Silica gel-encapsulated AtzA biocatalyst for atrazine biodegradation

Mechanistic and recent updates in nano-bioremediation for developing green technology to alleviate agricultural contaminants

The rise in environmental pollutant levels in recent years is mostly attributable to anthropogenic activities such as industrial, agricultural and other activities. Additionally, these activities may produce excessive levels of dangerous toxicants such as heavy metals, organic pollutants including pesticide and herbicide chemicals, and sewage discharges from residential and commercial sources. With a focus on environmentally friendly, sustainable technology, new technologies such as combined process of nanotechnology and bioremediation are urgently needed to accelerate the cost-effective remediation process to alleviate toxic contaminants than the conventional remediation methods. Numerous studies have shown that nanoparticles possess special qualities including improved catalysis and adsorption as well as increased reactivity. Currently, microorganisms and their extracts are being used as promising, environmentally friendly catalysts for engineered nanomaterial. In the long term, this combination of both technologies called nano-bioremediation may significantly alter the field of environmental remediation since it is more intelligent, safe, environmentally friendly, economical and green. This review provides an overview of soil and water remediation techniques as well as the use of nano-bioremediation, which is made from various living organisms. Additionally, current developments related to the mechanism, model and kinetic studies for remediation of agricultural contaminants have been discussed.

Insight into the enhancing mechanism of silica nanoparticles on denitrification: Effect on electron transfer and microbial metabolism

Although silica nanoparticles (SiNPs) are produced in large numbers for industrial manufacturing and engineering applications, the effect of SiNPs on biotransformation in the environment is still not clear. In the current study, the effect of SiNPs in enhancing denitrification was investigated, and its mechanism was explored from the perspectives of electron transfer, microbial metabolism and bacterial community structure for the first time. Batch experiments showed that a concentration of SiNPs ranging from 0.05 to 5 g/L enhanced the bioreduction of nitrate. The mechanism study showed that SiNPs accelerated the extracellular electron transfer in the denitrification process due to their electron donating capacity, bonding action, and the secretion of more electron shuttles. During the denitrification process, SiNPs promoted metabolic activity, which mainly consists of promoting enzyme activities and electron transport system activity; these metabolic activity assays were positively correlated with SiNPs according to the structural equation modeling analysis. Moreover, SiNPs affected the composition of the microbial community, including denitrifying functional bacteria, silicon-activating bacteria and electron transfer active bacteria exhibiting a synergistic symbiosis. In addition, it was shown, by investigating two functional group-modified SiNPs, that the carboxyl modified SiNPs had the potential to be applied in nitrogen removal due to their performance and non-toxicity. This study presented a better insight into the role of SiNPs in biological transformation.

Multiple Roles of Mesoporous Silica in Safe Pesticide Application by Nanotechnology: A Review

Pollution related to pesticides has become a global problem due to their low utilization and non-targeting application, and nanotechnology has shown great potential in promoting sustainable agriculture. Nowadays, mesoporous silica-based nanomaterials have garnered immense attention for improving the efficacy and safety of pesticides due to their distinctive advantages of low toxicity, high thermal and chemical stability, and particularly size tunability and versatile functionality. Based on the introduction of the structure and synthesis of different types of mesoporous silica nanoparticles (MSNs), the multiple roles of mesoporous silica in safe pesticide application using nanotechnology are discussed in this Review: (i) as nanocarrier for sustained/controlled delivery of pesticides, (ii) as adsorbent for enrichment or removal of pesticides in aqueous media, (iii) as support of catalysts for degradation of pesticide contaminants, and (iv) as support of sensors for detection of pesticides. Several scientific issues, strategies, and mechanisms regarding the application of MSNs in the pesticide field are presented, with their future directions discussed in terms of their environmental risk assessment, in-depth mechanism exploration, and cost-benefit consideration for their continuous development. This Review will provide critical information to related researchers and may open up their minds to develop new advances in pesticide application.

A Bacillus Spore-Based Display System for Bioremediation of Atrazine

Owing to human activities, a large number of organic chemicals, including petroleum products, industrial solvents, pesticides, herbicides (including atrazine [ATR]), and pharmaceuticals, contaminate soil and aquatic environments. Remediation of these pollutants by conventional approaches is both technically and economically challenging. Bacillus endospores are highly resistant to most physical assaults and are capable of long-term persistence in soil. Spores can be engineered to express, on their surface, important enzymes for bioremediation purposes. We have developed a Bacillus thuringiensis spore platform system that can display a high density of proteins on the spore surface. The spore surface-tethered enzymes exhibit enhanced activity and stability relative to free enzymes in soil and water environments. In this study, we evaluated a B. thuringiensis spore display platform as a bioremediation tool against ATR. The Pseudomonas sp. strain ADP atzA determinant, an ATR chlorohydrolase important to the detoxification of ATR, was expressed as a fusion protein linked to the attachment domain of the BclA spore surface nap layer protein and expressed in B. thuringiensis Spores from this strain are decorated with AtzA N-terminally linked on the surface of the spores. The recombinant spores were assayed for ATR detoxification in liquid and soil environments, and enzyme kinetics and stability were assessed. We successfully demonstrated the utility of this spore-based enzyme display system to detoxify ATR in water and laboratory soil samples.IMPORTANCE Atrazine is one of the most widely applied herbicides in the U.S. midwestern states. The long environmental half-life of atrazine has contributed to the contamination of surface water and groundwater by atrazine and its chlorinated metabolites. The toxic properties of ATR have raised public health and ecological concerns. However, remediation of ATR by conventional approaches has proven to be costly and inefficient. We developed a novel B. thuringiensis spore platform system that is capable of long-term persistence in soil and can be engineered to surface express a high density of enzymes useful for bioremediation purposes. The enzymes are stably attached to the surface of the spore exosporium layer. The spore-based system will likely prove useful for remediation of other environmental pollutants as well.

Bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application

The synthetic s-triazines are abundant, nitrogen-rich, heteroaromatic compounds used in a multitude of applications including, herbicides, plastics and polymers, and explosives. Their presence in the environment has led to the evolution of bacterial catabolic pathways in bacteria that allow use of these anthropogenic chemicals as a nitrogen source that supports growth. Herbicidal s-triazines have been used since the mid-twentieth century and are among the most heavily used herbicides in the world, despite being withdrawn from use in some areas due to concern about their safety and environmental impact. Bacterial catabolism of the herbicidal s-triazines has been studied extensively. Pseudomonas sp. strain ADP, which was isolated more than thirty years after the introduction of the s-triazine herbicides, has been the model system for most of these studies; however, several alternative catabolic pathways have also been identified. Over the last five years, considerable detail about the molecular mode of action of the s-triazine catabolic enzymes has been uncovered through acquisition of their atomic structures. These structural studies have also revealed insights into the evolutionary origins of this newly acquired metabolic capability. In addition, s-triazine-catabolizing bacteria and enzymes have been used in a range of applications, including bioremediation of herbicides and cyanuric acid, introducing metabolic resistance to plants, and as a novel selectable marker in fermentation organisms. In this review, we cover the discovery and characterization of bacterial strains, metabolic pathways and enzymes that catabolize the s-triazines. We also consider the evolution of these new enzymes and pathways and discuss the practical applications that have been considered for these bacteria and enzymes. One Sentence Summary: A detailed understanding of bacterial herbicide catabolic enzymes and pathways offer new evolutionary insights and novel applied tools.

Evaluating formulation and storage of Arthrobacter aurescens strain TC1 as a bioremediation tool for terbuthylazine contaminated soils: Efficacy on abatement of aquatic ecotoxicity

Recently, a bioremediation tool consisting of freshly grown cells of the Arthrobacter aurescens strain TC1 proved successful in the cleanup of terbuthylazine (TBA) contaminated soil, with potential to prevent TBA dispersal via the soil-water pathway. The present work aimed at examining the feasibility of preparing and formulating bioaugmentation bacterial cells in advance which retain adequate viability and herbicide-degrading activity during storage and transport to contaminated sites. Three different types of formulation of A. aurescens TC1 cells were performed, namely cell paste, lyophilized, and adsorbed onto the mineral carrier vermiculite. Vermiculite-based cell material and cell paste offered survival rates significantly higher (≥78% of cells recovered viable, when compared to the initial numbers) than lyophilized cells (≥65%) after storage at 4 °C for up to a maximum period of 30 days. Inocula prepared from the three types of formulated and stored cells supported adequate levels of herbicide-biodegradation activity, ultimately allowing an almost complete removal of TBA from either liquid buffer or soil. In soil microcosms, the efficacy of bioremediation of TBA-contaminated soil in terms of decontamination (%) based on the ecotoxicity assessment of soil eluates towards a freshwater microalga was found to differ within formulations in the order: lyophilized cells (~100% efficacy at the end of one or two weeks of bioremediation treatment with an initial inoculum of ~2.5 × 10⁷ viable cells/g of soil; similar to fresh cells) > vermiculite-adsorbed cells (81% with ~2.4 × 10⁸ cells/g) > cell paste (68% with ~2.4 × 10⁸ cells/g). The limitations and advantages of each type of bacterial formulation, together with the prediction of their applicability in the field are discussed.

Signal Disruption Leads to Changes in Bacterial Community Population

The disruption of bacterial signaling (quorum quenching) has been proven to be an innovative approach to influence the behavior of bacteria. In particular, lactonase enzymes that are capable of hydrolyzing the N-acyl homoserine lactone (AHL) molecules used by numerous bacteria, were reported to inhibit biofilm formation, including those of freshwater microbial communities. However, insights and tools are currently lacking to characterize, understand and explain the effects of signal disruption on complex microbial communities. Here, we produced silica capsules containing an engineered lactonase that exhibits quorum quenching activity. Capsules were used to design a filtration cartridge to selectively degrade AHLs from a recirculating bioreactor. The growth of a complex microbial community in the bioreactor, in the presence or absence of lactonase, was monitored over a 3-week period. Dynamic population analysis revealed that signal disruption using a quorum quenching lactonase can effectively reduce biofilm formation in the recirculating bioreactor system and that biofilm inhibition is concomitant to drastic changes in the composition, diversity and abundance of soil bacterial communities within these biofilms. Effects of the quorum quenching lactonase on the suspension community also affected the microbial composition, suggesting that effects of signal disruption are not limited to biofilm populations. This unexpected finding is evidence for the importance of signaling in the competition between bacteria within communities. This study provides foundational tools and data for the investigation of the importance of AHL-based signaling in the context of complex microbial communities.

Enhanced biodegradation of atrazine by bacteria encapsulated in organically modified silica gels

Biodegradation by cells encapsulated in silica gel is an economical and environmentally friendly method for the removal of toxic chemicals from the environment. In this work, recombinant E. coli expressing atrazine chlorohydrolase (AtzA) were encapsulated in organically modified silica (ORMOSIL) gels composed of TEOS, silica nanoparticles (SNPs), and either phenyltriethoxysilane (PTES) or methyltriethoxysilane (MTES). ORMOSIL gels adsorbed much higher amounts of atrazine than the hydrophilic TEOS gels. The highest amount of atrazine adsorbed by ORMOSIL gels was 48.91×10^-3μmol/mlgel, compared to 8.71×10^-3μmol/mlgel by the hydrophilic TEOS gels. Atrazine biodegradation rates were also higher in ORMOSIL gels than the TEOS gels, mainly due to co-localization of the hydrophobic substrate at high concentrations in close proximity of the encapsulated bacteria. A direct correlation between atrazine adsorption and biodegradation was observed unless biodegradation decreased due to severe phase separation. The optimized PTES and MTES gels had atrazine biodegradation rates of 0.041±0.003 and 0.047±0.004μmol/mlgel, respectively. These rates were approximately 80% higher than that measured in the TEOS gel. This study showed for the first time that optimized hydrophobic gel material design can be used to enhance both removal and biodegradation of hydrophobic chemicals.

Silica nanoparticle based techniques for extraction, detection, and degradation of pesticides

Silica nanoparticles (SiNPs) find applications in the fields of drug delivery, catalysis, immobilization and sensing. Their synthesis can be mediated in a facile manner and they display broad range compatibility and stability. Their existence in the form of spheres, wires and sheets renders them suitable for varied purposes. This review summarizes the use of silica nanostructures in developing techniques for extraction, detection and degradation of pesticides. Silica nanostructures on account of their sorbent properties, porous nature and increased surface area allow effective extraction of pesticides. They can be modified (with ionic liquids, silanes or amines), coated with molecularly imprinted polymers or magnetized to improve the extraction of pesticides. Moreover, they can be altered to increase their sensitivity and stability. In addition to the analysis of pesticides by sophisticated techniques such as High Performance Liquid Chromatography or Gas chromatography, silica nanoparticles related simple detection methods are also proving to be effective. Electrochemical and optical detection based on enzymes (acetylcholinesterase and organophosphate hydrolase) or antibodies have been developed. Pesticide sensors dependent on fluorescence, chemiluminescence or Surface Enhanced Raman Spectroscopic responses are also SiNP based. Moreover, degradative enzymes (organophosphate hydrolases, carboxyesterases and laccases) and bacterial cells that produce recombinant enzymes have been immobilized on SiNPs for mediating pesticide degradation. After immobilization, these systems show increased stability and improved degradation. SiNP are significant in developing systems for effective extraction, detection and degradation of pesticides. SiNPs on account of their chemically inert nature and amenability to surface modifications makes them popular tools for fabricating devices for 'on-site' applications.

Immobilized Biocatalyst for Detection and Destruction of the Insensitive Explosive, 2,4-Dinitroanisole (DNAN)

Accurate and convenient detection of explosive components is vital for a wide spectrum of applications ranging from national security and demilitarization to environmental monitoring and restoration. With the increasing use of DNAN as a replacement for 2,4,6-trinitrotoluene (TNT) in insensitive explosive formulations, there has been a growing interest in strategies to minimize its release and to understand and predict its behavior in the environment. Consequently, a convenient tool for its detection and destruction could enable development of more effective decontamination and demilitarization strategies. Biosensors and biocatalysts have limited applicability to the more traditional explosives because of the inherent limitations of the relevant enzymes. Here, we report a highly specific, convenient and robust biocatalyst based on a novel ether hydrolase enzyme, DNAN demethylase (that requires no cofactors), from a Nocardioides strain that can mineralize DNAN. Biogenic silica encapsulation was used to stabilize the enzyme and enable it to be packed into a model microcolumn for application as a biosensor or as a bioreactor for continuous destruction of DNAN. The immobilized enzyme was stable and not inhibited by other insensitive munitions constituents. An alternative method for DNAN detection involved coating the encapsulated enzyme on cellulose filter paper. The hydrolase based biocatalyst could provide the basis for a wide spectrum of applications including detection, identification, destruction or inertion of explosives containing DNAN (demilitarization operations), and for environmental restorations.

Toward Bioremediation of Methylmercury Using Silica Encapsulated Escherichia coli Harboring the mer Operon

Mercury is a highly toxic heavy metal and the ability of the neurotoxin methylmercury to biomagnify in the food chain is a serious concern for both public and environmental health globally. Because thousands of tons of mercury are released into the environment each year, remediation strategies are urgently needed and prompted this study. To facilitate remediation of both organic and inorganic forms of mercury, Escherichia coli was engineered to harbor a subset of genes (merRTPAB) from the mercury resistance operon. Protein products of the mer operon enable transport of mercury into the cell, cleavage of organic C-Hg bonds, and subsequent reduction of ionic mercury to the less toxic elemental form, Hg(0). E. coli containing merRTPAB was then encapsulated in silica beads resulting in a biological-based filtration material. Performing encapsulation in aerated mineral oil yielded silica beads that were smooth, spherical, and similar in diameter. Following encapsulation, E. coli containing merRTPAB retained the ability to degrade methylmercury and performed similarly to non-encapsulated cells. Due to the versatility of both the engineered mercury resistant strain and silica bead technology, this study provides a strong foundation for use of the resulting biological-based filtration material for methylmercury remediation.

Performance of a novel microwave-based treatment technology for atrazine removal and destruction: Sorbent reusability and chemical stability, and effect of water matrices

Transition metal-exchanged dealuminated Y zeolites were used to adsorb atrazine from aqueous solutions, followed by regeneration of the sorbents and destruction of the sorbed atrazine with microwave irradiation. Exchange of copper and iron into the zeolite's micropores significantly enhanced its sorption capacity and selectivity toward atrazine, and increased the microwave-induced degradation rate of the sorbed atrazine by 3-4-folds. Both the copper- and iron-exchanged zeolites could be regenerated and reused multiple times, while the catalytic activity of the latter was more robust due to the much greater chemical stability of Fe(3+) species in the micropores. The presence of humic acid, and common cations and anions had little impact on the sorption of atrazine on the transition metal-exchanged zeolites. In the treatment of atrazine spiked in natural surface water and groundwater samples, sorptive removal of atrazine was found to be impacted by the level of dissolved organic carbon, probably through competition for the micropore spaces and pore blocking, while the water matrices exhibited no strong effect on the microwave-induced degradation of sorbed atrazine. Overall, iron-exchanged dealuminated Y zeolites show great potential for removal and destruction of atrazine from contaminated surface water and groundwater in practical implementation of the novel treatment technology.

Silica Gel for Enhanced Activity and Hypochlorite Protection of Cyanuric Acid Hydrolase in Recombinant Escherichia coli

Chlorinated isocyanuric acids are widely used water disinfectants that generate hypochlorite, but with repeated application, they build up cyanuric acid (CYA) that must be removed to maintain disinfection. 3-Aminopropyltriethoxysilane (APTES)-treated Escherichia coli cells expressing cyanuric acid hydrolase (CAH) from Moorella thermoacetica exhibited significantly high CYA degradation rates and provided protection against enzyme inactivation by hypochlorite (chlorine). APTES coating or encapsulation of cells had two benefits: (i) overcoming diffusion limitations imposed by the cell wall and (ii) protecting against hypochlorite inactivation of CAH activity. Cells encapsulated in APTES gels degraded CYA three times faster than nonfunctionalized tetraethoxysilane (TEOS) gels, and cells coated with APTES degraded CYA at a rate of 29 µmol/min per mg of CAH protein, similar to the rate with purified enzyme. UV spectroscopy, fluorescence spectroscopy, and scanning electron microscopy showed that the higher rates were due to APTES increasing membrane permeability and enhancing cyanuric acid diffusion into the cytoplasm to reach the CAH enzyme. Purified CAH enzyme was shown to be rapidly inactivated by hypochlorite. APTES aggregates surrounding cells protected via the amine groups reacting with hypochlorite as shown by pH changes, zeta potential measurements, and infrared spectroscopy. APTES-encapsulated E. coli cells expressing CAH degraded cyanuric acid at high rates in the presence of 1 to 10 ppm hypochlorite, showing effectiveness under swimming pool conditions. In contrast, CAH activity in TEOS gels or free cells was completely inactivated by hypochlorite. These studies show that commercially available silica materials can selectively enhance, protect, and immobilize whole-cell biocatalysts for specialized applications.

Hypochlorite is used in vast quantities for water disinfection, killing bacteria on surfaces, and washing and whitening. In pools, spas, and other waters, hypochlorite is frequently delivered as chlorinated isocyanuric acids that release hypochlorite and cyanuric acid. Over time, cyanuric acid accumulates and impairs disinfection and must be removed. The microbial enzyme cyanuric acid hydrolase can potentially remove cyanuric acid to restore disinfection and protect swimmers. Whole bacterial cells expressing cyanuric acid hydrolase were encapsulated in an inert silica matrix containing an amine group. The amine group serves to permeabilize the cell membrane and accelerate cyanuric acid degradation, and it also reacts with hypochlorite to protect against inactivation of cyanuric acid hydrolase. Methods for promoting whole-cell biocatalysis are important in biotechnology, and the present work illustrates approaches to enhance rates and protect against an inhibitory substance.

Engineering of a silica encapsulation platform for hydrocarbon degradation using Pseudomonas sp. NCIB 9816-4

Industrial application of encapsulated bacteria for biodegradation of hydrocarbons in water requires mechanically stable materials. A silica gel encapsulation method was optimized for Pseudomonas sp. NCIB 9816-4, a bacterium that degrades more than 100 aromatic hydrocarbons. The design process focused on three aspects: (i) mechanical property enhancement; (ii) gel cytocompatibility; and (iii) reduction of the diffusion barrier in the gel. Mechanical testing indicated that the compressive strength at failure (σf ) and elastic modulus (E) changed linearly with the amount of silicon alkoxide used in the gel composition. Measurement of naphthalene biodegradation by encapsulated cells indicated that the gel maintained cytocompatibility at lower levels of alkoxide. However, significant loss in activity was observed due to methanol formation during hydrolysis at high alkoxide concentrations, as measured by FTIR spectroscopy. The silica gel with the highest amount of alkoxide (without toxicity from methanol) had a biodegradation rate of 285 ± 42 nmol/L-s, σf  = 652 ± 88 kPa, and E = 15.8 ± 2.0 MPa. Biodegradation was sustained for 1 month before it dropped below 20% of the initial rate. In order to improve the diffusion through the gel, polyvinyl alcohol (PVA) was used as a porogen and resulted in a 48 ± 19% enhancement in biodegradation, but it impacted the mechanical properties negatively. This is the first report studying how the silica composition affects biodegradation of naphthalene by Pseudomonas sp. NCIB 9816-4 and establishes a foundation for future studies of aromatic hydrocarbon biodegradation for industrial application.

Bacterial Cyanuric Acid Hydrolase for Water Treatment

Di- and trichloroisocyanuric acids are widely used as water disinfection agents, but cyanuric acid accumulates with repeated additions and must be removed to maintain free hypochlorite for disinfection. This study describes the development of methods for using a cyanuric acid-degrading enzyme contained within nonliving cells that were encapsulated within a porous silica matrix. Initially, three different bacterial cyanuric acid hydrolases were compared: TrzD from Acidovorax citrulli strain 12227, AtzD from Pseudomonas sp. strain ADP, and CAH from Moorella thermoacetica ATCC 39073. Each enzyme was expressed recombinantly in Escherichia coli and tested for cyanuric acid hydrolase activity using freely suspended or encapsulated cell formats. Cyanuric acid hydrolase activities differed by only a 2-fold range when comparing across the different enzymes with a given format. A practical water filtration system is most likely to be used with nonviable cells, and all cells were rendered nonviable by heat treatment at 70°C for 1 h. Only the CAH enzyme from the thermophile M. thermoacetica retained significant activity under those conditions, and so it was tested in a flowthrough system simulating a bioreactive pool filter. Starting with a cyanuric acid concentration of 10,000 μM, more than 70% of the cyanuric acid was degraded in 24 h, it was completely removed in 72 h, and a respike of 10,000 μM cyanuric acid a week later showed identical biodegradation kinetics. An experiment conducted with water obtained from municipal swimming pools showed the efficacy of the process, although cyanuric acid degradation rates decreased by 50% in the presence of 4.5 ppm hypochlorite. In total, these experiments demonstrated significant robustness of cyanuric acid hydrolase and the silica bead materials in remediation.

Use of silica-encapsulated Pseudomonas sp. strain NCIB 9816-4 in biodegradation of novel hydrocarbon ring structures found in hydraulic fracturing waters

The most problematic hydrocarbons in hydraulic fracturing (fracking) wastewaters consist of fused, isolated, bridged, and spiro ring systems, and ring systems have been poorly studied with respect to biodegradation, prompting the testing here of six major ring structural subclasses using a well-characterized bacterium and a silica encapsulation system previously shown to enhance biodegradation. The direct biological oxygenation of spiro ring compounds was demonstrated here. These and other hydrocarbon ring compounds have previously been shown to be present in flow-back waters and waters produced from hydraulic fracturing operations. Pseudomonas sp. strain NCIB 9816-4, containing naphthalene dioxygenase, was selected for its broad substrate specificity, and it was demonstrated here to oxidize fundamental ring structures that are common in shale-derived waters but not previously investigated with this or related enzymes. Pseudomonas sp. NCIB 9816-4 was tested here in the presence of a silica encasement, a protocol that has previously been shown to protect bacteria against the extremes of salinity present in fracking wastewaters. These studies demonstrate the degradation of highly hydrophobic compounds by a silica-encapsulated model bacterium, demonstrate what it may not degrade, and contribute to knowledge of the full range of hydrocarbon ring compounds that can be oxidized using Pseudomonas sp. NCIB 9816-4.

Silica–PEG gel immobilization of mammalian cells

In this study, human foreskin fibroblasts and mouse embryonic fibroblasts were encapsulated in mechanically reversible, THEOS and THEOS–PEG gels that completely immobilized them restricting their motility, growth and proliferation.