New perspectives on the anaerobic degradation of BTEX: Mechanisms, pathways, and intermediates.

Aromatic hydrocarbons like benzene, toluene, xylene, and ethylbenzene (BTEX) can escape into the environment from oil and gas operations and manufacturing industries posing significant health risks to humans and wildlife. Unlike conventional clean-up methods used, biological approaches such as bioremediation can provide a more energy and labour-efficient and environmentally friendly option for sensitive areas such as nature reserves and cities, protecting biodiversity and public health. BTEX contamination is often concentrated in the subsurface of these locations where oxygen is rapidly depleted, and biodegradation relies on anaerobic processes. Thus, it is critical to understand the anaerobic biodegradation characteristics as it has not been explored to a major extent. This review presents novel insights into the degradation mechanisms under anaerobic conditions and presents a detailed description and interconnection between them. BTEX degradation can follow four activation mechanisms: hydroxylation, carboxylation, methylation, and fumarate addition. Hydroxylation is one of the mechanisms that explains the transformation of benzene into phenol, toluene into benzyl alcohol or p-cresol, and ethylbenzene into 1-phenylethanol. Carboxylation to benzoate is thought to be the primary mechanism of degradation for benzene. Despite being poorly understood, benzene methylation has been also reported. Moreover, fumarate addition is the most widely reported mechanism, present in toluene, ethylbenzene, and xylene degradation. Further research efforts are required to better elucidate new and current alternative catabolic pathways. Likewise, a comprehensive analysis of the enzymes involved as well as the development of advance tools such as omic tools can reveal bottlenecks degradation steps and create more effective on-site strategies to address BTEX pollution.

A Two Bacteriocinogenic Ligilactobacillus Strain Association Inhibits Growth, Adhesion, and Invasion of Salmonella in a Simulated Chicken Gut Environment.

In this study, we aimed to develop a protective probiotic coculture to inhibit the growth of Salmonella enterica serovar Typhimurium in the simulated chicken gut environment. Bacterial strains were isolated from the digestive mucosa of broilers and screened in vitro against Salmonella Typhimurium ATCC 14028. A biocompatibility coculture test was performed, which identified two biocompatible strains, Ligilactobacillus salivarius UO.C109 and Ligilactobacillus saerimneri UO.C121 with high inhibitory activity against Salmonella. The cell-free supernatant (CFS) of the selected isolates exhibited dose-dependent effects, and the inhibitory agents were confirmed to be proteinaceous by enzymatic and thermal treatments. Proteome and genome analyses revealed the presence of known bacteriocins in the CFS of L. salivarius UO.C109, but unknown for L. saerimneri UO.C121. The addition of these selected probiotic candidates altered the bacterial community structure, increased the diversity of the chicken gut microbiota challenged with Salmonella, and significantly reduced the abundances of Enterobacteriaceae, Parasutterlla, Phascolarctobacterium, Enterococcus, and Megamonas. It also modulated microbiome production of short-chain fatty acids (SCFAs) with increased levels of acetic and propionic acids after 12 and 24 h of incubation compared to the microbiome challenged with S. Typhimurium. Furthermore, the selected probiotic candidates reduced the adhesion and invasion of Salmonella to Caco-2 cells by 37-39% and 51%, respectively, after 3 h of incubation, compared to the control. These results suggest that the developed coculture probiotic strains has protective activity and could be an effective strategy to control Salmonella infections in poultry.

Formulation of synthetic bacteria consortia for enzymatic biodegradation of polyaromatic hydrocarbons contaminated soil: soil column study.

As an efficient method to remove contaminants from highly polluted sites, enzyme biodegradation addresses unresolved issues such as bioremediation inefficiency. In this study, the key enzymes involved in PAH degradation were brought together from different arctic strains for the biodegradation of highly contaminated soil. These enzymes were produced via a multi-culture of psychrophilic Pseudomonas and Rhodococcus strains. As a result of biosurfactant production, the removal of pyrene was sufficiently prompted by Alcanivorax borkumensis. The key enzymes (e.g., naphthalene dioxygenase, pyrene dioxygenase, catechol-2,3 dioxygenase, 1-hydroxy-2-naphthoate hydroxylase, protocatechuic acid 3,4-dioxygenase) obtained via multi-culture were characterized by tandem LC-MS/MS and kinetic studies. To simulate in situ application of produced enzyme solutions, pyrene- and dilbit-contaminated soil was bioremediated in soil columns and flask tests by injecting enzyme cocktails from the most promising consortia. The enzyme cocktail contained about 35.2 U/mg protein pyrene dioxygenase, 61.4 U/mg protein naphthalene dioxygenase, 56.5 U/mg protein catechol-2,3-dioxygenase, 6.1 U/mg protein 1-hydroxy-2-naphthoate hydroxylase, and 33.5 U/mg protein protocatechuic acid (P3,4D) 3,4-dioxygenase enzymes. It was found that after 6 weeks, the average pyrene removal values showed that the enzyme solution could be effective in the soil column system (80-85% degradation of pyrene).

Evaluation of scale-up effect on cold-active enzyme production and biodegradation tests using pilot-scale bioreactors and a 3D soil tank.

Despite recent attention being paid to the biodegradation of petroleum hydrocarbons in cold environments, scale-up studies of biodegradation are lacking. Herein, the effect of scale-up on the enzymatic biodegradation of highly contaminated soil at low temperatures was studied. A novel cold-adapted bacteria (Arthrobacter sp. S2TR-06) was isolated that could produce cold-active degradative enzymes (xylene monooxygenase (XMO) and catechol 2,3-dioxygenase (C2,3D)). Enzyme production was investigated on 4 different scales (lab to pilot scale). The results showed a shorter fermentation time, and the highest production of enzymes and biomass (107 g/L for biomass, 109 U/mL, and 203 U/mL for XMO and C2,3D after 24 h) was achieved in the 150-L bioreactor due to enhanced oxygenation. Multi-pulse injection of p-xylene into the production medium was needed every 6 h. The stability of membrane-bound enzymes can be increased up to 3-fold by adding FeSO4 at 0.1% (w/v) before extraction. Soil tests also showed that biodegradation is scale-dependent. The maximum biodegradation rate decreased from 100% at lab-scale to 36% in the 300-L sand tank tests due to limited access of enzymes to trapped p-xylene in soil pores, low dissolved oxygen in the water-saturated zone, soil heterogeneity, and the presence of the free phase of p-xylene. The result demonstrated that formulation of enzyme mixture with FeSO4 and direct injection of enzyme mixture (third scenario) can increase the efficiency of bioremediation in heterogeneous soil. In this study, it was demonstrated that cold-active degradative enzyme production can be scaled up to an industrial scale and enzymatic treatment can be used to effectively bioremediate p-xylene contaminated sites. This study could provide key scale-up guidance for the enzymatic bioremediation of mono-aromatic pollutants in water-saturated soil under cold conditions.

Neuromicrobiology, an emerging neurometabolic facet of the gut microbiome?

The concept of the gut microbiome is emerging as a metabolic interactome influenced by diet, xenobiotics, genetics, and other environmental factors that affect the host's absorption of nutrients, metabolism, and immune system. Beyond nutrient digestion and production, the gut microbiome also functions as personalized polypharmacy, where bioactive metabolites that our microbes excrete or conjugate may reach systemic circulation and impact all organs, including the brain. Appreciable evidence shows that gut microbiota produce diverse neuroactive metabolites, particularly neurotransmitters (and their precursors), stimulating the local nervous system (i.e., enteric and vagus nerves) and affecting brain function and cognition. Several studies have demonstrated correlations between the gut microbiome and the central nervous system sparking an exciting new research field, neuromicrobiology. Microbiome-targeted interventions are seen as promising adjunctive treatments (pre-, pro-, post-, and synbiotics), but the mechanisms underlying host-microbiome interactions have yet to be established, thus preventing informed evidence-based therapeutic applications. In this paper, we review the current state of knowledge for each of the major classes of microbial neuroactive metabolites, emphasizing their biological effects on the microbiome, gut environment, and brain. Also, we discuss the biosynthesis, absorption, and transport of gut microbiota-derived neuroactive metabolites to the brain and their implication in mental disorders.

Simulation of novel jellyfish type of process for bioremediation application.

A bioinspired device was fabricated as a sustainable remedial method and its performance as a membrane-enzyme reactor with cyclic ultrafiltration was investigated. The body of the jellyfish-like device was composed of two parts: 1) Jellyfish arms: Mono and co-axial electrospinning have been utilized to synthesize the flexible parts (e.g., multilayer membrane PS-PVDF/PAN/PS-PVDF) used for immobilization of aliphatic degrading enzymes, and 2) Jellyfish tentacles: Hollow fiber membranes were selected for physical immobilization of polycyclic aromatic hydrocarbon (PAH) degrading enzymes. To study the behavior of the membrane/enzyme reactor, the hollow fiber enzyme reactor with pulsation was operated by recycling an enzyme solution to assess ultrafiltration efficiency. A mathematical model was suggested to describe the experimental data obtained in this study to predict the effectiveness of the reactor for PAH removal. When testing the performance of the jellyfish-like device, those equipped with nanofibers with an oil sorption capacity of (10. ±0.7gdilbit/gfiber) were more effective at removing oil particles before they touched the hollow fiber membrane surface. Moreover, the reaction rate measured in a free soluble enzyme and a recirculating immobilized enzyme solution exhibited a slight difference in the kinetic parameter, Km (0.03 and 0.021 mM) due to the internal diffusional resistance. Based on biodegradation studies, a synergistic effect between membrane adsorption, enzymatic degradation, and ultrafiltration was proposed for the removal of anthracene from the column of water.

Pilot-scale production and in-situ application of petroleum-degrading enzyme cocktail from Alcanivorax borkumensis.

Petroleum degrading enzymes can be used as an alternative way to improve petroleum bioremediation approaches. Alcanivorax borkumensis is an alkane-degrading bacteria that can produce petroleum degrading enzymes such as alkane hydroxylase and lipase. In this study, pilot-scale Alcanivorax borkumensis fermentation was developed for producing large volumes of petroleum degrading enzymes cocktail (∼900 L). Different process conditions, such as inoculum age 72 h and size 4% v/v, temperature 30 ± 1 °C, agitation speed at 150 rpm and, fermentation period 3 days were determined as the optimum for producing alkane hydroxylase and lipase activity. The oxygen transfer capacity was studied for obtaining better bacterial growth and higher enzyme activities in bioreactor process optimization as well as scale-up. Results showed that the maximum values of oxygen mass transfer coefficient (kLa), oxygen uptake rate (OUR), oxygen transfer rate (OTR), alkane hydroxylase, lipase, and cell count were 196.95 h-1, 0.92 mmol O2/L/h, 1.8 mmol O2/L/h, 222.49 U/mL, 325 U/mL, and 8.6 × 1010 CFU/mL, respectively. Compared with the bench-scale bioreactors, the 150 L fermenter showed a better oxygen transfer rate which affected the cell growth that doubled the number and enzymes production that increased. Then, the enzyme cocktail was used for a field test in a diesel source zone using a 5-spot well pattern. The results showed a significant reduction in concentrations of C10 - C50 (from 36% to > 99%) after one injection of enzyme cocktail, mainly for the contaminated soils located in the saturated zone of the unconfined aquifer. This study confirmed the scaling-up ofalkane-degrading enzyme production to an industrial-scale and its application for effective bioremediation of petroleum contaminated sites.

Enzymatic biodegradation of highly p-xylene contaminated soil using cold-active enzymes: A soil column study.

Enzymatic bioremediation is a sustainable and environment-friendly method for the clean-up of contaminated soil and water. In the present study, enzymatic bioremediation was designed using cold-active enzymes (psychrozymes) which catalyze oxidation steps of p-xylene biodegradation in highly contaminated soil (initial concentration of 13,000 mg/kg). The enzymes were obtained via co-culture of two psychrophilic Pseudomonas strains and characterized by kinetic studies and tandem LC-MS/MS. To mimic in situ application of enzyme mixture, bioremediation of p-xylene contaminated soil was carried out in soil column (140 mL) tests with the injection (3 pore volume) of different concentrations of enzyme cocktails (X, X/5, and X/10). Enzyme cocktail in X concentration contained about 10 U/mL of xylene monooxygenase (XMO) and 20 U/mL of catechol 2, 3 dioxygenases (C2,3D). X/5 and X/10 correspond to 5x and 10x dilution of enzyme cocktail respectively. The results showed that around 92-94% p-xylene removal was achieved in the treated soil column with enzyme concentration X, X/5 after second enzyme injection. While the p-xylene removal rate obtained by X/10 concentration of enzyme was less than 30% and near to untreated soil column (22.2%). The analysis of microbial diversity and biotoxicity assay (root elongation and seed germination) confirmed the advantage of using enzymes as a green and environmentally friendly approach for decontamination of pollutants with minimal or even positive effects on microbial community and also enrichment of soil after treatment.

Biodegradation of microplastics: Better late than never.

Plastics use is growing due to its applications in the economy, human health and aesthetics. The major plastic particles in the form of microplastics (MPs) released into the environment are made up of polyethylene (PE), polypropylene (PP), polyvinylchloride (PVC), and polyethylene terephthalate (PET). Tremendous usage and continuous accumulation of MPs in the environment pose a global threat to ecosystems and human health. The current knowledge of biotechnological, aerobic and aerobic biodegradation approaches emphasizes the microbial culture's potential towards MPs removal. This review selectively provides recent biotechnological advances such as biostimulation, bioaugmentation and enzymatic biodegradation that can be applied for MPs removal by biodegradation and bioaccumulation. This review summarizes the knowledge and the research exploration on the biodegradation of synthetic organic MPs with different biodegradability. However, further research is still needed to understand the underlying mechanism of MPs biodegradation in soil and water systems, leading to the development of an effective method for MPs removal.

Biodegradation of p-xylene-a comparison of three psychrophilic Pseudomonas strains through the lens of gene expression.

p-Xylene is considered a recalcitrant compound despite showing a similar aromatic structure to other BTEXs (benzene, toluene, ethylbenzene, xylene isomers). This study evaluated the p-xylene biodegradation potential of three psychrophilic Pseudomonas strains (Pseudomonas putida S2TR-01, Pseudomonas synxantha S2TR-20, and Pseudomonas azotoformans S2TR-09). The p-xylene metabolism-related catabolic genes (xylM, xylA, and xylE) and the corresponding regulatory genes (xylR and xylS) of the selected strains were investigated. The biodegradation results showed that the P. azotoformans S2TR-09 strain was the only strain that was able to degrade 200 mg/L p-xylene after 60 h at 15 °C. The gene expression study indicated that the xylE (encoding catechol 2,3-dioxygenase) gene represents the bottleneck in p-xylene biodegradation. A lack of xylE expression leads to the accumulation of intermediates and the inhibition of biomass production and complete carbon recovery. The activity of xylene monooxygenase and catechol 2,3-dioxygenase was significantly increased in P. azotoformans S2TR-09 (0.5 and 0.08 U/mg, respectively) in the presence of p-xylene. The expression of the ring cleavage enzyme and its encoding gene (xylE) and activator (xylS) explained the differences in the p-xylene metabolism of the isolated bacteria and can be used as a novel biomarker of efficient p-xylene biodegradation at contaminated sites.

Nanopore sensors for viral particle quantification: current progress and future prospects.

Rapid, inexpensive, and laboratory-free diagnostic of viral pathogens is highly critical in controlling viral pandemics. In recent years, nanopore-based sensors have been employed to detect, identify, and classify virus particles. By tracing ionic current containing target molecules across nano-scale pores, nanopore sensors can recognize the target molecules at the single-molecule level. In the case of viruses, they enable discrimination of individual viruses and obtaining important information on the physical and chemical properties of viral particles. Despite classical benchtop virus detection methods, such as amplification techniques (e.g., PCR) or immunological assays (e.g., ELISA), that are mainly laboratory-based, expensive and time-consuming, nanopore-based sensing methods can enable low-cost and real-time point-of-care (PoC) and point-of-need (PoN) monitoring of target viruses. This review discusses the limitations of classical virus detection methods in PoN virus monitoring and then provides a comprehensive overview of nanopore sensing technology and its emerging applications in quantifying virus particles and classifying virus sub-types. Afterward, it discusses the recent progress in the field of nanopore sensing, including integrating nanopore sensors with microfabrication technology, microfluidics and artificial intelligence, which have been demonstrated to be promising in developing the next generation of low-cost and portable biosensors for the sensitive recognition of viruses and emerging pathogens.

Sustainable production and co-immobilization of cold-active enzymes from Pseudomonas sp. for BTEX biodegradation.

Toluene/o-Xylene Monooxygenase (ToMO) is equipped with a broad spectrum of aromatic substrate specificity (such as BTEX; benzene, toluene, ethylbenzene, and isomers of xylenes). TOMO has can hydroxylate more than a single position of aromatic rings in two consecutive monooxygenation reactions. Catechol 1,2-dioxygenase (C1,2D) is an iron-containing enzyme able to cleave the ring of catechol (the converted product from ToMO) for complete detoxification of BTEX. In this study, cold-active ToMO and C1,2D were produced using newly isolated psychrophilic Pseudomonas S2TR-14 in the minimal salt medium supplemented with crustacean waste and different concentrations of used motor oil (0.2-2% (v/v)). Crude ToMO and C1,2D were immobilized into micro/nano biochar-chitosan matrices and used for BTEX biodegradation. The results showed that the highest enzyme production (12 U/mg for ToMO and 22 U/mg for C1,2D) was achieved at the presence of 0.5% v/v used motor oil compared to the control group without motor oil (0.07 and 0.06 U/mg). High immobilization yield was achieved due to covalent bonding of ToMO (92.26% for micro matrix and 77.20% for nano matrix) and C1,2D (87.57% for micro matrix and 74.79% for nano matrix) with matrices. FTIR spectra confirmed the immobilization of enzymes on the surface of microbiochar and nanobiochar-chitosan matrices as proper support. The immobilization increased the storage stability of the enzymes with more than 50% residual activity after 30 days at 4 ± 1 °C, while the free form of enzymes had less than 10% of its activity. Immobilized enzymes degraded more than 80% of BTEX (~200 mg/L in groundwater and ~10,000 mg/kg in soil) at 10 ± 1 °C in groundwater and soil. Therefore, integrated use of microbiochar and nanobiochar with chitosan for co-immobilization of ToMO and C1,2D can be a potential way to remove petroleum hydrocarbons with higher efficiency from contaminated groundwater and soil.

Psychrozymes as novel tools to biodegrade p-xylene and potential use for contaminated groundwater in the cold climate.

Sites contaminated by petroleum hydrocarbons in cold-climate regions have recently received significant attention due to their sensitive ecosystem and human health impacts. Two cold-adapted pseudomonas strains were isolated from contaminated groundwater and soil. As xylene monooxygenase from Pseudomonas synxantha S2TR-26 and catechol 2,3-dioxygenase from Pseudomonas mandelii S2TR-08, have a matching end product, they acted in symphony to degrade p-xylene. Their unique thermodynamic and kinetic behavior permits them to achieve rapid degradation of p-xylene at low temperatures (<15 °C). The results showed that the sequential action led to the conversion of 200 mg/l of p-xylene within 72 h and complete degradation after 120 h. The cocktail of these enzymes with a ratio of 1:1.5 (xylene monooxygenase: catechol 2, 3-dioxygenase) confirmed the complete degradation of p-xylene within 48 h at 15 °C. This approach will allow efficient biodegradation of p-xylene to minimize the bioremediation duration in cold-climate regions.

Bioremediation of Unconventional Oil Contaminated Ecosystems under Natural and Assisted Conditions: A Review.

It is a general understanding that unconventional oil is petroleum-extracted and processed into petroleum products using unconventional means. The recent growth in the United States shale oil production and the lack of refineries in Canada built for heavy crude processes have resulted in a significant increase in U.S imports of unconventional oil since 2018. This has increased the risk of incidents and catastrophic emergencies during the transportation of unconventional oils using transmission pipelines and train rails. A great deal of effort has been made to address the remediation of contaminated soil/sediment following the traditional oil spills. However, spill response and cleanup techniques (e.g., oil recuperation, soil-sediment-water treatments) showed slow and inefficient performance when it came to unconventional oil, bringing larger associated environmental impacts in need of investigation. To the best of our knowledge, there is no coherent review available on the biodegradability of unconventional oil, including Dilbit and Bakken oil. Hence, in view of the insufficient information and contrasting results obtained on the remediation of petroleum, this review is an attempt to fill the gap by presenting the collective understanding and critical analysis of the literature on bioremediation of products from the oil sand and shale (e.g., Dilbit and Bakken oil). This can help evaluate the different aspects of hydrocarbon biodegradation and identify the knowledge gaps in the literature.

Data on changes of NF-κB gene expression in liver and lungs as a biomarker and hepatic injury in CLP-induced septic rats.

Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is a ubiquitous transcription factor, which plays a key role in regulating immune response against infection. Increased and/or prolonged activation of NF-κB has been linked to cancer, inflammatory, autoimmune diseases and viral infection. The purpose of this set of data was to evaluate NF-κB gene expression in cecal ligation and puncture (CLP)- induced septic rats and associated hepatic cell changes. Here, we provide the information about the evaluation of NF-κB gene expression using Real-time PCR and histopathological data of liver-related to our study published in the Turkish Journal of Medical Sciences [1]. Also, the information of the primers and more details about gene expression evaluation by real-time PCR of the targeted gene is provided. The data present here introduced another biomarker in liver and lung of CLP- induced septic rats and also confirmed hepatic dysfunction based on the pathological data. The histopathologic assessment showed normal condition in control group, mild infiltration of neutrophils in the liver parenchyma and portal tracts in LAP group (laparotomy) but severe congestion, severe neutrophil infiltration in the liver parenchyma and portal tracts in the CLP group. The data from real-time PCR showed that NF-κB expression was significantly increased in the CLP group compared with the control and LAP group, so it can be a biomarker for (CLP)- induced sepsis. This set of data and our previous study underscored the powerful potential of using the real-time PCR method to determine the involvement of genes such as MPO, CD177, and NF-κB in infectious diseases like sepsis.

Expression changes of CD177 and MPO as novel biomarkers in lung tissue of CLP model rats

Background/aim: Sepsis is an unregulated systemic response to microbial invasion that can lead to multiple organ failure. This study aims at investigating the relationships among myeloperoxidase (MPO) and CD177 in major organ systems including whole blood, liver, and lung tissues in septic rats. Materials and methods: Sepsis was induced by cecal ligation and puncture (CLP) in female Wistar rats. Whole blood, liver, and lung samples were obtained from rats of 3 groups (n = 10 for each group, n total = 30: control as a wild-type group, laparotomy group (LAP), and CLP). Gene expression of MPO and CD177 in targeted tissues was determined by real-time PCR after CLP. MPO activity was also determined by ELISA method for the result validation of the real-time PCR. Results: Expression levels of MPO increased significantly in all targeted organs in the CLP group, while CD177 expression was upregulated only in lung tissue in response to sepsis (P < 0.05). The results obtained with ELISA analysis also show that MPO level was significantly increased in all the targeted tissues in the CLP group (P < 0.05). Conclusion: A high level of MPO as an inflammatory enzyme can be a potentially novel biomarker for sepsis in all organs. On the other hand, CD177 may be a marker in lung tissue.

Effect of metal sulfide pulp density on gene expression of electron transporters in Acidithiobacillus sp. FJ2.

In Acidithiobacillus ferrooxidans, one of the most important bioleaching bacterial species, the proteins encoded by the rus operon are involved in the electron transfer from Fe2+ to O2. To obtain further knowledge about the mechanism(s) involved in the adaptive responses of the bacteria to growth on the different uranium ore pulp densities, we analyzed the expression of the four genes from the rus operon by real-time PCR, when Acidithiobacillus sp. FJ2 was grown in the presence of different uranium concentrations. The uranium bioleaching results showed the inhibitory effects of the metal pulp densities on the oxidation activity of the bacteria which can affect Eh, pH, Fe oxidation and uranium extractions. Gene expression analysis indicated that Acidithiobacillus sp. FJ2 tries to survive in the stress with increasing in the expression levels of cyc2, cyc1, rus and coxB, but the metal toxicity has a negative effect on the gene expression in different pulp densities. These results indicated that Acidithiobacillus sp. FJ2 could leach the uranium even in high pulp density (50%) by modulation in rus operon gene responses.