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

Stress resistance of the biofilm and planktonic forms of Lactobacillus delbrueckii in adverse environments

Biofilm and planktonic forms are different kinds of self-protection mechanisms in microorganisms for resistance to adverse environments. The research explored the physicochemical properties, antimicrobial, and antioxidant activities of Lactobacillus delbrueckii (L. delbrueckii) 5E, focusing on the biofilm's stress tolerance. L. delbrueckii 5E's high lactic acid production (709.1 g·L-1) enhances its antimicrobial activity, which is pH-dependent and decreases when the supernatant is adjusted to pH 6.5. The cell-free fermentation supernatant, bacterial suspension, and cell-free extract of L. delbrueckii 5E showed significant scavenging activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH), hydroxyl, and superoxide anion radicals. L. delbrueckii 5E formed biofilms with a bacterial count of 9.00 × 106 CFU·mL-1 on polyacrylonitrile electrospun membranes. Stress-tolerance tests indicated that the biofilm form of L. delbrueckii 5E exhibited superior survival under high temperatures, osmotic pressures, bile salts, potassium sorbate, and H2O2 exposure. The biofilm consistently released free bacteria, maintaining a stable total colony count of 106 CFU·mL-1. The remarkable antibacterial and antioxidant properties of L. delbrueckii 5E, along with its resilience to harsh environments, establish its potential for applications in the food industry.

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.

Zymomonas mobilis as an emerging biotechnological chassis for the production of industrially relevant compounds

Zymomonas mobilis is a well-recognized ethanologenic bacterium with outstanding characteristics which make it a promising platform for the biotechnological production of relevant building blocks and fine chemicals compounds. In the last years, research has been focused on the physiological, genetic, and metabolic engineering strategies aiming at expanding Z. mobilis ability to metabolize lignocellulosic substrates toward biofuel production. With the expansion of the Z. mobilis molecular and computational modeling toolbox, the potential of this bacterium as a cell factory has been thoroughly explored. The number of genomic, transcriptomic, proteomic, and fluxomic data that is becoming available for this bacterium has increased. For this reason, in the forthcoming years, systems biology is expected to continue driving the improvement of Z. mobilis for current and emergent biotechnological applications. While the existing molecular toolbox allowed the creation of stable Z. mobilis strains with improved traits for pinpointed biotechnological applications, the development of new and more flexible tools is crucial to boost the engineering capabilities of this bacterium. Novel genetic toolkits based on the CRISPR-Cas9 system and recombineering have been recently used for the metabolic engineering of Z. mobilis. However, they are mostly at the proof-of-concept stage and need to be further improved.

Functional Gene Identification and Corresponding Tolerant Mechanism of High Furfural-Tolerant Zymomonas mobilis Strain F211

Furfural is a major inhibitor in lignocellulose hydrolysate for Zymomonas mobilis. A mutant F211 strain with high furfural tolerance was obtained from our previous study. Thus, its key tolerance mechanism was studied in the present study. The function of mutated genes in F211 was identified by functional complementation experiments, revealing that the improved furfural tolerance was resulted from the C493T mutation of the ZCP4_0270 gene promoting cell flocculation and the mutation (G1075A)/downregulation of ZCP4_0970. Comparative transcriptome analysis revealed 139 differentially expressed genes between F211 and the control, CP4, in response to furfural stress. In addition, the reliability of the RNA-Seq data was also confirmed. The potential tolerance mechanism was further demonstrated by functional identification of tolerance genes as follows: (I) some upregulated or downregulated genes increase the levels of NAD(P)H, which is involved in the reduction of furfural to less toxic furfuryl alcohol, thus accelerating the detoxification of furfural; (II) the mutated ZCP4_0270 and upregulated cellulose synthetase gene (ZCP4_0241 and ZCP4_0242) increased flocculation to resist furfural stress; (III) upregulated molecular chaperone genes promote protein synthesis and repair stress-damaged proteins; and (IV) transporter genes ZCP4_1623–1,625 and ZCP4_1702–1703 were downregulated, saving energy for cell growth. The furfural-tolerant mechanism and corresponding functional genes were revealed, which provides a theoretical basis for developing robust chassis strains for synthetic biology efforts.

Advances in engineered Bacillus subtilis biofilms and spores, and their applications in bioremediation, biocatalysis, and biomaterials

Bacillus subtilis is a commonly used commercial specie with broad applications in the fields of bioengineering and biotechnology. B. subtilis is capable of producing both biofilms and spores. Biofilms are matrix-encased multicellular communities that comprise various components including exopolysaccharides, proteins, extracellular DNA, and poly-γ-glutamic acid. These biofilms resist environmental conditions such as oxidative stress and hence have applications in bioremediation technologies. Furthermore, biofilms and spores can be engineered through biotechnological techniques for environmentally-friendly and safe production of bio-products such as enzymes. The ability to withstand with harsh conditions and producing spores makes Bacillus a suitable candidate for surface display technology. In recent years, the spores of such specie are widely used as it is generally regarded as safe to use. Advances in synthetic biology have enabled the reprogramming of biofilms to improve their functions and enhance the production of value-added products. Globally, there is increased interest in the production of engineered biosensors, biocatalysts, and biomaterials. The elastic modulus and gel properties of B. subtilis biofilms have been utilized to develop living materials. This review outlines the formation of B. subtilis biofilms and spores. Biotechnological engineering processes and their increasing application in bioremediation and biocatalysis, as well as the future directions of B. subtilis biofilm engineering, are discussed. Furthermore, the ability of B. subtilis biofilms and spores to fabricate functional living materials with self-regenerating, self-regulating and environmentally responsive characteristics has been summarized. This review aims to resume advances in biological engineering of B. subtilis biofilms and spores and their applications.

Microbial biofilms in biorefinery - Towards a sustainable production of low-value bulk chemicals and fuels

Harnessing the potential of biocatalytic conversion of renewable biomass into value-added products is still hampered by unfavorable process economics. This has promoted the use of biofilms as an alternative to overcome the limitations of traditional planktonic systems. In this paper, the benefits and challenges of biofilm fermentations are reviewed with a focus on the production of low-value bulk chemicals and fuels from waste biomass. Our study demonstrates that biofilm fermentations can potentially improve productivities and product yields by increasing biomass retention and allowing for continuous operation at high dilution rates. Furthermore, we show that biofilms can tolerate hazardous environments, which improve the conversion of crude biomass under substrate and product inhibitory conditions. Additionally, we present examples for the improved conversion of pure and crude substrates into bulk chemicals by mixed microbial biofilms, which can benefit from microenvironments in biofilms for synergistic multi-species reactions, and improved resistance to contaminants. Finally, we suggest the use of mathematical models as useful tools to supplement experimental insights related to the effects of physico-chemical and biological phenomena on the process. Major challenges for biofilm fermentations arise from inconsistent fermentation performance, slow reactor start-up, biofilm carrier costs and carrier clogging, insufficient biofilm monitoring and process control, challenges in reactor sterilization and scale-up, and issues in recovering dilute products. The key to a successful commercialization of the technology is likely going to be an interdisciplinary approach. Crucial research areas might include genetic engineering combined with the development of specialized biofilm reactors, biofilm carrier development, in-situ biofilm monitoring, model-based process control, mixed microbial biofilm technology, development of suitable biofilm reactor scale-up criteria, and in-situ product recovery.

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.

Physiological studies of the Pediococcus pentosaceus biofilm

Pediococcus pentosaceus, a bacterium recently used in human and animal probiotics, was used in combination with supports made from polylactic acid composite soybean meal was used to study biofilm formation, and it was found that dense biofilms developed by Day 1. Proteomic comparison between planktonic and biofilm cultures of P. pentosaceus showed distinct expression patterns of intracellular and extracellular proteins. Type I glyceraldehyde-3-phosphate dehydrogenase was upregulated in biofilm cultures and mediated cell adhesion and encouraged biofilm production. GMP synthase, which regulates GMP synthesis and acts as an intracellular signal molecule to control cell mechanisms and has been exploited in the development of new therapeutic agents, was also upregulated in the biofilm mode of growth. The present work serves as a basis for future studies examining the complex network of systems that regulate lactic acid bacterial (LAB) biofilm formation and can serve as a framework for studies of production of therapeutic agents from LAB.

The “Zero Miles Product” Concept Applied to Biofuel Production: A Case Study

To make biofuel production feasible from an economic point of view, several studies have investigated the main associated bottlenecks of the whole production process through approaches such as the “cradle to grave” approach or the Life Cycle Assessment (LCA) analysis, being the main constrains the feedstock collection and transport. Whilst several feedstocks are interesting because of their high sugar content, very few of them are available all year around and moreover do not require high transportation’ costs. This work aims to investigate if the “zero miles” concept could bring advantages to biofuel production by decreasing all the associated transport costs on a locally established production platform. In particular, a specific case study applied to the Technical University of Denmark (DTU) campus is used as example to investigate the advantages and feasibility of using the spent coffee grounds generated at the main cafeteria for the production of bioethanol on site, which can be subsequently used to (partially) cover the campus’ energy demands.

Concepts for flow chemistry with whole-cell biocatalysts

By combining continuous flow processing and biocatalysis, efficient, stable and cost-effective processes can be realised. In this review, an overview about different concepts for continuous flow processes based on the use of whole-cells as catalysts is given.

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.

Controlling biofilms using synthetic biology approaches

Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of biofilms due to the non-growing nature of biofilm bacteria and the physical barrier provided by the extracellular matrix, eradicating biofilms is a very difficult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling biofilms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate biofilms via protein engineering of biofilm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables beneficial applications of biofilms through the production of biomaterials and patterning biofilms with specific temporal and spatial structures. Advances in synthetic biology will add novel biofilm functionalities for future therapeutic, biomanufacturing, and environmental applications.

Valorising Agro-industrial Wastes within the Circular Bioeconomy Concept: the Case of Defatted Rice Bran with Emphasis on Bioconversion Strategies

The numerous environmental problems caused by the extensive use of fossil resources have led to the formation of the circular bioeconomy concept. Renewable resources will constitute the cornerstone of this new, sustainable model, with biomass presenting a huge potential for the production of fuels and chemicals. In this context, waste and by-product streams from the food industry will be treated not as “wastes” but as resources. Rice production generates various by-product streams which currently are highly unexploited, leading to environmental problems especially in the countries that are the main producers. The main by-product streams include the straw, the husks, and the rice bran. Among these streams, rice bran finds applications in the food industry and cosmetics, mainly due to its high oil content. The high demand for rice bran oil generates huge amounts of defatted rice bran (DRB), the main by-product of the oil extraction process. The sustainable utilisation of this by-product has been a topic of research, either as a food additive or via its bioconversion into value-added products and chemicals. This review describes all the processes involved in the efficient bioconversion of DRB into biotechnological products. The detailed description of the production process, yields and productivities, as well as strains used for the production of bioethanol, lactic acid and biobutanol, among others, are discussed.

Potential of Zymomonas mobilis as an electricity producer in ethanol production

BACKGROUND

Microbial fuel cell (MFC) convokes microorganism to convert biomass into electricity. However, most well-known electrogenic strains cannot directly use glucose to produce valuable products. Zymomonas mobilis, a promising bacterium for ethanol production, owns special Entner-Doudoroff pathway with less ATP and biomass produced and the low-energy coupling respiration, making Z. mobilis a potential exoelectrogen.

RESULTS

A glucose-consuming MFC is constructed by inoculating Z. mobilis. The electricity with power density 2.0 mW/m² is derived from the difference of oxidation-reduction potential (ORP) between anode and cathode chambers. Besides, two-type electricity generation is observed as glucose-independent process and glucose-dependent process. For the sake of enhancing MFC efficiency, extracellular and intracellular strategies are implemented. Biofilm removal and addition of c-type cytochrome benefit electricity performance and Tween 80 accelerates the electricity generation. Perturbation of cellular redox balance compromises the electricity output, indicating that redox homeostasis is the principal requirement to reach ideal voltage.

CONCLUSION

This study identifies potential feature of electricity activity for Z. mobilis and provides multiple strategies to enhance the electricity output. Therefore, additional electricity generation will benefit the techno-economic viability of the commercial bulk production for biochemicals or biofuels in an efficient and environmentally sustainable manner.

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.

Adaptively evolved Escherichia coli for improved ability of formate utilization as a carbon source in sugar-free conditions

BACKGROUND

Formate converted from CO₂ reduction has great potential as a sustainable feedstock for biological production of biofuels and biochemicals. Nevertheless, utilization of formate for growth and chemical production by microbial species is limited due to its toxicity or the lack of a metabolic pathway. Here, we constructed a formate assimilation pathway in Escherichia coli and applied adaptive laboratory evolution to improve formate utilization as a carbon source in sugar-free conditions.

RESULTS

The genes related to the tetrahydrofolate and serine cycles from Methylobacterium extorquens AM1 were overexpressed for formate assimilation, which was proved by the ¹³C-labeling experiments. The amino acids detected by GC/MS showed significant carbon labeling due to biomass production from formate. Then, 150 serial subcultures were performed to screen for evolved strains with improved ability to utilize formate. The genomes of evolved mutants were sequenced and the mutations were associated with formate dehydrogenation, folate metabolism, and biofilm formation. Last, 90 mg/L of ethanol production from formate was achieved using fed-batch cultivation without addition of sugars.

CONCLUSION

This work demonstrates the effectiveness of the introduction of a formate assimilation pathway, combined with adaptive laboratory evolution, to achieve the utilization of formate as a carbon source. This study suggests that the constructed E. coli could serve as a strain to exploit formate and captured CO₂.

Expression and Extracellular Secretion of Endo-glucanase and Xylanase by Zymomonas mobilis

Recombinant Zymomonas mobilis (pGEX-4T-3 BI 120-2) was constructed to encode endo-glucanase (CelA) and endo-xylanase (Xyn11) from Z. mobilis ZM4 (ATCC 31821) and an uncultured bacterium. The recombinant was genetically engineered with the N-terminus of a predicted SecB-dependent (type II) secretion signal from phoC of Z. mobilis to translocate the enzymes extracellularly. Both the enzymes were characterized regarding their functional optimum pH and temperature, with the highest multi-enzyme activities at pH 6.0 and a temperature of 30 °C, which approximates the optimum conditions for ethanol production by Z. mobilis. The crude intracellular and extracellular fractions of the recombinant were characterized in terms of substrate specificity using carboxymethyl cellulose (CMC), beechwood xylan, filter paper, Avicel, and pretreated rice straw. The crude extracellular and intracellular enzymes with cellulolytic and xylanolytic activities were more robustly produced and secreted from the recombinant strain compared to the wild-type and ampicillin-sensitive strains, using CMC and beechwood xylan as the substrates. Ethanol production by the recombinant strain was greater than the production by the wild-type strain when pretreated rice straw was used as a sole carbon source.

Furfural-tolerant Zymomonas mobilis derived from error-prone PCR-based whole genome shuffling and their tolerant mechanism

Furfural-tolerant strain is essential for the fermentative production of biofuels or chemicals from lignocellulosic biomass. In this study, Zymomonas mobilis CP4 was for the first time subjected to error-prone PCR-based whole genome shuffling, and the resulting mutants F211 and F27 that could tolerate 3 g/L furfural were obtained. The mutant F211 under various furfural stress conditions could rapidly grow when the furfural concentration reduced to 1 g/L. Meanwhile, the two mutants also showed higher tolerance to high concentration of glucose than the control strain CP4. Genome resequencing revealed that the F211 and F27 had 12 and 13 single-nucleotide polymorphisms. The activity assay demonstrated that the activity of NADH-dependent furfural reductase in mutant F211 and CP4 was all increased under furfural stress, and the activity peaked earlier in mutant than in control. Also, furfural level in the culture of F211 was also more rapidly decreased. These indicate that the increase in furfural tolerance of the mutants may be resulted from the enhanced NADH-dependent furfural reductase activity during early log phase, which could lead to an accelerated furfural detoxification process in mutants. In all, we obtained Z. mobilis mutants with enhanced furfural and high concentration of glucose tolerance, and provided valuable clues for the mechanism of furfural tolerance and strain development.

Adaptation to low pH and lignocellulosic inhibitors resulting in ethanolic fermentation and growth of Saccharomyces cerevisiae

Lignocellulosic bioethanol from renewable feedstocks using Saccharomyces cerevisiae is a promising alternative to fossil fuels owing to environmental challenges. S. cerevisiae is frequently challenged by bacterial contamination and a combination of lignocellulosic inhibitors formed during the pre-treatment, in terms of growth, ethanol yield and productivity. We investigated the phenotypic robustness of a brewing yeast strain TMB3500 and its ability to adapt to low pH thereby preventing bacterial contamination along with lignocellulosic inhibitors by short-term adaptation and adaptive lab evolution (ALE). The short-term adaptation strategy was used to investigate the inherent ability of strain TMB3500 to activate a robust phenotype involving pre-culturing yeast cells in defined medium with lignocellulosic inhibitors at pH 5.0 until late exponential phase prior to inoculating them in defined media with the same inhibitor cocktail at pH 3.7. Adapted cells were able to grow aerobically, ferment anaerobically (glucose exhaustion by 19 ± 5 h to yield 0.45 ± 0.01 g ethanol g glucose(-1)) and portray significant detoxification of inhibitors at pH 3.7, when compared to non-adapted cells. ALE was performed to investigate whether a stable strain could be developed to grow and ferment at low pH with lignocellulosic inhibitors in a continuous suspension culture. Though a robust population was obtained after 3600 h with an ability to grow and ferment at pH 3.7 with inhibitors, inhibitor robustness was not stable as indicated by the characterisation of the evolved culture possibly due to phenotypic plasticity. With further research, this short-term adaptation and low pH strategy could be successfully applied in lignocellulosic ethanol plants to prevent bacterial contamination.

Living together in biofilms: the microbial cell factory and its biotechnological implications

In nature, bacteria alternate between two modes of growth: a unicellular life phase, in which the cells are free-swimming (planktonic), and a multicellular life phase, in which the cells are sessile and live in a biofilm, that can be defined as surface-associated microbial heterogeneous structures comprising different populations of microorganisms surrounded by a self-produced matrix that allows their attachment to inert or organic surfaces. While a unicellular life phase allows for bacterial dispersion and the colonization of new environments, biofilms allow sessile cells to live in a coordinated, more permanent manner that favors their proliferation. In this alternating cycle, bacteria accomplish two physiological transitions via differential gene expression: (i) from planktonic cells to sessile cells within a biofilm, and (ii) from sessile to detached, newly planktonic cells. Many of the innate characteristics of biofilm bacteria are of biotechnological interest, such as the synthesis of valuable compounds (e.g., surfactants, ethanol) and the enhancement/processing of certain foods (e.g., table olives). Understanding the ecology of biofilm formation will allow the design of systems that will facilitate making products of interest and improve their yields.

Zymomonas mobilis as a model system for production of biofuels and biochemicals

Zymomonas mobilis is a natural ethanologen with many desirable industrial biocatalyst characteristics. In this review, we will discuss work to develop Z. mobilis as a model system for biofuel production from the perspectives of substrate utilization, development for industrial robustness, potential product spectrum, strain evaluation and fermentation strategies. This review also encompasses perspectives related to classical genetic tools and emerging technologies in this context.

Analysis of a taurine-dependent promoter in Sinorhizobium meliloti that offers tight modulation of gene expression

Background

Genetic models have been developed in divergent branches of the class Alphaproteobacteria to help answer a wide spectrum of questions regarding bacterial physiology. For example, Sinorhizobium meliloti serves as a useful representative for investigating rhizobia-plant symbiosis and nitrogen fixation, Caulobacter crescentus for studying cell cycle regulation and organelle biogenesis, and Zymomonas mobilis for assessing the potentials of metabolic engineering and biofuel production. A tightly regulated promoter that enables titratable expression of a cloned gene in these different models is highly desirable, as it can facilitate observation of phenotypes that would otherwise be obfuscated by leaky expression.

Results

We compared the functionality of four promoter regions in S. meliloti (P_araA, P_tauA, P_rhaR, and P_melA) by constructing strains carrying fusions to the uidA reporter in their genomes and measuring beta-glucuronidase activities when they were induced by arabinose, taurine, rhamnose, or melibiose. P_tauA was chosen for further study because it, and, to a lesser extent, P_melA, exhibited characteristics suitable for efficient modulation of gene expression. The levels of expression from P_tauA depended on the concentrations of taurine, in both complex and defined media, in S. meliloti as well as C. crescentus and Z. mobilis. Moreover, our analysis indicated that TauR, TauC, and TauY are each necessary for taurine catabolism and substantiated their designated roles as a transcriptional activator, the permease component of an ABC transporter, and a major subunit of the taurine dehydrogenase, respectively. Finally, we demonstrated that P_tauA can be used to deplete essential cellular factors in S. meliloti, such as the PleC histidine kinase and TatB, a component of the twin-arginine transport machinery.

Conclusions

The P_tauA promoter of S. meliloti can control gene expression with a relatively inexpensive and permeable inducer, taurine, in diverse alpha-proteobacteria. Regulated expression of the same gene in different hosts can be achieved by placing both tauR and P_tauA on appropriate vectors, thus facilitating inspection of conservation of gene function across species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-014-0295-2) contains supplementary material, which is available to authorized users.