Enhanced benzaldehyde tolerance in Zymomonas mobilis biofilms and the potential of biofilm applications in fine-chemical production

Engineering microbial metabolic homeostasis for chemicals production

Microbial-based bio-refining promotes the development of a biotechnology revolution to encounter and tackle the enormous challenges in petroleum-based chemical production by biomanufacturing, biocomputing, and biosensing. Nevertheless, microbial metabolic homeostasis is often incompatible with the efficient synthesis of bioproducts mainly due to: inefficient metabolic flow, robust central metabolism, sophisticated metabolic network, and inevitable environmental perturbation. Therefore, this review systematically summarizes how to optimize microbial metabolic homeostasis by strengthening metabolic flux for improving biotransformation turnover, redirecting metabolic direction for rewiring bypass pathway, and reprogramming metabolic network for boosting substrate utilization. Future directions are also proposed for providing constructive guidance on the development of industrial biotechnology.

Microbial biofilms as a platform for diverse biocatalytic applications

Microbial biofilms have gained significant traction in commercial wastewater treatment due to their inherent resilience, well-organized structure, and potential for collaborative metabolic processes. As our understanding of their physiology deepens, these living catalysts are finding exciting applications beyond wastewater treatment, including the production of bulk and fine chemicals, bioelectricity generation, and enzyme immobilization. While the biological applications of biofilms in different biocatalytic systems have been extensively summarized, the applications of artificially engineered biofilms were rarely discussed. This review aims to bridge this gap by highlighting the untapped potential of engineered microbial biofilms in diverse biocatalytic applications, with a focus on strategies for biofilms engineering. Strategies for engineering biofilm-based systems will be explored, including genetic modification, synthetic biology approaches, and targeted manipulation of biofilm formation processes. Finally, the review will address key challenges and future directions in developing robust biofilm-based biocatalytic platforms for large-scale production of chemicals, pharmaceuticals, and biofuels.

Biofilms for Production of Chemicals and Energy

The twenty-first century will be the century of biology. This is not only because of breakthrough advances in molecular biology tools but also because we need to reinvent our economy based on the biological principles of energy efficiency and sustainability. Consequently, new tools for production routines must be developed to help produce platform chemicals and energy sources based on sustainable resources. In this context, biofilm-based processes have the potential to impact future production processes, because they can be carried out continuously and with robust stationary biocatalysts embedded in an extracellular matrix with different properties. We review productive biofilm systems used for heterotrophic and lithoautotrophic production and attempt to identify fundamental reasons why they may be particularly suitable as future production systems.

Regulation of biofilm formation in Zymomonas mobilis to enhance stress tolerance by heterologous expression of pfs and luxS

Zymomonas mobilis is a potential alternative of Saccharomyces cerevisiae to produce cellulosic ethanol with strengths in cofactor balance, but its lower tolerance to inhibitors in the lignocellulosic hydrolysate restricts the application. Although biofilm can improve bacteria stress tolerance, regulating biofilm formation in Z. mobilis is still a challenge. In this work, we constructed a pathway by heterologous expressing pfs and luxS from Escherichia coli in Z. mobilis to produce AI-2 (autoinducer 2), a universal quorum-sensing signal molecule, to control cell morphology for enhancing stress tolerance. Unexpectedly, the results suggested that neither endogenous AI-2 nor exogenous AI-2 promoted biofilm formation, while heterologous expression of pfs can significantly raise biofilm. Therefore, we proposed that the main factor in assisting biofilm formation was the product accumulated due to heterologous expression of pfs, like methylated DNA. Consequently, ZM4::pfs produced more biofilm, which presented an enhanced tolerance to acetic acid. All these findings provide a novel strategy to improve the stress tolerance of Z. mobilis by enhancing biofilm formation for efficient production of lignocellulosic ethanol and other value-added chemical products.

Biofilm accumulation in new flexible gastroscope channels in clinical use

OBJECTIVE

Assess the accumulation of protein and biofilm on the inner surfaces of new flexible gastroscope (FG) channels after 30 and 60 days of patient use and full reprocessing.

DESIGN

Clinical use study of biofilm accumulation in FG channels.

SETTING

Endoscopy service of a public hospital.

METHODS

First, we tested an FG in clinical use before the implementation of a revised reprocessing protocol (phase 1 baseline; n = 1). After replacement of the channels by new ones and the implementation of the protocol, 3 FGs were tested after 30 days of clinical use (phase 2; n = 3) and 3 FGs were tested after 60 days of clinical use (phase 3; n = 3), and the same FGs were tested in phase 2 and 3. Their biopsy, air, water, and air/water junction channels were removed and subjected to protein testing (n = 21), bacteriological culture (n = 21), and scanning electron microscopy (SEM) (n = 28). Air-water junction channels fragments were subjected to SEM only.

RESULTS

For the FGs, the average number of uses and reprocessing cycles was 60 times. Extensive biofilm was detected in air, water, and air-water junction channels (n = 18 of 28). All channels (28 of 28) showed residual matter, and structural damage was identified in most of them (20 of 28). Residual protein was detected in the air and water channels of all FG evaluated (phases 1-3), except for 1 air channel from phase 2. Bacteria were recovered from 8 of 21 channels, most air or water channels.

CONCLUSIONS

The short time before damage and biofilm accumulation in the channels was evident and suggests that improving the endoscope design is necessary. Better reprocessing methods and channel maintenance are needed.

Biofilm application in the microbial biochemicals production process

Biofilms can be naturally formed through the attachment of microorganisms on the supporting materials. However, natural biofilms formed in the environment may cause some detrimental effects, such as the equipment contamination and food safety issues et al. On the contrary, biofilms mediated microbial fermentation provides a promising approach for the efficient biochemicals production owing to the properties of self-immobilization, high resistance to toxic reactants and maintenance of long-term cells activity. While few reviews have specifically addressed the biological application of biofilms in the microbial fermentation process. Accordingly, this review will comprehensively summarize the biofilms formation mechanism and potential functions in the microbial fermentation process. Furthermore, the construction strategies for the formation of stable biofilms through synthetic biology technology or the modification of suitable supporting materials will be also discussed. The application of biofilms mediated fermentation will provide an outlook for the biorefinery platform in the future.

Three-stage repeated-batch immobilized cell fermentation to produce butanol from non-detoxified sugarcane bagasse hemicellulose hydrolysates

To enable the production of butanol with undiluted, non-detoxified sugarcane bagasse hemicellulose hydrolysates, this study developed a three-staged repeated-batch immobilized cell fermentation in which the efficiency of a 3D-printed nylon carrier to passively immobilize Clostridium saccharoperbutylacetonicum DSM 14923 was compared with sugarcane bagasse. The first stage consisted of sugarcane molasses fermentation, and in the second stage, non-detoxified sugarcane bagasse hemicellulose hydrolysates (SBHH) was pulse-fed to sugarcane molasses fermentation. In the next four batches, immobilized cells were fed with undiluted SBHH supplemented with molasses, and SBHH-derived xylose accounted for approximately 50% of the sugars. Bagasse was a superior carrier, and the average xylose utilization (33%) was significantly higher than the treatment with the 3D-printed carrier (16%). Notably, bagasse allowed for 43% of the butanol to be SBHH-derived. Overall, cell immobilization on lignocellulosic materials can be an efficient strategy to produce butanol from repeated-batch fermentation of non-detoxified hemicellulose hydrolysates.

Perspectives and new directions for bioprocess optimization using Zymomonas mobilis in the ethanol production

Zymomonas mobilis is an ethanologenic microbe that has a demonstrated potential for use in lignocellulosic biorefineries for bioethanol production. Z. mobilis exhibits a number of desirable characteristics for use as an ethanologenic microbe, with capabilities for metabolic engineering and bioprocess modification. Many advanced genetic tools, including mutation techniques, screening methods and genome editing have been successively performed to improve various Z. mobilis strains as potential consolidated ethanologenic microbes. Many bioprocess strategies have also been applied to this organism for bioethanol production. Z. mobilis biofilm reactors have been modified with various benefits, including high bacterial populations, less fermentation times, high productivity, high cell stability, resistance to the high concentration of substrates and toxicity, and higher product recovery. We suggest that Z. mobilis biofilm reactors could be used in bioethanol production using lignocellulosic substrates under batch, continuous and repeated batch processes.

Growth Dynamics of Bacterial Populations in a Two-Compartment Biofilm Bioreactor Designed for Continuous Surfactin Biosynthesis

Biofilm bioreactors are promising systems for continuous biosurfactant production since they provide process stability through cell immobilization and avoid foam formation. In this work, a two-compartment biofilm bioreactor was designed consisting of a stirred tank reactor and a trickle-bed reactor containing a structured metal packing for biofilm formation. A strong and poor biofilm forming B. subtilis 168 strain due to restored exopolysaccharides (EPS) production or not were cultivated in the system to study the growth behavior of the planktonic and biofilm population for the establishment of a growth model. A high dilution rate was used in order to promote biofilm formation on the packing and wash out unwanted planktonic cells. Biofilm development kinetics on the packing were assessed through a total organic carbon mass balance. The EPS⁺ strain showed a significantly improved performance in terms of adhesion capacity and surfactin production. The mean surfactin productivity of the EPS⁺ strain was about 37% higher during the continuous cultivation compared to the EPS^- strain. The substrate consumption together with the planktonic cell and biofilm development were properly predicted by the model (α = 0.05). The results show the efficiency of the biofilm bioreactor for continuous surfactin production using an EPS producing strain.

Zymomonas mobilis Biofilm Reactor for Ethanol Production Using Rice Straw Hydrolysate Under Continuous and Repeated Batch Processes

Plastic composited corn silk was developed as a biotic/abiotic carrier for Zymomonas mobilis biofilm formation for the purpose of ethanol production. Furthermore, we explored the use of rice straw hydrolysate as substrate in both multistage continuous culture and repeated batch processes and compared the ethanol production efficiency by two strains of Z. mobilis. Biofilm formed by bacterial strains Z. mobilis ZM4 and TISTR551 were detected, and its proficiencies were compared under various conditions by scanning electron microscopy (SEM) and crystal violet assays. The greatest biofilm formed by both strains was found on day five after the inoculation. Z. mobilis strain ZM4 grown in repeated batch biofilm reactors produced higher yields of ethanol than TISTR551 grown under the same conditions, while TISTR551 produced higher yields of ethanol in the multistage continuous process. The yields were highly maintained, with no significant differences (p < 0.05) among the three consecutive repeated batches. These experiments highlight exciting uses for agricultural byproducts in the production of ethanol using Z. mobilis biofilm reactors.

Cell Aggregation and Aerobic Respiration Are Important for Zymomonas mobilis ZM4 Survival in an Aerobic Minimal Medium

Zymomonas mobilis produces ethanol from glucose near the theoretical maximum yield, making it a potential alternative to the yeast Saccharomyces cerevisiae for industrial ethanol production. A potentially useful industrial feature is the ability to form multicellular aggregates called flocs, which can settle quickly and exhibit higher resistance to harmful chemicals than single cells. While spontaneous floc-forming Z. mobilis mutants have been described, little is known about the natural conditions that induce Z. mobilis floc formation or about the genetic factors involved. Here we found that wild-type Z. mobilis forms flocs in response to aerobic growth conditions but only in a minimal medium. We identified a cellulose synthase gene cluster and a single diguanylate cyclase that are essential for both floc formation and survival in a minimal aerobic medium. We also found that NADH dehydrogenase 2, a key component of the aerobic respiratory chain, is important for survival in a minimal aerobic medium, providing a physiological role for this enzyme, which has previously been found to be disadvantageous in a rich aerobic medium. Supplementation of the minimal medium with vitamins also promoted survival but did not inhibit floc formation.IMPORTANCE The bacterium Zymomonas mobilis is best known for its anaerobic fermentative lifestyle, in which it converts glucose into ethanol at a yield surpassing that of yeast. However, Z. mobilis also has an aerobic lifestyle, which has confounded researchers with its attributes of poor growth, accumulation of toxic acetic acid and acetaldehyde, and respiratory enzymes that are detrimental for aerobic growth. Here we show that a major Z. mobilis respiratory enzyme and the ability to form multicellular aggregates, called flocs, are important for survival, but only during aerobic growth in a medium containing a minimum set of nutrients required for growth. Supplements, such as vitamins or yeast extract, promote aerobic growth and, in some cases, inhibit floc formation. We propose that Z. mobilis likely requires aerobic respiration and floc formation in order to survive in natural environments that lack protective factors found in supplements such as yeast extract.

Recombinant Escherichia coli BL21-pET28a-egfp Cultivated with Nanomaterials in a Modified Microchannel for Biofilm Formation

The application of whole cells as catalytic biofilms in microchannels has attracted increasing scientific interest. However, the excessive biomass formation and structure of biofilms in a reactor limits their use. A microchannel reactor with surface modification was used to colonize recombinant Escherichia coil BL21-pET28a-egfp rapidly and accelerated growth of biofilms in the microchannel. The segmented flow system of 'air/culture medium containing nanomaterials' was firstly used to modulate the biofilms formation of recombinant E. coil; the inhibitory effects of nanomaterials on biofilm formation were investigated. The results indicated that the segmental flow mode has a significant impact on the structure and development of biofilms. Using the channels modified by silane reagent, the culture time of biofilms (30 h) was reduced by 6 h compared to unmodified channels. With the addition of graphene sheets (10 mg/L) in Luria-Bertani (LB) medium, the graphene sheets possessed a minimum inhibition rate of 3.23% against recombinant E. coil. The biofilms cultivated by the LB medium with added graphene sheets were stably formed in 20 h; the formation time was 33.33% shorter than that by LB medium without graphene. The developed method provides an efficient and simple approach for rapid preparation of catalytic biofilms in microchannel reactors.

Rapid enzyme regeneration results in the striking catalytic longevity of an engineered, single species, biocatalytic biofilm

BACKGROUND

Engineering of single-species biofilms for enzymatic generation of fine chemicals is attractive. We have recently demonstrated the utility of an engineered Escherichia coli biofilm as a platform for synthesis of 5-halotryptophan. E. coli PHL644, expressing a recombinant tryptophan synthase, was employed to generate a biofilm. Its rapid deposition, and instigation of biofilm formation, was enforced by employing a spin-down method. The biofilm presents a large three-dimensional surface area, excellent for biocatalysis. The catalytic longevity of the engineered biofilm is striking, and we had postulated that this was likely to largely result from protection conferred to recombinant enzymes by biofilm's extracellular matrix. SILAC (stable isotopic labelled amino acids in cell cultures), and in particular dynamic SILAC, in which pulses of different isotopically labelled amino acids are administered to cells over a time course, has been used to follow the fate of proteins. To explore within our spin coated biofilm, whether the recombinant enzyme's longevity might be in part due to its regeneration, we introduced pulses of isotopically labelled lysine and phenylalanine into medium overlaying the biofilm and followed their incorporation over the course of biofilm development.

RESULTS

Through SILAC analysis, we reveal that constant and complete regeneration of recombinant enzymes occurs within spin coated biofilms. The striking catalytic longevity within the biofilm results from more than just simple protection of active enzyme by the biofilm and its associated extracellular matrix. The replenishment of recombinant enzyme is likely to contribute significantly to the catalytic longevity observed for the engineered biofilm system.

CONCLUSIONS

Here we provide the first evidence of a recombinant enzyme's regeneration in an engineered biofilm. The recombinant enzyme was constantly replenished over time as evidenced by dynamic SILAC, which suggests that the engineered E. coli biofilms are highly metabolically active, having a not inconsiderable energetic demand. The constant renewal of recombinant enzyme highlights the attractive possibility of utilising this biofilm system as a dynamic platform into which enzymes of interest can be introduced in a "plug-and-play" fashion and potentially be controlled through promoter switching for production of a series of desired fine chemicals.

A comparison of the response of twoBurkholderia fungorumstrains grown as planktonic cells versus biofilm to dibenzothiophene and select polycyclic aromatic hydrocarbons

In natural environments, bacteria often exist in close association with surfaces and interfaces by establishing biofilms. Here, we report on the ability of Burkholderia fungorum strains DBT1 and 95 to survive in high concentrations of hydrocarbons, and we compare their growth as a biofilm vs. planktonic cells. The 2 compounds tested were dibenzothiophene (DBT) and a mixture of naphthalene, phenanthrene, and pyrene (5:2:1) as representative compounds of thiophenes and polycyclic aromatic hydrocarbons (PAHs), respectively. The results showed that both strains were able to degrade DBT and to survive in the presence of up to a 2000 mg·L−1concentration of this compound both as a biofilm and as free-living cells. Moreover, B. fungorum DBT1 showed reduced tolerance towards the mixed PAHs (2000 mg·L−1naphthalene, 800 mg·L−1phenanthrene, and 400 mg·L−1pyrene) both as a biofilm and as free-living cells. Conversely, biofilms of B. fungorum 95 enhanced resistance against these toxic compounds compared with planktonic cells (P < 0.05). Visual observation through confocal laser scanning microscopy showed that exposure of biofilms to DBT and PAHs altered their structure: high concentrations of DBT triggered an aggregation of biofilm cells. These findings provide new perspectives on the effectiveness of using DBT-degrading bacterial strains in bioremediation of hydrocarbon-contaminated sites.

Hyperadherence of Pseudomonas taiwanensis VLB120ΔC increases productivity of (S)-styrene oxide formation

The attachment strength of biofilm microbes is responsible for the adherence of the cells to surfaces and thus is a critical parameter in biofilm processes. In tubular microreactors, aqueous‐air segmented flow ensures an optimal oxygen supply and prevents excessive biofilm growth. However, organisms growing in these systems depend on an adaptation phase of several days, before mature and strong biofilms can develop. This is due to strong interfacial forces. In this study, a hyperadherent mutant of Pseudomonas taiwanensis VLB120ΔCeGFP possessing an engineered cyclic diguanylate metabolism, was applied to a continuous biofilm process for the production of (S)‐styrene oxide. Cells of the mutant P.  taiwanensis VLB120ΔCeGFP Δ04710, showing the same specific activity as the wild type, adhered substantially stronger to the substratum. Adaptation to the high interfacial forces was not necessary in these cases. Thereby, 40% higher final product concentrations were achieved and the maximal volumetric productivity of the parent strain was significantly surpassed by P. taiwanensis VLB120ΔCeGFP Δ04710. Applying mutants with strong adhesion in biofilm‐based catalysis opens the door to biological process control in future applications of catalytic biofilms using other industrially relevant strains.

Phenotypic Variability in Synthetic Biology Applications: Dealing with Noise in Microbial Gene Expression

The stochasticity due to the infrequent collisions among low copy-number molecules within the crowded cellular compartment is a feature of living systems. Single cell variability in gene expression within an isogenic population (i.e., biological noise) is usually described as the sum of two independent components: intrinsic and extrinsic stochasticity. Intrinsic stochasticity arises from the random occurrence of events inherent to the gene expression process (e.g., the burst-like synthesis of mRNA and protein molecules). Extrinsic fluctuations reflect the state of the biological system and its interaction with the intra and extracellular environments (e.g., concentration of available polymerases, ribosomes, metabolites, and micro-environmental conditions). A better understanding of cellular noise would help synthetic biologists design gene circuits with well-defined functional properties. In silico modeling has already revealed several aspects of the network topology’s impact on noise properties; this information could drive the selection of biological parts and the design of reliably engineered pathways. Importantly, while optimizing artificial gene circuitry for industrial applications, synthetic biology could also elucidate the natural mechanisms underlying natural phenotypic variability. In this review, we briefly summarize the functional roles of noise in unicellular organisms and address their relevance to synthetic network design. We will also consider how noise might influence the selection of network topologies supporting reliable functions, and how the variability of cellular events might be exploited when designing innovative biotechnology applications.

Extracellular polymer substances and the heterogeneity of Clostridium acetobutylicum biofilm induced tolerance to acetic acid and butanol

Extracellular polymer substances limited the transfer of harmful substances, and thus diluted their concentration in order to protect biofilm cells, enabling the maintenance of stability and increased tolerance to environmental stress.

Increased Microbial Butanol Tolerance by Exogenous Membrane Insertion Molecules

Butanol is an ideal biofuel, although poor titers lead to high recovery costs by distillation. Fluidization of microbial membranes by butanol is one of the major factors limiting titers in butanol-producing bioprocesses. Starting with the hypothesis that certain membrane insertion molecules would stabilize the lipid bilayer in the presence of butanol, we applied a combination of in vivo and in vitro techniques within an in silico framework to describe a new approach to achieve solvent tolerance in bacteria. Single-molecule tracking of a model supported bilayer showed that COE1-5C, a five-ringed oligo-polyphenylenevinylene conjugated oligoelectrolyte (COE), reduced the diffusion rate of phospholipids in a microbially derived lipid bilayer to a greater extent than three-ringed and four-ringed COEs. Furthermore, COE1-5C treatment increased the specific growth rate of E. coli K12 relative to a control at inhibitory butanol concentrations. Consequently, to confer butanol tolerance to microbes by exogenous means is complementary to genetic modification of strains in industrial bioprocesses, extends the physiological range of microbes to match favorable bioprocess conditions, and is amenable with complex and undefined microbial consortia for biobutanol production. Molecular dynamics simulations indicated that the π-conjugated aromatic backbone of COE1-5C likely acts as a hydrophobic tether for glycerophospholipid acyl chains by enhancing bilayer integrity in the presence of high butanol concentrations, which thereby counters membrane fluidization. COE1-5C-mitigated E. coli K12 membrane depolarization by butanol is consistent with the hypothesis that improved growth rates in the presence of butanol are a consequence of improved bilayer stability.

Continuous cyclohexane oxidation to cyclohexanol using a novel cytochrome P450 monooxygenase from Acidovorax sp. CHX100 in recombinant P. taiwanensis VLB120 biofilms

The applications of biocatalysts in chemical industries are characterized by activity, selectivity, and stability. One key strategy to achieve high biocatalytic activity is the identification of novel enzymes with kinetics optimized for organic synthesis by Nature. The isolation of novel cytochrome P450 monooxygenase genes from Acidovorax sp. CHX100 and their functional expression in recombinant Pseudomonas taiwanensis VLB120 enabled efficient oxidation of cyclohexane to cyclohexanol. Although initial resting cell activities of 20 U gCDW (-1) were achieved, the rapid decrease in catalytic activity due to the toxicity of cyclohexane prevented synthetic applications. Cyclohexane toxicity was reduced and cellular activities stabilized over the reaction time by delivering the toxic substrate through the vapor phase and by balancing the aqueous phase mass transfer with the cellular conversion rate. The potential of this novel CYP enzyme was exploited by transferring the shake flask reaction to an aqueous-air segmented flow biofilm membrane reactor for maximizing productivity. Cyclohexane was continuously delivered via the silicone membrane. This ensured lower reactant toxicity and continuous product formation at an average volumetric productivity of 0.4 g L tube (-1) h(-1) for several days. This highlights the potential of combining a powerful catalyst with a beneficial reactor design to overcome critical issues of cyclohexane oxidation to cyclohexanol. It opens new opportunities for biocatalytic transformations of compounds which are toxic, volatile, and have low solubility in water.

Guiding efficient microbial synthesis of non-natural chemicals by physicochemical properties of reactants

The recent progress in sustainable chemistry and in synthetic biology increased the interest of chemical and pharmaceutical industries to implement microbial processes for chemical synthesis. However, most organisms used in biotechnological applications are not evolved by Nature for the production of hydrophobic, non-charged, volatile, or toxic compounds. In order to overcome this discrepancy, bioprocess design should consist of an integrated approach addressing pathway, cellular, reaction, and process engineering. Highlighting selected examples, we show that surprisingly often Nature provides conceptual solutions to enable chemical synthesis. Complemented by established methods from (bio)chemical and metabolic engineering, these concepts offer potential strategies yet to be explored and translated into innovative technical solutions enabling sustainable microbial production of non-natural chemicals.

Solvent optimization for bacterial extracellular matrices: a solution for the insoluble

Ionic liquids enable solvent optimization for different biofilms through solubility parameter concept.

Segmented flow is controlling growth of catalytic biofilms in continuous multiphase microreactors

Biofilm reactors are often mass transfer limited due to excessive biofilm growth, impeding reactor performance. Fluidic conditions play a key role for biofilm structural development and subsequently for overall reactor performance. Continuous interfacial forces generated by aqueous-air segmented flow are controlling biofilm structure and diminish mass transfer limitations in biofilm microreactors. A simple three step method allows the formation of robust biofilms under aqueous-air segmented flow conditions: a first-generation biofilm is developing during single phase flow, followed by the introduction of air segments discarding most of the established biofilm. Finally, a second-generation, mature biofilm is formed in the presence of aqueous-air segments. Confocal laser scanning microscopy experiments revealed that the segmented flow supports the development of a robust biofilm. This mature biofilm is characterized by a three to fourfold increase in growth rate, calculated from an increase in thickness, a faster spatial distribution (95% surface coverage in 24 h), and a significantly more compact structure (roughness coefficient <1), as compared to biofilms grown under single phase flow conditions. The applicability of the concept in a segmented flow biofilm microreactor was demonstrated using the epoxidation of styrene to (S)-styrene oxide (ee > 99.8%) catalyzed by Pseudomonas sp. strain VLB120ΔC cells in the mono-species biofilm. The limiting factor affecting reactor performance was oxygen transfer as the volumetric productivity rose from 11 to 46 g L tube (-1) day(-1) after increasing the air flow rate. In summary, different interfacial forces can be applied for separating cell attachment and adaptation resulting in the development of a robust catalytic biofilm in continuous microreactors.

Biofilm production by Zymomonas mobilis enhances ethanol production and tolerance to toxic inhibitors from rice bran hydrolysate

Microorganisms play a significant role in bioethanol production from lignocellulosic material. A challenging problem in bioconversion of rice bran is the presence of toxic inhibitors in lignocellulosic acid hydrolysate. Various strains of Zymomonas mobilis (ZM4, TISTR 405, 548, 550 and 551) grown under biofilm or planktonic modes were used in this study to examine their potential for bioconversion of rice bran hydrolysate and ethanol production efficiencies. Z. mobilis readily formed bacterial attachment on plastic surfaces, but not on glass surfaces. Additionally, the biofilms formed on plastic surfaces steadily increased over time, while those formed on glass were speculated to cycle through accumulation and detachment phases. Microscopic analysis revealed that Z. mobilis ZM4 rapidly developed homogeneous biofilm structures within 24 hours, while other Z. mobilis strains developed heterogeneous biofilm structures. ZM4 biofilms were thicker and seemed to be more stable than other Z. mobilis strains. The percentage of live cells in biofilms was greater than that for planktonic cells (54.32 ± 7.10% vs. 28.69 ± 3.03%), suggesting that biofilms serve as a protective niche for growth of bacteria in the presence of toxic inhibitors in the rice bran hydrolysate. The metabolic activity of ZM4 grown as a biofilm was also higher than the same strain grown planktonically, as measured by ethanol production from rice bran hydrolysate (13.40 ± 2.43 g/L vs. 0.432 ± 0.29 g/L, with percent theoretical ethanol yields of 72.47 ± 6.13% and 3.71 ± 5.24% respectively). Strain TISTR 551 was also quite metabolically active, with ethanol production by biofilm and planktonically grown cells of 8.956 ± 4.06 g/L and 0.0846 ± 0.064 g/L (percent theoretical yields were 48.37 ± 16.64% and 2.046 ± 1.58%, respectively). This study illustrates the potential for enhancing ethanol production by utilizing bacterial biofilms in the bioconversion of a readily available and normally unusable low value by-product of rice farming.

Whole-cell biocatalysis for selective and productive C-O functional group introduction and modification

During the last decades, biocatalysis became of increasing importance for chemical and pharmaceutical industries. Regarding regio- and stereospecificity, enzymes have shown to be superior compared to traditional chemical synthesis approaches, especially in C-O functional group chemistry. Catalysts established on a process level are diverse and can be classified along a functional continuum starting with single-step biotransformations using isolated enzymes or microbial strains towards fermentative processes with recombinant microorganisms containing artificial synthetic pathways. The complex organization of respective enzymes combined with aspects such as cofactor dependency and low stability in isolated form often favors the use of whole cells over that of isolated enzymes. Based on an inventory of the large spectrum of biocatalytic C-O functional group chemistry, this review focuses on highlighting the potentials, limitations, and solutions offered by the application of self-regenerating microbial cells as biocatalysts. Different cellular functionalities are discussed in the light of their (possible) contribution to catalyst efficiency. The combined achievements in the areas of protein, genetic, metabolic, and reaction engineering enable the development of whole-cell biocatalysts as powerful tools in organic synthesis.

Application of biofilm bioreactors in white biotechnology

The production of valuable compounds in industrial biotechnology is commonly done by cultivation of suspended cells or use of (immobilized) enzymes rather than using microorganisms in an immobilized state. Within the field of wastewater as well as odor treatment the application of immobilized cells is a proven technique. The cells are entrapped in a matrix of extracellular polymeric compounds produced by themselves. The surface-associated agglomerate of encapsulated cells is termed biofilm. In comparison to common immobilization techniques, toxic effects of compounds used for cell entrapment may be neglected. Although the economic impact of biofilm processes used for the production of valuable compounds is negligible, many prospective approaches were examined in the laboratory and on a pilot scale. This review gives an overview of biofilm reactors applied to the production of valuable compounds. Moreover, the characteristics of the utilized materials are discussed with respect to support of surface-attached microbial growth.

Optimisation of engineered Escherichia coli biofilms for enzymatic biosynthesis of l-halotryptophans

Engineered biofilms comprising a single recombinant species have demonstrated remarkable activity as novel biocatalysts for a range of applications. In this work, we focused on the biotransformation of 5-haloindole into 5-halotryptophan, a pharmaceutical intermediate, using Escherichia coli expressing a recombinant tryptophan synthase enzyme encoded by plasmid pSTB7. To optimise the reaction we compared two E. coli K-12 strains (MC4100 and MG1655) and their ompR234 mutants, which overproduce the adhesin curli (PHL644 and PHL628). The ompR234 mutation increased the quantity of biofilm in both MG1655 and MC4100 backgrounds. In all cases, no conversion of 5-haloindoles was observed using cells without the pSTB7 plasmid. Engineered biofilms of strains PHL628 pSTB7 and PHL644 pSTB7 generated more 5-halotryptophan than their corresponding planktonic cells. Flow cytometry revealed that the vast majority of cells were alive after 24 hour biotransformation reactions, both in planktonic and biofilm forms, suggesting that cell viability was not a major factor in the greater performance of biofilm reactions. Monitoring 5-haloindole depletion, 5-halotryptophan synthesis and the percentage conversion of the biotransformation reaction suggested that there were inherent differences between strains MG1655 and MC4100, and between planktonic and biofilm cells, in terms of tryptophan and indole metabolism and transport. The study has reinforced the need to thoroughly investigate bacterial physiology and make informed strain selections when developing biotransformation reactions.

Application of the adhesive bacterionanofiber AtaA to a novel microbial immobilization method for the production of indigo as a model chemical

The toluene-degrading bacterium Acinetobacter sp. Tol 5 shows high adhesiveness mediated by the bacterionanofiber protein AtaA, which is a new member of the trimeric autotransporter adhesin (TAA) family. In contrast to other reported TAAs, AtaA mediates the adhesion of Tol 5 to various abiotic surfaces ranging from hydrophobic plastics to hydrophilic glass and stainless steel. The expression of ataA in industrially relevant bacteria improves their adhesiveness and enables immobilization directly onto support materials. This represents a new method that can be alternated with conventional immobilization via gel entrapment and chemical bonding. In this study, we demonstrate the feasibility of this immobilizing method by utilizing AtaA. As a model case for this method, the indigo producer Acinetobacter sp. ST-550 was transformed with ataA and immobilized on a polyurethane support. The immobilized ST-550 cells were transferred directly to a reaction solution containing indole as the substrate. The immobilized ST-550 cells showed a faster indigo production rate at high concentrations of indole compared with planktonic ST-550 not expressing the ataA gene, implying that immobilization enhanced the tolerance of ST-550 to the substrate indole. As a result, the immobilized ST-550 produced fivefold higher levels of indigo than planktonic ST-550. These results proved that AtaA is useful for bacterial immobilization.

Biofilms as living catalysts in continuous chemical syntheses

Biofilms are resilient to a wide variety of environmental stresses. This inherited robustness has been exploited mainly for bioremediation. With a better understanding of their physiology, the application of these living catalysts has been extended to the production of bulk and fine chemicals as well as towards biofuels, biohydrogen, and electricity production in microbial fuel cells. Numerous challenges call for novel solutions and concepts of analytics, biofilm reactor design, product recovery, and scale-up strategies. In this review, we highlight recent advancements in spatiotemporal biofilm characterization and new biofilm reactor developments for the production of value-added fine chemicals as well as current challenges and future scenarios.

Real-time solvent tolerance analysis of pseudomonas sp. strain VLB120{Delta}C catalytic biofilms

Biofilms are ubiquitous surface-associated microbial communities embedded in an extracellular polymeric (EPS) matrix, which gives the biofilm structural integrity and strength. It is often reported that biofilm-grown cells exhibit enhanced tolerance toward adverse environmental stress conditions, and thus there has been a growing interest in recent years to use biofilms for biotechnological applications. We present a time- and locus-resolved, noninvasive, quantitative approach to study biofilm development and its response to the toxic solvent styrene. Pseudomonas sp. strain VLB120ΔC-BT-gfp1 was grown in modified flow-cell reactors and exposed to the solvent styrene. Biofilm-grown cells displayed stable catalytic activity, producing (S)-styrene oxide continuously during the experimental period. The pillar-like structure and growth rate of the biofilm was not influenced by the presence of the solvent. However, the cells experience severe membrane damage during styrene treatment, although they obviously are able to adapt to the solvent, as the amount of permeabilized cells decreased from 75 to 80% down to 40% in 48 h. Concomitantly, the fraction of concanavalin A (ConA)-stainable EPS increased, substantiating the assumption that those polysaccharides play a major role in structural integrity and enhanced biofilm tolerance toward toxic environments. Compared to control experiments with planktonic grown cells, the Pseudomonas biofilm adapted much better to toxic concentrations of styrene, as nearly 65% of biofilm cells were not permeabilized (viable), compared to only 7% in analogous planktonic cultures. These findings underline the robustness of biofilms under stress conditions and its potential for fine chemical syntheses.