A general model for multiple substrate biodegradation. Application to co-metabolism of structurally non-analogous compounds

Coupling pathway prediction and fluorescence spectroscopy to assess the impact of auxiliary substrates on micropollutant biodegradation

Some bacteria can degrade organic micropollutants (OMPs) as primary carbon sources. Due to typically low OMP concentrations, these bacteria may benefit from supplemental assimilation of natural substrates present in the pool of dissolved organic matter (DOM). The biodegradability of such auxiliary substrates and the impacts on OMP removal are tightly linked to biotransformation pathways. Here, we aimed to elucidate the biodegradability and effect of different DOM constituents for the carbofuran degrader Novosphingobium sp. KN65.2, using a novel approach that combines pathway prediction, laboratory experiments, and fluorescence spectroscopy. Pathway prediction suggested that ring hydroxylation reactions catalysed by Rieske-type dioxygenases and flavin-dependent monooxygenases determine the transformability of the 11 aromatic compounds used as model DOM constituents. Our approach further identified two groups with distinct transformation mechanisms amongst the four growth-supporting compounds selected for mixed substrate biodegradation experiments with the pesticide carbofuran (Group 1: 4-hydroxybenzoic acid, 4-hydroxybenzaldehyde; Group 2: p-coumaric acid, ferulic acid). Carbofuran biodegradation kinetics were stable in the presence of both Group 1 and Group 2 auxiliary substrates. However, Group 2 substrates would be preferable for bioremediation processes, as they showed constant biodegradation kinetics under different experimental conditions (pre-growing KN65.2 on carbofuran vs. DOM constituent). Furthermore, Group 2 substrates were utilisable by KN65.2 in the presence of a competitor (Pseudomonas fluorescens sp. P17). Our study thus presents a simple and cost-efficient approach that reveals mechanistic insights into OMP-DOM biodegradation.

Alkaline-thermal hydrolysate of waste activated sludge as a co-metabolic substrate enhances biodegradation of refractory dye reactive black 5

Aromatic azo dyes possess inherent resistance and are known to be carcinogenic, posing a significant threat to human and ecosystems. Enhancing the biodegradation of azo dyes usually requires the presence of co-metabolic substrates to optimize the process. In addressing the issue of excessive waste activated sludge (WAS) generation, this study explored the potential of utilizing alkaline-thermal hydrolysate of WAS as a co-metabolic substrate to boost the degradation of reactive black 5 (RB5) dyes. The acclimated microbial consortium, when supplemented with the WAS hydrolysate obtained at a hydrolysis temperature of 30 °C, achieved an impressive RB5 decolorization efficiency of 90.3% (pH = 7, 35 °C) with a corresponding COD removal efficiency of 45.0%. The addition of WAS hydrolysate as a co-substrate conferred the consortium with a remarkable tolerance to high dye concentration (1500 mg/L RB5) and salinity levels (4-5%), surpassing the performance of conventional co-metabolic sugars in RB5 degradation. 3D-EEM analysis revealed that protein-like substances rich in tyrosine and tryptophan, present in the WAS hydrolysate, played a crucial role in promoting RB5 biodegradation. Furthermore, the microbial consortium community exhibited an enrichment of dye-degrading species, including Acidovorax, Bordetella, Kerstersia, and Brevundimonas, which dominated the community. Notably, functional genes associated with dye degradation and intermediates were also enriched during the RB5 decolorization and biodegradation process. These findings present a practical strategy for the simultaneous treatment of dye-containing wastewater and recycling of WAS.

Enhanced removal of nitrate and refractory organic pollutants from bio-treated coking wastewater using corncobs as carbon sources and biofilm carriers

The quality of the bio-treated coking wastewater (BTCW) is difficult to meet increasingly stringent coking wastewater discharge standards and future wastewater recycling needs. In this study, the pre-treatment process of BTCW was installed including the two up-flow fixed-bed bioreactors (UFBRs) which were separately filled with alkali-pretreated or no alkali-pretreated corncobs used as solid carbon sources as well as biofilm carriers. Results showed that this pre-treatment process could significantly improve the biodegradability of BTCW and increase the C/N ratio. Thus, over 90% of residual nitrate in BTCW were removed stably. Furthermore, GC-MS analysis confirmed that the typical refractory organic matters decreased significantly after UFBRs pre-treatment. High-throughput sequencing analysis using 16S rRNA demonstrated that dominant denitrifiers, fermentative bacteria and refractory-organic-pollutants-degrading bacteria co-existed inside the UFBRs system. Compared with no alkali-pretreated corncobs, alkali-pretreated corncobs provided more porous structure and much stable release of carbon to guarantee the growth and the quantity of the functional bacteria such as denitrifiers. This study indicated that the UFBRs filled with alkali-pretreated corncobs could be utilized as an effective alternative for the enhanced treatment of the BTCW.

Metabolic routes involved in the removal of linear alkylbenzene sulfonate (LAS) employing linear alcohol ethoxylated and ethanol as co-substrates in enlarged scale fluidized bed reactor

In this study, the microbial community characterization and metabolic pathway identification involved in the linear alkylbenzene sulfonated (LAS) degradation from commercial laundry wastewater in a fluidized bed reactor (FBR) on an increased scale were performed using the Illumina MiSeq platform. Ethanol and non-ionic surfactant (LAE, Genapol C-100) were used as co-substrates. The FBR was operated in five operational phases: (I) synthetic substrate for inoculation; (II) 7.9 ± 4.7 mg/L LAS and 11.7 ± 6.9 mg/L LAE; (III) 19.4 ± 12.9 mg/L LAS, 19.6 ± 9.2 mg/L LAE and 205 mg/L ethanol; (IV) 25.9 ± 11 mg/L LAS, 19.5 ± 9.1 mg/L LAE and 205 mg/L ethanol and (V) 43.9 ± 18 mg/L LAS, 25 ± 9.8 mg/L LAE and 205 mg/L ethanol. At all operation phases, organic matter was removed from 40.4 to 85.1% and LAS removal was from 24.7 to 56%. Sulfate-reducing bacteria (SRB) were identified in the biofilm of FBR in all operational phases. Although the LAS promoted a toxic effect on the microbiota, this effect can be reduced when using biodegradable co-substrates, such as ethanol and LAE, which was observed in Phase IV. In this phase, there was a greater microbial diversity (Shannon index) and higher microorganism richness (Chao 1 index), both for the Domain Bacteria, and for the Domain Archaea.

Dracaena sanderiana endophytic bacteria interactions: Effect of endophyte inoculation on bisphenol A removal

Bisphenol A (BPA) is one of the most abundant endocrine-disrupting compounds which is found in the aquatic environment. However, actual knowledge regarding the effect of plant-bacteria interactions on enhancing BPA removal is still lacking. In the present study, Dracaena sanderiana endophytic bacteria interactions were investigated to evaluate the effect of bacterial inoculation on BPA removal under hydroponic conditions. Two plant growth-promoting (PGP) bacterial strains, Bacillus thuringiensis and Pantoea dispersa, which have high BPA tolerance and can utilize BPA for growth, were used as plant inocula. P. dispersa-inoculated plants showed the highest BPA removal efficiency at 92.32 ± 1.23% compared to other inoculated and non-inoculated plants. This was due to a higher population of the endophytic inoculum within the plant tissues which resulted in maintained levels of indole-3-acetic acid (IAA) for the plant's physiological needs and lower levels of reactive oxygen species (ROS). In contrast, B. thuringiensis-inoculated plants had a lower BPA removal efficiency. However, individual B. thuringiensis possessed a significantly higher BPA removal efficiency compared to P. dispersa. This study provides convincing evidence that not all PGP endophytic bacteria-plant interactions could improve the BPA removal efficiency. Different inocula and inoculation times should be investigated before using plant inoculation to enhance phytoremediation.

Removals of non-analogous OTC and BaP in AMCBR with and without primary substrate

Anaerobic biodegradation of mixed non-analogous two substrates was studied in a binary system with and without the primary substrate using an anaerobic multichamber bed (AMCBR). In the binary mixture, the biodegradation of less-degradable oxytetracycline (OTC) was restarted in the presence of more degradable benzo[a]pyrene (BaP) in the initial runs of the AMCBR, but enhanced biodegradation of the more recalcitrant OTC occurs in the later runs of the AMCBR due to enhanced biomass growth on dual substrates without the primary carbon source. The biodegradation yields of the OTC, BaP were discussed with sole-substrate systems and with the dual substrate system in the presence of the primary substrate. The maximum OTC and BaP yields were 93% in Run 3 with the primary substrate, while the maximum BaP and OTC yields were 95%, 98% in Run 3 without the primary substrate. A dual form of the Monod was found to adequately predict the substrate interactions in the binary mixture of OTC and BaP using only the parameters derived from batch experiments. At low BaP (4 mg L(-1)) and OTC (40 mg L(-1)) concentrations, a non-competitive inhibition does not affect the binding of the substrate and so the K(s) were was not affected while the µ(max) was lowered. At high BaP (10 mg L(-1)) and OTC (100 mg L(-1)) concentrations, the BaP and OTC were biodegraded according to competitive inhibition with increased K(s) while µ(max) was not affected. BaP and OTC were biodegraded according to Haldane at high concentrations (>10 mg L(-1) for BaP, 100 mg L(-1) OTC) where they were used as the sole substrate.

The comparative advantages of ethanol and sucrose as co-substrates in the degradation of an anionic surfactant: microbial community selection

The efficiency of linear alkylbenzene sulfonate (LAS) removal from laundry wastewater and the related microbial community was investigated in an anaerobic fluidized bed reactor (AFBR). The AFBR was operated in three stages, in addition to the biomass adaptation stage without LAS (stage I). The stages were differentiated by their supplementary co-substrates: stage II had sucrose plus ethanol, stage III had only ethanol, and stage IV had no co-substrate. The replacement of sucrose plus ethanol with ethanol only for the substrate composition favored the efficiency of LAS removal, which remained high after the co-substrate was removed (stage II: 52 %; stage III: 73 %; stage IV: 77 %). A transition in the microbial community from Comamonadaceae to Rhodocyclaceae in conjunction with the co-substrate variation was observed using ion sequencing analysis. The microbial community that developed in response to an ethanol-only co-substrate improved LAS degradation more than the community that developed in response to a mixture of sucrose and ethanol, suggesting that ethanol is a better option for enriching an LAS-degrading microbial community.

Triphenyltin biodegradation and intracellular material release by Brevibacillus brevis

Triphenyltin (TPT) is an endocrine disruptor that has polluted the global environment, and thus far, information regarding the mechanisms of TPT biodegradation and intracellular material release is limited. Here, TPT biodegradation was conducted by using Brevibacillus brevis. Degradation affecting factors, metabolite formation, ion and protein release, membrane permeability, and cell viability after degradation were investigated to reveal the biodegradation mechanisms. The results showed that TPT could be degraded simultaneously to diphenyltin and monophenyltin, with diphenyltin further degraded to monophenyltin, and ultimately to inorganic tin. During degradation process, B. brevis metabolically released Cl(-) and Na(+), and passively diffused Ca(2+). Protein release and membrane permeability were also enhanced by TPT exposure. pH ranging from 6.0 to 7.5 and relatively high biomass dosage in mineral salt medium improved TPT degradation. Biodegradation efficiency of 0.5 mg L(-1) TPT by 0.3 g L(-1)B. brevis at 25 °C for 5d was up to 80%.

Cometabolic degradation of organic wastewater micropollutants by activated sludge and sludge-inherent microorganisms

Municipal wastewaters contain a multitude of organic trace pollutants. Often, their biodegradability by activated sludge microorganisms is decisive for their elimination during wastewater treatment. Since the amounts of micropollutants seem too low to serve as growth substrate, cometabolism is supposed to be the dominating biodegradation process. Nevertheless, as many biodegradation studies were performed without the intention to discriminate between metabolic and cometabolic processes, the specific contribution of the latter to substance transformations is often not clarified. This minireview summarizes current knowledge about the cometabolic degradation of organic trace pollutants by activated sludge and sludge-inherent microorganisms. Due to their relevance for communal wastewater contamination, the focus is laid on pharmaceuticals, personal care products, antibiotics, estrogens, and nonylphenols. Wherever possible, reference is made to the molecular process level, i.e., cometabolic pathways, involved enzymes, and formed transformation products. Particular cometabolic capabilities of different activated sludge consortia and various microbial species are highlighted. Process conditions favoring cometabolic activities are emphasized. Finally, knowledge gaps are identified, and research perspectives are outlined.

Removal of trace organic chemicals in onsite wastewater soil treatment units: a laboratory experiment

Onsite wastewater treatment is used by 20% of residences in the United States. The ability of these systems, specifically soil treatment units (STUs), to attenuate trace organic chemicals (TOrCs) is not well understood. TOrCs released by STUs pose a potential risk to downstream groundwater and hydraulically-connected surface water that may be used as a drinking water source. A series of bench-scale experiments were conducted using sand columns to represent STUs and to evaluate the efficacy of TOrC attenuation as a function of hydraulic loading rate (1, 4, 8, 12, and 30 cm/day). Each hydraulic loading rate was examined using triplicate experimental columns. Columns were initially seeded with raw wastewater to establish a microbial community, after which they were fed with synthetic wastewater and spiked with 17 TOrCs, in four equal doses per day, to provide a consistent influent water quality. After an initial start-up phase, effluent from all columns consistently demonstrated >90% reductions in dissolved organic carbon and nearly complete (>85%) oxidation of ammonia to nitrate, comparable to the performance of field STUs. The results of this study suggest STUs are capable of attenuating many TOrCs present in domestic wastewater, but attenuation is compound-specific. A subset of TOrCs exhibited an inverse relationship with hydraulic loading rate and attenuation efficiency. Atenolol, cimetidine, and TCPP were more effectively attenuated over time in each experiment, suggesting that the microbial community evolved to a stage where these TOrCs were more effectively biotransformed. Aerobic conditions as compared to anaerobic conditions resulted in more efficient attenuation of acetaminophen and cimetidine.

Laboratory and field verification of a method to estimate the extent of petroleum biodegradation in soil

We describe a new and rapid quantitative approach to assess the extent of aerobic biodegradation of volatile and semivolatile hydrocarbons in crude oil, using Shushufindi oil from Ecuador as an example. Volatile hydrocarbon biodegradation was both rapid and complete-100% of the benzene, toluene, xylenes (BTEX) and 98% of the gasoline-range organics (GRO) were biodegraded in less than 2 days. Severe biodegradation of the semivolatile hydrocarbons occurred in the inoculated samples with 67% and 87% loss of the diesel-range hydrocarbons (DRO) in 3 and 20 weeks, respectively. One-hundred percent of the naphthalene, fluorene, and phenanthrene, and 46% of the chrysene in the oil were biodegraded within 3 weeks. Percent depletion estimates based on C(30) 17α,21β(H)-hopane (hopane) underestimated the diesel-range organics (DRO) and USEPA 16 priority pollutant PAH losses in the most severely biodegraded samples. The C(28) 20S-triaromatic steroid (TAS) was found to yield more accurate depletion estimates, and a new hopane stability ratio (HSR = hopane/(hopane + TAS)) was developed to monitor hopane degradation in field samples. Oil degradation within field soil samples impacted with Shushufindi crude oil was 83% and 98% for DRO and PAH, respectively. The gas chromatograms and percent depletion estimates indicated that similar levels of petroleum degradation occurred in both the field and laboratory samples, but hopane degradation was substantially less in the field samples. We conclude that cometabolism of hopane may be a factor during rapid biodegradation of petroleum in the laboratory and may not occur to a great extent during biodegradation in the field. We recommend that the hopane stability ratio be monitored in future field studies. If hopane degradation is observed, then the TAS percent depletion estimate should be computed to correct for any bias that may result in petroleum depletion estimates based on hopane.

Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories

The dynamic modelling of metabolic networks aims to describe the temporal evolution of metabolite concentrations in cells. This area has attracted increasing attention in recent years owing to the availability of high-throughput data and the general development of systems biology as a promising approach to study living organisms. Biochemical Systems Theory (BST) provides an accurate formalism to describe biological dynamic phenomena. However, knowledge about the molecular organization level, used in these models, is not enough to explain phenomena such as the driving forces of these metabolic networks. Dynamic Energy Budget (DEB) theory captures the quantitative aspects of the organization of metabolism at the organism level in a way that is non-species-specific. This imposes constraints on the sub-organismal organization that are not present in the bottom-up approach of systems biology. We use in vivo data of lactic acid bacteria under various conditions to compare some aspects of BST and DEB approaches. Due to the large number of parameters to be estimated in the BST model, we applied powerful parameter identification techniques. Both models fitted equally well, but the BST model employs more parameters. The DEB model uses similarities of processes under growth and no-growth conditions and under aerobic and anaerobic conditions, which reduce the number of parameters. This paper discusses some future directions for the integration of knowledge from these two rich and promising areas, working top-down and bottom-up simultaneously. This middle-out approach is expected to bring new ideas and insights to both areas in terms of describing how living organisms operate.

Biodegradation of phenol at high concentration by a novel fungal strain Paecilomyces variotii JH6

A novel phenol-degrading filamentous fungus, strain JH6, was isolated from activated sludge and identified as a member of Paecilomyces variotii based on standard morphological and phylogenetic analysis. The degradation assays suggested that the strain was able to utilize phenol as the sole source of carbon and energy at concentrations up to 1800 mg/l. The strain exhibited optimum phenol degradation performance with the addition of 100 mg/l glucose at pH 5, 37°C. Haldane's model could be fitted to the growth kinetics data well over a wide range of initial phenol concentrations (100-1800 mg/l), with kinetic values μ(max)=0.312 h(-1), K(s)=130.4 mg/l, and K(i)=200 mg/l. The decay coefficient was found to be 0.0073 h(-1). Complete phenol degradation by strain JH6 could be achieved in the presence of other toxicants, such as m-cresol and quinoline, which were often found in the real phenol-containing wastewater.

Predicting the accumulation of harmful metabolic byproducts during the treatment of VOC emissions in suspended growth bioreactors

A predicting model is proposed to evaluate metabolic byproducts accumulation and process performance in suspended growth reactors treating air emissions contaminated with volatile organic compounds (VOCs). The model presented integrates a multistep kinetic model and a general mechanistic model describing bioreactor operation. This integrated model is based on general equations modeling, both mass transport and the mechanisms underlying pollutant biotransformation and byproducts accumulation, and can be applied to a wide range of operating conditions (VOC substrate, O2, and nutrients limitation). The model was tested for predicting benzyl alcohol (BA) accumulation in a chemostat reactor treating toluene. BA accumulates in Pseudomonas putida F1 cultures degrading toluene as a result of methyl monooxygenation reaction parallel to the main TOD degradation pathway. The operational conditions leading to BA accumulation are evaluated through simulations assays. Simulation results indicate that BA accumulation occurs when other substrates rather than toluene are limiting. Therefore, operation under toluene limitation is highly recommended to ensure not only the detoxification goals but also to avoid potential mutagenic effects of BA over the microbial culture.

Quantitative steps in the evolution of metabolic organisation as specified by the Dynamic Energy Budget theory

The Dynamic Energy Budget (DEB) theory quantifies the metabolic organisation of organisms on the basis of mechanistically inspired assumptions. We here sketch a scenario for how its various modules, such as maintenance, storage dynamics, development, differentiation and life stages could have evolved since the beginning of life. We argue that the combination of homeostasis and maintenance induced the development of reserves and that subsequent increases in the maintenance costs came with increases of the reserve capacity. Life evolved from a multiple reserves - single structure system (prokaryotes, many protoctists) to systems with multiple reserves and two structures (plants) or single reserve and single structure (animals). This had profound consequences for the possible effects of temperature on rates. We present an alternative explanation for what became known as the down-regulation of maintenance at high growth rates in microorganisms; the density of the limiting reserve increases with the growth rate, and reserves do not require maintenance while structure-specific maintenance costs are independent of the growth rate. This is also the mechanism behind the variation of the respiration rate with body size among species. The DEB theory specifies reserve dynamics on the basis of the requirements of weak homeostasis and partitionability. We here present a new and simple mechanism for this dynamics which accounts for the rejection of mobilised reserve by busy maintenance/growth machinery. This module, like quite a few other modules of DEB theory, uses the theory of Synthesising Units; we review recent progress in this field. The plasticity of membranes that evolved in early eukaryotes is a major step forward in metabolic evolution; we discuss quantitative aspects of the efficiency of phagocytosis relative to the excretion of digestive enzymes to illustrate its importance. Some processes of adaptation and gene expression can be understood in terms of allocation linked to the relative workload of metabolic modules in (unicellular) prokaryotes and organs in (multicellular) eukaryotes. We argue that the evolution of demand systems can only be understood in the light of that of supply systems. We illustrate some important points with data from the literature.

A kinetic inhibition mechanism for maintenance

To fulfil their maintenance costs, most species use mobile pools of metabolites (reserve) in favourable conditions, but can also use less mobile pools (structure) under food-limiting conditions. While some empirical models always pay maintenance costs from structure, the presence of reserve inhibits the use of structure for maintenance purposes. The standard dynamic energy budgets (DEB) model captures this by simply supplementing all costs that could not be paid from reserve with structure. This is less realistic at the biochemical level, and involves a sudden use of structure that can complicate the analysis of the model properties. We here propose a new inhibition formulation for the preferential use of reserve above structure in maintenance that avoids sudden changes in the metabolites use. It is based on the application of the theory for synthesizing units, which can easily become rather complex for demand processes, such as the maintenance. We found, however, a simple explicit expression for the use of reserve and structure for maintenance purposes and compared the numerical behaviour with that of a classical model in oscillating conditions, by using parameters values from a fit of the models to data on yeasts in a batch culture. We conclude that our model can better handle variable environments. This new inhibition formulation has a wide applicability in modelling metabolic processes.

A multi-step kinetic model for substrate assimilation and bacterial growth: Application to benzene biodegradation

A multi-step kinetic model based on the concept of synthesizing unit (SU) was developed for describing benzene biodegradation in Pseudomonas putida F1. The model herein presented considered substrate arrival rates to the SU rather than concentrations, and provided a reasonable good fit of the dynamics of both catechol and biomass concentrations experimentally determined. It was based on very general assumptions and could be applied to any process accumulating metabolic intermediates. Conventional growth models considering a single step can be regarded as a particular case of this multi-step model. Despite the merits of this model, its applicability strongly depends on the knowledge of the complex induction-repression and inhibition mechanisms governing the different catabolic steps of the degradation pathway, which in most cases are difficult to elucidate experimentally and/or to model mathematically. In this particular case repression of benzene oxidation by catechol and self-inhibition of catechol transformation were experimentally confirmed and considered in the simulation, resulting in a good fit (relative average error of 6%) of the experimental data.

Behavior of lipids in biological wastewater treatment processes

Lipids (characterized as oils, greases, fats and long-chain fatty acids) are important organic components of wastewater. Their amount, for example, in municipal wastewater is approximately 30-40% of the total chemical oxygen demand. The concern over the behavior of lipids in biological treatment systems has led to many studies, which have evaluated their removal, but still the exact behavior of lipids in these processes is not well understood. In this review, we discuss the current knowledge of how lipids/fatty acids affect both aerobic and anaerobic processes and specific methods that have been used in an attempt to enhance their removal from wastewater. Overall, the literature shows that lipids/fatty acids are readily removed by biological treatment methods, inhibitory to microbial growth as well as the cause of foaming, growth of filamentous bacteria and floc flotation.

Modelling microbial adaptation to changing availability of substrates

In their natural environment microorganisms encounter changes in substrate availability, involving either nutrient concentrations or nutrient types. They have to adapt to the new conditions in order to survive. We present a model for slow microbial adaptation, involving the synthesis of new enzymes, in response to changes in the availability of substitutable substrates. The model is based on reciprocal (or mutual) inhibition of expression of both the substrate-specific carriers and the associated assimilatory machinery. The inhibition kinetics is derived from the kinetics of synthesizing units. An interesting property of the adaptation model is that the presence of a single limiting resource results in a constant maximum specific substrate consumption rate for fully adapted microorganisms. Because the maximum specific consumption rate is not a function of substrate concentration, for growth on one substrate, the Monod and Pirt models for instance are still valid. Other adaptation models known to us do not fulfil this property. The simplest version of our model describes adaptation during diauxic growth, using only one preference parameter and one initial condition. The applicability of the model is exemplified by fitting it to published data from diauxic growth experiments.