Revitalizing Urban Rivers with Biotechnological Strategies for Sustainability and Carbon Capture

Abstract

Urban rivers are essential resources for human societies; however, their degradation poses serious public health, economic, and environmental risks. Conventional physical remediation methods can partially mitigate pollution by targeting specific contaminants, but they are often limited in scope, lack long-term sustainability, and fail to restore ecological functions. In contrast, biotechnological approaches integrated with ecological engineering offer sustainable and nature-based solutions for river depollution, conservation, and revitalization. Although these strategies are supported by a solid theoretical framework and successful applications in other aquatic systems, their large-scale implementation in urban rivers has only recently begun to gain momentum. This review critically examines strategies for the revitalization of polluted urban rivers, progressing from conventional remediation techniques to advanced biotechnological interventions. It highlights real-world applications, evaluates their advantages and limitations, and discusses policy frameworks and management strategies required to promote the broader adoption of biotechnological solutions for sustainable urban river restoration. The goal is to demonstrate the transformative potential of integrated biotechnological, eco-engineering, and data-driven approaches—particularly microbial, phytoplankton-based, and biofilm systems—to reduce energy demand and carbon emissions in urban river restoration while highlighting the need for scalable designs, adaptive management, and supportive regulatory frameworks to enable their large-scale implementation.

1. Introduction

Urban rivers play a fundamental role in the development and functioning of human societies. Historically, they have supplied drinking water, food resources, transportation routes, communication corridors, recreational spaces, and areas for social interaction, which explains why many cities have emerged and expanded along their banks [1]. Rivers and streams are key components of watershed systems, acting as natural catchment areas that collect precipitation and surface runoff from diverse sources and channel them toward a common outlet. Within these systems, micro-basins may exist, in which all drainage converges into the main watercourse of a sub-basin [2].

Understanding the ecological and spatial dynamics of urban watersheds is therefore essential, as urban analyses often begin with the largest river traversing a populated area. This perspective helps reveal land-use patterns associated with housing, transportation infrastructure, industrial development, agriculture, and other anthropogenic activities that have significantly altered riverine ecosystems [3]. For example, contamination by fecal pathogens originating from agricultural runoff and dispersed settlements represents a major public health concern [4].

Pollution in urban rivers has been linked to a wide range of health impacts, including gastrointestinal illnesses, dehydration, skin and textile damage caused by iron oxidation, and, in severe cases, life-threatening conditions, particularly among vulnerable populations. Long-term exposure to chemical and biological contaminants may also lead to organ damage, developmental disorders, reproductive impairments, and an increased risk of cancer [5,6].

In addition to public health consequences, river pollution generates substantial economic impacts. The collapse of the Doce River ecosystem following a dam failure resulted in massive fish mortality, severely affecting fishermen, riverside populations, and Indigenous communities who lost their primary sources of income and subsistence [7]. Similarly, in the São Francisco River basin (Brazil), declining fish stocks have compelled many fishermen to abandon traditional livelihoods or migrate to urban centers, especially younger generations facing limited economic prospects [8]. Nature-based tourism, which depends on preserved aquatic and riparian ecosystems, is also adversely affected, as environmental degradation undermines its regenerative and economic potential [9].

The revitalization of urban rivers through improved sanitation, pollutant removal, and flow restoration is therefore essential for sustainable development. When properly managed, urban rivers can be transformed into transportation corridors, recreational areas, and cultural landmarks, enhancing real estate value and improving overall quality of life [10]. River restoration can also contribute to carbon capture by reestablishing ecological processes that sequester atmospheric carbon and stabilize it in sediments and biomass [11]. Successful revitalization initiatives worldwide include the Isar River (Austria and Germany) [12], Cheonggyecheon Stream (South Korea) [13], Medellín River (Colombia), Thames River (United Kingdom) [14], Seine River (France), and Anacostia River (United States).

This review critically examines strategies for the remediation and revitalization of polluted urban rivers, with emphasis on pollution types, sources, and mitigation approaches that promote ecological balance, human well-being, and carbon sequestration. Specifically, it addresses: (i) how biotechnological tools and ecological engineering can support urban river restoration through bio-based systems, and (ii) how these approaches provide more sustainable and resilient outcomes compared with conventional river pollution management practices. Finally, the review discusses key barriers to large-scale implementation, including regulatory challenges, the need for supportive public policies, engagement from sanitation companies, and the mobilization of private investment to enable the deployment of bio-based river revitalization projects.

2. Types and Sources of Urban River Pollution

Pollution sources in urban river systems are generally classified as point sources or non-point (diffuse) sources. Point-source pollution typically originates from identifiable discharges, such as domestic sewage and industrial effluents, whereas non-point pollution arises from rainwater runoff that transports contaminants from urban, rural, and atmospheric origins into aquatic environments [15].

While point sources can often be monitored, regulated, and controlled, non-point sources are inherently more difficult to quantify and manage [16]. In many regions, including Brazil, the scarcity of data on diffuse pollution limits the development of robust models to estimate pollutant generation, transport, and accumulation within watersheds [17]. As a result, even watercourses lacking visible point-source discharges may remain significantly contaminated. This situation has serious economic implications, particularly for water supply utilities and fisheries, since polluted streams frequently sustain little to no aquatic life and are unsuitable for recreation or abstraction [18].

Point-source pollution is commonly associated with industrial effluents, untreated or partially treated domestic sewage, and stormwater overflows. These discharges often contain high concentrations of toxic substances and occur intermittently, typically during specific operational periods, which facilitates detection and enforcement actions [19]. In contrast, diffuse-source pollution originates from agricultural runoff, urban drainage systems, and atmospheric deposition. Although individual contaminant concentrations are generally lower, their continuous input leads to accumulation over time, posing chronic environmental risks. In such cases, educational programs, land-use planning, and economic incentives may be more effective than purely punitive approaches for pollution mitigation [20].

Surface water pollution in rivers, lakes, and ponds encompasses a broad spectrum of biological and chemical contaminants, including heavy metals, nutrients, persistent organic pollutants, pathogens, human waste, and food residues derived from domestic and industrial sewage [19]. Common manifestations include sludge accumulation, septic conditions, oxygen depletion, nutrient imbalances (e.g., excess nitrogen and phosphorus), algal blooms, non-biodegradable organic matter, toxic compounds, surfactants, and metals such as arsenic, cadmium, chromium, copper, mercury, nickel, lead, and zinc [21,22,23].

An emerging and particularly critical concern is the dissemination of multidrug-resistant bacteria, especially those originating from hospital wastewater. Pathogens such as Mycobacterium tuberculosis, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Streptococcus pneumoniae, Salmonella spp., Shigella spp., and Neisseria gonorrhoeae represent a global health threat, as they reduce the effectiveness of existing antimicrobial therapies [24,25].

Hospital effluents are commonly discharged into municipal sewer systems and treated alongside domestic wastewater. However, insufficient treatment efficiency enables resistant microorganisms and resistance determinants to enter natural water bodies [26,27]. Once released, these pathogens can spread beyond clinical settings, facilitating the dissemination of antimicrobial resistance throughout aquatic ecosystems [28]. Urban rivers, which often receive untreated or inadequately treated hospital and industrial discharges, therefore represent not only ecological hotspots of contamination but also critical nodes within the broader public health and environmental safety framework [29,30].

3. Traditional Methods for River Revitalization

Historically, river revitalization efforts have relied primarily on physical and chemical remediation techniques to mitigate pollution and restore ecological balance. Among these conventional approaches, dredging, aeration, and chemical treatment represent the most widely applied interventions, each characterized by distinct mechanisms, efficiencies, and operational challenges. Although these methods can be effective for targeted pollution control and rapid water quality improvement, they also exhibit substantial environmental, economic, and sustainability limitations. These constraints underscore the need for more integrated, adaptive, and ecosystem-based restoration strategies.

3.1. Dredging for River Revitalization

Dredging involves the mechanical removal of contaminated sediments from riverbeds (Figure 1) using equipment such as cutter-suction dredgers, backhoes, or clamshell dredges. The excavated material is typically treated or disposed of in controlled facilities to prevent secondary contamination. Meta-analytical studies have demonstrated that dredging can significantly reduce pollutant loads in aquatic ecosystems, achieving average reductions in more than 77% in before–after assessments and up to 84% in control–impact models worldwide [31]. Substantial decreases in chlorophyll-a, total phosphorus (TP), and total nitrogen (TN) concentrations—often exceeding 30%—have also been reported [32].

Targeted dredging in highly contaminated zones has proven effective in removing heavy metals and persistent organic pollutants (POPs) [33]. Optimal dredging depths ranging from 40 to 60 cm are associated with the most pronounced water quality improvements, particularly when sufficient post-dredging recovery periods are allowed [32]. Moreover, precision dredging guided by ecological risk indices enables the identification of “critical-risk depths,” reducing operational costs by up to 45% compared with conventional blanket dredging approaches [34,35].

Despite its effectiveness, dredging can induce adverse environmental effects, including sediment resuspension, disruption of nutrient cycling, and the release of bound heavy metals during operations [36,37]. To mitigate these impacts and enhance restoration outcomes, dredging is increasingly combined with complementary techniques, such as aeration and biological treatments [38].

3.2. Aeration for River Revitalization

Aeration enhances dissolved oxygen (DO) concentrations in river water through the use of mechanical aerators, air diffusers, or artificial waterfalls (Figure 1). Increased oxygen availability stimulates aerobic microbial processes, thereby promoting the degradation of organic pollutants, sewage-derived contaminants, and ammonium nitrogen (NH₄⁺-N) [39]. Beyond pollutant removal, aeration improves habitat quality and supports the recovery of fish and invertebrate communities.

Aeration also plays an important role in controlling cyanobacterial blooms. For example, studies conducted in eastern Poland demonstrated that underwater aeration systems effectively suppressed cyanobacterial scum formation, contributing to improved ecosystem stability [40]. In addition, aeration influences greenhouse gas (GHG) dynamics by reducing emissions of CO₂, CH₄, and N₂O over time [41]. However, when applied in combination with dredging, careful monitoring is required, as short-term increases in N₂O emissions may occur following intervention.

The integration of aeration with other biotechnological systems further enhances treatment efficiency. Floating Treatment Wetlands (FTWs) combined with aeration have achieved removal efficiencies approaching 99% for chemical oxygen demand (COD), NH₄⁺-N, and Escherichia coli [42]. Similarly, the incorporation of sulfur–iron autotrophic denitrification into Moving Bed Biofilm Reactors (MBBRs) has significantly increased nitrogen and phosphorus removal, reaching up to 85.65% and 78.02%, respectively [41].

Advanced modeling tools are increasingly employed to optimize aeration-based interventions. Reaction–diffusion–advection models [43,44] and Laplace-transform approaches [45] provide predictive frameworks for sustaining oxygenation and enhancing pollutant degradation. Applications such as those in the Nkisa River (Nigeria) highlight the role of re-aeration in strengthening the natural self-purification capacity of river systems [43].

Conventional river revitalization techniques such as dredging and artificial aeration are widely applied to improve water quality, yet they are often associated with high energy consumption and significant carbon emissions. Dredging requires intensive mechanical operations, fuel-powered equipment, sediment transport, and disposal, resulting in substantial greenhouse gas emissions and disturbance of benthic habitats. In addition, the handling and treatment of dredged sediments may generate secondary emissions and environmental impacts, particularly when contaminated materials require specialized disposal. Similarly, continuous aeration systems rely on electricity-intensive blowers or pumps to maintain dissolved oxygen levels, leading to sustained energy demand and elevated operational costs. In contrast, biotechnological approaches—such as microbial bioremediation, phytoremediation, floating treatment wetlands, and microalgae-based systems—generally operate with lower energy inputs and reduced carbon footprints. These nature-based solutions harness biological metabolism and ecosystem processes to remove nutrients, organic pollutants, and metals, often while simultaneously sequestering carbon in biomass or sediments. Moreover, many biotechnological systems can be integrated into circular economy frameworks, enabling resource recovery, biomass valorization, and partial energy self-sufficiency, thereby further offsetting emissions. As a result, biotechnological strategies offer a more energy-efficient and climate-resilient pathway for long-term river revitalization compared to conventional engineering-intensive interventions.

3.3. Chemical Treatment for River Revitalization

Chemical treatment involves the application of agents such as coagulants (e.g., aluminum sulfate, ferric chloride), oxidants (e.g., ozone, hydrogen peroxide), and pH modifiers to neutralize, precipitate, or chemically degrade pollutants [46]. This approach enables rapid control of pathogens, nutrients, and organic contaminants, making it particularly valuable during pollution emergencies or acute contamination events. Chemical treatment is frequently combined with sedimentation, filtration, or physical separation processes to enhance overall effectiveness.

Despite its rapid action, chemical treatment presents notable risks, including secondary pollution from residual chemicals, toxicity to aquatic organisms when overdosing occurs, and challenges in achieving uniform distribution across large or dynamic water bodies. Consequently, continuous monitoring and careful dosage control are essential to minimize unintended ecological impacts [47,48].

Overall, traditional methods such as dredging, aeration, and chemical treatment remain indispensable tools for river revitalization, providing immediate and measurable improvements in water quality and ecosystem condition. However, their high operational costs, environmental trade-offs, and limited long-term sustainability necessitate a transition toward integrated, adaptive, and nature-based restoration approaches [47]. Future river management strategies should combine conventional techniques with ecological and biotechnological solutions to enhance system resilience and achieve global water sustainability objectives. The main challenges and bottlenecks associated with traditional river restoration methods are summarized in

Table 1. Major bottlenecks in traditional approaches to river restoration.

Category	Challenges	Details
Environmental Impacts	Habitat disturbance and pollution	Dredging disturbs benthic habitats and resuspends toxins.
		Aeration alters thermal profiles and disrupts sensitive biota.
		Chemical treatments can introduce new pollutants.
High Operational Costs	Expensive and energy-intensive	Dredging requires heavy equipment and complex logistics.
		Aeration demands constant energy input. Chemical treatments need recurrent chemical inputs and monitoring.
Sustainability Concerns	Symptom-focused and non-durable	Methods treat symptoms rather than sources of pollution.
		Risk of recontamination without upstream management.
		Delays in adopting nature-based, ecosystem-centered solutions.

.

3.4. Bacterial and Fungi Biotechnological Approaches to River Revitalization

Urban rivers are increasingly impacted by a broad spectrum of contaminants, including heavy metals, organic pollutants, nutrients, persistent organic pollutants (POPs), and pathogenic microorganisms, largely as a consequence of rapid urbanization and industrial expansion [5]. Although conventional remediation strategies, such as sediment dredging and sewage interception, can reduce pollutant loads, they often require extensive infrastructure, high energy input, and long implementation times. In contrast, biotechnological approaches—particularly those based on microbial bioremediation—offer more sustainable, decentralized, and cost-effective alternatives for addressing complex pollution scenarios in urban river systems.

Bioremediation exploits the intrinsic metabolic capabilities of microorganisms, plants, and enzymes to remove, transform, or detoxify environmental contaminants. Within this framework, microbial biotechnology (Figure 2) harnesses bacteria and fungi capable of degrading organic compounds, immobilizing or transforming heavy metals, and eliminating emerging contaminants such as pharmaceutical residues. These microorganisms employ multiple mechanisms, including biodegradation, biotransformation, biosorption mediated by extracellular polymeric substances (EPS), and intracellular bioaccumulation, enabling efficient detoxification of polluted aquatic environments [49,50,51].

3.4.1. Heavy Metal Removal by Microorganisms

When exposed to toxic metals or adverse environmental conditions, microorganisms activate stress-response pathways that enhance their survival and remediation capacity (Figure 3). These responses include the production of bound polysaccharides and EPS capable of chelating and adsorbing metal ions, regulating local pH, and reducing metal bioavailability [52,53]. In parallel, microorganisms induce enzymatic systems involved in stress management, contaminant transformation, and the repair of damaged cellular structures [54,55,56]. Intracellular enzymes further contribute to detoxification by transforming ionic metal species into less toxic forms.

Bacterial and fungal genera such as Sphingomonas and Fusarium have demonstrated strong potential for the removal of heavy metals (Table 2), including lead (Pb), cadmium (Cd), and arsenic (As), through mechanisms such as ion exchange, complexation, and biosorption [51]. Sphingomonas strains isolated from contaminated environments often exhibit high metal uptake capacities, while Fusarium species have shown notable efficiency in uranium biosorption [49]. Moreover, mixed bacterial–fungal consortia frequently outperform monocultures, as complementary metabolic pathways enhance overall pollutant removal efficiency, making such consortia particularly suitable for riverbank restoration and wastewater treatment applications [57].

In addition to metal remediation, microbial systems are effective in removing organic contaminants. For example, Fusarium culmorum has been employed for the removal of cadmium and zinc [58], while diverse bacterial and fungal species are capable of degrading petroleum hydrocarbons, including crude oil and polycyclic aromatic hydrocarbons (PAHs) [59]. These findings underscore the versatility of microbial bioremediation strategies for addressing the complex pollutant mixtures typically found in urban river environments.

Microbial remediation of heavy metals is especially critical due to the severe ecological and human health risks associated with these contaminants. Microorganisms mediate metal detoxification through enzymatic processes such as reduction, methylation, and precipitation. Rhizobacteria utilize organic or inorganic electron donors to reduce hexavalent chromium (CrO₄⁻) to the less toxic trivalent form, Cr(OH)₃ [51].

The effectiveness of microbial and fungal heavy metal remediation in urban rivers is governed not only by biological mechanisms—biosorption, bioaccumulation, biotransformation, and biomineralization—but also by environmental parameters that directly regulate these processes. Among the most influential factors are pH and temperature, which affect metal speciation, microbial metabolism, enzyme activity, and cell surface chemistry [60].

At the molecular level, biosorption relies primarily on negatively charged functional groups, including carboxyl, hydroxyl, phosphoryl, and amine moieties, present on microbial cell walls [61,62] and within EPS matrices [63]. The ionization state of these groups is pH-dependent and determines their metal-binding capacity. Under acidic conditions (pH < 4), protonation reduces surface negativity and limits cation binding due to competition with H⁺ ions [60]. As pH increases, deprotonation restores negative charges, enhancing electrostatic attraction and ion-exchange processes. Consequently, many bacterial and fungal species exhibit maximal biosorption capacities within a pH range of 5–8 [60,64]. In contrast, bioleaching processes driven by microbial acid production require highly acidic conditions to solubilize otherwise immobile metals [65].

Bioaccumulation and enzymatic biotransformation are similarly sensitive to pH, as these processes depend on active transport systems and redox enzymes whose structural stability and catalytic efficiency vary with proton availability. For instance, chromate reductases involved in CrO₄⁻ reduction show optimal activity near neutral pH, whereas the mercury resistance (MerA) enzyme system is inhibited under acidic conditions [66,67,68].

Temperature also modulates both passive and active remediation mechanisms. While biosorption is relatively insensitive to temperature fluctuations, higher temperatures generally enhance metal ion mobility and diffusion, facilitating passive uptake. In contrast, active processes such as bioaccumulation, enzymatic reduction, and biomineralization are strongly linked to microbial metabolic rates, which typically peak under mesophilic conditions (20–40 °C) [69,70,71]. Deviations from this range may impair enzyme stability or compromise membrane integrity, reducing remediation efficiency. Nevertheless, thermophilic and psychrophilic microorganisms remain metabolically active under extreme temperature conditions [72], enabling bioremediation strategies across diverse climatic regions.

Environmental conditions further influence metal speciation and solubility, directly affecting bioavailability. For example, CrO₄⁻ reduction to Cr(OH)₃ is favored under near-neutral pH and moderate temperatures, whereas carbonate and phosphate precipitation processes that immobilize Pb²⁺, Cd²⁺, and Zn²⁺ are more efficient under alkaline conditions [73]. Likewise, sulfate-reducing bacteria require anaerobic environments and moderate temperatures to produce sulfides that precipitate metals as insoluble metal sulfides.

From a critical standpoint, these mechanistic–environmental interactions indicate that microbial remediation is not universally effective under all conditions. Instead, its success is highly species-specific and dependent on the physicochemical characteristics of the contaminated environment. Fungi often exhibit greater tolerance to low pH and high metal concentrations than bacteria, largely due to their robust cell wall structures enriched in chitin and melanin, as well as their capacity to secrete organic acids that promote bioleaching. These traits make fungi particularly advantageous for remediation in acidic or heavily contaminated sediments. Conversely, bacterial consortia tend to perform optimally under moderate pH and temperature conditions, where synergistic mechanisms—biosorption, enzymatic transformation, and mineral precipitation—can operate simultaneously.

Effective implementation of microbial and fungal biotechnologies for urban river revitalization therefore requires careful alignment between microbial metabolic potential and site-specific environmental conditions. Accounting for these mechanistic and environmental dependencies is essential for the rational design of bioaugmentation strategies, the selection of functional microbial consortia, and the optimization of field-scale bioremediation systems in urban river ecosystems.

3.4.2. Nutrient Pollution and Eutrophication

Nutrient pollution represents another major challenge for urban river systems, particularly the excessive inputs of nitrogen and phosphorus derived from urban runoff, industrial effluents, and insufficiently treated wastewater, which collectively drive eutrophication processes (Figure 4). Microorganisms—especially bacteria and fungi—play a central role in nutrient attenuation through biochemical pathways such as nitrification, denitrification, and biological phosphorus removal. Nitrification, which converts ammonia (NH₃/NH₄⁺) into nitrate (NO₃⁻), followed by denitrification, where nitrate is reduced to inert nitrogen gas (N₂), constitutes the primary microbial route for mitigating nitrogen pollution in aquatic environments.

In parallel, phosphorus is removed through microbial assimilation and immobilization. Certain microorganisms accumulate phosphorus intracellularly as polyphosphate granules, while others mineralize organic phosphates, thereby reducing the risk of eutrophication [74,75]. Field-scale studies, such as those conducted in Guangzhou (China), demonstrate that microbial nutrient-removal processes are significantly enhanced when coupled with artificial aeration or submerged macrophyte restoration, leading to substantial reductions in sediment-bound nitrogen and phosphorus [74]. Likewise, bioretention systems employing washed sea sand have shown effective nitrogen removal efficiencies, highlighting their potential as cost-effective solutions for urban runoff management [76].

Microbial nitrogen and phosphorus removal in contaminated urban rivers is governed by highly coordinated biochemical pathways that are strongly influenced by environmental conditions. In nitrogen cycling, the heterotrophic nitrification–aerobic denitrification (HN–AD) pathway is particularly advantageous, as it enables microorganisms to oxidize and reduce nitrogen species simultaneously under oxic conditions. This metabolic flexibility is especially relevant in shallow or turbulent urban rivers, where dissolved oxygen concentrations fluctuate rapidly [77]. During nitrification, enzymes such as ammonia monooxygenase (AMO) and hydroxylamine oxidoreductase catalyze the stepwise oxidation of ammonium (NH₄⁺) to hydroxylamine (NH₂OH), nitrite (NO₂⁻), and nitrate (NO₃⁻) [78]. Denitrification subsequently proceeds through the sequential action of nitrate reductases (NapA or NarG), nitrite reductases (nirK/nirS), nitric oxide reductase, and nitrous oxide reductase (nosZ), ultimately yielding dinitrogen gas (N₂) [79]. These pathways are tightly regulated by enzyme expression, redox balance, and cellular energy availability, rendering nutrient removal highly sensitive to environmental stressors. In addition to dissimilatory pathways, many HN–AD bacteria assimilate nitrogen into biomass, contributing further to inorganic nitrogen depletion even under suboptimal conditions.

Phosphorus removal relies on equally complex microbial strategies. Unlike classical phosphate-accumulating organisms (PAOs), which require alternating anaerobic–aerobic cycles, several multifunctional HN–AD–syncretic nitrogen and phosphorus removal (HNAD–SNPR) strains can assimilate phosphate efficiently under strictly aerobic conditions [80]. These microorganisms import phosphate through high-affinity transport systems such as PstSCAB, enabling uptake even at low ambient phosphate concentrations [81]. Intracellular phosphorus is incorporated into nucleic acids, phospholipids, or stored as phosphate monoesters and diesters. While some strains synthesize polyphosphate via polyphosphate kinase (Ppk), many urban river isolates preferentially immobilize phosphorus within extracellular polymeric substances (EPS) [81]. EPS-rich biofilms can bind large quantities of phosphate, effectively retaining it on sediment surfaces, macrophyte roots, and riverbed substrates [82]. In iron-rich systems, phosphorus may also precipitate abiotically as iron phosphates (e.g., FePO₄), providing an additional removal pathway in metal-enriched urban rivers.

Temperature exerts a strong control over these microbial processes by regulating enzyme kinetics, membrane fluidity, and growth rates. Most HN–AD and HNAD–SNPR bacteria exhibit optimal activity between 25 and 37 °C [77], a range typical of tropical and subtropical rivers. Below approximately 20 °C, nitrification and denitrification rates decline sharply due to reduced AMO and reductase activity [83]. Nitrite-oxidizing bacteria (NOB) are particularly sensitive to low temperatures, often leading to nitrite accumulation and incomplete nitrogen removal [84]. Phosphorus uptake is similarly constrained, as reduced ATP generation suppresses Ppk activity and limits phosphate incorporation into cellular and extracellular pools [85]. Although some psychrotolerant strains maintain nitrate removal at temperatures as low as 5–10 °C, reaction rates remain slower and require extended hydraulic retention times for effective remediation [86,87].

pH is equally critical, as it influences nutrient speciation, proton gradients, and enzyme conformation. Most microbial nutrient-removal pathways operate optimally at neutral to slightly alkaline pH values (≈7.5–8.5). Within this range, the NH₄⁺/NH₃ equilibrium favors the substrate preferred by AMO, enhancing nitrification efficiency [88,89].

Denitrification is also favored due to stable nitrate reductase activity and efficient electron transport. Acidic conditions (pH ≤ 5) inhibit key redox enzymes, suppress nitrification, increase N₂O emissions, and reduce phosphorus uptake by limiting Ppk activity [90]. Conversely, highly alkaline conditions (pH > 10) increase free ammonia concentrations, which can be toxic to nitrifiers, although some specialized strains tolerate such extremes. Alkalinity also promotes chemical precipitation of phosphate as metal–phosphate complexes, partially compensating for reduced biological uptake under extreme conditions [90].

Collectively, these environmental controls determine the efficiency of microbially driven eutrophication mitigation in urban rivers. Temperature dictates the metabolic rate of microbial reactions, while pH defines the chemical framework in which these reactions occur. Given that urban rivers experience rapid shifts in temperature, dilution during storm events, industrial discharges, and diurnal pH fluctuations driven by photosynthetic activity, strong selective pressures act on microbial communities. The resilience of emerging HN–AD and HNAD–SNPR strains lies in their capacity to maintain functional enzyme systems across broad environmental gradients, making them promising candidates for nutrient remediation in highly urbanized and eutrophic river systems.

3.4.3. Persistent Organic Pollutants and Their Bioremediation

Persistent organic pollutants (POPs), including pesticides, industrial chemicals, pharmaceuticals, and combustion by-products, pose severe risks to urban river ecosystems due to their toxicity, chemical stability, bioaccumulative behavior, and resistance to natural attenuation. These compounds enter riverine environments primarily through industrial discharges, hospital effluents, domestic wastewater, and urban runoff, making polluted urban rivers major sinks for both legacy and emerging POPs [91,92,93].

The most frequently detected POP classes in urban rivers include polycyclic aromatic hydrocarbons (PAHs), such as phenanthrene and anthracene, derived from incomplete fossil fuel combustion and petroleum contamination, which preferentially accumulate in sediments [94,95]. Polychlorinated biphenyls (PCBs), formerly used as dielectric fluids, remain problematic due to their carcinogenicity and strong biomagnification potential [96,97]. Organochlorine pesticides (OCPs), including DDT, lindane, and endosulfan, persist as residues of historical agricultural practices [98,99]. Emerging contaminants, notably per- and polyfluoroalkyl substances (PFAS), are of particular concern due to the exceptional stability of carbon–fluorine bonds, which severely limits natural degradation processes [100,101]. Pharmaceuticals and personal care products (PPCPs), such as antibiotics, analgesics, and hormones, are increasingly reported in urban rivers as a consequence of inadequate wastewater treatment [102]. Highly toxic dioxins and furans (PCDD/Fs), unintentionally generated during combustion and chlorine-based industrial processes, further exacerbate ecological and human health risks even at trace concentrations [103].

Bioremediation offers a sustainable strategy for POPs mitigation and largely operates through natural self-purification processes mediated by interactions among microorganisms, aquatic vegetation, sediments, and hydrodynamics [104]. Streambed biofilms constitute particularly active zones, where bacteria, fungi, microalgae, and EPS retain, transform, and degrade contaminants [95,105]. These processes can be enhanced through biostimulation or bioaugmentation to promote specialized degraders capable of targeting recalcitrant compounds [93,106]. In engineered or highly contaminated systems, electro-bioremediation has emerged as a complementary approach, improving pollutant mobilization and bioavailability under low-intensity electric fields [107].

At the mechanistic level, POPs removal involves biosorption onto microbial and algal cell surfaces or EPS matrices via functional groups such as carboxyl, hydroxyl, and amine moieties [108,109]. Bioaccumulation contributes through active uptake and intracellular sequestration [108]. However, biodegradation and biotransformation are the most critical processes. Aerobic microorganisms utilize oxygenases to cleave aromatic rings, while anaerobic consortia in sediments perform reductive dehalogenation of chlorinated POPs, including PCBs and OCPs [110,111]. Fungal and bacterial enzymes, such as laccases and peroxidases, further enhance the breakdown of highly recalcitrant compounds [110]. Phytoremediation complements these processes through contaminant uptake and rhizodegradation, whereby root exudates stimulate microbial activity in contaminated sediments [98,112].

3.4.4. Pathogen Removal and Pollution Mitigation

In addition to chemical contaminants, urban rivers frequently harbor a wide range of microorganisms—pathogenic bacteria, viruses, and protozoa, as well as multicellular parasites such as helminths, posing significant risks to public health and aquatic ecosystems. Pathogen dynamics in river systems are governed by the interplay of physical, chemical, and biological processes, including microbial growth, natural mortality, light-induced inactivation, and particulate settling. The persistence of microbial contaminants, including Escherichia coli, Klebsiella pneumoniae, Enterococcus faecalis, Salmonella enterica, Shigella strains, Campylobacter jejuni and viral pathogens, is primarily regulated by microbial growth dynamics, natural mortality, light-induced inactivation, and particulate settling. While these intrinsic mechanisms underpin river self-purification, increasing anthropogenic pressures necessitate targeted bio-based strategies to enhance pathogen attenuation [113]. Although these intrinsic mechanisms underpin river self-purification, increasing anthropogenic pressures necessitate targeted biotechnological interventions to enhance pathogen attenuation.

Bioremediation plays a central role in pathogen control through microbial antagonism, enzymatic degradation, and competitive exclusion, each operating via distinct mechanisms (Figure 5).

Beneficial bacteria suppress pathogens by rapidly assimilating nutrients, while fungi such as Trichoderma spp. produce antimicrobial peptides that inhibit pathogen proliferation. Enzymatic activities, including chitinase and glucanase production, further disrupt pathogen cell walls and reduce viability [50]. These effects are amplified in biofilm-rich environments, where microbial density and metabolite concentrations exceed those in the bulk water phase.

Among nature-based solutions (Table 2), riverbank filtration (RBF) represents a key biotechnological interface between surface waters and subsurface ecosystems. During subsurface passage, pathogens are attenuated through hydrodynamic dilution, mechanical straining, physicochemical interactions (e.g., sorption and redox reactions), and microbial biodegradation. Viral reductions of up to 3.1 log units, including adenoviruses, have been reported during early filtration stages, although removal efficiency is strongly influenced by pH and ionic strength [114], underscoring the role of sediment-associated microbial communities. Other clinically important viral agents that must be addressed by such approaches include Coxsackieviruses and rotaviruses.

Conventional non-biological approaches, such as advanced oxidation and disinfection, can complement bio-based strategies in highly impacted river reaches. Ozonation disrupts microbial membranes, while ultraviolet (UV) irradiation induces irreversible nucleic acid damage [115]. Combined O₃/UV systems generate hydroxyl radicals (-OH), enabling non-selective oxidation of organic matter and reducing the dissemination of chromosomal antibiotic resistance genes (cARGs) through structural modification of dissolved organic matter [116]. However, high energy demand and operational costs limit large-scale deployment, reinforcing the need for sustainable biological alternatives.

Recent advances emphasize biological antagonism and pathogen capture as scalable solutions. Synthetic microbial communities (SMCs) performing heterotrophic nitrification–aerobic denitrification (HN–AD) simultaneously enhance nitrogen removal and suppress pathogens through metabolic competition. The production of organic acids, such as lactic and acetic acids, creates inhibitory microenvironments that restrict the growth of opportunistic bacteria, including Vibrio spp. [117]. These effects are most pronounced in low-flow, high-retention zones such as constructed wetlands, side channels, riverbank filtration areas, and polishing reaches downstream of wastewater treatment plants.

Functionalized biochar has also emerged as an effective bio-based material for pathogen capture in filtration and interception zones, including permeable reactive barriers and hybrid wetland–biofilter systems. Pathogens are immobilized through electrostatic and hydrophobic interactions and binding to surface functional groups, where oxidative stress and antagonistic microbial colonization further reduce viability [118].

Collectively, these bio-based mechanisms (Table 2) transform targeted river segments into self-sustaining biotechnological treatment hotspots, enabling continuous pathogen retention and inactivation at sediment–water interfaces and within engineered substrates. Although microfiltration technologies, such as ceramic membranes (~0.5 µm), can achieve near-complete E. coli removal [119], their cost and maintenance requirements limit widespread application. Moreover, persistent stressors, including PFAS contamination, may selectively favor pathogenic microorganisms over beneficial communities, challenging long-term system resilience. These findings support the conceptualization of urban rivers as biologically active purification systems, where integrated bio-based interventions harness microbial competition, material-assisted capture, and ecosystem processes to achieve resilient and sustainable pathogen control.

Table 2. Bio-based approaches, their target contaminants, and key findings from recent literature.

Target Pollutant	Approach	Efficiency of Removal	Reference
Heavy Metals (Pb, Cd, As, U)	Sphingomonas, Fusarium	80%	[51]
Heavy Metals (Cd, Pb, U)	Fusarium verticillioides (fungus)	90%	[120]
Heavy Metals (Cd, Zn)	Fusarium culmorum	85%	[58]
Hydrocarbons (Crude oil, PAHs)	Scedosporium apiospermum	70–75%	[59]
Heavy Metal (Cd)	Sphingomonas sp. M1-B02	95%	[121]
Nutrients (N, P)	Various bacteria and fungi (e.g., nitrifying bacteria)	60%	[74]
Nutrients (N)	Various bacteria (e.g., nitrifying bacteria)	70–80%	[75]
Nutrients (N)	Microbial communities in Bioretention Systems	50–60%	[76]
POPs (PCBs, DDT, Dioxins)	Dehalococcoides, Marinobacter hydrocarbonoclasticus SDK644	90%	[122]
POPs (PCBs, DDT, Dioxins)	Organophosphorus Acid Anhydrolase	87–97%	[123]
POPs (PCBs, DDT, Dioxins)	Bacterial consortium (e.g., Paraclostridium sp., Bacillus sp., Staphylococcus sp.)	80–90%	[124]
POPs (PCBs, DDT, Dioxins)	Bacteria (e.g., Dehalococcoides, Marinobacter)	85%	[125]
Pollutants (Nanoparticles, Heavy Metals)	Lemna, Phragmites (aquatic plants)	80%	[126]
Pollutants (Ammonia, BOD)	Canna indica (wetland plant)	60–70%	[127]
Pathogens (Bacteria)	Corbicula (freshwater mussels)	40–60%	[128]
Pathogens (E. coli, Antibiotic Resistance)	Microalgae-Bacteria Systems (MBS)	80% (E. coli reduction) and 70–80% (antibiotic resistance gene reduction)	[129]
Pathogens and Pollutants (Ammonia, COD)	HP-RPe-3 (microbial agent)	30% DO increase, 60% NH3-N reduction, 40% COD reduction	[130]
Heavy Metal (Pb)	Klebsiella sp. USL2D (Biosorption)	97%	[131]
Heavy Metal (CrO4−)	Sporosarcina saromensis M52 (Biosorption/Biotransformation)	100%	[132]
Heavy Metal (CrO4−)	Cellulosimicrobium sp. (Biosorption)	99.33%	[133]
Heavy Metal (Cu)	Sulfate-reducing bacteria (SRB) (In situ acid mine drainage remediation)	99.55%	[134]
Heavy Metal (CrO4−)	Proteus mirabilis (Bioreduction in tannery effluent)	99.00%	[135]
Heavy Metal (CrO4−)	Halomonas campaniensis (Bioreduction in tannery effluent)	98.68%	[135]
Heavy Metal (CrO4−)	Bacillus pumilus (Bioreduction in tannery effluent)	98.28%	[135]
Heavy Metal (Pb)	Cellulosimicrobium sp. (Biosorption)	99% (Nearly complete)	[133]
Heavy Metal (Zn)	Sulfate-reducing bacteria (SRB) (In situ acid mine drainage remediation)	94.59%	[134]

Table 2. Bio-based approaches, their target contaminants, and key findings from recent literature.

Target Pollutant	Approach	Efficiency of Removal	Reference
Heavy Metals (Pb, Cd, As, U)	Sphingomonas, Fusarium	80%	[51]
Heavy Metals (Cd, Pb, U)	Fusarium verticillioides (fungus)	90%	[120]
Heavy Metals (Cd, Zn)	Fusarium culmorum	85%	[58]
Hydrocarbons (Crude oil, PAHs)	Scedosporium apiospermum	70–75%	[59]
Heavy Metal (Cd)	Sphingomonas sp. M1-B02	95%	[121]
Nutrients (N, P)	Various bacteria and fungi (e.g., nitrifying bacteria)	60%	[74]
Nutrients (N)	Various bacteria (e.g., nitrifying bacteria)	70–80%	[75]
Nutrients (N)	Microbial communities in Bioretention Systems	50–60%	[76]
POPs (PCBs, DDT, Dioxins)	Dehalococcoides, Marinobacter hydrocarbonoclasticus SDK644	90%	[122]
POPs (PCBs, DDT, Dioxins)	Organophosphorus Acid Anhydrolase	87–97%	[123]
POPs (PCBs, DDT, Dioxins)	Bacterial consortium (e.g., Paraclostridium sp., Bacillus sp., Staphylococcus sp.)	80–90%	[124]
POPs (PCBs, DDT, Dioxins)	Bacteria (e.g., Dehalococcoides, Marinobacter)	85%	[125]
Pollutants (Nanoparticles, Heavy Metals)	Lemna, Phragmites (aquatic plants)	80%	[126]
Pollutants (Ammonia, BOD)	Canna indica (wetland plant)	60–70%	[127]
Pathogens (Bacteria)	Corbicula (freshwater mussels)	40–60%	[128]
Pathogens (E. coli, Antibiotic Resistance)	Microalgae-Bacteria Systems (MBS)	80% (E. coli reduction) and 70–80% (antibiotic resistance gene reduction)	[129]
Pathogens and Pollutants (Ammonia, COD)	HP-RPe-3 (microbial agent)	30% DO increase, 60% NH3-N reduction, 40% COD reduction	[130]
Heavy Metal (Pb)	Klebsiella sp. USL2D (Biosorption)	97%	[131]
Heavy Metal (CrO4−)	Sporosarcina saromensis M52 (Biosorption/Biotransformation)	100%	[132]
Heavy Metal (CrO4−)	Cellulosimicrobium sp. (Biosorption)	99.33%	[133]
Heavy Metal (Cu)	Sulfate-reducing bacteria (SRB) (In situ acid mine drainage remediation)	99.55%	[134]
Heavy Metal (CrO4−)	Proteus mirabilis (Bioreduction in tannery effluent)	99.00%	[135]
Heavy Metal (CrO4−)	Halomonas campaniensis (Bioreduction in tannery effluent)	98.68%	[135]
Heavy Metal (CrO4−)	Bacillus pumilus (Bioreduction in tannery effluent)	98.28%	[135]
Heavy Metal (Pb)	Cellulosimicrobium sp. (Biosorption)	99% (Nearly complete)	[133]
Heavy Metal (Zn)	Sulfate-reducing bacteria (SRB) (In situ acid mine drainage remediation)	94.59%	[134]

4. Role of Phytoplankton on Contaminated River Revitalization

Phytoplankton, including microalgae and cyanobacteria, have emerged as powerful agents for the restoration of polluted urban rivers, offering environmentally sustainable alternatives to conventional remediation technologies. Their capacity to remove nutrients and toxic contaminants, improve water quality, and simultaneously generate valuable biomass has been extensively demonstrated in wastewater treatment systems [136,137]. More recently, these attributes have attracted growing attention in the context of urban river revitalization, where phytoplankton-based processes can function as both remediation and resource recovery strategies (Figure 6).

Cyanobacteria such as Nostoc, Anabaena, Phormidium, and Oscillatoria have shown remarkable bioremediation performance in highly polluted environments. In the Yamuna River (Delhi, India), these organisms outperformed conventional wastewater treatment plants (WWTPs) by achieving substantially higher reductions in organic pollution. Oscillatoria removed up to 72.4 ± 4.11% of biological oxygen demand (BOD) and 63.90 ± 3.67% of chemical oxygen demand (COD), while Nostoc achieved BOD and COD removals of 59 ± 5.1% and 68.46 ± 3.87%, respectively, compared with approximately 25% removal by WWTPs. In addition, Nostoc exhibited a high capacity for chromium biosorption, removing 30.7 ± 2.13% of CrO₄⁻ within three days, highlighting the potential of cyanobacteria for heavy metal remediation in urban rivers [138].

Microalgae have similarly demonstrated strong phycoremediation capabilities. For instance, Selenastrum sp. cultivated in polluted river water under mixotrophic conditions significantly improved water quality by reducing pH, total dissolved solids (TDS), BOD, and COD, while producing lipid-rich biomass. The lipid fraction, dominated by saturated and monounsaturated fatty acids such as palmitic and oleic acids, was suitable for biofuel production, illustrating the added value of integrating bioremediation with biomass valorization [139].

Field-scale studies have further confirmed the effectiveness of indigenous microalgal strains. Chlorella sp., isolated from the Thirumanimutharu River, achieved reductions of 34.51% in BOD and 32.53% in COD, completely removed free ammonia, and increased dissolved oxygen (DO) by 88.47%. Fourier-transform infrared (FTIR) analysis identified functional groups involved in pollutant adsorption, while scanning electron microscopy (SEM) revealed morphological changes associated with contaminant binding [140].

Phytoplankton also play a significant role in heavy metal remediation. Species such as Synechococcus elongatus and Chlorococcum infusionum isolated from the Rio Doce River exhibited high removal efficiencies for iron (Fe) and manganese (Mn), with C. infusionum achieving up to 79% removal. Importantly, these species maintained metal removal capacity under saline conditions, underscoring their applicability across diverse and dynamic urban river environments [141].

In addition to pollutant removal, phytoplankton contribute to contaminant biotransformation. Freshwater microalgae such as Closterium aciculare and Pediastrum duplex have been shown to biotransform toxic arsenate (As(V)) into less toxic methylated arsenic species under varying salinity regimes, thereby reducing metal bioavailability and ecological risk [142].

Despite these advantages, phytoplankton-based remediation is associated with ecological risks when not properly managed. In nutrient-rich urban rivers, excessive phytoplankton growth can lead to harmful algal blooms, resulting in hypoxia, fish mortality, and toxin production. This phenomenon has been observed in urban rivers supplemented with reclaimed water, where elevated nitrogen concentrations favored the dominance of Chlorophyta and Bacillariophyta species such as Chlorella, Cyclotella, and Coscinodiscus. Although algal abundance declined from spring to autumn, spring conditions presented a particularly high bloom risk [143].

Bloom dynamics are influenced by multiple factors, including light intensity, nutrient availability, and metal ion concentrations. Predictive modeling using autoregressive integrated moving average (ARIMA) approaches has effectively captured seasonal changes in algal density, emphasizing the importance of managing environmental parameters to prevent unintended phytoplankton proliferation [143].

Another critical limitation of phytoplankton-based remediation is the potential for secondary pollution. Metal accumulation within phytoplankton biomass can pose risks if biomass is not adequately harvested and managed. Moreover, physiological stress caused by high salinity or metal overload may induce cell lysis and the release of intracellular contents, leading to the reintroduction of previously immobilized pollutants into the water column [142].

Overall, phytoplankton exhibit a dual role in urban river revitalization. On one hand, their capacity for nutrient removal, heavy metal biosorption, contaminant biotransformation, and biomass generation provides sustainable pathways for bioremediation and bioresource valorization. On the other hand, uncontrolled proliferation and improper biomass handling may result in eutrophication and secondary contamination. Consequently, effective phytoplankton-based restoration requires carefully designed, well-monitored strategies that integrate biological processes with conventional management approaches.

Despite their demonstrated potential, the large-scale implementation of microalgae-based remediation technologies remains constrained by a major bottleneck: the efficient and cost-effective harvesting of microalgal biomass [144]. Urban rivers typically contain low algal biomass concentrations, high loads of suspended solids, and highly variable environmental conditions, making solid–liquid separation technically and economically challenging. Biomass harvesting alone can account for 20–30% of total production costs, and in some cases up to 50% [145], due to intrinsic cellular properties such as small cell size, low culture density, and negatively charged cell surfaces that stabilize colloidal suspensions [146].

Conventional harvesting techniques—including centrifugation, membrane filtration, sedimentation, and flotation—exhibit significant trade-offs when applied to polluted river systems [147]. Centrifugation provides high recovery efficiencies but is energy-intensive and impractical for large-scale river restoration. Membrane filtration yields high-quality biomass but is prone to severe fouling in wastewater-derived cultures rich in algogenic organic matter [148]. Sedimentation is generally ineffective for small-celled microalgae and requires long retention times [149], while flotation technologies, such as dissolved air flotation (DAF) or electrolytic flotation, often require chemical additives or high energy inputs, particularly under fluctuating pH and ionic strength conditions typical of urban rivers [150].

Chemical and electro-assisted flocculation can improve harvesting efficiency but introduce environmental and operational constraints. Inorganic coagulants, although cost-effective, contaminate biomass with metals and limit downstream valorization. In contrast, bio-based flocculants, including chitosan and tannin-derived polymers, offer more sustainable alternatives by achieving high recovery efficiencies while preserving biomass quality and compatibility with complex pollutant matrices [151]. Nevertheless, flocculant dosage optimization, pH sensitivity, and process control remain important challenges. Electrocoagulation eliminates chemical inputs but is hindered by electrode degradation, scaling, and elevated energy demand. Hybrid strategies—such as flocculation–flotation or flocculation–filtration—have demonstrated high harvesting efficiencies (>95%) while reducing energy consumption and environmental impact [152].

To overcome these limitations, biofilm-based microalgae cultivation has emerged as a particularly promising approach. In contrast to suspended cultures, biofilm systems promote microalgal growth directly on solid substrates, greatly simplifying biomass recovery [153]. Mature biofilms can be harvested by simple mechanical scraping, eliminating the need for energy-intensive centrifugation or chemical flocculation [154]. This approach is especially attractive for urban river restoration, where large water volumes, low biomass densities, and decentralized deployment demand robust and low-cost harvesting solutions.

Biofilm-based systems also confer functional advantages under polluted river conditions, including improved light utilization, enhanced gas exchange, tolerance to hydrodynamic fluctuations, and reduced space and infrastructure requirements. Biofilm formation is mediated by extracellular polymeric substances (EPS), which facilitate cell adhesion and structural stability. Natural lignocellulosic carriers, such as pine wood and soybean shells, have proven particularly effective due to their hydrophilic functional groups (e.g., carboxyl, hydroxyl, methoxy) and porous microstructures that promote EPS binding and microalgal attachment [155,156]. These materials also exhibit high water retention capacity, supporting sustained growth under variable flow regimes. Reported biofilm productivities for Chlorella spp. reach 9–15 g m⁻² day⁻¹ under regrowth conditions, substantially exceeding those of suspended cultures [153].

When applied to river revitalization, algal biofilms offer distinct ecological and operational advantages: (i) modular deployment of carriers directly within river channels; (ii) enhanced nutrient and metal removal via combined adsorption and active uptake [157]; (iii) minimized pollutant resuspension during harvesting; and (iv) straightforward recovery of biomass for downstream applications such as biofertilizers, bioenergy, and biopolymer production [158]. Importantly, simplified harvesting reduces the risk of secondary pollution associated with biomass degradation or metal re-release—an issue of particular relevance when phytoplankton accumulate toxic metals or organic pollutants [159].

While conventional harvesting technologies impose major economic and operational constraints on phytoplankton-based remediation of urban rivers, biofilm-based cultivation represents a transformative strategy that directly addresses the challenge of algal–water separation. Integrating attached-growth phytoplankton systems with traditional phycoremediation approaches can significantly enhance process feasibility, environmental resilience, and biomass valorization potential. Future urban river restoration programs should therefore include comprehensive techno-economic assessments of biofilm-based microalgal systems as part of a scalable, low-cost, and sustainable framework for improving water quality.

5. Biotechnological Strategies for the Removal of Multidrug-Resistant Microorganisms and Genes from Rivers

It is well known that rivers worldwide are, to varying degrees, polluted with solid waste, biological residues, pesticides, and pharmaceutical contaminants, among which antimicrobials stand out [160]. These compounds, whether synthetic or natural, are classified as Contaminants of Emerging Concern (CECs) and are commonly discharged into wastewater, surface, and groundwater systems. Once disseminated into human and animal bodies or ecosystems, CECs can cause ecotoxicological and degrading effects, which are being increasingly studied from a One Health perspective [161]. Moreover, such contaminants exert selective pressure on microorganisms, potentially leading to resistance against various chemical agents such as heavy metals, disinfectants and antimicrobials [162,163].

The presence of multidrug-resistant microorganisms and resistance genes in aquatic ecosystems is especially concerning in areas with inadequate sanitation infrastructure, such as in parts of Latin America. This situation contributes to a rise in antimicrobial resistance cases, mortality rates, and contamination of habitats and living organisms [160,161]. Among the resistant organisms, Gram-negative bacilli are particularly concerning and are prioritized for the development of antimicrobial resistance mitigation strategies [25].

The primary sources of river contamination include untreated or inadequately treated effluents from hospitals, agriculture, domestic, and industrial sources. Often, these effluents are sent to wastewater treatment plants that function as reservoirs for a broad spectrum of contaminants and microorganisms [164]. These environments facilitate the transfer of resistance genes via plasmids, transposons, and other mobile genetic elements, both vertically (within the same species) and horizontally (across different species) [163].

Given this growing threat, researchers have been developing promising strategies to mitigate the issue. This chapter section highlights and discusses some of the most innovative techniques being developed in the fields of microbiology, nanotechnology, and molecular biology.

5.1. Bioremediation as a Strategy Against Resistance Genes

Bioremediation is one of the primary techniques used for removing organic and inorganic contaminants from polluted environments. This method is widely favored for its low cost and the potential use of native microorganisms or introduced strains suited to the target ecosystem [165]. It involves the degradation of chemical compounds by bacteria, fungi, or algae, which metabolize these compounds as carbon sources. The choice of microorganism depends on the physicochemical characteristics of the environment and the nature of the pollutants.

Although some plants may also be employed for remediation, microbial bioremediation is generally more effective due to faster generation times and easier cultivation and maintenance of microbial consortia [166]. Microorganisms remove antibiotics and other chemical pollutants either through immobilization, reducing their availability and spread, or mobilization, increasing bioavailability for degradation, albeit with a risk of wider environmental dissemination [166]. When microalgae are integrated into bioremediation processes, overall efficiency can be increased because they release oxygen and synthesize organic compounds that sustain and strengthen the microbial consortium, thus complementing the mechanisms described before [167]. Bioremediation can be performed in situ or ex situ, depending on specific goals.

One of the most cost-effective and ecologically safe methods for removing pharmaceutical residues is adsorption or biosorption. This process is typically carried out by bacteria such as Pseudomonas sp. and Bacillus sp., which bind pollutants to their cell surfaces via ionic interactions, especially when metallic elements are present [165,166]. Filamentous fungi, such as white-rot fungi, can also adsorb, transform, and mineralize various CECs, such as fluoroquinones and ampicillin, through laccase-catalyzed oxidation (also present in Pseudomonas sp. and Bacillus sp.), reducing selection by qnr, ampC, blaTEM and similar genes [168]. Other enzymes may also be involved in this process, depending on the species of microorganism, such as dioxygenases, hydroxylases, etc. Despite its promise, bioremediation has limitations. It is influenced by environmental conditions, is effective only for biodegradable compounds, and its scalability remains a challenge.

5.2. Phages as Biocontrol Agents Against Multidrug-Resistant Bacteria

Phages, or bacteriophages, are viruses that infect and destroy specific bacterial targets. Their mechanism involves binding to bacterial membranes via lock-and-key interactions and lysing the host cells through the lytic cycle [169]. This high specificity, determined by tail fibers, allows phages to target harmful bacteria without affecting beneficial microbial communities, a feature demonstrated even in human applications.

In aquatic and wastewater environments, bacteriophages act as natural regulators of bacterial abundance, diversity, and succession. Phage-mediated lysis releases intracellular metabolites and dissolved organic matter, influencing carbon turnover and nutrient cycling—processes that directly affect microbial fermentation pathways in activated sludge and biofilm-based treatment systems. From a fermentation and bioprocess perspective, bacteriophages represent key regulators of microbial population dynamics, metabolic fluxes, and community stability.

The dissemination of antimicrobial-resistant (AMR) bacteria in rivers and wastewater treatment plants (WWTPs) has intensified due to sanitation deficits, rapid urbanization, and the discharge of domestic, hospital, industrial, and agricultural effluents. These systems function as open, large-scale microbial reactors in which selective pressures favor resistant phenotypes and facilitate the spread of antimicrobial resistance genes (ARGs). In this context, bacteriophages emerge as promising biological control agents capable of modulating microbial communities without disrupting essential fermentation and biological treatment processes.

Phages also drive microbial evolution through horizontal gene transfer, shaping bacterial adaptation to operational stresses such as temperature fluctuations, oxygen gradients, nutrient loading, and exposure to xenobiotics, all of which are characteristic of Brazilian WWTPs operating under tropical conditions. These interactions position bacteriophages as intrinsic modulators of microbial fermentation efficiency and stability.

Phages are naturally abundant, easy to isolate, and fast to propagate [170,171]. They are already being explored for the treatment of waterborne multidrug-resistant pathogens, regardless of Gram classification [169]. Phages can even penetrate and destroy biofilms in wastewater [171], and contaminated rivers and effluents themselves can be a source of effective phages [172]. Moreover, phages can be combined in engineered consortial (algae–bacteria–phage) to simultaneously achieve pollutant removal and targeted suppression of multidrug-resistant bacteria, thereby establishing multifunctional platforms for ecological remediation [173]. This approach can be observed in the use of activated sludge in sewage treatment plants [173].

Phages can be applied as cocktails, targeting multiple species, or as single phage therapies, which are particularly useful for reducing foaming and biofilms in wastewater treatment [169,171]. One concern is the potential for phage therapy to facilitate horizontal gene transfer. Upon host cell lysis, resistance genes housed in plasmids may be released into the environment. Other challenges include regulatory and biosafety concerns in in situ applications and the need for long-term ecological monitoring.

Bacteriophages represent a biologically robust and environmentally compatible tool for controlling antimicrobial-resistant bacteria in rivers and wastewater fermentation systems. Their strategic integration into wastewater treatment processes may enhance microbial community stability, improve treatment performance, and reduce the environmental dissemination of antimicrobial resistance. Future research should focus on large-scale field validation, process integration studies, and regulatory frameworks to enable safe and effective phage-based applications within fermentation-driven treatment systems.

5.3. Nanotechnology: An Innovative Alternative for Destroying Bacterial Cells and Resistance Genes

Nanotechnology involves manipulating materials at the nanoscale (1–100 nm). The concept was first proposed by Richard Feynman in 1959 [174]. Materials are typically classified as metals, polymers, semiconductors, ceramics, or composites, with differences in composition, hardness, thermal and electrical conductivity, and optical properties. A nanomaterial must exhibit at least one physical or chemical property at the nanoscale that significantly differs from its bulk form [175,176]. Nanoparticles can also be found in nature, such as gold and silver nanoparticles that can be synthesized by microalgae of the species Sargassum incisifolium [177].

At this critical size, materials may show altered melting points, conductivity, and even color due to changes in particle size and morphology. These unique properties have opened up diverse industrial and biomedical applications. For example, silver nanoparticles are used in textiles to prevent odors, nanocapsules enhance drug delivery, and “cyborg cells” have been developed to selectively target cancer cells [178].

In environmental applications, the degradation of antibiotics, pesticides, resistance genes, and heavy metals is commonly achieved through the use of nanoparticles such as silver, gold, zinc oxide, magnetite, manganese oxide, and cerium dioxide [179,180]. Among these, magnetite nanoparticles are particularly notable for their ability to bind DNA fragments containing resistance genes, which can then be recovered through magnetic separation. Cerium monoxide is also under investigation for its potential use in tap water treatment and in nanofilters designed to enable both physical and chemical removal of pathogens and resistance genes [180]. These nanomaterials can be incorporated into filtration systems, immobilized on activated carbon, directly dispersed into water or soil, or adhered to microorganisms to form bio-nanocomposites [180]. In particular, the attachment of nanoparticles to microalgae has been shown to expand the spectrum of bioremediation activity while offering a more environmentally sustainable approach [181,182].

Combining photocatalytic nanomaterials, such as titanium dioxide, with natural biocides or disinfection methods, as UV light, enhances efficacy. These materials generate reactive oxygen species (ROS) under light exposure, such as zinc oxide, titanium monoxide, bismuth trioxide, and silver orthophosphate, leading to membrane and organelle damage in resistant bacteria [183].

Advantages include low toxicity (when using appropriate nanoparticles), reusability, limited horizontal gene transfer, and effectiveness against both bacteria and resistance genes. Compared to conventional disinfectants, nanotechnology offers promising alternatives that reduce the formation of toxic by-products and selective pressure on microbial communities [184]. However, large-scale implementation requires investment, studies on environmental persistence and toxicity, and appropriate regulation to ensure safety.

6. Sustainable Strategies for Urban River Revitalization

In addition to the remediation approaches discussed above, the sustainable revitalization of urban rivers requires the integrated application of ecological, infrastructural, and urban planning strategies. Urban river ecosystems have experienced extensive degradation as a result of rapid urbanization, industrial effluent discharge, and unsustainable land-use practices. Effective restoration therefore demands holistic frameworks that balance ecological integrity, social functionality, and economic feasibility [47]. Within this context, urban river revitalization must incorporate innovative and adaptive solutions capable of harmonizing environmental recovery with urban development objectives [5]. This section examines sustainable strategies that emphasize eco-engineering solutions, green infrastructure, and biotechnological approaches for riverbank restoration.

6.1. Eco-Engineering Solutions: Integrating Natural Processes and Engineering for Sustainable Outcomes

Eco-engineering solutions play a central role in urban river revitalization by harnessing natural processes to restore ecological function while addressing water quality and hydrological challenges. These approaches prioritize the design and implementation of systems that mimic or enhance ecosystem services such as nutrient cycling, sediment retention, and habitat creation [185]. By integrating ecological principles with engineering design, eco-engineering promotes multifunctional river corridors that support biodiversity, mitigate pollution, and increase resilience to urban stressors [186]. Compared with conventional gray infrastructure, eco-engineering solutions offer adaptive, cost-effective, and environmentally sustainable pathways for restoring degraded urban waterways.

Among the wide range of eco-engineering strategies, constructed wetlands and floating treatment wetlands represent well-established approaches that combine ecological processes with engineered design to improve water quality and ecosystem functionality. These systems are described in detail in the following subsections.

6.1.1. Constructed Wetlands

Constructed wetlands (CWs) are engineered systems designed to replicate the functions of natural wetlands and are widely used for the treatment of urban wastewater. They facilitate a combination of physical, chemical, and biological processes that promote the removal of organic matter, nutrients (nitrogen and phosphorus), heavy metals, and pathogens.

CWs are generally classified into surface flow and subsurface flow systems. Surface flow wetlands allow water to flow over a vegetated soil surface, resembling natural marsh ecosystems. In contrast, subsurface flow wetlands direct water through a gravel or sand matrix planted with macrophytes such as Phragmites australis and Typha spp. These plants play a critical role in oxygenating the rhizosphere and supporting diverse microbial communities capable of degrading and transforming pollutants [187].

Numerous studies have demonstrated that constructed wetlands can achieve reductions exceeding 70% in biochemical oxygen demand (BOD) and total nitrogen (TN), depending on hydraulic retention time, temperature, and pollutant loading rates [188]. Although the relatively large land area required may limit their application in densely urbanized settings, their low operational costs, minimal energy demand, and robustness make CWs particularly suitable for urban retrofitting and decentralized treatment, especially in developing regions [189].

6.1.2. Floating Treatment Wetlands

Floating treatment wetlands (FTWs) consist of buoyant platforms planted with emergent vegetation and deployed on the surface of water bodies. Unlike constructed wetlands, FTWs do not rely on soil substrates; instead, plant roots are suspended directly into the water column, where they provide extensive surfaces for microbial biofilm development and nutrient uptake [190].

FTWs are especially advantageous in urban rivers characterized by limited riparian space, channelized morphology, or impervious surroundings. The synergistic interaction between plant roots and associated microbial communities enhances nitrogen removal through coupled nitrification–denitrification processes and phosphorus removal via plant uptake and sedimentation. In addition, FTWs contribute to habitat creation and can mitigate urban heat island effects by shading the water surface [191]. Field-scale applications in urban rivers and lakes have reported phosphate removal efficiencies exceeding 50% and nitrate reductions of up to 70%, highlighting the potential of FTWs as modular, low-impact solutions for urban river restoration.

6.2. Green Infrastructure: Integrating Nature into Urban Planning

Green infrastructure encompasses networks of natural and semi-natural systems designed to deliver essential ecosystem services, including stormwater regulation, pollutant attenuation, air quality improvement, and thermal regulation. In urban river contexts, green infrastructure seeks to restore hydrological connectivity, enhance biodiversity, and reduce pollutant inputs to aquatic ecosystems [192].

Key components of green infrastructure include bioswales and rain gardens, which capture and filter stormwater runoff before it enters river systems; green roofs and living walls, which reduce runoff volume, moderate urban temperatures, and provide habitat; and permeable pavements, which facilitate water infiltration, reduce surface runoff, and promote groundwater recharge [193]. Implementation of green infrastructure across urban catchments has been shown to attenuate peak storm flows, reduce total suspended solids, and decrease nutrient loading to rivers. Moreover, embedding green infrastructure within urban planning and zoning regulations enhances climate resilience, improves urban aesthetics, and supports long-term biodiversity conservation.

6.3. Riverbank Restoration: Biotechnological Approaches to Riparian Revitalization

Riparian zones represent critical interfaces between terrestrial and aquatic ecosystems, yet they are frequently degraded by erosion, habitat fragmentation, and invasion by non-native species. Biotechnological approaches offer innovative tools for restoring riparian environments while reinforcing their ecological functions.

Phytoremediation involves the use of plants to remove, degrade, or immobilize contaminants in soils and water. In riverbank restoration, species such as Chrysopogon zizanioides, Salix spp., and Populus spp. are commonly employed to stabilize sediments and uptake pollutants, including heavy metals and hydrocarbons [194,195]. These species combine deep root systems with high biomass production, making them particularly effective for erosion control and contaminant sequestration.

Bioengineering techniques further integrate living plant materials with structural components such as fascines, coir logs, and brush mattresses to reinforce riverbanks, dissipate hydraulic energy, and establish stable vegetation cover. These systems are especially valuable in flood-prone environments, as they form adaptive, self-repairing structures that evolve alongside natural ecological succession [196].

Advances in environmental biotechnology have also highlighted the importance of beneficial microbial consortia in riparian restoration. The application of plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi as inoculants can significantly enhance plant establishment, nutrient acquisition, and tolerance to abiotic stress [197]. Such bioaugmentation strategies accelerate revegetation, improve soil structure, and increase microbial diversity, thereby strengthening the long-term stability and functionality of riparian zones. Inoculated plantings have consistently demonstrated higher biomass production, survival rates, and pollutant uptake capacity in contaminated or nutrient-poor riverbanks.

Beyond erosion control and pollution mitigation, restored riparian zones deliver a wide range of ecosystem services, including carbon sequestration, habitat provision, and recreational and aesthetic benefits. Socioeconomic assessments indicate that riverbank restoration can increase property values, promote ecotourism, and foster community engagement in environmental stewardship initiatives. In summary, sustainable urban river revitalization depends on the synergistic integration of ecological principles, engineering innovation, and societal participation [198]. Eco-engineering solutions such as constructed and floating wetlands provide effective, modular treatment systems; green infrastructure embeds water-sensitive design within urban landscapes; and biotechnological riverbank restoration promotes resilient, self-sustaining riparian ecosystems [199]. When implemented within a holistic watershed management framework, these strategies offer transformative potential for restoring urban rivers and safeguarding their long-term ecological integrity.

7. Circular Economy in Urban River Revitalization

The revitalization of urban rivers requires innovative and sustainable solutions that move beyond conventional, linear remediation strategies. The integration of circular economy principles—aimed at minimizing waste, maximizing resource efficiency, enabling continuous monitoring, and closing material and energy loops—has emerged as a transformative paradigm for urban river restoration (Figure 7). This section examines the application of waste-to-resource frameworks, resource recovery technologies, and closed-loop systems in urban river revitalization, grounded in recent scientific advances.

Urban rivers frequently function as terminal sinks for anthropogenic wastes, accumulating heavy metals, nutrients, and persistent organic contaminants. A circular economy perspective redefines these pollutants as recoverable resources, thereby reducing environmental burdens while generating economic and social value. Floating treatment wetlands (FTWs) exemplify this approach by combining pollutant removal with biomass generation (Figure 8). Emergent macrophytes grown on floating platforms remove contaminants through plant uptake, microbial degradation, and sedimentation without requiring additional land area [200]. Importantly, the harvested biomass can be valorized for bioenergy, biofertilizers, or other bioproducts, directly supporting circular bioeconomy objectives.

Similarly, calcite-rich residues generated during industrial effluent treatment have demonstrated strong potential as substitutes for commercial limestone in passive dispersed alkaline substrate systems for acid mine drainage remediation. Removal efficiencies of 90–100% for Fe, Al, and Cu have been reported, effectively transforming a treatment by-product into a valuable environmental resource [201]. In another example, drinking water treatment residues (DWTRs) have been successfully reused as soil amendments in mining-impacted areas, significantly reducing the bioavailability of toxic metals such as Pb and Cu and reinforcing zero-waste, resource-recovery strategies [202].

Biotechnology plays a central role in circular urban river revitalization by enabling the conversion of pollutants into valuable products. The ALGEBRA project illustrates this concept through the use of microalgae, including Chlorella vulgaris and Spirulina platensis, for the removal of heavy metals from contaminated waters. Simultaneously, algal cultivation produces biomass suitable for biofuels, fertilizers, and pharmaceutical applications, forming a closed-loop and regenerative system [203].

Bioeconomy-driven approaches further emphasize the use of biological diversity for pollution control and resource recovery. Through bioremediation, contaminated river sediments and waters become renewable sources of bioproducts (Figure 9), strengthening the bio-based economy while mitigating environmental impacts [204]. For example, Salix spp. have been applied successfully for the remediation of contaminated dredged sediments, with heavy metals predominantly retained in root tissues, enabling both phytoremediation and targeted nutrient or metal recovery [205].

The full realization of circular economy principles in urban river revitalization requires the design of closed-loop systems that continuously recycle resources while minimizing waste outputs. Green corridor initiatives, such as the Huatanay River restoration project in Cuzco, Peru, exemplify this approach by integrating riparian reforestation, ecological restoration, renewable energy generation via biodigesters, and public green spaces into self-sustaining urban ecosystems [206].

Additional examples include photovoltaic-powered drip irrigation systems in Egypt, which combine smart technologies, renewable energy, and efficient water use to address water scarcity while enhancing agricultural productivity [207]. Although urban river restoration remains complex—given the multiple stressors affecting most river systems—projects rooted in circular economy principles consistently demonstrate greater long-term sustainability than linear remediation approaches [5].

Recent assessments in cities such as Shenzhen, China, further emphasize the need to move beyond water quality metrics alone toward holistic ecosystem recovery, including biodiversity restoration and aquatic community rehabilitation [208]. Moreover, participatory and co-evolutionary governance models, such as those implemented in Kerala, India, highlight the importance of community engagement in sustaining circular river management strategies [209]. Ultimately, closing material and energy loops in urban river systems requires the co-development of technical, ecological, and social dimensions.

8. Real World Case Studies of Successful Biotechnological and Sustainable River Revitalization

Globally, urban rivers have experienced severe degradation due to industrial discharges, agricultural runoff, and unregulated urban expansion. Conventional restoration approaches are often costly, time-intensive, and reliant on disruptive engineering works. In contrast, recent biotechnological innovations provide scalable, cost-effective, and environmentally sustainable alternatives for river revitalization (

Table 3. Recent real-world biotechnological applications for river revitalization.

River (Country)	Biotechnological Approach	Microorganisms Used	Reference
Camarajipe River (Brazil)	Composting with microbial accelerators, biofertilizers, bioinsecticides, photonic bio-stimulation, phytoremediation, Eco-Plant for waste reuse	Bacillus thuringiensis, Trichoderma spp., Bacillus subtilis	[210,211,212]
Chengnan River (China)	Direct application of microbial agent (HP-RPe-3) in water and sediment	Proprietary microbial agent (unspecified)	[130]
Plankenburg River (South Africa)	Bioreactors with bioballs for biofilm growth and metal bioaccumulation	Pseudomonas, Sphingomonas, Bacillus spp.	[213]
Unnamed River near Chemko (Slovakia)	Application of indigenous bacterial consortia for PCB degradation in sediments	Achromobacter xylosoxidans, Stenotrophomonas maltophilia, Ochrobactrum anthropi, Rhodococcus ruber	[214]
Savannah River Site (USA)	In situ bioremediation with methane/air injection and nutrient delivery to stimulate indigenous methanotrophs	Indigenous methanotrophic bacteria (not specified by species)	[215]
Subarnarekha River (India)	Integration of biomonitoring (e.g., mollusks) and bioremediation (e.g., fungi), with ecological indices (WQI, PLI, BCF)	Benthic mollusks, fungi (species not specified)	[216]

).

A prominent example of urban river degradation driven by unplanned urbanization is Salvador, the capital of Bahia, Brazil. Rapid and disorderly expansion has severely impacted watersheds such as the Camarajipe River Basin. Pollution from clandestine sewage discharges, solid waste dumping, industrial effluents, and deforestation has significantly compromised water quality and public health.

To address these challenges, the project “Application of Biotechnological and Sustainable Strategies to Mitigate Environmental Degradation in the Camarajipe River Basin and to Control Aedes aegypti and Agricultural Pests in Family Farming Systems” proposes an integrated suite of biotechnological interventions. These include pilot-scale composting facilities for organic waste conversion into biofertilizers using microbial accelerators (Bacillus thuringiensis, Trichoderma spp., Bacillus subtilis), supporting riparian reforestation and soil recovery [212]. In parallel, locally isolated microbial consortia developed in collaboration with the International Centre for Genetic Engineering and Biotechnology (ICGEB) are applied as biofertilizers and bioinsecticides to rehabilitate degraded areas.

Additional strategies include photonic biostimulation to enhance microbial productivity and plant development, as well as the deployment of entomopathogenic B. thuringiensis strains to control Aedes aegypti populations in flood-prone zones, contributing to public health protection [210,211]. An innovative Eco-Plant facility further valorizes urban waste streams (e.g., coconut husks, plastics, tires, construction debris) into biocomposites used in modular wastewater treatment systems and urban infrastructure.

Riparian restoration efforts prioritize native species (Hymenaea courbaril, Handroanthus impetiginosus, Paubrasilia echinata) alongside aquatic macrophytes to enhance phytoremediation capacity. Extensive capacity-building initiatives—workshops, extension programs, and community engagement—ensure long-term sustainability and social inclusion. Collectively, these integrated biotechnological interventions provide a replicable model for urban river restoration across Brazil.

Comparable successes have been reported elsewhere. In China, direct application of a microbial agent (HP-RPe-3) to the Chengnan River resulted in significant improvements in dissolved oxygen, ammonia nitrogen, and COD, eliminating black-odor conditions without dredging or aeration [130]. In South Africa, biofilm-based bioreactors using bioballs achieved substantial heavy metal removal in the Plankenburg River, driven by Pseudomonas, Sphingomonas, and Bacillus species [213]. In Slovakia, indigenous bacterial consortia degraded up to 85% of PCB congeners in contaminated sediments [214]. At the Savannah River Site (USA), in situ stimulation of methanotrophic bacteria enhanced trichloroethylene removal beyond conventional extraction methods [215]. In India, integrated biomonitoring and bioremediation of the Subarnarekha River highlighted the functional role of aquatic biota in ecosystem-based river management [216].

Together, these case studies demonstrate that site-adapted biotechnological approaches can deliver effective and sustainable river restoration outcomes when guided by local environmental conditions and adaptive management strategies.

9. Challenges, Future Directions and Artificial Intelligence

The application of biotechnological and sustainable strategies for river ecosystem revitalization has advanced substantially in recent years. Nevertheless, major challenges remain in scaling these approaches, establishing appropriate regulatory frameworks, and ensuring their long-term environmental effectiveness. This section critically examines the principal technical, ecological, and policy-related constraints, while highlighting emerging research directions and the growing role of artificial intelligence (AI) in urban river management.

Scaling biotechnological solutions from laboratory and pilot-scale studies to full-scale river restoration presents considerable technical obstacles. Many bioengineering strategies—including microbial bioremediation, biofilm-based systems, and the deployment of engineered or selected plant species—require tightly controlled conditions to maintain performance. In open and dynamic river environments, these conditions are difficult to reproduce due to spatial heterogeneity, fluctuating water chemistry, temperature variability, and seasonal hydrological changes [217,218].

Environmental risks further complicate large-scale implementation. The introduction of engineered organisms or novel biological agents into natural ecosystems may lead to unintended consequences, such as disruption of native communities, altered trophic interactions, unexpected bioaccumulation of contaminants, or horizontal gene transfer. In addition, the long-term stability, persistence, and ecological behavior of bioengineered systems remain insufficiently characterized, raising concerns about potential secondary impacts and the durability of remediation outcomes [219,220,221].

Ecosystem heterogeneity represents an additional challenge. Rivers differ widely in flow regimes, sediment dynamics, nutrient composition, and biological assemblages, meaning that technologies effective in one system may perform poorly in another. Consequently, biotechnological river restoration must rely on adaptive, site-specific designs supported by comprehensive environmental risk assessments prior to field deployment.

Regulatory frameworks governing biotechnological interventions in river systems have not yet kept pace with technological innovation. In many jurisdictions, the environmental release of genetically modified organisms is subject to strict regulation or prolonged approval procedures. International agreements, such as the Cartagena Protocol on Biosafety, impose additional restrictions on the transboundary movement of living modified organisms, complicating the implementation of biotechnological solutions in shared river basins [222,223].

Clear and harmonized regulatory guidelines are therefore needed to evaluate, authorize, and monitor biotechnological river restoration initiatives. Existing environmental legislation often fails to distinguish adequately between chemical and biological remediation strategies, creating regulatory uncertainty and hindering innovation. Furthermore, policies must explicitly address liability, risk management, and remediation responsibility in cases where biotechnological interventions underperform or generate unintended impacts.

Public perception and societal acceptance are equally critical. The success of biotechnological river revitalization depends not only on technical effectiveness but also on public confidence in the safety, transparency, and benefits of these approaches. Open communication, stakeholder engagement, and participatory decision-making processes are essential for building trust and facilitating regulatory approval.

Several emerging technologies hold significant promise for advancing biotechnological river revitalization. Synthetic biology enables the rational design of microorganisms with enhanced pollutant-degradation capabilities or ecosystem service functions, incorporating built-in safety mechanisms such as genetic kill switches to prevent uncontrolled environmental spread. In parallel, environmental DNA monitoring provides a powerful, non-invasive tool for real-time assessment of biodiversity and microbial community dynamics, enabling adaptive optimization of biotechnological interventions [224].

Bioelectrochemical systems, including microbial fuel cells, represent another promising avenue by simultaneously treating contaminated water and generating renewable energy. Advances in nanobiotechnology, particularly the development of biocompatible and environmentally benign nanomaterials, offer opportunities to enhance pollutant adsorption, catalysis, and bioavailability without adversely affecting aquatic organisms.

AI, machine learning, and neural network approaches are increasingly recognized as transformative tools for urban river revitalization. These technologies enable high-resolution monitoring, predictive modeling, and optimization of depollution strategies in complex and highly dynamic aquatic systems [225,226]. Urban rivers are characterized by nonlinear interactions among industrial effluents, domestic wastewater, stormwater runoff, and diffuse agricultural inputs, necessitating advanced data-driven approaches capable of handling non-stationary, multivariate datasets [226].

AI-driven frameworks integrate real-time data from Internet of Things-based sensors to continuously monitor key water quality parameters, including pH, dissolved oxygen, turbidity, and heavy metal concentrations, supporting early detection of pollution events and adaptive management responses [226]. Deep learning architectures, particularly Long Short-Term Memory (LSTM) networks, have demonstrated superior performance in forecasting temporal variations in nutrients and metals compared to conventional statistical models [227,228,229]. AI-enhanced remote sensing further expands spatial coverage by enabling large-scale assessment of land-use change, algal blooms, and surface pollution using satellite and drone imagery [230,231].

Beyond monitoring and prediction, AI is increasingly applied to optimize treatment processes. Machine learning models, such as artificial neural networks and random forest algorithms, are used to fine-tune coagulation–flocculation systems, achieving high pollutant removal efficiencies while minimizing chemical consumption and sludge generation [232]. Similar approaches enhance performance prediction for membrane filtration, biochar-based adsorption, and chemical precipitation pathways for contaminant immobilization [233,234].

AI also supports advanced bioremediation strategies by enabling data-driven design of phytobial systems and microbial consortia. Real-time analysis of plant–microbe interactions and contaminant bioavailability improves the efficiency of arsenic and mercury removal [235]. At the microbial level, AI-assisted genomic screening and metabolic modeling facilitate the selection and optimization of microorganisms as tailored “cell factories” for treating oily sludge and industrial effluents [236].

Despite its substantial potential, the application of AI in river revitalization faces important limitations. Many deep learning models operate as “black boxes,” limiting mechanistic interpretability and complicating regulatory acceptance. This challenge underscores the need for explainable AI frameworks, such as SHAP and LIME, to improve transparency and trust [232,236]. Moreover, AI performance is highly dependent on data availability and quality; sparse or site-specific datasets increase the risk of overfitting and poor generalization under real river conditions [226,237]. Cross-system transferability remains a major obstacle, as models trained for one river often perform poorly when applied to systems with different hydrological, climatic, or pollution characteristics [232].

Nevertheless, AI is emerging as a central decision-support layer for future river revitalization strategies, capable of integrating monitoring, prediction, and process optimization into unified management frameworks. Addressing challenges related to transparency, data robustness, and model generalization will be essential for translating AI-driven approaches from experimental studies into reliable, large-scale tools for sustainable river depollution.

Future research must also prioritize system resilience and adaptability. Biotechnological and AI-assisted solutions capable of adjusting to variable environmental conditions and recovering from disturbances will be critical for long-term success. Achieving this goal will require close multidisciplinary collaboration among biotechnologists, ecologists, hydrologists, data scientists, and policymakers to develop restoration strategies that are ecologically sound, economically viable, and socially acceptable.

10. Concluding Remarks

The revitalization of urban rivers through biotechnological and sustainable strategies is a critical pillar of urban sustainability. Healthy river systems are fundamental to maintaining water quality, supporting biodiversity, and enhancing human well-being. Beyond ecological restoration, sustainable river management strengthens urban resilience, improves public health, and generates socio-economic opportunities for surrounding communities. By integrating environmentally friendly biotechnological solutions with circular economy principles, cities can transition toward regenerative urban landscapes that deliver long-term ecological, social, and economic benefits. Achieving effective urban river management requires the coordinated integration of biotechnological innovations, ecosystem-based approaches, and sustainable planning strategies. When embedded within holistic watershed management frameworks, these approaches offer transformative pathways for river revitalization. Collaboration among scientists, urban planners, policymakers, and local communities is essential for developing adaptive, site-specific solutions that address local environmental pressures while fostering long-term resilience. Continued investment in research, regulatory development, and community engagement will be decisive in ensuring the effectiveness and sustainability of future interventions. Ultimately, the success of urban sustainability agendas depends on the ability to restore and safeguard clean, resilient river systems for present and future generations.

The key findings of this review can be summarized as follows:

(I)

Traditional remediation methods can provide short-term improvements in urban river quality; however, their long-term effectiveness is constrained by environmental impacts, economic costs, and sustainability limitations. Integrated frameworks that combine conventional techniques with ecosystem-based and nature-based solutions are essential for achieving durable river resilience.

(II)

Biotechnological approaches—particularly those based on bacterial and fungal processes—offer environmentally friendly and versatile solutions for the remediation of polluted urban rivers. These strategies effectively target heavy metals, organic contaminants, and pathogens while supporting ecological recovery. Continued technological innovation and system integration are necessary to enable large-scale implementation.

(III)

Phytoplankton-based approaches represent a sustainable tool for river revitalization through pollutant removal and biomass generation. However, their application requires careful management to prevent adverse outcomes such as harmful algal blooms and secondary pollution. Long-term success depends on balanced strategies that integrate biological and conventional control measures.

(IV)

The incorporation of circular economy principles into urban river restoration promotes regenerative systems that convert waste streams into valuable resources. Evidence from successful applications demonstrates that closing material and energy loops not only enhances ecosystem recovery but also creates socio-economic value. Resilient river restoration therefore relies on the synergy of ecological, technological, and community-driven approaches.

(V)

Advanced biotechnological innovations, including targeted microbial applications and biofilm-based systems, provide effective and sustainable alternatives for river revitalization across diverse environmental contexts. Addressing challenges related to microbial stability, process control, and site specificity will be critical for scaling these technologies.

(VI)

Despite their transformative potential, biotechnological solutions face technical, environmental, and regulatory barriers. Future efforts must prioritize adaptive, site-specific designs, strengthened regulatory frameworks, and transparent stakeholder engagement to build public trust. Multidisciplinary collaboration and continued innovation will be essential to achieving robust, sustainable, and resilient outcomes in urban river revitalization.