Bioremediation process in soil

Bioremediation refers to a microbial process applied to remediate contaminated media, including water, soil, and sediments, by optimising environmental conditions to stimulate the growth of microorganisms, thereby degrading the target pollutants. Bioremediation of a contaminant can be achieved directly through enzymatic reactions by stimulating and bioagumenting the microorganism or indirectly through non-enzymatic reactions by the microbially-induced changes in soil properties impacting contaminant degradation.

The direct enzymatic bioremediation process covers a number of reactions including mineralisation, co-metabolism, polymerisation, and bioaccumulatiou (Luo et al. 2014). The in-direct non-enzymatic reactions include microbially-induced changes in pH and redox potential that impact the abiotic and biotic degradation processes. In the mineralization process, the contaminants can serve as a substrate for microbial growth, thereby facilitating their degradation. Mostly, the carbon in the contaminants is used as a source of energy and released as carbon dioxide (C02). In the cometabolism process, the contaminants do not serve as a direct source of energy but are transformed by metabolic reactions by the microorganisms. It is the most prevalent form of degradation of organic contaminants. Polymerisation is a microbially mediated, oxidative coupling reaction by which a contaminant or its intermediate compound combines with itself or with other residues and naturally occurring compounds to form a larger molecular polymer. In the bioaccumulation process, the contaminants are incorporated into microorganisms by both active uptake and physical absorption. Bioaccumulatiou can readily be used to remove contaminants in aquatic environments.

In non-enzymatic reactions, the microbes alter the environmental parameters, such as pH, redox potential, and salt concentration, which promote the secondary or non-enzymatic transformations of contaminants. For example, acidic pH is created by bacteria during the nitrification reaction (equation 1) and elemental sulphur oxidation (equation 2) reaction in soil (Bolan et al. 2003).

Therefore, when these elements (i.e., N and S) are added to stimulate microbial activity and functions, the change in pH is likely to impact the reactions of contaminants and their subsequent bioavailability and degradation. For example, after a period of exposure to organic contaminants, such as pesticides, certain groups of microorganisms proliferate rapidly and the pesticide is metabolised. The increase in the proportion of the functional-specific biochemically active species within the total microbial population is known as the enrichment effect. The characteristic of enrichment effect in soil is the accelerated degradation of subsequent applications of pesticides without a lag period (i.e.. enhanced degradation). Under natural conditions, mobilization of organic contaminants from soil and sediments, and then subsequent biodegradation, are dependent on the activity of indigenous microorganisms. Biodegradation is primarily influenced by the metabolic activity of microorganisms that degrade organic contaminants into non-toxic substances, which are then assimilated into natural biogeocliemical cycles (Ghattas et al. 2017).

Bioremediation of PAHs through composting

Composting is a biological process used to decompose organic solid substrates and to convert them into a beneficial soil amendment rich in bioavailable carbon (humic substances) and nutrients. The composting process has generated interest because it can be used in the bioremediation of soils and sediments as a means to accelerate the biodegradation and subsequent removal of organic contaminants including PAHs (Lukic et al. 2016). Composting is a biochemical process based on the ability of microorganisms to decompose organic substrates, resulting in the release of heat, CO„ and water, along with biologically stable material (i.e., compost) (Hubble et al. 2010). A number of processes are involved in the removal of organic contaminants including PAHs during the co-composting of contaminated substrates with organic solid materials (Figure 1) (Lukic et al.

2016). These include: (i) an increase in temperature during the composting process; (ii) the addition of carbon and nutrient sources (biostimulation effect); and (iii) the introduction of a wide number of microorganisms capable of degrading organic compounds (bioaugmentation effect). The elevated temperature during the composting process can accelerate the biochemical kinetics involved in the biodegradation process, including the solubility and mass transfer rate of contaminants, thus facilitating the ability of the contaminants to become more accessible and bioavailable to microorganisms for their metabolism and subsequent degradation of contaminants (Haritash and Kaushik 2009).

Composting is also used as a biostimulation and bioaugmentation strategy for PAH contaminated soils. Bioremediation of PAH contaminated soils and sediments by indigenous microorganisms can be stimulated by incorporating organic materials (Table 3) (Mattei et al. 2016). The new microorganisms in the compost also enhance the bioaugmentatiou process of bioremediation. Composting of organic waste using the biostimulation and bioaugmeutation strategy would improve microbial diversity, introduce new microorganisms, enrich the activity of microorganisms in contaminated environments, and increase the supply of moisture and nutrients (Lukic et al. 2017a, b).

Biostimulation of microbiological process in contaminated soils is achieved by promoting optimum environmental conditions, including using the proper pH for microbial growth and adding nutrients to the soil. Microorganisms effectively promote the metabolization of contaminants under favourable environmental conditions for their growth. Biostimulation has been applied successfully

Processes involved in compost-assisted bioremediation of organic contaminants

Figure 1. Processes involved in compost-assisted bioremediation of organic contaminants.

Table 3. Selected references on the bioremediation of polycyclic aromatic hydrocarbons (PAHs) with the addition of organic

amendments (modified from Lukic et al. 2017).


Organic waste


Bioremediation process details



Composted sewage sludge

Spiked soil

Moisture content 40%, temperature was raised from 20°C to 60°C by 5°C day1,21 days

Adenuga et al. 1992, Antizar-Ladislao et al. 2004

Naphthalene, acenaphthene, fluorene, phenanthrene, anthracene, fluoranthene, рутепе, benzo[a]anthracene, chrysene

Municipal sohd wastes and fertilizer




Constant temperature at 45°C, 15 days

Antizar-Ladislao et al. 2004, Civilmi 1994, Semple et al. 2001

Diesel oil

Biowaste - vegetable, fruit, and garden waste

Diesel oil- spiked soil

Soil-to-biowaste ratio 1:10,12 weeks

Лап Gestel et al. 2003

16 PAHs

Green tree waste and manure

Tar residues



Field scale, green tree waste (< 5 days old), manure:soil ratio 15:5:80, moisture 60%- 80% field capacity, temperature reached maximum at 42°C after 35 days, 224 days

Antizar-Ladislao et al. 2004, Guerin 2000

Anthracene, phenanthrene

Sewage sludge, sterilized sludge, sludge to mauitam pH, glucose plus N and P source

Soil of the former lake Texcoco

Temperature 22°C, 112 days

Femandez-Luqueno et al. 2008

19 PAHs

Cow manure, modified fertilizer, and activated sewage sludge

Reilly soil*- creosote manufacturing and wood preservmg

C:N:P 100:5:1, com cobs bulkmg agent, moisture 30%-35%, temperature 41°C to 53°C m the first 15 days and subsequently decreased to ambient temperature, 84 days

Antizar-Ladislao et al. 2004, Potter et al, 1999

16 PAHs

Green waste

Aged coal tar contammated soil

Constant temperature at 38°C, 55°C, and 70°C separately, and comparative studies using a temperature profile, moisture content of 40%, 60%, and 80% field capacity, soil-to- green waste ratio 0.6:1, 0.7:1,0.8:1, and 0.9:1,

8 weeks

Antizar-Ladislao et al. 2005, Sayara et al. 2010


Tall fescue, arbuscular mycorrhizal fungus and epigeic earthworms

Former gasworks soil

Temperature 28/21°C (day/night), N:Pi05:K:0 = 1:0.35:0.8, 60% of field water holding capacity, 120 days

Lu and Lu 2015

Table 3 Contd....

...Table 3 Contd.


Organic waste


Bioremediation process details


Anthracene, benzo[a]pyrene


Industrial soil

Temperature 25°C, dark room, air humidity

70%, 274 days

Baldantom et al. 2017


Compost, biochar

Spiked soil

Temperature 20°C, dark, 50% of the soil’s maximum water holdmg capacity', 120 days

Sigmund et al. 2018

16 PAHs

Green compost, meat compost

Spiked soil, coal tar contammated soil, coal ash contammated soil

Ratio of compost to soil 250 and 750 tha-1, incubation 3, 6 and 8 months

Wu et al. 2014


Sewage sludge, compost

Uncultivated agricultural soil

Temperature 21/18°C (day/night), air humidity = 75-80%, day-night cycle 16 kday ^ knight

Wlokaet al. 2017


Sewage sludge

Heavily contammated soil with creosote (> 310,000 mg kg’1)

Field scale, moisture content 70% field capacity', aeration every 2 weeks, C:N:P ratio 25:1:1, 10 months

Atagana 2004

* The Reilly series consists of veiy deep, excessively drained, rapidly permeable soils that formed in stratified alluvial deposits of mixed origin. These soils are in river valleys.

to promote the degradation and subsequent removal of PAHs from soils and sediments (Table 3) (Murrieta et al. 2016). For example, Straube et al. (2003) reported PAH removal efficiency of 86% with biostimulation using ground rice husks as a bulking agent and dried blood as a slow-release nutrient source. Similarly, Atagana (2004) demonstrated that co-composting PAH contaminated soil with poultry manure resulted in a rapid degradation of a number of PAH compounds. For example, in the presence of poultry manure, the 2- and 3-ring PAHs (naphthalene, anthracene, phenantlirene, and pyrrole) were removed below the remediation target of 1 mg/kg within four months, whereas in the absence of poultry manure it took more than 16 months to reach the remediation target (Figure 2). In the case of 4- and 5-ring PAHs (pyrene, chrysene, fluoranthene, and benzo(a)pyrene), while degr adation continued very slowly in the control, degradation in the compost system increased rapidly.

Composting of contaminants, including PAHs in the organic residues, can also facilitate bioaugmentation. Bioaugmeutation involves the introduction of specific but benign microorganisms that are efficient at degrading contaminants from environmental media including soil, sediments, and water (Lukic et al. 2016). In soils with high PAH concentrations, the indigenous microorganisms are generally low, and, hence, bioaugmentation with microorganisms through composting can promote and accelerate the degradation process. The performance of bioaugmentation in promoting biodegradation of contaminants in soils depends on a number of factors, including the viability of introduced microorganisms, the environmental conditions of the polluted soil promoting the functional activity of the microorganisms, and the bioavailability of contaminants (Mrozik and Piotrowska-Seget 2010). The viability of the introduced microorganisms can be impacted from the competition with indigenous microorganisms and also the presence of co-contaminants in the composting substrate that could be toxic to added strains. Therefore, it is important to use indigenous

Poultry manure compost-assisted bioremediation of various polycyclic aromatic hydrocarbons (PAH) compounds

Figure 2. Poultry manure compost-assisted bioremediation of various polycyclic aromatic hydrocarbons (PAH) compounds

(Atagana 2004).

microorganisms isolated from the contaminated soil and sediments, which are tolerant to the target contaminant bemg degraded (Abatenh et al. 2017).

The compost-integrated biodegradation efficiency of PAHs in soils and sediments depends on the physical, chemical, and biological properties of the contaminated matrix, organic compost substrate characteristics, and environmental conditions (Lukic et al. 2016. Poluszyiiska et al. 2017). Additionally, the composting substrate enriches the contaminated soil with microorganisms derived from the composting substrate, and it also increases the moisture retention capacity of soil, thereby facilitating the bioremediatiou of PAHs (Lukic et al. 2016). The compost-integrated bioremediation approach also facilitates the eco-friendly disposal of organic waste used as a composting substrate, since the waste is simultaneously decomposed (Potter et al. 1999, Lukic et al. 2016). The organic amendments used as a compost substrate are likely to improve the soil structure and oxygen transfer and provide an additional nutrient and carbon source for the microorganisms. A number of studies have demonstrated that addition of an organic compost substrate increases the capability of microorganisms for degrading PAHs (Table 3).

In the compost-integrated bioremediation process, most of the PAH degradation has been shown to occur during the active thermo-composting phase and very little degradation occurs during the final curing phase of the composting process (Kastner and Miltuer 2016, Lukic et al. 2016). For example, Antizar-Ladislao et al. (2004) have demonstrated that PAH degradation in soil during composting is more efficient with the addition of fresh organic substrates compared to the addition of mature compost, which may be attributed to the active composting of the fresh organic substrates, thereby facilitating the degradation of the contaminant.

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