A Threshold Substrate Concentration Is Required to Initiate the Degradation of 3-Phenylpropionic Acid in Escherichia coli

Sulfamethoxazole is Metabolized and Mineralized at Extremely Low Concentrations

The presence of organic micropollutants in water and sediments motivates investigation of their biotransformation at environmentally low concentrations, usually in the range of μg L-1. Many are biotransformed by cometabolic mechanisms; however, there is scarce information concerning their direct metabolization in this concentration range. Threshold concentrations for microbial assimilation have been reported in both pure and mixed cultures from different origins. The literature suggests a range value for bacterial growth of 1-100 μg L-1 for isolated aerobic heterotrophs in the presence of a single substrate. We aimed to investigate, as a model case, the threshold level for sulfamethoxazole (SMX) metabolization in pure cultures of Microbacterium strain BR1. Previous research with this strain has covered the milligram L-1 range. In this study, acclimated cultures were exposed to concentrations from 0.1 to 25 μg L-1 of 14C-labeled SMX, and the 14C-CO2 produced was trapped and quantified over 24 h. Interestingly, SMX removal was rapid, with 98% removed within 2 h. In contrast, mineralization was slower, with a consistent percentage of 60.0 ± 0.7% found at all concentrations. Mineralization rates increased with rising concentrations. Therefore, this study shows that bacteria are capable of the direct metabolization of organic micropollutants at extremely low concentrations (sub μg L-1).

Predicting and improving the microbial removal of organic micropollutants during wastewater treatment: A review

Organic micropollutants (OMPs) consist of widely used chemicals such as pharmaceuticals and pesticides that can persist in surface and groundwaters at low concentrations (ng/L to μg/L) for a long time. The presence of OMPs in water can disrupt aquatic ecosystems and threaten the quality of drinking water sources. Wastewater treatment plants (WWTPs) rely on microorganisms to remove major nutrients from water, but their effectiveness at removing OMPs varies. Low removal efficiency might be the result of low concentrations, inherent stable chemical structures of OMPs, or suboptimal conditions in WWTPs. In this review, we discuss these factors, with special emphasis on the ongoing adaptation of microorganisms to degrade OMPs. Finally, recommendations are drawn to improve the prediction of OMP removal in WWTPs and to optimize the design of new microbial treatment strategies. OMP removal seems to be concentration-, compound-, and process-dependent, which poses a great complexity to develop accurate prediction models and effective microbial processes targeting all OMPs.

Stoichiometric ratios for biotics and xenobiotics capture effective metabolic coupling to re(de)fine biodegradation

Preserving human and environmental health requires anthropogenic pollutants to be biologically degradable. Depending on concentration, both nutrients and pollutants induce and activate metabolic capacity in the endemic bacterial consortium, which in turn aids their degradation. Knowledge on such 'acclimation' is rarely implemented in risk assessment cost-effectively. As a result, an accurate description of the mechanisms and kinetics of biodegradation remains problematic. In this study, we defined a yield 'effectivity', comprising the effectiveness at which a pollutant (substrate) enhances its own degradation by inducing (biomass) cofactors involved therein. Our architecture for calculation represents the interplay between concentration and metabolism via both stoichiometric and thermodynamic concepts. The calculus for yield 'effectivity' is biochemically intuitive, implicitly embeds co-metabolism and distinguishes 'endogenic' from 'exogenic' substances' reflecting various phenomena in biodegradation and bio-transformation studies. We combined data on half-lives of pollutants/nutrients in wastewater and surface water with transition-state rate theory to obtain also experimental values for effective yields. These quantify the state of acclimation: the portion of biodegradation kinetics attributable to (contributed by) 'natural metabolism', in view of similarity to natural substances. Calculated and experimental values showed statistically significant correspondence. Particularly, carbohydrate metabolism and nucleic acid metabolism appeared relevant for acclimation (R² = 0.11-0.42), affecting rates up to 10^4.9(±0.7) times: under steady-state acclimation, a compound stoichiometrically identical to carbohydrates or nucleic acids, is 10^3.2 to 10^4.9 times faster aerobically degraded than a compound marginally similar. Our new method, simulating (contribution by) the state of acclimation, supplements existing structure-biodegradation and kinetic models for predicting biodegradation in wastewater and surface water. The accuracy of prediction may increase when characterizing nutrients/co-metabolites in terms of, e.g., elemental analysis. We discuss strengths and limitations of our approach by comparison to empirical and mechanism-based methods.

Determination of the lower limits of antibiotic biodegradation and the fate of antibiotic resistant genes in activated sludge: Both nitrifying bacteria and heterotrophic bacteria matter

Antibiotics can be biodegraded in activated sludge via co-metabolism and metabolism. In this study, we investigated the biodegradation pathways of sulfamethoxazole (SMX) and antibiotic resistant genes' (ARGs) fate in different autotrophic and heterotrophic microorganisms, by employing aerobic sludge, mixed sludge, and nitrifying sludge. A threshold concentration of SMX activating the degradation pathways in the initial stage of antibiotics degradation was found and proved in different activated sludge systems. Heterotrophic bacteria played an important role in SMX biodegradation. However, ammonia-oxidizing bacteria (AOB) had a faster metabolic rate, which was about 15 times higher than heterotrophic bacteria, contributing much to SMX removal via co-metabolism. As SMX concentration increases, the amoA gene and AOB relative abundance decreased in aerobic sludge due to the enrichment of functional heterotrophic bacteria, while it increased in nitrifying sludge. Microbial community analysis showed that functional bacteria which possess the capacity of SMX removal and antibiotic resistance were selected by SMX pressure. Potential ARGs hosts could increase their resistance to the biotoxicity of SMX and maintain system performance. These findings are of practical significance to guide antibiotic biodegradation and ARGs control in wastewater treatment plants.

Ciprofloxacin-degrading Paraclostridium sp. isolated from sulfate-reducing bacteria-enriched sludge: Optimization and mechanism

Ciprofloxacin (CIP), one of the most widely used fluoroquinolone antibiotics, is frequently detected in the effluents of wastewater treatment plants and aquatic environments. In this study, a CIP-degrading bacterial strain was isolated from the sulfate reducing bacteria (SRB)-enriched sludge, identified as Paraclostridium sp. (i.e., strain S2). The effects of critical operational parameters on CIP removal by the strain S2 were systematically studied and these parameters were optimized via response surface methodology to maximize CIP removal. Furthermore, the pathway and kinetics of CIP removal were investigated by varying the initial CIP concentrations (from 0.1 to 20 mg/L). The CIP removal was characterized by rapid sorption followed by biotransformation with a specific biotransformation rate of 1975.7 ± 109.1 µg/g-cell dry weight/h at an initial CIP concentration of 20 mg/L. Based on the main transformation products, several biotransformation pathways have been proposed including piperazine ring cleavage, OH/F substitution, decarboxylation, and hydroxylation as the major transformation reactions catalyzed by cytochrome P450 and dehydrogenases. Acute toxicity assessment apparently shows that CIP biotransformation by strain S2 resulted in the formation of less toxic intermediates. To the best of our knowledge, this is the very first study in which a key functional microbe, Paraclostridium sp., highly effective in CIP biotransformation, was isolated from SRB-enriched sludge. The findings of this study could facilitate in developing appropriate bioaugmentation strategy, and in designing and operating an SRB-based engineered process for treating CIP-laden wastewater.

Enantioselective degradation of ofloxacin and levofloxacin by the bacterial strains Labrys portucalensis F11 and Rhodococcus sp. FP1

Fluoroquinolones are a class of antibiotics widely prescribed in both human and veterinary medicine of high environmental concern and characterized as environmental micropollutants due to their ecotoxicity and persistence and antibacterial resistance potential. Ofloxacin and levofloxacin are chiral fluoroquinolones commercialized as racemate and in enantiomerically pure form, respectively. Since the pharmacological properties and toxicity of the enantiomers may be very different, understanding the stereochemistry of these compounds should be a priority in environmental monitoring. This work presents the biodegradation of racemic ofloxacin and its (S)-enantiomer levofloxacin by the bacterial strains Labrys portucalensis F11 and Rhodococcus sp. FP1 at a laboratory-scale microcosm following the removal and the behavior of the enantiomers. Strain F11 could degrade both antibiotics almost completely when acetate was supplied regularly to the cultures. Enrichment of the (R)-enantiomer was observed in FP1 and F11 cultures supplied with ofloxacin. Racemization was observed in the biodegradation of the pure (S)-ofloxacin (levofloxacin) by strain F11, which was confirmed by liquid chromatography - exact mass spectrometry. Biodegradation of ofloxacin at 450 µg L^-1 by both bacterial strains expressed good linear fits (R² > 0.98) according to the Rayleigh equation. The enantiomeric enrichment factors were comprised between - 22.5% to - 9.1%, and - 18.7% to - 9.0% in the biodegradation of ofloxacin by strains F11 and FP1, respectively, with no significant differences for the two bacteria under the same conditions. This is the first time that enantioselective biodegradation of ofloxacin and levofloxacin by single bacteria is reported.

Integrated liquid chromatography method in enantioselective studies: Biodegradation of ofloxacin by an activated sludge consortium

Ofloxacin is a chiral fluoroquinolone commercialized as racemate and as its enantiomerically pure form levofloxacin. This work presents an integrated liquid chromatography (LC) method with fluorescence detection (FD) and exact mass spectrometry (EMS) developed to assess the enantiomeric biodegradation of ofloxacin and levofloxacin in laboratory-scale microcosms. The optimized enantioseparation conditions were achieved using a macrocyclic antibiotic ristocetin A-bonded CSP (150×2.1mm i.d.; particle size 5μm) under reversed-phase elution mode. The method was validated using a mineral salts medium as matrix and presented selectivity and linearity over a concentration range from 5μgL(-1) (quantification limit) to 350μgL(-1) for each enantiomer. The method was successfully applied to evaluate biodegradation of ofloxacin enantiomers at 250μgL(-1) by an activated sludge inoculum. Ofloxacin (racemic mixture) and (S)-enantiomer (levofloxacin) were degraded up to 58 and 52%, respectively. An additional degradable carbon source, acetate, enhanced biodegradation up to 23%. (S)-enantiomer presented the highest extent of degradation (66.8%) when ofloxacin was supplied along with acetate. Results indicated slightly higher biodegradation extents for the (S)-enantiomer when supplementation was done with ofloxacin. Degradation occurred faster in the first 3days and proceeded slowly until the end of the assays. The chromatographic results from LC-FD suggested the formation of the (R)-enantiomer during levofloxacin biodegradation which was confirmed by LC-MS with a LTQ Orbitrap XL.

Biodegradation of ofloxacin, norfloxacin, and ciprofloxacin as single and mixed substrates by Labrys portucalensis F11

Fluoroquinolone (FQ) antibiotics are extensively used both in human and veterinary medicine, and their accumulation in the environment is causing an increasing concern. In this study, the biodegradation of the three most worldwide used FQs, namely ofloxacin, norfloxacin, and ciprofloxacin, by the fluoroorganic-degrading strain Labrys portucalensis F11 was assessed. Degradation occurred when the FQs were supplied individually or as mixture in the culture medium, in the presence of an easily degradable carbon source. Consumption of individual FQs was achieved at different extents depending on its initial concentration, ranging from 0.8 to 30 μM. For the lowest concentration, total uptake of each FQ was observed but stoichiometric fluoride release was not achieved. Intermediate compounds were detected and identified by LC-MS/MS with a quadrupole time of flight detector analyzer. Biotransformation of FQs by L. portucalensis mainly occurred through a cleavage of the piperazine ring and displacement of the fluorine substituent allowing the formation of intermediates with less antibacterial potency. FQ-degrading microorganisms could be useful for application in bioaugmentation processes towards more efficient removal of contaminants in wastewater treatment plants.

How to live at very low substrate concentration

Availability of carbon/energy sources and temperature are the two environmental factors that severely restrict heterotrophic growth in most ecosystems. DOC concentrations in ground, drinking and surface waters are typically in the range of 0.5-5 mg/L, but most of this is present in a polymeric, inaccessible form for microbes. Concentrations of microbiologically available carbon compounds (so-called assimilable organic carbon, AOC) are usually in the range of 10-100 μg/L, those of individual sugars or amino acids are not higher than a few μg/L. Until recently microbiologists assumed that such nutrient-poor (oligotrophic) environments are "deserts" for life, and that the majority of bacterial cells seen in the microscope are dead, dormant or at least severely starved. Nevertheless, despite the low concentrations of available carbon compounds, bacterial cell numbers recorded in these environments typically are in the range of 10(5)-10(6) per mL. Over the last years, we have learnt that most of these microbes are perfectly alive, metabolizing and ready to grow when given the chance. Hence, microbes have adapted and developed strategies to cope with this situation. Laboratory studies with pure cultures suggest that bacterial cells have developed two strategies to live under such conditions. The first strategy is to perform a "multivorous" way of life by taking up and metabolizing dozens of different carbon substrates simultaneously (i.e., they are NOT specializing on a particular substrate, which they can take up with very high affinity). This "mixed substrate growth" equips the cell with a kinetic advantage and metabolic flexibility. Simultaneous utilization of a multitude of carbon substrates allows fast growth at minute concentrations of individual substrates. The second strategy is to minimize maintenance requirements (unfortunately we still know little about how this is achieved). Recently, flow cytometry has been employed to study microbial growth in very dilute, nutrient-poor environments. The technique allows fast and easy quantification of microbial growth of natural bacterial communities, including "uncultivable" members, under environmental conditions. When combined with strain-specific fluorescent immunoprobes, this technique allows investigation of the growth and competition of pathogens with the indigenous microbial flora. This method is particularly suited for studying questions concerning microbial growth and survival in drinking water systems.

Thermodynamic analysis of biodegradation pathways

Microorganisms provide a wealth of biodegradative potential in the reduction and elimination of xenobiotic compounds in the environment. One useful metric to evaluate potential biodegradation pathways is thermodynamic feasibility. However, experimental data for the thermodynamic properties of xenobiotics is scarce. The present work uses a group contribution method to study the thermodynamic properties of the University of Minnesota Biocatalysis/Biodegradation Database. The Gibbs free energies of formation and reaction are estimated for 914 compounds (81%) and 902 reactions (75%), respectively, in the database. The reactions are classified based on the minimum and maximum Gibbs free energy values, which accounts for uncertainty in the free energy estimates and a feasible concentration range relevant to biodegradation. Using the free energy estimates, the cumulative free energy change of 89 biodegradation pathways (51%) in the database could be estimated. A comparison of the likelihood of the biotransformation rules in the Pathway Prediction System and their thermodynamic feasibility was then carried out. This analysis revealed that when evaluating the feasibility of biodegradation pathways, it is important to consider the thermodynamic topology of the reactions in the context of the complete pathway. Group contribution is shown to be a viable tool for estimating, a priori, the thermodynamic feasibility and the relative likelihood of alternative biodegradation reactions. This work offers a useful tool to a broad range of researchers interested in estimating the feasibility of the reactions in existing or novel biodegradation pathways.

Gene regulation in continuous cultures: a unified theory for bacteria and yeasts

During batch growth on mixtures of two growth-limiting substrates, microbes consume the substrates either sequentially (diauxie) or simultaneously. The ubiquity of these growth patterns suggests that they may be driven by a universal mechanism common to all microbial species. Recently, we showed that a minimal model accounting only for enzyme induction and dilution, the two processes that occur in all microbes, explains the phenotypes observed in batch cultures of various wild-type and mutant/recombinant cells (Narang and Pilyugin in J. Theor. Biol. 244:326-348, 2007). Here, we examine the extension of the minimal model to continuous cultures. We show that: (1) Several enzymatic trends, attributed entirely to cross-regulatory mechanisms, such as catabolite repression and inducer exclusion, can be quantitatively explained by enzyme dilution. (2) The bifurcation diagram of the minimal model for continuous cultures, which classifies the substrate consumption pattern at any given dilution rate and feed concentrations, provides a precise explanation for the empirically observed correlations between the growth patterns in batch and continuous cultures. (3) Numerical simulations of the model are in excellent agreement with the data. The model captures the variation of the steady state substrate concentrations, cell densities, and enzyme levels during the single- and mixed-substrate growth of bacteria and yeasts at various dilution rates and feed concentrations. This variation is well approximated by simple analytical expressions that furnish deep physical insights. (4) Since the minimal model describes the behavior of the cells in the absence of cross-regulatory mechanisms, it provides a rigorous framework for quantifying the effect of these mechanisms. We illustrate this by analyzing several data sets from the literature.

Environmental fate of pharmaceuticals in water/sediment systems

In recent years there has been growing interest on the occurrence and the fate of pharmaceuticals in the aquatic environment. Nevertheless, few data are available covering the fate of the pharmaceuticals in the water/sediment compartment. In this study, the environmental fate of 10 selected pharmaceuticals and pharmaceutical metabolites was investigated in water/sediment systems including both the analysis of water and sediment. The experiments covered the application of four 14C-labeled pharmaceuticals (diazepam, ibuprofen, iopromide, and paracetamol) for which radio-TLC analysis was used as well as six nonlabeled compounds (carbamazepine, clofibric acid, 10,11-dihydro-10,11-dihydroxycarbamazepine, 2-hydroxyibuprofen, ivermectin, and oxazepam), which were analyzed via LC-tandem MS. Ibuprofen, 2-hydroxyibuprofen, and paracetamol displayed a low persistence with DT50 values in the water/sediment system < or =20 d. The sediment played a key role in the elimination of paracetamol due to the rapid and extensive formation of bound residues. A moderate persistence was found for ivermectin and oxazepam with DT50 values of 15 and 54 d, respectively. Lopromide, for which no corresponding DT50 values could be calculated, also exhibited a moderate persistence and was transformed into at least four transformation products. For diazepam, carbamazepine, 10,11-dihydro-10,11-dihydroxycarbamazepine, and clofibric acid, system DT90 values of >365 d were found, which exhibit their high persistence in the water/sediment system. An elevated level of sorption onto the sediment was observed for ivermectin, diazepam, oxazepam, and carbamazepine. Respective Koc values calculated from the experimental data ranged from 1172 L x kg(-1) for ivermectin down to 83 L x kg(-1) for carbamazepine.