Halophiles as Chassis for Bioproduction

Advances in stress-tolerance elements for microbial cell factories

Microorganisms, particularly extremophiles, have evolved multiple adaptation mechanisms to address diverse stress conditions during survival in unique environments. Their responses to environmental coercion decide not only survival in severe conditions but are also an essential factor determining bioproduction performance. The design of robust cell factories should take the balance of their growing and bioproduction into account. Thus, mining and redesigning stress-tolerance elements to optimize the performance of cell factories under various extreme conditions is necessary. Here, we reviewed several stress-tolerance elements, including acid-tolerant elements, saline-alkali-resistant elements, thermotolerant elements, antioxidant elements, and so on, providing potential materials for the construction of cell factories and the development of synthetic biology. Strategies for mining and redesigning stress-tolerance elements were also discussed. Moreover, several applications of stress-tolerance elements were provided, and perspectives and discussions for potential strategies for screening stress-tolerance elements were made.

Haloarchaea as Promising Chassis to Green Chemistry

Climate change and the scarcity of primary resources are driving the development of new, more renewable and environmentally friendly industrial processes. As part of this green chemistry approach, extremozymes (extreme microbial enzymes) can be used to replace all or part of the chemical synthesis stages of traditional industrial processes. At present, the production of these enzymes is limited by the cellular chassis available. The production of a large number of extremozymes requires extremophilic cellular chassis, which are not available. This is particularly true of halophilic extremozymes. The aim of this review is to present the current potential and challenges associated with the development of a haloarchaea-based cellular chassis. By overcoming the major obstacle of the limited number of genetic tools, it will be possible to propose a robust cellular chassis for the production of functional halophilic enzymes that can participate in the industrial transition of many sectors.

Microbial communities in the Dead Sea and their potential biotechnological applications

The Dead Sea is unique compared to other extreme halophilic habitats. Its salinity exceeds 34%, and it is getting saltier. The Dead Sea environment is characterized by a dominance of divalent cations, with magnesium chloride (MgCl2) levels approaching the predicted 2.3 M upper limit for life, an acidic pH of 6.0, and high levels of absorbed ultraviolet radiation. Consequently, only organisms adapted to such a polyextreme environment can survive in the surface, sinkholes, sediments, muds, and underwater springs of the Dead Sea. Metagenomic sequence analysis and amino acid profiling indicated that the Dead Sea is predominantly composed of halophiles that have various adaptation mechanisms and produce metabolites that can be utilized for biotechnological purposes. A variety of products have been obtained from halophilic microorganisms isolated from the Dead Sea, such as antimicrobials, bioplastics, biofuels, extremozymes, retinal proteins, colored pigments, exopolysaccharides, and compatible solutes. These resources find applications in agriculture, food, biofuel production, industry, and bioremediation for the detoxification of wastewater and soil. Utilizing halophiles as a bioprocessing platform offers advantages such as reduced energy consumption, decreased freshwater demand, minimized capital investment, and continuous production.

Application of extremophile cell factories in industrial biotechnology

Due to the extreme living conditions, extremophiles have unique characteristics in morphology, structure, physiology, biochemistry, molecular evolution mechanism and so on. Extremophiles have superior growth and synthesis capabilities under harsh conditions compared to conventional microorganisms, allowing for unsterilized fermentation processes and thus better performance in low-cost production. In recent years, due to the development and optimization of molecular biology, synthetic biology and fermentation technology, the identification and screening technology of extremophiles has been greatly improved. In this review, we summarize techniques for the identification and screening of extremophiles and review their applications in industrial biotechnology in recent years. In addition, the facts and perspectives gathered in this review suggest that next-generation industrial biotechnology (NGIBs) based on engineered extremophiles holds the promise of simplifying biofuturing processes, establishing open, non-sterilized continuous fermentation production systems, and utilizing low-cost substrates to make NGIBs attractive and cost-effective bioprocessing technologies for sustainable manufacturing.

Third generation biobutanol production by Clostridium beijerinckii in a medium containing mixotrophically cultivated Dunaliella salina biomass

This study aims the third generation biobutanol production in P2 medium supplemented D. salina biomass mixotrophically cultivated with marble waste (MW). The wastes derived from the marble industry contain approximately 90% of carbon-rich compounds. Microalgal growth in mixotrophic conditions was optimized in the 0.4-2 g/L of MW concentration range. The highest microalgal concentration was obtained as 0.481 g/L in the presence of 1 g/L MW. Furthermore, some important parameters for the production of biobutanol, such as microalgal cultivation conditions, initial mixotrophic microalgal biomass loading (50-300 g/L), and fermentation time (24-96 h) were optimized. The highest biobutanol, total ABE, biobutanol yield and productivity were determined as 11.88 g/L, 13.89 g/L, 0.331 g/g and 0.165 g/L/h at the end of 72 h in P2 medium including 60 g/L glucose and 200 g/L microalgal biomass cultivated in 1 g/L MW, respectively. The results show that D. salina is a suitable raw material for supporting Clostridium beijerinckii DSMZ 6422 cells on biobutanol production. To the best of our knowledge, this is the first study on the use of MW which is a promising feedstock on the mixotrophic cultivation of D. salina for biobutanol production.

Recent advances in production and applications of ectoine, a compatible solute of industrial relevance

Extremophilic bacteria growing in saline ecosystems are potential producers of biotechnologically important products including compatible solutes. Ectoine/hydroxyectoine are two such solutes that protect cells and associated macromolecules from osmotic, heat, cold and UV stress without interfering with cellular functions. Since ectoine is a high value product, overviewing strategies for improving yields become relevant. Screening of natural isolates, use of inexpensive substrates and response surface methodology approaches have been used to improve bioprocess parameters. In addition, genome mining exercises can aid in identifying hitherto unreported microorganisms with a potential to produce ectoine that can be exploited in the future. Application wise, ectoine has various biotechnological (protein protectant, membrane modulator, DNA protectant, cryoprotective agent, wastewater treatment) and biomedical (dermatoprotectant and in overcoming respiratory and hypersensitivity diseases) uses. The review summarizes current updates on the potential of microorganisms in the production of this industrially relevant metabolite and its varied applications.

Chemoautotrophic production of gaseous hydrocarbons, bioplastics and osmolytes by a novel Halomonas species

BACKGROUND

Production of relatively low value, bulk commodity chemicals and fuels by microbial species requires a step-change in approach to decrease the capital and operational costs associated with scaled fermentation. The utilisation of the robust and halophilic industrial host organisms of the genus Halomonas could dramatically decrease biomanufacturing costs owing to their ability to grow in seawater, using waste biogenic feedstocks, under non-sterile conditions.

RESULTS

We describe the isolation of Halomonas rowanensis, a novel facultative chemoautotrophic species of Halomonas from a natural brine spring. We investigated the ability of this species to produce ectoine, a compound of considerable industrial interest, under heterotrophic conditions. Fixation of radiolabelled NaH14CO3 by H. rowanensis was confirmed in mineral medium supplied with thiosulfate as an energy source. Genome sequencing suggested carbon fixation proceeds via a reductive tricarboxylic acid cycle, and not the Calvin-Bensen-Bassham cycle. The mechanism of energy generation to support chemoautotrophy is unknown owing to the absence of an annotated SOX-based thiosulfate-mediated energy conversion system. We investigated further the biotechnological potential of the isolated H. rowanensis by demonstrating production of the gaseous hydrocarbon (bio-propane), bioplastics (poly-3-hydroxybutyrate) and osmolytes (ectoine) under heterotrophic and autotrophic CO2 fixation growth conditions.

CONCLUSIONS

This proof-of-concept study illustrates the value of recruiting environmental isolates as industrial hosts for chemicals biomanufacturing, where CO2 utilisation could replace, or augment, the use of biogenic feedstocks in non-sterile, industrialised bioreactors.

Synthetic biology of extremophiles: a new wave of biomanufacturing

Microbial biomanufacturing, powered by the advances of synthetic biology, has attracted growing interest for the production of diverse products. In contrast to conventional microbes, extremophiles have shown better performance for low-cost production owing to their outstanding growth and synthesis capacity under stress conditions, allowing unsterilized fermentation processes. We review increasing numbers of products already manufactured utilizing extremophiles in recent years. In addition, genetic parts, molecular tools, and manipulation approaches for extremophile engineering are also summarized, and challenges and opportunities are predicted for non-conventional chassis. Next-generation industrial biotechnology (NGIB) based on engineered extremophiles promises to simplify biomanufacturing processes and achieve open and continuous fermentation, without sterilization, and utilizing low-cost substrates, making NGIB an attractive green process for sustainable manufacturing.

Co-production of biofuel, bioplastics and biochemicals during extended fermentation of Halomonas bluephagenesis

Halomonas bluephagenesis TD1.0 was engineered to produce the biofuel propane, bioplastic poly-3-hydroxybutyrate (PHB), and biochemicals mandelate and hydroxymandelate in a single, semi-continuous batch fermentation under non-sterile conditions. Multi-product separation was achieved by segregation of the headspace gas (propane), fermentation broth ([hydroxy]mandelate) and cellular biomass (PHB). Engineering was performed by incorporating the genes encoding fatty acid photodecarboxylase (CvFAP) and hydroxymandelic acid synthase (SyHMAS) into a H. bluephagenesis hmgCAB cassette knockout to channel flux towards (hydroxy)mandelate. Design of Experiment strategies were coupled with fermentation trials to simultaneously optimize each product. Propane and mandelate titres were the highest reported for H. bluephagenesis (62 g/gDCW and 71 ± 10 mg/L respectively) with PHB titres (69% g/gDCW) comparable to other published studies. This proof-of-concept achievement of four easily separated products within one fermentation is a novel achievement probing the versatility of biotechnology, further elevating H. bluephagenesis as a Next Generation Industrial Biotechnology (NGIB) chassis by producing highly valued products at a reduced cost.

A new carbonic anhydrase identified in the Gram-negative bacterium (Chromohalobacter sp.) and the interaction of anions with the enzyme

In this study, the characterization and inhibition characteristic of α-class carbonic anhydrase from Chromohalobacter (ChCA) was documented for the first time. The carbonic anhydrase enzyme had 47.77% yield and 54.45-fold purity. The specific activity of the enzyme was determined as 318.52 U/mg proteins. Alternative substrate (4-nitrophenyl trifluoroacetate, 4-nitrophenyl phosphate, 4-nitrophenyl sulphate and 4-nitrophenyl acetate) were tested for the enzyme. K_M and V_max values for 4-nitrophenyl acetate were 4.57 mM and 4.29 EU/mL and for 4-nitrophenyl trifluoroacetate were 2.39 mM and 2.41 EU/mL. The anions, Cl^-, NO₂^-, NO₃^-, Br^-, ClO₃^-, ClO₄^-, I^-, CO₃^2- and SO₄^2-, inhibited the ChCA hydratase activity. Among nine anions, the strongest inhibitor activities were obtained with micro molar concentrations of NO₂^-, NO₃^-, Br^-, I^-, CO₃^2- (K_I values of 160-255 μM). Other four anions tested (Cl^-, ClO₃^-, ClO₄^- and SO₄^2-) showed moderate inhibitory activities (K_I values of 680-813.5 μM). The results obtained demonstrate that the anions we tested inhibit the Chromohalobacter CA (ChCA) enzyme as in other α-CAs in mammals; however, the susceptibility of ChCA resulted from anions differed significantly from that of other organism CAs.

Engineered Mutants of a Marine Photosynthetic Purple Nonsulfur Bacterium with Increased Volumetric Productivity of Polyhydroxyalkanoate Bioplastics

Polyhydroxyalkanoates (PHAs) are green and sustainable bioplastics that could replace petrochemical synthetic plastics without posing environmental threats to living organisms. In addition, sustainable PHA production could be achieved using marine photosynthetic purple nonsulfur bacteria (PNSBs) that utilize natural seawater, sunlight, carbon dioxide gas, and nitrogen gas for growth. However, PHA production using marine photosynthetic PNSBs has not been economically feasible yet due to its high cost and low productivity. In this work, strain improvement, using genome-wide mutagenesis coupled with high-throughput screening via fluorescence-activated cell sorting, we were able to create Rhodovulum sulfidophilum mutants with enhanced volumetric PHA productivity, with an up to 1.7-fold increase. The best selected mutants (E6 and E6M4) reached the stationary growth phase 1 day faster and accumulated the maximum PHA content 2 days faster than the wild type. Maximizing volumetric PHA productivity before the stationary growth phase is indeed an additional advantage for R. sulfidophilum as a growth-associated PHA producer.

A Polyhydroxyalkanoates-Based Carrier Platform of Bioactive Substances for Therapeutic Applications

Bioactive substances (BAS), such as small molecule drugs, proteins, RNA, cells, etc., play a vital role in many therapeutic applications, especially in tissue repair and regeneration. However, the therapeutic effect is still a challenge due to the uncontrollable release and instable physico-chemical properties of bioactive components. To address this, many biodegradable carrier systems of micro-nano structures have been rapidly developed based on different biocompatible polymers including polyhydroxyalkanoates (PHA), the microbial synthesized polyesters, to provide load protection and controlled-release of BAS. We herein highlight the developments of PHA-based carrier systems in recent therapeutic studies, and give an overview of its prospective applications in various disease treatments. Specifically, the biosynthesis and material properties of diverse PHA polymers, designs and fabrication of micro- and nano-structure PHA particles, as well as therapeutic studies based on PHA particles, are summarized to give a comprehensive landscape of PHA-based BAS carriers and applications thereof. Moreover, recent efforts focusing on novel-type BAS nano-carriers, the functionalized self-assembled PHA granules in vivo, was discussed in this review, proposing the underlying innovations of designs and fabrications of PHA-based BAS carriers powered by synthetic biology. This review outlines a promising and applicable BAS carrier platform of novelty based on PHA particles for different medical uses.

Physiological limitations and opportunities in microbial metabolic engineering

Metabolic engineering can have a pivotal role in increasing the environmental sustainability of the transportation and chemical manufacturing sectors. The field has already developed engineered microorganisms that are currently being used in industrial-scale processes. However, it is often challenging to achieve the titres, yields and productivities required for commercial viability. The efficiency of microbial chemical production is usually dependent on the physiological traits of the host organism, which may either impose limitations on engineered biosynthetic pathways or, conversely, boost their performance. In this Review, we discuss different aspects of microbial physiology that often create obstacles for metabolic engineering, and present solutions to overcome them. We also describe various instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.

Microbial halophilic lipases: A review

Microbial lipases are commercially significant due to their versatile catalytic function of hydrolysis triacylglycerol. Among these, lipases from extremophiles are optimal for industrial application. Halophilic microorganisms living in a high salinity environment, such as the ocean, salt lakes, salt wells, and so on, produce halophilic lipases. In recent decades, many remarkable achievements have been made related to the properties and application of halophilic lipases. This review offers information collected over the last decades on halophilic lipase sources as well as advances in production, factors influencing activity, stability under various conditions, structural characteristics, progress in industrial applications such as food flavor modification, biodiesel production, and waste treatment, to provide theoretical and methodological references for the research in this direction.

Hyperproduction of 3-hydroxypropionate by Halomonas bluephagenesis

3-Hydroxypropionic acid (3HP), an important three carbon (C3) chemical, is designated as one of the top platform chemicals with an urgent need for improved industrial production. Halomonas bluephagenesis shows the potential as a chassis for competitive bioproduction of various chemicals due to its ability to grow under an open, unsterile and continuous process. Here, we report the strategy for producing 3HP and its copolymer poly(3-hydroxybutyrate-co-3-hydroxypropionate) (P3HB3HP) by the development of H. bluephagenesis. The transcriptome analysis reveals its 3HP degradation and synthesis pathways involving endogenous synthetic enzymes from 1,3-propanediol. Combing the optimized expression of aldehyde dehydrogenase (AldDHb), an engineered H. bluephagenesis strain of whose 3HP degradation pathway is deleted and that overexpresses alcohol dehydrogenases (AdhP) on its genome under a balanced redox state, is constructed with an enhanced 1.3-propanediol-dependent 3HP biosynthetic pathway to produce 154 g L-1 of 3HP with a yield and productivity of 0.93 g g-1 1,3-propanediol and 2.4 g L-1 h-1, respectively. Moreover, the strain could also accumulate 60% poly(3-hydroxybutyrate-co-32-45% 3-hydroxypropionate) in the dry cell mass, demonstrating to be a suitable chassis for hyperproduction of 3HP and P3HB3HP.

Improved Exopolymer Production by Chromohalobacter canadensis Cultures for Its Potential Cosmeceutical Applications

Several exopolymers with different chemical composition and correspondingly variety in their physico-chemical properties from halophilic microorganisms have still been described, however, with a low production yield. Chromohalobacter canadensis 28 isolated from Pomorie saltern synthesized an unusual exopolymer (EP) containing 72% γ-polyglutamic acid (PGA), an essential cosmeceutical additive. Current work suggests a novel approach for effective EP synthesis by C. canadensis 28 using continuous cultures. Highest production was observed at low dilution rates reaching a level of 2.1 mg/mL at D = 0.035, similar to those in batch cultures (2.34 mg/mL), however avoiding all disadvantages of discontinuous fermentation processes. At steady state, the total quantities of the synthesized EP after 48 h cultivation for the given equipment volume in D = 0.035 h⁻¹ and D = 0.075 h⁻¹ were 8.67 and 12 g, correspondingly, while it was 2.9 g for batch culture. Process parameters did not change after a ten-day run at D = 0.35 h⁻¹. A degree of purity of EP fraction received from continuous cultures was significantly increased up to 93–96%. A lack of cytotoxicity and high cell viability were observed for human dermal fibroblast cells after 24 h incubation with crude EP from C. canadensis 28 and purified PGA fraction that could suggest its high potential for cosmetic applications.

A marine photosynthetic microbial cell factory as a platform for spider silk production

Photosynthetic microorganisms such as cyanobacteria, purple bacteria and microalgae have attracted great interest as promising platforms for economical and sustainable production of bioenergy, biochemicals, and biopolymers. Here, we demonstrate heterotrophic production of spider dragline silk proteins, major ampullate spidroins (MaSp), in a marine photosynthetic purple bacterium, Rhodovulum sulfidophilum, under both photoheterotrophic and photoautotrophic growth conditions. Spider silk is a biodegradable and biocompatible material with remarkable mechanical properties. R. sulfidophilum grow by utilizing abundant and renewable nonfood bioresources such as seawater, sunlight, and gaseous CO₂ and N₂, thus making this photosynthetic microbial cell factory a promising green and sustainable production platform for proteins and biopolymers, including spider silks.

Foong et al. demonstrate production of spider dragline silk proteins in Rhodovulum sulfidophilum, a marine photosynthetic purple bacterium. This platform generates promise for the sustainable production of valuable biocompounds in photosynthetic organisms.

Recent Development of Extremophilic Bacteria and Their Application in Biorefinery

The biorefining technology for biofuels and chemicals from lignocellulosic biomass has made great progress in the world. However, mobilization of laboratory research toward industrial setup needs to meet a series of criteria, including the selection of appropriate pretreatment technology, breakthrough in enzyme screening, pathway optimization, and production technology, etc. Extremophiles play an important role in biorefinery by providing novel metabolic pathways and catalytically stable/robust enzymes that are able to act as biocatalysts under harsh industrial conditions on their own. This review summarizes the potential application of thermophilic, psychrophilic alkaliphilic, acidophilic, and halophilic bacteria and extremozymes in the pretreatment, saccharification, fermentation, and lignin valorization process. Besides, the latest studies on the engineering bacteria of extremophiles using metabolic engineering and synthetic biology technologies for high-efficiency biofuel production are also introduced. Furthermore, this review explores the comprehensive application potential of extremophiles and extremozymes in biorefinery, which is partly due to their specificity and efficiency, and points out the necessity of accelerating the commercialization of extremozymes.

Synthesis and Characterization of Polyhydroxyalkanoate Organo/Hydrogels

Synthetic organogels/hydrogels are attracting growing interests due to their potential applications in biomedical fields, organic electronics, and photovoltaics. Photogelation methods for synthesis of organogels/hydrogels have been shown particularly promising because of the high efficiency and simple synthetic procedures. This study synthesized new biodegradable polyhydroxyalkanoates (PHA)-based organogels/hydrogels via UV photo-cross-linking using unsaturated PHA copolymer poly[(R)-3-hydroxyundecanoate-co-(R)-3-hydroxy-10-undecenoate] (PHU10U) with polyethylene glycol dithiol (PDT) as a photo-cross-linker. The PHU10U was synthesized by an engineered Pseudomonas entomophila and characterized via Fourier transform infrared spectroscopy, ¹H nuclear magnetic resonance (NMR), and ¹³C NMR. With decreasing the molar ratio of PHU10U to PDT, both the swelling ratio and pore size were decreased. Meanwhile, increasing densities of the gel networks resulted in a higher compressive modulus. Cell cytotoxicity studies based on the CCK-8 assay on both the PHU10U precursor and PHU10U/PDT hydrogels showed that the novel PHA-based biodegradables acting as hydrogels possess good biocompatibility.

Identification of a GntR family regulator BusRTha and its regulatory mechanism in the glycine betaine ABC transport system of Tetragenococcus halophilus

Glycine betaine is one of the most effective compatible solutes of the halophilic lactic acid bacterium Tetragenococcus halophilus, the transportation of which is essential for its survival under salinity stress condition. In the current study, we attempted to define a glycine betaine ABC transporter system of T. halophilus, busA_Tha, which plays an important role in adapting to salinity condition. The expression of busA_Tha enhanced the growth of the recombinant strain under high salinity. BusR_Tha, a transcription regulator that represses the expression of busA_Tha, was characterized, and the repression was abrogated under high salinity. The binding of the regulator was demonstrated through electrophoretic mobility shift assays, and the binding sites were characterized as 5'-AAA(T/G)TGAC(C/A)(G/A)T(C/A)C-3'. This is the first studied transcription regulator of T. halophilus, and our findings provide insights into the molecular mechanism of halophilic life and tools for further application of halophiles as chassis in industrial biotechnology.