alexa Application of Innovative Bioremediation Technique using Bacteria for Sustainable Environmental Restoration of Soils from Heavy Metals Pollution: A Review
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Journal of Bioremediation & Biodegradation
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  • Review Article   
  • Bioremed Biodeg, Vol 11(3)

Application of Innovative Bioremediation Technique using Bacteria for Sustainable Environmental Restoration of Soils from Heavy Metals Pollution: A Review

Hoyle-Gardner J*, Badisa VLD, Ibeanusi V, Mwashote B, Jones W and Brown A
School of the Environment, Florida A&M University, Tallahassee, Florida, USA
*Corresponding Author: Hoyle-Gardner J, School of the Environment, Florida A&M University, Tallahassee, Florida, USA, Tel: +18504127049, Email: [email protected]

Received Date: May 01, 2020 / Accepted Date: May 20, 2020 / Published Date: May 27, 2020


Currently, heavy metals pollution has become one of the highly concerned worldwide environmental issues due to their harmful effects. Rapid industrialization, urbanization, and various natural processes have led to the increased release of these toxic heavy metals into the soil and water that causes serious threat to the ecosystem and human health. Hence, there is a greater need for remediation of contaminated soils and water with suitable approaches and mechanisms for sustainable environmental restoration of soils and water from heavy metal pollution. The conventional methods of physical or chemical remediation procedures involve the physical removal of contaminants, and their disposition are expensive, non-specific and often make the soil unsuitable for agriculture and other uses by disturbing the microenvironment. To overcome these problems, there has been increased attention in eco-friendly and sustainable approaches such as bioremediation for the cleanup of contaminated sites. Bioremediation is the use of natural and recombinant microorganisms such as bacteria, fungi, and plants for the cleanup of environmental toxic pollutants. They help in detoxification and degradation of toxic pollutants either through intracellular accumulation or via enzymatic transformation to lesser or completely non-toxic compounds. This review mainly focuses on the bacterial bioremediation for cleaning-up toxic heavy metals from polluted soils.

Keywords: Heavy metals; Pollution; Soil; Bioremediation; Bacteria


Heavy metals are defined as the elements with high density greater than 4 – 5 g/cm3 and classified as a general group of inorganic hazardous chemicals [1]. They are not essential for growth of microorganisms, animals or plants [2-4] however, they are toxic even at very low concentrations [5-8]. The examples of heavy metals are copper, lead, arsenic, mercury, silver, chromium, and cadmium [9-11]. These heavy metals have high economic significance in industrial use; but they cause pollution in the environment due to the release of industrial wastes. Pollution is defined as the presence of any toxic chemical that cause huge disturbances in the ecological balance and health of living organisms [12].The heavy metals pollution in the environment has become a serious threat to living organisms and ecosystem [2,13-17].It became a great environmental concern because of their bioaccumulation and non-biodegradability in nature [18,19].They pose a danger to humans and the ecosystem by affecting the food chain, drinking water, land usage, and food quality [1]. Due to their non-degradability, heavy metals persist in the soil for a long period of time. They are capable of reducing plant growth due to reduced photosynthetic activities, plant mineral nutrition, and reduced activity of essential enzymes [6,7]. These toxic metals could accumulate in the human body by consumption of food such as leafy vegetables grown in polluted soils or fish or oysters contaminated through the food chain and could lead to health problems including cancer [20,21].

Recently, heavy metals pollution in the soil and water became a worldwide problem, therefore remediation methods are necessary to find a solution for removal of heavy metals to protect the environment and human health [22].Many conventional methods such as physical and chemical techniques are available to remove these heavy metals. The physical remediation techniques include washing of soil, soil extraction, soil solidification, and soil stabilization of heavy metals. Physical methods include migrating contaminated land, disposal in landfills, replacement of soil to replace or partially replace the contaminated soil with clean soil to reduce the concentration of pollutants of the particular area [23,24]. The chemical remediation techniques include vitrify technology, chemical leaching, chemical fixation and electrokinetic technology. The vitrify technology increases the soil temperature at range of 1400–2000 °C, to decompose the organic matter [25]. The chemical fixation includes the addition of reagents into the contaminated soil to form slightly insoluble materials, which reduces the movement of heavy metals into water, plants, and other environmental media causing soil remediation [26].The electrokinetic technology involves the application of very high voltage to create electric field gradient at the two poles resulting in movement of charged pollutants to poles through electro-migration, electroosmotic flow, and electrophoresis process [27]. These conventional physical and chemical methods are laborious, time consuming, and not economically viable methods. Most of these techniques are ineffective when the concentrations of heavy metals are less than 100 mg/L or 100 ppm [28]. In addition, salt compounds of most heavy metals are water-soluble and dissolved in wastewater, which means they cannot be separated by physical separation methods [29].

Bioremediation through the living organisms such as microorganisms and plants offer an attractive alternative to physicochemical methods for removal of heavy metals by changing environmental pollutants into less toxic forms [30]. Hence, remediation by using bacteria is a possible solution for heavy metal pollution since it includes sustainable remediation technologies to remove completely or reduce the heavy metals levels and restore the ecosystem to its original condition of soil. In this review, sources of soil pollution with heavy metals, effects of heavy metals on soil microorganisms, toxic effects of heavy metals on humans, bioremediation of soil using bacteria are mainly discussed.

Sources of Soil Pollution with Heavy Metals

Soil contains heavy metals naturally in the form of rocks. They are also produced as byproducts during industrial processes. Soils are polluted with heavy metals through natural and anthropogenic sources. The natural sources are weathering of minerals, erosion and volcanic activities, forest fires and biogenic source and particles released by vegetation [20] and their concentrations in soils varies according to the nature of the rock, its location and age. Refining and mining of rocks, pesticides, batteries, paper industries, tanneries, fertilizer industries, solid wastes disposal including sewage sludge, wastewater irrigation and vehicular exhaust are the anthropogenic sources of heavy metals pollution in the soil (Figure 1).Mining and manufacturing industries are the main sources of heavy metals that pollute the soil. Due to increased urbanization and industrialization, different kinds of sewage, irrigation, industrial waste, and sludge containing heavy metals are released into the soil [35-38]. Heavy metals are introduced into food chains such as grains and vegetables grown in polluted soils [39].


Figure 1: Graphical representation of pollution caused by different sources (Source: [34]).

Effects of Heavy Metals on Soil Microorganisms

Metals without biological function such as lead, mercury are generally toxic even in minute concentrations, whereas essential metals with biological functions such as iron, zinc are usually are toxic in higher concentrations [40]. The heavy metals show toxic effects on microorganisms like bacteria [41] and influence microbial populations and their biological activities in soil which affect soil fertility [42]. Bacteria are the first biota that undergoes direct and indirect impacts of heavy metals. Heavy metals cause detrimental effects on microorganisms, and the toxicity depends on the bioavailability of heavy metal and the absorbed dose [2,43]. The toxicity involves several mechanisms via changing the structure and activity of enzymes, production of reactive oxygen species (ROS), destructing ion regulation, and directly affecting the formation of DNA as well as protein [44,45]. Chromium Cr (III) may change the structure and activity of enzymes by reacting with their carboxyl and thiol groups and also interact with negatively charged phosphate groups of DNA, which could affect transcription, replication, and cause mutagenesis [46]. Heavy metals like copper catalyze the production of ROS via Fenton and Haber-Weis reactions and can cause severe injury to cytoplasmic molecules, DNA, lipids, and other proteins [47,48]. Aluminum (Al) can cause DNA damage by stabilizing superoxide radicals [49]. Heavy metals can affect vital enzymatic functions by competitive or noncompetitive interactions with substrates that will cause configurational changes in enzymes and ion imbalance by adhering to the cell surface [44,50]. Cadmium (Cd) and lead (Pb) show deleterious effects on microbes through damaging cell membranes and destroying the structure of DNA by the displacement of metals from their native binding sites or ligand interactions [51]. As a whole, heavy metals affect the morphology, metabolism, and growth of microbes by changing the nucleic acid structure, causing functional disturbance, disrupting cell membranes, inhibiting enzyme activity, and oxidative phosphorylation [52,53]. The effects of all metals on microorganisms are summarized in Table 1 [2].

Arsenic Deactivation of enzymes
Cadmium Denature protein, destroy nucleic acid, hinder cell division and transcription
Chromium Growth inhibition, elongation of lag phase, inhibition of oxygen uptake
Copper Disrupt cellular function, inhibit enzyme activities
Selenium Inhibits growth rate
Lead Destroyed nucleic acid and protein, inhibit enzyme actions and transcription
Mercury Denature protein, inhibit enzyme function, disrupt cell membrane
Nickel Upset cell membrane, hinder enzyme activities and oxidative stress
Silver Cell lysis, inhibit cell transduction and growth
Zinc Death, decrease in biomass, inhibits growth

Table 1: Factors that influence bioremediation of heavy metals (Source: [2]).

Toxic Effects of Heavy Metals on Humans

Heavy metals have ability to accumulate in living tissues and cause adverse health effects in humans [54]. Numerous human health problems are associated with exposure to Pb such as anemia, reproductive failure, impatience, renal failure, and neurodegenerative damage [55]. Lungs, kidney, liver, and skeletal systems are adversely affected by Cd toxicity. Itai-Itai disease manifested by severe bone deformation was the first report of Cd toxicity in humans due to consumption of Cd contaminated rice in Japan after the Second World War. Other heavy metals, such as manganese, zinc, and copper, may cause hypophosphatemia, heart disease, liver damage, and sensory disturbance [56]. Excessive human intake of copper may lead to severe mucosal irritation and corrosion, widespread capillary damage, hepatic and renal damage and central nervous system irritation followed by depression. Severe gastrointestinal irritation and possible necrotic changes in the liver and kidney can also occur. The effects of Nickel exposure vary from skin irritation to damage to the lungs, nervous system, and mucous membranes [57]. The toxic effects of all metals on humans are shown in Table 2 [34].

Heavy metals EPA(regulatory limits ppm) Toxic effects
Ag 0.1 Exposure may cause skin and other body tissues to turn gray or blue-gray, breathing problems, lung and throat irritation and stomach pain
As 0.1 Affects essential cellular processes such as oxidative phosphorylation and ATP synthesis
Ba 2 Cause cardiac arrhythmias, respiratory failure,    gastrointestinal dysfunction, muscle twitching, and elevated blood pressure
Cd 5 Dysfunction, muscle twitching, and elevated blood pressure, carcinogenic, mutagenic, endocrine disruptor, lung damage, and fragile bones, affects calcium regulation in biological systems
Cr 0.1 Hair loss
Cu 1.3 Brain and kidney damage, elevated levels result in liver cirrhosis, and chronic anemia, stomach and intestine irritation
Hg 2 Autoimmune diseases, depression, drowsiness, fatigue, hair loss, insomnia, loss of memory, restlessness, disturbance of vision, tremors, temper outbursts, brain damage, lung and kidney failure
Ni 0.2 Allergic skin diseases such as itching, cancer of the lungs, nose, sinuses, throat through continuous inhalation, immunotoxin, neurotoxic, genotoxic, affects fertility, hair loss
Pb 15 Excess exposure in children causes impaired development, reduced intelligence, short-term memory loss, disabilities in learning and coordination problems, risk of cardiovascular disease
Se 50 Dietary exposure of around 300 μg day−1 affects endocrine function, impairment of natural killer cells activity, hepatotoxicity, and gastrointestinal disturbances
Zn 0.5 Dizziness, fatigue etc

Table 2: The toxic effects of some heavy metals on the human health (Source: [34]).

Heavy Metals    Microorganisms               References
Pb Micrococcus luteus, Bacillus subtilis, B. firmus, B. megaterium,Aspergillus niger, andPenicillium species, Brevibacterium iodinium, Pseudomonas spp., Staphylococcus spp., Streptomyces spp. [87-90]
Cd Pseudomonas aeruginosa, Alcaligenes faecalis, Bacillus subtilis, B. megaterium [88],[89]
Cu Bacteria: Staphylococcus sp., Streptomyces sp., Enterobacter cloacae, Desulfovibrio desulfuricans (immobilize on zeolite), Flavobacterium spp., Methylobacterium organophilum, Arthrobacter strain, Enterobacter cloaceae, Micrococcus sp., Gemella spp., Micrococcus spp., Pseudomonas sp., Flavobacterium spp., A. faecalis (GP06), Pseudomonas aeruginosa (CH07) [87], [88],[91-96]
Ni Micrococcus sp., Pseudomonas spp., Acinetobacter sp. Desulfovibrio desulfuricans (immobilize on zeolite)  [87],[97],[102]
Hg Klebsiella pneumoniae, Pseudomonas aeruginosa, Vibrio parahaemolyticus (PG02), Bacillus licheniformis, Vibrio fluvialis [91],[98],[99], [103]
Cr Bacillus cereus, Acinetobacter spp. and Arthrobacter sp. [88],[100]
Zn Bacillus firmus, Pseudomonas spp. [87],[101]
Co Enterobacter cloacae [91]

Table 3: List of microorganisms used in biological remediation of soil contaminated with heavy metals.

Bioremediation of Heavy Metals in Soil Using Bacteria

Recently, bioremediation using living organisms, an alternative innovative technology to conventional physico-chemical methods for removal and recovery of the heavy metals in polluted water and soils is accepted as the standard practice for the restoration of heavy-metalcontaminated soils. It is an efficient, inexpensive, and eco-friendly technique. It was reported that bioremediation was able to reduce 50– 65% of cost in comparison to the conventional methods such as excavation and landfill [58,59]. It also offers high specificity in the removal of particular heavy metals of interest. In addition, the conventional methods produce significant amounts of toxic sludge and are ineffective when metal concentrations are low [60,61].

The basic principles of bioremediation involve changing pH, the redox reactions and adsorption of pollutants from polluted environment to reduce the solubility of pollutants and convert to less toxic chemicals that are more stable, less mobile or inert [62,63]. The effectiveness of bioremediation depends on several factors such suitability of environmental conditions for their growth and metabolism which include suitable temperature, pH, and moisture and the level of the pollutants in that polluted site [64,65]. Microorganisms such as bacteria and fungus and plants or both are used in bioremediation process [66-70].

Bacteria are the first line of defense against any toxic chemical or heavy metals pollution which have ability to develop various strategies for their survival in heavy metal-polluted habitats [73-76]. They do not degrade the heavy metals but transform these metals by changing their physical and chemical properties. They have evolved various adaptive mechanisms to survive in heavy metal contaminated environments. One of the mechanisms was through the variation of genetic material such as mer operon for mercury tolerance which can be located on plasmid(s), chromosome(s) or may even be a component of transposons [77-79]. Bacterial detoxifying mechanisms are primarily responsible for remediation process. They adopt different detoxifying mechanisms such as biosorption, bioaccumulation, biotransformation and bio-mineralization, and these mechanisms are exploited for bioremediation process. Several reports showed that bacteria have the ability to detoxify sewage sludge, industrial waste, and the remediation of sediments and soils polluted with heavy metals (Table 3) [34,35,80]. Many factors influence the bacterial bioremediation in the soil and are shown in Table 4 [2].

Factors Activities
Microbial Production of toxic metabolites
Enzymes induction
Mutation and horizontal gene transfer
Enrichment of capable microbial populations
Substrate Chemical structure of contaminants
Too low concentration of contaminants
Toxicity of contaminants
Solubility of contaminants
Environmental Inhibitory Environmental conditions
Depletion of preferential substrates
Lack of nutrients
Mass transfer limitations Oxygen diffusion and solubility
Solubility/miscibility in/with water
Diffusion of nutrients
Growth substrate vs. co-metabolism Microbial interaction(competition, succession, and predation)
Alternate carbon source present
Biological aerobic vs. anaerobic process Microbial population present in the site
Oxidation/reduction potential
Availability of electron acceptors

Table 4: The oxicity of heavy metals to microorganisms.

Bioremediation of soil with bacteria can be in-situ or ex-situ [81]. In-situ bioremediation is an onsite clean-up process of polluted environments [82,83]. Ex-situ bioremediation involves transfer of polluted soil from its original site to a different location for treatment [68,65]. Recently, a global survey was reported that showed the use of bioremediation technologies for addressing the environmental problems [84]. It mentioned that developed countries made higher use of low-cost in situ bioremediation technologies such as monitored natural attenuation, while their developing counterparts appeared to focus on occasionally more expensive ex-situ technologies [84].

Bacterial bioremediation in the soil can be enhanced by biostimulation and bioaugmentation [85]. In biostimulation process, the growth conditions of indigenous microorganisms are stimulated by optimizing factors such as nutrients, oxygenation, temperature, pH, possible addition of biosurfactants [85].Using recombinant DNA technology, the indigenous microorganisms are improved to degrade specific contaminants or new recombinant bacteria that have ability to tolerate metal stress by overexpression of metal-chelating proteins and peptides, and ability of metal accumulation are produced [82,83]. In bioaugmentation process, recombinant bacteria having better remediation ability are introduced into the soil. Recombinant Corynebacterium glutamicum that had overexpression of ars operons(ars1 and ars2) was used to decontaminate As-contaminated sites [86].


At high concentrations, heavy metal pollution poses a serious threat to the environment metals and are toxic to human, plants and microorganisms. They could be dispersed in soil and consequently in human beings through food chain biomagnifications that could cause serious health hazards. Microorganisms possess inherent biological mechanisms that enable them to survive under heavy metal stress and remove the metals from the environment. Importance of microorganisms, plants and fungi in bioremediation are immense as they perform multiple functions such as improved soil quality, enhanced plant growth, detoxification, and removal of heavy metal from soil. In the need of an ecologically and economically effective method for environmental remediation, bioremediation shows to be a promising solution, especially on a large scale. However, more information is needed to combat specific organism application.


The authors would like to acknowledge the Department of Energy (TOA/PO No.0000456319 ) for financial support.


Citation: Hoyle-Gardner J, Badisa VLD, Ibeanusi V, Mwashote B, Jones W, Brown A (2020) Application of Innovative Bioremediation Technique using Bacteria for Sustainable Environmental Restoration of Soils from Heavy Metals Pollution: A Review. J Bioremed Biodeg 11: 467.

Copyright: © 2020 Hoyle-Gardner J. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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