Conditioning Biomass for Biogas Plants: Innovative Pre-Treatment and Digestate Valorization Techniques to Enhance Soil Health and Fertility

Abstract

In line with the concept of sustainable agriculture, efforts should be made to increase the green energy yield and minimize the environmental impact of mineral fertilizers, maintaining high agricultural productivity. In alignment with the principles of sustainable development, plant biomass-based green energy is considered promising. A deep understanding of and enhancements to the anaerobic digestion process using plant biomass, along with digestate post-treatment for regenerative agriculture improvements, are key elements to achieve sustainability goals. This article describes innovative methods for plant biomass pre-treatment aimed at enhancing biogas yield and the fertilizing potential of the obtained digestate. Moreover, valuable insights into the process of digestate conditioning for valorization are discussed. Among these, separation and digestate stabilization techniques are emphasized. Furthermore, this article provides a comprehensive source of knowledge on the impact of digestate on soil quality, fertility, soil organic carbon sequestration, and microbiota. The findings contribute to a broader understanding of how digestate impacts regenerative agriculture.

1. Introduction

Optimizing biogas plant processes is essential for managing organic waste and producing renewable energy, especially given the need to reduce greenhouse gas emissions and decrease dependence on fossil fuels [1]. At the core of these actions lies anaerobic digestion, which transforms agricultural, food, and animal waste into biogas, providing both electricity and heat [2,3]. However, during this process, digestate is also generated, a by-product frequently treated as waste yet holding significant potential in the circular economy [4,5]. Because it contains key nutrients such as nitrogen, phosphorus, and potassium, digestate can act as a natural organic fertilizer, a viable alternative to synthetic fertilizers that helps minimize harmful environmental effects. Its composition depends heavily on the substrates used in biogas production. Besides the microbial biomass responsible for methanogenic fermentation, digestate also comprises undigested organic compounds and mineral substances. These remain in quantities similar to those present in the feedstock, constituting around 90–97% of the initial input [6]. Naturally, any contaminants in the raw materials also end up in the digestate, which is why the quality of the digestate closely reflects the quality of the inputs [7,8].

Table 1. Averaged composition of the solid and liquid digestate fractions from an agricultural biogas plant [6].

Parameter (Unit)	Solid Fraction	Liquid Fraction
Dry matter, %	22.00–27.0	2.70–4.30
Organic dry matter, %	89.00–94.5	58.00–62.00
Total nitrogen, %	0.40–0.80	0.29–0.75
Ammonium nitrogen, %	0.08–0.52	0.28–0.38
Phosphorus, %	0.10–0.28	0.03–0.05
Potassium, %	0.12–0.69	0.50–0.62
Calcium, %	0.22–0.43	0.05–0.07
Magnesium, %	0.06–0.17	0.01–0.02
Cadmium, mg Cd/kg	0.25–0.50	0.55–0.71
Chromium, mg Cr/kg	1.15–4.55	4.52–6.73
Nickel, mg Ni/kg	1.07–9.45	11.60–18.50
Lead, mg Pb/kg	0.50–2.16	4.12–6.01
Zinc, mg Zn/kg	27.8–105.0	9.40–11.5
Copper, mg Cu/kg	7.90–27.90	1.50–1.74

presents the average composition of the solid and liquid digestate fractions from an agricultural biogas plant operated in Poland [6].

Within ongoing efforts to refine biogas plant operations and advance environmental sustainability, digestate management has emerged as one of the most pressing challenges [9,10]. This issue has gained further prominence through the RePower EU initiative, which aims to achieve 35 billion cubic meters of biomethane production by 2030. In this context, digestate processing has been identified as a key approach for optimizing by-product handling. A critical step involves solid–liquid separation, followed by additional advanced technologies that enable further treatment of each fraction [9]. Despite the many benefits of using digestate in agriculture, implementing it effectively presents numerous hurdles. The variability in organic and mineral content significantly bothers its widespread adoption as a natural fertilizer [11]. Because the substrates for anaerobic digestion can vary and biogas plants operate under different conditions, the resulting fluctuations in digestate composition make precise fertilization challenging and necessitate adjustments in application techniques. In many cases, developing new methods for digestate storage and application is essential to minimize nutrient losses and enhance fertilizer efficiency [12].

Conditioning the biomass before anaerobic digestion can have a significant impact on both biogas yield and digestate quality [13,14]. By applying a range of pre-treatment techniques such as mechanical, biological, chemical, or thermal actions, operators can enhance nutrient release, improve the breakdown of organic matter and increase the availability of crucial molecules for the microbial community. For instance, particle size reduction broadens the contact surface for microbes, boosting the overall digestion process [15]. Meanwhile, high-temperature treatments not only break down complex, hard-to-degrade compounds but also help disinfect the incoming feedstock, particularly when working with substrates of animal origin [16]. When using digestate as a natural fertilizer, post-digestion processing also becomes essential. Composting is one potential method that refines digestate structure and stabilizes its composition; however, it can lead to ammonia emissions and carbon losses in the form of CO₂ [17]. Consequently, there is growing interest in alternative approaches such as further fermentation of digestate to produce bioethanol, thermal conversion to obtain syngas, and biochar or recirculation within the biogas plant to tap any remaining methane potential. These strategies collectively expand the scope of digestate utilization, enhance process efficiency, and reduce environmental impacts.

Sustainable digestate management and innovative biomass conditioning are central to enhancing biogas plant efficiency, reducing environmental impacts and advancing circular economy goals. By applying these methods, operators can not only improve soil health and fertility but also significantly lower greenhouse gas emissions, which is vital in addressing climate change. Effective digestate handling can make biogas facilities more sustainable, reducing their ecological footprint and supporting environmentally responsible farming practices. Backed by suitable legal frameworks, these technologies can enhance biogas production, cut emissions, and improve soil quality, thereby contributing to the broader ambitions of global climate and environmental policies.

The aim of this research was to discuss and analyze innovative methods of pre-treatment of plant biomass that increase biogas production efficiency and enhance the fertilizing value of the resulting digestate. The novelty of this publication lies in its comprehensive approach, which combines innovative biomass pre-treatment techniques with advanced methods of digestate conditioning and stabilization, thereby enabling its effective integration into regenerative agriculture. The proposed solutions align with the latest achievements in biogas plants based on green biotechnology, where the goal is to maximize green energy while simultaneously closing the nutrient cycle and improving soil health. The article demonstrates that the focus should shift from solely intensifying biogas plant processes to also improving digestate processing methods for a conscious and targeted application in circular agriculture.

2. Methods of Conditioning Plant Biomass

Plant biomass processing in agricultural biogas plants is problematic due to the high content of lignocellulose. Lignocellulosic biomass should be subjected to pre-treatment processes to depolymerize cellulose and lignin, which provide plant cells with rigidity and resistance to unfavorable conditions. Pre-treatment methods are focused on increasing the availability of the biomass surface for microorganisms involved in methane fermentation. In addition, the purpose of pre-treatment is to break down complex polymeric structures. The main methods used to improve the degradation of plant biomass are mechanical, biological, thermal, chemical, and hybrid technologies [18]. The selection of appropriate conditioning methods should be adapted to the substrate characteristics. What is more, each technological process requires optimization depending on the type of feedstock and the intended purpose. This is particularly important when choosing a method for pre-treatment of plant biomass, such as energy crops, fruit pomace, straw, and agricultural and forest residues, where the organic carbon content is different. This is especially pertinent considering that most biogas plant operating within the European Union utilize plant biomass as the primary substrate for biogas production [19]. Biomass conditioning is one of the key aspects of agricultural biogas plant operation. A properly processed feedstock affects the quality of the obtained biogas and digestate, as well as their subsequent management (Figure 1).

2.1. Mechanical Pre-Treatment

Mechanical methods aim to degrade the structure of plant biomass to increase the surface accessibility and break down complex structures that extend the hydrolysis time. Mechanical methods are the first step in processing feedstocks before the digestion process. Nevertheless, it should be considered that mechanical methods are often associated with various limitations and challenges, such as insufficient processing of lignocellulosic biomass, high energy consumption, and, in some cases, the necessity to purchase and operate expensive processing equipment, which ultimately impacts the overall profitability of the process [20]. Nonetheless, selecting the appropriate conditioning technology is crucial, as it represents one of the initial and most important stages of substrate preparation. Implementing necessary optimizations can enhance biogas production and reduce retention time in the reactor.

Among mechanical processing methods, homogenization can be distinguished, e.g., assisted by dispersion. This innovative method reduces the size of biomass particles, liquefies it and, thus, improves the fermentation efficiency. The use of a dispersant effectively cleaves bonds in the substrate under the influence of stresses and pressure drop. Another type of feedstock homogenization is ultrasonic homogenization (cavitation). It is applied for complex mixtures to disintegrate their particles. The range of ultrasonic waves is 18–50 kHz. The advantages of this type of conditioning include stable process conditions and high efficiency with the possibility of producing good quality biogas [21]. Another frequently mentioned method of mechanical pre-treatment is milling. Its purpose is to reduce the size of the substrate and at the same time reduce polymerization. Various techniques are used to achieve these goals, including wet milling.

However, despite the advantages of mechanical pre-treatment techniques, several significant limitations hold up widespread application, particularly in the processing of lignocellulosic biomass. The high energy consumption associated with mechanical methods such as milling, extrusion, and ultrasonic homogenization remains a critical barrier to economic feasibility. For instance, processes like milling require a high energy input, which increases operational costs and limit scalability. Additionally, the maintenance of specialized equipment can be too expensive for many facilities, particularly smaller biogas plants. The efficiency of mechanical methods in breaking down lignocellulosic structures is often insufficient to achieve satisfactory hydrolysis rates and requires the implementation of supplementary methods to enhance biogas production. What is more, among mechanical techniques, screw extrusion is often used to process wet biomass. This process applies heat, pressure, and shear for biomass conditioning. This results in improved biodegradability often with increased biogas yield [22]. Such mechanical pre-treatment is particularly useful before the anaerobic digestion of plant substrates such as corn and rice and wood or pulps processing [23].

Al Afif and Pfeifer [24] determined the effect of cotton stalk fragmentation on methane production. The authors used a hammer mill and a blender for pre-treatment. They obtained 0.5, 3, 10, and 30 mm long stalks, which they fermented in mesophilic conditions for 48 days. The highest methane content was obtained from the most fragmented samples, i.e., 0.5 mm cotton stalks. In addition, an increase in methane content was observed in 0.5 mm and 3 mm samples of 20% compared to mechanically unprocessed samples. Moreover, the retention time of the batches was shortened to 25 days [24]. Other studies focused on mechanical processing of landscape grasses. The authors of one study used a 55 kW cross mill, a ball mill driven by a 45 kW engine, and a mower. The digestion process was carried out at 45 °C for 50 days. Mechanical pre-treatment effectively accelerated the degradation of the feedstocks and increased the biogas quality compared to unprocessed samples. Due to the high lignin and cellulose contents, the pre-treatment also proved effective in depolymerization. In particular, the use of a ball mill for conditioning of grass gave positive results in the energy balance of the entire process [25]. In turn, Moretti et al. [26] proved in their research that separation of biomass by wet pressing is an effective pre-treatment method which improves anaerobic digestion efficiency. Authors used biological waste to study the methanogenic potential. Pre-treated waste improved the biogas production process.

2.2. Biological Modification of Biomass

The use of microorganisms for processing biomass, including lignocellulosic biomass, is crucial, especially when the efficiency of other methods is not satisfactory. A consortia of microorganisms can be applied to improve the hydrolysis process or increase methane production, although the selection of bacteria and fungi for a given type of feedstock and digestion conditions is an important issue. Some authors consider biological processes to still be low-efficient, although, they also emphasize their advantages, such as lower operating costs and ease of installation [23]. Prasad et al. [14] found that biological methods require low energy input and do not generate as much pollution as other processing methods. Furthermore, biological methods do not pose the same issues as the use of chemical additives. The anaerobic digestion can be enhanced through the implementation of two-stage fermentation, anaerobic or aerobic pre-treatment, and enzymatic additives [27]. The basic feature of biological conditioning with its limitations and optimization paths are presented in Figure 2.

Bioaugmentation involves the inoculation of the digester with preselected and cultivated microorganisms, typically cellulolytic bacteria or mixed microbial cultures that function synergistically [28].

Objectives of bioaugmentation as a biological conditioning technique are as follows:

• Improvement of the activity of methane digestion microorganisms;
• Increase in biogas yields;
• Acceleration of hydrolysis, the bottleneck of the substrate processing during anaerobic digestion;
• Enhancement of biomass degradation efficiency [28,29].

Anaerobic fungi convert polysaccharides to simple sugars as a result of bioaugmentation. The conversion leads to the production of lactate, ethanol, hydrogen, and acetate. The challenge is batch cultivation of these microorganisms, which is expensive and time consuming. In addition, the culture media should be properly prepared, containing buffers, carbon and nutrient sources, mineral salts, supplements, and reducing agents [29]. Bacterial strains are used more frequently due to their shorter multiplication time, rapid enzyme production, and ease of cultivation. Among the bacteria that enhance the feedstock conditioning, strains of Clostridium, Bacteroides, Firmicutes, and Pseudomonas, known for their production of cellulolytic enzymes, are commonly cited [30]. More and more studies are focused on determining the suitability and characterization of strains that can improve bioaugmentation results. For instance, Poddar and Khardenavis [31], in their genomic analysis of selected bacteria used in bioaugmentation, observed that the Serratia marcescens EGD-HP20 strain exhibits significant potential for application in bioaugmentation to enhance methane yield and facilitate the hydrolysis of protein-rich waste.

Among the biological methods of processing feedstocks is the implementation of enzymes. In general, enzymes can be divided into three groups, which results from the substrate specificity. The first group consists of lignolytic enzymes, produced most commonly by fungi, including white rot fungi (WRF), Actinomycetes, and some Proteobacteria. This type of enzyme focuses on the depolymerization of lignin. In turn, the action of cellulolytic enzymes results in the hydrolysis of cellulose to monomers. Cellulose decomposition can occur through endocellulolytic enzymes—acting on glycosidic bonds within polysaccharide chains and exocellulolytic enzymes, which cleave monomers located at the ends of the chain. On the other hand, hemicellulolytic enzymes include glycoside hydrolases and carbohydrate esterases, which hydrolyze glycosidic and ester bonds, respectively [30]. In order for the implementation of enzyme preparations to be effective, several issues need to be considered, including enzyme concentration and origin, pre-treatment conditions such as time, temperature and pH, and feedstock specificity [29]. Furthermore, it is crucial to gain knowledge of the reactions catalyzed by the selected enzyme while also accounting for possible undesirable transformations.

2.3. Thermal, Chemical, and Hybrid Methods

Processing feedstocks at different temperatures increases biomass surface availability during digestion and is commonly used in biogas plants due to its simplicity. Moreover, thermal treatment has been shown to reduce substrate viscosity and pathogen content in the feedstock, which is crucial for the subsequent use of the digestate. Thermal pre-treatment of biomass is generally divided into thermophilic and mesophilic treatment (

Table 2. Comparison of thermo- and mesophilic pre-treatment processes (based on Kasinath et al. [19]).

Temperature Conditions	Thermophilic Pre-Treatment	Mesophilic Pre-Treatment
Temperature range	49 °C–70 °C	30 °C–35 °C
Advantages of the process	- shorter feedstock processing time; - high biogas yield, - efficient removal of organic matter; - possibility of processing at higher organic load; - better removal of pathogens.	- easier process optimization; - stable biogas production process; - lower energy requirements, resulting in lower processing costs.
Disadvantages of the process	- requires high energy input; - higher risk of process inhibition due to temperature changes.	- longer processing time, especially with higher organic content in the feedstock; - limited pathogen removal efficiency at lower temperatures.
Scale of application	<10% of fermentation reactors worldwide	>90% of fermentation reactors worldwide

). However, thermophilic processes can also occur at temperatures significantly higher than 70 °C. High-temperature pre-treatment (HTPT) requires the temperature to be above 140 °C and is highly beneficial for the processing of lignin and cellulose [32]. Psychrophilic fermentation conditions can also be distinguished, although the temperature at which the process takes place, that is >25 °C, causes methane losses and is less effective in removing pollutants compared to meso- and thermophilic fermentation [33].

There is an undeniable positive effect of thermal conditioning on the amount of methane produced, hydraulic retention time, and lignocellulosic fiber content. For instance, the research by Rajput et al. [34] focused on the possibility of implementing thermal pre-treatment of substrates such as sunflower meal and wheat straw. Co-digestion of these two substrates gave positive results. Moreover, in the case of pre-treatment at 180 °C, an increase in biogas yield by 94.3% was observed compared to the control sample. The processing time was significantly shortened, and the amount of lignin and hemicellulose after pre-treatment and digestion decreased [34].

On the other hand, hydrothermal pre-treatment is applied to substrates with high moisture content. The increase in temperature and pressure stimulates the decomposition of bonds and, thus, improves the accessibility of the surface area. Hemicellulose undergoes dissolution into sugars, acids, aldehydes, and ketones, whereas lignin depolymerization proceeds at a slower rate, necessitating higher temperatures to achieve satisfactory results, often exceeding 180 °C. Hydrothermal pre-treatment can take place under supercritical and subcritical conditions [35].

Meanwhile, chemical processing in particular involves the large-scale use of acids. For instance, chemical pre-treatment of tomato pomace is an economically advantageous, frequently used method that allows for the breakdown of cell walls. On the other hand, the use of acids can lead to corrosion of equipment and poses a threat to the environment [36]. In addition, chemical conditioning involves the use of alkaline compounds and ionic liquids. The most commonly utilized alkalis for biomass pre-treatment are NaOH and Ca (OH)₂, which stimulate the dissolution of hemicellulose and lignin, improving their biodegradability. Meanwhile, among the frequently applied acids are sulfuric acid, phosphoric acid and hydrogen chloride. With regard to ionic liquids, such as N-methylmorpholine-N-oxide, they exhibit considerable potential for facilitating cellulose degradation [27].

Akbay et al. [37] determined the effect of various pre-treatment methods, including mechanical treatment by ultrasound at a frequency of 37 kHz, microwave radiation at a power of 200 and 400 W, chemical pre-treatment using 0.1–1 M H₂SO₄ and 0.1–1 M NaOH, thermal pre-treatment by autoclaving and hybrid methods, ultrasonic treatment with acid processing, and ultrasonic treatment with alkaline treatment. The substrate was solid food waste (apple, black carrot, and pomegranate), which were co-digested with sewage sludge. The best results were obtained after ultrasonic pre-treatment with alkaline treatment, where the methane yield increased by 49% due to enhanced porosity [37].

The research conducted on sewage sludge indicates that magnetic preconditioning of sewage sludge using low-intensity magnetic fields may be an effective method for improving the efficiency of biomethane production in the anaerobic digestion process, while the use of higher magnetic intensities may have adverse effects. High-throughput sequencing analysis revealed that the magnetic field influences the composition of the microbial community, causing specific shifts in populations of microorganisms responsible for anaerobic digestion [38].

Nevertheless, it should be noted that the application of hybrid methods may not yield the desired results. For instance, the study conducted by Show et al. [39] on the potential of combining autoclaving at 121 °C for 15 min with preliminary chemical treatment using 2% and 5% NaOH prior to the digestion of water hyacinth demonstrated that the NaOH concentration had a greater impact on biogas production than the additional thermal processing. The latter did not significantly enhance biomass degradation or biogas yield [39]. Therefore, the selection of the optimal method requires extensive research into different pre-treatment combinations. Similarly to mechanical and biological pre-treatment technologies, thermal, chemical, and hybrid processes also have certain limitations. The application of thermal methods, aside from the long-term requirement for high energy input, remains unstandardized in terms of optimal duration and temperature condition [22]. In the case of chemical methods, a major challenge is the potential formation of toxic by-products resulting from the specific chemical compounds used in organic matter decomposition, as well as their neutralization and the overall efficiency of this process on an industrial scale [20]. Additionally, the use of acids may lead to technical issues due to their corrosive and toxic properties [22].

A potential solution to the economic and efficiency challenges of individual methods lies in optimizing the conditioning process for specific substrate types, which necessitates extensive analysis and large-scale studies. In biogas technologies, the increasing adoption of hybrid methods is also expected to enhance the efficiency of waste conversion into biogas.

2.4. Optimization of Anaerobic Digestion

The efficiency of anaerobic digestion can be increased by implementing improved biogas production technologies and conditioning processes, and by optimizing process parameters. The key goal of research on new technologies is to obtain methods and concepts that fit into the idea of sustainable development, allowing for increased methane production and expanding the possibilities of using biogas as a renewable energy source [19]. According to Rocha-Meneses [40], the implementation of modeling and optimization systems in anaerobic digestion provides economic and environmental benefits. Modeling applied in the anaerobic digestion process includes, among others, reaction kinetics, fluid dynamics and neural networks. Another important issue is the optimization of parameters, which involves adjusting the C/N ratio, organic loading rate (ORL), temperature, pH, moisture, retention time, and mixing speed [33]. To select the appropriate optimization method, it is essential to first characterize the substrates used in biogas plants (Figure 3).

2.5. Increasing the Efficiency of Biogas Production Through Co-Digestion and Conditioning Methods

Co-digestion is often used to optimize the anaerobic digestion. At least two different substrates are applied to the reactor, which ensures stable conditions and improves C/N ratio. Moreover, the presence of co-substrate is an additional source of nutrients for methanogenic microorganisms [34]. Numerous analyses demonstrate the benefits of using co-substrates to optimize the anaerobic digestion process. For instance, studies by Tian et al. [41] confirm the validity of using co-substrates in anaerobic digestion. The research was conducted on pig manure and rice straw with different variable parameters, such as inoculum and substrate concentrations. A 30-day anaerobic digestion in mesophilic conditions allowed them to determine the effect of variables on biogas production efficiency and bioconversion stability. The authors report that at a manure-to-rice straw ratio of 1:5, the accumulation of volatile fatty acids increased, which had a significant effect on methane production efficiency [41]. Other tested co-substrates were microalgae biomass and Miscanthus × giganteus silage fermented in mesophilic conditions at HRT for 40 days. The study conducted by Dębowski et al. [42] in 2022, which tested various ratios of the dry matter of the mentioned substrates, demonstrated that to increase biogas production, the percentage of microalgae in the feedstock should be 40%. However, the highest methane content in biogas was obtained as a result of anaerobic digestion of only microalgae, without the addition of silage [42].

Pre-treatment methods of feedstocks are particularly important when the substrate for conversion contains significant amounts of lignocellulose. In these instances, pre-treatment enhances the performance of hydrolysis of complex compounds [38]. Lignocellulosic biomass presents a significant challenge due to the complexity of its substrates, which include phenolic polymers such as lignin and crystalline cellulose—a polysaccharide. These substrates vary considerably in terms of morphology, moisture content, organic compound composition, and solid fraction [14]. Consequently, further research is required to determine the most optimal processing method for a specific feedstock.

Conditioning methods that improve biogas production efficiency include all types of pre-treatment. Mechanical and chemical methods are generally most frequently used. These technologies aim to reduce the size of substrate particles, thereby increasing the contact surface between the feedstock and the bacteria responsible for the biochemical conversion of organic matter into biogas. What is more, the previously mentioned research by Akbay et al. [37] confirms that chemical reagents appropriately selected for the substrate, such as acetic acid, can stimulate the decomposition of lignocellulosic biomass by swelling it. The researchers used the aforementioned chemical compound and mechanical pre-treatment to pre-process corn stover, which increased biomethane yield by over 47%.

2.6. Reducing the Retention Time of Substrates in the Reactor

The retention time of the substrate is primarily influenced by its specificity and digestion conditions, including temperature. In the case of psychrophilic processes, it is assumed that the hydraulic retention time (HRT) values are the highest, reaching about 80 days. In turn, the higher the temperature, the more efficient the process is and requires a shorter time of substrate retention in the reactor. This means that in mesophilic conditions, HRT can be more than twice as short, i.e., about 30–40 days, while in thermophilic conditions, hydraulic retention time can only be 15 days. The formulas describing the hydraulic and solid retention time (SRT) are presented as (1) and (2). HRT refers to the average retention time of the substrate in the reactor, while SRT refers to the retention time of solids [33].

$$HRT={\displaystyle \frac{V\left(bioreactor\right)}{V\left(feedstock\right)/t}} \left[t/day\right]$$

(1)

Hydraulic retention time

$$SRT={\displaystyle \frac{m\left(dry matter, bioreactor\right)}{m\left(dry matter, feedstock\right)/t}} \left[t/day\right]$$

(2)

Solid retention time

Biological pre-treatment can be applied to shorten the retention time of feedstocks in the reactors. The duration of the pre-treatment process depends on the specific method implemented. The use of fungi, such as white or sort rot fungi, requires significantly more time compared to the application of bacteria or enzyme preparations, which can yield satisfactory results within a few hours of pre-treatment [14]. In addition, other conditioning technologies such as thermal, chemical, and hybrid methods of pre-treatment can significantly contribute to reducing hydraulic retention time [27]. An example of this is the research conducted by El Gnaoui et al. [43]. The application of thermal and biological pre-treatment of food waste significantly shortened lag phase time and increased biogas production rate. Moreover, it was observed that the maximum methane yield enhanced and amounted to 674.49 mL CH₄/g VS. Meanwhile, both thermal and acid conditioning of coffee pulp prior to anaerobic digestion allow for the reduction in hydraulic retention time. The experimental conditions of Nava-Valente et al. (2023) [44] included an hourly thermal pre-treatment at temperatures ranging from 50 °C to 90 °C, chemical conditioning with acetic acid at concentrations ranging from 2.5% to 10%, and subsequent neutralization with NaOH. In the case of thermal pre-treatment at 90 °C, the HRT was shortened by 5 days compared to the untreated feedstock [44].

It is assumed that high-rate anaerobic systems cause an increase in biogas yield and a reduction in retention time. Among the high-performance technologies, systems based on the operation of various types of reactors can be mentioned. Anaerobic contact reactors use continuous mixing with biomass recirculation, anaerobic baffled reactors contain baffles inside the reactor, and anaerobic membrane bioreactors utilize membranes [40]. Anaerobic membrane reactors (AnMBR) have many advantages. In addition to enabling the use of this type of reactor at lower HRT, these systems also perform well under higher organic loads and can contribute to an increase in the methane content of biogas. As reported by Ariunbaatar et al. [45], the application of an anaerobic bioreactor with polyvinylidene (PVDF) ultrafiltration membrane modules for the digestion of mixed food waste (including meat, cheese, fruits and vegetables, among others) under optimized conditions resulted in a reduction in HRT from 20 days to just 1 day.

In addition to the reactor design, the use of co-digestion also has an impact on shortening the digestion time. This is especially important when lignocellulosic biomass is used as one of the substrates. For instance, Chen et al. [46] co-digested corn stover and cow manure using a gradient anaerobic digestion reactor (GADR). The HRT ranged from 15 days to 30 days. The highest volumetric biogas production efficiency (2.73 L/L/d) was noted for HRT over 15 days.

3. Digestate Conditioning

A broad range of techniques is available for separating solid particles from liquids. Depending on factors such as the contaminant load, particle size distribution, and other physicochemical properties of the two phases, each technique operates according to a distinct mechanism and demonstrates varying efficiency in the solid fraction separation. Digestate is the material generated during anaerobic digestion, particularly in biogas facilities. It is a complex organic medium containing both a solid and liquid component. The ratio of these two phases in digestate fluctuates, depending on the feedstock used, process conditions, and the specific technology adopted for phase separation. In many scenarios, separation of the solid and liquid fractions is essential not only from a technological point view but also to address environmental requirements [47]. It also allows for the recovery of valuable constituents [48], which can be redeployed in processes such as biogas production, organic fertilizer manufacturing, or water treatment. The solid fraction may be used as organic fertilizer or be integrated into composting applications, while the liquid fraction can undergo further treatment and be used in technological processes or agricultural fertilization. To maximize separation efficiency and minimize operating costs, biogas installations frequently implement multiple methods such preliminary sedimentation, filtration, and centrifugation.

3.1. Solid–Liquid Separation Techniques

Separating the solid and liquid phases in digestate is a critical operation in biogas facilities and other biomass processing installations. A variety of methods can be employed to achieve this operation. The choice of the most suitable technique depends on the specific properties of the material and the required purity of separation, making it a decisive factor in overall process efficiency [10,49,50]. Also, the quality monitoring of the separation stage is vital to ensure compliance with environmental regulations and to optimize biogas production outcomes.

3.1.1. Filtration

Filtration is one of the most straightforward techniques for separating solid and liquid phases. In this process, digestate is passed through a filtration medium that captures solid particles while permitting the liquid to flow through. Various filtration approaches can be employed such as mechanical filters, filter presses or pressure filters [51]. When applied to digestate, filtration can be fairly effective; however, its efficiency depends on the particle size and the properties of the filtration medium. Depending on the system’s throughput requirements, filter presses can be implemented in both small-scale and large-scale biogas plants. It is also important to consider that filtration may demand relatively high energy input and can require periodic cleaning or replacement of the filtration medium.

3.1.2. Centrifugation

Centrifugation is among the most commonly employed methods of phase separation in digestate processing. It leverages centrifugal force to separate solid and liquid components according to their density differences. During centrifugation, heavier solid particles are driven outward toward the centrifuge’s perimeter, while the lighter liquid fraction remains closer to the center. This approach is particularly effective for suspensions containing a high proportion of solid matter and can be utilized in both small- and large-scale applications. Its overall performance is influenced by a range of technical parameters, most notably rotational speed and centrifugation duration [52].

3.1.3. Sedimentation

Sedimentation relies on gravitational forces to make the solid particles settle to the bottom of a tank. While this method is relatively slow, it can be effective for digestate with a low concentration of solid matter. It also requires large tanks and prolonged settling times, which may limit its feasibility on an industrial scale. Sedimentation can be enhanced by adding coagulants or flocculants, which help form larger particle aggregates and, thus, facilitate settling.

3.1.4. Ultrasounds

Ultrasonic methods for solid–liquid separation represent a relatively new approach, primarily investigated under laboratory conditions. By applying high-frequency sound waves, solid particles can be disrupted, facilitating their separation from the liquid phase. Although the process is energy-intensive, it achieves effective separation for very fine particles. Looking ahead, this technique holds promise especially when integrated with other separation processes such as filtration or sedimentation.

3.1.5. Osmosis and Nanofiltration

Osmosis and nanofiltration are membrane-based technologies designed to selectively separate solid particles from liquids [53,54]. During osmosis, water passes through a semipermeable membrane driven by osmotic pressure, leaving solid particles behind. Nanofiltration, on the other hand, can remove particles sized between 1 and 10 nanometers, making it highly effective at removing very fine solid matter from the liquid phase. Membrane technologies are increasingly being adopted in water treatment and separation processes across various industries, including biogas production facilities.

Despite the effectiveness of solid–liquid separation methods for digestate, there are still barriers to their large-scale industrial implementation. These include high technological costs, substantial energy demand, and environmental regulations, all of which affect the choice of a suitable technique. Looking ahead, advancements in nanomaterials applied into filtration could enhance both the efficiency and cost-effectiveness of these processes. Solid–liquid separation in digestate remains a core step in biomass processing and biogas generation. A broad range of techniques can be employed for this purpose, and the ultimate choice depends on the characteristics of the material as well as technological and economic considerations. Effective separation enables further industrial applications of digestate while minimizing environmental impact. Although various methods of digestate conditioning have been explored, significant challenges still remain, particularly concerning the reduction in heavy metal content and enhancing nutrient stability. Future research should focus on developing innovative digestate conditioning techniques aimed at reducing heavy metal concentrations or enhancing the nutrient value of material.

3.2. Addition of Biochar and Mineral Additives for Nutrient Enrichment

Digestate produced in biogas plants through anaerobic digestion of biomass is a valuable by-product containing essential nutrients such as nitrogen (N), phosphorus (P), and potassium (K). These nutrients make digestate suitable for use in agriculture as an organic fertilizer. However, despite its agronomic potential, digestate can present certain limitations, including low levels of plant-available nitrogen, high moisture content, and the risk of heavy metal accumulation in soil. To enhance the quality of digestate and improve its performance as fertilizer, various enrichment methods have arisen in recent years, notably the addition of biochar and mineral fertilizer supplements. Biochar, obtained via the pyrolysis of biomass, exhibits unique physical and chemical properties that can significantly upgrade the value of digestate. A high biochar capacity for adsorbing nutrients such as N, P, and K is its main advantage. By acting as a “storage reservoir”, biochar can release these nutrients gradually, enhancing fertilizer efficiency. Incorporating biochar into biogas digestate also improves the material’s structure, increases its stability and mitigates leaching losses of nutrients. Furthermore, biochar serves as a pH buffer, creating conditions that favor the activity of soil microorganisms. Thanks to its porous structure, biochar offers microsites where beneficial microorganisms involved in mineralization processes can thrive, boosting nutrient availability for crops. Some authors [55,56] demonstrated the utility of biochar derived from biogas digestate as a phosphorus source for producing magnesium ammonium phosphate (MAP). Through a combination of precipitation and physical adsorption processes, they recovered 99.3% of the phosphorus (P) and 96.4% of the nitrogen (N) contained in the digestate, culminating in the formation of a biochar-based fertilizer known as MAP@BRC [57]. This fertilizer provides vital crop nutrients that are released gradually into the soil. By employing MAP precipitation, the nutrients originally contained in digestate become strongly adsorbed onto the biochar, thereby reducing the likelihood of nutrient losses. The MAP@BRC product addresses the typical challenges of low nitrogen content and limited phosphorus availability in biochar derived from biogas digestate, while simultaneously leveraging biochar’s physicochemical properties to improve soil quality and facilitate positive interactions between the nutrients and the biochar matrix [55].

Mineral fertilizer additives can also substantially increase the effectiveness of biogas digestate. Their primary function is to supply missing nutrients in mineral form such as nitrogen (e.g., from urea or ammonium nitrate), phosphorus (e.g., from superphosphate), and potassium (e.g., from potash salts). This supplementation can be particularly beneficial in soils that are inherently low in these essential elements. By adding mineral fertilizers, the N:P:K ratio in enriched digestate becomes more aligned with crop requirements. Buratoa et al. showed that struvite was used as a mineral amendment in organo-mineral fertilizers, increasing the overall efficiency of digestate [57]. Skrzypczak et al. [58] focused on developing a granulated fertilizer technology that integrates amino acids into digestate derived from food waste. Pig hemoglobin served as an additional source of nitrogen and organic carbon. Cucumber plants were subjected to 10-day germination tests under normal, saline, and drought conditions. The results indicated that lower application rates of the amino acid-based fertilizer promoted root growth under normal conditions, while higher dosages benefited aboveground plant parts. When coupled with biochar, mineral fertilizer additives can be used even more efficiently by plants. Mineral supplements further improve soil nutrient availability for elements such as magnesium, calcium, and various micronutrients essential for healthy plant growth. Combining biochar with mineral fertilizers in digestate, thus, yields multiple benefits: it upgrades digestate properties (reducing moisture content and improving structure) and boosts plant productivity. Biochar not only captures and holds nutrients, ensuring more efficient uptake by crops, but also minimizes nutrient runoff to groundwater.

In summary, the addition of biochar and mineral fertilizers to biogas digestate is a promising enrichment strategy and substantially raises its agronomic value and nutrient-use efficiency. Biochar’s adsorptive capacity improves nutrient retention while positively influencing soil structure. Mineral fertilizers correct nutrient imbalances, enabling more balanced and effective fertilization. Together, they help to improve soil quality, enhance crop productivity, and foster the sustainable development of agriculture, minimizing adverse environmental impacts.

3.3. Stabilization of Digestate to Reduce Odor and Greenhouse Gases (GHGs) Emissions

Technologies that improve the stability of the digestate structure are desirable in order to reduce greenhouse gas emissions and unpleasant odors, especially those resulting from large amounts of nitrogen in digestate. Other chemical compounds causing odor nuisance include sulfides, aromatic hydrocarbons, acids, and BTEX. Their presence may be perceived not so much during the anaerobic digestion process itself, but rather during the preparation of feedstocks or the initial stages of digestate management [59]. Nitrogen emissions to the atmosphere mainly concern nitrous oxide and ammonia. Although ammonia itself is not a greenhouse gas, its release into the atmosphere can lead to the formation of other nitrogen compounds that contribute to soil acidification, eutrophication, and respiratory diseases. Furthermore, as previously mentioned, ammonia present in the digestate is also a source of unpleasant odors. One of the effective methods for mitigating odor emissions and reducing the release of gases into the atmosphere is the injection of digestate directly into the soil [60]. According to Korba et al. [61], injections can reduce ammonia emissions by up to 99% compared to conventional application of digestate as fertilizer.

Among the digestate processing technologies, thermal drying can be mentioned. Drying usually takes 7–10 days. It has been proven that this process effectively reduced the percentage of NH₃ in the digestate. In addition to stabilizing the digestate, water evaporation occurring at higher temperatures favors the storage and further transport of the fertilizer [62]. Another stabilization technology is solid–liquid separation. By altering the digestate structure, this process facilitates the management of solid and liquid fractions separately, which can help minimize the risk of GHG emissions (mainly methane and hydrogen sulfide), provided that the solid fraction undergoes further stabilization processes such as composting [63].

The most common method for stabilizing digestate is composting. This process, which takes place under aerobic conditions, reduces methane emissions, one of the main products of anaerobic digestion. Research conducted by Weldon et al. [64] additionally considered the effect of biochar on the composting process of digestate with garden waste. The structure of digestate was improved, and N₂O emissions were reduced by 65–70%. The study conducted by Cheng et al. [65] determined the validity of using intermittent aeration during digestate stabilization in the composting process. The authors noted a decrease in nitrous oxide and ammonia emissions and an improvement in humification. In the case of NH₃, its emissions were reduced in the range of 29% to over 75% compared to continuous aeration.

4. The Impact of Digestate on Soils

4.1. Regeneration of Degraded Soils

Soil consists of rocks and minerals, water, air, and organic matter, whose presence is essential for supporting plant growth. Soil formation is a long-term process during which weathered rock material becomes enriched with organic matter, transforming into soil. Under natural conditions, matter circulates continuously; substances taken up by plants eventually return to the soil. Unfortunately, agricultural use of soil interrupts this cycle—harvested crops remove nutrients, preventing their return to the soil, resulting in soil productivity loss. This process is known as soil degradation. Soil fertility describes the soil’s ability to meet plant needs by supplying water, nutrients, and air. Thus, declining soil fertility is detrimental, negatively impacting crop yield quantity and quality and contributing to further soil degradation. Soil degradation encompasses various negative physical, chemical, and biological processes that reduce soil quality and impair its essential functions. Understanding soil properties and processes is critical to achieving the United Nations Sustainable Development Goals (SDGs). Sustainable management and protection of soils are essential responsibilities to meet the SDGs by 2030 [66].

One of the consequences of soil degradation is a decline in soil fertility, which can subsequently lead to reduced crop yield quantity and quality. Along with declining fertility, soil productivity—the capacity of the soil to meet plant needs—also deteriorates. The primary indicator of soil fertility is humus content. Many factors can negatively impact soil fertility, including a reduction in organic matter, decreased soil microbial populations, excessive soil drying, improper agricultural practices, inadequate crop rotation, or its complete absence [67]. Soil fertility can also be reduced by the use of chemical agents and improper fertilization. A decline in fertility is additionally associated with reduced biological activity in the soil, which is a consequence of soil degradation. By applying soil degradation prevention methods, it is possible to increase humus content and enhance the soil’s sorption capacity [68]. According to the 2020 FAO (Food and Agriculture Organization of the United Nations) report, the loss of soil biodiversity has been recognized as one of the key global challenges [69]. It is estimated that approximately 33% of the world’s soils have undergone moderate to severe degradation due to erosion, salinization, compaction, acidification, and chemical contamination. According to the FAO report, the outlook is bleak, with predictions suggesting that by 2050, more than 90% of all soils could be degraded. In the European Union, 70% of land is in poor condition, and erosion affects 25% of agricultural land. Degraded soil lacks the capacity to retain water, reduces biological life, and suffers from diminished biodiversity. The agricultural production system and post-industrial soils are currently severely threatening ecosystem resilience and climate stability. Those soils are a large driver of increasing environmental degradation [70]. Biodiversity conservation strategies to mitigate the negative influence of soil degradation today is one of the most important issues worldwide, since soil rich in biodiversity is essential for obtaining the best ecosystem restoration, which is now a key aspect in the ever-deepening problem of soil quality. Microorganisms in the soil work as a natural filter; the water leaching through the soil profile undergoes purification, so the water treatment capacity and, thus, groundwater resources, as well as the need for water treatment plants of the soil, are determined by soil biodiversity. Therefore, the loss in biodiversity effects the sudden spread of pests, which can lead to the destruction of large-scale crops.

Available arable land is expected to be halved by 2050, potentially leaving future generations without soil suitable for food production. The key factor contributing to soil depletion and erosion is declining humus content, which also leads to a reduction in the processes of soil organic carbon (SOC) sequestration [71]. Moreover, expanding agricultural land and draining meadows and wetlands leads to an increasing release of carbon from the soil (Figure 4).

These emissions indicate the long-term release of carbon dioxide from peat soils, resulting from agricultural activities and land use changes. Unfortunately, FAOSTAT data indicate that expanding agricultural land into previously undisturbed peatlands results in massive CO₂ emissions into the atmosphere, leading to a continuous loss of soil organic matter. These findings highlight that instead of converting new land for agriculture, we must focus on improving and retaining CO₂ within existing farmlands. This requires incorporating organic matter into soils and maintaining their fertility to prevent the loss of their productive function. A necessary solution appears to be the use of fertilizers, preferably natural ones rich in organic matter. Exclusive reliance on mineral fertilization, especially in high doses, can lead to a decline in soil microbial populations, the activation of heavy metal compounds, and increased soil acidification. These factors further contribute to soil erosion and higher CO₂ emissions [73]. Excessive use of mineral fertilizers, especially on heavy and poorly permeable soils, can lead to the accumulation of salts in the soil. Elements such as sodium, potassium, magnesium, and chlorine present in fertilizers can contribute to soil salinization [74]. Increasing the content of soil organic matter (SOM) plays a crucial role in minimizing soil erosion and improving overall soil structure. One effective approach to enhancing SOM levels is the application of organic materials, such as digestate, which not only enrich the soil with organic matter but also supply essential nutrients. The regular use of digestate as a biofertilizer contributes to maintaining a sustainable balance of organic matter in agricultural soils, preventing degradation over time. Moreover, the incorporation of organic amendments improves soil water retention, enhances microbial activity, and fosters a more resilient agricultural ecosystem. By promoting the use of biofertilizers derived from organic sources, farmers can ensure long-term soil fertility while reducing dependence on synthetic fertilizers [75]. Restoring degraded soils plays a vital role in reducing CO₂ emissions by capturing carbon in the soil and promoting the formation of organic matter. Consequently, large-scale ecosystem restoration presents a significant, yet underutilized, opportunity for enhancing carbon sequestration.

4.2. Increase in Humus Content and Improvement of Soil Structure

The amount of organic matter significantly affects soil and plant health by supporting root system development, reducing soil crusting, and improving plants’ ability to absorb nutrients. Soil organic carbon (SOC) and soil biodiversity are often linked to three dimensions of food security: increasing food availability, restoring the productivity of degraded soils, and enhancing the resilience of food production systems. While organic carbon itself does not directly influence food production, it serves as an indicator of the amount of soil organic matter (SOM), which is one of the key components associated with various soil functions. Microbial soil carbon is typically included in aggregate SOC measurements, and soil microorganisms are a component of soil organic matter [68]. Therefore, in terms of mass, SOC/SOM and soil microorganisms are directly interconnected. Another important indicator of soil health is the development of soil organic matter, soil acidity, soil microbial biomass, and soil microbial activity. In long-term studies spanning over 50 years, the application of organic fertilizers, such as farmyard manure and alternative organic materials, significantly increased the accumulation of soil organic carbon (SOC), contributing to the improvement of soil quality and function. Additionally, it was confirmed that the highest humic acid content was obtained in soil fertilized with farmyard manure combined with liming. This can be explained by the fact that liming and the use of organic fertilizers promoted the polymerization of humic acids, which also created more favorable conditions for the long-term sequestration of soil organic carbon [76]. A two-year experiment on the application of digestate to soils demonstrated that the highest soil organic carbon (SOC) content was achieved with the maximum fertilization rate of the solid digestate fraction. The application of digestate contributed to an increase in the content of mobile humic substances (MHS), particularly in grasslands and crop rotation fields, indicating its positive impact on the humification process [77]. The advantages of incorporating digestate into the soil involve enriching it with organic matter, enhancing biological activity, recycling essential nutrients, strengthening soil structure, increasing resistance to erosion, supporting plant health by stimulating microbial communities, and supplying valuable humic substances [75].

The primary direction for utilizing digestate from agricultural biogas plant, considering its physicochemical properties, should be its use as a fertilizer. The simplest method of fertilizer application is the direct spreading of liquid digestate on agricultural land, separation into solid and liquid fractions, followed by field application, as well as more advanced methods such as composting or the production of organic and organo-mineral fertilizers or soil-improving substances [76]. Digestate from biogas plants has good fertilizing value, comparable to natural fertilizers. However, this value may vary depending on the type of feedstocks used in anaerobic digestion. The chemical composition of digestate produced from biomass anaerobic digestion in biogas plants depends on the substrates used. If the substrates include plant biomass or waste from the agri-food industry, the digestate is a safe and valuable fertilizer. Research shows that, compared to the use of sewage sludge and composts, the application of digestate from agricultural biogas plants does not include significant additional contamination with heavy metals, microplastics, or pharmaceuticals [78].

The digestate contains methanogenic microorganisms, undigested organic residues, and mineral components that are easily accessible to plants. It primarily consists of persistent organic compounds such as cellulose, lignin, and lipids, which serve as precursors of humic substances. Stable organic matter (OM), particularly lignin, contributes to an increase in soil organic carbon (Corg) due to its low degradability. As a result, digestates have the potential to supply a greater proportion of resistant Corg for the regeneration of soil organic matter compared to the original feedstock [79]. Moreover, compared to raw plant biomass that has not undergone digestion, digestate has a lower dry matter content, a favorable C:N ratio that promotes faster decomposition, and a high concentration of nutrients in plant-available forms, resulting in a rapid fertilizing effect. Additionally, digestate has a higher proportion of nutrients in mineral forms (directly available to plants, leading to a quicker fertilizing effect) and a greater share of ammonium nitrogen (N-NH₄) [51,80]. Digestate organic matter undergoes microbial decomposition and transformation in the soil. Microorganisms break down this organic matter, converting it into humic substances. The carbon from digestate becomes an additional input to the soil and partly integrates permanently into soil organic matter [75]. Additionally, Greenberg et al. [81] demonstrated that the liquid fraction of digestate from maize silage significantly increases SOC content compared to mineral fertilizers. This effect was particularly noticeable in soil aggregates under temperate conditions. Therefore, digestate application enhances soil carbon sequestration compared to conventional fertilizers. Field studies on the use of digestate and other organic fertilizers over a period of 14 years have confirmed that the content of organic matter, soil microporosity, and phosphorus (P) resources available to plants have a significant impact on the movement of dissolved substances and colloids in the soil matrix. Long-term use of biogas digestate clearly affects the distribution of water and mobile nutrients in sandy soils. It causes an increase in organic carbon content, which is associated with increased hydrophobicity and macroporosity, and consequently affects the transport of dissolved substances. The analysis showed that phosphorus accumulates mainly in the matrix of the surface layer of the soil, while preferential flow paths in the subsoil favor the loss of nutrients, which indicates a complex relationship between digestate application and soil properties [82]. For soil health and functionality, the microbial population is a key parameter. Investigating the effects of digestate on soil microorganisms is highly important for assessing the impact of its application. The correlation between SOM and soil microorganisms is very complicated, and the application of external organic matter also influences this correlation. Inappropriate or unbalanced application of digestate in soil can lead to environmental pollution through the emission of ammonia and nitrogen oxides into the atmosphere and the leaching of nitrates into groundwater and surface waters, which promotes eutrophication and algal blooms. The addition of exogenous organic matter (EOM) can affect native soil organic matter (SOM), causing a priming effect. Increased microbial biomass after EOM application can contribute to the accumulation of mineral-associated organic matter (MAOM). In turn, particulate organic matter (POM) can undergo more intensive depolymerization, which promotes the priming process, but at the same time can be stabilized inside soil aggregates. These processes lead to various soil reactions to EOM addition, which can result in the stabilization of more stable SOM fractions. The interactions of EOM, like digestate with SOM, connected with N cycling and organic carbon sequestration, are an issue still pending more research. Studies indicate that the particulate organic matter (POM) fraction is mainly composed of plant residues, and solid digestate in this experiment was the key source of unbound organic matter (OC). This resulted in the accumulation of OC in the POM fraction, which is a readily available source of nutrients and energy for microorganisms [83]. Analysis of the multi-year study showed that digestate application had a significant effect on the C/N ratio only in the POM fraction and only in samples with solid digestate addition. The C/N ratio increased significantly in the deeper soil layer regardless of time. Although the residual organic matter in the POM fraction is easily available to microorganisms, the dominant accumulation in this fraction rather than in the MAOM fraction suggests that solid digestate requires a longer time for complete decomposition and integration with MAOM [84]. The use of digestate, depending on its form, in the form of a liquid fraction, gives different effects. The liquid fraction has the greatest impact on the availability of biogenic components used for the rapid growth of plant biomass, and its effects are rather short-term. On the other hand, the solid fraction has a long-term effect, affecting the building of organic matter forms, carbon sequestration, and soil water capacity.

4.3. Sustainable Supply of Micro and Trace Elements

The digestate contains biogenic elements like nitrogen, phosphorus, and potassium. Compared to sewage sludge and compost, the digestate is recognized by a higher content of phosphorus (P) and potassium (K), which makes it a valuable source of these macronutrients for the soil [79]. In the screening research for Polish agricultural biogas plants, the values for potassium (K2O) content ranged between 1.30 and 16.3 kg∙Mg⁻¹ [85]. The nutrients contained in the digestate are easily accessible, and their average ratio (P:K) is about 1:3, which is particularly beneficial for cereal and rapeseed crops [86]. In order to avoid excessive accumulation of phosphorus and potassium in the soil, it is recommended to limit the amount of digestate used, which, however, may require additional supplementation of nitrogen deficiencies with mineral fertilizers. Analyses of digestate from agricultural biogas plants clearly indicate the fertilizing properties of digestate (

Table 3. Effects of digestate on soil properties.

Soil Parameter	Effect of Digestate Soil Application	Type of Digestate-Feedstock	Reference
Organic matter content	Topsoil (0–0.3 m): control 0.76 ± 0.08%, digestate: 1.00 ± 0.07% SD caused a significant displacement effect—the share of organic in POM (particulate organic matter) increased at the expense of MAOM (mineral-associated organic matter).	digested slurry, digestate corn and poultry, manure, solid SD, and liquid LD	[82,84]
Soil organic carbon (SOC)	Digestate I (Ctot) 1.13%, digestate II 1.17%, compared to control 1.09%. Slight increase in SOC (2–5% increase compared to unfertilized soil).	(digestate I) corn silage, cattle slurry, (digestate II) corn silage, pig slurry, farmyard manure, and hay; digestates from maize (M), clover and grass (CG), poultry manure (PM), cattle slurry (CS)	[87,88]
Soil pH	Digestate I: pH 6.95, digestate II: pH 7.05, control 6.80.	(digestate I) corn silage, cattle slurry, (digestate II) corn silage, pig slurry, farmyard manure, and hay	[87]
Total nitrogen content	LD increased the N content; this effect was more pronounced than in the case of SD. Digestates used as liquid fraction—have a high share of mineral nitrogen (NH4+ constitutes 35–81% of total N). Their application increases the availability of N in the soil, although the total TN content changes only slightly (differences in the order of several point percentages compared to the control).	digestate from corn silage, straw, chicken manure, pig slurry, corn-based distiller’s grain, cattle slurry; digestates from maize (M), clover and grass (CG), poultry manure (PM), cattle slurry (CS)	[88,89]
Available phosphorus	(PDL—double lactate-extractable P) in topsoil: control 3.99 ± 0.51 mg/kg, digestate: 5.24 ± 1.91 mg/kg increase; effects are dependent on the type of digestate: digestates from food waste and manure (e.g., PM, CS) show higher P values, while those from plant silage (M, CG) may be slightly lower; changes in the range of 10–30% compared to the initial values.	digested slurry digestates from maize (M), clover and grass (CG), poultry manure (PM), cattle slurry (CS)	[82,88]
Microbial activity	Food waste digestate with very high OM mineralization (Cm ≈ 60.9%, CO2 production—1900 mgCO2-C kg−1 of soil), the remaining digestates had Cm in the range of 16–22% (corresponding to mineralization, about 720 mgCO2-C kg−1 of soil.	Seven digestates: maize silage (M), clover and grass silage (CG), grass silage (G), food waste (FW), source-separated organic household waste (OW), poultry manure (PM), and cattle slurry (CS)	[79]
Soil structure	Soil aggregates stability (SAS); digestate I: 32.35%, digestate II: 36.47%, control—26.22%. Porosity of macropores (>36 mm3,), control 4.02 ± 0.90 vol%, digestate 6.16 ± 2.78 vol%.	(digestate I) corn silage, cattle slurry, (digestate II) corn silage, pig slurry, farmyard manure, and hay; digested slurry	[82,87]
Soil salinity	Electrical conductivity (EC) increase; control 181 μS/cm, solid digestate 215 μS/cm, liquid digestate 327–386 μS/cm.	digestate corn and poultry, manure, solid SD and liquid LD	[84]
Trace elements	Digestates may contain elevated concentrations of microelements, such as Cu, Zn, or Mn (e.g., PM, CS), and accumulation may occur with repeated use—typical concentrations of Cu and Zn may be 20–50% higher than in soils fertilized with traditional manures. LD, at higher doses, increased the available forms of Fe, Mn, Cu, and Pb (e.g., at the highest dose, an increase in available Fe by 6.9%, Mn by 12.4%, Cu by 21.9%, and Pb by 20% compared to the control).	digestates from maize (M), clover and grass (CG), poultry manure (PM), cattle slurry (CS) digestate from corn silage, straw, chicken manure, pig slurry, corn-based distiller’s grain, cattle slurry	[88,89]

). In liquid digestate, the dry matter content ranges from 2% to 15%, while in solid form it can reach 20–30%. Organic carbon constitutes 30–50% of TS, while organic matter is in a wide range from 50% to 85% of TS, depending on the consistency of the digestate. This indicates the significant potential of digestate as a source of organic matter supporting soil fertility and microbial activity [51]. There is no doubt that its application to the soil contributes to improving its properties. This is primarily due to the high content of the ammonium form of nitrogen (N-NH₄), which accounts for up to 80% of the total nitrogen [80]. This form is readily available to plants, allowing for its direct incorporation into organic compounds, thereby increasing fertilization efficiency compared to manure or slurry. Additionally, the use of digestate in its ammonium form helps reduce eutrophication, positively impacting aquatic ecosystems. In the research conducted by [87] it was found that digestate application (4-year application) did not improve soil organic matter as significantly as compost, but improved significantly the soil’s physical properties and water infiltration (Table 3). The soil application of liquid digestate (LD) caused a significant increase (about 80–100% higher EC than the control), which may indicate an increase in soil salinity, while SD (solid digestate) caused a smaller effect (about 20% increase). Single soil applications (investigated after 6 months) (SD or LD) did not significantly change total OC or TN concentrations, but SD changed the SOM distribution—increasing the share of the labile POM fraction at the expense of MAOM [84]. Häfner et al. [79] tested seven different digestates and concluded that differences in fertilizer value and OM degradability could be mainly related to compositional variations, and food waste digestate had the highest impact on OM degradability.

From the perspective of crop benefits, the key nutrient that directly influences and limits plant biomass production is nitrogen. In the European Union, the application of nitrogen fertilizers in agricultural fields is regulated by Council Directive 91/676/EEC of 12 December 1991, commonly referred to as the Nitrates Directive. This directive aims to protect water bodies from pollution caused by nitrates of agricultural origin. Under this regulation, the annual application of natural fertilizers must not exceed 170 kg of total nitrogen per hectare of agricultural land [90]. The conversion of organic nitrogen (N_org) into ammonium (NH_4⁺-N) increases the proportion of NH_4⁺-N in the total nitrogen pool (NH_4⁺/N), thereby improving the immediate accessibility of nitrogen for plant uptake [79]. Additionally, studies confirm that the proportion of nitrogen forms in digestate varies depending on whether the digestate is in its raw form, the liquid fraction obtained after separating the solid fraction, or the solid fraction itself (Figure 5).

Analyses of the average nitrogen content in digestate from 10 agricultural biogas plants indicate that in raw digestate, the dominant nitrogen form is N-NH₄, accounting for an average of 81% of total nitrogen, while organic nitrogen (N-org) constitutes approximately 13.9%, and nitrate nitrogen (N-NO₃) makes up 5.1% (Figure 5). In the liquid fraction after separation, the proportion of N-NH₄ slightly decreases to an average of 77.6%, while the share of N-org increases to 18%, suggesting a partial transfer of organic nitrogen into this fraction. The solid fraction differs significantly in nitrogen composition, with organic nitrogen as the dominant form (80.2%), while ammonium nitrogen content decreases to an average of 19.4%. Considering the fertilizing properties of liquid and solid digestate, they exhibit significantly different nitrogen composition profiles. The form of digestate for soil application also influences the final effect. In the research conducted by [84], the solid digestate contained five times more dry matter (DM) and 1.5 times more organic matter (OM) compared to the liquid fraction. Solid digestate also had a higher organic carbon (OC) content (42%) than liquid digestate (33%). Conversely, total nitrogen (TN) was greater in the liquid fraction (3.5%) compared to the solid fraction (1.4%), resulting in a threefold higher C/N ratio in solid digestate. Thus, solid digestate is better suited as a soil amendment, while liquid digestate serves effectively as a fertilizer. Digestate may also contain total Mg (% fresh matter- FM) 0.03–0.07, total Ca (% FM), 0.01–0.023, total S (% FM), 0.02–0.04, and other elements such as copper, zinc, iron, manganese. Elevated concentrations of certain micronutrients, such as Cu and Zn, found in some digestates, result from the use of pig and cattle slurry as feedstock. The phytotoxicity of the digestate product may result from high concentrations of heavy metals, as well as elevated levels of potassium, sodium, and chlorine. Furthermore, heavy metals can accumulate in the soil and plants, while increased soil salinity may negatively affect seed germination and plant development. In digestate studies, an elevated iron (Fe) content can be observed, which results from several key factors related to the anaerobic digestion process and the composition of the feedstock. In biogas plants, iron sulfate (FeSO₄) or iron chloride (FeCl₃) is often added to reduce hydrogen sulfide (H₂S) emissions. The studies recorded Fe concentrations ranging from 2 to 5 g/kg DM, with Zn being the second most abundant element at 0.2 g/kg DM and third is Mn 0.15–0.2 g/kg DM [89].

4.4. Importance for Circular Agriculture, Closing the Nutrient Cycle—Digestate as an Ecological Alternative to Mineral Fertilizers

Due to the high fertilizing value of digestate and the presence of organic matter, which can replace traditional organic fertilizers, biogas digestate is becoming increasingly popular as a soil fertility enhancer [75]. A valuable characteristic of digestate is its content of stable carbon compounds with a high humification potential, which promotes better plant growth, enhances carbon sequestration in the soil, and increases the soil’s capacity to retain water and nutrients. Long-term application of digestate improves soil structure, thereby stimulating the development of soil microorganisms and improving soil physical properties and water infiltration.

The broadly spread positive feedback from soil reclamation is reflected in improvement in the soil quality, restoration ecosystem functionality, improvement of the crop yield and food safety, and increased ecosystem capacity to sequester C. However, these overlapping dependencies of soil quality, climate change, biodiversity, and food security require a broader understanding [91]. The microbiological activity of the soil is responsible for the processing and, thus, the formation of stable and labile carbon fractions in the soil. Improvement of soil organic carbon (SOC) content is one of the most important elements improving soil functionality and productivity, contributing to changes in the circulation of nutrients and immobilizing toxic elements, lowering both soil toxicity and the potential risk of the contaminant’s magnification and flow. The improvement of SOC sequestration and increased biodiversity contribute to improved public health through better food security and climate. Therefore, such monitoring of regenerative agriculture decreases the possibility of potential crop damage, generating income at the transnational scale. Therefore, the understanding of changes in biodiversity and its dependency on C storage and climate change will make it easier to achieve the ambitious goal of the EU’s Biodiversity Strategy with the assumption of obtaining 25% of all croplands under organic farming cultivation by 2030. Among the methods of biodegradable waste treatment and recovery, there are two acknowledged methods backed up by years of research, namely, composting and anaerobic digestion (AD). Focusing on them is particularly important in the context of EU Fertilizing Product Regulation (FPR), which defined recovery rules for bio-waste transformed into composts and digestates. Most research on AD focuses on improving the efficiency of the process, often neglecting the quality of the digestate produced. The current research shall also focus on a paradigm shift in the approach to anaerobic digestion from “biogas optimization” to “integrated biogas-digestate optimization”.

Digestate, a byproduct of anaerobic digestion processes, enables the effective integration of organic waste into agricultural production by converting it into a valuable fertilizer. This approach not only minimizes the amount of waste sent to landfills but also recovers essential nutrients such as nitrogen, phosphorus, and potassium. Such a strategy is crucial for circular agriculture, where closing the nutrient cycle contributes to increased resource use efficiency and a reduction in the negative environmental impact. Sustainable development must be accompanied by a sustainable crop production system. Digestate, as an ecological alternative to mineral fertilizers, facilitates the long-term improvement of soil quality by enriching it with organic matter, which in turn enhances soil structure, increases water retention, and stimulates microbial activity [92]. The effective use of digestate aligns with the principles of sustainable development by reducing dependency on external, non-renewable sources of nutrients. Furthermore, the incorporation of digestate into agricultural practices not only promotes higher yields but also limits greenhouse gas emissions associated with the production and transportation of synthetic fertilizers. The growing number of biogas plants represents significant potential and an opportunity to transition towards regenerative agriculture that utilizes organic fertilizers based on digestate. In this framework, ecological and economic efficiency must go hand in hand. Closing the nutrient cycle through the use of digestate is a crucial element of circular agriculture, wherein organic waste is reintegrated into agricultural production. Such a system not only supports environmental protection by reducing eutrophication and minimizing the emission of harmful substances, but also delivers tangible economic benefits, enabling farmers to reduce costs related to the purchase of mineral fertilizers, thereby enhancing the resilience of agricultural enterprises to market price fluctuations and fostering a more sustainable development of the agricultural sector [93].

Circular agriculture, based on the principle of a closed nutrient cycle, represents an innovative approach to managing natural resources, allowing for the minimization of losses and the reduction in the negative environmental impact of agricultural production. A key element of this concept is the utilization of organic waste, that can be converted into digestate—an ecological organic fertilizer [92]. Scientific literature and sustainable development practices in agriculture have identified several indicators that can be used to assess circular agriculture, although there is no single universal list of indicators. Among the most frequently used metrics are the degree of nutrient cycle closure, resource use efficiency, the nitrogen and phosphorus balance, greenhouse gas emissions, soil health indicators, biodynamics, and biodiversity [85,94,95]. The precise indicators of circular agriculture may vary depending on the context and specificity of the farm, and the examples above constitute the basic set of metrics used to assess the efficiency of circular agricultural systems. In the literature and within sustainable development programs, further methods for standardizing these indicators are being sought to better monitor and compare the outcomes of implementing circular systems in agriculture.

5. Conclusions

Currently, the pursuit of sustainable development across various sectors of the economy plays a crucial role. In the energy and agriculture sectors, a key process worth focusing on is anaerobic digestion, particularly of waste suitable for processing, which, as a developing society, we generate in increasing quantities each year. The successful implementation of new and improved anaerobic digestion technologies in biogas plants depends on the ability to optimize process parameters, the efficiency of feedstock conditioning, and the quality of the resulting digestate. Digestate plays a vital role in improving soil fertility and microbiological activity.

One of the main challenges in biogas plants is the processing of substrates, particularly those with high content of organic matter and plant fibers. Biomass conditioning methods often rely on mechanical processing techniques such as grinding, cavitation, and extrusion. However, the effects of these methods are often insufficient, which has led to the development of innovative biological approaches that utilize bacteria, fungi and enzymes. These biological methods remain an emerging technology. Meanwhile, well-established thermal and chemical methods should continue to be refined to maximize methane yields, shorten retention time, and improve the economic feasibility of large-scale application.

Each of the methods discussed in this article has its limitations, and further research with adaptation is necessary to optimize the bioconversion of organic substrates into biogas. In addition, to stabilize conditions, co-digestion strategies and reactor selection should also be carefully considered to optimize process conditions.

Actual research needs to study the dependence between soil microorganism’s biodiversity and the dynamic and composition of SOC pool. As digestate treatment technologies develop, the future question is how innovate digestate-based fertilizing products’ influence biodiversity and SOC sequestration in agricultural and post-industrial soils. More research is needed on the impact on the physicochemical properties of soil, as well as its biodiversity, when digestate has been applied. Additionally, more research is needed for the investigation and utilization of the mechanisms in which the stable forms of organic C are built into agriculture and post-industrial digestate-amended soils.

The use of digestate as a fertilizer presents a wide range of logistical challenges especially due to its lower nutrient content compared to synthetic fertilizers, especially if the digestate is to be used in conventional agriculture. Urban and peri-urban facilities face challenges in transporting digestate to agricultural regions due to high costs caused by the low nutrient concentration in liquid digestate and the large volumes of digestate required to feed crops. The use of digestate as an ecological fertilizer in circular agriculture enables the efficient recovery and reuse of nutrients, which contributes to environmental protection, improved soil quality, and increased economic efficiency in agricultural production.

This paper emphasizes that the integration of biogas plants and the use of digestate constitute the foundation for establishing sustainable, circular agricultural systems that can significantly impact environmental protection and enhance the efficiency of agricultural production. Innovative biomass pre-treatment methods and advanced digestate conditioning techniques significantly increase biogas production efficiency and enable the effective integration of digestate in regenerative agriculture. The research findings underscore that a comprehensive approach based on green biotechnology is key for circular agriculture, allowing for the maximization of green energy while simultaneously closing the nutrient cycle and enhancing soil health.

Future research should focus on scaling and testing digestate-based fertilizers under various climatic and soil conditions to evaluate their agronomic effectiveness. There is also a need to develop strategies for reducing the cost and environmental footprint of digestate transportation and application. Moreover, further investigation is recommended into synergistic microbial consortia that can enhance biogas yields and improve digestate quality. To achieve this, future research should prioritize long-term field studies aimed at assessing the cumulative impact of digestate application on soil health, carbon sequestration potential, and overall agricultural productivity.