Targeting the Production of Biomolecules by Extremophiles at Bioreactor Scale

Phenanthrene removal from a spent sediment washing solution in a continuous-flow stirred-tank reactor

The issue of polycyclic aromatic hydrocarbons (PAHs) is widespread in marine sediments involving ecological systems and human health. Sediment washing (SW) has proven to be the most effective remediation approach for sediments polluted by PAHs, such as phenanthrene (PHE). However, SW still raises waste handling concerns due to a considerable amount of effluents generated downstream. In this context, the biological treatment of a PHE- and ethanol-containing spent SW solution can represent a highly efficient and environmentally-friendly strategy, but its knowledge is still scarce in scientific literature and no studies have so far been conducted in continuous mode. Therefore, a synthetic PHE-polluted SW solution was biologically treated in a 1 L aerated continuous-flow stirred-tank reactor for 129 days by evaluating the effect of different pH values, aeration flowrates and hydraulic retention times as operating parameters over five successive phases. A PHE removal efficiency of up to 75-94% was achieved by an acclimated PHE-degrading consortium mainly composed of Proteobacteria, Bacteroidota and Firmicutes phyla through biodegradation following the adsorption mechanism. PHE biodegradation, mainly occurring via the benzoate route due to the presence of PAH-related-degrading functional genes and a phthalate accumulation up to 46 mg/L, was also accompanied by a reduction of dissolved organic carbon and ammonia nitrogen above 99% in the treated SW solution.

Optimization of Lipopeptide Biosurfactant Production by Salibacterium sp. 4CTb in Batch Stirred-Tank Bioreactors

Halophilic microorganisms are potentially capable as platforms to produce low-cost biosurfactants. However, the robustness of bioprocesses is still a challenge and, therefore, it is essential to understand the effects of microbiological culture conditions through bioreactor engineering. Based on a design of experiments (DOE) and a response surface methodology (RSM) tailored and taken from the literature, the present work focuses on the evaluation of a composite central design (CCD) under batch cultures in stirred-tank bioreactors with the halophilic bacteria Salibacterium sp. 4CTb in order to determine the operative conditions that favor mass transfer and optimize the production of a lipopeptide. The results obtained showed profiles highlighting the most favorable culture conditions, which lead to an emulsification index (E₂₄%) higher than 70%. Moreover, through the behavior of dissolved oxygen (DO), it was possible to experimentally evaluate the higher volumetric coefficient of mass transfer in the presence of lipopeptide (k_La = 31 1/h) as a key criterion for the synthesis of the biosurfactant on further cell expansion.

Soft Sensor-Based Monitoring and Efficient Control Strategies of Biomass Concentration for Continuous Cultures of Haloferax mediterranei and Their Application to an Industrial Production Chain

Continuous bioprocessing using cell retention allows the achievement of high space-time yields for slow-growing organisms such as halophiles. However, the lack of efficient methods for monitoring and control limits the application of biotechnological processes in the industry. The aim of this study was to implement a control and online monitoring strategy for biomass in continuous cultures. For the first time, a feedforward cultivation strategy in a membrane-based cell retention system allowed to control the biomass concentration of the extreme halophilic Haloferax mediterranei at defined levels. Moreover, soft sensor-based biomass estimation allowed reliable monitoring of biomass online. Application of the combined monitoring and control strategy using industrial process water containing formate, phenol, aniline and 4,4′-methylenedianiline could for the first time demonstrate high throughput degradation in this extremophilic bioremediation process, obtaining degradation efficiencies of up to 100%. This process demonstrates the usefulness of continuous halophilic cultures in a circular economy application.

Demonstrating the viability of halolipase production at a mechanically stirred tank biological reactor

The definition of halophiles as "the coming stars of industrial biotechnology" in a recent review demands new research efforts for their efficient production at bioreactor scale. In this sense, the scarcity of information about halolipases production has furthered the research on the viability of Halomonas sp. LM1C culture in a mechanically stirred bioreactor. The operating conditions have been optimized by means of a Central Composite Face-Centered (CCFC) design. The operation at low aerations (0.25 vvm) and moderate agitation rates (583 rpm) led to activity levels near 8000 U/L, which clearly surpasses the typical values detected for other extremophilic enzymes. The process at optimum conditions has been kinetically characterized and the oxygen volumetric mass transfer coefficient (K_La) has been determined.

The production, properties, and applications of thermostable steryl glucosidases

Extremophilic microorganisms are a rich source of enzymes, the enzymes which can serve as industrial catalysts that can withstand harsh processing conditions. An example is thermostable β-glucosidases that are addressing a challenging problem in the biodiesel industry: removing steryl glucosides (SGs) from biodiesel. Steryl glucosidases (SGases) must be tolerant to heat and solvents in order to function efficiently in biodiesel. The amphipathic nature of SGs also requires enzymes with an affinity for water/solvent interfaces in order to achieve efficient hydrolysis. Additionally, the development of an enzymatic process involving a commodity such as soybean biodiesel must be cost-effective, necessitating an efficient manufacturing process for SGases. This review summarizes the identification of microbial SGases and their applications, discusses biodiesel refining processes and the development of analytical methods for identifying and quantifying SGs in foods and biodiesel, and considers technologies for strain engineering and process optimization for the heterologous production of a SGase from Thermococcus litoralis. All of these technologies might be used for the production of other thermostable enzymes. Structural features of SGases and the feasibility of protein engineering for novel applications are explored.

Unravelling the suitability of biological induction for halophilic lipase production by Halomonas sp. LM1C cultures

In this study, the viability of using biological induction as an alternative to the conventional chemical induction in lipase production by a novel halophilic microorganism, Halomonas sp. LM1C, has been demonstrated. Thus, a 9-times increase of lipase activity (3000U/L) was recorded when Staphylococcus equorum sp. AMC7 was present in the medium, which is competitive with the results obtained when Triton X-100 was added as chemical inducer. The GC-MS data allowed concluding the true nature of the biological inducer effect, as the existence of high percentages of isomeric forms of pentadecanoic acid were detected. The suitability of the proposed strategy was validated by operating at bench scale bioreactor, and the influence of bioreactor configuration on the biomass and lipolytic activity levels was studied. All the data were fitted to logistic and Luedeking & Piret models to characterize the bioprocess kinetics, concluding the growth-associated character of the produced lipolytic enzymes.

Understanding the interplay of carbon and nitrogen supply for ectoines production and metabolic overflow in high density cultures of Chromohalobacter salexigens

Background

The halophilic bacterium Chromohalobacter salexigens has been proposed as promising cell factory for the production of the compatible solutes ectoine and hydroxyectoine. This bacterium has evolved metabolic adaptations to efficiently grow under high salt concentrations by accumulating ectoines as compatible solutes. However, metabolic overflow, which is a major drawback for the efficient conversion of biological feedstocks, occurs as a result of metabolic unbalances during growth and ectoines production. Optimal production of ectoines is conditioned by the interplay of carbon and nitrogen metabolisms. In this work, we set out to determine how nitrogen supply affects the production of ectoines.

Results

Chromohalobacter salexigens was challenged to grow in media with unbalanced carbon/nitrogen ratio. In C. salexigens, overflow metabolism and ectoines production are a function of medium composition. At low ammonium conditions, the growth rate decreased importantly, up to 80%. Shifts in overflow metabolism were observed when changing the C/N ratio in the culture medium. ¹³C-NMR analysis of ectoines labelling revealed a high metabolic rigidity, with almost constant flux ratios in all conditions assayed. Unbalanced C/N ratio led to pyruvate accumulation, especially upon N-limitation. Analysis of an ect⁻ mutant demonstrated the link between metabolic overflow and ectoine biosynthesis. Under non ectoine synthesizing conditions, glucose uptake and metabolic overflow decreased importantly. Finally, in fed-batch cultures, biomass yield was affected by the feeding scheme chosen. High growth (up to 42.4 g L⁻¹) and volumetric ectoine yields (up to 4.21 g L⁻¹) were obtained by minimizing metabolite overflow and nutrient accumulation in high density cultures in a low nitrogen fed-batch culture. Moreover, the yield coefficient calculated for the transformation of glucose into biomass was 30% higher in fed-batch than in the batch culture, demonstrating that the metabolic efficiency of C. salexigens can be improved by careful design of culture feeding schemes.

Conclusions

Metabolic shifts observed at low ammonium concentrations were explained by a shift in the energy required for nitrogen assimilation. Carbon-limited fed-batch cultures with reduced ammonium supply were the best conditions for cultivation of C. salexigens, supporting high density growth and maintaining high ectoines production.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0643-7) contains supplementary material, which is available to authorized users.

Scale-up of naringinase production process based on the constant oxygen transfer rate for a novel strain of Bacillus methylotrophicus

Naringinase bioprocess based on Bacillus methylotrophicus was successfully scaled up based on constant oxygen transfer rate (OTR) as the scale-up criterion from 5-L bioreactor to 20-L bioreactor. OTR was measured in 5 and 20-L bioreactor under various operating conditions using dynamic method. The operating conditions, where complete dispersion was observed were identified. The highest OTR of 0.035 and 0.04 mMol/L/s was observed in 5 and 20-L bioreactor, respectively. Critical dissolved oxygen concentration of novel isolated strain B. methylotrophicus was found to be 20% of oxygen saturation in optimized medium. The B. methylotrophicus cells grown on sucrose had maximum oxygen uptake rate of 0.14 mMol/L/s in optimized growth medium. The cells produced the maximum naringinase activity of 751 and 778 U/L at 34 hr in 5 and 20-L bioreactors, respectively. The maximum specific growth rate of about 0.178/hr was observed at both the scales of operations. The maximum naringinase yield of 160 and 164 U/g biomass was observed in 5 and 20-L bioreactors, respectively. The growth and production profiles at both scales were similar indicating successful scale-up strategy for B. methylotrophicus culture.

Aflatoxin B1 degradation by liquid cultures and lysates of three bacterial strains

Aflatoxin contamination remains a daunting issue to address in food safety. In spite of the efforts geared towards prevention and elimination of this toxin, it still persists in agricultural commodities. This has necessitated the search for other measures such as microbial degradation to combat this hazard. In this study, we investigated the biodegradation of aflatoxin B1 (AFB1), using lysates of three bacterial strains (Pseudomonas anguilliseptica VGF1, Pseudomonas fluorescens and Staphylococcus sp. VGF2) isolated from a gold mine aquifer. The bacterial cells were intermittently lysed in the presence and absence of protease inhibitors to obtain protease free lysates, subsequently incubated with AFB1 for 3, 6, 12, 24, and 48h to investigate whether any possible AFB1 degradation occurred using high performance liquid chromatography (HPLC) for detection. Results obtained revealed that after 6h of incubation, protease inhibited lysates of Staphylococcus sp. VGF2 demonstrated the highest degradation capacity of 100%, whereas P. anguilliseptica VGF1 and P. fluorescens lysates degraded AFB1 by 66.5 and 63%, respectively. After further incubation to 12h, no residual AFB1 was detected for all the lysates. Lower degrading ability was however observed for liquid cultures and uninhibited lysates. Data on cytotoxicity studies against human lymphocytes showed that the degraded products were less toxic than the parent AFB1. From this study, it can thus be deduced that the mechanism of degradation by these bacterial lysates is enzymatic. This study shows the efficacy of crude bacterial lysates for detoxifying AFB1 indicating potential for application in the food and feed industry.

Ionic liquids for the concomitant use in extremophiles lysis and extremozymes extraction

Ionic liquids have been successfully proposed to modify membrane permeability in cultures of a model extremophilic bacterium Thermus thermophilus HB27, which makes up the first time that aqueous solutions of these molten salts are applied in downstream stages of this kind of microorganisms. The presence of 1g/L of C10MIMCl entails a great solubilisation of cell biomass, thus allowing the release of intracellular and membrane-bound enzyme. The influence on the enzyme activity of two inorganic salts such as Na2CO3 and (NH4)2SO4, selected on the basis of their high salting out potential and biocompatibility with enzymes, respectively, was investigated. In parallel, their ability to trigger phase segregation was confirmed in the presence of the enzyme crude, leading to very high levels of enzyme extraction (96%). The validity of the strategy was confirmed by operating at bioreactor scale, and the main bioprocess parameters were obtained by modelling the experimental data.

Novel physico-biological treatment for the remediation of textile dyes-containing industrial effluents

In this work, a novel remediation strategy consisting of a sequential biological and physical process is proposed to remove dyes from a textile polluted effluent. The decolorization ability of Anoxybacillus flavithermus in an aqueous effluent containing two representative textile finishing dyes (Reactive Black 5 and Acid Black 48, as di-azo and antraquinone class, respectively) was proved. The decolorization efficiency for a mixture of both dyes reached almost 60% in less than 12h, which points out the suitability of the selected microorganism. In a sequential stage, an aqueous biphasic system consisting of non-ionic surfactants and a potassium-based organic salt, acting as the salting out agent, was investigated. The phase segregation potential of the selected salts was evaluated in the light of different thermodynamic models, and remediation levels higher than 99% were reached.