biofilm formation for improved bioremediation practices. This review summarizes the complex regulatory networks that influence biofilm development in bacteria, with a major focus on the applications of bacterial biofilms for environmental restoration.

Detection of naphthenic acid uptake into root and shoot tissues indicates a direct role for plants in the remediation of oil sands process-affected water

Bitumen extraction from surface-mined oil sands deposits results in the accumulation of large volumes of oil sands process-affected water (OSPW). Naphthenic acids (NAs) are primary contributors to OSPW toxicity and have been a focal point for the development of OSPW remediation strategies. Phytoremediation is an approach that utilizes plants and their associated microbes to remediate contaminants from soil and groundwater. While previous evidence has indicated a role for phytoremediation in OSPW treatment through the transformation and degradation of NAs, there are no reports that demonstrate the direct uptake of NAs into plant tissue. Using NAs labelled with ¹⁴C radioisotopes (¹⁴C-NAs) paired with whole-plant autoradiography, we show that NAs representing aliphatic (linear), single-ring, and diamondoid compounds were effectively removed from hydroponic solution and OSPW-treated soil by sandbar willow (Salix interior) and slender wheatgrass (Elymus trachycaulus) and their associated microbiomes. The NA-derived ¹⁴C label accumulated in root and shoot tissues of both plant species and was concentrated in vascular tissue and rapidly growing sink tissues, indicating that ¹⁴C-NAs or their metabolic derivatives were incorporated into physiological processes within the plants. Slender wheatgrass seedlings grown under axenic (sterile) hydroponic and soil conditions also effectively removed all ¹⁴C-NAs, including a highly stable diamondoid NA, demonstrating that plants can directly take up simple and complex NAs without the assistance of microbes. Furthermore, root and shoot tissue fractionation into major biomolecule groups suggests that NA-derived carbon is allocated toward biomolecule synthesis rapidly after NA treatment. These findings provide evidence of plant-mediated uptake of NAs and support a direct role for plants and their associated microbes in the development of future large-scale OSPW phytoremediation strategies.

Differential protein expression during growth on model and commercial mixtures of naphthenic acids in Pseudomonas fluorescens Pf-5

Naphthenic acids (NAs) are carboxylic acids with the formula (Cn H2n+Z O2 ) and are among the most toxic, persistent constituents of oil sands process-affected waters (OSPW), produced during oil sands extraction. Currently, the proteins and mechanisms involved in NA biodegradation are unknown. Using LC-MS/MS shotgun proteomics, we identified proteins overexpressed during the growth of Pseudomonas fluorescens Pf-5 on a model NA (4'-n-butylphenyl)-4-butanoic acid (n-BPBA) and commercial NA mixture (Acros). By day 11, >95% of n-BPBA was degraded. With Acros, a 17% reduction in intensity occurred with 10-18 carbon compounds of the Z family -2 to -14 (major NA species in this mixture). A total of 554 proteins (n-BPBA) and 631 proteins (Acros) were overexpressed during growth on NAs, including several transporters (e.g., ABC transporters), suggesting a cellular protective response from NA toxicity. Several proteins associated with fatty acid, lipid, and amino acid metabolism were also overexpressed, including acyl-CoA dehydrogenase and acyl-CoA thioesterase II, which catalyze part of the fatty acid beta-oxidation pathway. Indeed, multiple enzymes involved in the fatty acid oxidation pathway were upregulated. Given the presumed structural similarity between alkyl-carboxylic acid side chains and fatty acids, we postulate that P. fluorescens Pf-5 was using existing fatty acid catabolic pathways (among others) during NA degradation.

Persulfate Oxidation Coupled with Biodegradation by Pseudomonas fluorescens Enhances Naphthenic Acid Remediation and Toxicity Reduction

The extraction of bitumen from the Albertan oilsands produces large amounts of oil sands process-affected water (OSPW) that requires remediation. Classical naphthenic acids (NAs), a complex mixture of organic compounds containing O₂^- species, are present in the acid extractable organic fraction of OSPW and are a primary cause of acute toxicity. A potential remediation strategy is combining chemical oxidation and biodegradation. Persulfate as an oxidant is advantageous, as it is powerful, economical, and less harmful towards microorganisms. This is the first study to examine persulfate oxidation coupled to biodegradation for NA remediation. Merichem NAs were reacted with 100, 250, 500, and 1000 mg/L of unactivated persulfate at 21 °C and 500 and 1000 mg/L of activated persulfate at 30 °C, then inoculated with Pseudomonas fluorescens LP6a after 2 months. At 21 °C, the coupled treatment removed 52.8-98.9% of Merichem NAs, while 30 °C saw increased removals of 99.4-99.7%. Coupling persulfate oxidation with biodegradation improved removal of Merichem NAs and chemical oxidation demand by up to 1.8× and 6.7×, respectively, and microbial viability was enhanced up to 4.6×. Acute toxicity towards Vibrio fischeri was negatively impacted by synergistic interactions between the persulfate and Merichem NAs; however, it was ultimately reduced by 74.5-100%. This study supports that persulfate oxidation coupled to biodegradation is an effective and feasible treatment to remove NAs and reduce toxicity.

Oil sands process affected water sourced Trichoderma harzianum demonstrates capacity for mycoremediation of naphthenic acid fraction compounds

Development of Alberta's oil sands requires large volumes of water, leading to the abundance of oil sands process affected water (OSPW) that must be remediated prior to discharge or reuse. OSPW contains a variety of dissolved organic compounds, however naphthenic acids (NAs) have been found to contribute significantly to the toxicity of OSPW. A fungus, Trichoderma harzianum, isolated directly from OSPW, has previously demonstrated a high tolerance and capacity for growth in the presence of commercial NAs. This study conducted microcosm experiments to elucidate and characterize the capacity of T. harzianum to degrade labile commercial NAs (Merichem), and OSPW-sourced naphthenic acid fraction compounds (NAFCs). Additionally, two model NA compounds, the simple single ring cyclohexane carboxylic acid (CHCA) and complex diamondoid 1-adamanatane carboxylic acid (ADA), were utilized to determine the influence of NA structure on degradation. T. harzianum degraded 14% of CHCA, 13% of ADA, and 23-47% of Merichem NAs. Additionally, Orbitrap mass spectrometry revealed a large change in Z-series within NAFCs. This removal and shift in composition correlated to a 59% and 52% drop in toxicity as per Microtox, for Merichem NAs and NAFCs respectively. This proof of concept experiment confirms that the fungal species T. harzianum can contribute to the biodegradation of complex dissolved organics found in OSPW, including cyclic and diamondoid structures.

Developments in Molecular Level Characterization of Naphthenic Acid Fraction Compounds Degradation in a Constructed Wetland Treatment System

The reclamation of oil sands process-affected water (OSPW) is a matter of environmental importance because of the aquatic toxicity to biota. This study describes refinements in advanced analytical methods to assess the performance of biological treatment systems for OSPW, such as constructed wetland treatment systems (CWTSs). Assessment of treatment efficiency by measurement of the degradation of naphthenic acid fraction compounds (NAFCs) in OSPW is challenging in CWTS due to potentially interfering constituents such as humic acids, organic acids, salts, and hydrocarbons. Here we have applied a previous weak anion exchange (WAX) solid-phase extraction (SPE) method and high-resolution Orbitrap-mass spectrometry (MS) to remove major interferences from the NAFC analysis. The refinements in data processing employing principal component analysis (PCA) indicates that the relative abundance of NAFCs decreased with time in the treated OSPW relative to the untreated OSPW. The most saturated NAFCs with higher carbon numbers were relatively more degraded as compared to unsaturated NAFCs. The use of Kendrick plots and van Krevelen plots for assessment of the performance of the CWTS is shown to be well-suited to detailed monitoring of the complex composition of NAFCs as a function of degradation. The developments and application of analytical methods such as the WAX SPE method and high-resolution Orbitrap-MS are demonstrated as tools enabling the advancement of CWTS design and optimization, enabling passive or semi-passive water treatment systems to be a viable opportunity for OSPW treatment.

Bioremediation of Hexanoic Acid and Phenanthrene in Oil Sands Tailings by the Microbial Consortium BioTiger™

Polycyclic aromatic hydrocarbons (PAHs) and naphthenic acids (NAs) are toxic contaminants of environmental concern found in process water and mature fine tailings, or tailings, from the oil sands industry. BioTiger™, a patented microbial consortium of twelve natural environmental isolates, was found to cometabolically biodegrade the NA hexanoic acid and the PAH phenanthrene in the presence of tailings. Hexanoamide was found to be produced and consumed during cometabolism of hexanoic acid. Mechanistic analysis demonstrated three of the BioTiger™ strains generated biosurfactants with the bacterial adhesion to hydrocarbons assay, seven with the methylene blue active substances assay, and nine with a hemolysis assay. Serial transfers of the BioTiger™ consortium demonstrated the stability of hexanoic acid degradation over several generations. The results demonstrate that BioTiger™ cometabolically biodegrades combinations of phenanthrene and hexanoic acid in tailings. This work reveals the potential for in situ bioremediation of tailings with this natural microbial consortium.

Biodegradation of naphthenic acids: identification of Rhodococcus opacus R7 genes as molecular markers for environmental monitoring and their application in slurry microcosms

Nowadays, the increase of the unconventional oil deposit exploitation and the amount of oil sands process-affected waters (OSPW) in tailing ponds emerges the importance of developing bio-monitoring strategies for the restoration of these habitats. The major constituents of such deposits are naphthenic acids (NAs), emerging contaminant mixtures with toxic and recalcitrant properties. With the aim of developing bio-monitoring strategies based on culture-independent approach, we identified genes coding for enzymes involved in NA degradation from Rhodococcus opacus R7 genome, after the evaluation of its ability to mineralize model NAs. R. opacus R7 whole-genome analysis unveiled the presence of pobA and chcpca gene clusters putatively involved in NAs degradation. Gene expression analysis demonstrated the specific induction of R7 aliA1 gene, encoding for a long-chain-fatty-acid-CoA ligase, in the presence of cyclohexanecarboxylic acid (CHCA) and hexanoic acid (HA), selected as representative compounds for alicyclic and linear NAs, respectively. Therefore, aliA1 gene was selected as a molecular marker to monitor the biodegradative potential of slurry-phase sand microcosms in different conditions: spiked with CHCA, in the presence of R. opacus R7, the autochthonous microbial community, and combining these factors. Results revealed that the aliA1-targeting culture-independent approach could be a useful method for bio-monitoring of NA degradation in a model laboratory system.

Diamondoids are not forever: microbial biotransformation of diamondoid carboxylic acids

Oil sands process‐affected waters (OSPW) contain persistent, toxic naphthenic acids (NAs), including the abundant yet little‐studied diamondoid carboxylic acids. Therefore, we investigated the aerobic microbial biotransformation of two of the most abundant, chronically toxic and environmentally relevant diamondoid carboxylic acids: adamantane‐1‐carboxylic acid (A1CA) and 3‐ethyl adamantane carboxylic acid (3EA). We inoculated into minimal salts media with diamondoid carboxylic acids as sole carbon and energy source two samples: (i) a surface water sample (designated TPW) collected from a test pit from the Mildred Lake Settling Basin and (ii) a water sample (designated 2 m) collected at a water depth of 2 m from a tailings pond. By day 33, in TPW enrichments, 71% of A1CA and 50% of 3EA was transformed, with 50% reduction in EC₂₀ toxicity. Similar results were found for 2 m enrichments. Biotransformation of A1CA and 3EA resulted in the production of two metabolites, tentatively identified as 2‐hydroxyadamantane‐1‐carboxylic acid and 3‐ethyladamantane‐2‐ol respectively. Accumulation of both metabolites was less than the loss of the parent compound, indicating that they would have continued to be transformed beyond 33 days and not accumulate as dead‐end metabolites. There were shifts in bacterial community composition during biotransformation, with Pseudomonas species, especially P. stutzeri, dominating enrichments irrespective of the diamondoid carboxylic acid. In conclusion, we demonstrated the microbial biotransformation of two diamondoid carboxylic acids, which has potential application for their removal and detoxification from vast OSPW that are a major environmental threat.

Profiling of individual naphthenic acids at a composite tailings reclamation fen by comprehensive two-dimensional gas chromatography-mass spectrometry

Naphthenic acids (NAs) are naturally occurring in the Athabasca oil sands region (AOSR) and accumulate in tailings as a result of water-based extraction processes. NAs exist as a complex mixture, so the development of an analytical technique to characterize them has been an on-going challenge. The aim of this study was to use comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry to monitor individual NAs within a wetland reclamation site in the AOSR. Samples were collected from four monitoring wells at the site and the extracts were found to contain numerous resolved isomers of classical (monocyclic-, bicyclic-, adamantane-, indane-, and tetralin-type carboxylic acids) and sulfur-containing NAs (thiamonocyclic- and thiophene-type carboxylic acids). The absolute abundances of the monitored NAs were compared between four monitoring wells and unique profiles were observed at each well. Few significant changes in absolute abundances were observed over the sampling period, with the exception of one well (Well 6A). In addition, isomeric percent compositions were calculated for each set of structural isomers, and one-way analysis of variance (ANOVA) and two-dimensional hierarchical cluster analysis revealed high spatial variation at the site. However, consistent distributions were observed at each of the monitoring wells for some sets of NA isomers (such as: adamantane NAs), which may be useful for forensic applications, such as identifying sources of contamination or demonstrating biodegradation. The methods and results presented in this study demonstrate the utility of monitoring individual NAs, since both changes in absolute abundances of individual NAs and the distribution of NA isomers have the ability to provide insight into their sources and the processes controlling their concentrations that are not only of relevance to the Alberta Oil Sands, but also to other petroleum deposits and environmental systems.

Aerobic granular sludge and naphthenic acids treatment by varying initial concentrations and supplemental carbon concentrations

Aerobic granular sludge (AGS) has previously been utilized in the treatment of toxic compounds due to its diverse and dense microbial structure. The present study subjected mature AGS to model naphthenic acids (NAs) representative of the Canadian oil sands. To this effect, three NA concentrations (10, 50 and 100 mg/L) and three supplemental carbon source concentrations (600, 1200 and 2500 mg/L) were studied in batch reactors for 5 days. The responding variables were chemical oxygen demand (COD), NA concentrations and nutrients. Cyclohexane carboxylic acid (CHCA), cyclohexane acetic acid (CHAA) and 1-adamantane carboxylic acid (ACA) were chosen to study structure-based degradation kinetics. The optimal COD according to the runs was 1200 mg/L. CHCA was removed completely with biodegradation rate constants increasing with lower NA concentrations and lower COD concentrations. CHAA was also removed completely, however, an optimal rate constant of 1.9 d^-1 was achieved at NA and COD concentrations of 50 mg/L and 1200 mg/L, respectively. ACA removal trends did not follow statistically significant regressions; however, degradation and sorption helped remove ACA up to 19.9%. Pseudomonas, Acinetobacter, Hyphomonas and Brevundimonas spp. increased over time, indicating increased AGS adaptability to NAs.

Evaluating in situ biodegradation of 13C-labelled naphthenic acids in groundwater near oil sands tailings ponds

Potential seepage of naphthenic acids (NAs) from tailings ponds into surface water and groundwater is one of the main environmental concerns associated with the Canadian Athabasca oil sands mining operations. Here we report the application of ¹³C-labelled NA surrogate compounds to evaluate intrinsic biodegradation along groundwater flow-paths originating from oil sands tailings ponds at two different sites: a glacio-fluvial aquifer (Site 1) and a low-lying wetland (Site 2). Microcosms containing the carboxyl group labelled (99%) NA surrogates (cyclohexanecarboxylic acid, CHCA; 1,2-cyclohexanedicarboxylic acid, CHDCA; 1-adamantanecarboxylic acid, ACA) were lowered into monitoring wells for several months to allow sufficient time for substrate degradation and formation of a biofilm in conditions characteristic of the local aquifer. Phospholipid fatty acids (PLFAs), biomarkers for the active microbial population, were extracted from the biofilms for stable carbon isotope (δ¹³C) analysis. At Site 1, highly ¹³C-enriched δ¹³C values (up to ~+7100‰) confirmed the in situ microbial breakdown of CHCA and CHDCA. At Site 2, δ¹³C-PLFA values from -60.6 to -24.5‰ indicated uptake of a ¹³C-depleted substrate such as biogenic methane and not ¹³C-labelled ACA. Determination of the microbial community using 16s RNA sequencing confirmed the presence of methane-oxidizing bacteria in the subsurface at Site 2. The in situ biodegradation of NAs at Site 1 demonstrates that the indigenous microbial population in the shallow subsurface near tailings ponds can readily break down some of these compounds prior to surface water discharge. The lack of evidence for microbial uptake of ¹³C-labelled ACA at Site 2 demonstrates that other NAs, in particular tricyclic diamondoid acids, may persist in the environment following seepage from tailings ponds or natural sources.

Aerobic Growth of Rhodococcus aetherivorans BCP1 Using Selected Naphthenic Acids as the Sole Carbon and Energy Sources

Naphthenic acids (NAs) are an important group of toxic organic compounds naturally occurring in hydrocarbon deposits. This work shows that Rhodococcus aetherivorans BCP1 cells not only utilize a mixture of eight different NAs (8XNAs) for growth but they are also capable of marked degradation of two model NAs, cyclohexanecarboxylic acid (CHCA) and cyclopentanecarboxylic acid (CPCA) when supplied at concentrations from 50 to 500 mgL-1. The growth curves of BCP1 on 8XNAs, CHCA, and CPCA showed an initial lag phase not present in growth on glucose, which presumably was related to the toxic effects of NAs on the cell membrane permeability. BCP1 cell adaptation responses that allowed survival on NAs included changes in cell morphology, production of intracellular bodies and changes in fatty acid composition. Transmission electron microscopy (TEM) analysis of BCP1 cells grown on CHCA or CPCA showed a slight reduction in the cell size, the production of EPS-like material and intracellular electron-transparent and electron-dense inclusion bodies. The electron-transparent inclusions increased in the amount and size in NA-grown BCP1 cells under nitrogen limiting conditions and contained storage lipids as suggested by cell staining with the lipophilic Nile Blue A dye. Lipidomic analyses revealed significant changes with increases of methyl-branched (MBFA) and polyunsaturated fatty acids (PUFA) examining the fatty acid composition of NAs-growing BCP1 cells. PUFA biosynthesis is not usual in bacteria and, together with MBFA, can influence structural and functional processes with resulting effects on cell vitality. Finally, through the use of RT (Reverse Transcription)-qPCR, a gene cluster (chcpca) was found to be transcriptionally induced during the growth on CHCA and CPCA. Based on the expression and bioinformatics results, the predicted products of the chcpca gene cluster are proposed to be involved in aerobic NA degradation in R. aetherivorans BCP1. This study provides first insights into the genetic and metabolic mechanisms allowing a Rhodococcus strain to aerobically degrade NAs.

Naphthalene biodegradation under oxygen-limiting conditions: community dynamics and the relevance of biofilm-forming capacity

Toxic polycyclic aromatic hydrocarbons (PAHs) are frequently released into the environment from anthropogenic sources. PAH remediation strategies focus on biological processes mediated by bacteria. The availability of oxygen in polluted environments is often limited or absent, and only bacteria able to thrive in these conditions can be considered for bioremediation strategies. To identify bacterial strains able to degrade PAHs under oxygen‐limiting conditions, we set up enrichment cultures from samples of an oil‐polluted aquifer, using either anoxic or microaerophilic condition and with PAHs as the sole carbon source. Despite the presence of a significant community of nitrate‐reducing bacteria, the initial community, which was dominated by Betaproteobacteria, was incapable of PAH degradation under strict anoxic conditions, although a clear shift in the structure of the community towards an increase in the Alphaproteobacteria (Sphingomonadaceae), Actinobacteria and an uncultured group of Acidobacteria was observed in the enrichments. In contrast, growth under microaerophilic conditions with naphthalene as the carbon source evidenced the development of a biofilm structure around the naphthalene crystal. The enrichment process selected two co‐dominant groups which finally reached 97% of the bacterial communities: Variovorax spp. (54%, Betaproteobacteria) and Starkeya spp. (43%, Xanthobacteraceae). The two dominant populations were able to grow with naphthalene, although only Starkeya was able to reproduce the biofilm structure around the naphthalene crystal. The pathway for naphthalene degradation was identified, which included as essential steps dioxygenases with high affinity for oxygen, showing 99% identity with Xanthobacter polyaromaticivorans dbd cluster for PAH degradation. Our results suggest that the biofilm formation capacity of Starkeya provided a structure to allocate its cells at an appropriate distance from the toxic carbon source.

Screening selectively harnessed environmental microbial communities for biodegradation of polycyclic aromatic hydrocarbons in moving bed biofilm reactors

Bacteria are often found tolerating polluted environments. Such bacteria may be exploited to bioremediate contaminants in controlled ex situ reactor systems. One potential strategic goal of such systems is to harness microbes directly from the environment such that they exhibit the capacity to markedly degrade organic pollutants of interest. Here, the use of biofilm cultivation techniques to inoculate and activate moving bed biofilm reactor (MBBR) systems for the degradation of polycyclic aromatic hydrocarbons (PAHs) was explored. Biofilms were cultivated from 4 different hydrocarbon contaminated sites using a minimal medium spiked with the 16 EPA identified PAHs. Overall, all 4 inoculant sources resulted in biofilm communities capable of tolerating the presence of PAHs, but only 2 of these exhibited enhanced PAH catabolic gene prevalence coupled with significant degradation of select PAH compounds. Comparisons between inoculant sources highlighted the dependence of this method on appropriate inoculant screening and biostimulation efforts.

Assessing the bioremediation potential of algal species indigenous to oil sands process-affected waters on mixtures of oil sands acid extractable organics

Surface mining extraction of bitumen from oil sand in Alberta, Canada results in the accumulation of oil sands process-affected water (OSPW). In attempts to maximize water recycling, and because its constituents are recognized as being toxic, OSPW is retained in settling basins. Consequently, research efforts are currently focused on developing remediation strategies capable of detoxifying OSPW to allow for eventual release. One potential bioremediation strategy proposes to utilize phytoplankton native to the Alberta oil sand region to sequester, break down, or modify the complex oil sands acid extractable organic (AEO) mixtures in OSPW. Preliminary attempts to quantify changes in total oil sands AEO concentration in test solutions by ESI-MS following a 14-day algal remediation period revealed the presence of unknown organic acids in control samples, likely released by the phytoplankton strains and often of the same atomic mass range as the oil sands AEO under investigation. To address the presence of these "biogenic" organic acids in test samples, ESI-MS in MRM mode was utilized to identify oil sands AEO "marker ions" that were a) present within the tested oil sands AEO extract and b) unique to the oil sands AEO extract only (e.g. atomic masses different from biogenic organic acids). Using this approach, one of the 21 tested algal strains, Stichococcus sp. 1, proved capable of significantly reducing the AEO marker ion concentration at test concentrations of 10, 30, and 100mgL(-1). This result, along with the accelerated growth rate and recalcitrance of this algal strain with exposure to oil sands AEO, suggests the strong potential for the use of the isolated Stichococcus sp. 1 as a candidate for bioremediation strategies.

A comparison of the response of twoBurkholderia fungorumstrains grown as planktonic cells versus biofilm to dibenzothiophene and select polycyclic aromatic hydrocarbons

In natural environments, bacteria often exist in close association with surfaces and interfaces by establishing biofilms. Here, we report on the ability of Burkholderia fungorum strains DBT1 and 95 to survive in high concentrations of hydrocarbons, and we compare their growth as a biofilm vs. planktonic cells. The 2 compounds tested were dibenzothiophene (DBT) and a mixture of naphthalene, phenanthrene, and pyrene (5:2:1) as representative compounds of thiophenes and polycyclic aromatic hydrocarbons (PAHs), respectively. The results showed that both strains were able to degrade DBT and to survive in the presence of up to a 2000 mg·L−1concentration of this compound both as a biofilm and as free-living cells. Moreover, B. fungorum DBT1 showed reduced tolerance towards the mixed PAHs (2000 mg·L−1naphthalene, 800 mg·L−1phenanthrene, and 400 mg·L−1pyrene) both as a biofilm and as free-living cells. Conversely, biofilms of B. fungorum 95 enhanced resistance against these toxic compounds compared with planktonic cells (P < 0.05). Visual observation through confocal laser scanning microscopy showed that exposure of biofilms to DBT and PAHs altered their structure: high concentrations of DBT triggered an aggregation of biofilm cells. These findings provide new perspectives on the effectiveness of using DBT-degrading bacterial strains in bioremediation of hydrocarbon-contaminated sites.

Removal and biodegradation of naphthenic acids by biochar and attached environmental biofilms in the presence of co-contaminating metals

This study evaluated the efficacy of using a combined biofilm-biochar approach to remove organic (naphthenic acids (NAs)) and inorganic (metals) contaminants from process water (OSPW) generated by Canada's oil sands mining operations. A microbial community sourced from an OSPW sample was cultured as biofilms on several carbonaceous materials. Two biochar samples, from softwood bark (SB) and Aspen wood (N3), facilitated the most microbial growth (measured by protein assays) and were used for NA removal studies performed with and without biofilms, and in the presence and absence of contaminating metals. Similar NA removal was seen in 6-day sterile N3 and SB assays (>30%), while biodegradation by SB-associated biofilms increased NA removal to 87% in the presence of metals. Metal sorption was also observed, with up to four times more immobilization of Fe, Al, and As on biofilm-associated biochar. These results suggest this combined approach may be a promising treatment for OSPW.

Evaluating the Metal Tolerance Capacity of Microbial Communities Isolated from Alberta Oil Sands Process Water

Anthropogenic activities have resulted in the intensified use of water resources. For example, open pit bitumen extraction by Canada’s oil sands operations uses an estimated volume of three barrels of water for every barrel of oil produced. The waste tailings–oil sands process water (OSPW)–are stored in holding ponds, and present an environmental concern as they are comprised of residual hydrocarbons and metals. Following the hypothesis that endogenous OSPW microbial communities have an enhanced tolerance to heavy metals, we tested the capacity of planktonic and biofilm populations from OSPW to withstand metal ion challenges, using Cupriavidus metallidurans, a known metal-resistant organism, for comparison. The toxicity of the metals toward biofilm and planktonic bacterial populations was determined by measuring the minimum biofilm inhibitory concentrations (MBICs) and planktonic minimum inhibitory concentrations (MICs) using the MBEC ™ assay. We observed that the OSPW community and C. metallidurans had similar tolerances to 22 different metals. While thiophillic elements (Te, Ag, Cd, Ni) were found to be most toxic, the OSPW consortia demonstrated higher tolerance to metals reported in tailings ponds (Al, Fe, Mo, Pb). Metal toxicity correlated with a number of physicochemical characteristics of the metals. Parameters reflecting metal-ligand affinities showed fewer and weaker correlations for the community compared to C. metallidurans, suggesting that the OSPW consortia may have developed tolerance mechanisms toward metals present in their environment.