Digital class 8. Biological methods for the remediation of contaminants in water and soils

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Biological methods for the remediation of contaminants in water and soils


Welcome to this last session of the Soil and Water Environmental Engineering course, I am very pleased to meet you in this session, in which we will close with the content of the course reviewing biological strategies for the removal of contaminants in water and soil.

These biotechnologies have advantages over physical and chemical methods since they are environmentally sustainable and this increases the degree of acceptance in society, in addition to being cheaper. However, they have limitations regarding the range of contaminants to which it can be applied and the time it takes to decontaminate the sites.

I invite you to know the biological methods for the remediation of water and soil.

Content developement

Natural attenuation

Natural attenuation also called passive or intrinsic recovery, is being used increasingly as it is a low-cost method of reclaiming contaminated soils and water (Mulligan and Yong, 2004). However, although it can be used in a wide variety of places, it is rarely applied individually since it is a much slower treatment than those that use engineering technologies. Natural abatement consists of using natural processes to contain the spread of pollution from chemical spills and reduce the concentration and quantity of toxic agents in contaminated areas. The natural processes that are invoked for recovery are biological, such as aerobic, anaerobic, and co-metabolic biodegradation, and physical-chemical processes such as volatilization, dispersion, dilution, radioactive decay, chemical, and biochemical stabilization, precipitation, and sorption of organic matter particles and soil clays. The success of each natural attenuation process will depend on the geological, hydrological, and microbiological characteristics of the affected area (Mulligan and Yong, 2004).

The reactions and transformations that take place during abiotic processes depend on the physicochemical properties of the pollutant and the soil and, for both inorganic and organic substances, including hydrolysis and oxidation-reduction reactions, formation of double bonds, and dehydrohalogenation. In addition to the biodegradation of organic compounds, microorganisms can influence the sorption of organic compounds and metals in soils and their products can even act as metal chelators in contaminated soils (Mulligan and Kamali, 2003).

Natural attenuation is mainly applied to treat BTEX compounds (benzene, toluene, ethylbenzene, and xylene) and more recently chlorinated hydrocarbons (Chiu et al., 2013). Other contaminants that can potentially be removed include pesticides (Pimmatta et al., 2013) and inorganic compounds (Park et al., 2016).

For natural attenuation to be effective, constant monitoring is necessary for as long as these natural processes are operating to eliminate risks to the environment and human health.

For this, it is very useful to carry out models that can predict the behavior and transport of pollutants (Agah et al., 2013).


If indigenous microbial populations are not capable of biodegrading toxic organic compounds, specific microorganisms that do carry it out can be added to the soil, a process known as bioaugmentation. The bioaugmentation includes the ex situ stimulation of indigenous microbial populations and their subsequent reinjection in the contaminated area, the addition of non-indigenous microorganisms to the soil that are capable of biodegrading or co-metabolizing the contaminating compounds, and the addition of genetically modified microorganisms with additional catabolic genes. specific to degrade (Tyagi et al., 2011)

One obstacle in the design of genetically modified organisms (GMOs) is bureaucratic problems when it comes to obtaining permits to use them in the environment, rather than the limitations when it comes to making genetic modifications.

GMOs have been designed, among others, to monitor the presence of non-indigenous bacteria by placing biomarkers on them, to measure the bioavailability of contaminants using biosensors (Jansson et al., 2000), and to degrade contaminants such as PCBs (Symons and Bruce, 2006) ), polycyclic aromatic hydrocarbons, chloroaromatics, explosives and other organic pollutants (Pieper and Reineke, 2000). To eliminate the risks associated with the use and activity of GMOs in the environment, some authors have even designed cell death strategies to program these organisms to commit suicide after decontamination (Pandey et al., 2005).

In any case, the use in biodegradation of genetically modified microorganisms is a wide field still to be explored and is not yet being used in large-scale in situ bio-recovery trials. Recently, the joint use of biodegradation and other soil reclamation techniques is opening up new fields of application.

Biotechnology is very important for science, since thanks to its studies, it offers great results and helps to improve and treat certain issues related to the environment.

On the other hand, environmental biotechnology helps reduce or counteract the effects of pollution on the environment; providing various solutions to problems that exist or may arise.

The following are environmental biotechnologies used to treat contaminated sites; These technologies are complementary to the previously reviewed treatments, representing an attractive alternative with high pollutant removal values.


When biodegradation cannot be carried out naturally because the microorganisms do not have the essential elements for it in the contaminated area, the intervention of engineering actions aimed at stimulating microbiological activity is required. Thus, assisted biodegradation accelerates biodegradation reactions, facilitating microbial growth and optimizing the environmental conditions of the area where microorganisms must carry out their decontamination function. For this approach to work, the contaminant must not be recalcitrant, that is, the microorganisms must have sufficient genetic and physiological capacity to degrade the substance.

Fundamentally, the stimulation of natural microbial activity (biostimulation) is carried out by controlling parameters such as redox potential and humidity conditions, and the addition of oxygen or other electron acceptors (such as nitrate or sulfate) and nutrients such as nitrogen and phosphorus. However, the addition of nitrogen and phosphorus is not strictly necessary because there are usually high concentrations of ammonia in most contaminated soils, and the recycling of phosphorus between soil, water, and bacteria are usually sufficient to support limited microbial activity (Kanissery and Sims, 2011).


Phytoremediation is an emerging technology that uses the ability of certain plant species to survive in environments contaminated with heavy metals and organic substances and at the same time extract, accumulate, immobilize or transform these pollutants from the soil. The plants used in phytoremediation have constitutive and adapted mechanisms to tolerate or accumulate a high content of metals in their rhizosphere and their tissues. The success of this treatment is controlled by the selection of the appropriate plant species to recover a given soil, as well as the careful selection of amendments (organic matter, chelating agents, lime, etc.) that allow to improve the properties of the soil and promote the survival and growth of plants.

Phytoremediation is a natural, clean, and economical treatment, alternative to other more invasive physical and chemical processes. According to Vázquez-Núñez et al. (2021), the following basic processes of containment (phytostabilization or phyto-immobilization) or elimination (phytoextraction, phytodegradation, phytovolatilization, and rhizofiltration) of pollutants can be distinguished by which plants can be used in the recovery of contaminated soils and water:

Microalgae and diatoms

Microalgae are a very diverse group of microorganisms classified into more than 50,000 species delimited by their microscopic features, which inhabit various aquatic environments (Ebenezer et al., 2012). Microalgae are photosynthetic and contain some pigments such as chlorophyll, for example. Besides being polyphyletic and eukaryotic, they can grow autotrophically or heterotrophically, taking advantage of a diversity of organic matter. They have a very efficient system for the bioconversion of light energy as it has a great fixation to the 𝐶𝑂2 with their own biochemical purposes (Santos et al., 2014). 

These microorganisms have a high content of proteins, lipids rich in unsaturated fatty acids and carbohydrates, among other important compounds at an industrial level (Galarza, 2019). Microalgae have very extensive potential and versatility that constitute genetic resources for biodiversity and biotechnology studies in the aspect of covering and being able to solve many current problems in various areas of the industry such as food, pharmaceutical, aquaculture, among others. The interest that has been generated about them and their applications are revolutionary. Nowadays it is even possible to see the existence of companies directed entirely to the development and implementation of these microorganisms on a large scale.

The use of microalgae in water bioremediation includes its purification capacity, known as phytoremediation, where the kinetics of nutrient consumption of these microorganisms are used. 

In the same way, the elimination of other pollutants such as drugs, heavy metals are achieved and greater detoxification of the wastewater is achieved, unlike the usual technologies used. 

In wastewater treatment, the aim is to eliminate the biochemical oxygen demand (BOD), suspended solids, nutrients, coliforms, and toxicity (Hernández-Pérez and Labbé, 2014).

Diatoms, on the other hand, are highly used in the monitoring of water quality, mainly in rivers with heavy metal contamination because in addition to being a type of species that is very easy to collect, they have a predictable and fast response to environmental alterations. in which they are with which you can keep track and control. 

There are studies in which it has been proven that diatoms are good indicators of changes in bodies of water, correlating their deformations with physical-chemical parameters, the eutrophication/pollution index, and based on the study of these microorganisms, that is, morphology. that they present under normal conditions or the growth rate they have.

  • In addition to the technologies presented, some are attractive due to the results obtained and the versatility with which they can be applied.
  • These new biotechnologies are the result of the hybridization of more than one environmental technology with the incorporation of biological components, i.e., living beings, biomolecules, or compounds similar to these.
  • Although the study of these biotechnologies indeed deserves a separate course, we consider it necessary that you know them in the fundamentals, with the applications, and under particular conditions.
  • Below we include a resource where you can learn about innovative biotechnologies, applications, and the most outstanding results. The document is not limiting and may be useful to start with the specific study of environmental biotechnologies if that is your interest.
  • Environmental biotechnologies are an attractive alternative given their versatility and efficiency in removing pollutants. Global interest in the development and application of eco-technologies has grown greatly in recent years, especially for those that are economical and from which by-products with high economic value can be obtained, favoring the development of sustainable practices and a circular economy. that allow promoting bioeconomies.
  • And you, did you know these biotechnologies applied to the environment? What do you think are the advantages compared to conventional technologies? Did you propose any biotechnology for the recovery of impacted sites? Under what conditions? In what particular cases?
  • In addition to the previous reflection, think about What biological resources that exist in your immediate environment could be used for environmental remediation processes? and, more importantly, what knowledge -new or previous- can you integrate into a proposal to attend impacted sites?
  • Surely the answer to these questions will be the beginning of new searches to solve environmental problems.


Environmental biotechnology has emerged as an affordable alternative for treating environmentally impacted sites. Various technologies are based on the use of organisms and biomolecules that are the product of their metabolism, to decontaminate soil and water.

Increasingly, there are new comprehensive proposals that allow expanding the range of pollutants to be removed, allowing the entry of these technologies, creating a balance in the use of traditional technologies with biological ones.

It is still necessary to have more studies in the field to ensure its proper functioning in varied environmental conditions and thus facilitate its access to the global market.

Information sources

Kaushik, G. (Ed.). (2015). Applied environmental biotechnology: Present scenario and future trends. Springer India.

Oves, M., Khan, MZ, & Ismail, IM (Eds.). (2018). Modern age environmental problems and their remediation. Springer International Publishing.

Anjum, NA, Pereira, ME, Ahmad, I., Duarte, AC, Umar, S., & Khan, NA (Eds.). (2012). Phytotechnologies: remediation of environmental contaminants. CRC Press.

Nayak, SK, Dash, B., & Baliyarsingh, B. (2018). Microbial remediation of persistent agro-chemicals by soil bacteria: an overview. Microbial Biotechnology, 275-301.

Sayler, GS, Sanseverino, J., & Davis, KL (Eds.). (2012). Biotechnology in the sustainable environment (Vol. 54). Springer Science & Business Media.

Evans, GG, & Furlong, J. (2011). Environmental biotechnology: theory and application. John Wiley & Sons.

Mulligan, CN, & Yong, RN (2004). Natural attenuation of contaminated soils. Environment International, 30 (4), 587-601.

Mulligan, CN, & Kamali, M. (2003). Bioleaching of copper and other metals from low-grade oxidized mining ores by Aspergillus niger. Journal of Chemical Technology & Biotechnology: International Research in Process, Environmental & Clean Technology, 78 (5), 497-503.

Chiu, HY, Hong, A., Lin, SL, Surampalli, RY, & Kao, CM (2013). Application of natural attenuation for the control of petroleum hydrocarbon plume: Mechanisms and effectiveness evaluation. Journal of Hydrology, 505, 126-137

Pimmata, P., Reungsang, A., & Plangklang, P. (2013). Comparative bioremediation of carbofuran contaminated soil by natural attenuation, bioaugmentation, and biostimulation. International Biodeterioration & Biodegradation, 85, 196-204

Park, JH, Han, YS, & Ahn, JS (2016). Comparison of arsenic co-precipitation and adsorption by iron minerals and the mechanism of arsenic natural attenuation in a mine stream. Water Research, 106, 295-303.

Agah, A., Ardejani, FD, & Ghoreishi, H. (2013). Two-dimensional numerical finite volume modeling of processes controlling distribution and natural attenuation of BTX in the saturated zone of a simulated semi-confined aquifer. Arabian Journal of Geosciences, 6 (6), 1933-1944.

Tyagi, M., da Fonseca, MMR, & de Carvalho, CC (2011). Bioaugmentation and biostimulation strategies to improve the effectiveness of bioremediation processes. Biodegradation, 22 (2), 231-241.

Jansson, JK, Björklöf, K., Elvang, AM, & Jørgensen, KS (2000). Biomarkers for monitoring efficacy of bioremediation by microbial inoculants. Environmental pollution, 107 (2), 217-223.

Symons, ZC, & Bruce, NC (2006). Bacterial pathways for degradation of nitroaromatics. Natural product reports, 23 (6), 845-850.

Pandey, G., Paul, D., & Jain, RK (2005). Conceptualizing “suicidal genetically engineered microorganisms” for bioremediation applications. Biochemical and biophysical research communications, 327 (3), 637-639.

Kanissery, RG, & Sims, GK (2011). Biostimulation for the enhanced degradation of herbicides in soil. Applied and Environmental Soil Science, 2011.

Edgar, VN, Fabián, FL, Mario, PCJ, & Ileana, VR (2021). Coupling Plant Biomass Derived from Phytoremediation of Potential Toxic-Metal-Polluted Soils to Bioenergy Production and High-Value By-Products — A Review. Applied Sciences, 11 (7), 2982.

Ebenezer, V., Medlin, LK, & Ki, JS (2012). Molecular detection, quantification, and diversity evaluation of microalgae. Marine Biotechnology, 14 (2), 129-142.

Santos, CA, & Reis, A. (2014). Microalgal symbiosis in biotechnology. Applied microbiology and biotechnology, 98 (13), 5839-5846.

Galarza, VO (2019). Carbohydrates and proteins in microalgae: potential functional foods. Brazilian Journal of Food Technology, 22

Hernández-Pérez, A., & Labbé, JI (2014). Microalgae, cultivation and benefits. Journal of Marine Biology and Oceanography, 49 (2), 157-173.