Anaerobic Fermentation and High-Value Bioproducts: A Brief Overview of Recent Progress and Current Challenges

The global community is in a perpetual search for alternative energy sources that can effectively supplant fossil fuels and contribute to environmental stewardship [1]. Equally, the production of various organic wastes, such as food wastes, municipal sewage sludge, animal manure and agricultural residues, as well as various industrial wastewaters grows annually. This growth coincides with the rise of the Earth’s population, posing a threat to humanity and the environment [2].

Sustainable waste management practices can be guided by the philosophy of transforming waste into valuable resources, leading to the production of industrially significant chemicals and biofuels derived from renewable sources. In this context, the global scientific community is actively exploring the concept of integrated biorefineries, which aim to effectively extract valuable substances from renewable materials [3]. This approach involves a comprehensive framework that encompasses various biological processes, allowing for the maximum utilization of waste materials. A single bioproduct or process-based strategy may have limitations in terms of comprehensive waste utilization, yield optimization, economic feasibility, waste management after-effects, and long-term sustainability. On the other hand, an integrated approach incorporates multiple biological processes, creating a cascading system that optimizes the extraction of all components from waste, maximizing resource utilization [4].

Anaerobic fermentation (AF) is a well-established biotechnology used to valorize the organic components of waste, including carbohydrates, proteins, and fats. This process consists of four distinct stages: hydrolysis, acidogenesis, acetogenesis, and methanogenesis, which are carried out by a diverse microbial community [5]. By controlling these stages using different microbial strains and consortia, and through regulating their metabolism, it is possible to produce biogas containing high-energy components such as hydrogen and methane. A variety of bioproducts can also be produced, such as organic acids. These biogasses and bioproducts can be produced in an environmentally friendly way and can contribute to the development of a bioeconomy [6]. However, the currently available AF technologies often struggle to compete with traditional chemical methods, due to their lower production efficiency, the heterogeneity of feedstock, the lower quality of the resultant products, and the lack of a comparable infrastructure [7,8]. Therefore, further research is needed to overcome these challenges in terms of process efficiency, product synthesis, and resource utilization.

The present Special Issue (SI) focuses on the latest research in anaerobic fermentation for the production of high-value bioproducts. A total of 11 papers were submitted for consideration for this SI, and all went through a rigorous review process. As a result, seven papers were ultimately selected for publication, including two review papers and five original research articles. These papers explore various aspects of AF, such as the use of nanomaterials [9], machine learning [10], substrate composition [11], microbial consortiums [12], pretreatment [13], and issues related to lignocellulose [14] and sugarcane [15] biorefineries in the context of the circular economy. The papers present innovative approaches to AF and related fields, contributing to the further development of this important technology.

Methanogenic AF can experience deterioration under high organic loads and in the presence of high ammonia levels, as found in chicken manure. This is explained by the inhibition of syntrophic organisms that normally transfer electrons to methanogens through intermediates such as hydrogen and formate. In the work of Ziganshin et al. [9], carbon nanotubes assisted in the methanogenic degradation of chicken manure by promoting the consumption of volatile fatty acids through a direct interspecies electron transfer pathway (Contribution 1). Carbon nanotubes between 5.0 and 6.5 g per liter enhanced the biodegradation of volatile fatty acids, primarily acetate, butyrate, and propionate, increasing the maximum production rate of methane by 15–16%.

Methane-rich biogas is a gaseous fuel that can be employed in compression-ignition engines with minor modifications in dual-fuel mode. Alruqi et al. [10] explored the use of an advanced machine learning model, XGBoost, to predict engine performance when biogas served as the primary fuel (Contribution 2). The implementation of a higher compression ratio contributed to enhanced brake thermal efficiency, while the reduced combustion temperature due to the low energy density of biogas facilitated a reduction in NOx emissions. These findings provide valuable insights into optimizing the performance of dual-fuel systems powered by waste-derived biogas, potentially contributing to emission reduction efforts in the transportation industry.

Methanogenesis being inhibited, AF can produce hydrogen as an energy source, as well as various soluble bioproducts, such as fatty acids and alcohols. The anaerobic degradation and hydrolysis rates of lipids, proteins, and carbohydrates vary, with lipids exhibiting the lowest rate. Consequently, lipid degradation is regarded as a rate-limiting step in the process. Considering the diverse dietary patterns observed across different regions, Yan et al. [11] conducted a comparative analysis of the potential impact of various lipid species present in food waste on acidogenic AF (Contribution 3). Their findings indicate that the presence of unsaturated fatty acids leads to a shift in the metabolic pathway, diverting it away from lactic acid production towards the production of ethanol, acetic acid, and butyric acid. Additionally, the lipids present in food waste do not contribute to the formation of soluble substances, resulting in a reduction ranging from 14% to 59.7%.

In addition to the composition of the substrate, the use of efficient microbial species and their combinations is crucial for ensuring high production rates and yields of biological products. In Contribution 4, García-Depraect and León-Becerril [12] employed a highly specialized bacterial consortium comprising lactic acid-producing bacteria and lactate-oxidizing, hydrogen-producing bacteria to generate either lactate or biohydrogen and butyrate from various agricultural and industrial waste materials using a dual-phase approach. This approach demonstrated the feasibility of this method, as it enabled the production of high yields of lactate, biohydrogen, and butyrate using all of the tested raw materials, offering an innovative bioprocessing method for the valorization of agricultural and industrial wastes through a trade-off strategy, ultimately customizing the metabolic pathway according to the desired product(s).

The pretreatment of feedstock is a crucial step in accelerating another limiting stage of AF, namely, hydrolysis. In their work, Mikheeva et al. [13] explored the impact of an innovative pretreatment method for cheese whey using a vortex layer apparatus (Contribution 5). This process, characterized by cavitation-like phenomena and the introduction of iron particles, resulted in remarkable improvements. The maximum potential hydrogen yields were enhanced by up to 45.8%, while the maximum hydrogen production rate was increased by up to eight times compared to the control. Additionally, the lag phase of the process was significantly reduced, with a decrease exceeding 50% as a function of the pretreatment time.

Lignocellulose-based biomass represents a sustainable and abundant source of raw material for the production of biofuels and biochemicals through thermochemical and biochemical processes. However, both of these approaches have limitations in terms of efficiency, which means that an integrated approach must be adopted to maximize the use of lignocellulose. In their review paper (Contribution 6), Yogalakshmi et al. [14] examined the concept and technology of lignocellulosic biorefining, as well as the key factors that affect the feasibility of the biorefineries from a techno-economic perspective and the market outlook for their commercialization. Their research helps to anticipate the future environmental and economic consequences of the scaling-up processes of lignocellulosic biorefineries.

The concept of a circular economy encompasses the entire material flow and circulation in an industrial process, from raw materials and inputs to products, coproducts, and residues, including the emissions of gasses. Carvalho et al. [15] used the example of a sugarcane biorefinery to illustrate the current state of ethanol production technology and recent advancements in the methanogenic AF of vinasse (Contribution 7). The authors also assessed the potential integration of the methanogenic AF of vinasse into an ideal biorefinery and explored potential bottlenecks and future directions for the development and widespread implementation of this technology.

Based on the analysis of the aforementioned papers published in this SI and the recent literature, a concise overview of the current challenges in AF can be further elaborated, which should be addressed in future research. Regarding the production of gaseous biofuels, methanogenic AF is a well-established technology with more than 132,000 large-scale digesters operating worldwide [16]. To further improve biogas yields, production rates, and quality, exploring cost-effective methods for pretreating feedstock, deepening our understanding of mechanisms of direct interspecies electron transfer, and predicting balanced trace element concentrations are among the most pressing topics [8,17]. In the context of anaerobic biorefinery approaches, integrating acidogenic (dark) and methanogenic AF has proven to be a viable option. In addition to methane, the transition from conventional methanogenic digesters to multiproduct biorefineries produces biohydrogen and various soluble bioproducts, primarily organic acids and alcohols [18,19,20]. Despite decades of research, there are still specific challenges related to yield and stability in dark fermentative hydrogen production. Substrate and inoculum pretreatment, the search for effective microbial strains, and the use of metal additives to stimulate hydrogenase activity are among the key areas of research aimed at addressing these issues and bringing this technology closer to the level of cost-effectiveness required for large-scale industrial applications [21,22,23]. Due to the inherent challenges in maintaining strict sterility in real feedstocks, the dark fermentation process faces the non-specific production of a mixture of low-chain organic acids. Currently, separating these acids is not economically feasible due to their high carbon-to-oxygen ratio. Therefore, research should focus on the integrated use of low-chain organic acids and alcohols as a substrate for producing biopolymers, medium-chain organic acids, and mixed alcohols, as well as biological nutrient removal [7]. To extract the accumulated acids, membrane technologies [24] should be developed, as well as other on-site and off-site VFA extraction techniques such as electrodialysis [25], which deserve more research in the future. A more intricate approach could involve the utilization of multi-omic techniques for a more profound analysis of taxonomic interactions, alterations in microbial ecosystems, and variations in the genetic regulation of crucial metabolic pathways under diverse operational and environmental conditions in acidogenic AF, which could also result in the identification of functional capabilities at the species level for both cultivable and uncultivable microbial populations [26]. In addition, new bioprocesses such as electrofermentation should be more actively explored in order to address redox and pH imbalances, as well as to promote carbon chain elongation or degradation. The ultimate goal is to increase overall biomass production and facilitate the production of specific bioproducts [27].

Thus, existing research has demonstrated the potential of AF biorefineries, and progress is being made in both upstream and downstream processing. Future research on feedstock pretreatment, fermentation, and product recovery will lead to the development of a waste-to-value chain that can compete with petrochemicals and promotes the circular bioeconomy.