Introduction

Bioremediation (BR) is a method that converts pollutants from soil, water, and different types of sources by using microorganisms (Huda et al., 2021). Microorganisms, such as bacteria, fungi, algae, protozoans, and others, are frequently used to degrade organic matter in a polluted environment (Mandal et al., 2021; Rizwan et al., 2014). Microorganisms are used with oxygen gas, fertilizer, and other factors during in BR process that helps their rapid growth as they remove organic pollutants (Pandey, 2018). These microbes, which are used specifically in genetic engineering and other molecular biological techniques, can be applied to break down pollutants and consume toxic chemical agents (Balciunas et al., 2013; Enamala et al., 2019; Rizwan et al., 2014). The main advantages of the BR method are highly efficient for example easily selects specific metals, easily minimizes chemical and biological sludge, as well as has no requirements for supplementary nutrition for recovery of heavy metals (Rizwan et al., 2014). Sometimes, the BR process may happen naturally as defined in an innate diminution or inherent BR (Kungwani et al., 2022). Different types of technologies such as bio-stimulation, hemofiltration, land farming, composting, phytoremediation, bioreactor, and bioventing are very common processes of BR (Huda et al., 2021; Thomassin-Lacroix et al., 2002). The in situ BR method removes the harmful and poisonous chemicals in the area (Karlapudi et al., 2018). The ex situ BR method needs to treat the polluted substances or poisonous materials by digging in the soil (Rizwan et al., 2014).

Nano-bioremediation (NBR) is a method for disposing of detrimental pollutants into secure molecules by treating the different types of microorganisms in connection with NMs that are smaller than100 nm (Mallikarjunaiah et al., 2020). Several NMs—Zn, Cu, Au, and Ag— are synthesized with a lot of microorganisms and plants that are accessible in the literature and useful in breaking down harmful contaminants (Gupta et al., 2020). Scientists have extensively investigated the different combinations of synthesized NMs. This combined process involves a wide range of potential applications with lower costs and the least impact on our environment when mediating contaminants in wastewater, groundwater, and sediments contaminated with heavy metals as either inorganic or organic compounds in the soil (Vázquez-Núñez et al., 2020). NMs have a special ability to remove toxic elements and develop the microbial action of the defined toxic item (Pandey, 2018). Agricultural soil remediation seems like a useful approach for dealing with pollution control by using biosynthetic NMs. The goal of this review is to provide a general overview of the biosynthesis of NMs from plants and microorganisms and the chemical compositions of NMs. This review article is a summary of the latest enhancements in the techniques of agricultural soil remediation for the various contaminated areas of our environment. The potential impact of using NMs on environmental pollution, especially in agricultural soil, is also presented and discussed.

NMs and nanotechnology

NMs can be applied in almost every field of science—agriculture, food, medicine, engineering, space, cosmetics, defense, automobiles, textiles, and the environment (Singh et al., 2020). With great achievements in the field of NMs and nanotechnology, their importance in supplying advanced and efficient keys to ecological contexts is becoming gradually more significant (Chauhan et al., 2020). NMs have gained much attention from researchers throughout the world in the different sectors of the sciences that are very closely related to the environment, specifically BR (Chauhan et al., 2020). The surface activity of NMs can be customized to develop their selectivity for sample removal (Chauhan et al., 2020; Zamborini et al., 2012; Huang et al., 2009). Different types of NMs with their chemical presentations, structures, and examples are described in Table 1.

Table 1 List of NMs with chemical composition with structure
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Nanoparticles, such as nano scale-zero-valent iron (nZVI), are metals that act as a reducing agent that transfers their electrons from iron and degrades a wide range of contaminants (Visentin et al., 2021). Nanocomposites are composed of different types of flexible and non-flexible NMs. Nanocrystals are composed of crystalline fragments of at least 1000 nm. For example, zinc sulfide is a nanocrystal that contains two different crystalline components: wurtzite and zincblende (Torres-Martinez et al., 2001). Nanopowder forms a massive number of atoms that bond to one another with a range from 1 to 100 nm. A nanosponge is a kind of nanomaterial that is a highly cross-linked carbon-containing polymer. These are tiny sponges porous in structure (Baglieri et al., 2013). Nanotube has, as so named, a tube structure, and a carbon nanotube (CNT) is a special carbon atom grapheme.

NMs consist of different types of chemical and physical materials, and their costs are high (Sebastian et al., 2014). The usage of harmful chemicals and the production of the poisonous secondary products have opened the way for the creation of biogenic NMs. Many researchers have described the different types of NMs, including iron (Fe), silver, zinc, copper, and gold, by using different types of microorganisms, such as bacteria, fungi, algae, yeasts, actinomycetes, and plant extracts (Das et al., 2018; Huq et al., 2022; Moholkar et al., 2020).

Using different biological factors in the biosynthesis of NMs is a growing research topic in green nanotechnology (Ganguly et al., 2018). Nowadays, many scientists have paid attention to the rise of nanotechnology as a plainer and more robust instrument. Nanotechnology has been applied to removing toxic pollutants that exist in small amounts in soil, air, and water (Das et al., 2015; O’Carroll et al., 2013; Dhillon et al., 2012). Nanotechnology also acts as a catalyst that reduces the number of objects used in the manufacturing procedure and reduces the production of detrimental wastes (Chauhan et al., 2020). Nanotechnology has given innovative scope to ecological cleanups, and it is an efficient substitute for commercial remediation as it facilitates both chemical reductions and rapid catalysis to reduce the contaminants of concern (Yaqoob et al., 2020). Nanotechnology has been used for dealing with the BR of uranium contamination, solid wastes, hydrocarbons, wastewater remediation, heavy metal contamination, soil pollution, and groundwater pollution (Alazaiza et al., 2021; Ojuederie & Babalola, 2017; Nematollahzadeh et al., 2015).

Principles and concepts of NBR

NBR can reduce the total expenditures on cleaning up major pollution with decreased clean up time (Enamala et al., 2019). The fundamental theory of NBR is termed as the deterioration of organic pollutants via nano-catalysts as a medium that permits them to enter deep inside the pollutants and deal with them carefully without influencing the nearby assistance of numerous microbes (Moholkar et al., 2020). These microbes appear in all places in the world and are struggling to live with the people on the earth. On the other hand, these microbes have different types of benefits like altering heavy metals into nonpoisonous forms, such as carbon dioxide and water, with the help of the mineralization of the organic pollutants. Even these can lead to various metabolic intermediates that can be used as metabolites for their development and growth (Enamala et al., 2019; Thakur et al., 2018). Besides, microbes protect their cell walls from the poisonous materials by producing degradable enzymes (Vardhan et al., 2019). When pollutants are consumed by microbes, they increase their unique surrounding membrane which helps them resist the entry of foreign materials into their cells (Murínová & Dercová, 2014). For a successful remediation method, researchers should consider the improvements of microorganisms mechanisms, such as development, growth, and movements in polluted sites (Enamala et al., 2019). The main idea about the NBR is that it describes the size of the NMs because their very small particles permit them to enter the polluted areas with different microbes, such as fungi, bacteria, and others.

Many scientists have included this study as part of their research because NMs can generate better outcomes when compared with the micro materials found in polluted areas (Enamala et al., 2019). The cleanup method is considerably delayed when compared to the usual BR technology. Some of the nano-based materials used for dealing with such polluted areas are nanocomposites, nanocrystals, nano-powders, nanotubes, and others. These NMs can be treated to immobilize the cells of microbes that then break down or be used in the recovery of precise chemicals depending upon the researcher’s interest (Enamala et al., 2019).

The science of NBR and biosynthesis of NMs

NBR is the main adaptable method for a strong environmental cleanup. The removal of environmental pollutants (for example, organic and inorganic contaminants and heavy metals) from polluted areas using NMs produced by microorganisms (for example, bacteria, and fungi) or plants with the help of nanotechnology is termed NBR (Chauhan et al., 2020; Ramezani et al., 2021; Vázquez-Núñez et al., 2020). NMs seem like an excellent substitute for existing techniques because of their price value, high competence, and friendliness to the environment. Iron (Fe) is regarded to be the first nanomaterial (NM) to be utilized for environmental cleanup (Chauhan et al., 2020). Several optimistic iron-based methods are accessible for the cleaning of polluted soil or for groundwater remediation (Chauhan et al., 2020). Zinc (Zn) as NMs have been widely used and investigated by scientists around the world because of its outstanding capability to break down organic dyes (Banerjee et al., 2021). As a semiconductor photocatalyst, Zn as an NM can contribute to the breaking down of a large variety of compounds from different types of dyes such as phenols and pharmaceutical medicines (Chauhan et al., 2020). NMs like as silver (Ag) and gold (Au) have an enormous application in a variety of areas, with the most significant application being the breakdown of organic dyes (Lu & Astruc, 2020). Copper (Cu) NM has also exhibited excellent results in breaking down organic dyes (Kim et al., 2018; Pandey, 2018; Shahwan et al., 2011).

The biosynthesis of NMs from plants and microorganisms and the remediation of different contaminants by NMs are shown in Table 2. NM such as nano iron is synthesized from plants (Sargassum muticum, Dodonaea viscose, Aloe vera, Azadirachta indica, Cartaya papaya, Green tea, etc.) and microorganisms (Escherichia coli, Shewanella oneidensis, Pleurotus sp., Klebsiella oxytoca, Aspergillus clavatus, etc.). Rubus glaucus, Ricinus communis, Nerium oleander, Calotropis gigantean, Nerium oleander, etc. are the plant sources for the biosynthesis of nano copper and the microorganism sources are Streptomyces sp., Fusarium oxysporum, Penicilium citrinum, Hypocrea lixii, etc.) (Table 2). Nanosilver is synthesized from Artemisia nilagirica, Nerium oleander, Sinapis arvensis, and other plant sources described in Table 2. Streptomyces naganishii, Brevibacterium casei, Trichoderma reesei, etc. are the plant sources for the biosynthesis of nanosilver. Nano zinc and gold are also synthesized from different plants and microorganisms (see details in Table 2). Yeast and fungi can also be utilized for the biosynthesis of NMs (Alghuthaymi et al., 2015). Whenever there is a need to produce huge quantities of NMs, fungi can be utilized as a result of their characteristic feature of having huge amounts of proteins (Pandey, 2018). In the biogenic manufacturing of metal NMs by a fungus, several decreasing enzymes with their catalytic results are made that lessen salts to their equivalent metallic solid NMs (Singh et al., 2020). This catalytic outcome is the main weakness of the microbial synthesis of NMs and requires making corrections for the wider application of this technique.

Table 2 Biosynthesis of NMs from plants and microorganisms with the remediation of different contaminants
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Engineered polymeric NMs for soil remediation

Some pollutants are found in the environment, for example, polynuclear aromatic hydrocarbons (PAHs) that are fixed to the soil. Therefore, it is very difficult to remove these pollutants from the soil (Patel et al., 2020; Loick et al., 2009). Recently, researchers have synthesized a few particles identified as amphiphilic polyurethane (APU) for the remediation of the soil polluted with PAHs (Mazarji et al., 2021; Rahman et al., 2022). The APU consists of polyurethane acrylate ionomers (PAIs) or polyethylene glycol. The colloidal dimension of APU is 17 − 97 nm by dynamic light scattering(Rizwan et al., 2014). APU can increase PAH’s desorption, stability, and independence in the aqueous stage (Johari et al., 2010). APU elements must be engineered to attain ideal features with a hydrophobic center region (Javaid et al., 2020). These elements also offer a high attraction for phenanthrene and hydrophilic surfaces, which then improves the elements’ mobility in the soil (Javaid et al., 2020). The affinity of APU elements may be controlled for pollutants by altering the dimension of the hydrophobic segment, for example, phenanthrene (Rizwan et al., 2014). The mobility of colloidal APU suspensions is controlled in the soil by the charge density. The capability to control particles features offers the potential to produce diverse NPS optimized for various pollutants and soil conditions (Rizwan et al., 2014).

An engineered iron NM solution is nonpoisonous, highly reactive, and very efficient, and it can quickly take away the soil pollutants (Reddy et al., 2016). This engineered iron NM is efficiently utilized for the removal of chlorinated hydrocarbons and different heavy metals present in the soil. First, the iron NM is inserted into the soil. Second, it reacts with the pollutants, and then it is absorbed into them as shown in Fig. 1. This method can also be applied to remediate the industrial pollutants from the agricultural soil (Enamala et al., 2019).

Fig. 1
figure 1

Outline the mechanism of soil remediation by NMs

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Challenges with NMs

While NMs have shown hopeful outcomes in removing polluted areas, there are some troubles related to their decreasing reactivity after a defined time, their conduction, and their outcomes on bacteria, fungi, and other microorganisms (Pandey, 2018). Iron (Fe) NMs have a reduction in their reactivity stage (after a defined time) and an obstructive outcome in the soil from blocking the holes in the soil thus confining the route of liquids. It has also been shown that a stabilizer (for example, lactate) may be treated to develop the dynamism of Fe NMs (Karimi & Mohseni Fard, 2017). A variety of guidelines under distinct situations have been carried out on the outcome of NMs on microorganisms. Among them, some of the guidelines have shown inhibitory results on microbes similar to Escherichia coli and Staphylococcus aureus (Pandey, 2018). Other studies have demonstrated the exciting outcome of NMs as electron contributors on microbes, for example, methanogens and bacteria (Chauhan et al., 2020).

Soil microbes are enormously significant to the normal series of nutrients in the environment, and they can break down the organic pollutants or diminish and arrest heavy metals (China et al., 2020). In this way, a severe reduction of the microbial inhabitants may result in the decline of the soil’s resistance to pollution (Pandey, 2018). The poisonous outcome of nano Fe can interrupt the cells’ membranes by making the reactive oxygen compounds that are responsible for the death of the microbial cells (Wang et al., 2019). Nano Fe compounds can obstruct the assimilation of nutrients via the cell membranes in the microorganism, which delays their development and growth (Hong et al., 2021). Compounds of Nano Fe have not proven to have any outcome on the development and growth of colonies of fungi. Studies have measured how the poisonous outcome of NMs can be reduced by covering them with some organic polymers (Pandey, 2018). Studies have also proved that microbes produce specific polysaccharides and enzymes that defend the poisonous action of NMs (Torres et al., 2019). In addition to their positive outcome on the exclusion of the pollutants, NMs might act together with both biotic and abiotic substances in positive and negative pathways. There are some characteristics of microorganisms, such as a high growth rate, less expenditure demand, simple culture techniques, and fewer environmental exposures, which help produce the biosynthesis of NMs (Alghuthaymi et al., 2015). Additionally, the utilization of NMs in an environment that has soils interacting with various organisms and NMs can influence the NBR of the polluted soils (Gomes et al., 2021). Some of the NMs utilized in this area contain carbon-related and metal-related NMs (Zhai et al., 2015; White et al., 2009).

BR and its significant role

BR is an advanced technique that proposes an environmentally amicable and economically viable substitute to eliminate pollutants from the environment (Rahman et al., 2022; Chauhan et al., 2020). The three major processes of BR are the utilization of plants, microbes, and enzymes (Rahman et al., 2022; Ojuederie & Babalola, 2017). The organic compounds are degraded from a contaminated environment by microbes such as bacteria, fungi, and yeast (Vieyra et al., 2015). Bacteria and fungi are utilized in the areas of breaking down different contaminants as shown in Table 3. The method of BR is significant in conserving and maintaining contaminated environments such as agricultural soil. Environmental biotechnology involves the application of genetic engineering to determine the competence and value of the utilization of microorganisms for reducing the environmental burden of toxic substances (Enamala et al., 2019). There are several microorganisms in an environment cultivating at different growth rates, and their plentiful diversity of functions has been observed (Stewart, 2012).

Table 3 List of bacteria and fungi used in BR techniques
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Bacteria

Bacteria are utilized in different applications in the environment through a variety of techniques. Among them, the BR technique is being used for a variety of purposes (Kadiyala et al., 2018). It was reported that the bacteria are used in breaking down the heavy metals and other pollutants via the route of BR (Khan et al., 2021). For example, bacteria identified as Deinococcusradioduranscan remedy heavy metals found in agricultural soil and is a non-pathogenic solvent bacterium (Appukuttan et al., 2006). Some of the genes recognized in Deinococcus radiodurans for breaking down metals, such as the merA reductase gene that encodes for the mercuric ion reductase, are extremely poisonous to humans (De et al., 2014). Some of the bacteria (such as Bacillus algicola, Sphingobium sp., Rhodococcus sp., Bosea sp., Phenylobacterium sp., Candida viswanathii, Bacillus subtilis, etc.) are used to degrade various pollutants (aromatic hydrocarbons, polynuclear aromatic hydrocarbons) in agricultural soils as shown in Table 3.

Fungi

Fungi also play a vital role in the areas of nanotechnology because their main task is the removal of poisonous pollutants (Huang et al., 2018). Some fungi produce extracellular synthesis (metabolites or enzymes) during their growth and development as a result of the BR. It was demonstrated that the catalytic outcomes of the enzymes being released by fungi, such as Fusarium oxysporum, Trichoderma viride, Aspergillus niger, Coriolus Versicolor, Candida glabrata, Aspergillus oryzae, and Fusarium semitectum, are applied to remove the exclusion contaminants and poisonous effluents nearby in the environment (Vázquez-Núñez et al., 2020) as shown in Table 3. Not only bacteria and fungi but also some species of algae (Chlorella sp.) and yeast (Lipomyceskononenkoae) may play an important role in breaking down pollutants.

Combined application of NMs and NBR in agricultural soil

The practice of combining NMs and NBR technology can remove pollutants from the environment as shown in Table 4. Different types of NMs have been used for the remediation of pollutants, for example, bimetallic nanoparticles (BNPs), enzymes, titanium dioxide (TiO2), nZVI, nanoscale zeolites, carbon nanotubes, and three metal oxides(nZVI, TiO2, and CNTs), which are applied in agricultural soil remediation (Table 4).

Table 4 Combined practice of NMs and NBR technology used in agricultural soil remediation
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Vázquez-Núñez et al. (2020) reported that responses of living organisms depend on the environmental conditions, types of pollutants, and NMs utilizations. Different types of NMs are being utilized to increase the microbial degradation of contaminants. Kim et al. (2012) observed that nano-bio treatment utilizing nZVI and diphenyl ether in a mixture using bacteria Sphingomonas sp. can remove polybrominated diphenyl ethers (PBDEs). Sphingomonas sp. PH-07 could produce in nZVI concentrations up to a high concentration of 5 gl−1 and contribute to the bio-deprivation of PBDEs (Kim et al., 2012). Similarly, Jing et al. (2018) found that the mixture of nZVI NM with any second metal or microorganism is used for the remediation of deeply contaminated places. The mixture also eliminates polychlorinated biphenyls (PCBs) from soil polluted by modifier oil. It was proved that nZVI significantly improved the soil washing efficacy by decreasing the interfacial tension between the oil and soil stages and removed 90% of PCBs (Bhattacharya et al., 2016). The mixture nZVI is utilized as pretreatment in the bioremediation of nitrate anions, PCBs, pesticides, heavy metals, radionuclides, and chlorinated volatile organic compounds (cVOCs) (Bhattacharya et al.,  2016; de Lima et al., 2012). Pereira et al. (2014) reported that a combination utilizing carbon nanotubes (CNT) and Arthrobacter sp. break down PCBs. They also found that the batch container with CNT was the highest breakdown percentage compared to other carbon NMS.

Hou et al. (2016) demonstrated the biodegradation of chlorophenol immobilized in magnetic NPS in a 100-mL batch container through Rhodococcus rhodochrous. The cells were immobilized by using k-carrageenan and Fe3O4 NPS and were capable of breaking down d-2-chlorophenol, 4-chlorophenol, 2, 3-dichlorophenol (Hou et al., 2016). Le et al. (2019) found that the combination of bimetallic iron dependent on NMs with tobacco plants is utilized to remove hexabromocyclododecane (HBCD). The unzipped carbon tube (CNT) combined with the enzyme organophosphate hydrolase removed the organophosphates and heavy metals from contaminated soil (Mechrez et al., 2014). Several previous studies have been attempted to increase the synergistic outcome of NM and BR practices and to elaborate on their biological and chemical interaction either in water or soil (Vázquez-Núñez et al., 2020).

Conclusions and prospects

The outcomes of nanoparticles on microorganisms in adjustable soil situations are critical to the remediation methods for the enhancement of the breakdown of soil pollutants. Nano bioremediation (NBR) relies primarily on the utilization of nanomaterials (NMs) to decrease the pollutants to equal levels that are favorable to biodegradation and then stimulate the biodegradation of the pollutants to spread the risk-based levels. The NMs are being used in various applications of NMs in building solids and in medicating several environmental contaminants. Consequently, the remediation of pollutants by the usage of current technology was not found to be efficient and effective in cleaning up the environment. It is helpful to develop the contaminant elimination competence and the combination of bioremediation (BR) technologies with NMs to eliminate contaminates. The NMs were applied to increase the exclusion of pollutants and narrate their interaction with abiotic and biotic elements during the remediation. So, NMs can be utilized for BR, which not only has a less toxic consequence on microorganisms but will also develop the microbial activity of the different pollutants in the agricultural soils, which offers an excellent opportunity for upcoming researchers.