Contemporary remediation technologies encompass methods that efficiently eliminate a wide range of pollutants from environmental matrices, generating minimal secondary waste that could negatively impact the environment. These technologies employ a synergistic combination of physicochemical and biological methods to facilitate the biotransformation and biodegradation of xenobiotics into non-toxic products and byproducts. This approach is designed to be economical, sustainable, and environmentally friendly. In the long term, it minimizes the production of harmful greenhouse gases and waste streams, thereby reducing the costs associated with additional remediation efforts [53,54]. The integration and synergy of diverse remediation techniques offer an optimal solution for achieving the desired quality and long-term benefits of environmental restoration processes. Among the naturally occurring processes, bioremediation and phytoremediation are particularly notable. These green biotechnologies are the focus of increasing scientific research and application for the oxidation, reduction, and biodegradation of various contaminants, including petroleum hydrocarbons, pesticides, pharmaceuticals, heavy metals, and other synthetic chemicals [55,56]. Phytoremediation is a biotechnology that exploits the inherent potential of plants to stabilize, absorb, or degrade various xenobiotics from contaminated soil, water, or air [57]. The biochemical mechanisms involved in this process include phytotransformation, phytostabilization, phytoextraction, and rhizofiltration [58,59]. Bioremediation has seen exponential growth over the past two decades, particularly in the areas of soil, water, and air pollution remediation. Unlike traditional physico-chemical remediation methods, bioremediation offers an alternative approach by utilizing the potential of microorganisms, including bacteria, fungi, and algae to degrade xenobiotic compounds [60]. Although bioremediation is more ecologically sustainable, certain challenges are inherent to this technology. These challenges include the duration of the biodegradation process, which is influenced by the adaptive capabilities of microorganisms and their specific growth and reproduction requirements, such as optimal temperature, pH, and nutrient availability [61]. Additionally, biodegradation can be constrained by the inhibition of enzyme activity critical for bioremediation in highly contaminated environments or the presence of specific toxic compounds that impede microbial proliferation [62]. In the context of bioremediation, enzymes synthesized by microorganisms play a pivotal role during their adaptation to pollutants. These enzymes facilitate the degradation of contaminants either intracellularly (intracellular enzymes) or extracellularly (extracellular enzymes) after being transported across the cellular membrane [63,64]. Enzymes, functioning as biocatalysts, reduce the activation energy and accelerate various biochemical reactions while remaining unchanged. To restrict enzyme mobility and ensure high catalytic efficiency, immobilization techniques are implemented. These techniques allow for the repeated use of biocatalysts, thus minimizing production or post-use filtration costs. Moreover, immobilization enhances the enzymes’ resistance to toxic environments and maintains their structural integrity and functionality during storage [65]. Enzymes that catalyze biotransformation and biodegradation processes encompass cytochrome P450, various laccases, dehalogenases, dehydrogenases, hydrolases, proteases, and lipases. Laccase enzymes are particularly notable for their capacity to reduce oxygen while oxidizing a broad spectrum of aromatic and other pollutant compounds via single-electron transfer. These laccase enzymes are produced by specific microorganisms, including Pseudomonas putida F6, which degrades synthetic dyes; Streptomyces cyaneus, which oxidizes the micropollutant bisphenol A; and Bacillus safensis, which decolorizes commercial dyes. The enzyme cytochrome P450 mediates electron transfer and catalysis through the oxidation/reduction of heme iron, thereby facilitating the degradation of steroids, fatty acids, and xenobiotics. This enzyme is synthesized by microorganisms such as Rhodococcus rhodochrous, which is involved in the degradation of hexogen, and Bacillus megaterium, which is responsible for the hydroxylation of polychlorinated dioxins. Dehalogenase enzymes cleave carbon-halogen bonds through three distinct mechanisms. Microorganisms producing this enzyme include Pseudomonas sp. TL and Ancylobacter aquaticus, which degrade halogenated acids; Bacillus sp., which degrades 2,4,6-trinitrobromophenol; and Ochrobactrum sp., which degrades tetrabromobisphenol A [66,67]. Examples of organisms with specific affinities for particular pollutants [68,69,70,71,72,73,74] are presented in Table 2.

Bioremediation technology can be enhanced by optimizing process parameters through biostimulation. This strategy involves stimulating the metabolic activity of microorganisms involved in the biotransformation and degradation of pollutants by adjusting factors such as oxygen concentration, essential metal availability, moisture content, salinity, and nutrient ratios (C/N/P), as well as controlling the temperature and pH of the system. Additionally, it is crucial to optimize the concentration of inhibitory and toxic substances that may adversely affect microbial biomass [75,76]. Bioaugmentation, a prominent bioremediation strategy, involves the deliberate introduction of indigenous or exogenous microbial cultures, either pure or mixed, into contaminated environments to enhance the efficiency and speed of the biodegradation processes [77]. The biological inoculum used in bioaugmentation is typically propagated in controlled bioreactors before being deployed into the polluted ecosystem. In practical applications, the introduced microbial biomass must contend with various biotic and abiotic stressors, including fluctuations in temperature, variations in humidity and pH levels, and the presence of high concentrations of toxic compounds. A critical challenge in bioaugmentation is the competitive interaction with native microbial communities already present in the contaminated site. To optimize the effectiveness of bioaugmentation, it is essential to thoroughly understand the environmental characteristics of the contaminated site and to carefully manage operational parameters within the system. This approach ensures minimal negative impacts on the vitality and biodegradation capabilities of the introduced microbial consortia [78,79]. An innovative approach in the realm of protecting and stabilizing inoculated biomass for in situ and ex situ bioremediation involves the utilization of organic, inorganic, or hybrid transport matrices. This immobilization method effectively regulates microbial activity, reduces the potential for migration from contaminated sites, and enhances the bioavailability of the pollutant substrate essential for microbial growth and proliferation [80,81]. The structural adaptability of transport matrices (such as biofilms, gels, granules, and powders) facilitates their economic feasibility and commercial application across diverse states of pollutant aggregation. This versatility allows for direct implementation in contaminated environments or bioreactors, as well as integration into biofilters for the purification of water and air. These matrices are composed of carriers including natural polymers like chitin and cellulose, synthetic materials such as silica gels, minerals with significant adsorption surfaces like natural clays or zeolites, and modern composite nanomaterials [82,83,84]. Exploring alternative strategies to enhance biodegradation or innovate new biological functionalities involves synthesizing insights from functional nanomaterials and natural systems [85]. Nanobiohybrids represent composite nanoscale materials (including metal nanoparticles, carbon nanomaterials, and quantum dots) integrated with biological entities such as microbial cells, plant cells or extracts, and enzymes. These hybrids aim to synergistically improve the degradation of pollutants within ecosystems [86,87,88]. Examples of integrated biological systems employing diverse carrier matrices are detailed in Table 3.

The application of hybrid technologies, such as nanobioremediation, facilitates enhanced removal of environmental pollutants by integrating nanomaterials with natural microbial degradation capabilities. Nanomaterials like carbon nanotubes (CNTs), graphene oxide, gold nanoparticles (AuNPs), silver nanoparticles (AgNPs), copper nanoparticles (CuNPs), and others, exhibit significant surface adsorption capacities, immobilizing pollutants and thereby catalyzing microbial activity [92]. Beyond microorganisms, these nanomaterials can also be synergistically combined with plant cultures to bolster plant resilience to toxic environments and expedite phytostabilization processes [93]. The aforementioned technology finds application in treating contaminated soils and wastewater, as well as in the removal of pollutants from air through integration into biofilters [94]. In addition to these methods, genetic engineering is increasingly pivotal in enhancing bioremediation effectiveness. Advances in biotechnology enable genetic modifications of microorganisms or modulation of biocatalysts to develop systems that surpass natural environmental processes in speed and efficiency [95]. Approaches such as metabolic or genetic engineering can enhance the degradation capabilities of microorganisms towards both new and persistent pollutants, improve responses to stressful conditions, or stimulate the synthesis of biologically active compounds for bioremediation applications [96]. The proposed approach has been extensively studied in the context of synthetically engineered strategies for bioremediation of Hg(II) using genetically modified E. coli [97]. By incorporating the mer operon (consisting of merA, merB, and transporters merT, merC, and merP), natural gene clusters found in bacteria capable of complexing and reducing mercury, E. coli can effectively convert toxic Hg(II) ions into less harmful elemental mercury [98]. Boyd et al. [99] examined the efficacy of genetically modified Deinococcus geothemalis, which, after introducing the mer operon, demonstrated a successful reduction of mercury ions in thermal environments. Figure 2 illustrates the biogeochemical cycle of mercury in nature and the application of bioremediation technology involving the mechanism of action of genetically modified E. coli for the reduction and attenuation of toxicity.