Factors affecting bioremediation

Various factors affect bioremediation, such as contaminant concentration, availability of the microbes, and environmental factors such as temperature, pH, the presence of oxygen or other electron acceptors, soil type, and nutrients status (Vidali et al. 2001, Parsons Corporation 2004, ICSCS 2006). Although the microbes exist in contaminated soil, they cannot be there in the numbers needed for bioremediatiou of the site. Their growth and activity must be stimulated, which usually requires the addition of nutrients and oxygen to help indigenous microorganisms (ESTCP 2005, Naik et al. 2012).

Nutrients are the vital building blocks of the microbe’s life and enable them to create the necessary enzymes to break down the contaminants (Shamra et al. 2018). Carbon is an essential element of living forms of life and is required in higher amounts than other elements. In addition to hydrogen, oxygen, and nitrogen, carbon constitutes about 95% of the weight of cells. Phosphorous and sulfur contribute 70% of the remainder (Boopathy 2000). The nutritional demand for carbon to nitrogen ratio is 10:1, and carbon to phosphorous is 30:1 (Vidali et al. 2001). Several factors’ optimum environmental conditions for the degradation of contaminants are given below in Table 2. Some of the additional information about important factors that affect biorenrediation have also been explained below.

Table 2. Optimum environmental conditions for the degradation of contaminants.


Condition required for microbial activity

Optimum value for oil degradation

Soil moisture

25-28% of water holding capacity


Soil pH



Oxygen content

Aerobic, minimum air-filled pore space of 10%


Nutrient content

N and P for microbial growth

C:N:P= 100:10:1

Temperature (°C)




Not too toxic

Hydrocarbon 5-10%

Heavy metals

Total content 2000 ppm

Type of soil

Low clay or silt content

Source: Vidali et al. (2001).

3.1 Contaminant concentrations

Pollutants instantly influence the microbial activity in the soil. When levels are too high, then they may have toxic effects on the existing bacteria. In contrast, low contaminant concentration may prevent the induction of bacterial degradation enzymes (ESTCP 2005, Shamia et al. 2018).

3.2 Contaminant bioavailability

The contaminant bioavailability depends on the degree to which they sorb to solids by molecules in contaminated areas and other factors such as whether contaminants are present in noil-aqueous phase liquid (NAPL) form. Bioavailability for microbial reactions is lower for pollutants that are more actively sorbed to solids, embedded in molecules’ matrices of contaminated media, likewise widely diffused in macropores of soil and sediments, or are present in NAPL form (ICSCS 2006).

3.3 Site characteristics

The location of the contaminated area has a significant impact on the effectiveness of any bioremediation approach. Site environmental conditions essential to consider for bioremediation applications include pH, temperature, water content, nutrient availability, and redox potential.

3.3.1 pH

pH influences the solubility and biological availability of nutrients, metals, and other constituents for optimal bacterial growth (ESTCP 2005).

3.3.2 Redox potential and oxygen content

Both the factors typify oxidizing or reducing conditions. Redox potential is influenced by the appearance of electron acceptors such as nitrate, manganese oxides, iron oxides, and sulfate (ICSCS 2006).

3.3.3 Nutrients

They are needed for microbial cell growth and division (ESTCP 2005). Suitable amounts of minimum nutrients for microbial growth are generally present, but nutrients can be supplied in a useable form or via an organic substrate supplement (Parsons Corporation 2004), which also serves as an electron donor, to stimulate bioremediation.

3.3.4 Temperature

It directly influences the rate of microbial metabolism and, consequently, microbial activity in the environment. The biodegradation rate, to an extent, increases with rising temperature and decreases with reducing temperature (ESTCP 2005).

Role of plant roots and associated microbes to clean contaminated sites

The root-associated microorganisms establish a synergism with plant roots and can help the plant to absorb nutrients improving plant performance and, consequently, the quality of soils (Barea et al. 2002, Yang et al. 2009, Coelho et al. 2015). Plants growing in metal contaminated soils harbor a diverse group of microorganisms that can tolerate high concentration of hearty metals and provide some benefits to both the soil and the plant. Several microorganisms are used in hearty metal remediation of contaminated sites (Barea et al. 2002, Verma et al. 2006, Dong et al. 2013). Among the microorganisms involved in hearty metal phytoremediation, the rhizospliere bacteria deserve attention because they can directly improve the phytoremediation process by changing the metal bioavailability through altering soil pH, the release of chelators (e.g., organic acids, siderophores) and oxidation/reduction reactions (Yang et al. 2009, Rajkumar et al. 2012).

Various metabolites (e.g., 1-aminocyclopropane-l-carboxylic acid deaminase, indole- 3-acetic acid, siderophores, organic acids, etc.) produced by plant root-associated microbes (e.g., plant growth-promoting bacteria, mycorrhizae) have been proposed to be involved in many biogeochemical processes operating in the plant root or rhizospliere (Barea et al. 2002). The salient functions include nutrient acquisition, cell elongation, metal detoxification, and alleviation of biotic/ abiotic stress in plants. Plant root rhizospliere microbes accelerate metal mobility or immobilization. Plants and associated microbes release inorganic and organic compounds possessing acidifying, chelating, and reductive power (Meagher 2000, Kuiper et al. 2004, Rajkumar et al. 2012).

These functions are implicated to play an essential role in plant metal uptake. Overall, the plant root-associated beneficial microbes enhance the efficiency of the phytoremediation process directly by altering the metal accumulation in plant tissues and indirectly by promoting the shoot and root biomass production (Rajkumar et al. 2012). Similarly, the metal-tolerant mycorrhizal

Table 3. Microbial strains characterized by their potential to mobilize metals to alter the plant metal uptake.

S. No.

Microbial metabolites/reactions


Microbial effects oil metals and its uptake by plants


Siderophores (Pyoverdme, pyochelin and alcaligm E)

Pseudomonas aeruginosa, Pseudomonas fluorescens

Enhanced Cr and Pb uptake by plants by facilitatuig their mobilization


Organic acids

Oxalic acid, Tartaric acid,

Formic acid Acetic acid

Burkholderia cepacia Pseudomonas aeruginosa

Solubilized ZnO, ZnC03 and CdC03 Solubilized ZnO and Zn3(P04)2


Biosurfactants Di-rhamnohpid

Pseudomonas aeruginosa BS2

Mobilized Cd and Pb


Polymeric substances and glycoprotem

Azotobacter spp.

Immobilized Cd and Cr and decreased then- uptake by Triticum aestivum


Oxidation and reduction reaction

A consortium of oxidizing sulfur bacteria Stenotrophomonas maltophilia

Increased bioavarlabrlity of Cu Reduced soluble and harmful Se (AO to msoluble and unavailable Se (0) and thereby decreased the plant Se uptake



Brevibacillus sp. B-I Serratia sp. MSMC541

Decreased the concentration of Zn in shoot tissues of Trifolium repens Reduced translocation of As, Cd, and Cu from roots to shoots m Lupinus luteus

Source: Rajkumar et al. (2012).

fungi have also been frequently reported in hyperaccumulators growing in metal-polluted soils, indicating that these fungi have evolved a heavy metal tolerance and that they may play a significant role in the phytoremediation. Table 3 given above summarizes the published studies on plant roots and associated microbes that clean contaminated soil through metabolites/actions on heavy metal mobilization/immobilization and their uptake by plants.

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