Introduction
Bioremediation is an essential biological process that entails the application of microorganism or their products in the decontamination of the environment. Microorganisms can degrade pollutants in their environment by using them as substrate materials for their enzymes in the generation of metabolic energy (Perpetuo et al., 2011). Increasing levels of pollutants in the environment have prompted the need for bioremediation because it is the safest way and an effective strategy. Usually, pollution causes the accumulation of contaminants in soil, water, and air, endangering human health and diminishing species diversity in the environment. Across the world, the occurrence of oil spills has contaminated water and threatened the existence of aquatic flora and fauna (Jaiswal et al., 2019). For instance, in the United States, about 450 sites have been marked as brownfields. However, advancements in biotechnology have led to the generation and production of microorganisms with the ability to degrade target contaminants in the environment. By examining bioremediation, this essay describes its application, the role of genomic techniques, the genetic modification of bacteria, the utilization of horizontal gene transfer occurs, and solutions to existing limitations.
The Application Bioremediation
An example of the application of bioremediation in the removal or degradation of oil spills in the environment using engineered bacteria. In their study, French et al. (2020) report the use of indigenous bacteria with the ability to degrade hydrocarbons in oil. Genetically modified bacteria possess specific genes, which codes for degrading enzymes of petroleum hydrocarbons. The analysis of the expression profiles revealed that Escherichia coli contains three essential genes, namely, almA, p450cam, and xylE, coding for enzymes with the ability to degrade petroleum hydrocarbons (French et al., 2020). The almA genes code for enzymes that dominate in the cytoplasm, while p450cam has an operon involved in the degradation of hydrocarbons in various micro-compartments in the cytoplasm. The style codes for dioxygenase that degrades partially in the cell membrane and largely in the micro-compartments of the cells. Since normal expression does not have a marked effect, over-expression of these genes causes significant degradation of about 60-99% of petroleum hydrocarbons present in an oil spill (French et al., 2020). The over-expression of these genes E. coli is critical since their enzymes have synergistic actions, resulting in the degradation of petroleum hydrocarbons and the achievement of bioremediation in oil spills.
Genomics and Sequencing
Genomics and sequencing play a critical role in bioremediation because they provide tools for genetic studies and modification of genes. The study of various genes of microorganisms requires the use of genomic tools and approaches. Genomic analysis has made it possible to compare genetic materials of different strains or species of organisms about their functions. The emergence of next-generation sequencing allows genome-wide analysis and identification of genes and their respective functions. Moreover, genome-editing tools, such as restriction enzymes, proteins associated with clustered regularly interspaced short palindromic repeats (CRISPR-Cas9), zinc-finger nucleases (ZFNs), and transcription activator-like effector nucleases (TALENs), aid in the identification and annotation of genes (Jaiswal et al., 2019). The design and creation of recombinant organisms rely on the efficient use of these genome-editing tools.
In the design and the creation of engineered bacteria to degrade hydrocarbons in oil spills, genomic and sequencing strategies apply. Extraction, amplification, and hybridization of genetic material into microarrays facilitate the identification of the structure and functions of diverse genes. Recombination of genes in E. coli using vectors designed by applying the genomic and sequencing tools, French et al. (2020) created engineered bacteria with unique attributes of degrading petroleum hydrocarbon. Genetically engineered cells of E. coli using restriction enzymes generated competent cells named DH5-Alpha, which allows horizontal gene transfer (French et al., 2020). Additionally, the analysis of the expression profiles of genes in the modified organism reveals phenotypic attributes of genes responsible for the bioremediation of petroleum hydrocarbons. Comparative analysis of the expression profiles of engineered and wild bacteria indicated the over-expression of five genes with the capacity to degrade crude oil, polyaromatic hydrocarbons, and long-chain hydrocarbons (French et al., 2020). Sequencing offers a method of understanding genetic structure and function through the application of bioinformatics.
Genetic Modification of Bacteria
With the application of genomics and bioinformatics tools, genetic modification of bacteria is possible to enable them to metabolize petroleum hydrocarbons and facilitate bioremediation of oil spills in the marine environment. Since over-expression of certain genes in E. coli contributes to the activity of metabolizing hydrocarbons, their transfer into wild bacteria through recombinant DNA technology would cause genetic modification. According to French et al. (2020), the transformation of bacteria with recombinant plasmids with xylE, almA, and p450cam enhances their metabolic capacity to degrade hydrocarbons in oil spills. Restriction digest of genes that codes for required enzymes and their insertion into competent plasmids with selectable markers, cloning sites, promoter, and origin of replication forms the basis of genetic modification of bacteria. Subsequently, the transformation of wild bacteria in culture by uptaking modified plasmids and acquiring genes of interest leads to the generation of engineered bacteria. In essence, the presence of plasmids in bacteria eases their modification because they uptake genetic materials in their environment and undergo a recombinant transformation.
Horizontal Gene Transfer
Horizontal gene transfer involves the process through which bacteria exchange their genetic material in their environments. The process of horizontal gene transfer can occur through transformation, transduction, and conjugation, depending on the bacteria’s environment. In a suitable culture media, bacteria can uptake plasmids from the surrounding environment, utilize them as their genetic material, and become transformed. In an environment where bacteriophages are common, they act as vectors of genetic bacteria because they feed on bacteria and carry with them the genetic material as they migrate from one colony to another. French et al. (2020) established that E. coli can transfer its modified plasmids with xylE, almA, and p450cam genes into wild bacteria through the process of conjugation. In this case, transformed E. coli can transform other wild bacteria through the process of conjugation.
Limits and Solutions
Although bioremediation is safe and effective, challenges such as unfavorable temperature, pH, nutrients, and moisture have negative effects. The availability of genomic tools for editing offers solutions. Genes that code for resistant proteins against harsh pH, temperature, and moisture is available to aid in the production of adaptive bacteria. Moreover, genes that can metabolize certain chemicals or hydrocarbons are present to help bacteria survive in nutrient deficient sites to undertake bioremediation. In a nitrogen deficient environment, the use of nitrogen-fixing bacteria promotes the bioremediation of hydrocarbon-degrading bacteria (Xu et al., 2018).
Conclusion
The application of bioremediation in the removal of oil spills in the environment is not only effective but also a safe strategy that protects the environment from further damage. The use of the recombinant E. coli with over-expressed genes of xylE, almA, and p450cam, which codes for enzymes that degrades petroleum hydrocarbons, has proved effective. Genomics and sequencing strategies play a major role in the process of bioremediation because they enable the generation of engineered bacteria.
References
French, K.E., Zhou, Z. & Terry, N. (2020). Horizontal ‘gene drives’ harness indigenous bacteria for bioremediation. Scientific Reports, 10, 1–11.
Jaiswal, S., Singh, D. K., & Shukla, P. (2019). Gene editing and systems biology tools for pesticide bioremediation: A review. Frontiers in Microbiology, 10(87), 1–11.
Perpetuo, E. A., Souza, C. B., & Nascimento, C. A. O. (2011). Engineering bacteria for bioremediation, progress in molecular and environmental bioengineering. IntechOpen, 28, 606–631. Web.
Xu, X., Liu, W., Tian, S., Wang, W., Qi, Q., Jiang, P., Gao, X., Li, F., Li, H., & Yu, H. (2018). Petroleum hydrocarbon-degrading bacteria for the remediation of oil pollution under aerobic conditions: A perspective analysis. Frontiers in Microbiology, 9, 1–11.