Nanoarchitectonics to entrap living cells in silica-based systems: encapsulations with yolk-shell and sepiolite nanomaterials

In the present work, the bottom-up fabrication of biohybrid materials using a nanoarchitectonics approach has been applied to entrap living cells. Unicellular microorganisms, that is, cyanobacteria and yeast cells, have been immobilized in silica and silicate-based substrates organized as nanostructured materials. In a first attempt, matrices based on bionanocomposites of chitosan and alginate incorporating sepiolite clay mineral and shaped as films, beads, or foams have been explored for the immobilization of cyanobacteria. It has been observed that this type of biohybrid substrates leads to serious problems regarding the long-time survival of the encapsulated microorganisms. Alternative procedures using silica-based matrices with low sodium content, generated by sol-gel methods, as well as pre-synthesised yolk-shell bionanohybrids have been studied subsequently. Optical microscopy and SEM confirm that the silica shell microstructures provide a reduced contact between cells. The inorganic matrix increases the survival of the cells and maintains their bioactivity. Thus, the encapsulation efficiency is improved compared to the approach using a direct contact of cells in a silica matrix. Encapsulated yeast produced ethanol over a period of several days, pointing out the useful biocatalytic potential of the approach and suggesting further optimization of the present protocols.

Regulating Bacterial Behavior within Hydrogels of Tunable Viscoelasticity

Engineered living materials (ELMs) are a new class of materials in which living organism incorporated into diffusive matrices uptake a fundamental role in material's composition and function. Understanding how the spatial confinement in 3D can regulate the behavior of the embedded cells is crucial to design and predict ELM's function, minimize their environmental impact and facilitate their translation into applied materials. This study investigates the growth and metabolic activity of bacteria within an associative hydrogel network (Pluronic-based) with mechanical properties that can be tuned by introducing a variable degree of acrylate crosslinks. Individual bacteria distributed in the hydrogel matrix at low density form functional colonies whose size is controlled by the extent of permanent crosslinks. With increasing stiffness and elastic response to deformation of the matrix, a decrease in colony volumes and an increase in their sphericity are observed. Protein production follows a different pattern with higher production yields occurring in networks with intermediate permanent crosslinking degrees. These results demonstrate that matrix design can be used to control and regulate the composition and function of ELMs containing microorganisms. Interestingly, design parameters for matrices to regulate bacteria behavior show similarities to those elucidated for 3D culture of mammalian cells.

Silica Hydrogels as Entrapment Material for Microalgae

Despite being a promising feedstock for food, feed, chemicals, and biofuels, microalgal production processes are still uneconomical due to slow growth rates, costly media, problematic downstreaming processes, and rather low cell densities. Immobilization via entrapment constitutes a promising tool to overcome these drawbacks of microalgal production and enables continuous processes with protection against shear forces and contaminations. In contrast to biopolymer gels, inorganic silica hydrogels are highly transparent and chemically, mechanically, thermally, and biologically stable. Since the first report on entrapment of living cells in silica hydrogels in 1989, efforts were made to increase the biocompatibility by omitting organic solvents during hydrolysis, removing toxic by-products, and replacing detrimental mineral acids or bases for pH adjustment. Furthermore, methods were developed to decrease the stiffness in order to enable proliferation of entrapped cells. This review aims to provide an overview of studied entrapment methods in silica hydrogels, specifically for rather sensitive microalgae.

Impact of hydrophilic polymers in organosilica matrices on structure, stability, and biocatalytic activity of immobilized methylotrophic yeast used as biofilter bed

The impact of hydrophilic polymers in an organosilica matrix on the features and performance of immobilized methylotrophic yeast cells used as biocatalysts was investigated and described. Yeast cells were immobilized in a matrix made of tetraethoxysilane (TEOS) and methyltriethoxysilane (MTES) by one-step sol-gel route of synthesis in the presence of polyethylene glycol (PEG) or polyvinyl alcohol (PVA). Organosilica shells were spontaneously built around cells as a result of yeast immobilization at a TEOS to MTES ratio of 85/15 vol% and hydrophilic polymer (PEG or PVA). As a structure-directing agent, PVA produces organosilica films. Stable high-performance biocatalysts active for one year, if stored at -18 °C, have been obtained by entrapment of methylotrophic yeast cells. A trickling biofilter with and without active aeration was designed using entrapped yeast cells to treat methanol polluted wastewater. A biofilter model with active aeration could halve methanol input thus demonstrating better performance compared to treatment without active aeration.

Sol-gel process: the inorganic approach in protein imprinting

Proteins play a central role in the signal transmission in living systems since they are able to recognize specific biomolecules acting as cellular receptors, antibodies or enzymes, being themselves recognized by other proteins in protein/protein interactions, or displaying epitopes suitable for antibody binding. In this context, the specific recognition of a given protein unlocks a range of interesting applications in diagnosis and in targeted therapies. Obviously, this role is already fulfilled by antibodies with unquestionable success. However, the design of synthetic artificial systems able to endorse this role is still challenging with a special interest to overcome limitations of antibodies, in particular their production and their stability. Molecular Imprinted Polymers (MIPs) are attractive recognition systems which could be an alternative for the specific capture of proteins in complex biological fluids. MIPs can be considered as biomimetic receptors or antibody mimics displaying artificial paratopes. However, MIPs of proteins remains a challenge due to their large size and conformational flexibility, their complex chemical nature with multiple recognition sites and their low solubility in most organic solvents. Classical MIP synthesis conditions result in large polymeric cavities and unspecific binding sites on the surface. In this review, the potential of the sol-gel process as inorganic polymerization strategy to overcome the drawbacks of protein imprinting is highlighted. Thanks to the mild and biocompatible experimental conditions required and the use of water as a solvent, the inorganic polymerization approach better suited to proteins than organic polymerization. Through numerous examples and applications of MIPs, we proposed a critical evaluation of the parameters that must be carefully controlled to achieve sol-gel protein imprinting (SGPI), including the choice of the monomers taking part in the polymerization.

Embedding live bacteria in porous hydrogel/ceramic nanocomposites for bioprocessing applications

In this work, we present a biocompatible one-pot processing route for ceramic/hydrogel nanocomposites in which we embed live bacteria. In our approach, we fabricate a highly stable alginate hydrogel with minimal shrinkage, highly increased structural and mechanical stability, as well as excellent biocompatibility. The hydrogel was produced by ionotropic gelation and reinforced with alumina nanoparticles to form a porous 3D network. In these composite gels, the bacteria Escherichia coli and Bacillus subtilis were embedded. The immobilized bacteria showed high viability and similar metabolic activity as non-embedded cells. Even after repeated glucose consumption cycles, the material maintained high structural stability with stable metabolic activity of the immobilized bacteria. Storing the bionanocomposite for up to 60 days resulted in only minor loss of activity. Accordingly, this approach shows great potential for producing macroscopic bioactive materials for biotechnological processes.

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

An adsorbent silica biogel material was developed via silica gel encapsulation of Pseudomonas sp. NCIB 9816-4, a bacterium that degrades a broad spectrum of aromatic pollutants. The adsorbent matrix was synthesized using silica precursors methyltrimethoxysilane and tetramethoxysilane to maximize the adsorption capacity of the matrix while maintaining a highly networked and porous microstructure. The encapsulated bacteria enhanced the removal rate and capacity of the matrix for an aromatic chemical mixture. Repeated use of the material over four cycles was conducted to demonstrate that the removal capacity could be maintained with combined adsorption and biodegradation. The silica biogel can thus be used extensively without the need for disposal, as a result of continuous biodegradation by the encapsulated bacteria. However, an inverse trend was observed with the ratio of biodegradation to adsorption as a function of log K_ow, suggesting increasing mass-transport limitation for the most hydrophobic chemicals used (log K_ow > 4).

The physics and chemistry of silica-in-silicates nanocomposite hydrogels and their phycocompatibility

Silicates-in-silica nanocomposite hydrogels obtained from sodium silicates/colloidal silica mixtures have previously been found to be useful for bacterial encapsulation. However the extension of synthesis conditions and the understanding of their impact on the silica matrix would widen the applicability of this process in terms of encapsulated organisms and the host properties. Here the influence of silicates and the colloidal silica concentration as well as pH conditions on the gel time, the optical properties, the structural and mechanical properties of silica matrices was studied. We show that gel formation is driven by silicate condensation but that the aggregation of silica colloids also has a major influence on the transparency and structure of the nanocomposites. Three different photosynthetic organisms, cyanobacteria Anabaena flos-aquae and two microalgae Chorella vulgaris and Euglena gracilis, were used as probes of the phycocompatibility of the process. The three organisms were highly sensitive to the silicate concentration, which impacts both the gelation time and ionic strength conditions. The Ludox content was crucial for cyanobacteria as it strongly impacts the Young's modulus of the matrices. The detrimental effect of acidic pH on cell suspension was compensated by the silica network. Overall, it is now possible to select optimal encapsulation conditions based on the physiology of the targeted cells, opening wide perspectives for the design of biosensors and bioreactors.

Microorganism mediated biosynthesis of metal chalcogenides; a powerful tool to transform toxic effluents into functional nanomaterials

Cadmium contained in soil and water can be taken up by certain crops and aquatic organisms and accumulate in the food-chain, thus removal of Cd from mining or industrial effluents - i.e. Ni-Cd batteries, electroplating, pigments, fertilizers - becomes mandatory for human health. In parallel, there is an increased interest in the production of luminescent Q-dots for applications in bioimaging, sensors and electronic devices, even the present synthesis methods are economic and environmentally costly. An alternative green pathway for producing Metal chalcogenides (MC: CdS, CdSe, CdTe) nanocrystals is based on the metabolic activity of living organisms. Intracellular and extracellular biosynthesis of can be achieved within a biomimetic approach feeding living organisms with Cd precursors providing new routes for combining bioremediation with green routes for producing MC nanoparticles. In this mini-review we present the state-of-the-art of biosynthesis of MC nanoparticles with a critical discussion of parameters involved and protocols. Few existing examples of scaling-up are also discussed. A modular reactor based on microorganisms entrapped in biocompatible mineral matrices - already proven for bioremediation of dissolved dyes - is proposed for combining both Cd-depletion and MC nanoparticle's production.

Fiber-Optic Chemical Sensors and Fiber-Optic Bio-Sensors

This review summarizes principles and current stage of development of fiber-optic chemical sensors (FOCS) and biosensors (FOBS). Fiber optic sensor (FOS) systems use the ability of optical fibers (OF) to guide the light in the spectral range from ultraviolet (UV) (180 nm) up to middle infrared (IR) (10 μm) and modulation of guided light by the parameters of the surrounding environment of the OF core. The introduction of OF in the sensor systems has brought advantages such as measurement in flammable and explosive environments, immunity to electrical noises, miniaturization, geometrical flexibility, measurement of small sample volumes, remote sensing in inaccessible sites or harsh environments and multi-sensing. The review comprises briefly the theory of OF elaborated for sensors, techniques of fabrications and analytical results reached with fiber-optic chemical and biological sensors.

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.

Alginate/porous silica matrices for the encapsulation of living organisms: tunable properties for biosensors, modular bioreactors, and bioremediation devices

The encapsulation of living cells within inorganic silica hydrogels is a promising strategy for the design of biosensors, modular bioreactors, and bioremediation devices, among other interesting applications, attracting scientific and technological interest. These hostguest multifunctional materials (HGFM) combine synergistically specific biologic functions of their guest with those of the host matrix enhancing their performance. Although inorganic immobilization hosts present several advantages over their (bio)polymer-based counterparts in terms of chemical and physical stability, the direct contact of cells with silica precursors during synthesis and the constraints imposed by the inorganic host during operating conditions have proved to influence their biological response. Recently, we proposed an alternative two-step procedure including a pre-encapsulation in biocompatible polymers such as alginates in order to confer protection to the biological guest during the inorganic and more cytotoxic synthesis. By means of this procedure, whole cultures of microorganisms remain confined in small liquid volumes generated inside the inorganic host, providing near conventional liquid culture conditions.Moreover, the fact of protecting the biological guest during the synthesis of the host, allows extending the synthesis parameters beyond biocompatible conditions, tuning the microstructure of the matrix. In turn, the microstructure (porosity at the nanoscale, radius of gyration of particles composing the structure, and fractal dimension of particle clusters) is determinant of macroscopic parameters, such as optical quality and transport properties that govern the encapsulation material’s performance. Here, we review the most interesting applications of the two-step procedure, making special emphasis on the optimization of optical, transport and mechanical properties of the host as well as in the interaction with the guest during operation conditions.

Transcriptomic responses of Synechocystis sp. PCC 6803 encapsulated in silica gel

Global gene expression of Synechocystis sp. PCC 6803 encapsulated in silica gel was examined by microarray analysis. Cultures were encapsulated in gels derived from aqueous precursors or from alkoxide precursors and incubated under constant light for 24 h prior to RNA extraction. Cultures suspended in liquid media were exposed to 500 mM salt stress and incubated under identical conditions for comparison purposes. The expression of 414 genes was significantly altered by encapsulation in aqueous-derived gels (fold change ≥1.5 and P value < 0.01), the expression of 1,143 genes was significantly altered by encapsulation in alkoxide-derived gels, and only 243 genes were common to both encapsulation chemistries. Additional qRT-PCR analyses of four selected genes, ggpS, cpcG2, slr5055, and sll5057, confirmed microarray results for those genes. These results illustrate that encapsulation stress is quite different than salt stress in terms of gene expression response. Furthermore, a number of hypothetical and unknown proteins associated with encapsulation and alcohol stress have been identified with implications for improving encapsulation protocols and rationally engineering microorganisms for direct biofuel production.