Functional characterization of an efficient ibuprofen-mineralizing bacterial consortium

Adaptive Laboratory Evolution of a Microbial Consortium Enhancing Non-Protein Nitrogen Assimilation for Feed Protein Production

The increasing global demand for protein underscores the necessity for sustainable alternatives to soybean-based animal feed, which poses a challenge to human food security. Thus, the search for sustainable, alternative protein sources is transforming the feed industry in its effort to sustainable operations. In this study, a microbial consortium was subjected to adaptive laboratory evolution using non-protein nitrogen (NPN) and wheat straw as the sole carbon source. The evolved microbial consortium was subsequently utilized to perform solid-state fermentation on wheat straw and NPN to produce feed protein. After 20 generations, the microbial consortium demonstrated tolerance to 5 g/L NPN, including ammonium sulfate, ammonium chloride, and urea, which represents a fivefold increase compared to the original microbial consortium. Among the three NPNs tested, the evolved microbial consortium exhibited optimal growth performance with ammonium sulfate. Subsequently, the evolved microbial consortium was employed for the solid-state fermentation (SSF) of wheat straw, and the fermentation conditions were optimized. It was found that the true protein content of wheat straw could be increased from 2.74% to 10.42% under specific conditions: ammoniated wheat straw (15% w/w), non-sterilization of the substrate, an inoculation amount of 15% (v/w), nitrogen addition amount of 0.5% (w/w), an initial moisture content of 70%, a fermentation temperature of 30 °C, and a fermentation duration of 10 days. Finally, the SSF process for wheat straw was successfully scaled up from 0.04 to 2.5 kg, resulting in an increased true protein content of 9.84%. This study provides a promising approach for the production of feed protein from straw and NPN through microbial fermentation, addressing protein resource shortages in animal feed and improving the value of waste straw.

Impact of ibuprofen on nitrogen removal performance and its biotransformation in a coupled sulfur autotrophic denitrification and anammox system

Ibuprofen (IBU), a commonly used non-steroidal anti-inflammatory drug, is frequently detected in wastewater treatment systems, where it can interfere with nitrogen removal. This study investigated the effects of IBU on nitrogen removal performance and its biotransformation in a coupled sulfur autotrophic denitrification and anammox (SAD/A) system. Moreover, key parameters, such as nitrogen removal efficiency, microbial activity, community structure, and IBU degradation products, were carefully monitored. While IBU concentrations of up to 1 mg/L had negligible impacts on nitrogen removal efficiency due to the counteracting effects of slight inhibition on anammox and enhancement of sulfur autotrophic denitrification, a significant inhibition of ammonia removal occurred when the concentration increased to 10 mg/L. Quantum chemical analyses revealed that IBU underwent biotransformation through decarboxylation and hydroxylation pathways, leading to the formation of two biotransformation products with high ecological toxicity. This study is the first to elucidate the mechanisms by which IBU influences microbial communities and metabolic activities in SAD/A systems. In addition, it highlights the resilience of these systems in maintaining nitrogen removal efficiency under varying IBU concentrations, as well as the environmental risks posed by the biotransformation products of IBU.

Genetic and species rearrangements in microbial consortia impact biodegradation potential

Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the re-organisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.

Microbes as Resources to Remove PPCPs and Improve Water Quality

The inadequate removal of pharmaceuticals and personal care products (PPCPs) by traditional wastewater treatment plants (WWTPs) poses a significant environmental and public health challenge. Residual PPCPs find their way into aquatic ecosystems, leading to bioaccumulation in aquatic biota, the dissemination of antibiotic resistance genes (ARGs), and contamination of both water sources and vegetables. These persistent pollutants can have negative effects on human health, ranging from antibiotic resistance development to endocrine disruption. To mitigate these risks, there is a growing interest in exploiting microorganisms and their enzymes for bioremediation purposes. By harnessing the metabolic capabilities of microbial communities, PPCPs can be efficiently degraded, transformed, or sequestered in water systems. Additionally, microbial communities exhibit remarkable adaptability and resilience to diverse PPCP contaminants, further underscoring their potential as sustainable and cost-effective solutions for water treatment. This review explores the promise of microbial bioremediation as an approach to addressing the complex challenges posed by persistent PPCP contamination, emphasising its potential to safeguard both environmental integrity and human well-being.

Characteristics and functional bacteria of an efficient benzocaine-mineralizing bacterial consortium

The extensive use of pharmaceutical and personal care products (PPCPs) has led to widespread residual pollution, which increases the risk of the development of drug resistance in pathogenic microorganisms. Benzocaine is a PPCP that is widely used medical anesthesia and in sunscreen. Microorganisms are essential for the degradation of residual PPCPs. However, no studies have reported the microbial degradation of benzocaine. In this study, through continuous enrichment of the initial consortium HJ1, the highly efficient benzocaine-degrading consortium HJ7 was obtained, HJ7 exhibited a degradation rate that was 1.92 times greater than that of HJ1. Methyl 4-aminobenzoate and 4-aminobenzoic acid were identified as major intermediate products during benzocaine biodegradation by consortium HJ1 or HJ7. Methylobacillus (57.8 % ± 0.9 %) and Pseudomonas (22.1 % ± 0.7 %), which are thought to harbor essential species for benzocaine degradation, were significantly enriched in consortium HJ7. Two benzocaine-degrading strains, Pseudomonas sp. A8 and Microbacterium sp. A741, and one methyl 4-aminobenzoate-degrading strain, Achromobacter sp. A5, were isolated from consortium HJ7, and they synergistically mineralized benzocaine. These findings not only provide new insights into the biotransformation of benzocaine but also provide strain resources for the bioremediation of residual benzocaine in the environment.

Identification of a Novel Ibuprofen Biotransformation Pathway in Streptomyces sp. D218 and Detoxification as Indicated by the Green Algae Scenedesmus obliquus

Ibuprofen, a widely used nonsteroidal anti-inflammatory drug, contaminates agricultural products and potentially threatens human health due to its frequent detection and poor biodegradability. Microbial metabolism dominates the elimination of residual ibuprofen in the environment. In mineral salt medium at pH 6 with 5 mM glucose, Streptomyces sp. D218 transformed ibuprofen concentrations ranging from 0.05 to 0.40 mM in 24 h. The optimal temperature, pH, and initial OD600 nm for ibuprofen transformation by strain D218 were 25-37 °C, 5.0-6.0, and 1.0-1.5, respectively. Strain D218 could simultaneously transform ibuprofen into the intermediates 2-hydroxyibuprofen and ibuprofen amide (IBUA). The two intermediates were further metabolized to 2-hydroxyibuprofen amide (2HIBUA), thus relieving the growth inhibition of ibuprofen in Scenedesmus obliquus. This is the first complete pathway reported for the detoxification of ibuprofen transformation by a Gram-positive strain. These findings further our understanding of the microbial catabolism of the IBU.

New bacterial strains for ibuprofen biodegradation: Drug removal, transformation, and potential catabolic genes

Ibuprofen (IBU) is a significant contaminant frequently found in wastewater treatment plants due to its widespread use and limited removal during treatment processes. This leads to its discharge into the environment, causing considerable environmental concerns. The use of microorganisms has recently been recognized as a sustainable method for mitigating IBU contamination in wastewater. In this study, new bacteria capable of growing in a solid medium with IBU as the only carbon source and removing IBU from a liquid medium were isolated from environmental samples, including soil, marine, mine, and olive mill wastewater. Four bacterial strains, namely Klebsiella pneumoniae TIBU2.1, Klebsiella variicola LOIBU1.1, Pseudomonas aeruginosa LOIBU1.2, and Mycolicibacterium aubagnense HPB1.1, were identified through 16S rRNA gene sequencing. These strains demonstrated significant IBU removal efficiencies, ranging from 60 to 100% within 14 days, starting from an initial IBU concentration of 5 mg per litre. These bacteria have not been previously reported in the literature as IBU degraders, making this work a valuable contribution to further studies in the field of bioremediation in environments contaminated by IBU. Based on the IBU removal results, the most promising bacteria, K. pneumoniae TIBU2.1 and M. aubagnense HPB1.1, were selected for an in silico analysis to identify genes potentially involved in IBU biodegradation. Interestingly, in the tests with TIBU2.1, a peak of IBU transformation product(s) was detected by high-performance liquid chromatography, while in the tests with HPB1.1, it was not detected. The emerging peak was analysed by liquid chromatography-mass spectrometry, indicating the presence of possible conjugates between intermediates of IBU biodegradation. The proteins encoded on their whole-genome sequences were aligned with proteins involved in an IBU-degrading pathway reported in bacteria with respective catabolic genes. The analysis indicated that strain HPB1.1 possesses genes encoding proteins similar to most enzymes reported associated with the IBU metabolic pathways used as reference bacteria, while strain TIBU2.1 has genes encoding proteins similar to enzymes involved in both the upper and the lower part of that pathway. Notably, in the tests with the strain having more candidate genes encoding IBU-catabolic enzymes, no IBU transformation products were detected, while in the tests with the strain having fewer of these genes, detection occurred.

Ibuprofen-enhanced biodegradation in solution and sewage sludge by a mineralizing microbial consortium. Shift in associated bacterial communities

Ibuprofen (IBP) is a widely used drug of environmental concern as emerging contaminant due to its low elimination rates by wastewater treatment plants (WWTPs), leading to the contamination of the environment, where IBP is introduced mainly from wastewater discharge and sewage sludge used as fertilizer. This study describes the application of a consortium from sewage sludge and acclimated with ibuprofen (consortium C7) to accelerate its biodegradation both in solution and sewage sludge. 500 mg L-1 IBP was degraded in solution in 28 h, and 66% mineralized in 3 days. IBP adsorbed in sewage sludge (10 mg kg-1) was removed after bioaugmentation with C7 up to 90% in 16 days, with a 5-fold increase in degradation rate. This is the first time that bioaugmentation with bacterial consortia or isolated bacterial strains have been used for IBP degradation in sewage sludge. The bacterial community of consortium C7 was significantly enriched in Sphingomonas wittichii, Bordetella petrii, Pseudomonas stutzeri and Bosea genosp. after IBP degradation, with a special increase in abundance of S. wittichii, probably the main potential bacterial specie responsible for IBP mineralization. Thirteen bacterial strains were isolated from C7 consortium. All of them degraded IBP in presence of glucose, especially Labrys neptuniae. Eight of these bacterial strains (B. tritici, L. neptuniae, S. zoogloeoides, B. petrii, A. denitrificans, S. acidaminiphila, P. nitroreducens, C. flaccumfaciens) had not been previously described as IBP-degraders. The bacterial community that makes up the indigenous consortium C7 appears to have a highly efficient biotic degradation potential to facilitate bioremediation of ibuprofen in contaminated effluents as well as in sewage sludge generated in WWTPs.

Highly effective degradation of ibuprofen by alkaline metal-doped copper oxides via peroxymonosulfate activation: Mechanisms, degradation pathway and toxicity assessments

Redox ratios of Cu2+/Cu+ and adsorbed oxygen species (Oads) have shown great activity toward radical generation by activating peroxymonosulfate (PMS). Herein, different alkaline metal oxides (CaO, MgO and BaO) and various amounts of CaO are incorporated into CuO, which could tune the main active sites of redox ratios of Cu2+/Cu+ and Oads. The results show that CaO-CuO-5% exhibits the outstanding performance of PMS activation toward ibuprofen (IBF) degradation with excellent kinetics (k = 0.812 min-1). The X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculation show that the CaO-CuO-5% has the higher electron density with superior electron transfer ability and lower PMS adsorption energy. Based on radical scavengers and electron paramagnetic resonance spectrometer (EPR), a nonradical process is proposed to play the dominant role. The degradation pathway and the corresponding toxicity of degraded intermediates with residue PMS after reaction is evaluated by LC-MS/MS and bioassay experiments, indicating the lower antagonistic influence on human hormone receptors after advanced oxidation process. Mitigation of the Cu leaching with cyclic stability can be achieved. This study provides a facile method to optimize high-performance catalysts to activate PMS and offer practical environmental applications in the remediation of emerging contaminants.

Progressive Biocatalysts for the Treatment of Aqueous Systems Containing Pharmaceutical Pollutants

The review focuses on the appearance of various pharmaceutical pollutants in various water sources, which dictates the need to use various methods for effective purification and biodegradation of the compounds. The use of various biological catalysts (enzymes and cells) is discussed as one of the progressive approaches to solving problems in this area. Antibiotics, hormones, pharmaceuticals containing halogen, nonsteroidal anti-inflammatory drugs, analgesics and antiepileptic drugs are among the substrates for the biocatalysts in water purification processes that can be carried out. The use of enzymes in soluble and immobilized forms as effective biocatalysts for the biodegradation of various pharmaceutical compounds (PCPs) has been analyzed. Various living cells (bacteria, fungi, microalgae) taken as separate cultures or components of natural or artificial consortia can be involved in biocatalytic processes under aerobic or anaerobic conditions. Cells as biocatalysts introduced into water treatment systems in suspended or immobilized form are used for deep biodegradation of PCPs. The potential of combinations of biocatalysts with physical-chemical methods of wastewater treatment is evaluated in relation to the effective removing of PCPs. The review analyzes recent results and the main current trends in the development of biocatalytic approaches to biodegradation of PCPs, the pros and cons of the processes and the biocatalysts used.