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Review

Microplastics, Antibiotics, and Heavy Metals in Anaerobic Digestion Systems: A Critical Review of Sources, Impacts, and Mitigation Strategies

by
Hongbo Liu
1,*,
Xiang Yuan
1,
Yuxuan Yao
1,
Lijin Yao
1,
Junbo Zhang
1 and
Claudia Maurer
2,*
1
School of Environment and Architecture, University of Shanghai for Science and Technology, Shanghai 200093, China
2
Water Quality and Waste Management, Institute of Sanitary Engineering, University of Stuttgart, Bandtäle 2, 70569 Stuttgart, Germany
*
Authors to whom correspondence should be addressed.
Recycling 2025, 10(3), 116; https://doi.org/10.3390/recycling10030116
Submission received: 30 April 2025 / Revised: 11 June 2025 / Accepted: 11 June 2025 / Published: 12 June 2025
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Versions Notes

Abstract

:
The widespread implementation of anaerobic digestion (AD) systems for organic waste treatment is increasingly challenged by emerging contaminants, including microplastics (MPs), antibiotics, and heavy metals (HMs), which exhibit environmental persistence and pose risks to ecological and human health. This review critically examines the sources, transformation pathways, and advanced mitigation strategies for these contaminants within AD systems. MPs, primarily derived from fragmented plastics and personal care products, accumulate in digestates and act as vectors for adsorbing toxic additives and pathogens. Antibiotics, introduced via livestock manure and wastewater, exert selective pressures that propagate antibiotic resistance genes (ARGs) while disrupting methanogenic consortia. HMs, originating from industrial and agricultural activities, impair microbial activity through bioaccumulation and enzymatic interference, with their bioavailability modulated by speciation shifts during digestion. To combat these challenges, promising mitigation approaches include the following: (1) bioaugmentation with specialized microbial consortia to enhance contaminant degradation and stabilize HMs; (2) thermal hydrolysis pretreatment to break down MPs and antibiotic residues; (3) chemical passivation using biochar or sulfides to immobilize HMs. Co-digestion practices inadvertently concentrate these contaminants, with MPs and HMs predominantly partitioning into solid phases, while antibiotics persist in both liquid and solid fractions. These findings highlight the urgency of optimizing mitigation strategies to minimize contaminant mobility and toxicity. However, critical knowledge gaps persist regarding the long-term impacts of biodegradable MPs, antibiotic transformation byproducts, and standardized regulatory thresholds for contaminant residues in digestate. This synthesis underscores the necessity for integrated engineering solutions and policy frameworks to ensure the safe resource recovery from AD systems, balancing energy production with environmental sustainability.

1. Introduction

Anaerobic digestion (AD) has emerged as a pivotal biotechnology for the sustainable management of organic wastes (e.g., livestock manure, crop residues, and food waste) and high-strength wastewater streams (e.g., swine effluent) through energy recovery [1,2]. Driven by renewable energy incentives, climate policies, and escalating waste disposal demands, global deployment of AD systems has expanded exponentially, with over 30 million commercial and household-scale digesters operational across Europe and Asia [3,4,5]. The process relies on synergistic microbial consortia to degrade organic substrates into methane-rich biogas under optimized operational parameters [6].
Despite its merits, AD faces critical challenges in digestate quality control due to co-introduced contaminants [7]. Co-digestion practices—integrating food waste with livestock manure or waste-activated sludge (WAS)—enhance methane yields but inadvertently introduce emerging pollutants with environmental persistence and bioaccumulative risks [8]. Three contaminant classes warrant urgent attention (Figure 1): (1) microplastics (MPs), derived from fragmented plastics (global production: 1.4 million tons in 1950 to 360 million tons in 2018) and personal care products, accumulate in WAS with >99% retention efficiency during wastewater treatment [9,10]; (2) antibiotics (e.g., ciprofloxacin, tetracyclines), extensively used in healthcare and intensive agriculture, enter AD systems via wastewater (30–90% excretion rates) and propagate antibiotic resistance genes (ARGs) through selective pressure [11,12]; (3) heavy metals (Cd, Zn, Cr), characterized by non-biodegradability and trophic transfer risks, exhibit speciation-dependent bioavailability that dictates their ecotoxicological impacts [13,14].
Notably, MPs act as vectors for adsorbing antibiotics and metal ions, creating compounded toxicity that disrupts methanogenic pathways [15,16]. Current knowledge gaps persist regarding the fate of microplastics (MPs), antibiotics, and heavy metals (HMs) in anaerobic digestion (AD), particularly the fragmentation pathways of biodegradable MPs, dissemination mechanisms of antibiotic resistance genes, and synergistic microbial inhibition by metal–organic complexes. This review critically examines their sources, transformation behaviors, and toxicity risks to methanogenesis and microbial consortia. Advanced remediation strategies such as biochar adsorption, microbial augmentation, and bioreactors are proposed to enable safer organic waste valorization via multi-level synergies.
To ensure a comprehensive and unbiased analysis, this review employed a systematic literature search across Scopus, Web of Science, and PubMed databases (2010–2024) using an expanded set of keywords for the search query as follows:
“anaerobic digestion” AND “microplastics”, “anaerobic digestion” AND “antibiotics”, “anaerobic
digestion” AND “heavy metals”, “anaerobic digestion” AND “methane”, “anaerobic digestion” AND
“biochar”, “anaerobic digestion” AND “heavy metals” AND “antibiotics”, “anaerobic digestion” AND
“heavy metals” AND “microplastics”, “anaerobic digestion” AND “antibiotics” AND “microplastics”,
“removl” OR “microplastics” OR “antibiotics” OR “heavy metals”
The initial screening of over 500 articles applied three key inclusion criteria: (1) peer-reviewed studies providing empirical data on contaminant behavior in AD systems, with particular attention to studies employing advanced analytical techniques like LC-MS/MS and ICP-MS; (2) papers that quantitatively assessed impacts on methane production kinetics or microbial community shifts using molecular methods; and (3) research proposing innovative mitigation strategies with demonstrable efficacy through controlled experiments. Exclusion criteria were carefully designed to remove non-English articles, purely theoretical models lacking experimental validation, and studies without proper control comparisons to ensure data reliability. The final selection of 156 references underwent a rigorous three-stage vetting process involving title/abstract screening, full-text evaluation, and cross-verification by multiple authors. Special priority was given to longitudinal studies (>6 months duration, 30 papers selected) tracking contaminant fate over time, investigations examining multi-contaminant interactions (12 papers included), and large-scale (pilot/industrial) experiments (20 papers retained) that could demonstrate practical engineering applicability. The review structure was organized to first establish the fundamental mechanisms of contaminant impacts (sources, transformation pathways), then systematically evaluate their effects on AD performance at different operational scales, and finally critically assess mitigation technologies with emphasis on their implementation feasibility and cost-effectiveness. This methodological approach ensured both comprehensive coverage of contaminant dynamics and practical emphasis on engineering solutions that could be readily implemented in real-world AD systems.

2. Sources and Pathways of Contaminants Transport to AD System

2.1. Microplastics

Microplastics is the subject of the contamination studies of the 14 papers we consider for this critical review. The pervasive use of plastics—global production reached 360 million metric tons in 2018—has led to irreversible environmental fragmentation, with an estimated 12 billion tons of plastic waste projected to accumulate in landfills and ecosystems by 2050 [17,18]. Secondary microplastics (MPs, 1 μm–5 mm) predominantly originate from the degradation of microplastics through mechanical abrasion, UV weathering, and microbial action, while primary MPs are intentionally manufactured for industrial applications (e.g., electronics coatings, personal care products) [19,20]. China alone discharges approximately 306.9 million tons of plastic microbeads annually into aquatic environments, exemplifying the scale of anthropogenic MP emissions [21].
Wastewater treatment plants (WWTPs) act as critical interception points, retaining >90% of influent microplastics (MPs) in sewage sludge through sedimentation and filtration processes [22,23]. However, this retention inadvertently transforms sludge into a concentrated MP reservoir, with digestates containing 5-fold higher MP concentrations than raw waste-activated sludge (WAS) [24]. Globally, PS, PVC, PP, PET, and PE dominate sludge-associated MPs, exhibiting morphological diversity (spheres, fibers, fragments) and size heterogeneity (0.1–5 mm) [25,26]. Regional studies reveal substantial variations: Italian WWTPs report PA and PET concentrations of 29.3–1470 μg/g in sludge [27], while Canadian facilities detect 50–150 μg/L polystyrene nanoplastics (PsNPs) in anaerobically digested sludge [28].
Notably, MPs’ high surface-area-to-volume ratio and hydrophobicity enable them to act as vectors for heavy metals, antibiotics, and pathogens through adsorption–desorption dynamics, amplifying contaminant mobility in AD systems [29,30]. Land application of MP-laden digestates introduces these composites into agricultural soils, posing long-term risks to food security—a critical nexus requiring regulatory intervention [31].

2.2. Antibiotics

Antibiotics is the subject of the contamination studies of 18 papers we consider for this critical review. Antibiotics, widely used as growth promoters in livestock and additives in personal care products, have experienced escalating environmental release due to surging global consumption [32]. Between 2000 and 2015, global antibiotic usage increased by 65%, with 30% allocated to livestock farming, while medical and aquaculture sectors accounted for 55% and 15%, respectively [33]. Approximately 17–90% of veterinary antibiotics are excreted as parent compounds or active metabolites, resulting in concentrations ranging from 100 μg/L to 500 mg/L in livestock manure [34]. To the best of our knowledge, there are four types of antibiotics including tetracyclines, sulfonamides, quinolones, and macrolides that were reportedly detected in the FW and related AD systems, as shown in Table 1. In China’s intensive farming systems, tetracyclines (TCs), sulfonamides (SAs), and fluoroquinolones (QNs) constitute >75% of the antibiotic load in swine manure, while enrofloxacin concentrations in poultry manure exceed those in swine/cattle manure by three orders of magnitude [35,36].
Antibiotics enter anaerobic digestion systems via two primary pathways: (1) co-digestion of livestock manure (e.g., TCs (tetracyclines): 21.4–152.0 μg/g dry weight) with municipal waste-activated sludge (WAS), directly suppressing methanogen metabolic activity [44,45]; (2) WAS-retained antibiotics (e.g., sulfamethoxazole: 3–9.4 μg/g) influencing microbial community function through extracellular polymeric substance-mediated adsorption–desorption dynamics [46]. Antibiotics with low MIC50 values (e.g., enrofloxacin MIC50 <0.06 μg/mL) inhibit key enzymatic activities via ribosomal targeting, reducing CH4 yield by 30–50% [47]. Concurrently, antibiotic-induced selective pressure drives horizontal transfer of antibiotic resistance genes (ARGs, e.g., sulfonamide resistance genes sul1 and sul2), increasing multidrug-resistant bacteria abundance by 2–3 orders of magnitude in AD sludge [48].
Despite the predominance of TCs and SAs (>75% detection rate in Chinese swine manure), global thresholds for antibiotic residues in agricultural digestate remain undefined [39]. Drawing from Germany’s regulatory model, integrated strategies should include source reduction (e.g., restricting high-risk antibiotics with MIC50 <1 μg/mL), process intervention (10% biochar addition achieves >90% sulfonamide adsorption), and legislative controls (ecotoxicology-based MRLs) to mitigate risks [49,50].

2.3. Heavy Metals

Heavy metals is the subject of the contamination studies of the 17 papers we consider for this critical review. The valorization of municipal sludge and livestock manure as organic fertilizers is hindered by heavy metal (HM) contamination, despite their rich nutrient content [51,52]. China generates over 60 million tons of sludge annually, with notable HM concentrations (e.g., Cu, Zn, Cd, Cr), where Fe, Mn, Cu, and Zn constitute >80% of total HMs in swine manure [53,54]. Table 2 shows the content of HMs in slurry. Total HM concentrations alone inadequately reflect ecological risks, as bioavailability and toxicity depend critically on chemical speciation—acid-soluble (F1) and reducible fractions (F2) exhibit high mobility, while oxidizable (F3) and residual fractions (F4) remain stable [55,56].
Within anaerobic digestion (AD) systems, HMs undergo dynamic speciation transformations. During initial hydrolysis-acidogenesis, organic acids lower pH to 5.5–6.0, enhancing dissolution of HM ions (e.g., Cu2+, Zn2+) [63]. As methanogenesis consumes volatile fatty acids, pH 7.5–8.5, establishing a reductive environment that facilitates HM stabilization through: (1) sulfide precipitation (e.g., CuS/ZnS) mediated by sulfate-reducing bacteria [13]; (2) humic acid (HA) complexation, with HA-Cu/HA-Zn exhibiting 2–3× higher stability than fulvic acid-bound forms [64]; (3) extracellular polymeric substance (EPS) adsorption, achieving 60–85% binding efficiency [65]. Ultimately, >90% of HMs accumulate in digestate solids, with 3–25 μm particles carrying >70% of the HM load [66,67].
Toxicity rankings follow Hg > Cd > Cr(III), where Cd poses the highest risk due to its bioaccumulation factor (BCF > 5) [14]. Although passivation strategies (e.g., composite additives) reduce Cu bioavailability by 40–60%, global standards for HM thresholds in agricultural digestate remain absent [68]. Future efforts must establish speciation-based risk assessment frameworks and develop microbial enhancement technologies targeting EPS synthesis or sulfur metabolism to achieve controlled HM risks in AD systems [66].

3. Conversion and Influence of Contaminants on AD System

Methane production, the core economic product of anaerobic digestion (AD), is a sensitive indicator for assessing the stability of pollutant-disturbed systems. Environmentally persistent, bioaccumulative, and ecotoxic microplastics, antibiotics, and heavy metals can reduce AD efficiency through a dual inhibitory mechanism: the direct inhibition of methane-producing archaeal activity and the disruption of microbial polymorphic structures. Polymeric particles (e.g., PE, PVC) impede mass transfer through organic matter adsorption; anti-microbial agents (e.g., tetracyclines TC/OTC, sulfonamides SDZ) induce resistance genes interfering with metabolism; and metal ions (e.g., Cu2+, Zn2+) deactivate key enzymes of methanogenesis. This review gathers as many studies as possible on the effects of these three pollutants on the AD system. In this critical review, 14 papers among those identified deal with microplastics, 18 papers deal with antibiotics, and 17 papers deal with heavy metals.

3.1. Conversion and Influence of Microplastics on AD System

Five types of most frequently detected MPs including polystyrene (PS), polycarbonate (PC), polyvinyl chloride (PVC), polyamide (PA 6), and polypropylene (PP) with different size ranges were summarized in Table 3.
Micro(nano)plastics (MNPs, defined as plastic particles ranging from 1 nm to 5 mm in size, derived from environmental degradation or industrial production) exert multidimensional toxicity mechanisms in anaerobic digestion (AD) systems. Concentration-effect studies reveal polystyrene nanoplastics (PSNPs) induce methane yield inhibition (r2 = 0.93) at 0.05–0.2 g/L through dual pathways: acidogenesis blockage (35–45% reduction in volatile fatty acids) and F420 coenzyme inactivation (60–75% activity loss) [29]. Particle size governs toxicity intensity—50 nm PS NPs generate 3.8-fold higher reactive oxygen species (ROS) than 1 μm counterparts due to their larger specific surface area (2.5 × 103 m2/g vs. 1.2 × 102 m2/g), causing mitochondrial damage via endocytosis [71,77].
Polymer-specific leaching effects demonstrate chemical toxicity divergence. Polycarbonate (PC) microplastics at 30 particles/g TS enhance methane yield by 24.7% via bisphenol A (BPA, 0.8–1.2 mg/L)-mediated superoxide dismutase activation (+25%), whereas high concentrations (200 particles/g TS) trigger ROS bursts (3.5-fold H2O2 increase) and 48% acetate kinase inhibition [72]. Polyvinyl chloride (PVC) >20 particles/g TS releases 1.5–2.0 mg/L BPA, reducing hydrolysis coefficient (k) by 0.12–0.15 d−1 through thiol group oxidation (−40% protease activity) and F420 conformational changes [78,79].
Microbial community restructuring underpins MNP-induced AD dysfunction. PS NPs decrease Candidatus Methanofastidiosum abundance by 2–3 orders of magnitude while enriching Mariniphaga (+450%) and Candidatus Microthrix (+320%), redirecting carbon flux from acetoclastic to hydrogenotrophic pathways [80]. Polyethylene (PE) microplastics increase Atopostipes (hydrolytic bacteria) and Psychrobacter (acid-tolerant genera) by 2.1- and 3.7-fold, respectively, but reduce Methanosaeta (acetoclastic methanogens) by 85%, decreasing VFA/CH4 conversion efficiency by 22–35% [81]. Crucially, MNPs promote antibiotic resistance gene (ARG) dissemination via horizontal transfer, with sul1 and tetB abundance showing linear correlation with PS NP concentration (R = 0.86), elevating environmental dissemination risks by 3–5-fold. When combined with antibiotics, microplastics exacerbate anaerobic digestion pollution through synergistic effects. Co-exposure enhances ARG propagation by disrupting microbial communities and enriching resistant strains, while also impeding methane production by 20–30% due to toxicity accumulation. The adsorption of antibiotics onto microplastics further prolongs their persistence, creating hotspots for resistance development. This dual contamination amplifies ecological risks, with ARG transfer efficiency increasing by 1.8–2.2 times compared to single pollutants, necessitating urgent mitigation strategies [82].

3.2. Conversion and Influence of Antibiotics on AD System

Antibiotics exhibit stage-specific and concentration-dependent inhibitory effects in anaerobic digestion (AD) systems. Table 4 shows the effects of several different antibiotics on anaerobic digestion. During the rate-limiting hydrolysis phase, chlorotetracycline (CTC) enhances hydrolysis rates by 30–40% through acid-forming bacterial activation (pH decrease 0.5–1.2 units), whereas azithromycin (AZM) increases hydrolytic community abundance by 25% [83,84]. In acidogenesis, sulfamethoxazole (SMX) ≥250 mg/L completely inhibits acetate synthesis and reduces butyrate production by 60–70%, attributable to irreversible inhibition of pyruvate dehydrogenase complexes [85]. Roxithromycin demonstrates dose-dependent effects (10–1000 μg/L), decreasing glucose degradation rates by 26.5–34.5% via 50S ribosomal subunit binding interference [86].
Methanogenesis exhibits heightened vulnerability through dual mechanisms: (1) suppression of acetoclastic pathway enzymes (e.g., 40–50% reduction in acetate kinase activity), diverting metabolism toward hydrogenotrophic routes; (2) selective inhibition of methanogens (2–3 orders of magnitude decrease in Methanosaeta abundance) coupled with proliferation of antibiotic-resistant genera (e.g., Clostridium spp.) [101,103]. Tetracycline displays threshold effects at 5.7–8.5 mg/L: low concentrations (1.65 mg/L) reduce methane yield by 10–20% while maintaining COD removal, whereas high concentrations (8.5 mg/L) inactivate propionate degraders and induce VFA accumulation [91,104]. Notably, long-term exposure triggers microbial adaptation—methanogenic function recovers to 80–90% baseline within 15–20 days post-cessation, indicating horizontal transfer of resistance genes (tetM, tetW).

3.3. Conversion and Influence of Heavy Metals on AD System

Seven types of the most frequently detected heavy metals including Cd, Fe, Zn, Hg, Cu, Ni, and Cr(III) with different concentrations were summarized in Table 5.
Heavy metals (HMs) exhibit biphasic concentration effects in anaerobic digestion (AD) systems, governed by well-defined threshold mechanisms. Trace levels of Cu2+ (0–100 mg/L), Fe2+ (50–4000 mg/L), Ni2+ (0.8–50 mg/L), and Zn2+ (0–5 mg/kg) enhance methanogenesis through activating key metabolic enzymes (e.g., 15–20% increase in cellulase activity) and stabilizing electron transport chains (30–50% upregulation of ferredoxin expression) [109,110]. Notably, Fe2+ demonstrates a pronounced dose–response relationship within 0–4000 mg/L, achieving peak biogas yield (+16.2%) at 1000 mg/L via sulfide chelation stabilization and cytochrome c oxidase activation [106,111].
Exceeding threshold concentrations triggers multidimensional inhibition. At Cu2+ > 300 mg/kg, cellulase activity declines by 5.86% with 40–60% reduction in microbial α-diversity, attributed to irreversible sulfhydryl group binding in enzyme active sites and ribosomal RNA structural damage [112,113]. Ni2+ exhibits a critical inhibitory threshold at 30 mg/L, beyond which methyl-coenzyme M reductase activity decreases by 25–35%, blocking the aceticlastic pathway [114]. Cd2+ displays the strongest biotoxicity, completely inhibiting F420 coenzyme synthesis at 1 mg/L and reducing system methane potential by 55% at 20 mg/L [105,115].
The methanogenic phase demonstrates heightened sensitivity to HM stress. Additionally, 5 mg/L Cu2+ increases Methanosarcina abundance by 2.5-fold, whereas 300 mg/kg reduces its relative abundance below detection limits [113]. Ni2+ dose–response curves reveal 2% biogas yield enhancement at 0.8 mg/L, but the methane content plummets from 60% to 35% beyond 30 mg/L [114]. This phase transition correlates with HM-induced microbial community restructuring—metal-resistant bacteria (e.g., Firmicutes) become selectively enriched, while methanogens (Methanothrix, Methanosarcina) decline by 50–80% [116,117].

4. Removal and Mitigation Strategies

The degradation of diverse substrates in anaerobic digestion (AD) systems involves distinct mechanisms, with pollutant concentrations and types (e.g., microplastics, antibiotics, heavy metals) largely determined by substrate sources [118]. Therefore, to effectively address the inhibitory effects of pollutants on AD systems, it is critical to develop universally applicable methods or tailored solutions for specific contaminants. This paper examines advanced treatment strategies, including biological pretreatment, bioreactors, and physicochemical treatment technologies for the removal and mitigation of contaminants.

4.1. Biological Pretreatment Technologies

Bioremediation technologies have emerged as the most promising strategy for removing contaminants in anaerobic digestion (AD) systems due to their cost-effectiveness and environmental compatibility [119]. These technologies rely on biosorption mechanisms involving ion exchange, surface complexation, and chemical precipitation, where interfacial interactions between non-viable biosorbents (e.g., agricultural wastes) and contaminants (heavy metals, antibiotics) play a dominant role. For instance, lignocellulosic biosorbents like rice husks exhibit ion exchange capacities of 2.1–3.8 mmol/g for Cd2+/Pb2+ under acidic conditions (pH 4–6), driven by sulfonic (-SO3H) and carboxyl (-COOH) functional groups. Surface complexation mechanisms are particularly effective for antibiotic removal, with tetracycline adsorption capacities exceeding 90% on cellulose-rich corncob biochar due to hydrogen bonding and π-π interactions [120,121]. Microbial pretreatment combined with physical grinding significantly enhances substrate accessibility; for instance, fungal-mechanical co-pretreatment increases methane yield from rice straw by 25–40% [122]. This process optimizes metabolic synergy between acidogens and methanogens, accelerating substrate decomposition during hydrolysis–acidogenesis and thereby boosting methane production rates at early AD stages [123].
Temperature-phased anaerobic digestion (TPAD) overcomes efficiency limitations of single-stage systems through thermophilic (50–70 °C) and mesophilic (35–40 °C) phase synergy. Akgul et al. [124] demonstrated that TPAD at 70 °C improves volatile solid (VS) degradation by 30–50% compared to single-stage thermophilic/mesophilic operations. The thermophilic phase achieves 85–90% lignin depolymerization via thermostable Caldicellulosiruptor spp., generating soluble aromatics that enhance acetoclastic methanogenesis in the mesophilic phase [124]. Kim et al. further verified that TPAD achieves 55% and 43% vs. degradation for primary and secondary biosolids, attributed to thermophilic-phase lignin depolymerization and mesophilic-phase acetogen enrichment [125]. In contrast, aerobic pretreatment depends on obligate microbial consortia for mineralizing complex organics into CO2, H2O, and nitrates under oxic conditions [126]. Although this method shortens methane stabilization periods in AD systems by 15–20 days through partial lignin removal (30–35%), its efficiency is constrained by biosolid properties (e.g., C/N ratio, particle size distribution). For high-C/N substrates (C/N > 30), aerobic pretreatment reduces nitrogen immobilization by 25%, but for fine particles (<0.5 mm), excessive mineralization lowers bioavailable carbon by 40%, negating methane yield improvements [127].

4.2. Use of Bioreactors in AD

Bioreactor technology significantly enhances the operational stability and pollutant degradation efficiency of anaerobic digestion (AD) systems through biomass enrichment, immobilization of functional microbial consortia, improved operational flexibility, and optimized treatment performance. Nevertheless, current mainstream anaerobic reactor systems for landfill leachate treatment—including Upflow Anaerobic Sludge Blanket (UASB) [128], Internal Circulation reactor (IC) [129], Moving Bed Biofilm Reactor (MBBR) [130], and Expanded Granular Sludge Bed (EGSB) [131]—still face critical challenges such as low microbial proliferation rates [132]. These systems frequently exhibit technical limitations including constrained treatment capacity, significant fluctuations in effluent pollutant concentrations, and inadequate sludge retention capabilities during practical operation.
Anaerobic membrane bioreactors (AnMBRs) integrate membrane separation with anaerobic digestion, achieving 95% chemical oxygen demand (COD) removal efficiency in high-suspended solids (SS) wastewater treatment [133]. Compared to conventional reactors (e.g., UASB, IC), AnMBR’s design with short hydraulic retention time (HRT) and long sludge retention time (SRT) enables deep organic mineralization while reducing sludge production by 40–60% [134], effectively addressing sludge disposal challenges in traditional systems [135]. The technology demonstrates unique advantages in treating swine wastewater and pharmaceutical effluents, where membrane modules (0.03–0.4 μm pore size) selectively retain functional microorganisms to prevent biomass loss and maintain system stability [136].
However, AnMBR’s large-scale application is hindered by membrane fouling—organic/inorganic pollutant accumulation reduces flux by 30–50% and increases transmembrane pressure (TMP) to 1.5–3.0 bar [137]. Innovative designs like dynamic membrane bioreactors (DMBRs) and electrochemical MBRs (eMBR) mitigate fouling rates by 60–80% through shear force optimization and electric field application (0.5–2.0 V/cm) [138,139]. For instance, eMBR coupling anodic oxidation with biodegradation achieves 98% removal efficiency for refractory pharmaceuticals like diclofenac [140].
For ammonia-inhibited substrates such as chicken manure, integrated strategies combining in situ ammonia stripping and hyper-thermophilic pretreatment (70–90 °C) enhance AnMBR methane yield by 25–35% while maintaining free ammonia concentrations below inhibitory thresholds (<200 mg/L) [141]. Future research must focus on synergistic optimization of antifouling membranes (e.g., graphene-coated membranes) and bioaugmentation techniques (e.g., electrogenic bacteria enrichment) to overcome AnMBR’s engineering limitations in complex matrices [142].

4.3. Physicochemical Treatment Technologies

Physicochemical technologies provide irreplaceable solutions for recalcitrant pollutants (e.g., microplastics) and complex toxicants (e.g., heavy metal complexes) through targeted molecular destruction or interfacial modulation. Fenton oxidation and photocatalysis achieve 70–85% mineralization of microplastics by breaking surface functional groups (-C=O, -OH) under pH 2.5–4.0 [143]. Ion-exchange resins exhibit selective adsorption capacities of 200–350 mg/g for Mn2+ and Cd2+, with coordination mechanisms effectively inhibiting metal re-dissolution [144,145]. Unlike biotreatment limited by enzymatic activity, these technologies demonstrate superior tolerance to extreme conditions (salinity > 5%, pH < 3), making them pivotal in emergency pollution control.
Composite passivators enhance heavy metal immobilization via multi-mechanistic synergy. Biochar (300–600 m2/g surface area) and humic acid form stable complexes with Cu2+/Zn2+ through carboxyl/phenolic groups, reducing acid-extractable metal fractions from 35–50% to 10–15% [63,146]. Simultaneously, passivators increase humification degree by 40–60%, further immobilizing metals via chelation.
Electrochemical pretreatment (EP) employs direct and indirect oxidation mechanisms. Direct mechanisms utilize high-voltage fields (5–15 kV) to induce cell lysis and polymer cleavage, while indirect mechanisms rely on electrogenerated radicals (·OH, ClO−) for non-selective degradation [147,148]. EP combined with sodium hypochlorite enhances sludge hydrolysis by 50–70% and methane yield by 25–35% [149].
However, scaling up physicochemical technologies requires balancing efficiency and cost. Microplastic (MP) enrichment in sludge reaches 75.7%, where source control (e.g., influent pretreatment) costs USD 0.2–0.5 per ton, and for end-of-life treatment, only 1/3–1/5 of end-of-pipe treatment [150,151]. Future efforts should focus on low-energy catalysts (e.g., non-noble metals) and smart process control systems to synergize pollutant removal with resource recovery.

5. Critical Analysis and Future Perspectives

Critical knowledge gaps persist regarding multiphase interactions of pollutants in anaerobic digestion (AD) systems. For microplastics (MNPs), systematic investigation is urgently needed on the synergistic effects of diverse MNP types during co-digestion of primary and waste-activated sludge, particularly focusing on fibrous MNPs (accounting for 60–75% of total sludge MNP load) and their interfacial behaviors. Standardized detection methods based on mass concentration (g/kg TS) rather than particle counts should be established to address data comparability issues caused by size heterogeneity [152]. Environmental fate studies of MNPs in biosolids must prioritize their role as vectors for antibiotic resistance genes (ARGs), especially the horizontal transfer efficiency of sul1 and tetW genes within soil–plant systems [153].
Breakthroughs in antibiotic removal technologies require deep mechanistic insights. Integrating metagenomics with metabolic flux analysis can elucidate electron transfer enhancement mechanisms at β-lactamase active sites by conductive materials like magnetite nanoparticles [154]. Hybrid AnMBR-UASB systems should be developed to optimize interphase mass transfer between biofilms and suspended sludge, achieving >95% removal efficiency for sulfonamide antibiotics [155]. Real-time biosensing systems using zebrafish embryo models are crucial for assessing the ecological toxicity of degradation intermediates [154].
Heavy metal (HM) bioremediation demands the directed development of resistant microbial resources. Genome editing of Methanosarcina spp. via CRISPR-Cas9 to introduce metallothionein expression modules could maintain >80% methanogenic activity under Cu2+ > 500 mg/L. A novel pyrolysis-AD cascade process (300–500 °C) could immobilize Cd/Pb in biochar matrices while enhancing methane yield by 30–45% [156]. Blockchain-based digestate traceability systems should be implemented for intelligent HM risk classification and land-use matching.

6. Conclusions

Anaerobic digestion (AD) systems confront a critical paradox: while achieving resource recovery from organic waste, they must simultaneously address escalating contamination challenges posed by microplastics (MPs), antibiotics, and heavy metals (HMs). Although AD systems function as biorefineries for methane recovery, they inadvertently concentrate persistent pollutants that threaten system stability. Polyethylene- and polypropylene-dominated MPs, coupled with tetracycline- and sulfonamide-class antibiotics, not only propagate antibiotic resistance genes but also suppress methanogenic archaeal activity. Furthermore, copper and zinc HMs compromise microbial vitality through bioaccumulation. Consequently, integrating AD with optimized reactor configurations, advanced materials, bioaugmentation strategies, and physicochemical technologies may present a promising multi-barrier approach for treating contaminated biowastes. This synergistic paradigm could potentially reconcile the dual objectives of waste valorization and contaminant mitigation in circular bioeconomy frameworks.

Author Contributions

Writing—review and editing, conceptualization, methodology, resources, supervision, project administration, funding acquisition, H.L.; writing—original draft preparation, X.Y.; data curation, visualization, Y.Y., L.Y. and J.Z.; writing—review and editing, C.M. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by Projects of International Cooperation Shanghai grant number [STCSM 23230711300].

Data Availability Statement

No new data were created or analyzed in this study.

Conflicts of Interest

The authors declare no conflicts of interest.

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Recycling 10 00116 g001
Figure 1. Schematic diagram of the effect of three contaminant classes (microplastics, antibiotics, heavy metals) on anaerobic digestion.
Figure 1. Schematic diagram of the effect of three contaminant classes (microplastics, antibiotics, heavy metals) on anaerobic digestion.
Recycling 10 00116 g001
Table 1. Antibiotic contents found in manure and digestates.
Table 1. Antibiotic contents found in manure and digestates.
CountryMatrixCTCDCOTCTCSDZSMZRef.
ChinaDairy cow feces1-5.11.1-0.46[37]
ChinaCattle manure--21.4124.69.4[38]
ChinaCow dung2.20.681.2---[35]
ChinaCow feces1.5--0.02--[39]
The NetherlandsSwine feces-1.90.16-0.13-[40]
BelgiumSwine manure-22.82-3-[41]
GermanySwine manure6.2-21.59.74.9-[38]
AustriaPig manure46-2923--[42]
GermanyPig manure37.427.413.61527.3-[43]
Note. -: It was not mentioned in the references.
Table 2. HMs contents in the slurry (mg/L).
Table 2. HMs contents in the slurry (mg/L).
Animal ManureTreatment ConditionCuZnCdAsPbCrNiMnRef.
PMMesophilic digestion16.3420.66-0.26----[57]
PMMesophilic digestion4.178.92--0.02--0.26[58]
PMMesophilic digestion1.323--0.040.053.62–22.1-[59]
PMMesophilic digestion
Mixed with corn silage		14.789.711.59-13.9--1.88[60]
CHMMesophilic digestion1.7912.67--0.050.116.91–31.4-[59]
CHMThermophilic digestion15.17124.510.1727.151.9439.75--[61]
DCMMesophilic digestion3.2917.45-0.06--1.51–4.96-[57]
China 0.520.010.050.20.10.2-
Note. Limit values according to standard for irrigation water quality in China (GB 5084-2021) [62]; PM: pig manure; CHM: chicken manure; DCM: dairy cattle manure; -: It was not mentioned in the references.
Table 3. Effects of MPs on anaerobic digestion.
Table 3. Effects of MPs on anaerobic digestion.
Micro(nano)plastics TypeCompoundConcentrationsMethane ProductionScaleRefs.
Polystyrene (PS)WAS150 µg/L−29.34%Lab[28]
Polystyrene (PS)WAS160 particles/g TS−11.04%Lab[69]
Polystyrene (PS)WAS150 µg/L−32.30%Lab[70]
Polyvinyl chloride (PVC)WAS2.4 g/g VS+34.90%Lab[71]
Polycarbonate (PC)WAS30 particles/g TS−24.70%Lab[72]
Polyvinyl chloride (PVC)WAS30 mg/g TS−15.62%Lab[73]
Polypropylene (PP)WASLow concentration (1–100 particles/g TS)−2.8%Industrial[74]
Polyamide 6 (PA6)WAS10 PA6 particles/g TS+39.50%Lab[75]
Polycarbonate (PC)WAS30 particles/g TS+24.70%Lab[72]
Polystyrene (PS)WAS50 mg/g TS−15.50%Lab[76]
Polyethylene (PS)WAS200 particles/g TS−27.50%Lab[76]
Note. TS: Total Solids; VS: Volatile Solids.
Table 4. Effects of antibiotics on anaerobic digestion.
Table 4. Effects of antibiotics on anaerobic digestion.
AntibioticCompoundConcentrations (mg/L)Biogas/Methane ProductionScaleRefs.
Sulfamethoxazole-1–45Biogas: 1004 ± 129 mL/d–96 mL/dLab[87]
SulfamethoxazoleMunicipal sewage6–100No inhibitionLab[88]
SulfamerazinePharmaceutical wastewaters10–90Methane content: 76–60%Pilot[89]
Sulfamerazinemanure≤280No impact on total biogas productionLab[90]
Sulfamethazinepiggery wastewater5.0–160InhibitedLab[90]
Tetracycline-1.65–5.7–8.5Biogas: 951–853–71 mL/dayLab[91]
Tetracyclinewastewater0.15–20Methane: 160–110 mLLab[92]
Tetracyclinepig diet550 mg/kg25% reduction in methaneLab[93]
Chlortetracyclinepig slurry500 mg/kgIncreasedPilot[94]
Chlortetracycline-2827.8% reduction in methaneLab[83]
Chlortetracycline-4050% reduction in methaneLab[95]
Oxytetracyclinepig slurry60, 100, 140 mg/kgReduce biogas production by 9.9, 10.4, and 14.1%Lab[96]
Oxytetracyclinedairy manure30, 60, 9079.1, 70.3, 68.6% of the control valuesLab[97]
Oxytetracyclineanimal manure125, 250No inhibitionLab[98]
Oxytetracyclineanimal manure3.1Reduce methane production by 27%Pilot[99]
Oxytetracycline Chlortetracyclinepig manure10, 50 and 100Reduced methane production by 56, 60 and 62%Lab[100]
Sulfamethoxazole
Erythromycin		-2.5 + 2.5 + 25DecreasedPilot[101]
Tetracycline-18–46Biogas production: 1247 mL/dayLab[102]
Sulfamethoxazole
Tetracycline		-20 + 1.5DecreasedLab[101]
Note. -: It was not mentioned in the references.
Table 5. Effects of heavy metals on anaerobic digestion.
Table 5. Effects of heavy metals on anaerobic digestion.
Heavy MetalCompoundConcentrationsMethane Production PerformanceInfluencing FactorsScaleRefs.
CdSewage sludge3.4–17.0 mg/kgInhibitionMethanogenic activity (55% biogas reduction)Pilot[105]
CdSludge0.1–0.3 mg/L (Promotion); 1.2 mg/L (Inhibition)Dual-phase effectMethanogenic activityPilot[105]
FeCow dung50–4000 mg/L (Promotion); 20,000 mg/L (Inhibition)Dual-phase effectCellulase activityLab[106]
ZnFood waste and wastewater co-digestion5 mg/L (Promotion); 50 mg/L (Inhibition)Dual-phase effectMethanogenic activityLab[1]
HgSewage sludge0.125 mg/kgInhibitionMethanogenic activity (60% biogas reduction)Pilot[105]
Cr(III)Sewage sludge1.55 and 3.10 mg/kg dry weightInhibitionMethanogenic activity (69% and 83% biogas reduction, respectively)Pilot[105]
CuReed straw and cow dung0–100 mg/L (Promotion); 500 mg/L (Inhibition)Dual-phase effectMethanogenic activity, cellulase activity, microbial community, VFA concentrationLab[107]
NiReed straw and cow dung0.8–50 mg/L (Promotion); 100 mg/L (Inhibition)Dual-phase effectCellulase activity and methanogenic activityLab[108]
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Liu, H.; Yuan, X.; Yao, Y.; Yao, L.; Zhang, J.; Maurer, C. Microplastics, Antibiotics, and Heavy Metals in Anaerobic Digestion Systems: A Critical Review of Sources, Impacts, and Mitigation Strategies. Recycling 2025, 10, 116. https://doi.org/10.3390/recycling10030116

AMA Style

Liu H, Yuan X, Yao Y, Yao L, Zhang J, Maurer C. Microplastics, Antibiotics, and Heavy Metals in Anaerobic Digestion Systems: A Critical Review of Sources, Impacts, and Mitigation Strategies. Recycling. 2025; 10(3):116. https://doi.org/10.3390/recycling10030116

Chicago/Turabian Style

Liu, Hongbo, Xiang Yuan, Yuxuan Yao, Lijin Yao, Junbo Zhang, and Claudia Maurer. 2025. "Microplastics, Antibiotics, and Heavy Metals in Anaerobic Digestion Systems: A Critical Review of Sources, Impacts, and Mitigation Strategies" Recycling 10, no. 3: 116. https://doi.org/10.3390/recycling10030116

APA Style

Liu, H., Yuan, X., Yao, Y., Yao, L., Zhang, J., & Maurer, C. (2025). Microplastics, Antibiotics, and Heavy Metals in Anaerobic Digestion Systems: A Critical Review of Sources, Impacts, and Mitigation Strategies. Recycling, 10(3), 116. https://doi.org/10.3390/recycling10030116

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