With the onset of the twentieth century, human beings have witnessed advancement in technologies related to food production, health, infrastructure, transport, and communications. Such activities require a vast quantity of new materials and energies destroying natural environmental components and the production of huge quantities of wastes resulting in environmental degradation (Mani and Kumar, 2014). The presence of toxic metals and metalloids in the waste generated from the industrial, domestic, and agricultural sectors causes significant damages to the ecosystem and associated lives (Pourret et al., 2016; Goyal et al., 2020; Leong and Chang, 2020). The contaminants are highly mobile and soluble, thus possessing the capability to be bioaccumulated in the food chain and causing serious damage with increasing tropic levels (Petavratzi et al., 2005; Zerizghi et al., 2020). When these contaminants enter the human body, they can cause various life-threatening diseases such as cancer, kidney and bone diseases, cardiovascular diseases, hypertension, low birth weight, Alzheimer diseases, and atherosclerosis (Nawrot et al., 2006; Ahern et al., 2011; Bernhoft, 2012; Flora et al., 2012; Muszynska and Hanus-Fajerska, 2015; Lee et al., 2017). Metal accumulated in biological tissues is hard to remove due to its non-biodegradability, and it becomes a major concern to global health (Ayangbenro and Babalola, 2017). Metal contamination leads to the alteration in soil physicochemical and biological properties such as an increase in bulk density and soil pH, as well as a decrease in soil fertility and water holding capacity, microbial diversity and soil enzyme activity (Wuana and Okieimen, 2011; Jin et al., 2019; Saha and Bauddh, 2020). They are also responsible for the alteration in microbial communities, leading to disturbing the proper function of the biogeochemical cycle and imbalance in the ecosystem (De Quadros et al., 2016; Feng et al., 2019). Heavy metals like As, Hg, Ni, Cr, Pb, and Cu can cause multiple indirect and direct effects on plant growth, such as chlorosis, necrosis, root injury, reduced carotenoid concentration, oxidative stress, inhibition of enzyme activities, osmotic imbalance, decreased photosynthetic activities, and imbalance of the nutrients (Lewis et al., 2001; Mascher et al., 2006; Shaibur et al., 2009; Yadav, 2010; Hasan et al., 2017; Sachan and Lal, 2017). Further, due to these environmental effects of metals, there are incessant efforts made to sustainably eliminate this toxic and excess amount of metals for stabilizing the ecosystem.

Various physicochemical techniques (such as extraction, immobilization, stabilization, coagulation, electrodialysis, vitrification, reverse osmosis, ion exchange, chemical reduction, evapotranspiration, and precipitation) have already been practicing to reduce metal contamination (Ali et al., 2013; Gupta and Kumar, 2017). However, these techniques are costly, require high energy, harsh chemicals with low removal efficiency, and can generate secondary environmental pollution (Tang et al., 2007; Acheampong et al., 2010; Ali et al., 2013; Gupta and Diwan, 2016; Suman et al., 2018). Therefore, there is a continuous demand for environmental friendly remediation methods that can be helpful to reduce its harmful effects on the environment.

Bioremediation is an ecologically sound technique that requires the use of green plants, microorganisms including fungi, bacteria, yeast, and algae or their enzymes to help the polluted sites return to their original states (Chakraborty et al., 2012; Mani and Kumar, 2014). The late 19^th century ascertained to be the golden period for bioremediation. With further improvement, the 20^th century marked the beginning of research in the field of microbial ecology, involving the identification and isolation of microbes that have the potential to degrade pollutants, e.g., Candidatus accumulibacter that is capable of accumulating excess amount of phosphorus as polyphosphates in their cells from the sewage treatment plants (Seviour et al., 2003). Later, the delineation of catabolic pathways to break pollutants, the genomic construction of recombinant microbes tailored to eliminate metals, and the application of molecular techniques to understand microbial activities have been explored (Siezen and Galardini, 2008; Ramos et al., 2011).

Soil microorganisms play an essential role in stabilizing soil macroaggregates by producing polysaccharides to maintain soil architectural patterns for plant productivity (Ghose, 2005). Such microorganisms including numerous species of bacteria, fungi, yeast, and algae contribute significantly to the decomposition and stabilization of inorganic and organic pollutants (Fulekar et al., 2012; Rahman et al., 2015; Leong and Chang, 2020). A number of studies have highlighted that various natural and genetically engineered microorganisms (GEM) such as Bacillus cereus, Chlorella pyrendoidosa, B. cereus XMCr-6, Pseudomonas veronii 2E, P. aeruginosa, Serratia marcescens, Sacharomyces cerevisiae, Penicillium canescens Spirogyra sp., Spirullina sp., and Cladophora sp. are responsible to remediate HMs such as Cd, Pb, As, Cr, Mn, Cu, U, Se, and Zn from contaminated land and water (Lee and Chang, 2011; Kumar et al., 2011b; Hrynkiewicz et al., 2012; Kanmani et al., 2012; Mane and Bhosle, 2012; Mani and Kumar, 2014; Farhan and Khadom, 2015; Lívia et al., 2015; Ojuederie and Babalola, 2017; Verma and Kuila, 2019).

There is a need for characterization and regular assessment of various contaminated sites such as mining dumpsites, nuclear waste, surface wastewater, sewage sludge pump sites, agricultural soils, and various industrial and commercial dumping zones. Recently a number of research studies and literature reviews have been focused on the phytoremediation potential of particular plant species and selected metals with different microorganisms or particular microorganism-based remediation strategies (Raza et al., 2020; Yan et al., 2020; Wang et al., 2021; Hao et al., 2021; Sharma et al., 2021).

In this review, we have covered some new aspects and dimensions of bioremediation of heavy metal-polluted soils. Here, we have reviewed the recent literature published mainly between the year 2019–2021. There is a critical examination of the bioremediation potential of different microorganisms, especially bacteria and fungi individually and in association with plants. Further, the different mechanisms adopted by the microorganisms to detoxify HMs have also been discussed. Moreover, the study attempts to explore the knowledge about field applications with several case studies, factors affecting bioremediation, challenges, as well as future prospects have been covered.

The relevant literature was searched and collected from the online database using Scopus, Web of Science, Google, Google Scholar, Springer Nature, Frontiers, Taylor and Francis, Science Direct, etc. The keywords used for the literature search include bioremediation, phytoremediation, phytoextraction, phytomanagement, remediation using living organisms, remediation through plant/microorganism, plant–microbe association for heavy metal removal, etc. In addition, particular focus journals such as International Journal of Phytoremediation, Bioremediation Journal, Frontiers in Microbiology, Journal of Environmental Management, Frontiers in Plant Science, Science of the Total Environment, Chemosphere, Water, Air, & Soil Pollution, Environmental Science and Pollution Research, Microbial Research, etc. were browsed volume-wise for track the relevant papers until July 2021. The literature includes journal articles, books, book chapters, conference papers, proceedings, and technical reports were referred in this review paper from which 92.91% were published between the years 2010 to 2021. In total, more than 400 documents were examined individually and eliminated the quotative and duplicate papers (Qi et al., 2018). Out of which 254 documents were selected for reference in this work.

Bioremediation is an emerging and highly acceptable practice for restoring heavy metal contaminated soils, because of its environment friendly and low cost as compared to other conventional methods such as dredging, capping, and incineration that are often very costly and ineffective when metal concentration level is low and often generates a significant amount of toxic byproducts (Ekperusi and Aigbodion, 2015; Ayangbenro and Babalola, 2017). A study has been shown that it costs about 100–500 USD/ton for cleaning metal-polluted sediments and soils through landfilling and chemical treatment, and 90–870 USD/ton for vitrification, whereas about 15–200 USD/ton for bioremediation and 5–40 USD/ton for phytoremediation (Meier et al., 2012). It estimates that bioremediation can save 50–65% for cleaning one acre of Pb-contaminated soil compared to traditional excavation and landfill (Blaylock et al., 1997; Chibuike and Obiora, 2014). In addition, bioremediation is a non-invasive method that can remove contaminants permanently, leave the environment intact, and can be hybridized with chemical and physical treatments (Mani and Kumar, 2014). The bioremediation processes rely entirely on natural biological potency. The majority of bioremediation methods depends on several parameters such as soil structure, pH of the polluted sites, moisture content, type of the pollutants, nutrient supplement, microbial diversity, the temperature of treatment sites, and oxygen availability (Atagana et al., 2003; Thapa et al., 2012; Mangunwardoyo et al., 2013; Mani and Kumar, 2014). Bioremediation can occur naturally in a polluted site, which is called natural attenuation.

Lombi and Hamon (2005) have divided bioremediation into ‘in-situ’ and ‘ex-situ’ strategies. In-situ or on-site bioremediation is the most preferred option for removing contaminants from polluted soil and water. In the in-situ process, the soils remain confined to their initial location throughout the reclamation process, ending up in minimal site disturbance, fewer public health risks associated with excavation and off-site transport of contaminated soil, and reduced the overall cost over other remediation technologies (Hellekson, 1999; Lombi and Hamon, 2005). The in-situ bioremediation is broadly classified into two types, intrinsic and engineered bioremediation (Hazen, 2010). Intrinsic bioremediation takes place through the stimulations of indigenous microorganisms by supplying them with nutrients and oxygen to boost their metabolic activity. This is an unstimulated, unmanipulated, and unenhanced biological remedy of contaminates. Whereas for engineered bioremediation, a specific type of microorganisms or genetically engineered bacteria are introduced into the contaminated place to accelerates the degradation process by creating a conducive physicochemical condition (Kumar et al., 2011).

On the other side, ex-situ bioremediation methods require the excavation of polluted soil and water from its original location for the treatment. This is further categorized as a solid-phase system and slurry phase system. Solid-phase bioremediation includes contaminated waste such as industrial waste, domestic waste, municipal solid waste, and sewage sludge with organic waste including manure, leaves, and agricultural waste. The treatment process includes composting, soil biopile, hydroponics, and land farming, which create suitable conditions for indigenous anaerobic and aerobic microorganisms to boost the reclamation process (Kumar et al., 2011; Rayu et al., 2012). From which in hydroponics methods plants are grown in the mineral nutrient solution. Nowadays, this method is a common step for screening the suitable plant for phytoremediation by characterization of its response to heavy metal stress. On the other hand, slurry phase bioremediation is a speedy process where contaminated soils are mixed with additives and water in a bioreactor to create an appropriate environment for microorganisms to eliminate the contaminants.

Both in-situ and ex-situ remediation methods work on the principle of biotransformation/biodegradation, removal, mobilization, immobilization, or decontamination of various pollutants from the environment through the action of microorganisms (bacteria, fungi, and yeast) and plants (Abatenh et al., 2017). Microbes use chemical contaminants as an energy source during biotransformation and metabolize the target contaminant into useable energy via redox reactions. There are usually less harmful by-products or metabolites released back into the environment compared to the primary pollutants. For instance, microorganisms can degrade petroleum hydrocarbons through aerobic respiration in the presence of oxygen. The hydrocarbon gets oxidized by losing electrons, whereas the oxygen reduces by gaining electrons. Water and carbon dioxide are formed as a by-product of this redox reaction (Nester et al., 2001).

The microorganisms play an important role in HM remediation from the contaminated soil as they have acquired various mechanisms to tolerate the toxic effects of HMs. Microorganisms can sequester, precipitate, biosorb, and change the oxidation states of various metals (Ndeddy Aka and Babalola, 2016; Yin et al., 2019; Rizvi et al., 2020; Ibrahim et al., 2021). Metal sequestration happens by cell wall components and by intercellular metal bindings peptides and proteins such as metallothionein, phytochelatins with bacterial siderophores (Ojuederie and Babalola, 2017; Balzano et al., 2020). Microorganisms convert the toxic metal into a less toxic or innocuous form with the help of enzymes (such as dioxygenases, peroxidases, and oxidoreductases). The mechanisms applied by microorganisms to remove HMs from the contaminated soil or convert to less toxic form have been presented in Figure 1. However, the biosorption mechanism is based on two way: first depends on cell metabolism and second on the location of the cell where the HM is removed.

Three key bioremediation ingredients are (1) the presence of a contaminant, (2) the acceptor of electrons, and (3) the existence of microorganisms that can degrade a specific contaminant. Generally, the biodegradation process is easy for the naturally occurring contaminant or those have chemical similarities with naturally occurring compounds. It is due to the potential of microorganisms to destroy the contaminants. For instance, petroleum hydrocarbons are naturally derived chemical products, therefore microorganisms are habituated for these contaminants and can degrade them easily. Different approaches applied in the microbial remediation process such as bioattenuation, biostimulation, bioaugmentation for removing the toxic pollutants from the contaminated land, have been described below.

Plants are used for bioremediation either alone or in combination with microbes (Ramos et al., 2005) instead of depending on microbes and their efficacy in achieving bioremediation of any contaminated medium. The application of green plants to clean up any contaminated medium or surface is not a novel concept. Plants were proposed for treating the wastewater around 300 years ago (Hartman, 1975). Presently a number of plant species such as Amaranthus spinosus, A. hypochondriacus Chrysopogon zizanioides, Brassica juncea, Ricinus communis, Chromolaena odorata, Ageratum conyzoides, Ipomoea carnea, Prosopis juliflora, Lantana camara, Parthenium hysterophorus, Fagopyrum esculentum, Odontarrhena chalcidica, Tagetes patula, T. erecta, and Odontarrhena chalcidica, have been identified which helpremediate HM contaminated soil (Bauddh and Singh, 2012; Bauddh and Singh, 2015; Huang et al., 2019; Chen et al., 2020a; Raza et al., 2020; Biswal et al., 2021; Cui et al., 2021; Gonzaga et al., 2021; Nugroho et al., 2021; Singh et al., 2021). In addition, plants like Nicotiana tabacum, Arabidopsis thaliana, Beta vulgaris and Sedum alfredii have been genetically modified with suitable bacterial genes from Caenorhabditis elegans, Saccharomyces cerevisiae, Streptococcus thermophilus, Pseudomonas fuorescens and employed for remediating the targeted contaminants (Daghan et al., 2013; Liu et al., 2015a; Wang et al., 2019; Nedjimi, 2021). For instance, mercury (Hg) reductase bacterial genes, e.g., merA and merB have been applied in plants for the detoxification of methyl-Hg (Li et al., 2020a). In addition, various biostimulators, such as manure and organic amendments (e.g., various plant biochar, biosolids, and litter) are used in this plant-based bioremediation. Use of different chelators such as citric acid, ethylene diamine tetraacetic acid (EDTA), [S,S]-ethylenediaminedisuccinic acid (EDDS), ethylenediamine-di-o-hydroxyphenylacetic acid (EDDHA), diethylenetriaminepentaacetic acid (DTPA), ethylene glycol tetraeacitic acid (AGTA), nhydroxyethylenediaminetriacetic acid (HEDTA), fulvic acids, salicyclic acid, and tartaric acid control metal sorption, and precipitation through the formation of metal chelate complexes, which consequently enhance the bioavailability of these metals and also improve phytoextraction efficiency (Caporale and Violante, 2016; Acuña et al., 2020; Saleem et al., 2020). The addition of chelates in soils can move more metals into soil solution via the suspension of precipitated compounds and desorption of sorbed species. Plants can also naturally produce various phytosiderophores, organic acids, and carboxylates, which can enhance metal mobility, solubility, and bioavailability in soils, thus increasing the phytoremediation potential of plants (Vithanage et al., 2012; Gupta and Singh, 2017). For instance, Miscanthus sinensis can detoxify Al by producing various phytosiderophores such as citric acid, malic acid, and chlorogenic acid and stored the metal in cell walls (Haruma et al., 2019).

Plant-based bioremediation is considered a potential tool for the accumulation, transformation, and immobilization of a low level of contaminants (Rayu et al., 2012). The mechanisms behind plants facilitate the reclamation of the polluted soils and groundwater are presented in Table 1. The approach of plant-based bioremediation has several merits such as cost-effectiveness, public acceptance, and the ability to remove inorganic and organic contaminants simultaneously. In a study, mixed mercury-trichloroethylene (Hg-TCE) pollutants are removed by transgenic alfalfa plants pKHCG co-expressing human P450 2E1 (CYP2E1) genes and glutathione S-transferase (GST; Zhang et al., 2013). A major synergistic effect caused by simultaneous expression of CYP2E1 and GST leads to increased accumulation and resistance of heavy metal–organic complex pollutants. Another study by Tammam et al. (2021) found that the plant Glebionis coronaria can eliminate Pb from the contaminated soil. It is also recorded that the foliar spray of Indole-3-acetic acid (IAA) and gibberellic acid (GA3) enhanced the growth significantly and increase the phytostabilization capacity of the studied plant. The application of bamboo biochar with the Salix psammophila to remediate the multi-metal contaminated soil, enhance the translocation factor (TF) and bioconcentration factors (BCF) of Cd, Cu and Zn (Li et al., 2021a). The higher TF for Zn (TF > 1) and BCF for Cd (BCF > 1) makes S. psammophila a potential candidate for the phytoremediation in BBC amendment soil. Recently several studies found that the application of nanoparticles such as Ag nanoparticles (AgNPs), nano-TiO₂ particles, nanoscale zero-valent iron (nZVI), salicylic acid nanoparticles (SANPs) and magnesium oxide (MgO) nanoparticles along with plants Zea mays, Glycine max, Isatis cappadocica, Lolium perenne, Boehmeria nivea and Raphanus sativus enhance the growth and phytoextraction of HMs Cd and Pb (Khan and Bano, 2016; Singh and Lee, 2016; Gong et al., 2017; Souri et al., 2017; Huang et al., 2018; Hussain et al., 2019).

Plants are effective in extracting inorganic and organic pollutants from the ground through the roots, they can also be transported and accumulated (phytoextraction/accumulation) in the harvestable parts of the plant (Pranaw et al., 2020). Transpiration to the atmosphere via leaf stomata (phytovolatilization) occurs in some instances (Rascio and Navari-Izzo, 2011). Phytodegradation of organic compounds are metabolized by plants in three sequential steps (namely transformation, conjugation, compartmentalization, respectively) with the aid of enzymes, e.g., cytochrome (CY) P450 and GT–glycosyltransferase (GT), which results in the storage of contaminant in the vacuole, incorporation into the cell wall, or excretion from the cell. In addition, plant-associated microorganisms in the rhizosphere (rhizodegradation) can degrade organic contaminants (Truu et al., 2015). By releasing root exudates and other compounds (e.g., organic acids) to the surrounding soil along with providing a surface for microbe colonization, plants can promote the biodegradation of pollutants, thereby contributing to the increased density and metabolic activity of microorganisms (rhizosphere effect) and contaminant bioavailability. Plant supplements nutrients to endophytic bacteria and stimulates catabolic gene expression. In turn, endophytic bacteria degrade organic contaminants, thereby reducing phytotoxicity and producing hormones (Shukla et al., 2020).

Since metal bioavailability in soils is relatively poor under most conditions, plants have very active metal uptake systems that utilize transporter molecules such as Zn-regulated transporter protein, Cu transporter protein, etc. (Krämer et al., 2007). In addition, plants are capable of acidifying the soil and mobilize soil-bound metals by secreting metal-chelating molecules to the surrounding soil, such as siderophores (catechol and hydroxymate), organic acids (e.g., citrate and malate), biosurfactants (rhamnolipids), protons from the root exudates (Yan et al., 2020; Bruno et al., 2021). Heavy metals cannot be biodegraded inside the plant, unlike organic contaminants, but can only be converted from one oxidation state/organic complex to another. It ends up in metal accumulation inside the plant. There are nearly 450 hyperaccumulator plants varies from annual to perennial herbs, shrubs, and trees (e.g., Brassica juncea, Zea mays, Ricinus communis, nicotiana tabacum, Helianthus annuus, Pteris vittata, Thlaspi caerulescens, Russian thistle, Sesbania drummondii, Salix matsudana, Populus deltoides), which have been identified to accumulate, metabolize and depollute extraordinary high concentration of metal ions (such as Cd, Pb, Ni, Co, Mn, Zn) in their above-ground tissues (Meagher, 2000; Padmavathiamma and Li, 2007; Shah and Nongkynrih, 2007; Sheoran et al., 2009; Palanivel et al., 2020).

The capacity of microorganisms to degrade contaminants depends on their metabolic system through which the pollutants alter to innocuous form via the redox process (Jan et al., 2014). They help plants alleviate metal toxicity by sequestration of metals in cell wall components, alteration of the biochemical pathway to block metal uptake, reduction of the intercellular metal concentration via a precise efflux system, and conversion of poisonous metals to a less harmful state (Jan et al., 2014; Ojuederie and Babalola, 2017). Microorganisms (such as bacteria and fungi) play a vital role in the microbial bioremediation process. In addition, microorganisms contain several genes located in transposons and plasmids, which encode heavy metal resistant proteins and transporters. Recently, Kang et al. (2016) found that four bacterial strains, namely Enterobacter cloacae KJ-46, E. cloacae KJ-47, Sporosarcina soli B-22, and Viridibacillus arenosi B-21 had synergistic effects on the remediation of Cd, Pb, and Cu from contaminated soil. Moreover, the combination of bacteria strains shows greater resistance and efficacy for metal bioremediation compared to a single strain after 48 h of experiments. Microbes secrete several metabolites that play a significant role in bioremediation of contaminated sites (Sobrinho et al., 2013; Dixit et al., 2015; Coelho et al., 2015; Ahemad, 2019; Figure 2).

Bacteria generate siderophores that can diminish metal bioavailability and are subsequently eliminated from contaminated land (Ahemad, 2019). It is recorded that bacterial cell can alter their morphology to increase the production of siderophores for promoting the intercellular accumulation of metals (Manoj et al., 2020). Chibuike and Obiora (2014) found that a sulfate-reducing bacterium Desulfovibrio desulfuricans can alter sulfate to hydrogen sulfate, which further reacts with HMs (Cd and Zn) and then form insoluble metal sulfides. The biomolecules of microbial cell walls contain negatively charged functional groups such as phosphate, hydroxyl, and carbonyl, which bind quickly with toxic metal ions and help them in bioremediation (Coelho et al., 2015; Dixit et al., 2015). Besides, bacteria can be grown and survive in any control and intense environmental conditions, making them a perfect bioremediation agent (Srivastava et al., 2015).

Likewise, fungi can be grown in harsh environmental conditions and detoxify metal ions by accumulation, valence transformation, and extra and intracellular precipitations (Ayangbenro and Babalola, 2017). In addition, fungi act as a promising biocatalyst in the bioremediation process, where they absorb toxic chemicals into their spores and mycelium. Recently, Hassan et al. (2020a) showed the bioremediation capability of fungal consortia of Ascomycota and Basidiomycota, suggesting fungal bioaugmentation helps decontaminate heavy metal from contaminated land. A number of investigations are carried to study the microorganism bioaccumulation and biosorption capacity for effectively remediate metal-contaminated environment (Table 2).

Recently researchers have been isolated various heavy metal resistance microorganism from contaminated lands, mining dumping and abandoned sites, industrial waste dumping yards, and the rhizosphere of plants growing in metal-contaminated sites (Banerjee et al., 2019; Aguilar et al., 2020; Akhter et al., 2020; Nurfitriani et al., 2020; Din et al., 2021; Sharma and Shukla, 2021b). The isolated bacterial genera (such as Arthrobacter, Enterobacter, Corynebacterium, Stenotrophomonas, Bacillus, and Pseudomonas) and fungi (such as Aspergillus flavus, Aspegillus awamori, Saccharomyces cerevisiae, Phanerochaete chrysosporium, Penicillium oxalicum, and Trichoderma viride) play a significant role in bioremediation process. Bacteria and fungi precisely used to eliminate the specific metals in recent years have been reviewed and presented in Tables 3, 4, respectively.

The microorganism-plant-based remediation has gain popularity currently due to its higher removal efficiency compared to plant-based remediation process. These microorganisms are involved in the various biochemical process such as carbon and nitrogen mineralization, nitrogen fixation, and decomposing organic matter, which contributes to soil formation, nutrient cycling and transfer of energy. Soil microorganisms are also affected by HMs in contaminated areas. However, with continuous exposer, they tend to tolerate and develop unique features with few specific microbial populations. These types of specific microbes can be employed for remediating toxic metals from contaminated lands. Further, soil microorganisms that form a symbiotic association with host plants are the most successful species in the soil reclamation process. The mycorrhizal fungi form intimate symbiotic relationship with host plants, which have been applied in many bioremediation processes (Yang et al., 2015; Gunathilakae et al., 2018; González-Chávez et al., 2019; Rubin and Görres, 2021). The arbuscular mycorrhizae as the most well-known symbiotic fungi are frequently used in phytoremediation due to their ubiquity in soil. They can develop several mechanisms to tolerate high metal concentrations in soils, thus promoting plant growth (Janoušková et al., 2005; Fasani et al., 2018). In addition, plant growth-promoting bacteria (PGPB) can also stimulate plant growth activities and help plants cope with the contaminated ecosystem. They can enhance plant growth through direct and indirect mechanisms that are discussed in the separated section below.

There are two aspects of plant–microbe-based bioremediation process. First of all is the microorganisms help the host plant sustain in the harsh environmental condition by providing nutrients. Second, the plant plays a critical role by maintaining favorable environmental conditions such as improving soil organic matter, available P, K, and N, where soil microorganisms can thrive and enhance the reclamation process. Recently, a number of studies have been highlighted both side benefits of the plant–microbe-based bioremediation process. A study recorded that planting of Trifolium repens in heavy metal contaminated sites improves soil enzymatic activities (Lin et al., 2021). Wang et al. (2021) also showed that plantation of Salix in Cd contaminated soil increased beneficial microorganisms diversity, such as genera of bacteria include Arthrobacter, Bacillus, Flavobacterium, Niastella, Novosphingobium, Niabella, Anaeromyxobacter, Rmlibacter, Solitalea, Devosia, Mesorhizobium Nitrospira, Thermomonas, Flavisolibacter, Pedomicrobium, Lysobacter, Rubrivivax Phyllobacterium, and mycorrhizal genera of fungi include Actinomucor, Conocytes, Amanita, Cryptococcus, Xylaria, Ramicandelaber, Spizellomyces, Sporobolomyces, Rhodotorula Umbilicaria, Claroideoglomus, Tilletiopsis, and Cirrenalia in plant rhizosphere.

The most important factor affecting bioremediation efficiency is site characteristics. Secondly, environmental factors such as water content, temperature, pH, nutrient availability, moisture content, and pollutant bioavailability can also hinder the efficiency of bioremediation (Freitas et al., 2013; Azubuike et al., 2016; Khodaverdiloo et al., 2020; Leong and Chang, 2020). Apart from this, the bioremediation process is a complex system that is optimized and controlled by many factors. The interactions among the contaminants, microbes, nutrient availability and environmental factors affect the bioavailability and biodegradation of the contaminants.

The bioremediation methods are diverse and show effectiveness in restoring the polluted sites contaminated with multiple HMs. However, there are some important factors to be considered before implementing bioremediation practices. There is a need for regular investigation and assessment of the level of HMs and other pollutant concentrations in the contaminated sites before proposing bioremediation. The selection of an appropriate type of microbes and plant species is a very hefty task for the sites where the presence of multi-metals and other organic pollutants at the same site. Secondly for the plant-based bioremediation, the presence of volatile metals and metalloids such as Si, Hg, and As in the site may get volatilized into the atmosphere in their toxic form which may affect the living organisms. Third, if edible plants are used for bioremediation purposes, there is a risk that they can be consumed by animals, insects and which may further contaminate the food chain and ultimately reach humans and cause serious health complications. For this, nonedible and nonpalatable phytoremediator plant species can be preferred or in the case of the edible plants, proper protection during cultivation, and harvesting must be taken to avoid future complications. With the presence HMs deeper into the ground where plant roots cannot reach, in situ phytoremediation becomes difficult.

Further research, assessment, and investigation are required to enhance our knowledge and understanding of best management practices for efficient bioremediation of HMs. There is a need for futuristic clarification of mechanisms, metabolites, and novel approaches/methods are required. For simple and efficient plant-based bioremediation, utilization of hyperaccumulator plants to efficiently remove of HMs from the contaminated soil need novel strategies for its further progress. This can be achieved in two ways, first by finding and validating the various diversity of new hyperaccumulator plant species, and second by developing the hyperaccumulator plant using genetic engineering. In addition, we can consider the hyperaccumulator plants with deep root plants for, e.g., woody plants or tree such as Populus × canescens, Rinorea bengalensis, Schima superba and Pycnandra acuminata with high translocation rate, high biomass and growth rates and more tolerant plant species.

Biotechnological intervention including genetic engineering, for example, the rate-limiting step in a known metabolic pathway can be manipulated genetically to enhance the transfer and biodegradation rates, or by introducing a completely new metabolic pathway into the microbe for higher accumulation of HMs or degradation of recalcitrant compounds. In addition, overexpression of foreign genes into a non-tolerant plant with having higher biomass for HM remediation from the soil may be a feasible strategy. The advanced way to study hologenomics of plants microorganism will be helpful for the manipulation of microbial niches which help to enhance the resistance against toxic metal contamination. For multi-metal contaminated and multi-stress environmental conditions, there is a need to development of suitable amendments to enhance the survival of the suitable plant species. Although there are several organic and inorganic amendments and metal chelators are available there is a need for further investigation to find out more suitable and eco-friendly amendments which can be applied for the treatment of multi-metal contaminated and multi-stressed soil. There is a necessity for coordination and contribution of researchers, scientists, policymakers, government, industrial sectors, and individuals that can help to success and reliability of bioremediation.

Man-made activities have been introducing a high amount of toxic metals into the environment, affecting the life processes of all living organisms in direct and indirect ways. It has been reported that more than one type of heavy metal is simultaneously present in the contaminated land and the available conventional methods are not significantly efficient to detoxify the pollutants compared to the bioremediation process. It has been proved that bioremediation methods are easily affordable compared to other physicochemical remediation techniques. A number of bacterial and fungal strains have been isolated and identified from different metal-contaminated and mining abandoned soils in recent years. Pseudomonas spp., Bacillus spp., Aspergillus spp., and Penicillium spp. are found frequently and show high metal tolerance and bioremediation potential. Currently, bioremediation has been practiced in various contaminated sites globally with varying degrees of success. Recently by applying the various plants and microorganisms to remediate the contaminants from the environment has been noted like Alaska oil spill remediation, China’s Aleutian island bioremediation operation and other decontamination cases of HMs from the industrial and agricultural fields. The addition of proper supplements and enhancing environmental conditions are the prime concern for the significant yield of bioremediation. To overcome the above problem, the addition of organic matter and a consortium of microorganisms can enhance microbial metabolic activity and may improve bioremediation potential. In addition, more investigations are still required to screen the more suitable microorganisms, hyperaccumulator plants that will have a high capacity to tolerate multi-metal contaminated and multi-stress environmental conditions sites and accumulate multi-metals at once. Further attention will be required to plant–microbe-based bioremediation strategies to identify the novel plant–microbe pairs that will have high metal removal efficiency along with creating a favorable environment to accommodate other microbial diversity for indirectly improving the soil health. Additionally, further research on the application of nanomaterials and biochar along with microbes to enhance bioremediation efficiency is needed.

All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.

This work is carried out at the College of Resources and Environment, Southwest University, supported by the Fundamental Research Funds for the Central Universities (No. SWU 020010), the Natural Science Foundation of Chongqing (No. cstc2021jcyj-msxmX0827) and Chongqing Returned Overseas Students’ Entrepreneurship and Innovation Support Program (No. cx2021001).

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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