Unveiling the Sustainable and Biological Remediation of Heavy Metals Contaminations in Soils and Water Ecosystems Through Potential Microbes—A Review

Abstract

This review provides a critical summary of the biological remediation of heavy metals by leveraging the potential of microbes in soils and water ecosystems, highlighting major research findings and practical obstacles. Heavy metals (HMs) pose a severe threat to environmental health due to their toxicity and persistence, necessitating effective remediation strategies. Biological remediation, especially through microorganisms and enzymatic actions, offers a promising alternative to conventional methods due to its eco-friendly and cost-effective nature. The review discusses various microbes, including bacteria, fungi, and algae known for their metal-binding capacities and transformation abilities. It delves into the mechanisms of bioremediation, such as biosorption, bioaccumulation, and biotransformation, facilitated by microbial enzymes like oxidoreductases and hydrolases that remove or bind the chemical structure of HMs. This paper also explores genetic engineering approaches to enhance microbial efficacy in HMs’ uptake and resistance. Furthermore, the review addresses the significant challenges in scaling bioremediation from a laboratory to the field, such as the complexity of environmental conditions, the presence of mixed contaminants, and the need for system optimization to improve efficiency and sustainability. It also evaluates the current legislative framework governing bioremediation practices, suggesting a need for clearer policies to support the integration of biological methods into mainstream remediation strategies. Conclusively, while microbial and enzymatic remediation presents considerable potential, extensive research is needed to overcome existing hurdles and develop robust, field-applicable systems. This paper calls for a multidisciplinary approach combining microbiology, engineering, and environmental sciences to advance this promising field.

1. Introduction

In a global context, heavy metal (HM) contamination has become a critical environmental concern due to persistence, ubiquity in every component of the environment, and widespread transformation throughout the environment [1]. In general, HMs are natural elements derived from the earth’s crust, but many anthropogenic activities, including improper industrial discharge, rigorous mining, irrigation through metal-rich groundwater, and unscrupulous solid waste management, can augment the HMs concentration in arable soils and terrestrial ecosystems, including plant, microbial, and animal life [2]. Typically, there are two major classifications of HMs, namely essential HMs and non-essential HMs. Essential HMs pertain to the physiology of plants and biota at certain tolerable concentrations but become toxic at higher concentrations [3]. In contrast, non-essential HMs are highly toxic, even at lower concentrations, both for soil biota and the human food chain. Earlier studies have noticed that the toxicity of HMs may cause chronic cancer (lung and abdominal cancer), kidney damage, acute and chronic respiratory difficulties, and disruptions of cellular functions in humans [2]. Similarly, reduced cell division, damage to DNA and protein, cell necrosis, and chlorophyll imbalances are experienced by HM-affected plants. Thus, HM toxicity applies to both plant cells and the human body, is critical, and can be chronic if the HM contamination persists without proper diagnosis.

According to research of the past decade, HMs have been found in fresh vegetables, fruits, dairy, and meat samples both in fresh and processed conditions [4]. In particular, the concentration of HMs was higher than the tolerable limit set by the WHO/FAO. The crisis of HM pollution is regarded as a global dilemma due to the non-biodegradability and biotransformation of HMs from one environmental component to another through food chain transfer [5]. As a result, global regulatory bodies, including the FAO (Food and Agriculture Organization) and the WHO (World Health Organization), have expressed their concerns for setting the maximum tolerable limit (MTL) of exposure to HMs in edible and food items [6]. In addition, several risk factor assessments were also suggested for those HMs related to contamination of food safety. However, the consequence of HMs contamination is evident in the way it affects global environmental concern, manipulating the sustainable development goal (SDG) themes (i.e., SDG 1, SDG 2, SDG 3, SDG 6, SDG 11, SDG 12, SDG 13, and SDG 15) [7]. Recent studies displayed the higher concentrations of HMs in fresh and processed food materials, indicating the biotransformation and bioaccumulation of HMs through edible foodstuffs. The abundance of HMs in the foodstuffs of developing countries has shown an alarming circumstance leading to a potential and protracted risk for food chain toxicity [8].

Thus, several innovative and contemporary approaches have been employed for effective and sustainable remediation of HM-contaminated soils and water samples [9]. The physical approaches include soil washing through chelating agents, and soil tilling that can reduce HMs concentration through dilution and adsorption mechanisms [10]. Furthermore, thermal desorption, incineration, and electrokinetic processes have been employed as popular physical methods for HMs removal [11]. On the other hand, several innovative chemical processes (i.e., the advanced oxidation process (AOP), catalysis, Fenton reactions, and ozonation) were employed as popular and robust chemical weapons for the efficient remediation of HMs contamination [6]. Although physical and chemical approaches are effective against HMs contamination, the sustainability of those approaches is still debatable due to the risk of secondary pollution and high-cost requirements [1].

To overcome the existing challenges of physical and chemical remediation techniques for tackling HM contaminations, biological drivers, including potential microbes and hyperaccumulating plant species, are considered effective, eco-friendly, and green strategies with affordable costs [12,13]. Metal-tolerant microbes, including bacteria, fungi, algae, and yeast, either in pristine or engineered forms, are an excellent driving force for sustainable and green remediation of HMs [14]. In recent days, genetic engineering coupled with multi-OMICS approaches (i.e., genomics, transcriptomics, proteomics, and metabolomics) has been found to be more effective than the conventional microbial process [15]. The microbial consortia, on the other hand, were a wondrous option. In this review, a critical assessment of research trends regarding potential microbes and their functional enzymes is performed, with a focus on deciphering these microbes and microbial consortia as potent and green weapons against toxic metal-contaminated samples, both in soils and water ecosystems. The specific goals of this study are as follows: (i) to comprehend the existing research trend of microbial bioremediation of HMs contaminations, (ii) to pinpoint the key limitations of microbial remediation of HMs and decipher possible solutions, (iii) to combine microbe-oriented approaches with a compatible approach for enhanced bioremediation of heavy metals by combining methods, and (iv) to summarize specific recommendations for the advancement of microbial bioremediation for HMs and related emerging pollutants.

2. Global Challenge of Heavy Metal Pollution

Heavy metal contamination has been identified as a growing global concern, with estimates indicating that approximately 14% to 17% of the world’s arable land is contaminated by at least one heavy metal, translating to nearly 242 million hectares of affected land [16]. This widespread contamination poses substantial risks to agricultural productivity and public health. It has been estimated that between 900 million and 1.4 billion people reside in regions classified as high-risk zones for heavy metal exposure. In one study, Lake Maurepas exhibited alarmingly high concentrations of heavy metals and nutrients, with arsenic levels reaching up to 420% above the acceptable limit for lakes and 6300% over the EPA’s threshold for drinking water [17]. Additionally, lead and cadmium were detected at concentrations substantially exceeding safe limits, while nickel, copper, and manganese were also observed above environmental safety thresholds. In urban soil studies, lead (95.8 mg/kg) and barium (86.8 mg/kg) emerged as the most prevalent contaminants [18]. Moderate levels of chromium (13.8 mg/kg) and arsenic (5.14 mg/kg) were also reported, with selenium, cadmium, and silver detected at lower concentrations (below 1 mg/kg) [18]. Elevated levels of copper, nickel, and zinc were particularly noted in the Lower Mississippi River Valley, which also exhibited moderate to high concentrations of cadmium, chromium, lead, nickel, and iron. Similarly, the River Swat demonstrated elevated concentrations of arsenic. In certain soil samples, nickel concentrations reached up to 214.4 mg/kg, surpassing international soil quality standards, and were attributed primarily to geogenic sources [19].

2.1. Sources of Heavy Metal Contamination

Heavy metals (HMs), including lead (Pb), mercury (Hg), cadmium (Cd), arsenic (As), and chromium (Cr), among others, originate from both natural and anthropogenic sources [20]. Natural sources of heavy metals include geological weathering, which releases metals into soils and water systems as rocks erode over time [21]. Volcanic eruptions are another significant source, propelling HMs such as Hg and Cd into the atmosphere, from here they can settle on the Earth’s surface [22]. Additionally, forest fires can mobilize the HMs stored in vegetation and soil, dispersing them through smoke and ash into the environment [23]. HMs contamination originates from various human activities, including mining operations, industrial processes (such as foundries, smelters, oil refineries, petrochemical plants, and chemical manufacturing), as well as the application of untreated sewage sludge [1]. Additionally, diffuse sources contribute to the problem, including metal piping, vehicular emissions, and by-products from the combustion of coal in power plants [24,25,26]. The industrial revolution has markedly increased the dispersal of heavy metals into the environment, making them ubiquitous contaminants in air, water, and soils (Figure 1a).

2.2. Toxicity and Persistence

The toxicity of HMs is well documented, with numerous studies indicating their potential to cause severe health issues in humans and wildlife [10,24]. Heavy metals, particularly Hg, Pb, Cd, As, and Cr, are toxic because they can interfere with biological processes, causing cellular and organ damage [25]. For example, lead affects neurological development in children, mercury can impair neurological and kidney function, and arsenic exposure is linked to skin lesions and an increased risk of cancer (Figure 1b). A particularly concerning characteristic of HMs is their enduring nature; they remain in the environment without breaking down into less hazardous forms over time [26]. Instead, HMs accumulate in soils, sediments, and living organisms, leading to bioaccumulation and biomagnification [20,27]. This implies that an accumulation of heavy metals can occur up the food chain, resulting in significant health hazards being posed to organisms at higher trophic levels, including humans. HMs persistence in the environment, combined with their ability to travel long distances through water and air, makes managing heavy metal contamination a global challenge. Addressing this issue requires effective pollution control measures, remediation of contaminated sites, and careful monitoring of environments at risk.

2.3. Effects on Biota

Heavy metals exert profound and diverse effects on biota, impacting organisms across various ecosystems. These effects range from sub-lethal to lethal, affecting individual organisms, populations, and entire communities. In aquatic ecosystems, heavy metals can be particularly toxic to fish, invertebrates, and algae [28]. They disrupt physiological processes, reduce reproductive success, and can cause acute and chronic toxicity, leading to decreased biodiversity and altered species composition. Soil-dwelling microorganisms, crucial for nutrient cycling and soil fertility, can be adversely affected by heavy metal contamination [29]. HMs such as cadmium, copper, and lead can inhibit microbial growth and enzyme activity, disrupting soil ecosystems and affecting plant health [30,31].

HMs accumulate in the tissues of organisms without being metabolized or excreted, leading to bioaccumulation [32]. Through the food chain, these metals can be biomagnified, posing significant risks to higher trophic levels. Predators, including humans, can be exposed to high levels of HMs through the consumption of contaminated prey [33]. Heavy metals can be toxic to plants, inhibiting seed germination, root and shoot growth, and photosynthesis [34]. This not only reduces crop yields and quality but also compromises the survival of native plant species, altering habitat structure and function.

In wildlife and humans, heavy metals can weaken immune systems and cause reproductive problems. Exposure to certain metals, like Pb and Hg, has been linked to decreased fertility, developmental abnormalities, and an increased susceptibility to disease [35]. HMs can cause genetic mutations and DNA damage, leading to cancer and other heritable conditions in humans and wildlife [25]. This genetic impact can have long-term consequences for the viability of populations.

2.4. Food Safety Concerns

The contamination of food with HMs is a significant public health concern. Crops grown in contaminated soil or irrigated with polluted water can accumulate heavy metals, posing risks to human health when consumed [36]. Similarly, the consumption of contaminated fish and shellfish can lead to the intake of hazardous levels of metals like Hg and Pb [37]. Elevated concentrations of heavy metals have been detected in various food items, raising significant concerns regarding food safety and human health. Studies have reported cadmium levels in rice exceeding 0.4 mg/kg, surpassing the maximum permissible limits set by international food safety authorities [38]. Lead concentrations in vegetables have been detected up to 2.1 mg/kg, while mercury levels in certain fish species have reached 0.8 mg/kg, which have been shown to be harmful to the human food chain owing to a violation of the maximum tolerated limits [39]. The chronic intake of such contaminated food has been associated with bioaccumulation and potential toxic effects, highlighting the urgent need for monitoring and regulatory control. The implications for food safety are far-reaching, with potential consequences including developmental problems in children, compromised immune systems, and chronic health conditions in adults [40]. Given the widespread occurrence and persistence of heavy metal contamination in environmental and food matrices, the implementation of stricter regulatory policies is warranted to mitigate the associated risks. Such policies would enhance monitoring, limit permissible exposure levels, and promote safer agricultural and industrial practices. A more rigorous framework is essential to address the long-term implications for ecosystem integrity and public health.

2.5. Biosafety Standards in Nano-Bioremediation

Nanotechnology and biological systems are great for the environment because they can get rid of heavy metals, but they also make people worry about biosafety. Nano-bioremediation uses modified bacteria, nanoparticles (NPs), and GMOs; therefore, it must be safe for living beings. This is to make sure that health and the environment do not get hurt in ways that are not intended. Nanoparticles could change the bacteria on Earth since they are small, have a surface that reacts, and can pass through biological barriers. They could potentially stop enzymes from working and cause oxidative stress in animals that are not the target [41]. Scientists need to study how nanoparticles act on land and in water as part of biosafety research. They need to know how they stick to, break up, and build up in living things and stay there [42].

Bioremediation uses genetically engineered microorganisms, or GEMs, to speed up the transmission of genes and change the way regular microbial ecosystems work. The Cartagena Protocol on Biosafety advises that you should think about the hazards of letting out live modified organisms, keep an eye on them, and control them [43]. Manganyi et al. [44] reported that biosensors and molecular tools can be used for real-time biosurveillance to check GEMs and find unintended gene transfers and microbial dysbiosis. The results of lab tests on nano-bioremediation may not be the same as those in the field because pH, soil composition, ionic strength, and organic matter can all affect how nanomaterials behave and how harmful they are [45]. This method needs to be tested in small- and medium-sized groups to help a lot of people. The European Food Safety Authority (EFSA) and the U.S. Environmental Protection Agency (EPA) have set standards for studies on how safe and biodegradable nanomaterials are [46]. Natural or green nanoparticles are better for the environment and safer because they do not last as long [47]. Before using nano-bioremediation technology, think about the good and bad things about it. Always put safety first so you may use it safely, responsibly, and for a long time.

3. Current Global Trend of HMs Remediation Strategies

Heavy metal remediation strategies encompass a range of techniques aimed at reducing the concentrations of toxic metals in the environment to mitigate their harmful effects on human health and ecological systems. These strategies are essential for restoring contaminated sites and preventing further pollution. There are several remediation strategies utilized for HMs remediation, such as physical (adsorption, filtration, membrane technologies, soil washing), chemical (immobilization, advanced oxidation processes, ion exchange, redox reactions), and biological (bioremediation, phytoremediation) methods (Figure 2). Nano-remediation techniques, which often integrate surface adsorption, redox reactions, and catalytic functions, may be more appropriately classified under an interdisciplinary physical–chemical category. Each method presents distinct advantages and limitations. Physical methods such as filtration and adsorption are simple and rapid but may lack selectivity. Chemical treatments offer high efficiency but often involve secondary pollution and higher operational costs. Biological approaches, particularly microbial remediation, are eco-friendly and cost-effective, although they may require longer treatment times and are sensitive to environmental conditions. Highlighting these contrasts underscores the growing importance and potential of microbial strategies in sustainable heavy metal remediation.

Adsorption processes for HMs remediation involve using materials with high surface areas to capture and remove toxic metals from water or soil [24,48]. These processes are efficient, cost-effective, and widely used for environmental cleanup, utilizing various adsorbents like activated carbon, biochar, and nanomaterials to target specific heavy metals [10,49]. The soil washing method involves the use of chemical agents to extract HMs from contaminated soils [50]. The extracted metals can then be recovered or safely disposed of, while the decontaminated soil is returned to the site. Soil washing is effective for treating soils with high levels of contamination, but it can be costly and may require treatment of the wash water. Electrokinetic Remediation utilizes an electrical current to mobilize charged species, including heavy metals, in soil or sediment [11]. The metals move towards the electrodes, where they can be collected and removed. This technique is particularly useful for fine-grained soils, where other methods may be less effective.

Chemical immobilization involves the addition of amendments to the soil that react with heavy metals to form less bioavailable compounds [51]. Lime, phosphates, and biochar are common agents that can effectively immobilize metals, reducing their mobility and bioavailability [52]. Advanced Oxidation Processes (AOPs) generate highly reactive species, such as hydroxyl radicals, which can break down complex contaminants into less harmful substances or even into harmless end products [53,54]. Advanced Oxidation Processes (AOPs) play a crucial role in the removal of heavy metals through the generation of highly reactive species, primarily hydroxyl (^•OH) and sulfate (SO₄^•−) radicals [55]. These reactive intermediates facilitate the oxidation of metal ions, their transformation into less toxic or more stable forms, and, in some cases, the precipitation of released ions as insoluble hydroxides or oxides. Furthermore, AOPs can enhance the breakdown of complex metal–organic species, thereby improving overall removal efficiency in contaminated water and soil systems. [56,57].

Bioremediation uses potential microorganisms to remove or immobilize heavy metals [58]. Certain bacteria and fungi are capable of altering the chemical state of metals, making them less toxic and mobile. Genetic engineering is being explored to enhance the natural metal-remediation abilities of these microorganisms [59]. Phytoremediation involves the use of plants to remove, stabilize, or detoxify heavy metals from soil and water [1]. Different mechanisms are employed, including phytoextraction (the accumulation of metals in plant tissues), phytostabilization (the reduction of metal mobility in soil), and rhizofiltration (using plant roots to absorb metals from water) [60].

Nano-remediation, which includes the use of nanoparticles to remove heavy metals from soil and water, is an emerging field of research [61]. Nanoparticles can adsorb or chemically react with heavy metals, facilitating their removal. This method offers high efficiency and specificity, but raises concerns regarding the fate and toxicity of nanoparticles in the environment. The electrocoagulation process involves the use of electrical currents to induce the coagulation of heavy metals in water, allowing them to be easily separated and removed [62]. Electrocoagulation is effective for treating industrial wastewater and is valued for its simplicity and efficiency.

The selection of a remediation strategy depends on various factors, including the type and concentration of heavy metals, the characteristics of the contaminated site (such as soil type and hydrology), the presence of other contaminants, cost considerations, and environmental impact. Ideally, remediation efforts should aim not only to remove or stabilize heavy metals but also to restore the ecological integrity of the contaminated site. Moreover, the sustainability of remediation technologies is becoming increasingly important. Strategies that offer a potential for metal recovery and recycling, minimal secondary pollution, and the rejuvenation of ecosystems are particularly valued. As research progresses, the development of more effective, efficient, and environmentally friendly remediation technologies continues to be a critical area of focus in the field of environmental science and engineering.

Microbial bioremediation is gaining popularity over traditional remediation methods for several compelling reasons, reflecting its effectiveness, sustainability, and economic advantages [58]. This approach harnesses the natural processes of microorganisms to remove, transform, or immobilize contaminants, including heavy metals, in the environment [63].

Figure 2. Contemporary strategies for the remediation of heavy metals in soils and water ecosystems (adapted and modified from [1,58]).

Figure 2. Contemporary strategies for the remediation of heavy metals in soils and water ecosystems (adapted and modified from [1,58]).

4. Microbial Bioremediation of HMs—An Overview

Bioremediation, a promising technique that harnesses the power of living organisms to clean polluted areas, has shown remarkable effectiveness in tackling environmental heavy metal contamination [58]. Hence, in the past few years, there has been a growing focus on microbiological treatment for addressing the issue of heavy metal contamination. This type of pollution poses a significant threat to ecosystems and human health and hinders progress towards sustainable development [58]. Traditional methods of remediation are costly and produce harmful byproducts that have a detrimental impact on the environment. As a result, a sustainable approach utilizing diverse biological agents, primarily bacteria, algae, yeasts, and fungi, has proven to be highly effective in removing and recovering heavy metals [64,65,66,67,68,69]. This green technology offers significant advantages, such as efficient removal, affordability, and widespread availability. Moreover, the rapid growth and ease of manipulation of these biological agents make them indispensable in the field of remediation [63,70]. For example, a recent in silico study emphasized the use of Pseudomonas putida for its metallothionein-mediated biosorption of lead and cadmium, and its ability to identify vital binding sites (e.g., GLU30, GLN21) that coordinate metal binding, paving the way for a targeted increase of its remedial potential [71]. Similarly, a fungal remediation study observed that Aspergillus niger can absorb up to 36.7 mg Cd/g under 50 ppm of cadmium stress, demonstrating strong intracellular sequestration and cell-wall adsorption mechanisms [72].

Microbial strategies such as biosorption, bioaccumulation, biomineralization, and enzymatic transformation allow for the efficient removal, immobilization, or recovery of heavy metals without introducing secondary pollutants (Figure 3). Furthermore, microbes can be genetically engineered or selectively enriched to enhance their remediation potential. These advantages, combined with their cost-effectiveness and broad environmental applicability, underscore the necessity to prioritize microbial approaches in modern remediation efforts [73]. Hence, promoting the use of microorganisms as viable bioremediation agents is crucial for advancing sustainable and eco-friendly solutions to heavy metal pollution. Moreover, integrated approaches that combine microbial and plant systems (e.g., plant growth-promoting rhizobacteria in phytoremediation) can further enhance bioremediation efficiency, opening avenues for future research.

4.1. Bacterial Bioremediation

Bacteria, the most predominant microorganisms on Earth, thrive in diverse environmental conditions. Their small size, rapid growth, and ease of cultivation make them valuable for removing heavy metal pollutants from the environment. Various heavy metal remediation methods utilizing bacteria like Staphylococcus, Pseudomonas, Micrococcus, and Bacillus are presented in this study. Heavy metal ions are typically adsorbed onto the polysaccharide slime layers of bacteria via functional groups like phosphate, amino, carboxyl, and sulfate groups, resulting in effective accumulation. The uptake capabilities of bacteria for heavy metal ions generally fall within the range of 1 mg/g to 500 mg/g [74,75]. The binding of metal ions to a bacterium’s cell surface during metabolism-independent biosorption comprises mechanisms like chemical or physical interactions, diffusion, complexation, precipitation, or surface adsorption [76]. Both living and dead bacterial biomasses can serve as efficient biosorbents for remediating toxic metals, even at considerably lower concentrations [77,78].

4.2. Fungal Bioremediation

Fungi are vital microbes for efficient remediation of HMs contamination without compromising the surrounding ecosystem. In particular, Mycoremediation, which involves the use of fungi to remove pollutants from various environmental niches, whether alive or dead, is a cost-effective method that prevents the generation of harmful waste products. This makes it a holistic solution due to its complete breakdown of pollutants in an environment [79,80]. The success of mycoremediation depends heavily on identifying and utilizing specific fungal species tailored to the targeted heavy metals (HMs) or other pollutants. Fungi have a remarkable ability to accumulate HMs in their fruit bodies, making them either inaccessible or reducing their presence in the environment [81]. Fungal cell walls play a crucial role in the absorption of HMs, facilitated by various functional groups, such as amino, sulfate, hydroxyl, carboxyl, and phosphate groups, as well as glucans, pigments, proteins, polysaccharides, and lipids; this involves various mechanisms such as intracellular precipitation, ion exchange, complexation, and valence transformation [82,83]. Fungi have shown significant effectiveness in HM cleanup due to their innate capacity to adapt and grow in challenging environments characterized by extreme temperatures, fluctuating pH levels, and limited availability of nutrients [84]. Consequently, fungi have gained significant attention for their potential in adsorbing heavy metal ions and exhibiting a remarkable capacity for metal uptake, as shown in Table 1.

4.3. Algal Bioremediation

Algae, a type of photosynthetic organism, have the ability to thrive in both freshwater and seawater environments. Recent studies have shown that algae possess a remarkable capacity to absorb heavy metal ions. This is achieved through the production of various peptides by algae, which not only facilitate the accumulation of heavy metal ions but also serve as a protective mechanism against their toxicity [85]. Moreover, macro-algae (brown, green, and red) and micro-algae have different cell wall compositions, which consist of chitin, polysaccharides, cellulose, polymers, alginic acid, proteins, and lipids. These components contain essential functional groups such as amino (NH₂), carboxyl (COO), sulfate (SO₄²⁻), and carboxyl (COO), hydroxyl (OH) groups, which play a crucial role in the biosorption process of heavy metals by algae [67,86]. Algae are widely recognized as the predominant biosorbent utilized in comparison to other biosorbents, primarily due to their abundant availability, cost-effective processing, and exceptional efficiency [67]. As a result, numerous research endeavors have been undertaken to address heavy metal contamination by employing various species of algae (Table 1).

4.4. Microbial Consortia-Based Bioremediation

Microbial remediation has been widely utilized in bioremediation efforts to address various contaminants. However, the use of pure cultures of microorganisms in practical applications is hindered by their limited adaptability, efficiency, and ability to handle multiple contaminants. On the other hand, mixed cultures of microorganisms, which involve the symbiosis of two or more microorganisms, have shown great promise. These mixed cultures combine the characteristics of each species or strain, making them highly effective in bioremediation efforts targeting organic or heavy metal pollutants [87]. The shift towards using mixed cultures has been driven by their synergistic metabolism, which enhances the degradation efficiency of hydrocarbons and other chemicals [88,89]. Additionally, mixed cultures are capable of handling multiple contaminants due to the unique functions possessed by each strain within the consortium. As a result of their superior degradation capabilities for complex compounds, microbial consortia are now preferred over single strains in environmental remediation practices [90]. Various types of microbial consortia, such as fungi–fungi, bacteria and yeast, bacteria–bacteria, and microalgae–bacteria, have shown great potential in removing heavy metals and recovering valuable metals. The recovery of these valuable metals not only offers broad development potential and high commercial value but also brings about significant social benefits [91,92]. Furthermore, the treatment of sewage microbial consortia has seen significant advancements, with the addition of microalgae to activated sludge leading to improved adsorption and degradation efficiency for various compounds, including heavy metals, in sewage [93].

Microbial consortia have proven to be more advantageous than single strains when it comes to degrading complex compounds. This is because they are more adaptable and stable within their growth environment, providing a suitable catalytic environment for the enzymes required in a biodegradation pathway. With advancements in synthetic biology and gene-editing tools, artificial microbial consortia systems can now be designed to be even more efficient, stable, and robust. These systems can produce high-value-added products due to their strong degradation capabilities [94,95]. Numerous research investigations have demonstrated the partial or complete degradation of heavy metals using mixed microbial cultures (Table 1).

Table 1. Screened list of potential microbes and their bioremediation potential for heavy metal reclamation.

Microbial Group	Species Name	Heavy Metals	Results or Key Findings	Reference
Bacteria	Bacillus strain MRS-2 (ATCC 55674)	Lead	High Pb biosorption capacity at the rate of 206.5 qmax (g/L) from wastewater	[64]
	Pseudomonas aeruginosa	Mercury	Capable of removing Hg under saline conditions	[96]
	Bacillus megaterium and Rhizopus stolonifera	Nickel and cadmium	Remediate Ni and Cd by bioaccumulation	[97]
	Sphingobium sp. SA2	Mercury	Able to volatilize 79% Hg in Hg-supplemented culture solutions after 6 h	[98]
	Bacillus sp., Microbacterium sp., Micrococcus sp., and Shigella sp.	Arsenic and uranium	Significantly remove As and U	[65]
	Staphylococcus hominis AMB-2	Cadmium and lead	Biosorption of Pb and Cd	[30]
	Pannonibacter phragmitetus BB	Chromium	99% Cr removal efficiency from soil	[99]
	Micrococcus luteus DE2008	Copper and lead	Able to absorb Pb and Cu	[31]
	Staphylococcus aureus	Lead	90% Pb removal capacity	[100]
	Sphingomonas paucimobilis 20006FA	Chromium	Cr removal efficiency of 90% from artificial contaminated soil	[101]
	Bacillus sp. MNU16	Chromium	75% Cr reduction capacity	[102]
Fungi	Aspergillus niger	Chromium	100% reduction of Cr at concentrations ranging from 10 to 50 mg/L.	[103]
	Saccharomyces cerevisiae	Nickel, mercury, and lead	Remediated Pb (86%), Ni (47%), and Hg (69%) from aqueous medium	[104]
	Penicillium sp., Trichoderma sp., and Aspergillus sp.	Cobalt and copper	High biosorption capacity of Cu and Co	[66]
	Fusarium sp.	Lead, chromium, and copper.	Remediated Pb (83%), Cd (93%), and Cr (84%) from wastewater	[105]
	Aspergillus nomius JAMK1	Lead, copper, and nickel.	Remediated Pb (99.25%), Ni (80%), and Cu (86.31%) from aqueous medium at a concentration of 100 ppm	[106]
	Ganoderma lucidum	Cadmium and lead	High Cd and Pb adsorption capacity from polluted water through precipitation mechanism	[107]
	Aspergillus flavus	Arsenic	Capable of converting soluble As into As particles, which have less toxicity	[108]
	Trichoderma sp.	Cadmium	Efficiently reduce Cd content and increase spinach growth	[109]
	Penicillium sp.	Cadmium, lead, and mercury	Remediation efficiency of 80% for Cd, 99.6% for Hg, and 92.4% for Pb	[23]
Algae	Cladophora glomerate and Enteromorpha intestinalis	Chromium	Efficient in the removal of Cr from aqueous solution	[110]
	Chlorococcum humicola	Cobalt	Remediate Co with 44% efficiency through biosorption	[111]
	Chlorella vulgaris	Manganese	99% efficiency in the removal of Mn	[112]
	Chlorophyceae sp.	Copper	88% efficiency in the removal of Cu by bioaccumulation	[112]
	Oedogonium westi	Nickel	60–90% efficiency in the removal of Ni	[113]
	Chlorophyceae sp.	Zinc	92% efficiency in the removal of Zn	[112]
	Phormidium ambiguum	Cadmium	86% efficiency in the removal of Hg by bioaccumulation and biosorption	[114]
	Enteromorpha intestinalis	Chromium	93% efficiency in the removal of Cr by biosorption	[115]
	Ulva Reticulata	Arsenic	60% efficiency in the removal of As by biosorption	[116]
	Phormidium ambiguum	Mercury	97% efficiency in the removal of Hg through bioaccumulation and biosorption	[114]
	Desmodesmus sp. AARLG074	Copper	80% efficiency in the removal of Cu by bioaccumulation and biosorption	[117]
	Ulva lactuca	Mercury	98% efficiency in the removal of Hg via bioaccumulation and biosorption	[118]
Yeast	Gelidium amansii	Lead	Pb biosorption with 100% efficacy	[68]
	Candida tropicalis	Chromium	60–70% Cr removal efficacy	[119]
	Saccharomyces cerevisiae	Chromium	96% Cr removal efficacy	[120]
Microbial consortia	Bacillus subtilis and Staphylococcus aureus	Lead, chromium, arsenic, nickel, and zinc	High remediation of heavy metals from polluted soil potential	[121]
	Saccharomyces cerevisiae and Pseudomonas aeruginosa	Chromium	99% Cr remediation efficiency from tannery effluents	[122]
	Antrodia serialis, Paecilomyces lilacinus, and Penicillium cataractum	Arsenic, iron, copper, manganese, and chromium	Significantly reduce heavy metal contamination in soil by bioaugmentation	[123]
	Pseudomonas aeruginosa and Bacillus subtilis	Chromium	Almost 100% Cr remediation efficiency from tannery effluents	[120]
	Streptomyces sp. M7, Streptomyces sp. MC1, Streptomyces sp. A5, and Amycolatopsis tucumanensis	Chromium	86% Cr removal efficiency from artificial contaminated soil	[69]
	Acinetobacter sp. and Arthrobacter sp.	Chromium	78% Cr remediation efficiency	[124]
	Saccharomyces cerevisiae and Bacillus subtilis	Chromium	97% Cr remediation efficiency from tannery effluents	[120]
	Daldinia starbaeckii, Perenniporia subtephropora, Phanerochaete concrescens, Fusarium equiseti, Cerrena aurantiopora, Polyporales sp., Aspergillus fumigatus, Trametes versicolor and Aspergillus niger	Arsenic, iron, copper, manganese, and chromium	Significantly reduce heavy metal contamination in soil through bioaugmentation	[69]
	Penicillium sp. A1 and Fusarium sp. A19	Chromium, lead, copper, and zinc	Efficiently accumulate heavy metals	[124]
	Pseudomonas pyogenes, Serratia marcescens, Erwnia amylovora, and Enterobacter cloacae	Lead, chromium, arsenic, nickel, and zinc	High remediation of heavy metals from polluted soil potential	[121]

Table 1. Screened list of potential microbes and their bioremediation potential for heavy metal reclamation.

Microbial Group	Species Name	Heavy Metals	Results or Key Findings	Reference
Bacteria	Bacillus strain MRS-2 (ATCC 55674)	Lead	High Pb biosorption capacity at the rate of 206.5 qmax (g/L) from wastewater	[64]
	Pseudomonas aeruginosa	Mercury	Capable of removing Hg under saline conditions	[96]
	Bacillus megaterium and Rhizopus stolonifera	Nickel and cadmium	Remediate Ni and Cd by bioaccumulation	[97]
	Sphingobium sp. SA2	Mercury	Able to volatilize 79% Hg in Hg-supplemented culture solutions after 6 h	[98]
	Bacillus sp., Microbacterium sp., Micrococcus sp., and Shigella sp.	Arsenic and uranium	Significantly remove As and U	[65]
	Staphylococcus hominis AMB-2	Cadmium and lead	Biosorption of Pb and Cd	[30]
	Pannonibacter phragmitetus BB	Chromium	99% Cr removal efficiency from soil	[99]
	Micrococcus luteus DE2008	Copper and lead	Able to absorb Pb and Cu	[31]
	Staphylococcus aureus	Lead	90% Pb removal capacity	[100]
	Sphingomonas paucimobilis 20006FA	Chromium	Cr removal efficiency of 90% from artificial contaminated soil	[101]
	Bacillus sp. MNU16	Chromium	75% Cr reduction capacity	[102]
Fungi	Aspergillus niger	Chromium	100% reduction of Cr at concentrations ranging from 10 to 50 mg/L.	[103]
	Saccharomyces cerevisiae	Nickel, mercury, and lead	Remediated Pb (86%), Ni (47%), and Hg (69%) from aqueous medium	[104]
	Penicillium sp., Trichoderma sp., and Aspergillus sp.	Cobalt and copper	High biosorption capacity of Cu and Co	[66]
	Fusarium sp.	Lead, chromium, and copper.	Remediated Pb (83%), Cd (93%), and Cr (84%) from wastewater	[105]
	Aspergillus nomius JAMK1	Lead, copper, and nickel.	Remediated Pb (99.25%), Ni (80%), and Cu (86.31%) from aqueous medium at a concentration of 100 ppm	[106]
	Ganoderma lucidum	Cadmium and lead	High Cd and Pb adsorption capacity from polluted water through precipitation mechanism	[107]
	Aspergillus flavus	Arsenic	Capable of converting soluble As into As particles, which have less toxicity	[108]
	Trichoderma sp.	Cadmium	Efficiently reduce Cd content and increase spinach growth	[109]
	Penicillium sp.	Cadmium, lead, and mercury	Remediation efficiency of 80% for Cd, 99.6% for Hg, and 92.4% for Pb	[23]
Algae	Cladophora glomerate and Enteromorpha intestinalis	Chromium	Efficient in the removal of Cr from aqueous solution	[110]
	Chlorococcum humicola	Cobalt	Remediate Co with 44% efficiency through biosorption	[111]
	Chlorella vulgaris	Manganese	99% efficiency in the removal of Mn	[112]
	Chlorophyceae sp.	Copper	88% efficiency in the removal of Cu by bioaccumulation	[112]
	Oedogonium westi	Nickel	60–90% efficiency in the removal of Ni	[113]
	Chlorophyceae sp.	Zinc	92% efficiency in the removal of Zn	[112]
	Phormidium ambiguum	Cadmium	86% efficiency in the removal of Hg by bioaccumulation and biosorption	[114]
	Enteromorpha intestinalis	Chromium	93% efficiency in the removal of Cr by biosorption	[115]
	Ulva Reticulata	Arsenic	60% efficiency in the removal of As by biosorption	[116]
	Phormidium ambiguum	Mercury	97% efficiency in the removal of Hg through bioaccumulation and biosorption	[114]
	Desmodesmus sp. AARLG074	Copper	80% efficiency in the removal of Cu by bioaccumulation and biosorption	[117]
	Ulva lactuca	Mercury	98% efficiency in the removal of Hg via bioaccumulation and biosorption	[118]
Yeast	Gelidium amansii	Lead	Pb biosorption with 100% efficacy	[68]
	Candida tropicalis	Chromium	60–70% Cr removal efficacy	[119]
	Saccharomyces cerevisiae	Chromium	96% Cr removal efficacy	[120]
Microbial consortia	Bacillus subtilis and Staphylococcus aureus	Lead, chromium, arsenic, nickel, and zinc	High remediation of heavy metals from polluted soil potential	[121]
	Saccharomyces cerevisiae and Pseudomonas aeruginosa	Chromium	99% Cr remediation efficiency from tannery effluents	[122]
	Antrodia serialis, Paecilomyces lilacinus, and Penicillium cataractum	Arsenic, iron, copper, manganese, and chromium	Significantly reduce heavy metal contamination in soil by bioaugmentation	[123]
	Pseudomonas aeruginosa and Bacillus subtilis	Chromium	Almost 100% Cr remediation efficiency from tannery effluents	[120]
	Streptomyces sp. M7, Streptomyces sp. MC1, Streptomyces sp. A5, and Amycolatopsis tucumanensis	Chromium	86% Cr removal efficiency from artificial contaminated soil	[69]
	Acinetobacter sp. and Arthrobacter sp.	Chromium	78% Cr remediation efficiency	[124]
	Saccharomyces cerevisiae and Bacillus subtilis	Chromium	97% Cr remediation efficiency from tannery effluents	[120]
	Daldinia starbaeckii, Perenniporia subtephropora, Phanerochaete concrescens, Fusarium equiseti, Cerrena aurantiopora, Polyporales sp., Aspergillus fumigatus, Trametes versicolor and Aspergillus niger	Arsenic, iron, copper, manganese, and chromium	Significantly reduce heavy metal contamination in soil through bioaugmentation	[69]
	Penicillium sp. A1 and Fusarium sp. A19	Chromium, lead, copper, and zinc	Efficiently accumulate heavy metals	[124]
	Pseudomonas pyogenes, Serratia marcescens, Erwnia amylovora, and Enterobacter cloacae	Lead, chromium, arsenic, nickel, and zinc	High remediation of heavy metals from polluted soil potential	[121]

5. Underlying Mechanisms of Microbial Bioremediation

Microbial bioremediation of heavy metals is a complex process and consists of several vital processes, including biosorption, biotransformation, bioaccumulation, and bioleaching. In particular, biochemical processes such as metal chelation, the transformation of toxic metal into non-toxic metal intermediates, ion exchange, metal precipitation, and metal efflux were identified (Figure 4). Recombinant DNA technology, a form of genetic engineering, can be used to alter the genetic material of microorganisms. This process involves exchanging genes between microbes, resulting in genetically engineered microorganisms (GEMs) or genetically modified microorganisms (GMMs) [125]. One of the emerging bioremediation approaches that shows great promise is the utilization of genetic engineering to enhance the capabilities of microorganisms in removing various heavy metals simultaneously [126]. It offers the benefit of creating microbial strains that can withstand challenging environmental conditions. These strains can be used as bioremediators in complex and diverse environments. The potential of genetic engineering in bioremediation has been recognized by molecular biologists and microbiologists.

However, a major challenge in utilizing these GEMs under real-world conditions is maintaining the population of recombinant bacteria in the soil, due to varying environmental factors and competition from native microbial communities [127]. Evaluations of the potential health risks linked to GEMs and the prevention of uncontrolled proliferation, horizontal gene transfer, and the spread of GEMs are still challenging. However, the implementation of programmed cell death in synthetic microorganisms following heavy metal bioremediation can be an effective option to mitigate the potential hazards associated with horizontal gene transfer and undesirable consequences such as unregulated growth and proliferation.

The use of microorganisms has proven to be a time-saving solution for bioremediation, especially considering the complexities associated with traditional soil remediation methods. However, a drawback of bioremediation is that certain microorganisms cannot convert toxic heavy metals into non-toxic forms, leading to inhibitory effects on microbial activity. To address this issue and boost the biodegradation capabilities of microorganisms, genetic engineering enables the transfer of desired traits from one species to another, creating specific strains tailored for the bioremediation of soil, sludge, or contaminated water [128,129].

6. Multi-Omics Approach for Enhanced Bioremediation

The extensive application of potential microbes, either in their pristine form or a genetically modified form, can be hindered by many limiting factors due to natural mutations and ineffectiveness. In general, potential microbes from diverse groups (e.g., bacteria, fungi, algae, and yeast) have been effective for heavy metal remediation under laboratory conditions. However, the functions of these potential microbes could be decreased under varied field conditions. Advanced biotechnological approaches can offer a holistic solution to tackle these shortcomings with pristine microbes. The time frame for studying microbiome composition shifted from relying on culture-based methods [130] to metagenomics, a technique that has potential in determining the genetic diversity of environmental microbes and in searching for novel functional genes connected with pollutant degradation [131]. Functional metagenomics proves to be quite useful in exploring the functions of genes. Function-based metagenomic analysis, which includes a process of DNA extraction from environmental samples, determines the role of proteins that are encoded [132].

Furthermore, Metagenomics, sometimes referred to as environmental genomics, offers a valuable perspective on microbial diversity at the genetic level and the associated metabolic pathways in a given environment through an analysis of the genetic material held by a microbial community [133]. Currently, functional and sequence-based approaches to metagenomics are being conducted. Sequence-based metagenomic investigations give molecular data regarding composition, dominance, and diversity in microbial communities [134,135]. Transcriptomics examines the entire transcriptome of an organism (which includes coding and non-coding messenger RNAs as well as various regulatory RNAs). The field is predominantly reliant on high-throughput techniques, especially microarrays and RNA sequencing, to study changes in gene expression caused by specific factors in experimental setups. Besides high-throughput technologies, quantitative reverse transcription PCR can be used to target gene expression levels [136]. Also, Proteomics refers to the total proteome/protein of an organism or cellular system at a given time in specific conditions [135]. More specifically, proteomics includes the differential expression of proteins, protein–protein interactions, protein turnover, and post-translational modifications. New molecular approaches, including proteomics, transcriptomics, metagenomics, and others, have opened new possibilities and strategies in environmental management [39]. These techniques have greatly facilitated the understanding of microbial community structures—which until recently relied on culture-based methods [130]. They can help to determine the genetic diversity of the microorganisms relevant to an environment and investigate new functional genes presumed to be involved in pollutant degradation [131]. Omics technology refers to a molecular biological approach that enables a simultaneous analysis of biomolecules such as DNA, RNA, proteins, and metabolites from individual organisms or even entire communities [137,138,139].

7. Prospects and Limitations

Microorganisms, being small in size, have the advantage of easily coming into contact with pollutants, enabling a swift and efficient process of treating or reducing contaminants to a safer level. The effectiveness of microbial remediation relies on various factors such as the type of microbes present, the characteristics of the pollutants, as well as the chemical and geological conditions of the contaminated area. Additionally, key elements that influence the efficiency of bioremediation by microorganisms include pH levels, temperature, oxygen availability, soil composition, nutrient content, the presence of heavy metals, and moisture level [140,141].

Bioremediation proves to be a valuable method when specific environmental conditions are met for the growth and function of microbes. Despite its uniqueness, bioremediation using microbes presents several challenges, such as safeguarding biodiversity, developing a reliable and cost-effective biological system for the efficient removal of heavy metals from contaminated sites, preventing heavy metal-related diseases in living beings, and preventing the contamination of air, water, and soils with HMs. Microbes are widely utilized in the remediation of heavy metals due to their rapid growth and ability to adapt to various heavy metal ions in the environment. They demonstrate remarkable tolerance and resilience against these contaminants. Further research is necessary to fully understand the efficacy and potential consequences of bioremediation technology [141,142].

Genetically Engineered Microbes and Their Prospects

Recombinant DNA technology, a form of genetic engineering, can be used to alter the genetic material of microorganisms. This process involves exchanging genes between microbes, resulting in genetically engineered microorganisms (GEMs) or genetically modified microorganisms (GMMs) [125]. One of the emerging bioremediation approaches that shows great promise is the utilization of genetic engineering to enhance the capabilities of microorganisms in removing various heavy metals simultaneously [126]. It offers the benefit of creating microbial strains that can withstand challenging environmental conditions. These strains can be used as bioremediators in complex and diverse environments. The potential of genetic engineering in bioremediation has been recognized by molecular biologists and microbiologists (Table 2). However, a major challenge in utilizing these GEMs in real-world conditions is maintaining the population of recombinant bacteria in soil. This is due to the varying environmental conditions and competition from native bacterial populations [127]. Evaluations of the potential health risks linked to GEMs and the prevention of uncontrolled proliferation, horizontal gene transfer, and the spread of GEMs are still challenging. However, the implementation of programmed cell death in synthetic microorganisms following heavy metal bioremediation can be an effective option to mitigate the potential hazards associated with horizontal gene transfer and undesirable consequences such as unregulated growth and proliferation.

The use of microorganisms has proven to be a time-saving solution for bioremediation, especially considering the complexities associated with traditional soil remediation methods. However, a drawback of bioremediation is that certain microorganisms lack the ability to convert toxic heavy metals into non-toxic forms, leading to inhibitory effects on microbial activity. To address this issue and boost the biodegradation capabilities of microorganisms, genetic engineering enables the transfer of desired traits from one species to another, creating specific strains tailored for the bioremediation of soil, sludge, or contaminated water [128,129].

Table 2. Genetically engineered microbes for enhanced bioremediation of heavy metals.

Microbial Species	Studied Heavy Metals	Genetic Modification	Enhancement of Outcomes	Reference
Saccharomyces cerevisiae	Arsenic	Expression of WaarsM gene	Improve As tolerance via volatization	[129]
Bacillus subtilis BR151 (pTOO24)	Cadmium	Luminescent cadmium sensors	Increase Cd bioavailability in soil	[143]
Escherichia coli		Overexpression of Metalloregulatory protein ArsR	Improve specificity and affinity for As, which allow 100% As accumulation	[144]
Caulobacter crescentus JS4022/p723–6H	Cadmium	RsaA-6His fusion protein	Enhance Cd retrieving capacity in water	[145]
Acidithiobacillus ferrooxidans	Mercury	Mercury ion transporter gene expression	High potential in the uptaking of Hg	[146]
Bacillus Idriensis and Sphingomonas desiccabilis	Arsenic	Overexpression of the arsM gene	Augment As removal through biovolatization in soil and aqueous systems	[147]
Pseudomonas putida	Chromium	Overexpression of ChrR	Increase Cr reduction	[148]
Escherichia coli SE5000	Nickel	Nickel transport system and metallothionein	Improve Cd uptake from aqueous solution	[149]
Pseudomonas fluorescens OS8; Escherichia coli MC1061; Bacillus subtilis BR151 and Staphylococcus aureus RN4220	Cadmium, mercury, and zinc	MerR/CadC/ZntR/Pmer/PcadA/PzntA	Enhance bioavailability of Cd, Zn, and Hg in soil	[150]
Methylococcus capsulatus	Chromium	CrR genes for Cr (VI) reductase activity	Increase bioremediation of Cr	[151]
Escherichia coli	Mercury	MerE protein encoded by transposon Tn21	Boost Hg uptake	[152]
Achromobacter sp. AO22	Mercury	Mercury reductase expressing mer gene	Improve in situ bioremediation of Hg	[153]
Escherichia coli JM109	Mercury	Metalloregulatory protein MerR using an INP anchor	Enhance biosorption of Hg	[154]
Escherichia coli	Arsenic	Co-expression of fMT with a specific arsenic transporter GlpF	Increase arsenic accumulation	[155]
Deinococcus radiodurans	Mercury	Hg (II) resistance gene (merA)	Highly efficient in reducing Hg at higher temperatures and at ionizing radiation	[156]
Pseudomonas putida 06909	Cadmium	Expression of metal-binding peptide EC20	Improve Cd binding and alleviate the cellular toxicity of Cd	[127]
Escherichia coli	Nickel and cobalt	Overexpression of Serin acetyltransferase	Enhance resistance against Ni and Co	[157]
Mesorhizobium huakuii B3	Cadmium	Phytochelatin synthase (PCS) gene expression	Increase Cd accumulation	[158]
Escherichia coli	Mercury	Expression of polyphosphate kinase and metallothionein	Boost Hg accumulation and tolerance	[159]

Table 2. Genetically engineered microbes for enhanced bioremediation of heavy metals.

Microbial Species	Studied Heavy Metals	Genetic Modification	Enhancement of Outcomes	Reference
Saccharomyces cerevisiae	Arsenic	Expression of WaarsM gene	Improve As tolerance via volatization	[129]
Bacillus subtilis BR151 (pTOO24)	Cadmium	Luminescent cadmium sensors	Increase Cd bioavailability in soil	[143]
Escherichia coli		Overexpression of Metalloregulatory protein ArsR	Improve specificity and affinity for As, which allow 100% As accumulation	[144]
Caulobacter crescentus JS4022/p723–6H	Cadmium	RsaA-6His fusion protein	Enhance Cd retrieving capacity in water	[145]
Acidithiobacillus ferrooxidans	Mercury	Mercury ion transporter gene expression	High potential in the uptaking of Hg	[146]
Bacillus Idriensis and Sphingomonas desiccabilis	Arsenic	Overexpression of the arsM gene	Augment As removal through biovolatization in soil and aqueous systems	[147]
Pseudomonas putida	Chromium	Overexpression of ChrR	Increase Cr reduction	[148]
Escherichia coli SE5000	Nickel	Nickel transport system and metallothionein	Improve Cd uptake from aqueous solution	[149]
Pseudomonas fluorescens OS8; Escherichia coli MC1061; Bacillus subtilis BR151 and Staphylococcus aureus RN4220	Cadmium, mercury, and zinc	MerR/CadC/ZntR/Pmer/PcadA/PzntA	Enhance bioavailability of Cd, Zn, and Hg in soil	[150]
Methylococcus capsulatus	Chromium	CrR genes for Cr (VI) reductase activity	Increase bioremediation of Cr	[151]
Escherichia coli	Mercury	MerE protein encoded by transposon Tn21	Boost Hg uptake	[152]
Achromobacter sp. AO22	Mercury	Mercury reductase expressing mer gene	Improve in situ bioremediation of Hg	[153]
Escherichia coli JM109	Mercury	Metalloregulatory protein MerR using an INP anchor	Enhance biosorption of Hg	[154]
Escherichia coli	Arsenic	Co-expression of fMT with a specific arsenic transporter GlpF	Increase arsenic accumulation	[155]
Deinococcus radiodurans	Mercury	Hg (II) resistance gene (merA)	Highly efficient in reducing Hg at higher temperatures and at ionizing radiation	[156]
Pseudomonas putida 06909	Cadmium	Expression of metal-binding peptide EC20	Improve Cd binding and alleviate the cellular toxicity of Cd	[127]
Escherichia coli	Nickel and cobalt	Overexpression of Serin acetyltransferase	Enhance resistance against Ni and Co	[157]
Mesorhizobium huakuii B3	Cadmium	Phytochelatin synthase (PCS) gene expression	Increase Cd accumulation	[158]
Escherichia coli	Mercury	Expression of polyphosphate kinase and metallothionein	Boost Hg accumulation and tolerance	[159]

8. Practical Challenges and Recommendations

The bioremediation of HMs is a classical and sustainable research strategy to tackle contaminated sites due to its cost effectiveness, facile technology, and eco-friendly applications. However, several key research pitfalls hinder the extensive application of this promising technology in real-field conditions. The following are the vital limitations and practical challenges concerning the bioremediation of HMs:

i. Single strain versus microbial consortia: A single strain of a potential microbe is not effective under real-field conditions due to hostile climatic factors and the natural mutation of potential microbial strains over time. Thus, microbial consortia (a combination of potential and compatible microbes from diverse genera) will be a wondrous solution to enhance the process of bioremediation under real-field conditions with hostile factors. Thus, microbial consortia or the effective microorganism concept can be applied instead of a single potential strain under adverse climatic factors.

ii. Coupling bioremediation for enhanced performance: The bioremediation process using only screened strain (e.g., bioaugmentation) is not a sustainable option for a robust remediation of pollutants. The innate potential of screened strains may be lost during the complete mineralization of HMs. Thus, the coupling of bioremediation with other compatible and promising strategies will boost the bioremediation of HMs. For instance, the coupling of bioremediation with nanotechnology will emerge as a new eco-friendly approach to remediate a HM-contaminated site (e.g., nano-bioremediation). Similarly, the nano-bioremediation approach can be boosted in the presence of phytoaccumulating plant species for efficient remediation of HMs contamination.

iii. Combined processes: In most cases, the solitary effect of a screened microbe strain is not a feasible option under varied climatic conditions. To overcome this shortcoming, several win–win combinations of bioremediation with other emerging strategies have been suggested by recent studies [160]. For example, HM bioremediation mediated by potential microbes in the presence of biochar or an organic amendment would be a great option. The chemical and biological health of soil is a key concern for the success of microbial bioremediation of HMs. If organic amendments will augment the exogenous organic matter and improve overall soil health, bioremediation will be enhanced to tackle global HMs contamination.

iv. Genetic engineering or advanced biotechnology: The advancement of biotechnological tools is necessary for enhancing the bioremediation process. In general, the potential strains that are super active under laboratory assay will be inactive in real-field conditions. These constraints of microbial bioremediation can be resolved by employing advanced biotechnological toolkits and genetic engineering approaches. As a thumb rule, the microbial strains isolated from metal-contaminated sites will act as good candidates for managing metal-contaminated soils and sediments. Even the effective strains will be employed for treating HM-contaminated wastewater. The stress tolerance of metal can be enhanced through advanced biotechnology. Engineered microbes (like bacteria, yeast, or fungi whose genetic material has been intentionally modified using biotechnology to perform specific tasks) will be explored for large-scale bioremediation both in the field and in wastewater treatment plants.

v. Horizontal gene transfer (HGT): Horizontal gene drives will boost bacteria-mediated bioremediation. In general, the diverse genera of bacteria, particularly plant growth-promoting bacteria (PGPB), are key biological drivers for remediating HMs contamination both in pilot-phase lab trials and real-field studies. PGPB are typically fast-growing bacteria and will persist until the log growth phase without any engineering. However, horizontal gene transfer (the transfer of genetic material between organisms without reproduction) is a robust technology for harnessing classical bioremediation through indigenous bacterial strains. Usually, the vector-mediated HGT will be active even after the bacterial log growth phase has disappeared. Thus, HGT will provide sustainable bioremediation after the disappearance of traditional bacteria.

vi. Economic feasibility: The critical concern associated with the commercial application of bioremediation is cost-effectiveness. There are several convenient approaches that have already been explored for efficient HMs remediation, including chemical, catalytic, and biological approaches. Among the available approaches, the most suitable approach will be assessed for sustainable bioremediation in terms of an economic perspective (this involves evaluating how affordable, scalable, and sustainable the method is for both researchers and end-users). The most affordable approach will be accepted by both the research community and end-users.

9. Conclusions

Microorganisms have biological processes that allow them to tolerate severe metal stress and eliminate metals from the environment. Microbe-assisted phytoremediation works best at sites with relatively low pollution levels that are amenable to processes like biomineralization, biostimulation, mycoremediation, cyanoremediation, phytodegradation, phytostabilization, hyperaccumulation, dendroremediation, and rhizofiltration for a long time. Many microbes can naturally break down metals, but this is insufficient on a global scale. As a result, genetic engineering can be used to create designed microorganisms as a solution to this problem. Although transgenic microorganisms and plants have the potential to effectively repair heavy metal and organically polluted environments, their usage should be subjected to strict biosafety standards to verify that there are no health or environmental risks. Researchers in the area should look into new species that have a lot of potential in the future. Bioremediation is only effective when environmental circumstances allow for microbial growth and activity, and it is a highly safe and accommodating method because it relies on bacteria that naturally occur in the soil and pose no risk to the environment or the people who live there. Despite the availability of diverse bioremediation sources, such as bacteria, archaea, yeasts, fungi, algae, and plants, biological therapy alone is insufficient to remove pollutants or polluted locations. This review summarizes the current scientific advances in using biotechnological methods for environmental management in the burgeoning field of bioremediation (with the help of microorganisms and plants) to reduce pollution concerns around the world. Although extremely effective microorganisms are produced for a range of applications, the beneficial potential of microorganisms in the field of bioremediation and phytoremediation remains large and untapped. More research is needed, however, to determine the precise and unambiguous mechanisms involved in heavy metal removal by bacteria, fungi, and algae.