Genetically-manipulated microorganisms and their products in the oil service industries

A Systematic Review on Biosurfactants Contribution to the Transition to a Circular Economy

Since they are more environmentally acceptable than their chemically synthesized counterparts, biosurfactants are used in a wide range of environmental applications. However, less research has been done on biosurfactants within the context of the circular economy, despite their theoretical potential to fulfill a number of circular economy ambitions, including closing the consumption loop, regenerating natural systems, and maintaining resource value within the system. Hence, the main objective of this review is to identify and analyze the contributions of biosurfactants to the implementation of the circular economy. A final sample of 30 papers from the Web of Science database was examined. We identified five broad categories of contributions: waste stream-derived production, combating food waste, strengthening soil health, and improving the efficiency of water resources. We concluded that, while manufacturing biosurfactants from waste streams can reduce production costs, optimizing yield remains a contentious issue that complicates the adoption of biosurfactants into the circular economy framework.

Deployment of Engineered Microbes: Contributions to the Bioeconomy and Considerations for Biosecurity

Engineering at microscopic scales has an immense effect on the modern bioeconomy. Microbes contribute to such disparate markets as chemical manufacturing, fuel production, crop optimization, and pharmaceutical synthesis, to name a few. Due to new and emerging synthetic biology technologies, and the sophistication and control afforded by them, we are on the brink of deploying engineered microbes to not only enhance traditional applications but also to introduce these microbes to sectors, contexts, and formats not previously attempted. In microbially managed medicine, microbial engineering holds promise for increasing efficacy, improving tissue penetration, and sustaining treatment. In the environment, the most effective areas for deployment are in the management of crops and protection of ecosystems. However, caution is warranted before introducing engineered organisms to new environments where they may proliferate without control and could cause unforeseen effects. We summarize ideas and data that can inform identification and assessment of the risks that these tools present to ensure that realistic hazards are described and unrealistic ones do not hinder advancement. Further, because modes of containment are crucial complements to deployment, we describe the state of the art in microbial biocontainment strategies, current gaps, and how these gaps might be addressed through technological advances in synthetic engineering. Collectively, this work highlights engineered microbes as a foundational and expanding facet of the bioeconomy, projects their utility in upcoming deployments outside the laboratory, and identifies knowns and unknowns that will be necessary considerations and points of focus in this endeavor.

Rhamnolipid the Glycolipid Biosurfactant: Emerging trends and promising strategies in the field of biotechnology and biomedicine

Rhamnolipids (RLs) are surface-active compounds and belong to the class of glycolipid biosurfactants, mainly produced from Pseudomonas aeruginosa. Due to their non-toxicity, high biodegradability, low surface tension and minimum inhibitory concentration values, they have gained attention in various sectors like food, healthcare, pharmaceutical and petrochemicals. The ecofriendly biological properties of rhamnolipids make them potent materials to be used in therapeutic applications. RLs are also known to induce apoptosis and thus, able to inhibit proliferation of cancer cells. RLs can also act as immunomodulators to regulate the humoral and cellular immune systems. Regarding their antimicrobial property, they lower the surface hydrophobicity, destruct the cytoplasmic membrane and lower the critical micelle concentration to kill the bacterial cells either alone or in combination with nisin possibly due to their role in modulating outer membrane protein. RLs are also involved in the synthesis of nanoparticles for in vivo drug delivery. In relation to economic benefits, the post-harvest decay of food can be decreased by RLs because they prevent the mycelium growth, spore germination of fungi and inhibit the emergence of biofilm formation on food. The present review focuses on the potential uses of RLs in cosmetic, pharmaceutical, food and health-care industries as the potent therapeutic agents.

Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications

BACKGROUND

Biosafety is a key aspect in the international Genetically Engineered Machine (iGEM) competition, which offers student teams an amazing opportunity to pursue their own research projects in the field of Synthetic Biology. iGEM projects often involve the creation of genetically engineered bacterial strains. To minimize the risks associated with bacterial release, a variety of biosafety systems were constructed, either to prevent survival of bacteria outside the lab or to hinder horizontal or vertical gene transfer.

MAIN BODY

Physical containment methods such as bioreactors or microencapsulation are considered the first safety level. Additionally, various systems involving auxotrophies for both natural and synthetic compounds have been utilized by iGEM teams in recent years. Combinatorial systems comprising multiple auxotrophies have been shown to reduced escape frequencies below the detection limit. Furthermore, a number of natural toxin-antitoxin systems can be deployed to kill cells under certain conditions. Additionally, parts of naturally occurring toxin-antitoxin systems can be used for the construction of 'kill switches' controlled by synthetic regulatory modules, allowing control of cell survival. Kill switches prevent cell survival but do not completely degrade nucleic acids. To avoid horizontal gene transfer, multiple mechanisms to cleave nucleic acids can be employed, resulting in 'self-destruction' of cells. Changes in light or temperature conditions are powerful regulators of gene expression and could serve as triggers for kill switches or self-destruction systems. Xenobiology-based containment uses applications of Xeno-DNA, recoded codons and non-canonical amino acids to nullify the genetic information of constructed cells for wild type organisms. A 'minimal genome' approach brings the opportunity to reduce the genome of a cell to only genes necessary for survival under lab conditions. Such cells are unlikely to survive in the natural environment and are thus considered safe hosts. If suitable for the desired application, a shift to cell-free systems based on Xeno-DNA may represent the ultimate biosafety system.

CONCLUSION

Here we describe different containment approaches in synthetic biology, ranging from auxotrophies to minimal genomes, which can be combined to significantly improve reliability. Since the iGEM competition greatly increases the number of people involved in synthetic biology, we will focus especially on biosafety systems developed and applied in the context of the iGEM competition.

Microbial production of rhamnolipids: opportunities, challenges and strategies

Rhamnolipids are a class of biosurfactants which contain rhamnose as the sugar moiety linked to β-hydroxylated fatty acid chains. Rhamnolipids can be widely applied in many industries including petroleum, food, agriculture and bioremediation etc. Pseudomonas aeruginosa is still the most competent producer of rhamnolipids, but its pathogenicity may cause safety and health concerns during large-scale production and applications. Therefore, extensive studies have been carried out to explore safe and economical methods to produce rhamnolipids. Various metabolic engineering efforts have also been applied to either P. aeruginosa for improving its rhamnolipid production and diminishing its pathogenicity, or to other non-pathogenic strains by introducing the key genes for safe production of rhamnolipids. The three key enzymes for rhamnolipid biosynthesis, RhlA, RhlB and RhlC, are found almost exclusively in Pseudomonas sp. and Burkholderia sp., but have been successfully expressed in several non-pathogenic host bacteria to produce rhamnolipids in large scales. The composition of mono- and di-rhamnolipids can also be modified through altering the expression levels of RhlB and RhlC. In addition, cell-free rhamnolipid synthesis by using the key enzymes and precursors from non-pathogenic sources is thought to not only eliminate pathogenic effects and simplify the downstream purification processes, but also to circumvent the complexity of quorum sensing system that regulates rhamnolipid biosynthesis. The pathogenicity of P. aeruginosa can also be reduced or eliminated through in vivo or in vitro enzymatic degradation of the toxins such as pyocyanin during rhamnolipid production. The rhamnolipid production cost can also be significantly reduced if rhamnolipid purification step can be bypassed, such as utilizing the fermentation broth or the rhamnolipid-producing strains directly in the industrial applications of rhamnolipids.

Bioaugmentation: An Emerging Strategy of Industrial Wastewater Treatment for Reuse and Discharge

A promising long-term and sustainable solution to the growing scarcity of water worldwide is to recycle and reuse wastewater. In wastewater treatment plants, the biodegradation of contaminants or pollutants by harnessing microorganisms present in activated sludge is one of the most important strategies to remove organic contaminants from wastewater. However, this approach has limitations because many pollutants are not efficiently eliminated. To counterbalance the limitations, bioaugmentation has been developed and consists of adding specific and efficient pollutant-biodegrading microorganisms into a microbial community in an effort to enhance the ability of this microbial community to biodegrade contaminants. This approach has been tested for wastewater cleaning with encouraging results, but failure has also been reported, especially during scale-up. In this review, work on the bioaugmentation in the context of removal of important pollutants from industrial wastewater is summarized, with an emphasis on recalcitrant compounds, and strategies that can be used to improve the efficiency of bioaugmentation are also discussed. This review also initiates a discussion regarding new research areas, such as nanotechnology and quorum sensing, that should be investigated to improve the efficiency of wastewater bioaugmentation.

Synthetic bugs on the loose: containment options for deeply engineered (micro)organisms

Synthetic Biology (SynBio) has brought up again questions on the environmental fate of microorganisms carrying genetic modifications. The growing capacity of editing genomes for deployment of man-made programs opens unprecedented biotechnological opportunities. But the same exacerbate concerns regarding fortuitous or deliberate releases to the natural medium. Most approaches to tackle these worries involve endowing SynBio agents with containment devices for halting horizontal gene transfer and survival of the live agents only at given times and places. Genetic circuits and trophic restraint schemes have been proposed to this end in the pursuit of complete containment. The most promising include adoption of alternative genetic codes and/or dependency on xenobiotic amino acids and nucleotides. But the field has to still overcome serious bottlenecks.

Simultaneous polyhydroxyalkanoates and rhamnolipids production by Thermus thermophilus HB8

The ability of Thermus thermophilus HB8 to produce simultaneously two environmentally-friendly biodegradable products, polyhydroxyalkanoates (PHAs) and rhamnolipids (RLs), using either sodium gluconate or glucose as sole carbon source, was demonstrated. The utilization of sodium gluconate resulted in higher levels of PHAs and RLs production than when glucose was used as sole carbon source. The initial phosphate concentration (as PO43-) influences both PHAs and RLs productions that were increased during cultivation time. PHAs accumulation was enhanced (> 300 mg/L) after 72 h of cultivation in an initial [PO43-] of 25 mM, while RLs production (> 200 mg/L) was started after 35 h and continued until 72 h of cultivation, in a phosphate-limited medium containing initially 5 mM of [PO43-]. In addition, the combine effect of initial [PO43-] and cultivation time on biomass, PHAs and RLs production was evaluated from 2D contour plots. The results revealed that low initial phosphate concentrations (up to 5 mM) and long incubation time (72 h) promoted RLs biosynthesis while higher initial phosphate concentrations (up to 25 mM) where favorable for biomass and PHAs production. The molecular composition of the produced bio-products was identified. The accumulated PHAs were co-polymers which mainly consisted of 3-hydroxydecanoate (3HD) as resulted by gas chromatography (GC) analysis. The secreted RLs were extracted and their total mixture contained both mono- and di- RLs identified by thin-layer chromatography (TLC). Moreover, the molecular composition of the produced RLs characterized in details by LC-MS analysis showed a plethora of diversity including mono-, and di-RLs, di-rhamno-monolipidic congeners differing in the length of the lipidic chain, which additionally were found to be saturated or unsaturated in some cases.

Continuous bioconversion of n-octane to octanoic acid by recombinant Escherichia coli (alk(+)) growing in a two-liquid-phase Chemostat

Escherichia coli is able to grow on sugars in the presence of a bulk n-alkane phase. When E. coli is equipped with the alk genes from Pseudomonas oleovorans, the resulting recombinant strain converts n-alkanes into the corresponding alkanoic acids. To study the effects of growth rate and exposure to a bulk apolar phase on the physiology and the productivity of E. coli, we have grown this microorganism in two-liquid-phase continuous cultures containing 5% (v/v) n-octane.In contrast to batch cultures of wild-tape E. coli grown in the presence of n-octane, cells remained viable during the entire continuous culture, which lasted 200 h. Bioconversion of n-octane to n-octanoic acid by a recombinant E. coli (alk(+)) in a two-liquid-phase continuous culture was made possible by optimizing both the recombinant host strain and the conditions of culturing the organism. Continuous production in such two-phase systems has been maintained for the least 125 h without any changes in the product concentration in the fermentation medium. The volumetric productivity was determined as a function of growth rate and showed a maximum at a dilution rate D = 0.32 h(-1), reaching a continuous production rate of 0.5 g octanoate/L . h (4 tons/m(3) . year).

Microbial enhanced separation of oil from a petroleum refinery sludge

Petroleum refineries around the world have adopted different technological options to manage the solid wastes generated during the refining process and stocking of crude oil. These include physical, chemical and biological treatment methods. In this investigation bacterial mediated oil separation is effected. Two strains of Bacillus were isolated from petroleum-contaminated soils, and inoculated into slurry of sludge, and sludge-sand combinations. The bacteria could effect the separation of oil so as to form a floating scum within 48h with an efficiency of 97% at < or =5% level of sludge in the sludge-sand mixture. The activity was traced to the production of biosurfactants by bacteria.

Environmental applications for biosurfactants

Biosurfactants are surfactants that are produced extracellularly or as part of the cell membrane by bacteria, yeasts and fungi. Examples include Pseudomonas aeruginosa which produces rhamnolipids, Candida (formerly Torulopsis) bombicola, one of the few yeasts to produce biosurfactants, which produces high yields of sophorolipids from vegetable oils and sugars and Bacillus subtilis which produces a lipopeptide called surfactin. This review includes environmental applications of these biosurfactants for soil and water treatment. Biosurfactant applications in the environmental industries are promising due to their biodegradability, low toxicity and effectiveness in enhancing biodegradation and solubilization of low solubility compounds. However, more information is needed to be able to predict and model their behaviour. Full scale tests will be required. The role of biosurfactants in natural attenuation processes has not been determined. Very little information is available concerning the influence of soil components on the remediation process with biosurfactants. As most of the research until now has been performed with rhamnolipids, other biosurfactants need to be investigated as they may have more promising properties.

Toxicity comparison of biosurfactants and synthetic surfactants used in oil spill remediation to two estuarine species

The relative environmental toxicities of synthetic and biogenic surfactants used in oil spill remediation efforts are not well understood. Acute and chronic toxicities of three synthetic surfactants and three microbiologically produced surfactants were determined and compared in this study for the estuarine epibenthic invertebrate, Mysidopsis bahia and the inland silverside, Menidia beryllina. The toxicities of the surfactant were determined in standard laboratory static and static-renewal tests of 4-7 d duration. Results were specific to the surfactant, response parameter and test species. The LC50 values (nominal concentrations) for M. bahia ranged from 3.3 mg/l (Triton X-100) to >1000 mg/l (PES-61) and 2.5 mg/l (Triton X-100) to 413.6 mg/l (PES-61) for M. beryllina. Chronic first-effect concentrations (mg/l) for the six surfactants ranged from 2.3 to 465.0 (M. beryllina) and 1.0 to >1000.0 (M. bahia) based on reductions in growth and fecundity. Few generalizations could be made concerning the results due to their variability but M. bahia was generally the more sensitive species and the toxicities of the biosurfactants were intermediate to those of the synthetic surfactants.

Characterization of rhizosphere colonization by luminescent Enterobacter cloacae at the population and single-cell levels

A bioluminescence marker system was used to characterized colonization of the rhizosphere by a bacterial inoculum, both in terms of population activity and at the single-cell level. Plasmid pQF70/44, which contains luxAB genes under the control of a strong constitutive phage promoter, was introduced into the rhizobacterium and model biocontrol agent Enterobacter cloacae. Light output from the lux-modified strain was detected by luminometry of samples from growing cultures of E. cloacae and from inoculated soil and wheat root samples. The minimum detection limits for fully active cells under optimum conditions were 90 and 445 cells g-1 for liquid culture and soil, respectively. The metabolic activities of the lux-marked population of E. cloacae, characterized by luminometry, contrasted in rhizosphere and nonrhizosphere soil. Cells in the rhizosphere were active, and there was a linear relationship between light output and cell concentration. The activity of cells in nonrhizosphere coil could not be detected unless the soil was supplied with substrate. Novel use of a charge-coupled device is reported for the spatial characterization of rhizosphere colonization by E. cloacae (pQF70/44) at the single-cell and population levels. Used macroscopically, the charge-coupled device identified differences in colonization due to competition from indigenous soil organisms. The lux-marked bacterium was able to colonize all depths of roots in the absence of competition but was restricted tot he spermosphere in the presence of competition (nonsterile soil).(ABSTRACT TRUNCATED AT 250 WORDS)

Production of rhamnolipid biosurfactants

Biosurfactants are of increasing interest due to their broad range of potential applications. A large variety of microbial surfactants is known at present, some of which may be used for specific applications. Towards the large scale industrial production of biosurfactants, the physiology, biochemistry and genetics of biosurfactant synthesis has to be well understood. A fully integrated process has to be developed, allowing high productivities under optimized conditions. In the past few years, we have investigated the molecular biology of rhamnolipid biosynthesis have been partially purified and characterized. The structural and regulatory genes encoding the rhamnolipid synthesis pathway have been isolated and characterized. The knowledge of the complex mechanisms involved in rhamnolipid synthesis facilitates the overproduction of these extracellular compounds. Furthermore, the transfer of the relevant genes into other species allows the production of rhamnolipids in heterologous hosts under controlled conditions. An integrated process for the production of rhamnolipids on an industrial scale has been developed. This process involves continuous cultivation under optimized media and growth conditions and makes use of refined methods of cell recycling, gas exchange and downstream processing, thus allowing high yields and productivities.

Cloning and heterologous expression of a gene encoding an alkane-induced extracellular protein involved in alkane assimilation from Pseudomonas aeruginosa

Pseudomonas aeruginosa PG201 produces a 16-kDa extracellular protein in media containing n-hexadecane as a carbon source but not in media containing glycerol or glucose. This protein was purified, and the N-terminal amino acid sequence was determined. The amino acid composition of the protein was found to be very similar to that of the so-called protein-like activator for n-alkane oxidation (PA) from P. aeruginosa S7B1. This extracellular protein was previously characterized (K. Hisatsuka, T. Nakahara, Y. Minoda, and K. Yamada, Agric. Biol. Chem. 41:445-450, 1977) and found to stimulate the growth of P. aeruginosa on n-hexadecane and to possess emulsifying activity. To study the role(s) of the PA protein and to make it accessible for possible future applications, we have cloned the PA-encoding (pra) gene and determined its nucleotide sequence. This analysis revealed a protein-coding region of 162 amino acids, with the first 25 residues being reminiscent of those of a typical bacterial signal sequence. The pra gene was inactivated by insertional mutagenesis, and the resulting strain was found to lack extracellular PA protein and to be retarded in its growth in n-hexadecane-containing media. These results are consistent with the growth stimulatory role of the PA protein. The pra gene was expressed in Escherichia coli, and substantial amounts of the recombinant protein were found in the extracellular growth medium. The recombinant protein was purified by metal chelate affinity chromatography. The ability to produce secreted PA protein by E. coli provides a simple and safe means to analyze its function(s) in alkane assimilation in the future.

Hydrocarbon assimilation and biosurfactant production in Pseudomonas aeruginosa mutants

We isolated transposon Tn5-GM-induced mutants of Pseudomonas aeruginosa PG201 that were unable to grow in minimal media containing hexadecane as a carbon source. Some of these mutants lacked extracellular rhamnolipids, as shown by measuring the surface and interfacial tensions of the cell culture supernatants. Furthermore, the concentrated culture media of the mutant strains were tested for the presence of rhamnolipids by thin-layer chromatography and for rhamnolipid activities, including hemolysis and growth inhibition of Bacillus subtilis. Mutant 65E12 was unable to produce extracellular rhamnolipids under any of the conditions tested, lacked the capacity to take up 14C-labeled hexadecane, and did not grow in media containing individual alkanes with chain lengths ranging from C12 to C19. However, growth on these alkanes and uptake of [14C]hexadecane were restored when small amounts of purified rhamnolipids were added to the cultures. Mutant 59C7 was unable to grow in media containing hexadecane, nor was it able to take up [14C]hexadecane. The addition of small amounts of rhamnolipids restored growth on alkanes and [14C]hexadecane uptake. In glucose-containing media, however, mutant 59C7 produced rhamnolipids at levels about twice as high as those of the wild-type strain. These results show that rhamnolipids play a major role in hexadecane uptake and utilization by P. aeruginosa.

Bioconversion of N-Octane to Octanoic Acid by a Recombinant Escherichia Coli Cultured in a Two-Liquid Phase Bioreactor

The alk genes from the catabolic OCT plasmid of Pseudomonas oleovorans, which encode the enzymes involved in the oxidation of n-alkanes to carboxylic acids, were introduced into E. coli W3110. The resulting recombinant converts n-octane in a two-liquid phase medium into the corresponding alkanoate and excretes this compound into the aqueous phase. The rate of octanoic acid production by the recombinant E. coli is equal to or better than the alkane oxidation rate of P. oleovorans, suggesting that two-liquid phase fermentations with E. coli might have future industrial applications.

Applications of microbial surfactants

Biosurfactants are amphiphilic compounds produced by microorganisms that are capable of decreasing surface and interfacial tensions. They are useful in remediation of insoluble organic pollutants in soil and marine environments. There are also a large number of industrial uses for biosurfactants. This paper reviews recent research on applications of microbially-produced surfactants.

Enhanced Removal of Exxon Valdez Spilled Oil from Alaskan Gravel by a Microbial Surfactant

Remediation efforts for the oil spill from the Exxon Valdez tanker in Alaska have focused on the use of pressurized water at high temperature to remove oil from the beaches. We have tested a biological surfactant from Pseudomonas aeruginosa for its ability to remove oil from contaminated Alaskan gravel samples under various conditions, including concentration of the surfactant, time of contact, temperature of the wash, and presence or absence of xanthan gum. The results demonstrate the ability of the microbial surfactant to release oil to a significantly greater extent (2 to 3 times) than water alone, particularly at temperatures of 30 degrees C and above.

Microbial degradation of synthetic recalcitrant compounds

Synthetic compounds, particularly highly chlorinated aromatics, comprise the bulk of the environmental pollutants that somehow must be removed from the environment. Microbial degradation of such compounds is usually very slow, making them highly persistent in nature. Some synthetic compounds, with a lower degree of chlorination are, however, biodegradable; biochemical, genetic, and molecular studies demonstrate the evolution of new plasmid-encoded enzymatic activities specifically designed for the chlorinated substrates. Nucleotide sequences of many of the genes encoding such enzymatic activities demonstrate considerable homology either near the active sites or throughout the molecules with the chromosomal genes encoding enzymes catalyzing analogous reactions. In some cases, unique repeated sequences, reminiscent of prokaryotic insertion sequence elements, are present at or near the newly evolved genes. This suggests gene duplication and divergence as well as recombinational events mediated by transposable type elements as key ingredients in the evolution of new degradative functions. An understanding of such evolutionary processes is an essential feature for the development of genetically-improved bacteria capable of utilizing and thereby removing highly chlorinated environmental pollutants from our environment.