write an essay on two methods of bioremediation

• Biology Article
• Bioremediation

Process of Bioremediation

What is bioremediation.

Bioremediation is a biotechnical process, which abates or cleans up contamination. It is a type of waste management technique which involves the use of organisms to remove or utilize the pollutants from a polluted area.

There are several remedies where contaminated water or solid is purified by chemical treatment, incineration, and burial in a landfill. There are other types of waste management technique which include solid waste management , nuclear waste management, etc. Bioremediation is different as it uses no toxic chemicals.

Microorganisms like Bacteria and Fungi are the main role player when it comes to executing the process of Bioremediation. Bacteria are the most crucial microbes in this process as they break down the waste into nutrients and organic matter. Even though this is an efficient process of waste management but bioremediation cannot destroy 100% contaminants. Bacteria can easily digest contaminants like chlorinated pesticides or clean oil spills but microorganisms fail to destroy heavy metals like lead and cadmium.

Types of Bioremediation

Bioremediation is of three types –

1) Biostimulation

As the name suggests, the bacteria is stimulated to initiate the process. The contaminated soil is first mixed with special nutrients substances including other vital components either in the form of liquid or gas. It stimulates the growth of microbes thus resulting in efficient and quick removal of contaminants by microbes and other bacterias.

2) Bioaugmentation

At times, there are certain sites where microorganisms are required to extract the contaminants. For example – municipal wastewater. In these special cases, the process of bioaugmentation is used. There’s only one major drawback in this process. It almost becomes impossible to control the growth of microorganisms in the process of removing the particular contaminant.

3) Intrinsic Bioremediation

The process of intrinsic bioremediation is most effective in the soil and water because of these two biomes which always have a high probability of being full of contaminants and toxins. The process of intrinsic bioremediation is mostly used in underground places like underground petroleum tanks. In such place, it is difficult to detect a leakage and contaminants and toxins can find their way to enter through these leaks and contaminate the petrol. Thus, only microorganisms can remove the toxins and clean the tanks.

Other methods of Waste Management

Incineration.

This is a process where wastes and other unwanted substances are burnt. During combustion, the organic waste turns into ash, flue gas, and heat. The inorganic constituents of the waste remain in the form of an ash. It is also termed as thermal treatment.

Phytoremediation

In this scenario, plants are directly used to clean up or contain contaminants in the soil. This method of bioremediation will help mitigate the environmental problem without the need to excavate the contaminant material and dispose of it elsewhere.

Phytoremediation = Phyto (Plant) + Remedium (Restoring balance or Remediation)

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• A General Essay on Bioremediation of Contaminated Soil

A General Essay on Bioremediation                                         of Contaminated Soil

Dana L. Donlan and J.W. Bauder, Professor, Montana State University-Bozeman MSSE Graduate Student and Professor, respectively

Bioremediation is defined as use of biological processes to degrade, break down, transform, and/or essentially remove contaminants or impairments of quality from soil and water. Bioremediation is a natural process which relies on bacteria, fungi, and plants to alter contaminants as these organisms carry out their normal life functions. Metabolic processes of these organisms are capable of using chemical contaminants as an energy source, rendering the contaminants harmless or less toxic products in most cases. This paper summarizes the general processes of bioremediation within the soil environment, focusing on biodegradation of petroleum hydrocarbons. The effect of soil conditions on rate of biodegradation of hydrocarbons is addressed. Further, limitations and potential of both ex situ and in situ bioremediation as viable alternatives to conventional remediation are explained and addressed.

Many substances known to have toxic properties have been introduced into the environment through human activity. These substances range in degree of toxicity and danger to human health. Many of these substances either immediately or ultimately come in contact with and are sequestered by soil. Conventional methods to remove, reduce, or mitigate toxic substances introduced into soil or ground water via anthropogenic activities and processes include pump and treat systems, soil vapor extraction, incineration, and containment. Utility of each of these conventional methods of treatment of contaminated soil and/or water suffers from recognizable drawbacks and may involve some level of risk.

The emerging science and technology of bioremediation offers an alternative method to detoxify contaminants. Bioremediation has been demonstrated and is being used as an effective means of mitigating:

• hydrocarbons
• halogenated organic solvents
• halogenated organic compounds
• non-chlorinated pesticides and herbicides
• nitrogen compounds
• metals (lead, mercury, chromium)
• radionuclides

Bioremediation technology exploits various naturally occurring mitigation processes: natural attenuation, biostimulation , and bioaugmentation . Bioremediation which occurs without human intervention other than monitoring is often called natural attenuation . This natural attenuation relies on natural conditions and behavior of soil microorganisms that are indigenous to soil. Biostimulation also utilizes indigenous microbial populations to remediate contaminated soils. Biostimulation consists of adding nutrients and other substances to soil to catalyze natural attenuation processes. Bioaugmentation involves introduction of exogenic microorganisms (sourced from outside the soil environment) capable of detoxifying a particular contaminant, sometimes employing genetically altered microorganisms (Biobasics, 2006).

During bioremediation, microbes utilize chemical contaminants in the soil as an energy source and, through oxidation-reduction reactions, metabolize the target contaminant into useable energy for microbes. By-products (metabolites) released back into the environment are typically in a less toxic form than the parent contaminants. For example, petroleum hydrocarbons can be degraded by microorganisms in the presence of oxygen through aerobic respiration. The hydrocarbon loses electrons and is oxidized while oxygen gains electrons and is reduced. The result is formation of carbon dioxide and water (Nester et al., 2001). When oxygen is limited in supply or absent, as in saturated or anaerobic soils or lake sediment, anaerobic (without oxygen) respiration prevails. Generally, inorganic compounds such as nitrate, sulfate, ferric iron, manganese, or carbon dioxide serve as terminal electron acceptors to facilitate biodegradation (State of Mississippi, Department of Environmental Quality, 1998).

Three primary ingredients for bioremediation are: 1) presence of a contaminant, 2) an electron acceptor, and 3) presence of microorganisms that are capable of degrading the specific contaminant. Generally, a contaminant is more easily and quickly degraded if it is a naturally occurring compound in the environment, or chemically similar to a naturally occurring compound, because microorganisms capable of its biodegradation are more likely to have evolved (State of Mississippi, Department of Environmental Quality, 1998). Petroleum hydrocarbons are naturally occurring chemicals; therefore, microorganisms which are capable of attenuating or degrading hydrocarbons exist in the environment. Development of biodegradation technologies of synthetic chemicals such DDT is dependent on outcomes of research that searches for natural or genetically improved strains of microorganisms to degrade such contaminants into less toxic forms.

Microorganisms have limits of tolerance for particular environmental conditions, as well as optimal conditions for pinnacle performance. Factors that affect success and rate of microbial biodegradation are nutrient availability, moisture content, pH, and temperature of the soil matrix. Inorganic nutrients including, but not limited to, nitrogen, and phosphorus are necessary for microbial activity and cell growth. It has been shown that “treating petroleum-contaminated soil with nitrogen can increase cell growth rate, decrease the microbial lag phase, help to maintain microbial populations at high activity levels, and increase the rate of hydrocarbon degradation” (Walworth et al., 2005). However, it has also been shown that excessive amounts of nitrogen in soil cause microbial inhibition. Walworth et al. (2005) suggest maintaining nitrogen levels below 1800 mg nitrogen/kg H 2 O for optimal biodegradation of petroleum hydrocarbons. Addition of phosphorus has benefits similar to that of nitrogen, but also results in similar limitations when applied in excess (State of Mississippi, Department of Environmental Quality, 1998).

All soil microorganisms require moisture for cell growth and function. Availability of water affects diffusion of water and soluble nutrients into and out of microorganism cells. However, excess moisture, such as in saturated soil, is undesirable because it reduces the amount of available oxygen for aerobic respiration. Anaerobic respiration, which produces less energy for microorganisms (than aerobic respiration) and slows the rate of biodegradation, becomes the predominant process. Soil moisture content “between 45 and 85 percent of the water-holding capacity (field capacity) of the soil or about 12 percent to 30 percent by weight” is optimal for petroleum hydrocarbon degradation (US EPA, 2006, “Landfarming”).

Soil pH is important because most microbial species can survive only within a certain pH range. Furthermore, soil pH can affect availability of nutrients. Biodegradation of petroleum hydrocarbons is optimal at a pH 7 (neutral); the acceptable range is pH 6 – 8 (US EPA, 2006, “Landfarming”; State of Mississippi, Department of Environmental Quality, 1998).

Temperature influences rate of biodegradation by controlling rate of enzymatic reactions within microorganisms. Generally, “speed of enzymatic reactions in the cell approximately doubles for each 10 oC rise in temperature” (Nester et al., 2001). There is an upper limit to the temperature that microorganisms can withstand. Most bacteria found in soil, including many bacteria that degrade petroleum hydrocarbons, are mesophiles which have an optimum temperature ranging from 25 degree C to 45 degree C (Nester et al., 2001). Thermophilic bacteria (those which survive and thrive at relatively high temperatures) which are normally found in hot springs and compost heaps exist indigenously in cool soil environments and can be activated to degrade hydrocarbons with an increase in temperature to 60 degree C. This finding “suggested an intrinsic potential for natural attenuation in cool soils through thermally enhanced bioremediation techniques” (Perfumo et al., 2007).

Contaminants can adsorb to soil particles, rendering some contaminants unavailable to microorganisms for biodegradation. Thus, in some circumstances, bioavailability of contaminants depends not only on the nature of the contaminant but also on soil type. Hydrophobic contaminants, like petroleum hydrocarbons, have low solubility in water and tend to adsorb strongly in soil with high organic matter content. In such cases, surfactants are utilized as part of the bioremediation process to increase solubility and mobility of these contaminants (State of Mississippi, Department of Environmental Quality, 1998). Additional research findings of the existence of thermophilic bacteria in cool soil also suggest that high temperatures enhance the rate of biodegradation by increasing the bioavailability of contaminants. It is suggested that contaminants adsorbed to soil particles are mobilized and their solubility increased by high temperatures (Perfumo et al., 2007).

Soil type is an important consideration when determining the best suited bioremediation approach to a particular situation. In situ bioremediation refers to treatment of soil in place. In situ biostimulation treatments usually involve bioventing, in which oxygen and/or nutrients are pumped through injection wells into the soil. It is imperative that oxygen and nutrients are distributed evenly throughout the contaminated soil. Soil texture directly affects the utility of bioventing, in as much as permeability of soil to air and water is a function of soil texture. Fine-textured soils like clays have low permeability, which prevents biovented oxygen and nutrients from dispersing throughout the soil. It is also difficult to control moisture content in fine textured soils because their smaller pores and high surface area allow it to retain water. Fine textured soils are slow to drain from water-saturated soil conditions, thus preventing oxygen from reaching soil microbes throughout the contaminated area (US EPA, 2006, “Bioventing”). Bioventing is well-suited for well-drained, medium, and coarse-textured soils.

In situ bioremediation causes minimal disturbance to the environment at the contamination site. In addition, it incurs less cost than conventional soil remediation or removal and replacement treatments because there is no transport of contaminated materials for off-site treatment. However, in situ bioremediation has some limitations: 1) it is not suitable for all soils, 2) complete degradation is difficult to achieve, and 3) natural conditions (i.e. temperature) are hard to control for optimal biodegradation. Ex situ bioremediation, in which contaminated soil is excavated and treated elsewhere, is an alternative.

Ex situ bioremediation approaches include use of bioreactors, landfarming, and biopiles. In the use of a bioreactor, contaminated soil is mixed with water and nutrients and the mixture is agitated by a mechanical bioreactor to stimulate action of microorganisms. This method is better-suited to clay soils than other methods and is generally a quick process (US EPA, 2006, “Guide”).

Landfarming involves spreading contaminated soil over a collection system and stimulating microbial activity by allowing good aeration and by monitoring nutrient availability (US EPA, 2006, “Landfarming”).

Biopiles are mounds of contaminated soils that are kept aerated by pumping air into piles of soil through an injection system (US EPA, 2006, “Biopiles”).

In each of these methods, conditions need to be monitored and adjusted regularly for optimal biodegradation. Use of landfarming and biopiles also present the issue of monitoring and containing volatilization of contaminants. Like in situ methods, ex situ bioremediation techniques generally cost less than conventional techniques and apply natural methods. However, they can require a large amount of land and, similar to in situ bioremediation, complete degradation is difficult to achieve, and evaporation of volatile components is a concern (US EPA, 2006, “Landfarming”; US EPA, 2006, “Biopiles”).

If the challenges of bioremediation, particularly of in situ techniques, can be overcome, bioremediation has potential to provide a low cost, non-intrusive, natural method to render toxic substances in soil less harmful or harmless over time. Currently, research is being conducted to improve and overcome limitations that hinder bioremediation of petroleum hydrocarbons. On a broader scope, much research has been and continues to be developed enhance understanding of the essence of microbial behavior as microbes interact with various toxic contaminants. Additional research continues to evaluate conditions for successful introduction of exogenic and genetically engineered microbes into a contaminated environment, and how to translate success in the laboratory to success in the field (US DOE, 2006).

Biobasics: The Science and the Issues. 9 Feb 2006. 24 Nov 2006 http://www.biobasics.gc.ca/english/View.asp?x=741

Nester, Eugene W., Denise G. Anderson, C. Evans Roberts Jr., Nancy N. Pearsall, and Martha T. Nester. 2001. Microbiology: A Human Perspective. 3 rd ed. New York: McGraw-Hill.

Perfumo, Amedea, Ibrahim M. Banat, Roger Marchant, and Luigi Vezzulli. 2007. “Thermally Enhanced Approaches for Bioremediation of Hydrocarbon-Contaminated Soils.” Chemosphere 66: 179-184.

State of Mississippi. Department of Environmental Quality. 1998. Fundamental Principles of Bioremediation. April 1998. 27 Nov 2006 <http://www.deq.state.ms.us/MDEQ.nsf/pdf/ GARD_Bioremediation/$File/Bioremediation.pdf? Verified 12/15/2006.

United States. Department of Energy, Office of Science. 2006. Bioremediation Research Needs. 2 January 2002. 1 December 2006 http://www.er.doe.gov/production/ober/nabir/needs.html . Verified 12/15/2006.

United States. Environmental Protection Agency. 2006. A Citizen’s Guide to Bioremediation. April 1996. 24 Nov 2006 http://www.epa.gov/tio/download/citizens/a_citizens_guide_to_bioremediation.pdf . Verified 06/29/2006.

United States . Environmental Protection Agency. Biopiles. 9 March 2006 . 24 Nov 2006 http://www.epa.gov/oust/cat/biopiles.htm . Verified 06/26/2015.

United States . Environmental Protection Agency. Bioventing. 9 March 2006 . 24 Nov 2006 http://www.epa.gov/oust/cat/biovent.htm . Verified 06/26/2015.

United States . Environmental Protection Agency. Landfarming. 9 March 2006 . 24 Nov 2006 http://www.epa.gov/oust/cat/landfarm.htm . Verified 06/26/2015.

Walworth, James, Andrew Pond, Ian Snape, John Rayner, Susan Ferguson, and Paul Harvey. 2005. “Fine Tuning Soil Nitrogen to Maximize Petroleum Bioremediation.” ARCSACC (2005): 251-257.

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Tel: (406) 994-7381 Fax: (406) 994-3933 E-mail: [email protected] Location: Marsh Labs, Room 2

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Bioremediation Technology Essay (Article)

Reasons for the technology, factors of bioremediation, bioremediation techniques, recommendations, future study.

The breakdown decomposition degradation or removal of toxic contaminants from the environment is called bioremediation (Aislabie, 2012). Microorganisms are introduced into the contaminated soil to carry out normal functions (Nester, 2001). Microorganisms act on the contaminated soils to neutralize the contaminants. The organisms include bacteria, fungi, and plants to mention a few (Perfumo, 2007).

The organisms alter the composition of the contaminants by carryout their normal life activities. The waste management technique can be done on the site of contamination or on a neutral waste disposal site. Advanced technologies are employed in the treatment of contaminants (Walworth, 2007). The techniques include bioventing, bioaugmentation, and bioleaching to mention a few. The organisms utilized during bioremediation are called bioremediators.

The organisms are introduced on the site of contamination to degrade the contaminants. Waste management is a necessity because of the effect of the contaminants to human health. These contaminants pose health risk to humans and the environment. A study conducted by Simon revealed that waste managements could reduce the effect of toxic spills by 13 percent (2010).

Environmental studies suggest that oil contaminant causes severe health challenges. This accounts for the rise in toxic related diseases and infant mortality. Bioremediation technology mitigates these contaminants (Walworth, 2007). Observations are ongoing to ascertain the effects of bioremediation on the soil and its effect on human health.

Human beings and Plants suffer similar risk to contamination of the soil. The polluted soil makes it difficult to cultivate crops and grow animals. Contaminants block the passage of soil nutrients and the blockage affects the circulation of soil nutrients. Such situations make the soil infertile and toxic for agriculture.

The contaminants reduce the fertility of the soil. Three important agents are present during bioremediation processes. The agents are; the contaminant, the electron acceptor and a suitable microorganism. The degraded material adds nutrients to the environment. For example, degraded hydrocarbons react with oxygen to cause aerobic respiration. Although these microorganisms have their limits, they combine well under favorable conditions to influence the degradation of various contaminants (Swannell, 2010).

Industrial waste constitutes 65 percent of the world’s toxic materials. The emergence of bioremediation technology is a positive development in curbing the effects of the contaminants. Sveum suggested the use of five microorganisms to reduce the toxicity of industrial contaminants (2008). These microorganisms include; Pseudomonas, Staphylococcus, Aspergillus, Bacillus cereus and aeruginosa. These organisms combine to reduce the toxicity of industrial contaminants.

The effects of industrial waste are so severe that chief executives have careful minimize oil spills. Industrial waste can be recycled using bioremediation to reduce the effect on the environment. Mass protests and demonstrations occur daily because of industrial spillage and soil contamination. A proper management system is the only way of reducing the effects of industrial contamination (Swannell, 2010).

Bioremediation is a complex process which is controlled by different factors (Walworth, 2007). The factors include: the presence of a suitable organism, the presence of the contaminants, favourable environmental conditions suitable for microbial growth to mention a few.

Microbial populations in bioremediation process

The presence of microorganisms in the contaminants influences bioremediation. The organisms can survive in extreme conditions. The nature of their growth makes them suitable for bioremediation. The organisms can be categorized into four groups.

a. Anaerobic organisms: Anaerobic organisms survive without oxygen. This makes them suitable in the control of biphenyls contaminants and the compounds of chloroform. Composting and land farming techniques favors anaerobic organisms. The compost stimulated the growth of the organisms in extreme temperature.

b. Aerobic organism: They function with oxygen. The microbes include Alcaligenes and Rhodococcus to mention a few.

Methylotrophs microbes: The microbes grow with oxygen and little methane.

Ligninolytic fungi: This group of microorganism can be used to degrade hazardous waste.

Environmental factors affecting bioremediation

Microorganisms are the principal agents in the bioremediation process. To degrade much contaminant, the population of a suitable microorganism must be balanced (Aislabie, 2012). Thus, microorganisms suitable for bioremediation require favourable environmental conditions to boost their growth.

The nutrients must be available in equal proportions suitable for microbial growth. Microbial organisms require carbon, nitrogen, oxygen, hydrogen, sodium, calcium, chloride to mention a few. Microbial growth and degradation is influenced by the conditions suitable for microbial development.

Bioremediation is influenced by soil moisture, temperature, pH, oxygen level, and temperature, nature of the contaminants, soil type and the nature of heavy metals. The nature of the soil influences the rate of degradation and microbial growth. The presence or absence of oxygen is influenced by the contaminants. The presence of oxygen requires aerobic microorganisms while the absence of oxygen in the soil will require anaerobic bacterial to complete the degradation processes.

The population of the microbes can be simulated by biostimulation techniques (Perfumo, 2007). The addition of oxygen and other favourable nutrients suitable for microbial growth is called biostimulation. The presence of heavy metals affects the growth of microorganisms.

In extreme cases, soil nutrients are introduced in the soil to boost microbial growth. Aerobic organisms will require aerated soils and this can be achieved thorough soil tillage. This will allow easy passage of nutrients suitable for the development of the microorganism.

The nature of the contaminants determines the technique used on the site of contamination. Bioremediation strategies require two broad procedures. In-situ and Ex-situ are two major techniques employed in bioremediation processes. In-situ bioremediation is used when the contaminants are degraded on the contaminated soil.

Microorganisms are introduced at the site of contamination (Swannell, 2010). Large contaminations will require excavation of the contaminants to another site for treatment, which is called Ex-situ bioremediation. The introduction of suitable microorganisms in the soil is called bioaugmentation. Bioaugmentation is affected by two factors.

a. The introduced organism may not adapt with the indigenous microbes in the soil. Thus, population growth may be limited.

b. Indigenous microbes have potentials to carry out bioremediation processes.

In-situ bioremediation

The degradation of contaminants at the site of contamination is called In-situ bioremediation. It is a cheap technique compared to the excavation of contaminated soil to a new facility. Its disadvantage is caused by the soil type. The soil type influences the level of degradation. Aerated soils degrade faster and biostimulation is easy. In-situ bioremediation can be achieved in different ways.

Bioventing : It involves the supply of nutrients and oxygen in equal amounts through wells. The quantity of oxygen is controlled to produce stable growth of the microorganism.

Biodegradation : Gaseous solutions are supplied on the site of contamination to circulate the nutrient requirements suitable for microbial growth. The procedure requires the use of groundwater to distribute oxygen and microbial nutrients on the contaminated site.

Bioaugmentation : The supply of internal or external microorganisms into the site of contamination is called bioaugmentation. One disadvantage of exogenous microbe is the performance ratio. Exogenous microorganisms may not grow in extreme temperature. Extreme temperature will limit the population of the microorganism.

Biosparging : The site of contamination is pressurized to induce the availability of oxygen. The injection of pressurized air alters the concentration of groundwater at the contaminated site.

Ex-situ bioremediation

The techniques include land farming, composting, biopiles and bioreactors.

Land farming : The process requires the excavation of the contaminated soil to a prepared facility suitable for degradation. The microbes are stimulated with oxygen and microbial nutrients to increase its population (Walworth, 2007).

Compost: The combination of the contaminated soil with manure or agricultural products is called composting. The manure stimulates microbial growth and facilitates the development of ingenious microorganisms. The temperature of the soil is controlled to influence the production of anaerobic organisms.

Biopiles : The combination of land farming and compost is called biopiles. Engineered organisms are used to degrade contaminants. The technique is suitable for aerobic and anaerobic microbes.

Bioreactors : The use of treated vessels to decontaminate the soil is another bioremediation technique. The contaminants are transported to an engineered facility. The process is monitored under a controlled temperature (Nester, 2001).

Advantages of bioremediation

1. Bioremediation is a natural process and the residues do not pose a health risk.

2. Bioremediation is useful in the degradation of heavy metals and other toxic waste.

3. Contaminants can be destroyed or neutralized at the site of contamination. The procedure reduces the risk of transporting hazardous waste from the site of contamination to a free zone.

4. Except in extreme cases, the process of bioremediation does not disrupt the ecological system of the contaminated site.

5. Bioremediation is a cheap method of decontamination compared with various decontamination techniques.

Disadvantages of bioremediation

1. The decontamination of the soil is a limited process. Most contaminations cannot be degraded by microorganisms.

2. The introduction of microorganisms may cause severe damage to the ecological system.

3. The chances of success are slim because of the absence of microbial population. It is difficult to estimate the quantity of microbial organisms required for the decontamination process.

4. The process requires time. The evacuation and transportation of the contaminated soil to the treated facility lengthens the time of biodegradation.

5. The processes of bioremediation cannot be justified. The extent of damage cannot be determined.

The treatment of industrial waste requires bioremediation. Unlike other methods of waste managements, bioremediation mitigates these contaminants. Bioremediation benefits man and the environment. Oil spills and heavy metals, which are major soil contaminants are treated with suitable microorganisms.

A combination of two or more microorganisms can create an atmosphere suitable for the degradation of contaminants. Although the treatment is cost-effective, it reduces the effects of toxic wastes on the environment. A practical approach must be used to degrade contaminants in large quantity.

The process is suitable for degradation of contaminated sites. The cost of the procedure makes it suitable for large decontamination. The risk associated with the process cannot be ascertained; however the process provides the best technique for decontamination.

I will recommend further studies to determine the extent of damage during the cleanup. Regulatory agencies must reduce the occurrence of oil spillage and soil contamination.

Aislabie, J. (2012). Bioremediation of hydrocarbon-contaminated soils . USA, New York: McGraw-Hill.

Nester, E. (2001). Microbiology: A human perspective and approach . USA, New York: McGraw-Hill.

Perfumo, A. (2007). Thermal enhanced approaches for bioremediation of hydrocarbons . USA, New York: McGraw-Hill.

Simon, M. (2010). Evaluation of bioaugmentation for remediation of petroleum in a wetland. USA, New York: McGraw-Hill.

Sveum, P. (2008). Hydrocarbon bioremediation and its benefits . Sydney, Australia: Ibex Press.

Swannell, R. (2010). The use of bioremediation to treat an oiled shoreline . Sydney, Australia: Maxon Press.

Walworth, J. (2010). Fine tuning soil nitrogen to maximize petroleum bioremediation. South Melbourne, Australia: Maxon Press.

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The Application of Bioremediation

Introduction, the application bioremediation, genomics and sequencing, genetic modification of bacteria, horizontal gene transfer, limits and solutions.

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.

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 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.

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 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.

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).

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.

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. 

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37.5.1: Bioremediation

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• Page ID 75368

• Matthew R. Fisher
• Oregon Coast Community College via OpenOregon

Bioremediation is a waste management technique that involves the use of organisms such as plants, bacteria, and fungi to remove or neutralize pollutants from a contaminated site. According to the United States EPA, bioremediation is a “treatment that uses naturally occurring organisms to break down hazardous substances into less toxic or non toxic substances”.

Bioremediation is widely used to treat human sewage and has also been used to remove agricultural chemicals (pesticides and fertilizers) that leach from soil into groundwater. Certain toxic metals, such as selenium and arsenic compounds, can also be removed from water by bioremediation. Mercury is an example of a toxic metal that can be removed from an environment by bioremediation. Mercury is an active ingredient of some pesticides and is also a byproduct of certain industries, such as battery production. Mercury is usually present in very low concentrations in natural environments but it is highly toxic because it accumulates in living tissues. Several species of bacteria can carry out the biotransformation of toxic mercury into nontoxic forms. These bacteria, such as Pseudomonas aeruginosa , can convert Hg 2+ to Hg, which is less toxic to humans.

Probably one of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of oil spills. The importance of prokaryotes to petroleum bioremediation has been demonstrated in several oil spills in recent years, such as the Exxon Valdez spill in Alaska (1989) (Figure \(\PageIndex{1}\)), the Prestige oil spill in Spain (2002), the spill into the Mediterranean from a Lebanon power plant (2006,) and more recently, the BP oil spill in the Gulf of Mexico (2010). To clean up these spills, bioremediation is promoted by adding inorganic nutrients that help bacteria already present in the environment to grow. Hydrocarbon-degrading bacteria feed on the hydrocarbons in the oil droplet, breaking them into inorganic compounds. Some species, such as Alcanivorax borkumensis , produce surfactants that solubilize the oil, while other bacteria degrade the oil into carbon dioxide. In the case of oil spills in the ocean, ongoing, natural bioremediation tends to occur, inasmuch as there are oil-consuming bacteria in the ocean prior to the spill. Under ideal conditions, it has been reported that up to 80 percent of the nonvolatile components in oil can be degraded within 1 year of the spill. Researchers have genetically engineered other bacteria to consume petroleum products; indeed, the first patent application for a bioremediation application in the U.S. was for a genetically modified oil-eating bacterium.

There are a number of cost/efficiency advantages to bioremediation, which can be employed in areas that are inaccessible without excavation. For example, hydrocarbon spills (specifically, oil spills) or certain chlorinated solvents may contaminate groundwater, which can be easier to treat using bioremediation than more conventional approaches. This is typically much less expensive than excavation followed by disposal elsewhere, incineration, or other off-site treatment strategies. It also reduces or eliminates the need for “pump and treat”, a practice common at sites where hydrocarbons have contaminated clean groundwater. Using prokaryotes for bioremediation of hydrocarbons also has the advantage of breaking down contaminants at the molecular level, as opposed to simply chemically dispersing the contaminant.

Contributors and Attributions

• “Bioremediation” is licensed under CC BY 4.0 . “Prokaryotic Diversity” by OpenStax is licensed under CC BY 4.0 . Modified from originals by Matthew R. Fisher.

Microbiology Notes

Bioremediation – Definition, Types, Application

Table of Contents

What is Bioremediation?

Bioremediation is a process used to clean up and detoxify polluted sites by utilizing microorganisms, plants, or their enzymes to break down and degrade environmental contaminants. It involves the natural or deliberate introduction of these biological agents to enhance the rate of degradation and transformation of pollutants.

The concept of bioremediation includes biodegradation, which refers to the breakdown and detoxification of contaminants by microorganisms and plants. This natural process can be enhanced through various methods:

• Biostimulation: This involves providing nutrients, carbon sources, or electron donors to stimulate the growth and activity of indigenous microorganisms. By supplementing the natural microbial community, biostimulation enhances their ability to degrade pollutants.
• Biorestoration: Similar to biostimulation, biorestoration involves creating favorable conditions for the indigenous microorganisms to degrade contaminants. This can include optimizing temperature, pH, oxygen levels, and moisture content in the environment.
• Bioaugmentation: In bioaugmentation, an enriched culture of microorganisms with specific characteristics is introduced to the polluted site. These specialized microorganisms have the ability to degrade the targeted contaminants at a faster rate than the indigenous microorganisms. This method can be particularly effective when the indigenous microbial community lacks the necessary capabilities to degrade certain pollutants.

The goal of bioremediation is to reduce pollutant levels to undetectable, nontoxic, or acceptable levels set by regulatory agencies. Ideally, the contaminants are completely transformed into harmless byproducts such as carbon dioxide, water, and mineral salts through a process called mineralization.

Bioremediation offers a sustainable and environmentally friendly approach to address pollution issues, as it relies on natural biological processes to remediate contaminated sites. It can be applied to various types of pollution, including organic pollutants like petroleum hydrocarbons, pesticides, and solvents, as well as inorganic contaminants such as heavy metals and nitrates.

Definition of Bioremediation

Bioremediation is the use of microorganisms, plants, or their enzymes to clean up and detoxify polluted environments by breaking down and degrading contaminants.

Principle of Bioremediation

The principle of bioremediation is based on harnessing the natural capabilities of certain microorganisms to break down and degrade environmental contaminants. The process involves the following key elements:

• Contaminant Utilization: Bioremediation relies on specific microbes that can use contaminants as a source of food and energy. These microorganisms have the ability to metabolize and transform pollutants, such as oil, solvents, and pesticides, into simpler, less harmful substances.
• Microbial Conversion: The selected microbes consume the contaminants and convert them into smaller amounts of harmless byproducts, primarily water and gases like carbon dioxide. This conversion process reduces the toxicity and concentration of the contaminants, effectively cleaning up the polluted site.
• Optimal Conditions: To ensure effective bioremediation, the right conditions must be provided for the growth and activity of the target microbes. This includes maintaining the appropriate temperature, supplying necessary nutrients and food sources for the microbes, and ensuring adequate oxygen levels.
• Environmental Amendments: If the natural conditions are not conducive to bioremediation, amendments can be added to the environment. These amendments, such as molasses, vegetable oil, or increased aeration, create optimal conditions for the microbes to thrive and carry out the bioremediation process more efficiently.
• Timeframe : The duration of the bioremediation process can vary significantly depending on various factors. The size of the contaminated area, the concentration of contaminants, temperature, soil density, and the choice between in situ (on-site) or ex situ (off-site) bioremediation methods all contribute to the overall timeline. Bioremediation can range from a few months to several years.

By understanding and applying the principles of bioremediation, it is possible to harness the natural abilities of microorganisms and create conditions that facilitate the breakdown and removal of environmental contaminants. This approach offers a sustainable and environmentally friendly solution to clean up polluted sites.

Types of Bioremediation (Classification of Bioremediation)

Bioremediation methods can be classified into different types based on the approach used and the location of the remediation process:

• Natural Attenuation or Intrinsic Bioremediation: This method relies on the natural processes and capabilities of microorganisms present in the environment to degrade and attenuate contaminants without any additional intervention. The existing microbial populations break down the pollutants over time.
• Biostimulation: Biostimulation involves the enhancement of bioremediation by stimulating the growth and activity of indigenous microorganisms. This is achieved by adding nutrients, such as fertilizers, to the contaminated medium. The added nutrients increase the bioavailability of contaminants and promote microbial degradation.
• In Situ Bioremediation: In situ bioremediation refers to the treatment of contaminated materials directly at the site where they are located. It avoids the need for excavation or removal of the polluted materials. In this approach, bioremediation processes are conducted in the subsurface, groundwater, or soil, depending on the nature and extent of contamination.
• Ex Situ Bioremediation: Ex situ bioremediation involves the removal of contaminated materials from their original location and their treatment at a different location. This method is often used when the contamination is widespread, the site is inaccessible, or the contaminants are highly concentrated. The polluted materials are excavated and transported to a controlled facility or bioreactor for treatment.

Both in situ and ex situ bioremediation methods have their advantages and limitations, and the selection of the appropriate method depends on factors such as the type and extent of contamination, site characteristics, regulatory requirements, and cost considerations.

In Situ Bioremediation

• These methods involve treating polluted substances at the source of pollution.
• It requires no excavation and minimal or no soil disturbance during construction.
• These procedures ought to be more cost-effective than ex-situ bioremediation techniques.
• Some in-situ bioremediation procedures, such as bioventing, biosparging, and phytoremediation, may be improved, while others, such as intrinsic bioremediation and natural attenuation, may continue without modification.
• Sites polluted with chlorinated solvents, heavy metals, dyes, and hydrocarbons have been satisfactorily remedied using in-situ bioremediation approaches.

Advantages of in-situ bioremediation

• Methods of in-situ bioremediation do not involve the excavation of contaminated soil.
• This approach treats both dissolved and solid pollutants using volumetric treatment.
• Frequently, expedited in-situ bioremediation can cure subsurface pollutants more quickly than pump-and-treat techniques.
• It may be possible to convert all organic pollutants into harmless substances such as carbon dioxide, water, and ethane.
• It is a cost-effective solution because site disruption is minimised.

Disadvantages of Advantages of in-situ bioremediation

• Some toxins may not be completely turned into safe compounds depending on the place.
• If transformation ceases at an intermediate component, the intermediate may be more hazardous and/or mobile than the original chemical; refractory pollutants are not biodegradable.
• Due to the combination of nutrients, electron donor, and electron acceptor, injection wells may get clogged with abundant microbiological growth if administered improperly.
• Concentrations of heavy metals and organic chemicals impede the action of indigenous microorganisms.
• In-situ bioremediation typically requires acclimatisation of microorganisms, which may not occur for spills and stubborn substances.

Types of in-situ bioremediation

There are two types of in-situ bioremediation: intrinsic and engineered bioremediation.

1. Intrinsic bioremediation

• Intrinsic bioremediation, also known as natural reduction, is an in-situ bioremediation method involving the passive remediation of polluted environments, without the need of external force (human intervention).
• This procedure involves the promotion of the indigenous or native microbial population.
• Using both aerobic and anaerobic microbial mechanisms to biodegrade contaminating elements, including those that are resistant.
• Due to the lack of external force, the procedure is less expensive than other in-situ techniques.

2. Engineered in-situ bioremediation

• The second method involves introducing certain microorganisms to the contaminated region.
• Genetically Engineered microorganisms used in in-situ bioremediation expedite the degradation process by promoting the proliferation of microorganisms by increasing the physicochemical conditions.

Methods of In Situ Remediation

1. bioaugmentation.

• Bioaugmentation refers to the introduction of specialised microorganisms, either naturally occurring or genetically created, into polluted soil or water for their remarkable ability to breakdown or detoxify a specific contaminant or contaminant group.
• To expedite the remediation process, microorganisms having the potential to utilise or detoxify pollutants are typically identified, cultivated in the laboratory, and then delivered to contaminated locations.
• Dehalococcoides sp., which dechlorinates trichloroethylene (TCE) to ethene, has the potential to be used as a bioaugmentation agent in TCE-contaminated groundwater rehabilitation.
• Bioremediation of BTEX-contaminated soils is effective when inoculated with microbial populations capable of metabolising benzene, toluene, ethylbenzene, and xylene (BTEX).
• Bioaugmentation has proven successful with groupings of microorganisms from the same or different taxonomic groups (e.g., microbial mats and assemblages of bacteria–microalgae/cyanobacteria).

Limitations of Bioaugmentation

• Extensive studies of treatability and site characterisation may be required.
• The risk of contaminant leakage into groundwater must be mitigated due to the increased mobility of contaminants.

2. Bioventing

• Bioventing is a promising new method that provides oxygen to promote the natural in situ aerobic biodegradation of pollutants by microorganisms already present at the site.
• Popular groundwater pollutants, BTEX chemicals, are readily biodegradable by aerobic microorganisms; hence, the addition of oxygen to contaminated aquifers to induce aerobic degradation has been regarded as a common bioremediation approach.
• In order to provide enough oxygen for the sustaining of microbial activity, only modest air flow rates are maintained in the vadose zone.
• Commonly, oxygen is injected directly into soil containing residual pollution. Due to the sluggish movement of vapours through biologically active soil, not only the adsorbed fuel residuals but also the volatile compounds are biodegraded as a result of bioventing.

Applicability

• Soils contaminated with petroleum hydrocarbons, non-chlorinated solvents, pesticides, wood preservatives, and other organic contaminants have been successfully remedied by bioventing.

Limitations

The following reasons may hinder the effectiveness of bioventing:

• Soils with poor permeability
• Vapor accumulation in basements inside the influence radius of air injection wells.
• Extremely low moisture content.
• monitoring of soil surface emissions.
• In certain situations, a remediation procedure could be slowed by the low temperature.

3. Nitrate-Enhanced In Situ Bioremediation

• To oxidise a substrate, the microbial metabolic process requires an electron giver and an electron acceptor.
• Nitrate enhancement is yet another new bioremediation approach in which nitrate acts as an alternative electron acceptor for microbial activity, hence accelerating the breakdown of organic molecules.
• This approach employs the circulation of nitrate throughout the contaminated area of the groundwater in order to accelerate the breakdown of the contaminant.
• This technique is efficient for treating groundwater contaminated with BTEX.

Among the variables that may limit the efficacy of this technology are the following:

• Subsurface heterogeneity.
• Requirement for a groundwater circulation system to prevent contaminants from escaping the biodegradation zone.
• Since nitrate is regulated by drinking water standards, regulatory acceptance.

4. Cometabolic Process

• Some microbes may not utilise the intended contamination for their growth, but they can cometabolize the contaminant while utilising another molecule for growth.
• For instance, methane monooxygenase, an enzyme produced by methanotrophic bacteria during the oxidation of methane, can convert chlorinated solvents such as TCE.
• Cometabolic process is an innovative in situ bioremediation approach utilised for nonpetroleum hydrocarbons, such as chlorinated solvents, by utilising enzymes generated during the decomposition of certain chemicals.
• Cometabolism is contingent upon the presence of a suitable substrate whose metabolism can result in the transformation of the target pollutant.
• Water containing methane and oxygen is pumped into groundwater to boost the methanotrophic bacteria’ capacity for cometabolic breakdown of chlorinated organic solvents.
• Since it is difficult to circulate methane solution across each portion of a contaminated zone, the efficacy of the cometabolic process depends on the subsurface’s homogeneity.

5. Monitored Natural Attenuation

• Monitored natural attenuation (MNA) entails dependence on natural processes to obtain pollutant cleanup.
• Consideration of MNA for remediation of contaminated aquifers and groundwater systems typically necessitates modelling and evaluation of contaminant degradation rates, exposure pathways, impacts on sensitive receptors, and prediction of contaminant concentrations downgradient to the migrating contaminant plume.
• Typically, the appropriateness of MNA is evaluated on a case-by-case basis. Evaluation of MNA is not an easy task; it requires multidisciplinary skills in microbiology, chemistry, hydrogeology, and geochemistry, among others.
• MNA has been effective, particularly for hydrocarbon fuels. Typically, fuel and volatile organic compounds containing halogen are examined for MNA.

Among the problems that may restrict the use and efficacy of MNA is the need for site-specific data for modelling.

• not being suitable for locations with impending dangers.
• It is possible for the rate of pollutant migration to exceed the rate of contaminant degradation.
• Products of degradation may be more hazardous and mobile.
• It may take more time than an active cleanup approach.
• When many contaminants are included in a spill, some of the toxins may not decompose in the subsoil.
• Before considering MNA, the necessary must designate contamination both horizontally and vertically.
• Over time, the geochemical and hydrologic conditions that are conducive to MNA may alter and remobilize the stable pollutants.
• necessity for contaminated source elimination prior to MNA adoption.
• Long-term surveillance and related expenditures.

6. Bioslurping

• This method combines vacuum-enhanced pumping, soil vapour extraction, and bioventing to remediate soil and ground water by indirect oxygenation and promotion of pollutant biodegradation.
• This technology is intended for the recovery of products from capillary, light non-aqueous phase liquids (LNAPLs), unsaturated and saturated zones during remediation.
• This method is utilised to decontaminate soils contaminated with volatile and semi-volatile organic pollutants.
• The approach employs a “slurp” that spreads into the layer of free product and draws liquids from this layer.
• By ascending, the pumping machine takes LNAPLs to the surface, where they are isolated from air and water. In this method, soil moisture limits air permeability and decreases the oxygen transfer rate, hence decreasing microbial activity.
• Although this method is unsuitable for low-permeable soil restoration, it is a cost-effective operation process since it uses less ground water and reduces storage, treatment, and disposal expenses.

7. Biosparging

• This method is similar to bioventing in that air is pumped into the subsurface of the soil to promote microbial activity and accelerate the removal of pollutants from polluted locations.
• Bioventing, on the other hand, involves injecting air into the saturated zone, which facilitates the upward migration of volatile organic molecules into the unsaturated zone, so accelerating the biodegradation process.
• The effectiveness of biospraying depends on two primary aspects, namely soil permeability and the biodegradability of pollutants.
• In bioventing and soil vapour extraction (SVE), biosparging is closely related to the in-situ air sparging (IAS) technology, which relies on high air-flow rates for pollutant volatilization, whereas biosparging promotes biodegradation.
• Biosparging has often been employed to treat diesel and kerosene-contaminated groundwater.

8. Phytoremediation

• Phytoremediation decontaminates polluted soils. This technique utilises physical, chemical, biological, microbiological, and biochemical plant interactions to reduce the toxicity of pollutants at contaminated locations.
• Involved in phytoremediation are a number of mechanisms, including as extraction, degradation, filtration, accumulation, stability, and volatilization, which are dependent on pollutant quantity and kind.
• Heavy metals and radionuclides are typically eliminated through extraction, transformation, and sequestration.
• Organic pollutants such as hydrocarbons and chlorinated chemicals are typically eliminated through degradation, rhizoremediation, stabilisation, and volatilization; however, mineralization is possible when certain plants such as willow and alfalfa are utilised.
• The root system, which may be fibrous or tap depending on the depth of the pollutant, the above-ground biomass, the toxicity of the pollutant to the plant, the existence of the plant and its adaptability to the prevailing environmental conditions, the plant’s growth rate, site monitoring, and, most importantly, the time required to achieve the desired level of cleanliness are all important factors of plant as a phytoremediator.
• Additionally, the plant must be disease- and insect-resistant. Pollutant removal in phytoremediation involves uptake and transfer from roots to shoots. Additionally, translocation and accumulation are contingent upon transpiration and partitioning.
• However, the method may be altered based on variables such as the nature of the pollutant and the facility.
• The majority of plants growing in contaminated areas are effective phytoremediators. Therefore, the effectiveness of any phytoremediation strategy rests primarily on enhancing the remediation potentials of native plants growing on polluted areas, either by bioaugmentation using endogenous or foreign plant material.
• Some precious metals can bioaccumulate in some plants and be recovered after remediation, a process known as phytomining. This is one of the key benefits of utilising plants to rehabilitate polluted sites.

9. Permeable reactive barrier (PRB)

• As a physical method for remediating polluted groundwater, this technique is frequently observed.
• However, the biological mechanisms used in the PRB approach for pollution removal are precipitation degradation and sorption.
• To incorporate the biotechnology and bioremediation aspects of the technique, the words biological PRB, bio-enhanced PRB, and passive bioreactive barrier have been proposed as substitutes.
• In general, PRB is an in-situ technology used to remove heavy metals and chlorinated chemicals from polluted groundwater.

Ex Situ Bioremediation 

• Ex-situ bioremediation approaches entail excavating pollutants from contaminated locations and moving them to a new location for treatment.
• Ex-situ bioremediation procedures are frequently evaluated based on the depth of contamination, kind of pollutant, level of contamination, cost of treatment, and geographic location of the contaminated site.
• Additionally, performance guidelines govern the selection of ex-situ bioremediation procedures.

Types of Ex-situ bioremediation

There are two types of Ex-situ bioremediation;

1. Solid-phase treatment

• Solid-phase bioremediation is an ex-situ process that involves the excavation and piling of contaminated soil.
• It also comprises domestic, industrial, and municipal trash, as well as organic wastes such as leaves, animal dung, and agricultural wastes.
• Pipes are utilised to transport bacterial growth throughout the piles.
• Ventilation and microbial respiration require air to flow through the pipes.
• In comparison to slurry-phase procedures, solid-phase systems necessitate a vast amount of area and require more time to clean up.
• Solid-phase treatment methods include biopiles, windrows, land farming, and composting, among others.

2. Slurry-phase bioremediation

• Slurry-phase bioremediation is a somewhat faster treatment method than the others.
• In the bioreactor, contaminated soil is blended with water, nutrients, and oxygen to produce the optimal environment for microorganisms to breakdown soil pollutants.
• This procedure involves separating rocks and debris from contaminated soil.
• The concentration of additional water is dependent on the quantity of contaminants, the rate of biodegradation, and the physicochemical parameters of the soil.
• Using vacuum filters, pressure filters, and centrifuges, the soil is extracted and dehydrated following this procedure.
• The succeeding steps involve disposing of the soil and treating the resulting fluids in advance.

Methods Ex Situ Remediation

1. biopiles.

• Biopiles is a treatment technology in which excavated soils are combined with soil amendments and placed in above-ground enclosures equipped with an aeration system and a leachate collection system.
• Biodegradation is frequently utilised to remediate petroleum hydrocarbons in excavated soils.
• In order to decrease the possibility of contaminants seeping into groundwater or uncontaminated soil, the treatment area is typically lined with an impermeable membrane. Diverse fertiliser and supplement formulas are utilised to increase microbial activity in biopiles.
• Dirt piles can reach a height of up to 6 metres, although the optimum height is 2–3 metres. Typically, a vacuum or positive pressure air distribution system is constructed beneath the soil and maintained. The biopiles are covered with a plastic sheet to reduce runoff, evaporation, and volatilization, which can also result in increased solar heating.
• If there are volatile organic compounds (VOCs) in the soil, it may be necessary to clean the air leaving the soil prior to its release into the sky. The operation of biopiles might take anywhere between a few weeks and several months.
• Biopile treatment has been demonstrated to be effective for fuel hydrocarbons and non-halogenated VOCs. This method has also been used to treat halogenated VOCs and pesticides; however, the success rate will vary and some chemicals may be inapplicable.

Among the issues that may limit the efficacy of biopile treatment are:

• The demand for soil excavation.
• Tests of treatability to measure oxygenation and nutrient loading.
• Unlike methods involving periodic mixing, static treatment processes do not result in uniform treatment.

2. Composting

• Composting (windrows) is a controlled biological process in which excavated contaminated soil is mixed with bulking agents and organic amendments (wood chips, hay, manure, green waste, etc.) in a proper proportion to provide the proper balance of carbon and nitrogen required for thermophilic microbial activity.
• Under aerobic and anaerobic conditions, microbial activities convert organic pollutants (such as polycyclic aromatic hydrocarbons (PAHs) and 1,1,1-trichloro-2,2-bis(p-chlorophenyl) ethane (DDT)) into harmless stable compounds.
• During the composting process, the heat produced by indigenous microorganisms during the decomposition of organic materials will result in a thermophilic phase (55–65 degrees Celsius), which is essential for the transformation of hazardous pollutants.
• Maintaining adequate oxygenation (through windrow rotation), moisture content (by irrigation), and temperature can increase degradation efficiency.
• The various composting designs include (1) aerated static piles, in which compost piles are aerated through blowers or vacuum pumps, (2) in-vessel composting with mechanical agitation, in which compost is placed in a reactor vessel and mixed and aerated, and (3) windrow composting, a more cost-effective method in which compost is placed in long piles called windrows and mixed periodically with mobile equipment.
• Using the composting process, biodegradable pollutants in soils and sediments can be removed. Pilot and large-scale operations have provided evidence that aerobic, thermophilic composting can reduce the content of explosives such as trinitrotoluene (TNT), RDX, HMX, and ammonium picrate to tolerable levels.
• Also suitable to PAHs and DDT residues is this method.

Limitations of the composting process include the need for a large amount of area.

• any uncontrolled VOC emissions related with soil excavation.
• Due to the need for additions, there is a rise in material quantity.

3. Land Farming

• Land farming is a large-scale bioremediation technique in which excavated contaminated soil is deposited on lined beds of a predefined depth and aerated by periodic turning or tilling (plow depth about 4–12 in).
• During this procedure, soil parameters such as moisture content, aeration, pH, and amendments such as soil bulking agents, fertilisers, etc. are manipulated to achieve the highest possible rate of pollutant breakdown.
• This mechanism enables aerobic microbial digestion through the availability of oxygen, nutrients, and moisture.
• Land cultivation has been effective for treating petroleum hydrocarbons. More chlorinated and nitrated substances decay slowly.
• Diesel fuel, fuel oils, oil sludge, wood preservation wastes, coke wastes, and insecticides are also successfully treated.
• The need for a big amount of area is one of the variables that may limit the efficiency of land farming.
• Some of the elements governing microbial proliferation and decomposition, such as precipitation and temperature, are out of control and may lengthen the duration of degradation.
• need for handling volatile substances to avoid these gases from migrating off-site and into the environment.
• required for the construction of a facility for collecting and monitoring runoff debris.
• For optimal facility design, it is necessary to analyse the site’s topography, erosion, climate, and permeability, among other factors.

4. Slurry-Phase Bioreactors

• Slurry-phase biological treatment is combining excavated contaminated soil or sediment with water and other additives in a bioreactor under regulated conditions to produce aqueous slurry.
• The amount of water given to soil is dependent on the concentration of the pollutant, its rate of biodegradation, and the soil’s physicochemical qualities.
• During the treatment process, the solids are kept in slurry suspension in the reactor and combined with nutrients and oxygen to bring microorganisms into contact with soil constituents.
• If an appropriate indigenous population of microorganisms capable of degrading specific pollutants is not present in the soil, it is possible to introduce such organisms.
• The pH will be adjusted to the desired level, if necessary, in the reactor vessel. After biodegradation is complete, the slurry can be dewatered and the treated soil can be discarded.
• It has been demonstrated that slurry-phase bioreactors are effective for remediating soils and sediments contaminated with petroleum hydrocarbons, explosives, solvents, pesticides, and other contaminants.
• When treating diverse and impermeable soils, as well as when faster treatments are necessary, bioreactors are preferable to in situ biological methods.

Among the constraints of slurry-phase biotreatment are:

• The obligation to excavate polluted soil.
• The amount of soil that can be introduced to the reactor, especially when treating huge quantities of contaminated soil.
• The expense associated with dewatering treated soil.
• locating a safe and appropriate method of wastewater disposal.

5. Fungal Remediation

• The metabolism of fungi has been linked to the breakdown of numerous organic pollutants, particularly hydrocarbons.
• One type of fungi , specifically white-rot fungus (Phanerochaete chrysosporium), may decompose a wide range of organic pollutants, such as PCBs, PAHs, and explosives.
• These enzymes, lignin peroxidases, are generated by these fungi and are responsible for their wide biodegradability.
• It has been established that white-rot fungus may decompose chlorinated hydrocarbons, PAHs, PCBs, polychlorinated(p)dioxins, pesticides (lindane and DDT), and some azodyes.
• Also, white-rot fungi have been demonstrated to degrade PAHs such as benzo(a)pyrene, pyrene, fluorene, and phenanthrene; however, breakdown is favoured under nitrogen-limited and low pH circumstances.

Among the conditions that impede fungal remediation are:

• Their awareness of biological processes.
• their incapacity to effectively grow in suspension systems.
• mixing’s deleterious influence on enzyme synthesis.
• The inability of fungi to adhere to fixed media.
• chemical adhesion
• conflict with native microorganisms
• Transformation ability that is sluggish.

Advantages of ex-situ bioremediation

• Compatible with a wide variety of pollutants
• Suitability is reasonably straightforward to evaluate using site investigation data.
• The contaminated environment is more manageable, controllable, and predictable in a bioreactor system than in solid-phase systems.

Disadvantages of ex-situ bioremediation

• Not applicable to contamination with heavy metals or chlorinated hydrocarbons like trichloroethylene.
• Non-permeable soil requires further preparation.
• Before introducing a contamination into a bioreactor, the contaminant can be removed from the soil through soil washing or physical extraction.

Factors affecting the bioremediation

Various environmental factors, such as temperature, salinity, pH, and oxygen availability, have the potential to influence petrochemical waste bioremediation. There is an inverse link between salinity and the solubility of petroleum hydrocarbons, since an increase in salt increases aromatic hydrocarbon absorption. It has been documented for pyrene in several types of sediments, with salting out effects identified in both solution and solid phases as a likely source for this increase in degradation. Moreover, in some instances, hypersalinity inhibits microbial growth and, consequently, metabolic processes, while promoting the growth of unidentified halophytic archaea during biodegradation. Several other environmental variables are discussed in detail below:

1. Temperature

• Temperature exerts a crucial influence on both in situ and ex situ microbial metabolism and hydrocarbon breakdown.
• At low temperatures, microbial growth and multiplication decrease, resulting in a sluggish rate of petrochemical degradation.
• In contrast, numerous studies have demonstrated that a rise in temperature enhances the solubility of hydrocarbons in the medium, making petrochemical hydrocarbons readily accessible to microbes.
• The breakdown rate of petrochemical wastes is typically rapid at temperatures between 30 and 40 degrees Celsius in soil and 15 and 20 degrees Celsius in aquatic or marine environments.
• However, some thermophilic bacteria (e.g., Bacillus thermoleovorans) have been shown to change phenanthrene, naphthalene, and anthracene efficiently even at higher temperatures.
• Variations in pH conditions significantly influenced the microbial decomposition of petrochemical wastes in soil or aquatic medium.
• Diverse research support the advantageous mineralization of petroleum hydrocarbons close to pH neutrality.
• A little change in pH can have a substantial effect on the overall biological degradation processes in an aquatic environment.
• It has been found that certain fungi and acidophilic microorganisms can grow and have biodegradation capacity in highly acidic settings.

3. Oxygen availability

• The presence of oxygen determines whether a given environmental condition is aerobic or anaerobic.
• It has been noted that the degradation of petrochemical hydrocarbons occurs predominantly in aerobic conditions and occasionally in anaerobic environments.
• Biodegradation in anaerobic conditions occurs primarily in aquifers and submerged marine sediments with a negligible degradation rate, and is primarily limited to halogenated aromatics.
• Oxygen is important for the activity of mono- and dioxygenase enzymes during aromatic ring oxidation, which is required for the aerobic breakdown of petrochemicals. To promote aromatic compound oxidation in an anaerobic environment, substituted electron acceptors such as ferrous iron, nitrate, and sulphate are important.
• However, the reduction of electron acceptors such as ferric iron, nitrate, and sulphate under anaerobic circumstances releases substantial quantities of phosphorus and ferrous iron, further contaminating the natural ecosystem.
• In addition, under anaerobic breakdown of petrochemical hydrocarbons, greenhouse gas emissions (CH4, NO2, etc.) and an increase in pH have been reported.
• Thus, oxygen availability plays a crucial role in aromatic chemical bioremediation.

4. Concentration of pollutant

• Individual contaminants’ degradation rates may be affected by the interactions between substrates.
• Due to its probable impact in bacterial sensitivity and metabolism, the evaluation of substrate-substrate interactions at varying concentrations has been deemed a crucial factor.
• The synergistic interactions between a contaminant’s many components can enhance breakdown rates and catabolic enzyme activities.
• In a batch culture investigation, it was revealed that the growth rate of Pseudomonas putida was reduced at high substrate concentrations.
• Due to their complicated interactions, BTEX chemicals (at specific doses) had an inhibiting influence on microbiological processes.

5. Nutrients availability

• Nutrients (such as carbon, nitrogen, phosphorus, potassium, and calcium) are essential for microbial development and activity; hence, their availability plays a crucial role in regulating the breakdown rates of various pollutants.
• In addition, relative nutrient availability has a significant regulatory effect on pollutant degradation. At a contaminated site with higher levels of organic carbon in the contaminants, for instance, the microbial activity is reported to be significantly higher, resulting in the rapid depletion of bioavailable nutrients such as nitrogen, phosphorus, potassium, and iron in the early phase, followed by a decrease in degradation as a result of the depletion of these essential elements.
• On the contrary, increased availability of N, P, and K has been observed to have a deleterious effect on aromatic hydrocarbon decomposition.

6. Microbial adaptation (acclimatization)

• Petroleum waste decomposition is potentially influenced by microbial adaptability.
• The adaptation of microbial populations to aromatic organic compounds increases their efficiency of breakdown.
• Alcaligenes xylosoxidans Y234, for instance, decomposed benzene and toluene more effectively under adapted conditions than under non-adapted ones.
• Non-acclimatized microorganisms exhibit the quickest biodegradation rates in both single-component and multicomponent-based confinement systems.

7. Bioavailability

• Accessibility of organic contaminants to microorganisms is one of the most important determinants of biodegradation rate.
• The bioavailability of hydrocarbons depends on their physical properties and chemical composition.
• Some compounds generated from bacteria may operate as additives that accelerate the breakdown of petroleum hydrocarbons.
• Biosurfactants, a rich source of carbon, produced by diverse microbes (e.g., bacteria and fungus), have the potential to contribute to the uptake and mineralization of petroleum hydrocarbons.

8. Redox Potential

• Redox Potential and oxygen content are indicative of oxidising or reducing circumstances, respectively.
• The presence of electron acceptors such as nitrate, manganese oxides, iron oxides, and sulphate influences redox potential (ICSS 2006).

Microorganisms used in bioremediation

Microorganisms play a crucial role in nutritional chains, which are an integral aspect of the biological equilibrium of life. Bioremediation is the process of removing contaminated materials using bacteria, fungi, algae, and yeast. In the presence of toxic substances or any waste stream, microorganisms can flourish at temperatures below zero and at high temperatures. The adaptability and biological systems of microorganisms make them useful for the cleanup process. Carbon is the essential component for microbial action. In various conditions, a consortium of microorganisms performed bioremediation. These microbes include Achromobacter, Arthrobacter, Alcaligenes, Bacillus, Corynebacterium, Pseudomonas, Flavobacterium, Mycobacterium, Nitrosomonas, and Xanthobacter, among others.

There are various microbe groups utilised in bioremediation, including:

• Aerobic : Aerobic bacteria such as Pseudomonas, Acinetobacter, Sphingomonas, Nocardia, Flavobacterium, Rhodococcus, and Mycobacterium have the ability to breakdown complex substances. According to reports, these bacteria breakdown insecticides, hydrocarbons, alkanes, and polyaromatic chemicals. Numerous of these bacteria utilise the pollutants as a source of carbon and energy.
• Anaerobic: Anaerobic bacteria are utilised less frequently than aerobic bacteria. Aerobic bacteria utilised for bioremediation of chlorinated aromatic chemicals, polychlorinated biphenyls, and dechlorination of the solvent trichloroethylene and chloroform, decomposing and converting contaminants to less hazardous forms, are gaining growing attention.

Bioremediation approaches used for dye degradation

Dye decolorization is initiated by an anaerobic reduction reaction performed by azo-reductases or azo-bonds breaking under aerobic or anaerobic conditions, which results in the creation of aromatic amines due to the physiological and metabolic activities of the mixed bacterial community. The following is a detailed description of various dye degradation processes:

1. Aerobic treatment

• There are very few reports on the bacterial degradation of azo-dyes; yet, several microorganisms have demonstrated their capacity for dye reduction.
• Pseudomonas aeruginosa has been shown to degrade the commercially used textile and tannery dye Navitan Fast Blue SSR in an aerobic medium including glucose as a carbon source.

2. Anaerobic treatment

• Under anaerobic conditions, azo-dye reduction is accomplished through the dissolution of azo-bonds.
• Under anaerobic conditions, dyes are cleaved, producing poisonous aromatic amines via bacterial metabolism.

3. Anoxic treatment

• Various studies show the anaerobic degradation of various colours by facultative anaerobic and mixed aerobic bacteria.
• Although a number of bacteria are capable of flourishing in an aerobic environment, the dye is only destroyed in anaerobic conditions.
• A number of pure bacterial cultures , including Pseudomonas luteola, Aeromonas hydrophila, Bacillus subtilis, and Proteus mirabilis, are known to digest azo-dyes anaerobically.

4. Sequential degradation of dyes

• It has been proposed that aromatic amines generated by the anaerobic decomposition of azo-dyes can be degraded in an aerobic environment.
• First, the applicability of this method was demonstrated for the sulfonated azo-dye Mordant Yellow. Following aeration, full microbial mineralization of amine is seen.

Different Categories of Bioremediation

Bioremediation can be categorized into two main types: microbial remediation and phytoremediation.

a. Microbial Remediation:

Microbial remediation involves the use of microorganisms such as bacteria, fungi, yeasts, and actinomycetes to break down and remove contaminants from the environment. These microorganisms have the ability to degrade a wide range of organic compounds and absorb inorganic substances. Key points about microbial remediation include:

• Microorganisms are diverse, abundant, and readily available for use in bioremediation processes.
• Different microbial systems can be employed for the removal of toxic and other contaminants from the environment.
• Microorganisms can be used in both in situ (on-site) and ex situ (off-site) conditions, and they can thrive in extreme environmental conditions.
• Synergistic interactions among mixed cultures of microorganisms are often beneficial in bioremediation, particularly for the degradation of crude oil in soil.
• Various bacteria, including Pseudomonas, Aeromonas, Moraxella, Nocardia, Bacillus, and Cyanobacteria, are commonly used for the removal of petroleum hydrocarbon contaminants from soil.

b. Phytoremediation:

Phytoremediation is a bioremediation process that utilizes plants to remove, transfer, stabilize, or destroy contaminants in the soil and groundwater. Different mechanisms are involved in phytoremediation, including:

• Rhizosphere biodegradation: Plants release natural substances through their roots, providing nutrients to soil microorganisms, which enhance the biological degradation of contaminants.
• Phyto-stabilization: Chemical compounds produced by plants immobilize contaminants, preventing their movement and reducing their toxicity.
• Phyto-accumulation (phytoextraction): Plant roots absorb contaminants, along with other nutrients and water, which accumulate in the shoots and leaves. This method is primarily used for contaminants containing metals.
• Hydroponic systems for treating water streams (rhizofiltration): Plants are grown in greenhouses with their roots in water, allowing the plants to absorb contaminants from the water. The saturated roots are harvested and disposed of.
• Phyto-volatilization: Plants absorb water containing organic contaminants and release the contaminants into the air through their leaves.
• Phyto-degradation : Plants metabolize and destroy contaminants within their tissues.
• Hydraulic control : Trees indirectly remediate by controlling the movement of groundwater. The dense root mass of trees takes up large quantities of water, helping to regulate the water table and limit the spread of contaminants.

Overall, microbial remediation and phytoremediation offer valuable approaches for the cleanup of contaminated environments, utilizing the natural capabilities of microorganisms and plants to mitigate pollution.

What is Slurry phase bioremediation?

• Slurry phase bioremediation is a batch treatment approach in which excavated soil or sediments are combined with water and treated in bioreactor vessels or ponds.
• To reduce the viscosity of contaminated soil, removal of stones and rubbles from the soil is required during soil processing.
• The soil is then combined with a specific quantity of water to create slurry.
• Thus, slurry phase treatment is a three-phase system consisting of water, air, and suspended particulate matter, including the desired microorganism.
• The amount of water added depends on the quantity of contaminants, the rate of biodegradation, and the soil’s physical characteristics (USEPA, 2006). In addition to ensuring appropriate aeration and mixing, nutrients are always provided, along with surfactants or dispersants as necessary.
• In bioreactor vessels, optimal pH and temperature conditions are also provided.
• With slurry phase systems, soil and sediments contaminated with a wide variety of organic chemicals, such as pesticides, petroleum hydrocarbons, pentachlorophenol, polychlorinated biphenyls (PCBs), etc., have undergone effective bioremediation.
• There are three biologically distinct types of slurry phase bioreactors: aerated lagoons, lowshear airlift reactors, and fluidized-bed soil reactors.
• A slurry bioreactor is a vessel and apparatus used to create a three-phase (solid, liquid, gas) mixing condition to increase the rate of bioremediation of soil-bound and water-soluble pollutants as a water slurry of contaminated soil and biomass (typically indigenous microorganisms) capable of degrading target contaminants.
• In general, the pace and amount of biodegradation are larger in a bioreactor system than in situ or solid-phase systems because the enclosed environment is more manageable and, thus, more predictable.
• Despite the benefits of bioreactor systems, there are downsides, such as the need to pre-treat contaminated soil (e.g., excavation) or remove contaminants from the soil via soil washing or physical extraction (e.g., vacuum extraction) prior to placing the soil in a bioreactor.

What is Solid phase bioremediation?

• The solid phase system consists of organic wastes, manures, sewage sludge, and municipal solid wastes.
• Traditional cleanup methods include the informal processing of organic debris and the generation of compost, which can be used as a soil amendment.
• Solid phase bioremediation involves the excavation and piling of contaminated soil.
• A network of pipes that are dispersed throughout the piles stimulates bacterial development. By drawing air through pipes, microbial respiration is given with the necessary ventilation.
• Spraying the soil with water introduces moisture. Solid-phase systems demand a substantial amount of area, and cleanups take longer than slurry-phase procedures.
• Land farming chemical groups on mineral surfaces, reactive organic chemicals, and inorganic metals are some solid-phase treatment techniques.
• The precise method by which microorganisms respond to insecticides is not understood. It is possible for microorganisms to acquire genetic material encoding the biochemical pathways required to handle a potential substrate.
• The process of microbial bioremediation can occur under both aerobic and anaerobic environments. In an aerobic environment, bacteria use air oxygen for their metabolic processes in order to produce carbon dioxide and water through pesticide breakdown.
• In the absence of oxygen, however, bacteria use these chemical compounds in the soil as substrate, breaking them down to obtain the energy they require.

Applications of Bioremediation

Bioremediation has a wide range of applications in the cleanup of various contaminants and polluted sites. Some key applications of bioremediation include:

• Remediation of Metals, Radionuclides, and Pesticides: Bioremediation can be used to address contamination by heavy metals, radioactive substances, and pesticides. Specific microbial or plant-based strategies can target these contaminants and facilitate their degradation or immobilization.
• Treatment of Explosives, Fuels, VOCs, and SVOCs: Bioremediation is effective in treating pollutants such as explosives (e.g., TNT), fuels (e.g., gasoline, diesel), volatile organic compounds (VOCs), and semi-volatile organic compounds (SVOCs). Microorganisms can break down these contaminants into less harmful substances.
• Phytoremediation of Perchlorate: Phytoremediation, a form of bioremediation using plants, shows promise in addressing perchlorate contamination in surface and groundwater systems. Research is being conducted to understand the role of plants in removing this persistent contaminant.
• Cleanup of Soil and Groundwater: Bioremediation is commonly used to clean up contaminants found in soil and groundwater. Microorganisms or plants are introduced to the polluted sites to break down or remove the pollutants, restoring the environmental quality.
• Remediation of Petroleum Products: Bioremediation is highly effective in treating petroleum products, such as gasoline and diesel fuel, which may contaminate soil and groundwater. Microorganisms can metabolize and degrade these hydrocarbons.
• Treatment of Production-related Chemicals: Bioremediation can address contamination caused by leaked or released production-related chemicals, including both difficult-to-remediate heavy metals and minor pollutants. Certain microorganisms have the ability to biologically eliminate these pollutants.
• Landfill Remediation: Overfilled, leaking, or closed landfills can benefit from bioremediation. This approach can help regulate methane gas, a common byproduct of landfill waste, through air stripping and scrubbing techniques.
• Remediation of Over-Fertilized Farms: Bioremediation can be applied to farms that have been excessively fertilized, addressing both synthetic fertilizers and animal waste. Microorganisms can break down the excess nutrients and restore the balance in the soil.
• Cleanup of Wood Preservative Contamination: Bioremediation efforts can remove pollutants from lumber processing yards, where wood preservatives have seeped into the soil and groundwater. Microorganisms can break down these contaminants.
• Treatment of Failed Septic Tanks and Disposal Fields: Onsite sewage systems that fail and contaminate the soil and groundwater can be effectively treated using bioremediation. Biological treatment methods can help restore the affected areas.
• Remediation of Mine Tailings: Toxic mine tailings can be remediated through bioremediation techniques. Efforts to decontaminate old mine quarries and pits using bioremediation have shown promising results.
• Cleanup of Chemical Leaks along Traffic Routes: Accidental chemical spills, including road salts and petroleum spills along traffic routes, can be remedied through biological treatments. Bioremediation helps break down and remove these pollutants.

Advantage of bioremediation

Bioremediation offers several advantages over other cleanup methods, making it a favorable choice for addressing environmental contamination:

• Environmentally Friendly: Bioremediation is a natural process that utilizes the existing microbial and plant-based mechanisms in the environment. It causes less damage to ecosystems and is considered a green method of cleanup.
• Minimal Disruption: Bioremediation can be conducted underground, allowing amendments and microbes to be pumped into groundwater and soil without causing significant disruption to nearby communities or surface activities.
• Safe and Harmless Byproducts: The process of bioremediation converts contaminants and pollutants into harmless byproducts such as water and carbon dioxide. It generates few harmful byproducts, reducing the risk of creating additional environmental hazards.
• Cost-Effective: Bioremediation is generally a cost-effective method compared to other cleanup methods. It requires minimal equipment and labor, making it an affordable option for remediation projects.
• Tailored Approach: Bioremediation can be tailored to the specific needs of the polluted site. The selection of appropriate microbes and the optimization of growth-promoting factors allow for targeted degradation of pollutants.
• Minimal Effort and On-Site Treatment: Bioremediation can be performed on-site with minimal effort. It does not require the transfer of contaminated material off-site, reducing transportation costs and potential risks associated with waste disposal.
• Complete Breakdown of Contaminants: Bioremediation promotes the complete breakdown of contaminants. Hazardous substances can be converted into less harmful products, ensuring the effective removal and disposal of pollutants.
• No Hazardous Chemicals: Bioremediation does not rely on the use of hazardous chemicals. Instead, it often involves the addition of nutrients or fertilizers to stimulate microbial growth, resulting in the conversion of contaminants into harmless substances.
• Sustainable and Eco-Friendly : Bioremediation methods align with sustainable and eco-friendly practices. They utilize natural processes and minimize the need for external interventions, contributing to environmental preservation.

Overall, the advantages of bioremediation make it a viable and preferred approach for the cleanup of contaminated sites, offering an environmentally friendly, cost-effective, and efficient solution to environmental pollution.

Disadvantage of bioremediation

Bioremediation, while offering numerous advantages, also has certain disadvantages that should be considered:

• Unknown Toxicity and Bioavailability: The toxicity and bioavailability of by-products generated during biodegradation processes are not always well understood. It is important to assess the potential risks associated with these by-products to ensure they do not pose a threat to ecosystems or human health.
• Mobilization and Bioaccumulation: Degradation by-products may be mobilized in groundwater or bio-accumulated in animals, potentially leading to the transfer of contaminants through the food chain. The fate and potential impacts of these accumulated contaminants need to be carefully evaluated.
• Fate of Contaminants in Plant Metabolic Cycle: Further research is required to determine the fate of contaminants within the plant metabolic cycle. It is crucial to understand whether plant droppings, leaves, or wood release harmful chemicals into the environment, particularly when they are utilized as mulch or firewood.
• Disposal of Harvested Plants: The disposal of harvested plants that contain high levels of heavy metals can be challenging. Proper handling and disposal methods must be implemented to prevent the release of contaminants into the environment.
• Treatment Limitations: Bioremediation, including phytoremediation, is often limited to shallow soils, streams, and groundwater. The depth of contaminants can restrict the effectiveness of treatment in deeper soil layers.
• Seasonal and Climatic Influences: The success of phytoremediation can be affected by seasonal variations and climatic factors. Different plants may exhibit varying levels of effectiveness depending on the location and specific environmental conditions.
• Ecological Ramifications: Introducing new plant species for remediation purposes can have widespread ecological consequences. The potential impacts on native flora and fauna should be thoroughly studied and monitored to avoid unintended ecological ramifications.
• Plant Survival and Contaminant Concentrations: High concentrations of contaminants may inhibit plant growth and survival. If contaminant levels are too high, the plants may not be able to thrive or effectively remediate the site.
• Media Transfers: Phytoremediation may transfer contaminants across different environmental media, such as from soil to air, posing challenges in managing and controlling the movement of contaminants.
• Land Requirement: Phytoremediation often requires a large surface area of land to achieve effective remediation. This can limit its applicability, particularly in densely populated areas or sites with limited available land.

Considering these disadvantages, careful assessment and monitoring are essential when implementing bioremediation strategies to ensure the effectiveness of the remediation process while minimizing potential risks to the environment and human health.

What is Phytoremediation?

• Phytoremediation is a type of bioremediation that uses plants to remove toxins by healing and rebuilding the soil and ground and surface water.
• The plants utilised in the method absorb the toxins from the soil, store them inside their plant tissues , and bind them until they are decomposed by the roots.
• The plants extract pollutants from the soil through their roots, which then accumulate in the stems. Plants absorb toxic substances from the soil and release them into the atmosphere via transpiration and evaporation.
• Metals, pesticides, chlorinated solvents, polychlorinated biphenyls, and petroleum hydrocarbons are just a few of the contaminants that plants may eliminate.
• Indian Mustard, Indian Grass, Brown Mustard, Sunflower plants, Barley Grass, Pumpkin, Poplar trees, Pine trees, and White Willows are examples of plants that can be utilised for phytoremediation.
• These possess renewing and energising properties that aid the procedure.

What is Mycoremediation?

• Fungi are recognised as the decomposers of nature. They decompose the majority of the plant and woody debris on Earth, resulting in the renewal of the soil.
• Using their metabolic enzymes, fungi breakdown substances such as metals and diverse insecticides.
• By breaking down bigger hydrocarbon chains into smaller ones, fungi operate as a catalyst for microbes and plants, making their processes simpler.
• The fungi absorb the chemicals by degrading them with the aid of enzymes and then store the nutrients in the fleshy portions, which are known as mushrooms.

What is bioremediation?

Bioremediation is a process that uses living organisms, such as bacteria, fungi, and plants, to degrade or detoxify contaminants in the environment.

What types of contaminants can bioremediation address?

Bioremediation can be used to address a wide range of contaminants, including petroleum hydrocarbons, chlorinated solvents, pesticides, and heavy metals.

How does bioremediation work?

Bioremediation works by using microorganisms to break down contaminants into less harmful substances. This can be done through different mechanisms, such as metabolic transformation or adsorption.

What are the benefits of bioremediation?

Bioremediation offers several benefits, such as being cost-effective, environmentally friendly, and producing minimal waste. It can also be used in situ, meaning it can be performed on site, reducing the need for transportation and disposal of contaminated materials.

What are the limitations of bioremediation?

Bioremediation has some limitations, such as the need for specific environmental conditions and the length of time required for the process to work effectively. Additionally, some contaminants may be resistant to biodegradation.

What are some examples of successful bioremediation projects?

Some examples of successful bioremediation projects include the cleanup of the Exxon Valdez oil spill in Alaska, the restoration of a contaminated industrial site in Spain, and the treatment of groundwater contaminated with chlorinated solvents in California.

What are the different types of bioremediation?

There are several types of bioremediation, including natural attenuation, bioaugmentation, biostimulation, and phytoremediation.

What is natural attenuation?

Natural attenuation is a type of bioremediation that relies on naturally occurring microorganisms to degrade contaminants without human intervention.

What is phytoremediation?

Phytoremediation is a type of bioremediation that uses plants to absorb, degrade, or stabilize contaminants in the soil or water. Different plants have different abilities to remediate different contaminants.

Is bioremediation safe?

Bioremediation is generally considered safe, as it relies on naturally occurring processes and does not involve the use of harsh chemicals. However, as with any environmental remediation process, precautions should be taken to ensure the safety of workers and the surrounding community.

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Phytoremediation pp 1–26 Cite as

Principles of Phytoremediation

• Brian R. Shmaefsky 3  
• First Online: 20 March 2020

981 Accesses

3 Citations

Part of the book series: Concepts and Strategies in Plant Sciences ((CSPS))

Phytoremediation, a form of bioremediation, is one viable option for removing pollution from contaminated soil and water. Bioremediation was developed as an inexpensive, environmentally friendly, and sustainable alternative to traditional chemical and physical pollution remediation methods. Bioremediation began with the use of bacteria and later other microorganisms, to extract or degrade inorganic and organic contaminants in soil and water in situ. It then evolved to other applications in combination with traditional chemical and physical remediation methods. Phytoremediation was came about from basic research studies on the physiology of halophytic and hyperaccumulating plants. At first, plants provided successful for extracting salts, metals, and radionuclides from soil and water. Further, studies discovered that plant roots and the rhizosphere were capable of extracting or degrading organic pollutants such as pesticides and petrochemicals. The in situ case studies showcased in this book demonstrate how phytoremediation is a sustainable means of pollution remediation in economically emerging countries and is consistent with the United Nations Sustainable Development Goals.

• Bioremediation
• Environmental pollution
• Phytoremediation
• Phytotechnology
• Traditional remediation

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Adams GO, Fufeyin PT, Okoro SE, Ehinomen I (2015) Bioremediation, biostimulation and bioaugmention: a review. Int J Environ Bioremediat Biodegradation 3(1):28–39

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Shmaefsky, B.R. (2020). Principles of Phytoremediation. In: Shmaefsky, B. (eds) Phytoremediation. Concepts and Strategies in Plant Sciences. Springer, Cham. https://doi.org/10.1007/978-3-030-00099-8_1

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Bioremediation

Last updated on October 9, 2023 by ClearIAS Team

The use of living microbes to treat contaminated environments is known as bioremediation. Bacteria, fungi, algae, and other microbes are used here. Scientists have successfully created many bioremediation technologies to restore contaminated settings.

As part of this process, harmful compounds are detoxified, reduced, degraded, or changed into less dangerous ones. Pesticides, agrochemicals, xenobiotic compounds, heavy metals, plastics, organic halogens, greenhouse gases, and other contaminants have no effect on the microorganisms used in bioremediation. This technology is also used to treat nuclear waste.

Also read: Energy Flow Through an Ecosystem

Table of Contents

Bioremediation is the use of microorganisms to break down environmental contaminants into less dangerous forms. The microorganisms may be indigenous to the contaminated area, or they may have been isolated elsewhere and brought to the contaminated site.

The Oxidation Reduction Potential, or redox, in soil and groundwater, together with pH, temperature, oxygen content, electron acceptor/donor concentrations, and breakdown product concentrations, can indirectly monitor the bioremediation process (e.g. carbon dioxide).

Bioremediation can be effective only when the environmental conditions allow for microbial growth and activity.

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Bioremediation Strategies

Bioremediation strategies mainly include in-situ bioremediation techniques and ex-situ bioremediation techniques.

In situ Bioremediation Techniques

In situ bioremediation is the use of on-site decontamination technologies to remediate polluted soil or groundwater while causing minimal damage to the soil structure.

• Because excavation processes are avoided, these bioremediation methods are less expensive.
• The cost of building and installing complicated equipment to boost biotic activity in bioremediation, on the other hand, is a considerable concern.
• In situ bioremediation techniques have been used to detoxify chlorinated solvents, dyes, nutrients, heavy metals, and organic waste sites.

In situ, bioremediation techniques include bioventing, biosparging, and bioaugmentation.

• Bioventing is an in situ bioremediation technique that promotes aerobic decomposition.
• It boosts the innate potential of indigenous microorganisms to break down organic contaminants adsorbed to the soil by supplying oxygen into an unsaturated zone.
• Air is fed directly into the contaminated zone using vertical and horizontal wells.
• In this technique, only the amount of air required for degradation is utilized. Pollutant volatilization and discharge into the environment are also reduced.
• Bioventing was one of the first large-scale technologies to be developed in the 1990s, and it is now widely used in commercial applications.
• Bioventing can be performed actively or passively.
• In passive bioventing, gas exchange from vent wells is merely affected by atmospheric pressure, whereas in active bioventing, the air is forced into the ground by a blower, sometimes in conjunction with vacuum extraction of the gas.

Biosparging

• The method of injecting pressurised air or gas into a contaminated area to increase in-situ aerobic biological activity is known as biosparging.
• This approach targets chemical substances that can be biodegraded under aerobic circumstances, such as mineral oils and benzene, toluene, ethylbenzene, xylene, and naphthalene (BTEXN), and is used to remediate soluble and residual pollutants in the saturation zone.
• The injection of air (and gaseous nutrients if needed) encourages the development of the aerobic microbial population and so increases the bioavailability of contaminants by providing oxygen to the microorganisms and enhancing the interactions between air, water, and the aquifer.
• A sparging system aims to promote pollutant biodegradation while reducing volatile and semi-volatile organic compound volatilization.
• The flow rate of air injection is set to provide the amount of oxygen required to promote bacterial contamination degradation. However, depending on the operation mode and design chosen, some volatilization may occur, needing air capture and treatment.

Bioaugmentation

• It entails investigating local indigenous varieties to determine whether biostimulation is feasible.
• Bioaugmentation refers to adding more archaea or bacterial cultures to increase pollutant breakdown, whereas biostimulation refers to providing nutritional supplements to increase bacterial metabolism.
• If the indigenous bacteria detected in the area are capable of metabolizing the pollutants, more indigenous bacterial cultures will be introduced into the area to hasten the breakdown of the contaminants.
• If the indigenous species lack the metabolic ability to heal itself, exogenous microorganisms with such sophisticated pathways are introduced.
• Industrial wastes that contain inhibiting or harmful constituents that can be addressed using bioaugmentation products include acetone, acrylic acid, ammonia, nitrite, furfural, phenolic compounds, and methyl ethylamine.

Also read: Ecosystem- In layman’s Language

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Ex-situ Bioremediation Techniques

Ex-situ bioremediation is a biological approach in which excavated soil is placed in a lined above-ground treatment area and then aerated to assist the indigenous microbial population in degrading organic contaminants.

• Under aerobic conditions, organic pollutants such as petroleum hydrocarbon mixtures, polycyclic aromatic hydrocarbons (PAH), phenols, cresols, and some pesticides can be used as a source of carbon and energy by specific microbes and then degraded to carbon dioxide and water.
• Although adding microbial communities is uncommon, it is usual to need to assess nutrient requirements and supplement the soil’s basic nutrients and organic substrate if any of these elements are insufficient or lacking.
• Oxygen (via the introduction of air) is essential to allow the microbial population to form cultures capable of sustaining degradation.

Ex-situ, bioremediation techniques include Landfarming, Biopiles, Bioreactors, Composting

Landfarming

• Land farming is the most fundamental kind of bioremediation.
• Before being tilled into the ground, contaminated soils are combined with soil additives such as bulking agents and fertilisers.
• Inland farming, they are excavated and spread them in layers of around 0.3m thickness on a lined treatment area.
• Bioremediation can be aided by regular bed flipping and the addition of nutrients.
• Contaminants are degraded, converted, and immobilized by microbiological and oxidative processes.
• Controlling soil conditions optimizes the rate of pollutant breakdown.
• Moisture content, aeration frequency, and pH are all modifiable variables.
• Landfarming techniques require huge areas and are often not feasible for small sites due to the restricting thickness of soil layers (0.3m), yet they can be the most cost-effective type of bioremediation.
• A Biopile is a sort of ex-situ treatment that employs biological processes to convert pollutants into non-hazardous byproducts.
• It is frequently used to reduce petroleum component concentrations in soils through the bioremediation process. Biopiles are a form of remediation technology that is only employed for a limited duration.
• Excavated soil or silt is placed over an impermeable base or pad with aeration to increase and manage the rate of biodegradation.
• Pads are frequently provided with a cover and adequate drainage to manage precipitation exposure, as well as probes to measure temperature, moisture content, and pollutant concentrations.
• Optional equipment may include a moisture addition system, leachate collection system, and off-gas treatment, depending on the site’s attributes and regulatory needs.

Also Read: E-Waste: Causes, Concerns and Management – ClearIAS

Bioreactors

• A bioreactor is any piece of manufactured equipment or system that supports a biologically active environment.
• The bioreactor method is a biochemical processing system that uses microbes to remove toxins from wastewater or pumped groundwater, as well as the solid and liquid (slurry) stages of contaminated soil remediation.
• This process could be aerobic or anaerobic.
• These bioreactors are commonly cylindrical in design, with diameters ranging from liters to cubic meters, and are made of stainless steel.
• Slurry bioreactors are one of the most sophisticated bioremediation systems on the market, as well as one of the most successful ex-situ options for treating polluted soils with resistant pollutants in a controlled environment.
• A slurry bioreactor’s proper operation is based on the presence of balanced suspension, aeration, and mixing conditions.
• Compost bioremediation is the use of a biological system of microorganisms in a mature, cured compost to adsorb or break down contaminants in water or soil.
• The two most common composting processes are aerated static pile composting (compost is shaped into heaps and aerated with blowers or vacuum pumps) and windrow composting (compost is dumped in long piles (windrows) and occasionally stirred with mobility equipment).
• Windrow composting is frequently regarded to be the most cost-effective technique of composting, however, it may also produce the most fugitive emissions.
• Compost is referred to as “tailored” or “designed” compost in bioremediation since it is made precisely to treat specific pollutants at specific places.
• Excavated contaminated soil is mixed with bulking agents and organic additions such as wood chips, hay, manure, and vegetable (e.g., potato) wastes.
• Compost bioremediation has successfully decomposed or altered several types of contaminants, including chlorinated and non-chlorinated hydrocarbons, wood-preserving chemicals, solvents, heavy metals, pesticides, petroleum products, and explosives.
• The ultimate goal of any remediation operation is to return the land to its pre-contamination state, which often includes revegetation to sustain the treated soil.
• Compost helps to achieve this goal by boosting plant development while also lowering pollution levels.
• Compost is both a soil conditioner and a source of nutrients for a wide variety of plants.

Also read: Functions of Ecosystem: Ecological succession and Homeostasis

Phytoremediation

• Live plants are employed in phytoremediation technologies to clean up contaminated soil, air, and water.
• It is defined as “the use of green plants and associated bacteria, as well as appropriate soil amendments and agronomic approaches, to either contain, eliminate, or render harmless dangerous environmental chemicals.”
• Several plants, such as mustard, alpine pennycress, hemp, and pigweed, have been shown to hyper-accumulate toxins at toxic waste sites.
• Phytoremediation has been effectively utilized to restore abandoned metal mine workings, sites where polychlorinated biphenyls were deposited during production, and mitigation of ongoing coal mine discharges, reducing pollutants in soils, water, and air.
• Phytoremediation efforts around the world have reduced metals, pesticides, solvents, explosives, and crude oil and its derivatives.

Also Read: Plastic Waste Management: Rules and Regulations – ClearIAS

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Benefits of Bioremediation

• The most notable advantage of using bioremediation technology is the favorable environmental impact. In bioremediation, nature is used to repair nature.
• When performed properly by competent employees using specialized bioremediation equipment, this is the safest and least invasive soil and groundwater treatment.
• Bioremediation can treat organic pathogens, arsenic, fluoride, nitrate, volatile organic compounds, metals, and a number of other pollutants like ammonia and phosphates.
•  It effectively removes pesticides and herbicides from aquifers, as well as seawater intrusion. There is no transportation risk: The majority of work is done on-site, reducing transportation concerns.
• Other than a few particular parts, very little equipment is necessary.
• Maintenance and input expenses are both minimal.
• Because poisons are less likely to escape, liability is minimized.
• Compared to incineration and landfilling, there is very little energy consumed.

Disadvantages of Bioremediation

• The main limitation of the bioremediation technique is that it can only treat biodegradable pollutants.
• Researchers have also discovered that the new product formed as a result of biodegradation is sometimes more damaging to the environment than the original component.
• Finally, the technique takes time, especially ex-situ bioremediation, which requires excavation and pumping.

Bioremediation is increasingly commonly used as a treatment for pharmaceutical pollution. However, the key barriers to converting lab-scale research to the field are a lack of understanding of microbial processes in the contaminated niche, pollutant bioavailability, non-native species survival, and a lack of an integrated multi-disciplinary approach.

Article Written By: Atheena Fathima Riyas

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What is Bioremediation? | 4 Real-World Examples of Bioremediation

Environmental pollutants continue to be a major global concern. However, thanks to the evolution of bioremediation technology, we are able to diminish some of the damaging effects that these pollutants have had on our environment. The following 3 examples will help you gain a better understanding of bioremediation and its uses. 

Bioremediation is the process of using biological organisms to break down hazardous substances into less toxic or nontoxic substances. According to Cornell University , “Bioremediation provides a technique for cleaning up pollution by enhancing the same biodegradation processes that occur in nature.” Although bioremediation happens naturally over time, scientists have developed ways to speed up the process through bioremediation technology.

3 Examples of Bioremediation

Sure, you probably learned about bioremediation in your high school science class. But how does it apply to real world situations? There are several branches of bioremediation, each with its own specialized methods and qualifications. It is important to note that while these branches share the same title, bioremediation, they are handled differently and their services do not overlap.

• Crime scene cleanup. Bioremediation in this sense involves the cleanup of blood and bodily fluids that can pose health risks such as hepatitis, HIV, and MRSA. Rather than using standard cleaning agents like bleach or ammonia, crime scene cleaners use enzyme cleaners to rid the scene of harmful substances. Aftermath is a company that specializes in this area of bioremediation and has almost 20 years of experience in the field. Aftermath does not remediate environmental pollutants.
• The cleanup of contaminated soil. Human activity has introduced many toxic substances into the environment’s soil and groundwater. According to an essay published by Montana State University , “During bioremediation, microbes utilize chemical contaminants in the soil as an energy source and, through oxidation-reduction reactions, metabolize the target contaminant into useable energy for microbes.”
• Bioaugmentation. The injection of a small amount of oil-degrading microbes into an affected area.
• Biostimulation. The addition of nutrients to stimulate the growth of innate oil-degrading microbes to increase the rate of remediation.

There are several companies that handle oil spill and contaminated soil cleanup. To learn more about these companies,  this list can help.

Aftermath is committed to providing active leadership and support to the communities we serve through public education. To learn more about crime scene cleanup techniques, browse through some of our blogs .

———- Sources:

http://ei.cornell.edu/biodeg/bioremed/ http://abcnews.go.com/US/deepwater-horizon-oil-spill-years/story?id=30432672 https://microbewiki.kenyon.edu/index.php/Microbial_Response_to_Deepwater_Horizon_Oil_Spill http://waterquality.montana.edu/docs/methane/Donlan.shtml http://www.aftermath.com/blog/biotales/aftermath-helps-decrease-liability-risk-improve-safety-atp-testing/ http://www.aftermath.com/contact-24-7-365/ http://w3.ualg.pt/~jvarela/biotecnol/pdf/biorm-polut.pdf http://www.epa.gov/tio/download/citizens/a_citizens_guide_to_bioremediation.pdf

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Phytoremediation, Bioaugmentation, and the Plant Microbiome

Understanding plant biology and related microbial ecology as a means to phytoremediate soil and groundwater contamination has broadened and advanced the field of environmental engineering and science over the past 30 years. Using plants to transform and degrade xenobiotic organic pollutants delivers new methods for environmental restoration. Manipulations of the plant microbiome through bioaugmentation, endophytes, adding various growth factors, genetic modification, and/or selecting the microbial community via insertion of probiotics or phages for gene transfer are future areas of research to further expand this green, cost-effective, aesthetically pleasing technology—phytoremediation.

Short abstract

A perspective on phytoremediation, its promise, and how it developed into a powerful green technology for cleaning hazardous waste sites.

Introduction

Phytoremediation, the modern use of plants to help clean the environment, began in the early 1980s as a research area with studies on the uptake of metals by hyperaccumulating plants 1 and the toxicity of pesticides to crop and nontarget plants. 2 However, in fact, the history of plants to improve soil quality goes back millennia to Greek and Roman times when fava beans (legumes) were used to provide soil cover and nitrogen fertilization for vineyards. In northern Europe in the 1700s, lupine was planted to improve poor quality sandy soils by adding organic carbon and nutrients via nitrogen fixation and root turnover. 3 Likely, these were the first plants grown for land remediation (phytoremediation) purposes. However, plants were unknown for their potential to remediate contaminated soil and hazardous waste sites until recently.

Considering that most of the land on Earth is covered by plants, it stands to reason that they influence the fate and transport of chemicals and xenobiotic compounds to a large extent. Twenty-nine percent of the Earth’s surface is land, and most of that land, 71%, is habitable (the remainder is glaciated or barren). 4 Of habitable land, plants cover 98%, consisting of 50% in agriculture, 37% in forests, and 11% in shrubs and grassland. 4 Trees and forests account for roughly one-half of all primary production and carbon sequestration. Moreover, because of their enormous biomass, plants represent the greatest oxidative enzymatic power on Earth, with catabolic enzyme systems evolved for respiration, detoxification, and plant protection that can fortuitously biodegrade many toxic organic chemicals.

Remarkably, plants comprise 82% of all living biomass on Earth, 450 billion metric tons of carbon (out of 550 GtC). 5 They capture carbon dioxide from the atmosphere to partially offset human greenhouse gas emissions, and they photosynthesize 100 billion metric tons of carbon per year (100 GtC/year), which serves as food for all living things. It is no wonder that bacteria, fungi, and an entire ecosystem of decomposers reside in, on, and around plants as nature’s primary producers of carbon substrate (food). The next largest category of biomass on Earth is bacteria (∼10% of all living biomass), while human biomass is relegated to a paltry 0.01%. 5

Phytoremediation Background

As authors, we credit many researchers, students, postdoctoral fellows, and consulting firms since the 1980s with unraveling the mysteries of phytoremediation and employing it at thousands of hazardous waste sites. At the University of Iowa, an energetic and creative Ph.D. student, Louis Licht, was the first to see the potential of “phyto”. 6 We called it “vegetative remediation” at the time, for lack of a better moniker. 7 , 8 We worked especially with hybrid poplar ( Populus spp.) as buffer zones along stream margins to intercept nutrients and biodegrade pesticides before they impacted water quality ( Figure ​ Figure1 1 ).

Hybrid poplar plantation and riparian zone buffer strip from the Ph.D. research of Louis Licht at Amana, Iowa. Photo was taken in 1997, approximately 7 years after planting. 6 − 8

Why poplar? Although we employed many different plants, including trees, grasses, and wetland species, most of our research dealt with hybrid poplar trees as model plants because of their incredible versatility and deep-rooting capability. Poplar trees ( Populus spp.) are extremely fast growing (5–8 ft per year, 7.5 tons of dry matter per acre per year) and can flourish geographically from boreal midcontinental regions to subtropical zones. They transpire large quantities of water (up to 100 gal per mature tree each day) when it is available, thus exerting some hydraulic control on soluble soil and groundwater contaminants. Poplars can withstand flooded conditions for short periods (a couple of weeks to months), but generally, their roots need to remain aerobic. This is facilitated by aerenchyma, gas passages through the vascular structure, which allows poplar to transport oxygen downward to maintain root systems and the rhizosphere. Thousands of hybrid poplar cultivars are commercially available throughout the world, mostly developed by traditional plant breeding techniques. They can be clonally propagated. We plant genetically identical male clones because most property owners do not want the airborne “cotton”, which disperses the seeds from female poplar trees. Poplars are among tree species that can undergo coppicing, that is, they can grow back from a cut stump more vigorously, leaving the perennial roots in place and producing a bushier, more productive plant. Lastly, Populus is considered a “model plant” because the entire genome has been sequenced and is mostly annotated. 9 It is also a model plant in the sense that poplars are widely utilized by phytoengineers at actual contaminated sites as the species of choice to transpire water and to facilitate biodegradation of contaminants. Often, nothing will grow at these sites, yet the hardy poplar can be viewed as an instrument of phytoremediation and also as the first step in improving poor soils (adding carbon and nitrogen from root turnover) such that native species can eventually be planted to restore the ecology of the site.

Pesticides in runoff were the first obvious target compounds for research because agrochemical companies had not published the uptake and active mechanisms of herbicides and insecticides for proprietary reasons. 7 , 10 In 1982, Briggs, Bromilow, and Evans studied the physical chemistry for uptake of nonionic organic chemicals by barley. 2 However, it was not until 1994 that researchers realized that plant uptake and metabolism of xenobiotic chemicals was analogous to metabolism in higher organisms. Sandermann proposed the “green liver” model for plant metabolism of organics. 11 Coleman developed the concept further emphasizing three phases of biotransformation and detoxification. Phase I: activation to a more polar metabolite such as hydroxylation by cytochrome P450 monooxygenases. Phase II: conjugation by enzymes such as glutathione- S -transferase (GST), glucuronosyltransferases (UDT), or sulfotransferases (SULT). Phase III: sequestration or compartmentation of the large, conjugated molecule into the plant cell wall or vacuoles out of harm’s way. 12 Discoveries of plant enzymes involved in the degradation of xenobiotics, largely led by phytoremediation research, are today at the front line of research aiming to address the critical concern of nontarget site resistance (NTSR) in weeds. 13

Environmental scientists and engineers had not much considered the power of catabolic enzymes in plants which have evolved through eons for detoxification, plant protection, secondary metabolite formation, and respiration. 14 Biodegradation and catabolism were thought to be the domain of bacteria, fungi, and decomposers—not plants, the primary producers so ubiquitous on Earth. Some doubted that organic xenobiotic chemicals could pass through the membrane and Casparian strip of rooted plants to a sufficient extent to be uptaken and metabolized.

Physical Chemistry and Plant Uptake

Burken and Schnoor began to study the physical chemistry necessary for the uptake of nonionic toxic organic chemicals. 15 They reported that some chemicals were too hydrophobic and not bioavailable to plants for uptake, but there was a “sweet spot” in the range of log K ow 1.5–4. 15 Many chemicals could be uptaken by plants and without phytotoxicity. 16 , 17 However, some chemicals were too toxic or insoluble (e.g., 2,4,6-trinitrotoluene, TNT) to allow a viable application of phytoremediation. 18 In addition, of course, some groundwater contaminants were too deep in the subsurface (>15 ft bgs) for plant roots to access without pumping groundwater up to irrigate the root zone of plants. We concluded that for cleanup to be successful at a site, xenobiotic organic chemicals in the subsurface were required to be somewhat hydrophilic (bioavailable) and not too toxic and that it was necessary for roots to explore the entire contaminated zone for suitable mass transfer to occur.

Microbial Processes in the Rhizosphere vs Plant Uptake

Somewhere along the way, we realized that phytoremediation for many neutral hydrophobic chemicals in soils occurred mainly in the rhizosphere by bacteria, not in the plant itself. Microbes found a suitable habitat in the root zone and were apparently aided by dissolved oxygen, exudates, and secondary metabolites leaked from plants. 19 − 21 Exudates served as auxiliary substrates for cometabolism of aromatics like benzene/toluene/ethylbenzene/xylenes (BTEX), polynuclear aromatic hydrocarbons (PAHs), and long-chain alkanes in petroleum hydrocarbons. 21 , 22 In some cases, exudates were inhibitory to metabolic degraders because they represented a readily bioavailable and degradable carbon source, causing diauxic or catabolic repression in the degradation of target compounds. 23 , 24

Microzones and variable redox conditions allowed both aerobic and anoxic degradation pathways to exist in the same contaminated plant/soil systems for polychlorinated biphenyls (PCBs) phytoremediation. 25 − 27 However, oxygen is critical for the aerobic degradation of total petroleum hydrocarbons (TPH) in the subsurface by phytoremediation. 19 Often, a “smear zone” exists at former refineries and tank farm sites—an oily phase at a depth under low oxygen conditions through which roots cannot penetrate. 28 Aerobic bacteria may express dioxygenase enzymes for the rapid oxidation of petroleum hydrocarbons in the root zone. We have seen hybrid poplar trees grow through pools of weathered surface oil but only if their root systems can track through zones of sufficient oxygen in soil gas to survive. Plant uptake and transformation of BTEX compounds may play a role in TPH phytoremediation, but it is mostly the bacteria in the rhizosphere that do the work. Dominant families include Actinobacteria, Proteobacteria, and Bacteriodetes. Long-term phytoremediation of petroleum hydrocarbons in soils at former tank farm sites has been successfully demonstrated. 29

For several years, we tried to understand exactly what the plants were doing to biodegrade toxic organic chemicals versus the role that associated microbes played. We used various “controls” and attempted to poison the microbes to be able to observe solely plant biodegradation of chemicals in the absence of microbes. These attempts mostly failed because high concentrations of antibiotics or sterilizing agents were necessary to kill bacteria and fungi, but they also proved phytotoxic. Thus, we tried to raise sterile (axenic) plant tissues—callus, root, and shoot cultures. Apical meristems from plants were surface sterilized to serve as pluripotent stem cells (without bacteria and fungi). Despite our best efforts, we could not separate the role of microbes from the plants because it turns out that a whole world of microbes lives within the plant (as endophytes) and cannot be killed by surface sterilization! We found that ubiquitous bacteria and fungi lived in, on, and around plant leaves, shoots, and roots. Some were beneficial to the plant, protecting it from infection by microbes and protozoa, and some were opportunistic pathogens. Plant/microbe associations were often mutualistic, with microbes receiving substrates (food) from the plants and plants receiving minerals, nutrients, vitamins, or growth hormones from the microbes (auxins and cytokinins such as indole-3-acetic acid and cis -zeatin).

Schnoor credits Benoit Van Aken, a postdoctoral and research scientist in our lab, with the “Eureka” moment in ca. 2004, “It’s the ecology, stupid!” That is when we discovered that our axenic shoot cultures (surface sterilized with alcohol) had multiple bacteria and fungi living inside (endophytes). In addition, some of the microbes were novel, never having been seen or documented before. Simply by serendipity, we stumbled upon Methylobacterium populi bacteria living inside hybrid poplar. We walked into the lab one morning to observe, to our surprise, that the shoot cultures displayed a pink-pigmented α-proteobacter shining brightly red on the surface of our agar ( Figure ​ Figure2 2 ). We never thought, as engineers, we would discover a new organism or publish it in a systematics journal, but we did! 30 − 32 Our true discovery was that phytoengineers and scientists must learn to appreciate the entire plant/microbe/rhizosphere ecosystem to fully understand and apply phytoremediation. 33 It is impossible to separate the role of plants versus microbes because they work together—it is all part of a mutualistic ecosystem, the microbiome. We stand transfixed by the remarkable coevolution that has accrued through time and its enzymatic transformative power to degrade xenobiotic contaminants.

Inextricable mutualism between plants and attendant microbes. (A) Axenic poplar shoot culture growing in minimal agar with the leakage of the endophyte, Methylobacterium populi , emanating from inside the plant shoot onto the agar, revealing itself. (B) (Right) Agar plate shows the slow growth of M. populi on minimum agar. (Left) Plate shows how a small piece of living plant tissue (callus cell culture of Populus deltoides x nigra , DN34) provides carbon substrate (fructose) for vigorous growth of the endophyte bacteria, M. populi . In turn, the callus cells receive growth hormones (indole-3-acetic acid and cis -zeatin) from the bacteria.

Still, we lacked a fundamental understanding of plant transformations of toxic organic chemicals because catabolic processes had been ignored for so long. It turned out that hybrid poplar could, by itself, mineralize 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) in plant tissues, although microbial processes by rhizosphere bacteria are likely faster. 34 Plant uptake and biotransformation occur in parallel with rhizosphere biodegradation for many soluble compounds like ethers 1,4-dioxane, methyl- tert -butylether (MTBE), and explosives RDX and 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctane (HMX). 35 − 39 The powerful idea of coring or sampling plant tissues for phytoscreening of subsurface-contaminated zones (phytoforensics) was championed by Joel Burken and his students beginning in 2002. 40 Sometimes, volatile organic chemicals like TCE could be transpired by poplar to the atmosphere, but many alkenes and VOCs are rapidly oxidized in the atmosphere by the cleansing power of hydroxyl radicals. 41 Furthermore, some xenobiotic chemicals can be transformed within the translucent leaves with the aid of the sun, a.k.a. phytophotolysis. 42

Molecular Biology and Phyto

It became important to answer the following question: what genes encode for the plant enzymes necessary to biodegrade toxic organic chemicals? Regulatory authorities needed multiple lines of evidence and a documented explanation for how cleanup occurs in risk-based phytoremediation. Arabidopsis was the first plant whose genome was completely sequenced and appeared on a microarray chip around 2005. 43 Affymetrix ATH1 GeneChip microarrays represented 22 810 genes of 7 Arabidopsis thaliana accessions. 44 It was not long before the complete genome was available (but not well annotated) for Populus trichocarpa . 9 Phytoresearchers began to use plant microarrays and real-time reverse-transcription PCR to determine which genes were up- or downregulated by common contaminants like TCE, BTEX, PCBs, petroleum hydrocarbons, pesticides, and explosive compounds. We then searched for the mRNA transcripts active in biodegradation (transcriptomics) and their translated enzymes (proteomics). Benoit Van Aken led the charge in our laboratory of this pursuit. 45 Many phytoresearchers became involved with the “omics” revolution. We were fortunate to unravel some of the genes upregulated and involved in the transformation of 2,4-D and 2,4,5-T by A. thaliana ( 46 , 47 ) and RDX and TNT by poplar. 48 , 49 Much of this molecular biology research with plants led us to explore improvements in the rhizosphere that could be achieved through bioaugmentation. 50

Bioaugmentation and Growth Factors

Recent studies have explored bioaugmented phytoremediation to enhance the treatment of xenobiotic compounds, including explosives, 32 PCBs, 50 chlorinated solvents, 51 hydrocarbons, 52 pesticides, 53 and heavy metals. 54 , 55 Building on our previous work, 35 , 36 our recent efforts have focused on optimizing bioaugmentation of the poplar microbiome to treat 1,4-dioxane contamination. Because 1,4-dioxane was used as a stabilizer for chlorinated solvents, it is often found comingled with TCE, cis -DCE, TCA, and DCA. 56 At some sites, the 1,4-dioxane plumes can reach for miles, possibly threatening the drinking water of nearby communities. Phytoremediation is well suited for these large and dilute plumes, where traditional remedial techniques are often prohibitively expensive. For example, poplars readily uptake and metabolize TCE into trichloroacetic acid (TCAA), dichloroacetic acid, and trichloroethanol ( Figure ​ Figure3 3 ). 57 Anaerobic zones in the rhizosphere also allow for microbial reductive dechlorination of these solvents. 58 1,4-Dioxane is also readily uptaken by poplar, but due to its high miscibility in water (log K ow = −0.27), the majority of dioxane (76.5 ± 3.9%) is transpired directly to the atmosphere. 35 By bioaugmenting the poplar root zone with dioxane-degrading bacteria, we can increase dioxane metabolism in the rhizosphere and minimize the amount of dioxane transpired to the atmosphere ( Figure ​ Figure3 3 ).

Concept of bioaugmented phytoremediation showing the synergy between the two technologies deployed together for the biodegradation of 1,4-dioxane and co-occurring chlorinated solvents, including trichloroethylene (TCE), cis -dichloroethylene (cDCE), 1,1,1-trichloroethane (TCA), and dichloroethane (DCA).

During this work, we confirmed that through uptake and evapotranspiration, poplar trees alone can achieve low dioxane concentrations (∼1 μg/L) in the laboratory with simulated contaminated groundwater. We also demonstrated that bioaugmenting the rhizosphere with dioxane-metabolizing organisms, including Pseudnocardia dioxanivorans CB1190 and Mycobacterium dioxanotrophicus PH-06, speeds the treatment of dioxane. 59 CB1190 can utilize root extract as an auxiliary carbon source, making it well equipped to colonize the poplar root zone. 36 However, the root extract’s presence also caused catabolite repression in CB1190, slowing dioxane metabolism. In contrast, PH-06 cannot utilize root extract but was not sensitive to catabolite repression.

We also evaluated dozens of enrichment cultures and other dioxane-metabolizing organisms as bioaugmentation candidates for the poplar rhizosphere. We hypothesized that these strains required growth factors (i.e., amino acids or vitamins) not typically included in minimal microbial media. Through another stroke of serendipity, we discovered Rhodococcus ruber strain 219 rapidly grows on and degrades dioxane when supplemented with thiamine (vitamin B1). 60 This strain had been previously reported only to grow very slowly on dioxane. 61 In addition, when grown with thiamine, the strain had the fastest kinetics for dioxane metabolism reported to date. This discovery also underscored the complex syntrophic relationships between plants and microbes in the rhizosphere. Furthermore, many growth factors may be supplied by rhizospheric bacteria, fungi, or root exudates. 62 − 66 Harnessing these syntrophic relationships is an important emerging area of research in bioaugmented phytoremediation. Engineering the microbiome of the plant rhizosphere is key to further progress and wider application of bioaugmented phytoremediation.

Genetically Modified Plants, Bacteria, and Editing the Microbiome

Recent efforts have been made to bolster phytoremediation by optimizing plant cultivars through either conventional (traditional crossbreeding) or engineered (transgenics) techniques. The selective cultivation and screening of tree hybrids (e.g., Populus and Salix spp.) has shown promise in identifying genotypes and/or superior clones to maximize tree survival and remediation performance. This work can assist in selecting varieties best suited for the conditions and contaminants present at a site. 67 , 68 Alternatively, transgenic plants have been produced by introducing exogenous genes to improve the uptake or metabolism of contaminants. For example, work by Doty et al. enhanced the treatment of TCE by inserting cytochrome P450 monooxygenases into poplar via a bacterial vector. 69 Furthermore, Bruce et al. engineered Arabidopsis , tobacco, switchgrass, and wheatgrass to express a bacterial gene for phytoremediation of RDX. 70 − 74 Transgenic plants have also been used to improve plant tolerance, uptake, and treatment of various metals, including lead, cadmium, mercury, and selenium. 75 − 78 In addition, transgenic plants have been developed to excrete increased root exudates, in turn supporting increased biodegradation in the root zone. 79

Another approach to enhance phytoremediation is through the use of genetically engineered bacteria. Successful bioaugmentation of the rhizosphere often hinges on strain survival postinoculation. This is often most successful if the bacteria are well adapted to the plant’s rhizosphere. 80 However, isolating endophytic or rhizospheric bacteria capable of transforming contaminants has proven difficult. An alternative strategy is to engineer endophytic strains to express contaminant-degrading genes. This approach has been used to insert a toluene monooxygenase into plant-growth-promoting bacteria, Burkholderia cepacia VM1468. 81 Subsequent inoculation into the poplar rhizosphere and exposure to toluene improved plant growth, decreased phytotoxicity, and enhanced toluene degradation in the root zone. However, upon closer investigation, the researchers could not detect or recover the initially inoculated strains. Instead, the inserted gene had horizontally transferred to various other endophytic strains. This remarkable unintended result highlights a potential added benefit to bioaugmented phytoremediation. One of the strains which received the horizontally transferred toluene gene has also been used to enhance degradation of TCE in the poplar rhizosphere. 82 , 83 Genetically modified endophytes have also been used to improve tolerance and uptake of nickel. 84

An alternative strategy to improve inoculated strain survival is to engineer the plant microbiome before inoculation. Because the plant microbiome can support a highly diverse microbial community, this can increase competition for inoculated strains. 85 For example, desirable bioaugmented strains may not effectively colonize the rhizosphere due to competition for required resources (e.g., carbon source, oxygen, growth factors). To better understand plant–microbe interactions, researchers have utilized metagenomic analyses to ensure the colonization and survival of inoculated strains. 86 Other techniques suggest altering selective pressures to improve strain survival. 85 Recent progress has also been made in “niche clearing” using bacteriophages. 87 Employing this technique, researchers can perform precise microbiome editing, allowing for the suppression of specific microbial activities, which may open niches for inoculated strains. Furthermore, this technique may improve various plant traits, such as increased drought and disease resistance. Other emerging technologies, such as specific gene editing using CRISPR, will streamline the engineering of plants, endophytes, and the plant microbiome, opening new frontiers for phytoremediation research.

The future outlook for phytoremediation and its various off-shoots is indeed bright. Applications to emerging contaminants seem likely, such as per- and polyfluoroalkyl substances (PFAS), brominated and organophosphate flame retardants, synthetic musks and other personal care product ingredients, industrial chemical additives, stabilizers, adjuvants, and hormonally active compounds. Natural treatment systems for water and wastewater (green infrastructure) with low carbon footprints are expanding rapidly and have gained the confidence of consulting engineers. Low-impact development (LID) to slow down stormwater, which improves infiltration and groundwater recharge, often employs plant-based strategies. Constructed wetlands, floating mats, rain gardens, bioswales, green roofs, and riparian zone buffer strips are gaining acceptance for improvement of water quality and LID. Increasingly, architects and landscapers utilize green walls on buildings and plants for indoor air filtration and purification systems. Phytoremediation can clean water, air, and soil in a cost-effective, natural green system.

Probably the greatest environmental challenge facing humanity is how to stabilize the chemistry of our atmosphere and control climate change. Massive plantations of native trees and grasses on previously degraded marginal lands are a potent and cost-effective climate solution. It is already underway as a Great Green Wall by China in the Gobi Desert and as an African Union Project in the Sahel in Sub-Saharan Africa. Replanting temperate and boreal forests worldwide could remove CO 2 from the atmosphere (negative emissions) and restore organic carbon to soils. When forests reach climax, they could be harvested for products like biochar to sequester carbon long term as a soil conditioner and applied on land to facilitate replanting and regrowing the forests as a long-lasting solution.

Acknowledgments

J.L.S. gratefully acknowledges the ACS Division of Environmental Chemistry, Environmental Science & Technology , and Environmental Science and Technology Letters for the 2022 Outstanding Achievements in Environmental Science & Technology Award given “in recognition of pioneering research on phytoremediation and water quality engineering science”. We also thank SERDP/ESTCP for grants ER-2719 on “Utilizing the Plant Microbiome to Degrade 1,4-Dioxane and Co-Contaminants,” and ER21-5096 on “Bioaugmented Phytoremediation to Treat 1,4-Dioxane Contaminated Groundwater” and the Center for Global and Regional Environmental Research at the University of Iowa, which helped to support the authors while conducting this research. Finally, we thank three reviewers for their excellent comments, which have improved the manuscript significantly.

Jerald Schnoor is the Allen S. Henry Chair in Engineering, Professor of Civil and Environmental Engineering, Professor of Occupational and Environmental Health, and Co-director of the Center for Global & Regional Environmental Research at the University of Iowa. His research interests include phytoremediation, water sustainability, and climate change. He is a member of the US National Academy of Engineering, elected in 1999 for “research and engineering leadership in development, validation, and utilization of mathematical models for global environmental decision-making”. He served as Editor-in-Chief of Environmental Science & Technology , 2002–2014, and as the founding Editor-in-Chief of Environmental Science and Technology Letters , 2012–2014.

The authors declare no competing financial interest.

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