Classification, techniques and cellular processes of microbial remediation

In the previous article, the concept of bioremediation was introduced as an answer to the rising instances of environmental pollution. Although the act of bioremediation can be performed by a wide range of organisms including plants, fungi and microorganisms. Microbial remediation has proven to be the most advantageous and efficient process owing to its wide span of metabolic pathways and enzymes. In this article, bioremediation as a process has been classified, on the basis of application and cellular level processes by the microorganisms. 

Microbial remediation can be classified on the basis of the scale of the bioremediation activity. The large scale practical applications also known as in-situ bioremediation and the cellular level processes of the microorganisms are involved. Practical applications of microbial remediation deals with different techniques of undertaking bioremediation at the site of contamination, the cellular level processes of bioremediation involves various metabolic pathways that microbes use in remediating or transforming the contaminant molecules.

Factors influencing microbial remediation

Bioremediation methods involve designing of cost-effective and reliable treatment plans of a contaminated site on the basis of environmental and nutrient or pollutant factors (1). Furthermore, these factors (shown below) influence the cellular processes of the microorganisms involved and since suitable environmental conditions is required for effective microbial growth at the site, bioremediation approaches often require varying levels of environmental manipulation for success (2).

Factors Conditions necessary
Contaminant or pollutant Optimal concentration and high bioavailability for microbial growth and remediation.
Site characteristics
pH 6.5 – 8.0
Temperature Based on type of microorganism involved (15°- 45°C)
Moisture content 12-25%
Oxygen content More than 0.2 mg/L or 10% minimum air filled pore space
Redox Potential Optimal Levels of Electron Acceptors (iron oxides, nitrates, sulfates etc.) and/or Electron Donors (organic compounds)
Nutrients Optimal levels of Nitrogen, Carbon, Phosphorus and Oxygen as well as trace elements
Soil properties Low clay or silt content

Factors influencing bioremediation processes, (Source: Sharma 2012)

In-Situ microbial bioremediation

In-situ bioremediation has been classified into multiple approaches on the basis of the extent of human intervention and additional nutrient requirement (3). The table below shows a comparison of different bioremediation approaches on the basis of cost, area of contamination and degree of human intervention. Intrinsic bioremediation refers to naturally occurring processes as a result of existing microorganism population at the site of contamination and requires no human intervention (4). Where naturally occurring bioremediation can be time consuming. Acceleration of the metabolic processes and supplementing microbial growth by addition of oxygen by bioventing or biosparging or nutrients by biosimulation at the site of contamination is advantageous (4).

The process of biosorption has been defined by Kotrba (2012) as a property of living and dead biomass to bind and concentrate inorganic and organic compounds. It involves two processes:

  1. Passive biosorption; property shown by dead biomass and fragments of cells or tissues.
  2. Active biosorption; active sorption or uptake of compounds by live cells (5,6).

This type of bioremediation process requires addition of dead biomass or specific strains of microbes at the site of contamination in order to encourage sorption of the contaminant. For the purpose of transforming the pollutant to a less toxic form, bioaugmentation technique is applied. Furthermore, it involves introduction of pollutant degrading microbes in the contaminated environment for supplementing the indigenous population as well as speeding up the degradation process (7).

Bioremediation strategy Area of contamination Human involvement Cost
Intrinsic bioremediation Large None Minimal to none
Bioventing and biosparging Medium High High
Biosimulation Medium Initial phase Medium-high
Biosorption (passive) Large Initial phase Low
Biosorption (active) Medium Medium High
Bioaugmentation Medium Initial phase High

Types of in-situ bioremediation strategies

Cellular microbial bioremediation

At the cellular level, the process of microbial remediation can occur in multiple ways based on the chemical nature of the pollutant. The microorganisms undertake metabolically dependent or independent pathways of remediating the contaminant compound. The physico-chemical process of biosorption has been categorized into different processes like (8):

  1. Native biosorption,
  2. Complexation (Enzymatic or Extracellular)
  3. Precipitation

Native biosorption is the process of passive adsorption of charged compounds onto the microbial surface as a result of electrostatic interaction. It occurs passively without any microbial energy loss. Complexation and precipitation both occur in an actively dependent manner. Precipitation occurs when there is change in speciation of the pollutant as a result of its interaction with a precipitant or by changing levels of environmental pH. It leads to the formation of an insoluble pollutant compound that precipitates on or around the microbial surface (9). The most common examples of precipitants released by microbes are phosphates, carbonates and sulfides produced and released by bacteria for precipitation of soluble metal ions from their surrounding matrix (4,9).

Different metabolism,iIndependent and dependent pathways of microbial remediation

                Different metabolism pathways in microbial remediation

Complexation of pollutants

Complexation of pollutants can be enzyme dependent on microbial surface or through extracellular complexation. Microbes often secrete extracellular compounds such as extracellular polymeric substances (EPS), slime or capsule. It interacts with certain pollutants and immobilizes or precipitates them (8). For example extracellular polymeric substances commonly secreted by microbes helps in biofilm formation. It has the ability to entrap metal ions as well as particulate metal precipitates leading to their immobilization and separation from the environment (10).

Furthermore, microbial remediation by cell surface enzymatic complexation helps in breaking down of the pollutant or direct transformation of the pollutant in the environment without entering the cell (11). This metabolically dependent enzymatic bioremediation happens in the cell by transformation to a less toxic compound or bioassimilation (12).

Consequently, microbial remediation techniques can be selected and applied on the basis of:

  1. Overall costs.
  2. The extent of human intervention possible.
  3. The pollutant and the indigenous microbial community at the site of contamination.

Introduction of specific strains of microorganisms or genetically modified organisms (GMOs) at the site of contamination will require thorough pilot testing as well as review of unpredictable changes in the local ecosystem.



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Chandrika Kapagunta

Chandrika Kapagunta

Research Analyst at Project Guru
Chandrika is a nature enthusiast with special love for the marine world. Her Master’s degree in Marine Biotechnology and Scuba Diving experience has made her a strong advocate of environment and marine conservation, especially through bioremediation. She believes in finding solutions of everyday human problems in nature, be it medicines, technology or philosophy. Having worked as a volunteer at The Bombay Natural History Society and as a Senior Research Fellow at Central Institute of Fisheries Education, she has had exposure to the current state of the academic research, specifically in the field of environmental biotechnology.
Chandrika Kapagunta

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