Recycling of Organic Wastes in Agriculture: Serving for Sustainable Agriculture

1. Introduction

The transition toward sustainable agriculture is increasingly shaped by two converging pressures: the need to secure food production under climate and resource constraints and the imperative to reduce environmental burdens associated with linear “take–make–dispose” systems [1]. Within this context, the recycling and valorization of organic wastes has emerged as a practical pathway to strengthen circularity in agri-food systems. Organic waste streams—originating from livestock production, municipal services, agro-industrial processing, and wastewater treatment—are commonly rich in organic matter and essential nutrients. When properly managed, their agricultural reuse can support soil organic matter restoration, improve nutrient cycling, and reduce dependence on mineral fertilizers while simultaneously alleviating challenges related to waste storage and disposal [2].

At the same time, the agricultural use of organic wastes raises legitimate concerns that must be addressed with equal rigor. Alongside beneficial constituents, organic residues may introduce undesirable contaminants (e.g., heavy metals, emerging pollutants, microplastics, pathogens) and may contribute to gaseous losses during treatment and application, potentially offsetting environmental gains if not mitigated [3,4]. These trade-offs make it essential to evaluate organic waste recycling through an integrated lens—one that considers not only agronomic performance but also soil quality, environmental risk, and socio-economic feasibility [5,6].

This Special Issue, “Recycling of Organic Wastes in Agriculture: Serving Sustainable Agriculture” (Agronomy, section “Agricultural Biosystem and Biological Engineering”), was conceived to showcase recent advances that help maximize the environmental and agronomic benefits of organic waste utilization while recognizing and managing associated risks. We welcomed contributions spanning the valorization of diverse organic waste streams, assessment of fertilizer potential, impacts on soil properties and crop productivity, identification of potential contaminants and approaches to reduce their occurrence, and broader socio-economic analyses linked to implementation at farm and regional scales.

The nine papers published in this Special Issue collectively reflect the breadth and interdisciplinarity of the field. Several contributions emphasize waste-to-input pathways that convert residues into value-added products capable of supporting soil fertility and plant performance. These include the development of organo-mineral fertilizers from industrial residues (e.g., deinking paper sludge) and soil organic amendments derived from municipal solid waste fractions (biochar and compost), demonstrating the continued innovation in converting heterogeneous waste streams into more standardized agricultural inputs. The issue also highlights biological and microbiome-oriented approaches—such as circular biostimulant development using winery wastewater as a cultivation substrate and studies on manure-derived inputs affecting soil microbial communities—underscoring the role of biological processes in improving nutrient use efficiency and soil functioning.

Composting and process optimization constitute another important theme. Work on biochar-amended pig manure composting advances the toolbox for assessing compost maturity and immobilizing metals such as Cu and Zn, directly tackling a common barrier to safe land application of manure-derived products. Complementarily, research on sewage sludge composting explores strategies to curb nitrogen losses through targeted amendments (e.g., biochar combined with “garbage enzyme”), linking process control with microbial mechanisms of nitrogen transformation [7].

Risk assessment and environmental safeguards are addressed explicitly in the Special Issue through geospatial modeling of agricultural microplastic hotspots associated with biosolid application [8,9]. Such contributions reinforce that sustainable recycling is not solely about nutrient recovery—robust monitoring, modeling, and preventive management are equally necessary to avoid the unintended spread of pollutants across landscapes. Finally, a state-of-the-art review on biomethane production in the Mediterranean region broadens the perspective from field-scale reuse to system-level circular bioeconomy models, where anaerobic digestion can simultaneously deliver renewable energy and nutrient-rich digestate for agricultural soils [10].

Taken together, the contributions demonstrate that “closing the loop” in agriculture is a multi-criteria challenge: it requires technological solutions for valorization, agronomic evidence of performance, and risk-informed frameworks that account for contaminants, emissions, and implementation barriers. This introduction introduces the rationale and scope of the Special Issue, then synthesizes the published papers into coherent thematic threads before outlining key takeaways and future research directions for advancing organic waste recycling as a pillar of sustainable and resilient agriculture [11].

2. An Overview of Published Articles

Contribution 1 addresses the recycling of animal-derived organic wastes in agriculture by evaluating the short-term effects of cattle manure and poultry litter application on soil chemical properties and bacterial communities. Based on a 60-day field experiment, the study demonstrates that poultry litter induced more pronounced changes in soil chemistry and microbial community structure than cattle manure, particularly through increases in soil organic carbon and phosphorus availability and reductions in soil acidity. The results indicate that the observed shifts in soil microbiota were primarily driven by changes in soil chemical properties rather than by the direct transfer of microorganisms from the applied residues. Overall, this contribution highlights the potential of recycling organic waste as an effective strategy to improve soil fertility while supporting sustainable agriculture.

Contribution 2 explores the valorization of municipal solid waste through the conversion of its combustible and compostable fractions into biochar and compost for agricultural use. The study is based on a controlled pot experiment in which sunflower was cultivated for 75 days in soils amended with municipal solid waste–derived biochar and compost applied individually and in combination at different doses. The results demonstrate that the combined application of biochar and compost, particularly at a medium dose, led to marked improvements in key soil health indicators, including soil organic matter, cation exchange capacity, water-holding capacity, and the availability of essential nutrients. These improvements translated into enhanced sunflower growth, yield, and oil content, with performance comparable to that achieved using conventional chemical fertilizers. Importantly, the study shows that increasing amendment rates did not necessarily result in proportional yield gains, highlighting the importance of optimized application strategies.

Contribution 3 presents an innovative approach to recycling industrial organic waste by valorizing deinking paper sludge from the paper recycling industry for the production of organo-mineral fertilizers. The study combines acid-hydrolyzed deinking sludge with poultry litter ash to formulate PK-type fertilizers enriched with organic matter, secondary nutrients, and micronutrients. The resulting fertilizers were comprehensively characterized in terms of nutrient composition, heavy metal content, and phosphorus speciation, followed by an eight-week soil incubation experiment to assess their behavior under controlled conditions. The results demonstrate that the fertilizers met regulatory requirements for organo-mineral fertilizers and provided a substantial proportion of potentially bioavailable phosphorus, with a gradual release pattern favorable for reducing nutrient losses. Soil incubation studies revealed improvements in soil pH, organic carbon content, phosphorus availability, and microbial activity, as indicated by increased catalase activity.

Contribution 4 presents a GIS-based geospatial modeling approach to assess the risk of agricultural microplastic transport associated with the land application of biosolids. The study combines spatial data on rainfall, soil properties, land use, and proximity to waterways to map the relative risk of microplastic movement through three pathways: surface runoff, retention in soil, and groundwater infiltration. The results show that the risk of microplastic pollution is highest in agricultural areas located near rivers, in regions with higher rainfall, and in soils that favor particle mobility. By clearly identifying high- and low-risk zones, the study demonstrates how spatial risk mapping can support more informed decisions on where biosolids can be safely applied and where their use may increase the risk of microplastic pollution.

Contribution 5 describes the development of a circular, microbe-based biostimulant that combines a plant growth–promoting Bacillus strain with winery flotation wastewater as a low-cost growth medium. A bacterial isolate from the grapevine rhizosphere, named Bacillus sp. 10/R, was thoroughly analyzed for its biochemical characteristics, enzyme production, and plant growth–promoting traits. At the same time, winery flotation wastewater was assessed as a cultivation substrate by tracking nutrient use and enzyme production during bacterial growth. The resulting bacterial cultivation broths were then tested as seed treatments to examine their effects on barley germination and early seedling growth. The findings show that Bacillus sp. 10/R has a broad enzymatic capacity and strong pectin-degrading activity, supporting its potential as a plant growth–promoting microorganism. Winery flotation wastewater has been shown to promote bacterial growth and metabolite production while reducing the wastewater’s organic nutrient content. The authors therefore suggest further research to better understand plant responses, optimize application methods and dosage, and evaluate the technical and economic feasibility of this biostimulant approach under greenhouse and field conditions.

Contribution 6 presents a study on Opuntia spp., with a particular focus on residue valorization and circular economy practices in Mexico. The article combines a bibliometric analysis of international literature with a critical review of applied Mexican studies to identify research trends, regional gaps, and opportunities for closing production cycles through the reuse of cladode residues. The study shows that three main valorization pathways are composting, anaerobic fermentation, and direct soil application of Opuntia residues, with composting being the most popular. The authors argue that these practices fit well with smallholder farming systems and circular economy principles, but their wider use is limited by the lack of standardized methods, long-term field validation, and policy support. Overall, the article highlights composting and residue reuse as practical strategies to close nutrient cycles and improve the sustainability of Opuntia-based production systems in Mexico.

Contribution 7 explores strategies to reduce nitrogen losses during sewage sludge composting by using additives such as garbage enzyme, biochar, and pelelith. The research highlights that combining garbage enzyme with biochar or pelelith can improve nitrogen retention, enhance ammonia-oxidizing microbial activity, and promote more efficient nitrogen transformation. These additives also influence the structure and function of ammonia-oxidizing microbial communities, contributing to higher-quality compost and reduced environmental impacts. The findings suggest that integrating enzymatic and carbon-based amendments offers a promising, sustainable approach to improve composting efficiency and nutrient management, while further studies are needed to fully understand the underlying microbial mechanisms.

Contribution 8 presents an innovative approach to evaluating compost maturity and heavy metal passivation in biochar-amended pig manure using self-organizing maps (SOM) integrated with three-dimensional excitation–emission matrix fluorescence spectroscopy. The research examined different biochar dosages and their effects on compost quality, organic matter transformation, and Cu/Zn stabilization. The findings demonstrate that higher biochar additions accelerate compost maturation and enhance heavy metal passivation, though moderate dosages can achieve comparable results while offering better cost-effectiveness. By combining SOM with advanced spectroscopic techniques, the authors successfully tracked organic matter evolution and identified key microbial communities responsible for metal stabilization. This work provides a novel methodology for real-time compost quality assessment and offers practical insights for optimizing biochar application in livestock waste management systems.

Contribution 9 examines biomethane production in the Mediterranean region as a renewable energy solution. The authors evaluate how anaerobic digestion can convert organic waste, such as olive pomace, citrus peel, grape residues, livestock manure, and municipal biowaste, into clean energy and valuable fertilizer. The study highlights the dual benefits of this technology: producing biomethane as a replacement for natural gas while creating digestate that improves soil health in areas affected by degradation and desertification. The review discusses upgrading technologies that transform biogas into high-quality biomethane, along with policy frameworks like the EU Renewable Energy Directive that support sector growth. Case studies from Italy, Spain, France, Greece, and Tunisia demonstrate the practical application of these systems in rural and island communities. Despite the clear potential, challenges remain, including variable feedstock availability, limited infrastructure, and inconsistent policies across countries. The authors conclude that biomethane can play a central role in achieving energy independence, reducing greenhouse gas emissions, and supporting sustainable agriculture in the Mediterranean within a circular economy approach.

3. Conclusions and Future Perspectives

3.1. Conclusions

The contributions collected in this Special Issue confirm that recycling organic waste streams into agriculture can simultaneously support soil functioning, nutrient cycling and productivity—provided that agronomic benefits are pursued together with rigorous risk management. Across the presented studies, a consistent message emerges: organic amendments and derived products (e.g., composts, digestates, organic–mineral fertilizers and biochar-based materials) can improve soil fertility indicators, enhance nutrient availability, and, in several cases, contribute to stabilizing soil organic matter or improving soil physical properties. At the same time, the “circularity dividend” is not automatic. Outcomes depend on feedstock origin, processing technology, product stability, application rate and timing, as well as site-specific conditions such as soil type, climate and management history.

Importantly, the studies also underscore that the safe return of organic residues to land must address multiple, partly interacting hazards. These include the persistence and mobility of potentially toxic elements, the presence of pathogens and antibiotic resistance determinants, the fate of emerging contaminants and microplastics, and climate-relevant gaseous emissions during storage and after field application. Several contributions point toward practical pathways to mitigate these risks, including improved stabilization and sanitation during processing, blending strategies (e.g., organic–mineral formulations), and decision-support approaches that optimize sourcing and allocation of organic resources at the landscape scale. Overall, the Special Issue supports a shift from viewing organic wastes as uniform “fertilizer substitutes” toward treating them as engineered, quality-controlled soil inputs whose performance and safety must be demonstrated within local agroecosystems and governance frameworks.

3.2. Future Perspectives

Building on the evidence and challenges discussed in this Special Issue, several priorities can guide research and implementation:

• Long-term, system-level field evidence. Multi-year field trials across contrasting soils and climates are needed to quantify yield stability, soil carbon trajectories, nutrient balances and resilience outcomes under repeated applications, including interactions with cropping systems and reduced mineral fertilization strategies.
• Harmonized quality metrics and fit-for-purpose standards. Comparable analytical protocols and transparent criteria are needed for product maturity/stability, nutrient release patterns and contaminant thresholds (including emerging pollutants and microplastics). Linking these metrics to intended agronomic functions (fertility building, carbon management, remediation) would strengthen certification and market confidence.
• Integrated risk assessment for multiple stressors. Future work should move beyond single-contaminant approaches toward frameworks that combine chemical hazards (potentially toxic elements, organic pollutants), biological risks (pathogens, antibiotic resistance) and physical contaminants (microplastics), accounting for co-occurrence, transformation during processing and bioavailability after land application.
• Emission-aware circularity. Nutrient-loop closure should be evaluated together with greenhouse gas and reactive nitrogen emissions (CH₄, N₂O, NH₃) along the full chain—from collection and treatment to storage, transport and field application. Mitigation options (e.g., covers, additives, incorporation timing, biochar co-application) deserve standardized testing under realistic conditions.
• Design of advanced products and blends. Organic–mineral fertilizers, biochar-enhanced amendments and tailored compost/digestate formulations offer opportunities to improve nutrient use efficiency and reduce losses. Research should clarify mechanism-based design rules (e.g., sorption, pH buffering, microbial interactions) and quantify trade-offs between performance, cost and safety.
• Spatial planning and decision support at the landscape scale. Because feedstock availability, transport constraints and environmental sensitivity vary across regions, models combining GIS, logistics, soil vulnerability and regulatory limits can support optimal allocation of organic resources. This is crucial to avoid local over-application of phosphorus or contaminants while maximizing benefits where soils are most responsive.
• Governance, adoption and economics. Key barriers include stakeholder acceptance, regulatory harmonization, traceability and liability, and stable business models for waste-derived products. Coupling agronomic trials with techno-economic and life-cycle assessments can translate scientific findings into implementable circular strategies.

Taken together, these directions point toward an integrated agenda in which organic waste recycling is treated as a managed, evidence-based intervention—optimizing agronomic value while ensuring environmental protection and societal trust.