Advancements in Bioremediation due to Synthetic Biology

By - Tehseen Bukhari

An estimated 12.6 million people died in 2012 due to an unhygienic environment, approximately 1 in 4 of total global deaths. However, bioremediation plays a pivotal role in eradicating air, water, and soil pollutants via effective remediation strategies. Now, what is Bioremediation? It is a process invented by George M. Robinson, a petroleum engineer. It breaks down environmental pollutants by consuming micro-organisms that are naturally occurring or deliberately introduced to clean a polluted site. The pollutants in our surroundings are categorized into two types:

1. Organic: Persistent organic pollutants include some polycyclic aromatic hydrocarbons, along with halogenated aromatics. Additional emerging pollutants include plasticizers and nanoparticles (NPS). These are classified as possibly carcinogenic to humans by IARC, effective in enhancing bioaccumulation in food chains and promoting bacterial resistance in the environment.

2. Inorganic: The primary inorganic pollutants are ‘heavy metals,’ which are bioaccumulating in tissues and living organisms. Additionally, nitrogen and phosphate cause eutrophication in water bodies due to the surface runoff of fertilizers.

Bioremediation has made monumental advancements in Microbial remediation, which uses micro-organisms for degrading pollutants. It is further grouped into two types:

1. Indigenous micro-organisms: This refers to micro-organisms already present at the site to be bio-remediated and only require optimum observational conditions for survival.

2. Exogenous micro-organisms: This refers to micro-organisms introduced into the soil deliberately for remediation.

There are also different types of remediations for different conditions:

1. Microbial bioremediation: It utilizes micro-organism or their derivatives (enzymes or spent biomass) to purify the environment by converting pollutants into small amounts of water and harmless gasses like carbon dioxide.

2. Phytoremediation: Plants disseminate toxic material from the soil or groundwater and hold onto them in their tissues until it is broken down in the roots and released into the atmosphere by transpiration and evaporation. The plants can clean up a few pollutants: metals, pesticides, chlorinated solvents, polychlorinated biphenyls, and petroleum hydrocarbons. Some plants which can be used for phytoremediation are Indian Mustard, Indian Grass, Brown mustard, Sunflower plants, Barley Grass, Pumpkin, Poplar trees, Pine trees, and White Willows.

3. Mycoremediation: In this process, fungi act as a catalyst for micro-organisms and plants. It breaks down metals and varied pesticides with larger hydrocarbon chains into smaller pieces, making their process easy. Biosorption is a process in which mushrooms absorb pollutants into their mycelium, hence neutralizing the site. The following fungi, Trichoderma, Aspergillus, and Pleurotus, are effective in the removal of Cadmium, Nickel, Lead, Chromium, Mercury, Arsenic, Boron, Iron, and Zinc in wastewater, on land, and in the Marine.

4. Bioremediation of Wastewater: Aerobic bacteria consume organic contaminants and mold the less soluble part while releasing nitrogen gas as a by-product. Water is aerated to maintain aerobic conditions for bacteria to grow.

There are two effective techniques for bioremediation:

1. In-situ technique: In-situ indicates that the location of the bioremediation has occurred at the contamination site without the translocation of the polluted materials by directly neutralizing pollutants such as chlorinated compounds, nitrates, toxic metals, etc.

2. Ex-situ technique: Ex-situ bioremediation processes involve excavating contaminated soil or pumping groundwater. Ex-situ techniques include Slurry-phase bioremediation and Solid-phase bioremediation.

Bioremediation has advanced progressively over time and provides multiple solutions for pollution, including:

1. Treatment of oil spillage:

2. Treatment of rivers, streams, and estuaries:

3. Sewage (wastewater) treatment:

4. Compost bioremediation: The contaminants are removed by the micro-organisms present in the compost

5. Bioaugmentation: It develops super decomposers that eradicate contaminants. It is often achieved by genetic manipulation of natural decomposers.

In 2007, American scientist Craig Venter published the complete sequence of his genome in PLOS Biology. This publication brought a new way of thinking for the scientist. Three years later, he built the genome of a bacterium and incorporated it into a cell. From there on, synthetic biology started to revolutionize various fields, including bioremediation. Biology offers enormous potential as a tool to develop microbial and plant-based solutions to remediate and restore our environment by developing advanced technology like:

1. Biosensors: Bacteria, such as Geobacter sulfurreducens and Shewanella oneidensis grow as highly conductive biofilms with pili. These form basis of microbial fuel cells that produce electrical current from the degradation of organic pollutants. The output voltage from MFCs is used to demonstrate biosensors for p-nitrophenol in industrial wastewater and biomonitoring of copper from mine effluent.

1. Artificial organelles: This removes the concentration of inorganic pollutants away from sensitive cellular environments. A recent study has successfully targeted proteins to the luminal side of an artificial bacterial microcompartment. This paved the way for proteins to be bound with metal within artificial organelles, enabling hyperaccumulation of a specific metal for efficient removal.

1. Bioremediation of Mercury: Mercury is ranked third in the priority list of hazardous substances by the Agency for Toxic Substances and Disease Registry. An exciting study by Tay et al. combined MerR and an operon encoding a mercury-absorbing, extracellular protein nanofiber, or curli, into E.coli. These curli fibers form a biofilm that is only produced when mercury contamination is present and provide a large surface area for Hg2+ absorption to negate the toxicity of intracellularly accrued Hg2+ ions. This work paves the way for developing on-demand living biofilm materials that can operate autonomously as heavy-metal absorbents.

1. Biodegradation of polyethylene terephthalate (PET): Plastic is designed to resist degradation that promotes the accumulation of microplastics in the environment. PET is a plastic used in textile manufacturing and as packaging for food and liquids globally. It is dangerous for aquatic life as these microplastics enter food chains and/or suffocate marine animals. Several enzymes with activity towards PET have been characterized. The most promising species mined for PET-degrading enzymes are Ideonella sakaiensis 201-F6, PET hydrolase, and MHET hydrolase.

1. Biodegradation of aliphatic chlorinated compounds: Bacteria, including Xanthobacter autotrophicus, break down a broad range of halogenated aliphatic compounds. 1,2-dichloroethane is a priority pollutant and probable human carcinogen. Dehalogenase genes dhlA and dhlB from X, Autotrophicus were incorporated into tobacco alcohol and aldehyde dehydrogenase and are used to create a synthetic route for the degradation of 1,2-DCA. F 1,2,3-trichloropropane has been engineered into E.coli to optimize 1,2,3-TCP degradation by microbial communities in the rhizosphere of plants. It has been demonstrated that metabolites released by plant roots into this zone can enhance the biodegradation of 1,2- dichloroethylene. Combining genetically modified -plants and -rhizosphere-dwelling bacteria seems to be the next logical step.

1. Phytoremediation of explosive compounds: Explosive compounds like 2,4,6-trinitrotoluene (TNT) and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) are used extensively by the military and are significant environmental pollutants. Bacteria able to degrade RDX are used in bioaugmentation studies in RDX-contaminated aquifers. The genes responsible, xplA and xplB, have been engineered into rhizosphere-colonizing bacteria and Arabidopsis thaliana. Both xplA and xplB, along with a bacterial nitroreductase that detoxifies the co-contaminant and phytotoxic TNT, have been engineered into switchgrass (Panicum virgatum), wheatgrass (Pascopyrum smithii), and creeping bentgrass (Agrostis stolonifera)

In conclusion, synbio has advanced bioremediation and provides cost-effective, environmentally friendly, and advanced technology/methods to solve pollution problems efficiently. The use of synbio technologies for remediation is still in its infancy but already offers exciting possibilities for the use of engineered organisms to provide a cleaner, safer environment.