Adsorption and Biodegradation of Aromatic Chemicals by Bacteria Encapsulated in a Hydrophobic Silica Gel

Biotransformation characteristics of tetracycline by strain Serratia marcescens MSM2304 and its mechanism evaluation based on products analysis and genomics

Microbial biotransformation is a recommended and reliable method in face of formidable tetracycline (TC) with broad-spectrum antibacterial activity. Herein, comprehensive characteristics of a newfound strain and its molecular mechanism in process of TC bioremediation were involved in this study. Specifically, Serratia marcescens MSM2304 isolated from pig manure sludge grew well in presence of TC and achieved optimal removal efficiency of 61% under conditions of initial TC concentration of 10 mg/L, pH of 7.0, cell inoculation amount of 5%, and tryptone of 10 g/L as additional carbon. The pathways of biotransformation include EPS biosorption, cell surface biosorption and biodegradation, which enzymatic processes of biodegradation were occurred through TC adsorbed by biofilms was firstly broken down by extracellular enzymes and part of TC migrated towards biofilm interior and degraded by intracellular enzymes. Wherein extracellular polysaccharides in extracellular polymeric substances (EPS) from biofilm of strain MSM2304 mainly performed extracellular adsorption, and changes in position and intensity of CO, =CH and C-O-C/C-O of EPS possible further implied TC adsorption by it. Biodegradation accounting for 79.07% played a key role in TC biotransformation and could be fitted well by first-order model that manifesting rapid and thorough removal. Potential biodegradation pathway including demethylation, dihydroxylation, oxygenation, and ring opening possibly involved in TC disposal process of MSM2304, TC-degrading metabolites exhibited lower toxicity to indicator bacteria relative to parent TC. Whole genome sequencing as underlying molecular evidence revealed that TC resistance genes, dehydrogenases-encoding genes, monooxygenase-encoding genes, and methyltransferase-encoding genes of strain MSM2304 were positively related to TC biodegradation. Collectively, these results favored a theoretical evaluation for Serratia marcescens MSM2304 as a promising TC-control agent in environmental bioremediation processes.

"3-in-1" Hybrid Biocatalysts: Association of Yeast Cells Immobilized in a Sol-Gel Matrix for Determining Sewage Pollution

This study presents a novel ″3-in-1″ hybrid biocatalyst design that combines the individual efficiency of microorganisms while avoiding negative interactions between them. Yeast cells of Ogataea polymorpha VKM Y-2559, Blastobotrys adeninivorans VKM Y-2677, and Debaryomyces hansenii VKM Y-2482 were immobilized in an organosilicon material by using the sol-gel method, resulting in a hybrid biocatalyst. The catalytic activity of the immobilized microorganism mixture was evaluated by employing it as the bioreceptor element of a biosensor. Optical and scanning electron microscopies were used to examine the morphology of the biohybrid material. Elemental distribution analysis confirmed the encapsulation of yeast cells in a matrix composed of methyltriethoxysilane (MTES) and tetraethoxysilane (TEOS) (85 and 15 vol %, respectively). The resulting heterogeneous biocatalyst exhibited excellent performance in determining the biochemical oxygen demand (BOD) index in real surface water samples, with a sensitivity coefficient of 50 ± 3 × 10-3·min-1, a concentration range of 0.3-31 mg/L, long-term stability for 25 days, and a relative standard deviation of 3.8%. These findings demonstrate the potential of the developed hybrid biocatalyst for effective pollution monitoring and wastewater treatment applications.

Cleanup of Cr(VI)-polluted groundwater using immobilized bacterial consortia via bioreduction mechanisms

Cr(VI) bioreduction has become a remedial alternative for Cr(VI)-polluted site cleanup. However, lack of appropriate Cr(VI)-bioreducing bacteria limit the field application of the in situ bioremediation process. In this study, two different immobilized Cr(VI)-bioreducing bacterial consortia using novel immobilization agents have been developed for Cr(VI)-polluted groundwater remediation: (1) granular activated carbon (GAC) + silica gel + Cr(VI)-bioreducing bacterial consortia (GSIB), and (2) GAC + sodium alginate (SA) + polyvinyl alcohol (PVA) + Cr(VI)-bioreducing bacterial consortia (GSPB). Moreover, two unique substrates [carbon-based agent (CBA) and emulsified polycolloid substrate (EPS)] were developed and used as the carbon sources for Cr(VI) bioreduction enhancement. The microbial diversity, dominant Cr-bioreducing bacteria, and changes of Cr(VI)-reducing genes (nsfA, yieF, and chrR) were analyzed to assess the effectiveness of Cr(VI) bioreduction. Approximately 99% of Cr(VI) could be bioreduced in microcosms with GSIB and CBA addition after 70 days of operation, which caused increased populations of total bacteria, nsfA, yieF, and chrR from 2.9 × 10⁸ to 2.1 × 10¹², 4.2 × 10⁴ to 6.3 × 10¹¹, 4.8 × 10⁴ to 2 × 10¹¹, and 6.9 × 10⁴ to 3.7 × 10⁷ gene copies/L. In microcosms with CBA and suspended bacteria addition (without bacterial immobilization), the Cr(VI) reduction efficiency dropped to 60.3%, indicating that immobilized Cr-bioreducing bacteria supplement could enhance Cr(VI) bioreduction. Supplement of GSPB led to a declined bacterial growth due to the cracking of the materials. The addition of GSIB and CBA could establish a reduced condition, which favored the growth of Cr(VI)-reducing bacteria. The Cr(VI) bioreduction efficiency could be significantly improved through adsorption and bioreduction mechanisms, and production of Cr(OH)₃ precipitates confirmed the occurrence of Cr(VI) reduction. The main Cr-bioreducing bacteria included Trichococcus, Escherichia-Shigella, and Lactobacillus. Results suggest that the developed GSIB bioremedial system could be applied to cleanup Cr(VI)-polluted groundwater effectively.

Effect of Fenton oxidized lignin support on immobilized β-glucosidase activity

In this study, the Fenton oxidized lignin was prepared to investigate the effect of Fenton oxidation modification on the activity of lignin immobilized β-glucosidase (β-GL). The results demonstrated that Fenton oxidation could significantly improve the activity and stability of immobilized β-GL. This is because the Fenton oxidation increased the electrostatic, hydrogen bonding, and hydrophobic forces between lignin and β-GL, resulting in increased lignin adsorption onto β-GL. The Fenton oxidation also changed the chemical structure of lignin, altering the lignin-β-GL binding site and reducing the negative effect of lignin on the β-GL catalytic domain. This research will improve understanding of the effect of Fenton lignin oxidation on immobilized β-GL activity and expand the use of lignin in enzyme immobilization.

The Use of Diethoxydimethylsilane as the Basis of a Hybrid Organosilicon Material for the Production of Biosensitive Membranes for Sensory Devices

Biomembranes based on an organosilica sol-gel matrix were used to immobilize bacteria Paracoccus yeei VKM B-3302 as part of a biochemical oxygen demand (BOD) biosensor. Diethoxydimethylsilane (DEDMS) and tetraethoxysilane (TEOS) were used as precursors to create the matrix in a 1:1 volume ratio. The use of scanning electron microscopy (SEM) and the low-temperature nitrogen adsorption method (BET) showed that the sol-gel matrix forms a capsule around microorganisms that does not prevent the exchange of substrates and waste products of bacteria to the cells. The use of DEDMS as part of the matrix made it possible to increase the sensitivity coefficient of the biosensor for determining BOD by two orders of magnitude compared to a biosensor based on methyltriethoxysilane (MTES). Additionally, the long-term stability of the bioreceptor increased to 68 days. The use of such a matrix neutralized the effect of heavy metal ions on the microorganisms' catalytic activity in the biosensor. The developed biosensor was used to analyze water samples from water sources in the Tula region (Russia).

Engineered Living Hydrogels

Living biological systems, ranging from single cells to whole organisms, can sense, process information, and actuate in response to changing environmental conditions. Inspired by living biological systems, engineered living cells and nonliving matrices are brought together, which gives rise to the technology of engineered living materials. By designing the functionalities of living cells and the structures of nonliving matrices, engineered living materials can be created to detect variability in the surrounding environment and to adjust their functions accordingly, thereby enabling applications in health monitoring, disease treatment, and environmental remediation. Hydrogels, a class of soft, wet, and biocompatible materials, have been widely used as matrices for engineered living cells, leading to the nascent field of engineered living hydrogels. Here, the interactions between hydrogel matrices and engineered living cells are described, focusing on how hydrogels influence cell behaviors and how cells affect hydrogel properties. The interactions between engineered living hydrogels and their environments, and how these interactions enable versatile applications, are also discussed. Finally, current challenges facing the field of engineered living hydrogels for their applications in clinical and environmental settings are highlighted.

Long-term dechlorination of cis-DCE to ethene with co-immobilized Dehalococcoides mccartyi BAV1 and Clostridium butyricum in silica gel system

Chloroethenes are common groundwater pollutants, and have been classified as toxic and carcinogenic to humans. The metabolites of chloroethenes, cis-dichloroethene (cis-DCE) and vinyl chloride (VC) commonly accumulate in groundwater due to their recalcitrant reductive dechlorination under anaerobic conditions. Dehalococcoides mccartyi (Dhc) is the key anaerobic bacteria for complete dechlorination of chloroethene, and Clostridium butyricum (C. butyricum) can provide hydrogen for supporting the growth of Dhc. In this study, we co-immobilized Dhc strain BAV1 and C. butyricum in a silica gel to determine the ability of the complete dechlorination of cis-DCE. Our results showed that our immobilized system could protect BAV1 from a high concentration (8 mM) of cis-DCE to carry out complete dechlorination. After the long-term use of our immobilized system, the activity of complete dechlorination was maintained for more than 180 consecutive days. Furthermore, we applied the immobilized system to remediate contaminated groundwater and uncovered the complete dechlorination of cis-DCE into ethene, a non-toxic product, within 28 days. Therefore, this novel co-immobilized system could serve a solution for bioremediation at chloroethene-contaminated sites.

Porous Aluminum-Based Metal-Organic Framework-Aminoclay Nanocomposite: Sustainable Synthesis and Ultrahigh Sorption of Cephalosporin Antibiotics

A novel sorbent was synthesized based on MIL-53(Al) MOF grown over an aminoclay (AC) platform, called MIL-53(Al)@AC nanocomposite, via a green and facile hydrothermal method. The nanocomposite was characterized using FT-IR, PXRD, BET, TEM, FESEM, EDS, XPS, TGA, DLS, and zeta potential analyses. BET analysis represented the porous nature and great surface area of MIL-53(Al)@AC. The high crystalline structure for the synthesized nanocomposite was verified using the PXRD pattern. FESEM, EDS, TEM, and XPS analysis proved the successful decoration of MIL-53(Al) over the AC platform. Cephalosporin antibiotics cefixime (CFX) and cephalexin (CPX), which are often present in wastewaters, were utilized to examine the sorption capacity of the nanocomposite. The significant influential factors such as pH, temperature, sorbent amount, ionic strength, and impurity were discussed. At an initial pH of 7.0 ± 0.1, the highest sorption capacities of CFX and CPX on MIL-53(Al)@AC were 784.14 and 747.91 mg g^-1 (T = 298 K, and sorbent amount = 0.1 g L^-1), which were 1.43 and 1.47 times greater compared to that of MIL-53(Al), respectively. The evaluation of experimental results was implemented through the Langmuir and Freundlich isotherm equations. The isothermal data were described nobly by the Freundlich isotherm, which confirmed multilayer adsorption on heterogeneous surfaces (R² > 0.970). A kinetic study indicated that the nanocomposite could adsorb the majority of cephalosporin antibiotics within 30 min. In addition, the experimental data were evaluated via pseudo-first-order, pseudo-second-order, and intraparticle diffusion models. The results indicated that the pseudo-second-order equation agreed more closely with the kinetic data (R² > 0.990). Furthermore, the processes of adsorption were exothermic and spontaneous. The electrostatic attraction, hydrophobic interaction, π-π electron donor-acceptor effect, H-bond, and π-π stacking constituted the main sorption mechanisms. Finally, MIL-53(Al)@AC presented an excellent regeneration performance. Thus, the results revealed the potential application of the MIL-53(Al)@AC nanocomposite for water remediation.

Preparation of Hybrid Sol-Gel Materials Based on Living Cells of Microorganisms and Their Application in Nanotechnology

Microorganism-cell-based biohybrid materials have attracted considerable attention over the last several decades. They are applied in a broad spectrum of areas, such as nanotechnologies, environmental biotechnology, biomedicine, synthetic chemistry, and bioelectronics. Sol-gel technology allows us to obtain a wide range of high-purity materials from nanopowders to thin-film coatings with high efficiency and low cost, which makes it one of the preferred techniques for creating organic-inorganic matrices for biocomponent immobilization. This review focuses on the synthesis and application of hybrid sol-gel materials obtained by encapsulation of microorganism cells in an inorganic matrix based on silicon, aluminum, and transition metals. The type of immobilized cells, precursors used, types of nanomaterials obtained, and their practical applications were analyzed in detail. In addition, techniques for increasing the microorganism effective time of functioning and the possibility of using sol-gel hybrid materials in catalysis are discussed.

Cleanup chlorinated ethene-polluted groundwater using an innovative immobilized Clostridium butyricum column scheme: A pilot-scale study

In this study, the developed innovative immobilized Clostridium butyricum (ICB) (hydrogen-producing bacteria) column scheme was applied to cleanup chlorinated-ethene [mainly cis-1,2-dichloroethene (cis-DCE)] polluted groundwater in situ via the anaerobic reductive dechlorinating processes. The objectives were to assess the effectiveness of the field application of ICB scheme on the cleanup of cis-DCE polluted groundwater, and characterize changes of microbial communities after ICB application. Three remediation wells and two monitor wells were installed within the cis-DCE plume. In the remediation well, a 1.2-m PVC column (radius = 2.5 cm) (filled with ICB beads) and 20 L of slow polycolloid-releasing substrate (SPRS) were supplied for hydrogen production enhancement and primary carbon supply, respectively. Groundwater samples from remediation and monitor wells were analyzed periodically for cis-DCE and its degradation byproducts, microbial diversity, reductive dehalogenase, and geochemical indicators. Results reveal that cis-DCE was significantly decreased within the ICB and SPRS influence zone. In a remediation well with ICB injection, approximately 98.4% of cis-DCE removal (initial concentration = 1.46 mg/L) was observed with the production of ethene (end-product of cis-DCE dechlorination) after 56 days of system operation. Up to 0.72 mg/L of hydrogen was observed in remediation wells after 14 days of ICB and SPRS introduction, which corresponded with the increased population of Dehalococcoides spp. (Dhc) (increased from 3.76 × 103 to 5.08 × 105 gene copies/L). Results of metagenomics analyses show that the SPRS and ICB introduction caused significant impacts on the bacterial communities, and increased Bacteroides, Citrobacter, and Desulfovibrio populations were observed, which had significant contributions to the reductive dechlorination of cis-DCE. Application of ICB could effectively result in increased populations of Dhc and RDase genes, which corresponded with improved dechlorination of cis-DCE and vinyl chloride. Introduction of ICB and SPRS could be applied as a potential in situ remedial option to enhance anaerobic dechlorination efficiencies of chlorinated ethenes.

Carbon source type can affect tetracycline removal by Pseudomonas sp. TC952 through regulation of extracellular polymeric substances composition and production

The objective of this work is to elucidate the mechanism of tetracycline (TC) removal by Pseudomonas sp. TC952. The TC removal characteristics of strain TC952 under various environmental conditions were studied. Results showed that the bio-removal efficiency was significantly affected by initial TC and peptone concentration, pH values, divalent metal ion (Zn²⁺) and carbon source, and the strain TC952 efficiently removed approximately 72.8% of TC within 6 days with 10 g/L peptone. The best conditions for strain TC952 to remove TC are as follows: initial TC concentration is 50 mg/L, solution initial pH is 7, Zn²⁺ concentration is 0.1 μg/L, carbon source is peptone. And through intra- and extracellular fractions assay and extracellular polymeric substances (EPS) component analysis, TC removal by strain TC952 was mainly attributed to the adsorption by bacterial EPS and bacterial cell. Furthermore, different carbon source affected the EPS production content and component of strain TC952, so EPS produced under peptone and serine conditions could bio-adsorb TC and formed a buffer area outside the cells, thus reducing or preventing TC from entering the bacteria cells. All the results obtained showed that secretion of EPS and adsorption of TC by EPS and bacterial cell wall may be a common way for bacteria to reduce TC in the environment, which brought novel insights for better management of TC contamination by functional bacteria and for understanding the natural removal process of antibiotics by microorganisms in the environment.

Label-Free Detection of Staphylococcus aureus Based on Bacteria-Imprinted Polymer and Turn-on Fluorescence Probes

The effective identification and quantitative determination of Staphylococcus aureus is a major public health concern. Here, an innovative strategy that combines a bacteria-imprinted polydimethylsiloxane film for bacterial recognition and fluorescence resonance energy transfer platform for turn-on fluorescence sensing is demonstrated. The bacteria-imprinted polydimethylsiloxane film was facilely fabricated to generate corresponding specific sites on the polydimethylsiloxane surface via stamp imprinting using Staphylococcus aureus as template followed by modification with 1H,1H,2H,2H-perfluorooctyltriethoxysilane. The fluorescence resonance energy transfer platform was developed through electrostatic interaction between citrate-functional copper clusters and dopamine-stabilized gold nanoparticles. When the Staphylococcus aureus are present, the 1H,1H,2H,2H-perfluorooctyltriethoxysilane-modified bacteria-imprinted polydimethylsiloxane film can precisely capture the target; subsequently, the negatively charged bacteria compete with citrate-functional copper clusters and bind to dopamine-stabilized gold nanoparticles, leading to the fluorescence recovery of citrate-functional copper clusters. The entire detection process was achieved within 135 min, showing a wide linear calibration response from 10 to 1 × 10⁷ cfu mL^-1 with a low detection limit of 11.12 cfu mL^-1. Furthermore, the recoveries from spiked samples were from 97.7 to 101.90% with relative standard derivations lower than 10%. The established label-free assay of measuring Staphylococcus aureus is rapid, sensitive, specific, and efficient.

Self-Assembly of Asymmetrically Functionalized Titania Nanoparticles into Nanoshells

Titania (anatase) nanoparticles were anisotropically functionalized in water-toluene Pickering emulsions to self-assemble into nanoshells with diameters from 500 nm to 3 μm as candidates for encapsulation of drugs and other compounds. The water-phase contained a hydrophilic ligand, glucose-6-phosphate, while the toluene-phase contained a hydrophobic ligand, n-dodecylphosphonic acid. The addition of a dilute sodium alginate suspension that provided electrostatic charge was essential for the self-limited assembly of the nanoshells. The self-assembled spheres were characterized by scanning electron microscopy, elemental mapping, and atomic force microscopy. Drug release studies using tetracycline suggest a rapid release dominated by surface desorption.

Viability and distribution of bacteria immobilized on Sawdust@silica: The removal mechanism of phenanthrene in soil

Immobilized cells (ICs) have been widely used to enhance the remediation of organic-contaminated soil (e.g., polycyclic aromatic hydrocarbons, PAHs). Once ICs are added to the heterogeneous soil, degradation hotspots are immediately formed near the carrier, leaving the remaining soil lack of degrading bacteria. Therefore, it remains unclear how ICs efficiently utilize PAHs in soil. In this study, the viability of Silica-IC (Cells@Sawdust@Silica) and the distribution of inoculated ICs and phenanthrene (Phe) in a slurry system (soil to water ratio 1:2) were investigated to explore the removal mechanism of PAHs by the ICs. Results showed that the Silica-IC maintained (i) good reproductive ability (displayed by the growth curve in soil and water phase), (ii) excellent stability, which was identified by the ratio of colony forming units in the soil phase to the water phase, the difference between the colony number and the DNA copies, and characteristics of the biomaterial observed by the FESEM, and (iii) high metabolic activity (the removal percentages of Phe in soil by the ICs were more than 95% after 48 h). Finally, the possible pathways for the ICs to efficiently utilize Phe in soil are proposed based on the distribution and correlation of Phe and ICs between the soil and water phase. The adsorption-degradation process was dominant, i.e., the enhanced degradation occurred between the ICs and carrier-adsorbed Phe. This study provided new insights on developing a bio-material for efficient bio-remediation of PAHs-contaminated soil.

Rational Design of PMPC/PDMC/PEGDA Hydrogel Micropatterns onto Polylactic Acid with Enhanced Biological Activity

Polylactic acid (PLA) is one of the biodegradable materials that has been used in the areas of surgical healing lines, cancer treatment, and wound healing. However, the application of PLA is still rather limited due to its high hydrophobicity and poor antibacterial activity. In order to enhance the antifouling and antibacterial performances of PLA, here we modified the surface of PLA with various sizes of hydrogel micropatterns in negative or positive mode using plasma treatment, the photomask technique, and UV-graft polymerization. The hydrogel micropatterns consist of poly(ethylene glycol) diacrylate (PEGDA), poly(2-methacryloyloxyethylphosphorylcholine) (PMPC), and poly(methacryloyloxyethyltrimethylammonium chloride) (PDMC). Compared to PLA, the patterned PLA (PLA-PMPC/PDMC/PEGDA) shows obviously enhanced antifouling and antibacterial activities. For PLA-PMPC/PDMC/PEGDA with either positive or negative micropatterns, the antifouling and antibacterial properties are gradually increasing with decreasing the size of micropatterns. Compared with PLA-PMPC/PDMC/PEGDA bearing positive and negative micropatterns in the same size, the PLA-PMPC/PDMC/PEGDA with negative micropatterns exhibits slightly better biological activity and the PLA-PMPC/PDMC/PEGDA with 3 μm negative hydrogel micropatterns shows the best hydrophilicity, antifouling, and antibacterial properties. Combining the in vitro hemolysis assay, cytotoxicity, water absorption test, and degradation test results, it is suggested that the fabrication of hydrogel micropatterns onto the PLA surface could significantly improve biological activities of PLA. We expect that this work would provide a new strategy to potentially develop PLA as a promising wound dressing.

Genetical Surface Display of Silicatein on Yarrowia lipolytica Confers Living and Renewable Biosilica-Yeast Hybrid Materials

In this work, a biological engineering-based biosilica-yeast hybrid material was developed. It was obtained by the aggregation of Yarrowia lipolytica through biosilicification catalyzed using genetically displayed silicatein on its cell surface. With orthosilicate or seawater as the substrate, the silicatein-displayed yeast could aggregate into flocs with a flocculation efficiency of nearly 100%. The resulting floc was found to be a sheetlike biosilica-yeast hybrid material formed by the biosilica-mediated immobilization of yeast cells via cross-linking and embedding, turning the original hydrophilicity of yeast cells into hydrophobicity. In addition, this material was characterized to be porous with an average pore diameter of approximately 10 μm and porosity of over 70%. Because of these properties, this hybrid material could achieve enhanced removal efficiencies for chromium ions and n-hexadecane, which were both above 99%, as compared to the free cells of Y. lipolytica in aqueous environments. Importantly, this hybrid material could be recultivated to generate new batches of yeast cells that maintain parallel properties to the first generation so that the same hybrid material could be reproduced with unchanged highly efficient removal of chromium and n-hexadecane to those of the first generation, demonstrating that this biosilica-yeast hybrid material was living and renewable. This work presented a novel way of harnessing silicatein and Y. lipolytica to achieve biological synthesis of a living inorganic-organic hybrid material that has potential to be applied in water treatment.

Rapid and selective recognition of Vibrio parahaemolyticus assisted by perfluorinated alkoxysilane modified molecularly imprinted polymer film

Molecular imprinting technology offers a means of tailor-made materials with high affinity and selectivity for certain analysts. However, the recognition and separation of specific bacteria in complex matrices are still challenging. Herein, a bacteria-imprinted polydimethylsiloxane (PDMS) film was facilely prepared and modified with 1H,1H,2H,2H-perfluorooctyltriethoxysilane (POTS). Employing Vibrio parahaemolyticus as a model bacterium, the imprinted surface exhibited three-dimensionality cavities with mean size of 1000 × 800 nm in square and 100 nm in depth. After incubation for 2 h with 6 × 10⁷ CFU mL⁻¹ of V. parahaemolyticus, the imprinted polymer film can reach a 62.9% capture efficiency. Furthermore, the imprinted POTS-modified PDMS film based solid phase extraction combined with polymerase chain reaction and agarose gel electrophoresis allows for detecting 10⁴ CFU mL⁻¹ with excellent selectivity in fresh oyster samples. As a result, the developed selective sample pretreatment method using molecular imprinting technology provides a promising platform for separation, identification, and analysis of pathogens.

Molecular imprinting technology offers a means of tailor-made materials with high affinity and selectivity for certain analysts.

Enhanced reductive dechlorination of trichloroethene with immobilized Clostridium butyricum in silica gel

Deteriorated environmental conditions during the bioremediation of trichloroethene (TCE)-polluted groundwater cause decreased treatment efficiencies. This study assessed the effect of applying immobilized Clostridium butyricum (a hydrogen-producing bacterium) in silica gel on enhancing the reductive dechlorination efficiency of TCE with the slow polycolloid-releasing substrate (SPRS) supplement in groundwater. The responses of microbial communities with the immobilized system (immobilized Clostridium butyricum and SPRS amendments) were also characterized by the metagenomics assay. A complete TCE removal in microcosms was obtained within 30 days with the application of this immobilized system via reductive dechlorination processes. An increase in the population of Dehalococcoides spp. was observed using the quantitative polymerase chain reaction (qPCR) analysis. Results of metagenomics assay reveal that the microbial communities in the immobilized system were distinct from those in systems with SPRS only. Bacterial communities associated with TCE biodegradation also increased in microcosms treated with the immobilized system. The immobilized system shows a great potential to promote the TCE dechlorination efficiency, and the metagenomics-based approach provides detailed insights into dechlorinating microbial community dynamics. The results would be helpful in designing an in situ immobilized system to enhance the bioremediation efficiency of TCE-contaminated groundwater.

Developing a Protein Scaffolding System for Rapid Enzyme Immobilization and Optimization of Enzyme Functions for Biocatalysis

Immobilization of enzymes is required for most biocatalytic processes, but chemistries used in enzyme immobilization are limited and can be challenging. Genetically encoded protein-based biomaterials could provide easy-to-use immobilization platforms for biocatalysts. We recently developed a self-assembling protein scaffold that covalently immobilized SpyTagged enzymes by engineering the bacterial microcompartment protein EutM from Salmonella enterica with a SpyCatcher domain. We also identified a range of EutM homologues as robust protein nanostructures with diverse architectures and electrostatic surface properties. In this work, we created a modular immobilization platform with tunable surface properties by developing a toolbox of self-assembling, robust EutM-SpyCatcher scaffolds. Using an alcohol dehydrogenase as model biocatalyst, we show that the scaffolds improve enzyme activity and stability. This work provides a modular, easy-to-use immobilization system that can be tailored for the optimal function of biocatalysts of interest.

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.

Enhancement of biocatalyst activity and protection against stressors using a microbial exoskeleton

Whole cell biocatalysts can perform numerous industrially-relevant chemical reactions. While they are less expensive than purified enzymes, whole cells suffer from inherent reaction rate limitations due to transport resistance imposed by the cell membrane. Furthermore, it is desirable to immobilize the biocatalysts to enable ease of separation from the reaction mixture. In this study, we used a layer-by-layer (LbL) self-assembly process to create a microbial exoskeleton which, simultaneously immobilized, protected, and enhanced the reactivity of a whole cell biocatalyst. As a proof of concept, we used Escherichia coli expressing homoprotocatechuate 2,3-dioxygenase (HPCD) as a model biocatalyst and coated it with up to ten alternating layers of poly(diallyldimethylammonium chloride) (PDADMAC) and silica. The microbial exoskeleton also protected the biocatalyst against a variety of external stressors including: desiccation, freeze/thaw, exposure to high temperatures, osmotic shock, as well as against enzymatic attack by lysozyme, and predation by protozoa. While we observed increased permeability of the outer membrane after exoskeleton deposition, this had a moderate effect on the reaction rate (up to two-fold enhancement). When the exoskeleton construction was followed by detergent treatment to permeabilize the cytoplasmic membrane, up to 15-fold enhancement in the reaction rate was reached. With the exoskeleton, we increased in the reaction rate constants as much as 21-fold by running the biocatalyst at elevated temperatures ranging from 40 °C to 60 °C, a supraphysiologic temperature range not accessible by unprotected bacteria.