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The role multidrug resistance efflux pumps (MDREPs) play in clinical antibiotic resistance is well understood but our understanding of their role in different environments such as hydrocarbon remediation, corrosion, agriculture, and aquaculture is far less comprehensive. Initially discovered for their role in antibiotic resistances, these proteins have broad substrate profiles which are specific yet promiscuous. The substrates range from antibiotics, antiseptics, fluoroquinolones, biocides, toxic and DNA intercalating dyes, and heavy metals. Here, we overview the families of MDREPs and discuss the role of the MDREPs in these diverse environments and how they impact mitigation strategies and animal stock handling practices. We look into which specific genes are expressed in which environment and the key methods used in these studies. We also discuss the state of research in this emerging field as it applies to environmental studies and branches beyond clinical studies and the challenges faced therein.

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.

Moving bed biofilm reactors (MBBRs) are an effective biotechnology for treating industrial wastewater. Biomass retention on moving bed biofilm reactor (MBBR) carriers (biofilm support materials), allows for the ease-of-operation and high treatment capacity of MBBR systems. Optimization of MBBR systems has largely focused on aspects of carrier design, while little attention has been paid to enhancing strategies for harnessing microbial biomass. Previously, our research group demonstrated that mixed-species biofilms can be harvested from an industrial wastewater inoculum [oil sands process water (OSPW)] using the Calgary Biofilm Device (CBD). Moreover, the resultant biofilm communities had the capacity to degrade organic toxins (naphthenic acids—NAs) that are found in OSPW. Therefore, we hypothesized that harnessing microbial communities from industrial wastewater, as biofilms, on MBBR carriers may be an effective method to bioremediate industrial wastewater.Here, we detail our methodology adapting the workflow employed for using the CBD, to generate inoculant carriers to seed an MBBR.In this study, OSPW-derived biofilm communities were successfully grown, and their efficacy evaluated, on commercially available MBBR carriers affixed within a modified CBD system. The resultant biofilms demonstrated the capacity to transfer biomass to recipient carriers within a scaled MBBR. Moreover, MBBR systems inoculated in this manner were fully active 2 days post-inoculation, and readily degraded a select population of NAs. Together, these findings suggest that harnessing microbial communities on carriers affixed within a modified CBD system may represent a facile and rapid method for obtaining functional inoculants for use in wastewater MBBR treatment systems.

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.

In an effort to prevent the formation of pathogenic biofilms on hydroxyapatite (HA)-based clinical devices and surfaces, we present a study evaluating the antimicrobial efficacy of Spherical biogenic Se-Nanostructures Embedded in Organic material (Bio Se-NEMO-S) produced by Bacillus mycoides SelTE01 in comparison with two different chemical selenium nanoparticle (SeNP) classes. These nanomaterials have been studied as potential antimicrobials for eradication of established HA-grown biofilms, for preventing biofilm formation on HA-coated surfaces and for inhibition of planktonic cell growth of Pseudomonas aeruginosa NCTC 12934 and Staphylococcus aureus ATCC 25923. Bio Se-NEMO resulted more efficacious than those chemically produced in all tested scenarios. Bio Se-NEMO produced by B.mycoides SelTE01 after 6 or 24h of Na 2 SeO 3 exposure show the same effective antibiofilm activity towards both P.aeruginosa and S.aureus strains at 0.078mgml −1 (Bio Se-NEMO 6 ) and 0.3125mgml −1 (Bio Se-NEMO 24 ). Meanwhile, chemically synthesized SeNPs at the highest tested concentration (2.5mgml −1 ) have moderate antimicrobial activity. The confocal laser scanning micrographs demonstrate that the majority of the P.aeruginosa and S.aureus cells exposed to biogenic SeNPs within the biofilm are killed or eradicated. Bio Se-NEMO therefore displayed good antimicrobial activity towards HA-grown biofilms and planktonic cells, becoming possible candidates as new antimicrobials.

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.

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.

Oil sands surface mining for bitumen results in the formation of oil sands process water (OSPW), containing acutely toxic naphthenic acids (NAs). Potential exists for OSPW toxicity to be mitigated by aerobic degradation of the NAs by microorganisms indigenous to the oil sands tailings ponds, the success of which is dependent on the methods used to exploit the metabolisms of the environmental microbial community. Having hypothesized that the xenobiotic tolerant biofilm mode-of-life may represent a feasible way to harness environmental microbes for ex situ treatment of OSPW NAs, we aerobically grew OSPW microbes as single and mixed species biofilm and planktonic cultures under various conditions for the purpose of assaying their ability to tolerate and degrade NAs. The NAs evaluated were a diverse mixture of eight commercially available model compounds. Confocal microscopy confirmed the ability of mixed and single species OSPW cultures to grow as biofilms in the presence of the NAs evaluated. qPCR enumeration demonstrated that the addition of supplemental nutrients at concentrations of 1 g L(-1) resulted in a more numerous population than 0.001 g L(-1) supplementation by approximately 1 order of magnitude. GC-FID analysis revealed that mixed species cultures (regardless of the mode of growth) are the most effective at degrading the NAs tested. All constituent NAs evaluated were degraded below detectable limits with the exception of 1-adamantane carboxylic acid (ACA); subsequent experimentation with ACA as the sole NA also failed to exhibit degradation of this compound. Single species cultures degraded select few NA compounds. The degradation trends highlighted many structure-persistence relationships among the eight NAs tested, demonstrating the effect of side chain configuration and alkyl branching on compound recalcitrance. Of all the isolates, the Rhodococcus spp. degraded the greatest number of NA compounds, although still less than the mixed species cultures. Overall, these observations lend support to the notion that harnessing a community of microorganisms as opposed to targeted isolates can enhance NA degradation ex situ. Moreover, the variable success caused by NA structure related persistence emphasized the difficulties associated with employing bioremediation to treat complex, undefined mixtures of toxicants such as OSPW NAs.

The caustic hot water extraction process used to release bitumen from the Alberta oil sands generates large volumes of tailings waste, or oil sands process water (OSPW). OSPW contains several components of environmental concern including diluents, polyaromatic hydrocarbons, heavy metals, and naphthenic acids (NAs); the latter are of particular concern as they are acutely toxic to aquatic organisms and mammals. Studies have demonstrated that the naturally occurring OSPW bacteria are capable of metabolizing the NAs. However, this in situ process takes place over hundreds of years, and is incomplete, leaving a recalcitrant fraction of NAs intact. In this study we explore options for recovering and harnessing the naturally occurring OSPW bacteria for potential future use in an aerobic ex situ OSPW treatment system. Here we evaluate our recovered microbes on their ability to degrade two model NAs, cyclohexane carboxylic acid and cyclohexane acetic acid. Using OSPW as a source for a bacterial inoculum, we were able to compare single and multispecies OSPW cultures, grown as either a biofilm, or as a planktonic suspension. Furthermore, we examined the effect of available nutrients on the ability of these cultures to degrade NAs. All biofilms were grown using the Calgary Biofilm Device. GC–MS, and GC-FID reveal that multispecies biofilm and planktonic cultures are each capable of degrading both NAs; a trait not observed for single species cultures. Moreover, complementary carbon sources have a tangible effect on the ability of the cultures to initiate the degradation of the NAs.