Genetically Engineered Methanotroph as a Platform for Bioaugmentation of Chemical Pesticide Contaminated Soil

Synthetic biology tools for environmental protection

Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.

Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.

Engineered bacterium-binding protein promotes root recruitment of functional bacteria for enhanced cadmium removal from wastewater by phytoremediation

Functional bacteria promote the efficiency of phytoremediation by enhancing plant growth and participating in decontamination. However, their activity is frequently compromised by the weakness of their interaction with plant roots. In this study, we designed the artificial protein LcGC composed of a bacterium-binding domain, a GFP fluorescence reporter, and a carbohydrate-binding domain to function as a physical contact between functional bacteria and plant roots. This protein was then expressed in an engineered yeast cell factory and extracted to assess its effect on rhizosphere microbiome composition, plant growth, and cadmium removal in a simulated phytoremediation system containing the remediation plant Lemna minor and the functional heavy metal-capturing bacteria Cupriavidus taiwanensis and Pseudomonas putida. LcGC efficiently bound bacterial cell wall components and glucan, endowing it high efficiency to bind both functional bacteria and plant roots. Scanning microscopy and microbiome analysis revealed that LcGC enhanced root recruitment and colonization of functional bacteria on the root surfaces. Furthermore, LcGC with the aid of single C. taiwanensis or of C. taiwanensis and P. putida in combination promoted plant growth, enhanced tolerance to cadmium-induced oxidative stress, and consequently improved cadmium-removing capacity of the plants, with the percent of cadmium removal reaching up to 91% for LcGC plus C. taiwanensis, and to 96% for LcGC plus C. taiwanensis and P. putida on day 7. This study provided a physical contact-based strategy to enhance the interaction between functional microbes and plant roots for efficient phytoremediation.

Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes

Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5'-phosphate-dependent enzymes, which have pivotal roles in microbe-microbe and plant-microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.

Pesticides Xenobiotics in Soil Ecosystem and Their Remediation Approaches

Globally, the rapid rise in the human population has increased the crop production, resulting in increased pesticide xenobiotics. Despite the fact that pesticide xenobiotics toxify the soil environment and ecosystem, synthetic pesticides have increased agricultural yields and reduced disease vectors. Pesticide use has increased, resulting in an increase in environmental pollution. Various methods of controlling and eliminating these contaminants have been proposed to address this issue. Pesticide impurity in the climate presents a genuine danger to individuals and other oceanic and earthly life. If not controlled, the pollution can prompt difficult issues for the climate. Some viable and cost-effective alternative approaches are needed to maintain this emission level at a low level. Phytoremediation and microbial remediation are effective methods for removing acaricide scrapings from the atmosphere using plants and organisms. This review gives an overview of different types of xenobiotics, how they get into the environment, and how the remediation of pesticides has progressed. It focuses on simple procedures that can be used in many countries. In addition, we have talked about the benefits and drawbacks of natural remediation methods.

Synthetically engineered microbial scavengers for enhanced bioremediation

Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review, we introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbial scavengers on ecosystems. In addition, we discuss recent achievements in the biodegradation of fastidious pollutants, greenhouse gases, and microplastics using engineered microbial scavengers. Using synthetic microbial scavengers and multidisciplinary technologies, toxic pollutants could be more easily eliminated, and the environment could be more efficiently recovered.

Exploration of an Efficient Electroporation System for Heterologous Gene Expression in the Genome of Methanotroph

One-carbon (C1) substrates such as methane and methanol have been considered as the next-generation carbon source in industrial biotechnology with the characteristics of low cost, availability, and bioconvertibility. Recently, methanotrophic bacteria naturally capable of converting C1 substrates have drawn attractive attention for their promising applications in C1-based biomanufacturing for the production of chemicals or fuels. Although genetic tools have been explored for metabolically engineered methanotroph construction, there is still a lack of efficient methods for heterologous gene expression in methanotrophs. Here, a rapid and efficient electroporation method with a high transformation efficiency was developed for a robust methanotroph of Methylomicrobium buryatense 5GB1. Based on the homologous recombination and high transformation efficiency, gene deletion and heterologous gene expression can be simultaneously achieved by direct electroporation of PCR-generated linear DNA fragments. In this study, the influence of several key parameters (competent cell preparation, electroporation condition, recovery time, and antibiotic concentration) on the transformation efficiency was investigated for optimum conditions. The maximum electroporation efficiency of 719 ± 22.5 CFU/μg DNA was reached, which presents a 10-fold improvement. By employing this method, an engineered M. buryatense 5GB1 was constructed to biosynthesize isobutyraldehyde by replacing an endogenous fadE gene in the genome with a heterologous kivd gene. This study provides a potential and efficient strategy and method to facilitate the cell factory construction of methanotrophs.