Solid waste management is increasingly becoming challenging. Improper treatment generates hazardous by-products, posing human health hazards and is proving to be deleterious to the environment (Sapuay, 2016). Nearly 2 billion tonnes of municipal solid wastes are generated globally, of which over 30% remains uncollected. Out of the total collected waste, 70% ends up in landfills or dumpsites, close to 19% is recycled, and the remaining 11% is used for energy recovery (Nanda and Berruti, 2021). Organics constitute 40 to 50% of municipal solid waste, mostly biodegradable, and comprise domestic and agricultural waste (Ramachandra et al., 2018). They are predominantly managed through incineration and landfills (Kumar and Agrawal, 2020), with significant environmental costs (Shah et al., 2022).

Composting is touted as a viable alternative, since it ensures valorization, and is environment friendly. However, composting is time-consuming complex microbial process with uncertain quality of resulting fertilizer and hence of low value. It also generates aspirational inconveniences, such as malodor and infection (Sharma et al., 2024; Kumar and Agrawal, 2020). A major reason for the slow process is the recalcitrance of lignocellulosic organic waste (Zoghlami and Paës, 2019; mainly plant based biomass) and the presence of antimicrobial defense metabolites. There are physical and chemical methods (Nait M’Barek et al., 2023) are available for pretreatment of lignocellulosic biomass such as strong acid or alkali or microwave. These treatments reduce the recalcitrance and improve biodegradability. Alternatively, anaerobic digestion is an efficient microbial treatment method for organic waste and nutrient recycling, converting 95% of organic waste into useful products viz., biogases and digestate (Patel et al., 2021). Integration of multiple intermediate steps (biomass pretreatment, fermentation and downstream processing) allows for the generation of value-added products, including biofuels, biodegradable polymers, and enzymes for industrial and medical applications (Patel et al., 2021). Though efficient and well adopted, they suffer from prohibitive cost and difficulties in maintaining optimal operational conditions. Moreover, the system is more applicable for large farms and centralized facilities and improper management of digestate also cause environmental issues (Lin et al., 2018).

On the other hand, wastewater poses different issues concerning sanitation, health, and hygiene, when compared to solid waste. They serve as a conduit for infection and contribute to malnutrition leading to a significant health burden (Subhash et al., 2022). The main cause of infection is improper treatment and discharge of wastewater into the receiving water bodies (Jahne et al., 2017), creating an ideal nutritional ambience for the proliferation of pathogens (Cai and Zhang, 2013). The widely adopted disinfection strategies fall into chemical and physical methods (Al-Gheethi et al., 2018), that suffer from disadvantages such as inefficient removal of pathogens, the release of hazardous disinfection by-products (DBPs), high energy requirements and frequent maintenance (Collivignarelli et al., 2021; Salim et al., 2022a). Another ignored issue associated with wastewater is malodour, which has negative implications on health, hygiene, and sanitation. Malodourants include biogenic hydrogen sulfide, methanethiol, ammonia, dimethyl sulfide, methane, and short-chain fatty acids (Salim et al., 2021; Sarat et al., 2023). Most notable is the lack of effective and affordable methods for malodour mitigation (Cai and Zhang, 2013).

Since, organic solid wastes and wastewater pose unique sets of problems, and their mitigation strategies suffer from myriad insufficiencies, the need of the hour is a biorefinery-like approach that conflates unit operations, and concertedly attempts to address these problems. This concept is gaining traction due to its potential to convert plant biomass into spectrum of high value products (Calvo-Flores and Martin-Martinez, 2022; Kalkanis et al., 2022). For example, 90% of waste from fruit processing industries serves as a feed stock for the extraction of various bioactive molecules such as polyphenols, phytosterols, terpenoids, carotenoids, tocopherols and glucosinolates, alkaloids, Poly Unsaturated Fatty Acids (PUFA) and peptides. These products further find use in therapeutic and healthcare sectors (Ritika et al., 2024). Likewise, onion peel is a major source of bioactive compounds viz., quercetin, quercetin glucoside, isoquercetin, vanillic acid, morin, ferulic acid, kaempferol, isorhamnetin etc. (Kumar et al., 2022). To take a specific example of bioactivity exhibited by the aforementioned bioactive compounds, quercetin is antimicrobial, anti-cancerous and antidiabetic. Alternatively, plant extracts can be used to synthesize engineered nanomaterials (ENMs) such as silver nanoparticles that are effective against MDR (multi drug resistant) plant pathogens. Moreover, their distinctive physicochemical characteristics, potent activity against diverse bacterial, fungal, and viral pathogens, and suitability for use in agricultural environments, position them as promising tools for efficient plant disease management (Kim et al., 2024).

Functionally, biorefinery approach catenates compatible processes to generate valuable products or energy. For example, combining phytochemical extraction with microbial fermentation generates bioactive components that are prospective in terms of economic viability and environmental applications. Compatibility is due to the favorable pre-processing of the feedstock by solvent extraction, rendering it ideal for fermentation through reduction of resident microbial load and substrate modification by the solvent.

In the described study, we propose a novel two-step valorization workflow that can simultaneously manage plant-biomass waste and wastewater disinfection and malodour. The initial step extracts small bioactive molecules from plant-biomass waste using organic solvents, favorably sterilizing (partially) the resultant residues. The study involved lignocellulosic plant biomass viz., Cocos nucifera, Allium cepa, Artocarpus hirsutus and Swietenia mahagoni, since they are used at commercial scale in food, and timber industry and generate large volume of recalcitrant organic byproducts, such peels and saw dust. The final step uses the post-extraction this residue (only used Allium cepa) after extraction as a feedstock for fermentation by B. clausii. The bioactive extracts from the first step and the supernatants from the second hold potential for applications in wastewater remediation. The proposed workflow is also advantageous to its amenability to adopt and process varied plant-biomass waste.

Solid waste management is in the limelight today, sometimes for the wrong reasons. Improper biowaste treatment may serve as a breeding ground for infection and as a source of malodour (Omang et al., 2021; Shekdar, 2009). The overwhelming volume of biomass, incommensurate with the ability of treatment systems to handle waste, is responsible for improper management and, hence, the associated issues. The proposed study aims to address this issue through a biorefinery-inspired, two-step valorisation process: one involving the isolation of useful small molecules and another enabling efficient treatment and retrieval of bioactive supernatants through submerged fermentation involving B. clausii, a GRAS (Generally Recognized as Safe) organism. The solvent extraction process also coincidently, yet favorably sterilizes the residue, rendering it suitable for inoculum addition and controlled fermentation. Moreover, the solvent treatment also improved the availability of carbohydrates, thereby converting the onion peel as a better feedstock for fermentation. Supernatant resultants from fermentation can also be employed for disinfection and malodour mitigation in wastewater (Figure 8).

The proposed strategy is a deviation from conventional physicochemical counterparts in adopting compatible and viable methods which yield useful products and, at the same time, achieve bioremediation objectives, viz. disinfection and malodour removal. The modular nature of the method makes it convenient and amenable for processing different types of agro waste apart from the one used in the study. Moreover, efficient resource recovery associated with this strategy results in better disposal of wastes from plant-based industries. Favorable feedstock modifications rendered by the solvent extraction process through the removal of antimicrobial compounds, such as quercetin (in the case of onion peel) (Nguyen and Bhattacharya, 2022), make them more suitable for fermentation. Additionally, improving unit processes for scale-up will help achieve efficient processing of feedstock, eventually resulting in better bulk reduction.

Infection and malodour are the problems associated with wastewater and have serious implications for health, hygiene, and sanitation. Owing to the ability of plant extracts and bioactive supernatants to reduce pathogens and malodour-causing microbes, makes the strategy suitable for wastewater applications. Restricted selectivity exhibited by the spent media in the inhibition of S. enterica and S. dysenteriae, when compared to other gram-negative and positive organisms (Supplementary Figure S7), could be advantageous since disinfection and malodour mitigation can be achieved without interfering with the associated bioremediation process. Further corroboration is required to leverage this characteristic effectively.

Onion peel MEK, among different chosen biowaste extracts, showed significant inhibition (MIC₉₀ = 4.5 mg/mL) of 1log post 6 h and a 70% reduction in biogenic H₂S production in post 6 h for 2 mg/mL concentration. The smell reduction is due to the reduction in viable cells of S. enterica. The reduced viability could be implicated in the presence of an antimicrobial agent, quercetin (Wang et al., 2018; Zheng et al., 2017). Reports abound on the antimicrobial, antioxidant, antifungal, and antiviral activities of quercetin (Nguyen and Bhattacharya, 2022). An interesting observation on the activity of column fractions, especially H and B, is that they possessed contrasting activity; the former promoted the growth of S. enterica, and the latter inhibited it. The presence of quercetin or its glycoside could be attributed to this differential activity (Hervert-Hernández and Goñi, 2011). HPLC and LC–MS data revealed the traces of quercetin in fraction B and its glycoside in fraction H. Inhibitory activity of quercetin and growth promotion characteristics of its glycoside are well documented (Chodak, 2012) and could be responsible for the contrasting activity.

Biorefinery approach demands conflation of compatible unit processes in order to improve its productivity and efficiency (Calvo-Flores and Martin-Martinez, 2022; Chojnacka, 2023). Combining extraction with fermentation provides two advantages viz., sterilization and substrate modification, which are pre-requisite for fermentation. The residue resultant from solvent extraction had sufficient carbon (60.9% carbohydrates) but was limiting in nitrogen (3.85% protein) (Supplementary Table S4). Solvent extraction also marginally improves the nutrients, which, when read along with the ability of the solvents to sterilize the residue partially (Supplementary Figure S6), proves advantageous for submerged fermentation. The residue requires supplementation in order to rectify its nutrient limitations, especially with regards to nitrogen and other macronutrients. These factors play out favorably in the fermentation process improving the growth of B. clausii significantly, when compared to the fermentation of raw feedstock (not being subjected to solvent extraction; Figures 7A,B).

Con.OPR72 and Con.OPR48 can also find potential application in wastewater, owing to their antimicrobial activity leading to disinfection and malodour mitigation. The activity could be attributed to hydrolytic enzymes such as proteases present in the supernatant, especially in the stationary phase of bacteria when they undergo metabolic stress because of competition from other bacteria. Interestingly, though, in the study, the protease activity was lost during the concentration of the supernatant. This implies that some other components are responsible for the activity. The supernatant, on the contrary, contains amylase, which is reported to possess biofilm inhibition activity (Lahiri et al., 2021; Solihin et al., 2021) This fact, when read along with the reports on the inhibitory activity of small molecules such as quercetin on amylase, points to favorable feedstock processing through solvent extraction (Pandurangan et al., 2017; Shen et al., 2023; Martinez-Gonzalez et al., 2019). Feedstock devoid of amylase inhibitors will prove conducive for amylase production by B. clausii, thereby ensuring antibiofilm activity of the resultant supernatant along with the elusive bactericidal action (Jee et al., 2020).

Inefficient management and disposal of solid waste may lead to environmental and health-related issues. A large proportion of agricultural waste, along with domestic waste, is disposed of improperly, in situ or ex-situ, such as in landfills, aggravating the issue further. Additionally, improper maintenance and monitoring of landfills generate gasses, viz. methane, carbon dioxide, sulfides and ammonia, contributing to global warming in general and local ecosystem perturbations in specific. Strategies such as this, with trains of modular unit processes with emphasis on valorization, certainly will improve the efficiency of bioremediation, improve economic viability, and leave a minimal environmental footprint.

Finally, like any other, this proof-of-concept study, invokes questions on its amenability for translation. The proposed strategy leans heavily on the concept of biorefinery and adopts features that are successfully translated. Large scale solvent extraction with different feedstocks, is carried out at industrial scale, with efficient solvent recovery and reuse (Isci and Kaltschmitt, 2022; Patra et al., 2022). Similarly, fermentation is also well established and adopted rampantly for large-scale applications. For example, 20 million liters of ethanol is generated from about 100 thousand tonnes of wheat straw, in a facility at Khuzestan, a wheat growing province of Iran (Hasanly et al., 2018). In United States, more than 10 gigalitres of bioethanol is generated from 84 million tonnes of corn stover (Karimi Alavijeh and Karimi, 2019). Catenation of these processes presents advantages in terms of enhanced valorisation and improves the associated processes and thereby making them synergistic.

Potential commercial viability and customizability for varied applications, makes the described strategy promising for scale up and eventual deployment. This biorefinery-inspired approach involves choosing unit processes that complements each other. Solvent extraction of onion peel for example, renders them partially sterile and amenable for the next step, which is fermentation. Moreover, retrieval of quercetin and its glycosides processes the feedstock by removing these antimicrobial compounds thereby preparing the substrate for efficient fermentation. The study establishes the proof of concept through the isolation of quercetin and its glycoside from onion peel waste in the first step, followed by the generation of a bioactive supernatant through fermentation with B. clausii. The onion peel residue after solvent extraction was rendered partially sterile and more suitable for the next step. The solvent treatment also improved the availability of carbohydrates, thereby promoting the fermentation process. In concordance with that, post extracted onion peel residue fermentation media (POCFM) promoted B. clausii better than its counterpart, raw onion peel fermentation media (ROCFM). An increase of 1 log and 85% were observed after 48 and 72 h respectively, when compared to ROCFM. Both the MEK extract, and bio active supernatants hold the potential for disinfection and malodour reduction in the wastewater. Maximum of 4 log inhibition was achieved with 5.5 mg/mL of onion peel MEK extract against S. enterica. There was an associated significant reduction of biogenic H₂S production by 70% (at sub MIC₉₀ concentration of 2 mg/mL). Additionally, concentrated bioactive supernatants, Con.OPR48 and Con.OPR72 showed inhibition in the growth of S. enterica and S. dysenteriae after 6 h of incubation, with the former being less effective than the latter. Like the extracts, supernatants also showed effective reduction in the emanation of biogenic H₂S. In conclusion, the modular nature of the proposed strategy will make it amenable for adoption in the management of various other plant-based organic wastes, other than the onion peel used in the study.