Bacterial Biorefineries: Transforming Agro-Industrial Waste into Sustainable Solutions for a Circular Bioeconomy

1  Introduction

Agricultural waste refers to surplus materials generated during the cultivation, harvesting, and processing of crops, including fruits, vegetables, dairy, poultry, meat, and other agricultural products [1]. Priya et al. [2] noted that substantial biomass waste arises from post-harvest and post-processing operations. The rapidly growing global population has transformed the food and agro-industrial sectors, significantly boosting productivity and, as a result, producing vast quantities of agro-industrial waste [3]. Currently, this waste is estimated at 1.03 billion tons annually, with most being burned or dumped in landfills [4]. Consequently, greenhouse gas (GHG) emissions have surged and are projected to increase by 60% by 2030. Blasi et al. [5] reported that such disposal methods release toxic compounds, contributing to pollution, health hazards, and climate change.

Agricultural processing generates a wide range of solid waste, including rice husks, wheat straw, leaves, stems, jute fiber residues, rusk, livestock waste, post-harvest leftovers, fruit and vegetable scraps, peels, skins, shells, edible oil waste, cooking oil, vegetable oil residues, poultry byproducts, feathers, egg discards, meat scraps, and forestry debris [6]. Agro-industrial waste, primarily composed of lignocellulosic biomass, has attracted growing interest in material and chemical engineering due to its mechanical strength, thermal stability, renewability, abundance, non-toxicity, affordability, and biodegradability [6]. These solid wastes can be transformed into valuable products through microbial biorefineries [7]. Microbial biorefineries offer sustainable methods for converting agricultural waste into marketable products. They focus on utilizing agro-industrial byproducts as feedstock to produce biofuels, bioenergy, biopolymers, bioactive compounds, and other high-value materials, promoting environmental sustainability [8]. This approach supports the development of bio-based industries by reducing pollution and conserving natural resources. The linear economy has contributed to excessive agro-industrial pollution [9,10], while the circular economy offers a promising solution for converting waste into useful products.

However, several challenges and future directions must be addressed to ensure successful implementation and advancement of this technology [1]. These include overcoming technical barriers and promoting environmental protection, resource efficiency, food security, and modern agricultural practices [10,11].

This review explores the sustainable use of agro-industrial waste through bacteria-driven biorefineries and evaluates current industrial efforts to produce valuable products via microbial conversion. It provides a comprehensive overview of the complexity of agro-industrial waste and the pretreatment methods needed to enhance microbial access. By identifying challenges and research gaps, the review emphasizes the need for greater visibility and integration of circular bioeconomy principles. It introduces a novel framework that combines microbial pathways, feedstock diversity, and industrial scalability—an approach often overlooked in previous studies. Additionally, the review addresses key questions such as how bacterial systems can be optimized for various waste streams, which pretreatment strategies best balance efficiency and sustainability, and how microbial biorefineries can be integrated into existing industrial systems. It also examines the socio-economic and policy factors influencing adoption, offering a strategic roadmap for advancing microbial biorefineries as scalable, low-carbon solutions for waste valorization.

2  Various Sources of Agro-Industrial Waste

Agriculture plays a vital role in contributing to the global economy across various resource sectors [12]. According to Bala et al. [13], unprocessed agro-industrial waste generates significant greenhouse gas emissions, which in turn intensify climate change through multiple pathways. Additionally, this results in the release of unwanted gaseous byproducts. Agricultural waste primarily originates from farming activities; however, it is not confined to production alone, as food processing also contributes to waste generation. Biorefineries can function as multipurpose facilities, particularly in waste management, by converting biomass waste into valuable products such as bioplastics, biofuels, organic acids, and chemicals [14,15]. The main sources of biomass waste include agricultural residues, food industry byproducts, and municipal waste streams [16]. Agricultural waste can be further categorized into lignocellulosic materials and green biomass [16], while food industry waste may consist of filtered grains and fibers, molasses, and shells. Fig. 1 below presents a broad classification of agricultural waste based on its various sources.

Figure 1: General schematic of different types of pre-treatment process of biorefineries of agricultural waste (Created using Adobe Illustrator)

Post-harvest waste refers to losses occurring throughout the entire food supply chain, beginning from the moment crops are harvested until their final consumption [17]. These losses can be categorized into weight reduction due to rotting, quality deterioration, nutritional depletion, reduced seed viability, and commercial loss. Waste generated from the agricultural industry contributes to GHG emissions and has several adverse environmental impacts. Like other production enterprises, the aquaculture industry requires various inputs to produce goods and materials [18]. Kumar and colleagues [18] noted that such wastes often hold little or no economic value and frequently act as environmental pollutants. Additionally, chemical usage in farming can be harmful to ecosystems. Hazardous substances such as pesticides, herbicides, and insecticides applied to crops may leach into groundwater and soil. Unused and leftover chemicals are considered toxic waste, posing significant risks to environmental health.

3  Common Practices in Agro-Industrial Waste Management

Identifying effective strategies for managing agricultural residues has become a critical priority in the agricultural sector, emerging as one of the most urgent challenges of the 21st century [19]. Conventional methods such as composting, recycling, landfilling, and incineration offer moderate reductions in carbon emissions. For instance, composting emits approximately from 30–400 kg CO2 equivalent per metric ton of biowaste (Fig. 2), whereas microbial biorefineries processing agro-waste can emit as little as 15–35 g CO2 equivalent per ton, depending on process design and post-treatment [20]. Biorefineries offer a more transformative solution by converting agro-waste into high-value products such as biofuels, bioplastics, biosurfactants, and pharmaceutical precursors. Life-cycle assessments indicate that optimized biorefinery systems can reduce emissions by up to 80%–90% compared to fossil-based production, with some advanced configurations achieving net-negative carbon balances through carbon capture and biochar generation. This not only enhances carbon savings by displacing fossil fuels but also improves resource efficiency and economic viability. Unlike conventional waste treatment, biorefineries enable cascading valorization, extracting maximum utility from biomass at each stage, in alignment with green chemistry and sustainability principles. While agro-waste management is locally scalable and accessible, biorefineries offer broader systemic impact, positioning them as strategic platforms for climate-smart innovation and sustainable industrial development (Fig. 2). Among waste management practices, landfilling remains the most widely used, with over 71% of municipal solid waste in the U.S. disposed of in landfill sites annually [21]. The United States Environmental Protection Agency categorizes landfills into five types: municipal solid waste landfills, bioreactor landfills, industrial waste landfills, hazardous waste landfills, and polychlorinated biphenyl landfills [22]. Landfills involve burying toxic waste in engineered pits, allowing slow decomposition. This method can be effective for farm or agro-industrial disposal if managed properly within a bioreactor landfill. However, a major concern is the degradation of soil and water quality during landfilling [23]. Potential hazards include the emission of gases and leachate. Moreover, poorly managed landfill sites can deteriorate into open dumps. Despite these risks, landfills can serve as a source of conventional energy if waste is carefully treated within the landfill environment [21].

Figure 2: Some of the common examples of agro-waste management globally and the carbon footprint (Created using Canva.com)

Composting is a green technology that transforms organic matter into a humidified and stable product through microbial activity. For effective composting, key parameters such as temperature, pH, moisture content, and the carbon-to-nitrogen ratio must be properly regulated [24]. Various strategies have been developed to compost organic waste. Chang et al. [25] utilized black soldier fly larvae to assist in composting, co-processing organic waste with agricultural residues to produce biofertilizers and larval biomass, which was subsequently used as animal feed. The larval biomass is nutritionally rich and suitable for feeding fish and poultry. Similarly, Peng et al. [26] demonstrated that co-composting kitchen waste with agricultural and forestry residues on an industrial scale results in an efficient composting process.

Vermicomposting is another method for processing organic waste. This biotechnology technique converts organic matter into compost through the combined action of red worms and bacteria [24]. Numerous studies have investigated composting and vermicomposting of food processing waste to ensure safe disposal and promote environmental sustainability. Recent reports suggest that vermicomposting is more effective than traditional composting in reducing greenhouse gas emissions and enhancing the quality of the final product [27]. It is also efficient in breaking down lignocellulose-rich materials, improving compost quality [28]. However, vermicomposting of municipal excess sludge has been associated with increased microplastic traces [27].

Traditional agro-industrial waste management practices such as landfilling, composting, and incineration present notable environmental and economic drawbacks compared to biorefinery-based solutions. Landfilling contributes significantly to methane emissions and groundwater contamination, with life cycle assessments indicating high global warming potential and ecotoxicity [29]. Incineration reduces waste volume but emits toxic gases and requires high capital and operational costs. Composting is more environmentally friendly but offers limited scalability and economic return, even with advanced systems, which still fall short of full valorization [30].

In contrast, biorefineries represent a circular economy model by converting waste into high-value products such as biofuels, bioplastics, and enzymes, thereby improving sustainability and reducing net emissions. Although biorefineries demand substantial initial investment, their long-term cost-effectiveness is supported by diversified revenue streams and reduced environmental liabilities. Bio-waste refineries offer dual benefits: they process waste from local communities and refine it into valuable bio-products. Usmani et al. [31] described biorefinery sustainability as a balanced coexistence between bioprocessing industries and the environment, meeting socioeconomic needs without compromising product quality. This includes utilizing bio-resources, especially bio-waste, to manufacture commodities economically. However, transitioning to this system may be gradual and vary across countries [32]. Sustainability assessments can aid in evaluating techno-economic feasibility and life cycle impacts [31]. To enhance biorefinery efficiency, Sukhla and Khan [33] discussed the use of microbial electrosynthesis (MES) to decarbonize carbon sources and support a green circular economy. Yet, challenges in stack design, anodic reaction efficiency, and reliable extraction methods can hinder full operational potential. Resolving these issues could significantly improve technology performance and feedstock conversion [34]. Additionally, De Buck et al. (2020) proposed refinery designs and supply chain models to improve sustainability and economic viability. Given the diverse and extensive composition of waste for these refineries, variability in feedstock size and type poses a major challenge. Therefore, a stable supply chain and logistics network are essential for successful biorefinery operations [35].

In another perspective, Regueira et al. [36] highlighted the restricted and inefficient use of microbes, suggesting flexible resource allocation models to address substrate utilization inefficiencies. Moreover, biowaste generated within biorefineries can be repurposed as a biosorbent for removing synthetic methylene blue dye from water, promoting sustainable practices in the biorefining industry [37].

4  Microbial Biorefineries

Biorefinery is a widely adopted concept that enables the comprehensive and integrated utilization of biomass often generated from microbes into a diverse array of bio-based products and bioenergy sources [20]. From conventional biorefineries to more advanced systems employing various processing technologies, such as thermochemical and biochemical methods, the full potential of biorefineries remains to be fully explored and optimized [38]. Fig. 3 illustrates the transformation of agro-industrial waste into valuable products.

Figure 3: Sustainable processing of biomass into marketable products (Created using Adobe Illustrator)

Galbe and Wallberg [39] defined biorefineries as a sustainable counterpart to petroleum refineries, with the key distinction being the source of raw materials. Their study also emphasized that biomass can be refined into a wide spectrum of chemicals and energy products, contributing to the advancement of the circular economy. Among the most promising feedstocks is lignocellulosic biomass an abundant and renewable resource that has emerged as a viable alternative to fossil carbon for producing value-added chemicals. However, due to its complex structure, along with that of other agricultural wastes, lignocellulosic biomass is not easily broken down [40]. To address this challenge, biomass must undergo specific processing steps. Awogbemi and Von Kallon [40] noted that pretreatment methods are essential operations applied to biomass to overcome its initial resistance to direct conversion. These methods facilitate the breakdown of structural barriers, enabling more efficient transformation into desired bio-products.

Microbial communities [41,42] or specific enzymes such as esterases, lyases [43], and β-mannanases [44] are commonly employed to convert biowaste into value-added products (Fig. 4). Most biorefineries utilize thermophilic or extremotolerant microorganisms to enhance biomass conversion, particularly for lignocellulosic biomass. This type of biomass, derived from plant material, is notoriously difficult to break down due to its dense crystalline structure and strong glycosidic bonds [45]. The low yield from such substrates often results in commercially unviable processes. Therefore, pretreatment of biowaste is essential to facilitate enzymatic hydrolysis [35]. Bedoić et al. [16] identified wet biomass from garden waste—such as cuttings, grasses, and cover crops—as another excellent source of biowaste, which would otherwise be discarded or used as compost. Lignocellulosic biomass primarily consists of biopolymers like cellulose, hemicellulose, and lignin, with trace amounts of inorganic minerals and organic extractives [45]. Its composition varies depending on the source and origin [46]. The estimated annual production of lignocellulosic biomass is approximately 181.5 billion tons. Table 1 presents the classification of predominant bacterial types into two general categories.

Figure 4: Biological pre-treatment of the agro-industrial waste requires the use of bacteria, fungi and enzymes to convert the agro-waste into simple sugars to be utilized for the bioproduction of valuable products (Created using Adobe Illustrator)

The dominant bacterial type significantly influences the characteristics of the treatment system by utilizing the organic components in the waste. These include species capable of metabolizing a wide range of organic materials and reproducing rapidly. Once the organic substrate is depleted, most bacteria die and lyse, releasing their biological components, which in turn support the growth of other microbial populations. Secondary predominance often arises from the overdesign of biological treatment systems for safety purposes. Beyond metabolic traits, the ability of bacteria to flocculate is a critical feature. For complete stabilization, all aerobic biological waste treatment systems rely on the separation of microorganisms from the liquid phase through flocculation [47].

Microorganisms have played a vital role in helping society address various environmental challenges. They have been successfully applied in the treatment of municipal and industrial waste, genetic engineering, and human and animal health. Microbial applications have enabled feasible and cost-effective solutions that would be difficult to achieve through chemical or physical engineering methods [47]. Moreover, microbial technologies have proven effective in tackling a wide range of environmental issues, particularly those related to waste management.

4.1 Bacterial Cellulose (BC) Biosynthesis

Bacterial cellulose (BC) is a highly pure, biodegradable biopolymer synthesized by aerobic bacteria. Unlike plant-derived cellulose, BC lacks lignin and hemicellulose, resulting in exceptional crystallinity, tensile strength, and biocompatibility qualities that make it ideal for biomedical, food, and textile applications [48,49]. Its nanofibrillar network provides high water retention, elasticity, and mechanical integrity, supporting cell adhesion and proliferation in tissue engineering contexts [49]. Despite these advantages, BC production faces economic and scalability challenges. A major limitation is the high cost of the fermentation medium, which accounts for 50%–65% of total production expenses [50]. Additionally, conventional static culture methods yield low quantities of BC, making industrial-scale manufacturing inefficient [50]. To overcome these constraints, researchers have emphasized the need for low-cost fermentation strategies that optimize media composition for maximum yield. Extensive efforts have focused on replacing expensive synthetic media with renewable nutrient sources, particularly agro-industrial waste streams such as dairy wastewater, winery residues, and textile effluents [51]. This approach not only reduces production costs but also promotes environmental sustainability by mitigating industrial waste disposal and pollution [52]. Recent advancements in fed-batch cultivation and dynamic bioreactor systems have further improved BC yield and quality, offering scalable solutions for biomedical and industrial applications [53]. These integrated strategies highlight the importance of techno-economic assessments and circular bioeconomy models to bridge the gap between laboratory innovation and commercial viability.

One accessible agro-industrial waste is banana peel, which has been used as a carbon source in BC biosynthesis [54]. A promising concentration of BC of 19.46 g/L was reported after 15 days of fermentation. Other agricultural wastes such as coconut water and fruit juices showed similar results when fermented by Acetobacter xylinum [54]. Additionally, whey protein contains various nutritional compounds that serve as a nitrogen source. Revin et al. [55] investigated the use of dairy and winery industry waste for cost-effective BC biosynthesis by Gluconacetobacter sp., successfully improving BC yield after just three days of fermentation. These findings suggest that whey products are a viable low-cost nitrogen source for BC production. Cotton textiles also hold potential as a sustainable resource for BC synthesis while addressing environmental concerns. A study by Kuo et al. [56] demonstrated that BC yield from discolored hydrolysate was higher than from colored hydrolysate. This may be due to the removal of colored reducing sugars via chitosan adsorption, which otherwise inhibits the metabolic activity of Gluconacetobacter sp. during BC biosynthesis.

Soemphol and colleagues [57] found that BC production improved when crude glycerol was used as an alternative substrate fermented by Gluconacetobacter sp. However, increasing glycerol concentrations beyond a certain threshold reduced BC biosynthesis, likely due to pollutants in crude glycerol affecting bacterial activity. Another study indicated that adding pineapple peel extract to crude glycerol enhanced BC biosynthesis. In addition to boosting BC production, utilizing these biofuel industry wastes helps reduce environmental impact and lowers reliance on non-renewable energy sources [57].

A recent study by Quiñones-Cerna and colleagues [58] employed Komagataeibacter rhaeticus, cultivated using asparagus waste. Additionally, agro-industrial wastes such as palm date, fig, and sugarcane molasses have been utilized for cost-effective BC production, either supplementing or replacing the widely used Hestrin-Schramm (HS) medium [59]. The researchers successfully synthesized highly crystalline BC (81.89%) with an ideal fiber size of 178 nm. Further investigations explored the use of various agro-waste substrates to assess BC yield. Residues from cucumber, tomato, apple, melon, and kiwi have been processed into hydrolysates for fermentation [60], while hydrolysates from mandarin fruit, lemon, grapefruit, and orange have also been used to produce BC [61]. Industrial waste products are increasingly recognized as promising candidates for BC production. However, their practical viability depends on the affordability of raw materials, which is influenced by factors such as geographic location and climate [51]. Consequently, agro-industrial by-products from agricultural export zones present a viable option for BC production substrates (Fig. 5). In microbial refineries focused on BC synthesis from lignocellulosic biomass, several bacterial taxa exhibit distinct metabolic pathways and substrate specificities that enhance their effectiveness. Komagataeibacter species, particularly K. xylinus and K. sucrofermentans, are well-known for producing high-purity BC via the pentose phosphate pathway and gluconeogenesis. These strains show strong specificity for glucose and xylose derived from fruit peels, sugarcane bagasse, and detoxified lignocellulosic hydrolysates [55,62]. In natural kombucha or yeast co-cultures, Komagataeibacter spp. work synergistically with saccharolytic partners to convert complex polysaccharides into fermentable sugars. This metabolic collaboration expands their substrate range to include starch-rich agro-residues such as cassava peels, rice bran, and sweet potato waste, which are first degraded by yeasts before being transformed into cellulose or acids by Komagataeibacter [63,64]. Gluconacetobacter spp., now largely reclassified under Komagataeibacter, share similar metabolic traits and can produce BC under acidic conditions using sugar-rich waste streams [65]. Acetobacter spp., traditionally associated with acetic acid fermentation, have also demonstrated BC synthesis when cultivated on ethanol or glucose-based lignocellulosic substrates, especially under optimized aeration and pH conditions [65]. Enterobacter spp., though not classical BC producers, have shown potential under tailored conditions due to their ability to metabolize both hexoses and pentoses via the Embden-Meyerhof-Parnas pathway. Their facultative anaerobic nature offers flexibility in fermentation setups [65]. Lactiplantibacillus plantarum, primarily known for lactic acid fermentation, has recently been explored for BC production through co-culturing or genetic modification. It utilizes hexoses from lignocellulosic hydrolysates and tolerates inhibitory compounds such as furfural [62]. Notably, Achromobacter spp. have emerged as promising BC producers, with strains capable of utilizing pectin-rich substrates like mango peel waste (MPW). Their metabolic versatility includes strong pectinase activity and efficient sugar uptake, resulting in enhanced BC yield and crystallinity compared to conventional media [65]. Collectively, these bacterial taxa represent a metabolically diverse and substrate-adapted toolkit for converting complex lignocellulosic feedstocks into high-value BC (Table 2).

Figure 5: (A) Schematic illustration of the production of BC using low-cost effective media (Adapted under the terms of the Creative Commons Attribution 4.0 International License from Ref. [68], Copyright 2022, Springer Nature SharedIt); (B) Production and extraction of BC using the culture of K. Saccharivorans MD1 and the BC film (Adapted under the terms of the Creative Commons Attribution 4.0 International License from Ref. [59], Copyright 2020, Springer Nature SharedIt)

4.2 Bio Textiles from Lignocellulose

One of the major drawbacks of both the fashion and agriculture industries is their significant carbon footprint. As a result, bio-textiles have emerged as a potential solution to the environmental challenges posed by these sectors. Jayaprakash and colleagues [82] reported that millions of people worldwide, particularly in developing countries, are engaged in natural fiber production, spanning both small- and large-scale operations. In recent years, the bioprocessing of cellulosic agricultural biomass has gained considerable attention. Biomass derived from palm oil, corn stalks, bamboo, banana, pineapple, and rice husk is increasingly recognized for its benefits and is considered a secondary source of fiber [82].

Bio-textiles made from microbial cellulose involve the bioengineering and bio-fabrication of specific microbes such as Acetobacter xylinus to produce textiles for the clothing and footwear industries. Agro-waste is often converted into bacterial nanocellulose, which is then processed for use in textile manufacturing. Compared to conventional material production, bio-fabrication requires fewer chemicals, less water, and less energy, resulting in a smaller carbon footprint. Notably, the “Bio Couture” textile brand was founded as a research initiative exploring bacterial cellulose through Kombucha fermentation. Since then, extensive research has focused on producing nanocellulose using A. xylinus under aerobic conditions (Fig. 6). These bacteria biosynthesize extracellular cellulose nanofibrils that self-assemble into a highly organized, crystalline 3D structure [49].

Figure 6: Microbial biofabrication from agro-industrial waste and development of bio-textiles from microbial cellulose (Adapted under the terms of the Common Creative BY-NC 3.0 license from [83], Copyright 2022, Royal Society of Chemistry)

A study by Stenton and colleagues [84] reported that the fashion sector contributes approximately 10 percent of global GHG emissions, including 4 percent of worldwide carbon dioxide emissions, with projections indicating a rise to 25 percent by 2050. Currently, only 65 percent of fibers used in the textile industry originate from natural sources, while a substantial amount of natural fiber is wasted in the form of food excess. For instance, the banana industry alone generates an estimated 270 million tons of waste annually [85]. In 2018, the biotechnology company Bolt Threads developed a plant-based synthetic leather called “Mylo,” suitable for use in clothing. Mylo is derived from mycelium, the root-like structure found in mushrooms, and serves as an eco-friendly alternative to conventional vegan leathers. Agrowaste fabric is another animal-free textile that offers a promising vegan substitute, with a texture and appearance similar to real silk [86]. Banana fibers present an environmentally friendly option to silk and cotton, holding significant potential for commercial applications in the textile and fiber industries. Enhancing the mechanical properties of banana fibers through softening treatments could expand their usability across a broader range of textile products. Bacterial cultures such as Bacillus aryabhattai, Bacillus licheniformis, and Bacillus subtilis have been employed to soften banana fibers for the development of sustainable bio-textiles [87]. These fibers possess a natural sheen and extremely fine inner strands within the stalk, enabling them to replicate the texture of silk.

4.3 Conversion into Biofuels

Biofuels have gained significant attention as environmentally friendly sources of green energy and are considered promising alternatives to fossil fuels due to their economic and ecological benefits. They are sustainable and emit up to ten times fewer harmful gases than fossil fuels during consumption [40]. The biofuel industry is expected to benefit substantially from agricultural waste. Lignocellulosic biomass, the most abundant, sustainable, and cost-effective form of biomass, has become a central focus for generating not only thermal and electrical energy but also biofuels such as ethanol and biodiesel. Research has demonstrated the potential of this feedstock, including its use by Escherichia coli to produce ethanol, 1,2-propanediol, and L-lactate. Additionally, novel microbes capable of converting agro-waste into biofuel have been discovered near oil-contaminated sites, with Pseudomonas sp. and Ochrobactrum sp. being notable examples [40]. Pseudomonas aeruginosa WD23, isolated from petroleum refinery effluent, was recently found to degrade up to 27% of crude oil in seawater with minimal supplementation [88], paving the way for biofuel production from agro-waste.

The Melle-Boinot process is the conventional method for bioethanol production via batch fermentation. Saccharomyces cerevisiae is the most commonly used microorganism for fermenting sugar-rich feedstocks. This yeast has long been employed in ethanol production. Schizosaccharomyces pombe is also utilized due to its ability to tolerate high osmotic pressures and solid content [89]. In response to growing interest, researchers have explored other microorganisms for bioethanol production, including Zymomonas mobilis, Klebsiella oxytoca, Escherichia coli, Thermoanaerobacter ethanolicus, Pichia stipitis, Candida shehatae, and Mucor indicus. Kluyveromyces marxianus is considered a promising alternative to S. cerevisiae, although further research is needed to optimize its performance at industrial scale [89] (Fig. 7).

Figure 7: Summary of methods and technologies involved in the production of biofuel from agro-industry waste (Created using the Adobe Illustrator)

In addition to ethanol, biomass fermentation can produce n-butanol using microorganisms from the genus Clostridium, a process known as Acetone-Butanol-Ethanol (ABE) fermentation or the Weizmann process [90]. This method has been implemented at industrial scale, with facilities producing multiple tonnes per day. Hydrogen (H2) gas has also attracted global interest as a highly promising, renewable, and eco-friendly energy source [91]. H2 is versatile and can be produced by various organisms under specific conditions. For example, microalgae use light energy to split water molecules and generate hydrogen, while cyanobacteria typically consume carbohydrates to store energy from photosynthesis and produce H2 from water molecules [92].

4.4 Conversion into Biosurfactants

Biosurfactants are increasingly recognized as eco-friendly alternatives to synthetic surfactants due to their biodegradability, non-toxicity, and wide-ranging applications in biotechnology, healthcare, and agriculture [93]. However, their commercial viability is often limited by high production costs, particularly those associated with fermentation media and downstream processing. A promising solution lies in the valorization of agro-industrial waste, which provides a cost-effective, renewable, and abundant substrate for microbial biosurfactant synthesis. Waste materials from fruit and vegetable processing, oil refining, starch and sugar industries, and dairy effluents have been successfully repurposed to support biosurfactant production, while simultaneously addressing environmental pollution and waste disposal challenges [94]. This approach not only lowers overall production costs but also aligns with circular bioeconomy principles by converting low-value residues into high-value biomolecules. Additionally, biosurfactant production from agro-waste promotes waste minimization, improves resource efficiency, and supports sustainable industrial practices [93]. As such, agro-industrial waste emerges as a strategic enabler for scaling biosurfactant technologies while reinforcing environmental stewardship.

Microorganisms such as bacteria, fungi, and yeasts are capable of producing various biosurfactants that can replace synthetic chemical compounds [95]. These biosurfactants possess both hydrophilic and hydrophobic properties, consisting of distinct moieties that reduce surface tension and facilitate the formation of emulsions or micelles [96]. The nonpolar hydrophobic tail typically comprises hydrocarbon chains of varying lengths and complexities, while the polar hydrophilic head includes carbohydrates, amino acids, peptides, alcohols, or phosphate carboxylic acids. Despite their advantages, the high cost of biosurfactant production particularly due to fermentation media and downstream processing poses a challenge for large-scale manufacturing. To address this, recent developments have focused on utilizing industrial agricultural waste as renewable raw substrates for biosurfactant synthesis [97]. These include waste from fruit and vegetable processing, starch residues, sugar industry byproducts, and distillery effluents (Table 3). Microbes from the genera Bacillus, Candida, and Pseudomonas are commonly known for biosurfactant production, typically as metabolic byproducts during fermentation. Optimizing fermentation conditions such as temperature, pH, and oxygen levels is essential for maximizing yield [98]. Biosurfactants are classified based on their chemical structure, microbial origin, and functional characteristics. Common types include glycolipids, lipopeptides, fatty acids, ionic, and polymeric biosurfactants [99]. Notably, biosurfactants can be co-produced with other valuable products such as biofuels and enzymes during biorefinery processes (Fig. 8).

Figure 8: Schematic diagram of the biosynthesis of biosurfactant agro-industrial waste using microbial fermentation (Created using BioRender.com)

Bioplastics currently account for just 1% of the 335 million tonnes of plastic produced annually, but the market is expanding rapidly as new biopolymers, applications, and products emerge [100]. The widespread use of conventional plastics has significant environmental consequences, prompting increased interest in biodegradable alternatives [101]. Bioplastics are bio-based, biodegradable, or compostable materials that serve as substitutes for fossil-based polymers [102]. Key types include poly(butylene succinate) (PBS), poly(butylene adipate-co-terephthalate) (PBAT), polycaprolactone (PCL), polylactic acid (PLA), and polyhydroxyalkanoates (PHA) [103]. Microbial fermentation remains one of the most innovative approaches for bioplastic production.

PLA and PHA are bacterial-based bioplastics [104], synthesized and polymerized by microorganisms such as Azotobacter beijernickii, Cupriavidus necator, and strains from Bacillus, Pseudomonas, Rhodococcus, and Lactobacillus genera. PHA is biosynthesized in response to excess carbon and nutrient-limited conditions [105], while PLA is produced through microbial conversion of substrates into lactic acid [106]. Despite their promise, high production costs remain a barrier to industrial-scale commercialization [107]. Recent research highlights the potential of agro-waste and food byproducts to reduce costs in bacterial bioplastic production [105]. These bioplastics are manufactured using renewable biomass sources such as corn, rice, palm fiber, potatoes, and wood cellulose, in contrast to conventional plastics derived from petroleum and natural gas [108] (Fig. 9). Careful selection of microorganisms and carbon substrates can significantly lower production costs. Utilizing agricultural and industrial waste as renewable carbon sources not only addresses waste management challenges but also supports a sustainable future [109]. Replacing synthetic plastics with biodegradable alternatives could reduce global greenhouse gas emissions by up to 800 million tons annually [110].

Figure 9: Schematic diagram of the production of bacterial based bioplastic PLA and PHA biosynthesized from agro-industrial waste (Created using BioRender.com)

5  Challenges and Future Direction of Sustainable Agro-Waste Conversion Using Microbial Biorefineries

Agro-industrial waste, once considered a disposal challenge, is now increasingly recognized as a valuable resource for sustainable innovation and economic development [47]. To fully unlock the potential of bacterial biorefineries in valorizing such waste, supportive policy models and regulatory frameworks are essential. National bioeconomy strategies should prioritize microbial biorefineries through mission-oriented R&D funding, public–private partnerships, and innovation clusters that help de-risk early-stage technologies [119]. Regulatory frameworks must evolve to include tiered biosafety assessments for microbial strains, streamlined approval pathways for non-pathogenic and genetically optimized organisms, and waste-to-resource certification schemes that legitimize agro-waste as industrial feedstock [1]. Extended Producer Responsibility (EPR) policies can further incentivize industries to adopt biodegradable inputs and invest in microbial valorization platforms. Technologically, scaling bacterial biorefineries requires advanced genetic tools such as CRISPR-Cas systems, gene shuffling, and in situ mutagenesis algorithms to enhance strain performance and unlock novel metabolic pathways [120–122]. The integration of multi-omics, whole genome sequencing, and bioinformatics platforms will optimize enzyme efficiency and metabolite yield [120]. Additionally, modular bioreactor designs, real-time biosensors, and AI-driven techno-economic modeling—including digital twins—are critical for simulating, monitoring, and scaling production systems efficiently [123]. Together, these policy and technological strategies can transform bacterial biorefineries into cornerstone platforms for a circular bioeconomy and climate-resilient manufacturing (Fig. 10).

Figure 10: Schematic representation on the improved production involved in sustainably employing various microbial systems to develop bio-based products

Environmental concerns, resource scarcity, and the growing demand for renewable and bio-based products are the key drivers behind the sustainable development paradigm in agro-industry conversion [124]. However, converting agro-waste into useful products faces several major challenges, including the absence of robust policy or legal frameworks, limited resources, technological constraints in processing diverse agro-industrial waste sustainably, and a lack of financial support, public awareness, and transportation infrastructure (Fig. 11). In order to overcome these barriers, future research efforts must focus on developing integrated biorefineries capable of simultaneously processing various types of agro-waste into valuable products [125]. Agro-waste conversion also holds significant potential for environmental remediation and effective waste management. Overall, the future of sustainable agro-waste conversion is promising, offering opportunities for bioeconomy development, production of high-value goods, bioremediation, and improved waste handling [126]. These advancements could pave the way for a more sustainable and circular agricultural system, promoting greener and more efficient resource use [127,128]. By adopting innovative technologies and sustainable practices, we can transform agro-waste into a valuable resource, generate new employment opportunities, and contribute to a cleaner, more resource-efficient planet [129].

Figure 11: Schematic illustration on the challenges faced in the sustainable agro-waste conversion using microbial biorefineries (Created using Canva.com)

6  Conclusion

The agricultural sector generates substantial quantities of agro-industrial processing waste, animal waste, pesticides, and fertilizers, all of which contribute significantly to environmental pollution. This review highlights the potential of converting agro-waste into valuable secondary metabolites, bioactive compounds, bioenergy, and sustainable food packaging materials. The global market for products derived from agricultural waste is experiencing rapid and exponential growth. Beyond reducing production costs, these innovations offer promising solutions to urgent environmental challenges. Microbial transformation of agro-industrial waste enhances the sustainability of industrial processes by promoting resource efficiency and circularity. This review also explores strategies to maximize the yield of high-value products and investigates novel types of agro-industrial waste as viable substrates for bioconversion. However, challenges persist in scaling up production and addressing existing knowledge gaps. These gaps can be bridged through targeted research, unlocking vast opportunities in the valorization of agro-industrial residues. In order to advance this field, research efforts must focus on optimizing pretreatment methods and downstream recovery processes. The objective is to develop efficient, scalable technologies for producing sustainable products that are safe for both human health and the environment. A multidisciplinary approach is essential to ensure the long-term viability of these processes. By integrating expertise across scientific and industrial domains, we can minimize waste, reduce environmental impact, and foster the development of eco-friendly products and technologies that benefit both society and the planet.

Acknowledgement: Not applicable.

Funding Statement: The authors would like to thank the Postgraduate Research Grant (PGRG) by Universiti Malaysia Terengganu [UMT/PGRG/2024/ 55527] for the financial support.

Author Contributions: Conceptualization: Sevakumaran Vigneswari; Lakshiminarayanan Rajamani. Writing—original draft preparation: Sevakumaran Vigneswari; Muhammad Shahrul Md Noor; Fazilah Ariffin; Azila Adnan; Amirah Alias; Lakshmanan Muthulakshmi; Nurul Nadhirah Ruzelan; Hemalatha Murugaiah; Nor Omaima Harun. Writing—review and editing: Sevakumaran Vigneswari; Azila Adnan. Visualization: Sevakumaran Vigneswari. Supervision: Sevakumaran Vigneswari; Lakshiminarayanan Rajamani. Project administration: Sevakumaran Vigneswari. Funding acquisition: Sevakumaran Vigneswari. All authors reviewed the results and approved the final version of the manuscript.

Availability of Data and Materials: Not applicable (This article does not involve data availability, and this section is not applicable).

Ethics Approval: Not applicable (This study does not involve humans or animals).

Conflicts of Interest: The authors declare no conflicts of interest to report regarding the present study.

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