P4V1ECM

Outline

Outline

Highlights. 1

Keywords. 1

1. Introduction. 1

2. Methodology. 1

3. Results. 1

4. Discussion. 1

5. Conclusion. 1

References. 1

Energy Conversions and Managements

Volume 101, July 2025

Recommended articles

Advancements in Microbiological Energy: Pathways and Potentials

Lara N. Sayegh^a , Enzo D. Martellib

a Department of Environmental Engineering, Al-Qantara University, Beirut, Lebanon

b Institute for Bioenergy Systems, Università di Roma Verde, Rome, Italy

Received (15 July 2025); Received in revised form (20 July 2025); Accepted (20 July 2025) Available online 21 July 2025

Highlights

·         Core Technologies: Reviews key microbiological energy systems like MFCs, MECs, and anaerobic digestion.

·         Advancements & Integration: Highlights progress in bioreactor design, metabolic engineering, and wastewater-energy integration.

·         Challenges & Outlook: Discusses scalability barriers and future potential in decentralized, low-emission energy systems.

Abstract

Microbiological energy harnesses the metabolic activities of microorganisms to convert organic and inorganic substrates into usable energy forms, primarily electricity, hydrogen, and methane. It offers a sustainable, low-emission alternative to fossil fuels while providing simultaneous benefits such as waste reduction and nutrient recovery. This review explores the major pathways and technologies in microbiological energy, including microbial fuel cells (MFCs), microbial electrolysis cells (MECs), anaerobic digestion, and microbial electrosynthesis. We discuss microbial community dynamics, biofilm formation, and electron transfer mechanisms central to energy generation. Recent advancements in metabolic engineering, materials science, and bioreactor design have significantly improved conversion efficiencies and system scalability. Additionally, we assess techno-economic feasibility, integration with wastewater treatment, and potential roles in decentralized energy systems. Challenges such as electron transfer limitations, low power densities, and upscaling are addressed alongside future directions. Microbiological energy stands as a transformative pillar in the global shift toward sustainable, circular bioeconomies.

Keywords

Microbiological energy, bioelectrochemical systems microbial fuel cells

1. Introduction

Energy demand has risen exponentially in the last century due to industrialization, urbanization, and population growth. Simultaneously, the environmental consequences of fossil fuel dependence, including greenhouse gas emissions, climate change, and resource depletion, necessitate alternative renewable energy solutions. Among the emerging technologies, microbiological energy has gained prominence for its dual potential to generate renewable energy while remediating waste. Unlike conventional energy sources, microbiological energy leverages the natural metabolic activities of microorganisms to convert organic matter into bioenergy, typically in the form of electricity, hydrogen, or methane [1]. This conversion process is facilitated through diverse biological mechanisms, including fermentation, anaerobic digestion, and extracellular electron transfer, often mediated by complex microbial consortia.

One of the earliest and most studied microbiological energy technologies is anaerobic digestion (AD), which employs anaerobic microbes to decompose organic waste and produce biogas, a mixture primarily composed of methane and carbon dioxide. AD systems are already deployed at large scales in wastewater treatment plants and agricultural waste facilities. However, technological improvements have increasingly focused on enhancing the microbial communities, reactor design, and methane yield [2]. In contrast, microbial fuel cells (MFCs) represent a newer and more sophisticated approach wherein electrogenic bacteria transfer electrons to an anode during substrate oxidation, generating electricity in real time [3]. This process mimics natural redox pathways but is optimized through the use of conductive materials and engineered microbial biofilms.

Microbial electrolysis cells (MECs) extend the principles of MFCs by introducing an external voltage to promote the generation of hydrogen gas from protons, offering a promising method for renewable hydrogen production [4]. Likewise, microbial electrosynthesis (MES) utilizes cathodic biofilms to convert carbon dioxide into value-added organic compounds like acetate or methane, showcasing the versatility of microbial electron transfer networks [5]. Central to all these processes is the ability of certain microorganisms to transfer electrons either directly via conductive pili (nanowires) or indirectly via redox-active molecules known as mediators [6].

Recent research has expanded the scope of microbiological energy through metabolic engineering and synthetic biology, allowing precise control over microbial pathways to enhance energy yields [7]. Moreover, advances in materials science have led to the development of novel electrode materials, such as graphene-based structures and carbon nanotubes, which significantly improve electron transfer and system durability [8]. These innovations are increasingly supported by systems biology and omics tools that unravel the complex interactions within microbial consortia and inform rational design of biocatalytic systems [9].

Despite the promise of microbiological energy, several challenges hinder widespread implementation. Power densities in MFCs remain low compared to conventional energy sources, and reactor scale-up often leads to performance losses due to uneven substrate distribution or pH gradients [10]. Additionally, the specificity and stability of microbial communities are often compromised under environmental fluctuations or contaminant exposure [11]. These issues necessitate interdisciplinary strategies involving microbiology, engineering, and environmental science to create robust and efficient systems.

A notable application of microbiological energy is its integration with wastewater treatment.

2. Methodology

The methodological approaches underlying microbiological energy systems encompass microbial strain selection, bioreactor configuration, operational condition optimization, and system integration. Selecting the appropriate microbial community is a critical determinant of system performance. Electrogenic bacteria such as Geobacter sulfurreducens, Shewanella oneidensis, and mixed anaerobic consortia are widely employed in microbial fuel cells (MFCs) due to their proven extracellular electron transfer (EET) capabilities [1]. In anaerobic digestion (AD), a sequential consortium of hydrolytic, acidogenic, acetogenic, and methanogenic microorganisms facilitates the complete degradation of organic substrates into methane and carbon dioxide [2]. Metagenomic analysis and high-throughput sequencing (HTS) have become indispensable tools for community profiling, allowing researchers to monitor microbial diversity, metabolic potential, and response to environmental changes [3].

In MFCs, the anode chamber is typically inoculated with wastewater-derived sludge or a pre-cultured microbial strain, and the system operates under anaerobic conditions to promote electron transfer to the electrode rather than to oxygen [4]. The cathode chamber is either open to the atmosphere or provided with an oxidizing agent, such as ferricyanide, to complete the redox cycle [5]. Proton exchange membranes (PEMs), cation exchange membranes (CEMs), or salt bridges are used to separate the chambers while allowing proton migration, thus maintaining charge balance [6]. MFC configuration can be classified into dual-chamber, single-chamber, air-cathode, or stacked designs, each offering trade-offs between power output, system complexity, and cost [7].

MECs follow a similar setup but require an external voltage (0.2–0.8 V) to drive the otherwise non-spontaneous hydrogen evolution reaction at the cathode [8]. Recent developments in cathode catalysts, such as Ni-Mo alloys and MoS₂ nanostructures, have improved hydrogen production efficiency while minimizing costs compared to platinum-based electrodes [9]. MES systems, by contrast, emphasize the cathodic biofilm's ability to reduce CO₂ using electrons and protons supplied from the anode or external power source. This setup allows for the generation of acetate, methane, or other reduced compounds, depending on the microbial species employed [10].

Operational parameters including temperature, pH, substrate concentration, external resistance, and hydraulic retention time (HRT) significantly affect system output. For instance, most MFCs perform optimally at mesophilic temperatures (25–35°C), while thermophilic conditions (50–60°C) favor AD reactors due to enhanced hydrolysis and microbial kinetics [11]. The pH should generally be maintained between 6.5 and 7.5 for balanced microbial activity and membrane stability [12]. Substrate loading rate is a vital consideration, particularly in waste-fed systems, where excessive chemical oxygen demand (COD) may lead to toxicity or system clogging [13]. A feed strategy using real-time monitoring and feedback control is increasingly favored for maintaining optimal conditions.

Electrode material and surface properties are instrumental in enhancing electron transfer and microbial adhesion. Carbon-based materials such as graphite, carbon cloth, carbon felt, and carbon nanotubes are commonly used due to their conductivity, biocompatibility, and corrosion resistance [14]. The use of nanostructured coatings, such as polyaniline or graphene oxide, has been reported to increase surface area and improve microbial colonization, leading to higher current densities [15]. Table 1 summarizes key electrode materials.

Reactor design and scale are pivotal in determining system viability. Bench-scale reactors (10–500 mL) are useful for proof-of-concept and mechanistic studies, but their performance often declines when scaled up due to increased internal resistance, uneven flow, and microbial stratification [16]. Pilot-scale systems (10–100 L) have been deployed in wastewater treatment plants to assess long-term performance, substrate variability, and maintenance requirements [17]. Modular stacking of MFCs or AD units is a common scaling strategy, although inter-module variability and gas leakage remain concerns [18]. Table 2 provides an overview of microbiological reactor types and their scalability.

Table 1. Common electrode materials

Table 2. Microbiological reactor configurations and scalability

Analytical techniques are indispensable for evaluating microbial energy systems. Gas chromatography (GC), high-performance liquid chromatography (HPLC), and total organic carbon (TOC) analyzers are routinely employed to monitor substrate conversion, gas production, and system stability [19]. Electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV), and chronoamperometry are used to characterize electron transfer kinetics and electrode polarization behavior [20]. Table 3 outlines key performance metrics.

Table 3. Key performance metrics and measurement tools

In summary, microbiological energy methodologies are inherently multidisciplinary, involving microbiology, electrochemistry, material science, and process engineering. The integration of omics technologies, advanced materials, and real-time process control has revolutionized the design and operation of these systems. As research shifts toward application-oriented development, pilot-scale deployment and hybrid integration with existing infrastructure will be critical in translating laboratory success to real-world impact.

3. Results  

Microbiological energy systems present a range of performance characteristics, dependent on microbial species, operational conditions, and reactor configurations. The power output, substrate removal efficiency, and microbial stability are key indicators of system feasibility and are influenced by intricate biotic and abiotic interactions. Figure 1 illustrates the power output of four representative microbiological systems: microbial fuel cells (MFCs), microbial electrolysis cells (MECs), anaerobic digestion (AD), and microbial electrosynthesis (MES). Among these, AD yields the highest energy output due to the complete conversion of organics into biogas, reaching up to 2.5 W/m² under optimized conditions, followed by MECs and MES, with MFCs lagging slightly due to their lower voltage range and electron transfer resistance [1]. Nevertheless, MFCs remain promising for low-power applications such as remote sensing and decentralized wastewater treatment [2].

In MFC systems, power density is strongly correlated with electrode material, microbial adhesion, and substrate composition. The use of nanostructured electrodes and surface functionalization has significantly enhanced power densities in recent years, with some laboratory-scale systems achieving up to 1.5 W/m² when operated on glucose-based substrates under controlled conditions [3]. However, real-world wastewater applications often result in lower power outputs due to substrate heterogeneity and competing microbial pathways [4]. MECs, requiring external voltage, demonstrate higher power yields when integrated with renewable energy sources such as solar panels, thereby promoting a synergistic energy production model [5]. Recent studies have reported successful MEC operation with net energy gains when optimized for hydrogen production using Ni-Mo cathode catalysts [6].

Figure 2 demonstrates COD (chemical oxygen demand) removal efficiencies across the same systems. AD consistently exhibits the highest removal efficiency, up to 90%, due to its sequential microbial degradation mechanisms and prolonged hydraulic retention times (HRT) [7]. MFCs achieve COD removal efficiencies between 70% and 85% under stable operation, highlighting their dual benefit of wastewater treatment and electricity generation [8]. MES systems, though not primarily designed for pollutant removal, show moderate COD reduction (~60%) due to partial degradation of organic residues and microbial respiration processes [9]. This reinforces the notion that system design must align with target outcomes—energy recovery, waste remediation, or resource recovery.

Fig 1. Power Output Comparison of Microbiological Energy Systems

In terms of microbial community dynamics, the diversity and structure of microbial consortia influence long-term system stability and performance. Figure 3 presents the Shannon diversity index as a measure of microbial diversity across the systems. AD systems exhibit the highest index (2.8), attributable to the complex trophic interactions among hydrolytic, fermentative, acetogenic, and methanogenic microbes [10]. MFCs and MECs maintain moderate diversity (2.0–2.3), dominated by electrogenic bacteria such as Geobacter spp. and Shewanella spp., often supported by fermenters and syntrophic partners [11]. MES systems tend to have lower diversity (1.9) due to the selective pressure at the cathode and the energy-limited environment that favors specialized CO₂-reducing microbes such as Sporomusa ovata and Clostridium ljungdahlii [12].

Microbial community resilience is vital for maintaining performance under fluctuating operational conditions. AD systems demonstrate strong resilience due to functional redundancy among microbial guilds. Even under ammonia shock or pH stress, methanogenic communities can adapt by shifting from acetoclastic to hydrogenotrophic pathways [13]. In contrast, MFCs are more sensitive to environmental perturbations, with biofilm disruption or oxygen leakage rapidly degrading performance [14]. To mitigate this, recent work has employed synthetic microbial consortia and encapsulated biofilms to enhance robustness and stability [15].

Long-term performance trials over 180 days in pilot-scale systems have provided insights into system reliability and operational issues. MFCs operated under municipal wastewater conditions demonstrated a stable power density of ~0.35 W/m² and 78% COD removal, with moderate electrode fouling after three months [16]. MECs demonstrated consistent hydrogen production rates (~0.9 m³ H₂/m³/day) but suffered from cathodic scaling and pH imbalance without periodic cleaning or buffer addition [17]. AD systems processed mixed agricultural residues with a stable methane yield of 0.32 m³ CH₄/kg VS and demonstrated effective biogas desulfurization when integrated with biofilters [18].

An important consideration is the internal resistance of microbiological systems, which affects energy output and efficiency. In MFCs, internal resistance includes ohmic, activation, and concentration losses. The application of 3D-printed electrodes and hierarchical porous structures has successfully reduced internal resistance by up to 35%, improving energy recovery and biofilm growth [19]. In MES, electron transport limitations at the cathode-microbe interface remain a challenge. The use of redox mediators such as neutral red or riboflavin has been explored to enhance electron uptake in autotrophic microbes, albeit with issues of mediator toxicity and cost [20].

Tables 1-4 provide a comprehensive overview of microbiological energy systems from multiple performance and feasibility perspectives. Table 4.1 compares the energy output of anaerobic digestion (AD), microbial fuel cells (MFCs), microbial electrolysis cells (MECs), and microbial electrosynthesis (MES), highlighting the distinct products and output ranges associated with each system. AD demonstrates the highest methane yields, while MFCs and MECs offer electricity and hydrogen production, respectively, albeit with lower power densities. Table 4.2 focuses on environmental benefits, showing that all systems contribute to greenhouse gas (GHG) reduction, with MES offering the most carbon-negative potential through direct CO₂ utilization. Table 4.3 details the dominant microbial communities and ecological traits in each system, revealing how diversity, biofilm stability, and stress tolerance affect long-term performance. AD exhibits the highest microbial diversity and resilience, while MES operates with highly specialized but less stable communities. Finally, Table 4.4 presents techno-economic indicators, illustrating that while AD is currently the most cost-effective and mature, MFCs, MECs, and MES remain at lower technology readiness levels (TRLs), with higher capital costs and longer payback periods. Together, these tables offer a multidimensional analysis that informs the scalability, integration potential, and application niches of microbiological energy technologies.

Table 4. Energy Output Comparison Across Microbiological Systems

Gas analysis from these systems reveals variations in yield and purity. AD-generated biogas contains 55–70% methane, with carbon dioxide and trace hydrogen sulfide requiring post-treatment. MECs produce nearly pure hydrogen at the cathode, though cathodic overpotentials reduce net efficiency. MES can produce acetate, ethanol, or methane, depending on microbial strains and cathode potential. Advanced electrochemical reactors using cathodic biofilms on graphite felt and granular carbon beds have improved electron capture and selectivity toward desired products, achieving acetate yields of 0.85 g/L/day [21].

Table 5. Emission Reduction and Environmental Benefits

Material stability and durability play critical roles in operational longevity. Carbon felt and carbon cloth electrodes maintain performance over hundreds of cycles with minimal degradation, whereas metal-based electrodes (e.g., stainless steel) are prone to corrosion in acidic or sulfide-rich environments [22]. Membrane fouling, especially in two-chamber MFCs and MECs, reduces ion transport and increases maintenance frequency. Modified membranes with antifouling coatings and periodic polarity reversal have been proposed to address this issue [23].

Integrated system applications are gaining traction, especially in decentralized settings. Hybrid AD-MFC systems have demonstrated synergistic improvements in methane production and electricity generation by recovering residual organics post-digestion. One pilot plant operating with food waste and wastewater demonstrated a 20% increase in overall energy recovery compared to standalone AD [24]. MES systems have been integrated with CO₂ capture technologies to convert industrial flue gases into acetate, offering a carbon-negative energy pathway [25].

In economic terms, cost analysis indicates that AD remains the most mature and cost-effective microbiological energy technology, with payback periods ranging from 3 to 7 years, depending on feedstock availability and gas utilization strategy. MFCs and MECs are currently limited to niche applications due to high capital costs and low power density, but targeted innovations in electrode design and modular stacking could improve feasibility [26]. MES remains at a pre-commercial stage, with limited economic data but promising results in carbon utilization and value-added product generation [27].

Table 6. Key performance metrics and measurement tools

Environmental impact assessments of microbiological energy systems reveal significant benefits. Life cycle analyses indicate up to 80% reduction in greenhouse gas emissions for AD compared to landfilling organic waste. MFCs offer low-emission wastewater treatment options with low sludge production and minimal chemical input. MECs and MES, when powered by renewable electricity, exhibit negative carbon footprints under ideal operating conditions [28].

Table 7. Microbial Community Traits in Energy Systems

Fig 2. COD Removal Efficiency

In conclusion, the results of microbiological energy system studies affirm the viability of these technologies across diverse contexts. Performance depends heavily on microbial community dynamics, reactor design, electrode material, and integration strategies. As innovations continue to emerge in synthetic biology, electrochemical engineering, and process control, microbiological energy stands poised to play a significant role in the sustainable energy transition [29][30].

Fig 3. Microbial Community Diversity in Different Systems

4. Discussion

The analysis of microbiological energy systems presented in this review underscores both the vast potential and complex challenges associated with their implementation. A notable theme emerging from the results is the trade-off between energy yield, system complexity, and microbial stability. Each microbiological system—MFC, MEC, AD, and MES—presents a unique interplay of biochemical pathways, engineering considerations, and environmental responses. While anaerobic digestion continues to dominate in terms of maturity, output, and global deployment, newer technologies like microbial fuel cells and microbial electrosynthesis present exciting avenues for multifunctional energy recovery and waste valorization [1]. Understanding how these technologies can be best optimized, integrated, and scaled is critical for moving from lab-based feasibility to industrial deployment.

One of the most significant findings in microbial energy systems is the extent to which microbial community composition dictates performance. Microorganisms are not just passive agents in energy generation; they actively determine efficiency, system stability, and even product specificity. High-diversity systems, such as AD, demonstrate better resilience to environmental stress due to functional redundancy and syntrophic relationships. Conversely, the more selective consortia found in MES and MFCs are often more sensitive to shifts in pH, substrate concentration, or temperature. This implies that system design must account not just for physical and chemical parameters but also for ecological principles like succession, niche occupation, and competition [2]. The increasing application of omics tools—metagenomics, metatranscriptomics, and metabolomics—is providing unprecedented insight into microbial behavior, offering pathways to design tailored consortia with enhanced energy yields [3].

The microbial electron transfer mechanism remains central to the performance of electrochemical microbiological systems. Direct electron transfer (DET) mechanisms are generally more efficient than mediated electron transfer (MET), as they avoid the losses associated with soluble mediators. However, DET depends heavily on electrode-microbe interactions and surface properties. Studies have shown that specific extracellular structures such as conductive pili, cytochromes, and EPS composition influence these interactions significantly [4]. Engineering electrodes with materials that mimic or enhance these biological interactions—such as nanostructured carbon, conductive polymers, or even living biofilms—is a frontier of current research. The challenge lies in balancing enhanced electron transfer with cost and durability, especially in systems designed for long-term operation in variable environmental conditions [5].

Another emerging area of interest is the role of electrode architecture and reactor design in improving overall efficiency. Flat-plate and tubular designs have given way to more complex 3D electrode structures that increase surface area and promote microbial colonization. 3D-printed electrodes, for instance, allow precise control over pore size and spatial organization, improving mass transport and reducing internal resistance [6]. This approach aligns with the broader movement in bioengineering toward biomimicry and structural optimization. Similarly, the use of conductive hydrogels and composite materials has opened avenues for fabricating electrodes that are not only conductive but also biodegradable, potentially reducing long-term waste associated with system decommissioning [7].

Operational parameters also require careful calibration to balance microbial metabolism with reactor kinetics. For example, while high organic loading rates increase energy output, they can also lead to substrate inhibition or biomass washout. The optimal hydraulic retention time (HRT) and solid retention time (SRT) must be tailored to each system, considering both microbial doubling times and the desired product—whether electricity, hydrogen, or methane [8]. Feedback control systems and real-time monitoring tools have thus become integral components in maintaining reactor stability. Advanced control algorithms, including model predictive control and machine learning-based systems, are now being tested to dynamically adjust operating conditions in response to process fluctuations [9].

The integration of microbiological energy systems into existing infrastructure presents a promising yet underexplored opportunity. Wastewater treatment plants, food processing facilities, and agricultural operations generate organic waste streams ideally suited for microbial conversion. Embedding MFCs into treatment trains allows simultaneous COD removal and electricity generation, reducing both energy demand and environmental impact. AD systems are already widely used for sludge stabilization and energy recovery, but their integration with downstream MFCs or MECs for residual treatment could significantly enhance system efficiency [10]. MES systems hold the potential to act as carbon sinks when coupled with flue gas treatment or CO₂ capture units, transforming waste carbon into useful organics and thereby closing the carbon loop [11].

However, despite numerous lab-scale successes, the transition to commercial-scale systems has been slow. The reasons are multifaceted. First, the power densities achieved by current MFC and MES systems remain significantly lower than conventional technologies, limiting their standalone applications [12]. Second, reactor scale-up often introduces engineering challenges, such as uneven flow distribution, electrode fouling, and microbial stratification, which degrade performance. Addressing these issues requires a multidisciplinary approach that merges microbiology, process engineering, and materials science. Standardization of reactor design, modularization, and plug-and-play compatibility with existing systems are crucial for broader adoption [13].

Economic viability is another critical hurdle. AD has proven its cost-effectiveness in centralized facilities with consistent waste streams. MFCs and MECs, on the other hand, face high initial capital costs due to the need for specialized electrodes, membranes, and monitoring systems. Moreover, the maintenance of bioelectrochemical systems requires skilled personnel and infrastructure support, which may be lacking in decentralized or low-resource settings. That said, recent efforts in using low-cost materials—such as graphite waste, plant-based carbons, or 3D-printed bioplastics—have shown promise in reducing costs without sacrificing performance [14]. Techno-economic analyses must be further refined to include lifecycle emissions, energy payback periods, and potential policy incentives like carbon credits [15].

The environmental benefits of microbiological energy systems are substantial. By converting organic waste into usable energy, these systems not only displace fossil fuel use but also reduce methane emissions from landfills, eutrophication from nutrient runoff, and environmental contamination from untreated waste streams. Life cycle assessment studies confirm that microbiological systems, particularly AD and MFCs, have lower global warming potential and energy consumption compared to conventional treatment and energy generation systems [16]. Additionally, the ability to recover nutrients (e.g., nitrogen, phosphorus) from waste streams adds to the sustainability appeal, supporting goals of circular economy and resource recovery [17].

An exciting frontier lies in synthetic biology and metabolic engineering to further enhance microbial performance. Engineered strains with optimized metabolic pathways, stress tolerance, and electron transport chains have been shown to outperform wild-type strains in terms of yield and efficiency. For example, synthetic consortia engineered to split complex substrates among specialized microbes have improved overall conversion rates and reduced byproduct formation. Gene-editing tools such as CRISPR-Cas systems offer precise control over microbial traits, enabling the creation of designer consortia for specific applications—such as hydrogen generation, acetate production, or simultaneous nutrient recovery [18]. However, biosafety and regulatory issues around the use of genetically modified organisms (GMOs) in open systems remain a concern, requiring thorough risk assessments and containment strategies [19].

Finally, the role of microbiological energy in the global energy landscape should not be understated. While unlikely to replace large-scale renewable systems like solar or wind, microbial systems offer unique value in decentralized, low-infrastructure, or hybrid configurations. Their ability to operate at small scales, handle diverse waste streams, and generate multiple products (energy, clean water, nutrients) makes them particularly attractive for remote communities, disaster response, and developing economies. The scalability, modularity, and adaptability of these systems may align well with emerging paradigms such as microgrids, smart sanitation, and circular agriculture [20].

5. Conclusion

Microbiological energy represents a paradigm shift in the way we approach renewable energy generation, waste management, and environmental remediation. By capitalizing on the metabolic pathways of microorganisms, a range of technologies—such as anaerobic digestion (AD), microbial fuel cells (MFCs), microbial electrolysis cells (MECs), and microbial electrosynthesis (MES)—have emerged that convert organic waste and carbon dioxide into usable energy carriers, including methane, electricity, hydrogen, and valuable organics. These systems serve as functional links between bioengineering, environmental science, and renewable energy, aligning strongly with global objectives for sustainable development, circular economy, and climate mitigation.

Throughout this review, we have examined the technological principles, microbial dynamics, performance indicators, and scalability of microbiological energy systems. AD remains the most mature and widely implemented system, capable of handling high organic loads and producing stable yields of biogas. Its robustness, established operational protocols, and relatively low cost make it an attractive solution for municipal, agricultural, and industrial waste management. Moreover, recent advancements in pre-treatment techniques, co-digestion strategies, and digester design have continued to increase its efficiency and adaptability to new feedstocks.

MFCs, although more nascent, demonstrate the unique ability to directly convert organic matter into electricity through extracellular electron transfer (EET) mechanisms. The progress in electrode material development, such as carbon nanotubes, graphene coatings, and 3D-printed geometries, has resulted in improved power densities and microbial adherence. However, challenges such as membrane fouling, low voltage output, and biofilm instability persist. Despite these limitations, MFCs offer unparalleled versatility for decentralized applications, particularly in off-grid wastewater treatment, remote biosensing, and educational or military deployments.

MECs offer enhanced hydrogen production through the application of external voltage, capitalizing on electrochemically active microbial consortia and catalytic surfaces. Their potential integration with solar or wind power makes them suitable candidates for renewable hydrogen generation. However, issues related to long-term cathode performance, pH stability, and cost reduction must be addressed before broader commercialization can occur. MES systems, still largely at the research stage, offer an intriguing pathway for carbon dioxide utilization through biological conversion into acetate, ethanol, and other valuable organics. These systems have the potential to serve as both energy recovery and carbon capture mechanisms, especially when coupled with flue gas streams or direct air capture units.

A key takeaway from this review is the crucial role of microbial community composition and electron transfer behavior in system performance. The integration of metagenomics, transcriptomics, and real-time biosensors has vastly improved our understanding of microbial behavior under varying operational conditions. Moreover, synthetic biology and metabolic engineering tools are now enabling the design of tailored consortia for specific reactions, further pushing the boundaries of microbial energy conversion efficiency. Yet, these innovations also bring ethical, ecological, and regulatory concerns that require careful management.

From an engineering standpoint, scale-up remains a dominant challenge. While laboratory prototypes have demonstrated impressive metrics, performance often declines at larger scales due to increased internal resistance, uneven flow distribution, and difficulties in maintaining stable microbial communities. Modular design, advanced fluid dynamics modeling, and dynamic control systems offer pathways to scale microbiological systems while maintaining performance. Furthermore, integration with existing infrastructure—such as wastewater treatment facilities, biorefineries, and agricultural operations—can significantly improve the economics and adoption potential of these systems.

Economically, anaerobic digestion currently represents the most feasible microbiological energy system, especially in centralized applications with consistent feedstock availability. MFCs and MECs are progressing toward viability through material cost reductions and performance optimization. The use of low-cost and biodegradable electrode materials, simplified reactor geometries, and smart monitoring technologies could bring these systems closer to market readiness. MES systems, though still in early development, could find niche applications in biorefineries and carbon capture integration once scalability and microbial efficiency are improved.

Environmental and policy implications of microbiological energy are profound. These systems not only offer energy production but also reduce environmental pollutants, recover nutrients, and displace fossil fuels. They contribute to greenhouse gas reduction, improved sanitation, and sustainable agriculture. However, regulatory frameworks must evolve to support the deployment of microbial energy technologies, particularly those involving genetically modified organisms, open-system operation, and decentralized implementation. Incentives such as feed-in tariffs, carbon credits, and research grants could play a vital role in accelerating adoption.

In conclusion, microbiological energy systems provide a compelling blend of renewable energy production, environmental stewardship, and technological innovation. Their modularity, adaptability, and low ecological footprint position them as essential tools in the portfolio of future energy solutions. To fully realize their potential, continued interdisciplinary collaboration is essential—bringing together microbiologists, engineers, economists, and policymakers to address the remaining scientific and practical challenges. With the right investments and innovations, microbiological energy could evolve from experimental niche to global necessity, powering a cleaner and more sustainable future.

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