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Fermentation
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The Future of Fermentation Technology in the Biorefining Process: 3rd...
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The Future of Fermentation Technology in the Biorefining Process: 3rd Edition

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Industrial Fermentation".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 9266

Special Issue Editor

Dr. Bartłomiej Zieniuk

E-Mail Website
Guest Editor
Department of Chemistry, Institute of Food Sciences, Warsaw University of Life Sciences-SGGW, 159C Nowoursynowska Str., 02-776 Warsaw, Poland
Interests: enzyme biosynthesis; enzymatic synthesis of compounds with antioxidant activity; lipases; Yarrowia lipolytica; chemistry of natural compounds
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The transition from a fossil-based economy to a circular bioeconomy requires the development of a high industrial symbiotic readiness level, continuous scientific innovations, and radical changes in the infrastructure of current industries. Biorefineries can play a crucial role in establishing this new type of economy, increasing the efficiencies of raw materials with the circular use of biomass and promoting the production of biochemicals and high-added-value compounds from industrial by-products and waste streams.

The aim of this Special Issue is to showcase the latest advancements in fermentation technology and bioprocessing for upgrading key industrial sectors into modern biorefineries, raising the awareness of all stakeholders on opportunities for utilizing waste and by-product streams from major industrial activities for the production of platform chemicals and biopolymers. Special attention will be given to the following research topics: (i) fermentation as the core bioprocess in biorefinery development; (ii) alternative raw materials as potential feedstocks for industrial biotechnology applications; (iii) innovative pretreatment (fractionation of raw materials) and advanced downstream processing (product separation and recovery) technologies coupled with efficient and innovative fermentation processes; (iv) pilot-scale, demo-scale, and commercial-scale case studies on biorefineries using fermentation as the main process; and (v) sustainability assessment tools to measure the socio-economic and environmental performance of these innovative facilities.

Dr. Bartłomiej Zieniuk
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fermentation is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • bioprocessing
  • biorefinery
  • alternative raw materials
  • utilization of industrial side streams
  • sustainability assessment

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Related Special Issue

Published Papers (6 papers)

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Research

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14 pages, 895 KB  
Article
Adding Digestive Enzymes to Anaerobic Co-Digestion of Cattle Manure and Industrial Corn Grain Waste
by Laís Medeiros Cintra, Roberta Passini, Luana Alves Akamine, Kedinna Dias de Sousa, Frank Freire Capuchinho, Sérgio Botelho de Oliveira and Silvia Robles Reis Duarte
Fermentation 2025, 11(12), 696; https://doi.org/10.3390/fermentation11120696 - 16 Dec 2025
Viewed by 178
Abstract
Brazil is one of the world’s largest producers of grains and cattle, activities that generate a large amount of organic waste, which has high potential for biogas and methane production. Cattle manure (CM) and industrial waste from corn processing are substrates with significant [...] Read more.
Brazil is one of the world’s largest producers of grains and cattle, activities that generate a large amount of organic waste, which has high potential for biogas and methane production. Cattle manure (CM) and industrial waste from corn processing are substrates with significant potential for biogas and methane generation, particularly through the process of anaerobic co-digestion (AcoD). This study aimed to assess the biogas and methane yield, as well as the stability of the AcoD process involving CM and corn grain residues (CG) derived from a grain processing agroindustry, in conjunction with the application of an enzyme complex. The experiment was conducted in plug-flow biodigesters, with a total volume of 28 L, under a semi-continuous feeding regime (OLR = 0.84 g vs. L d−1) at ambient temperature. The findings indicated increases in daily biogas and methane production for AcoD, without the addition of enzymes, of 52.1% and 44.4%, respectively, in comparison to CM mono-digestion. The incorporation of the enzyme complex did not yield beneficial effects, irrespective of the substrate composition. The utilization of enzymes in semi-continuous biodigesters to enhance methane yields necessitates further investigation to achieve favorable outcomes and validate its efficiency. Full article
(This article belongs to the Special Issue The Future of Fermentation Technology in the Biorefining Process: 3rd Edition)
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19 pages, 3219 KB  
Article
Improving Carbon Fixation and Acetate Production from Syngas Fermentation: On-Demand Versus Continuous Feeding
by Marta Pacheco, Tiago P. Silva, Carla Silva and Patrícia Moura
Fermentation 2025, 11(11), 640; https://doi.org/10.3390/fermentation11110640 - 12 Nov 2025
Viewed by 781
Abstract
Syngas fermentation is a promising carbon capture and utilization (CCU) technology for producing carboxylic acids while transforming low-cost waste gas into high-value products. This study evaluates the two bioreactor feeding strategies for synthesis gas (syngas) fermentation by Eubacterium callanderi (formerly Butyribacterium methylotrophicum) [...] Read more.
Syngas fermentation is a promising carbon capture and utilization (CCU) technology for producing carboxylic acids while transforming low-cost waste gas into high-value products. This study evaluates the two bioreactor feeding strategies for synthesis gas (syngas) fermentation by Eubacterium callanderi (formerly Butyribacterium methylotrophicum) strain Marburg—on-demand feeding (ODF) and continuous feeding (CF)—with a synthetic syngas mixture of 23 vol% CO2, 29 vol% CO, 32 vol% H2, and 16 vol% CH4, mimicking the syngas from lignocellulosic gasification. The ODF assay achieved a maximum syngas consumption rate of 112 mL/h, yielding 24.1 g/L acids, namely 22.9 g/L acetate and 1.3 g/L butyrate. CF of syngas at 223 mL/h required more gas (62.9 L) to produce 22.7 g/L total acids, from which 19.0 g/L acetate and 3.7 g/L butyrate were achieved. The CF-specific production rate (gproduct/gdry_cell_weight/hour) reached 0.5 g/gDCW/h (acetate) and 0.17 g/gDCW/h (butyrate), outperforming ODF with 0.3 and 0.02 g/gDCW/h, respectively. ODF minimized gas wastage and enabled CH4 accumulation inside the bioreactor up to approximately 78 vol%, while CF led to CO2 accumulation, indicating a need for more efficient CO2 utilization strategies, such as sequential fermentations. This work highlights the critical impact of the two feeding options studied with regard to scaling up the carbon-efficient production of carboxylic acids, and indicates that both strategies can have potential applications. ODF is ideal for increasing carbon fixation and achieving, simultaneously, gas cleaning, while CF fermentations are better suited to maximizing the acid production rate. Full article
(This article belongs to the Special Issue The Future of Fermentation Technology in the Biorefining Process: 3rd Edition)
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13 pages, 2095 KB  
Article
Combination Strategy of Bioenzymes and Sophorolipid Pretreatments Enhance Volatile Fatty Acid Production Based on Co-Fermentation of Waste Activated Sludge and Rubberwood Hydrolysates
by Fen Yin, Wenxuan Bie, Xiaojun Ma, Jianing Li, Yingying Zheng and Dongna Li
Fermentation 2025, 11(8), 486; https://doi.org/10.3390/fermentation11080486 - 21 Aug 2025
Viewed by 762
Abstract
In this study, we developed a combination strategy of bioenzymes and sophorolipid (SL) co-pretreatment to enhance volatile fatty acids (VFAs) in co-fermentation of waste activated sludge (WAS) and rubberwood hydrolysates (RWHs). Among all the pretreatments, SL and laccase co-pretreatment markedly increased soluble bioavailable [...] Read more.
In this study, we developed a combination strategy of bioenzymes and sophorolipid (SL) co-pretreatment to enhance volatile fatty acids (VFAs) in co-fermentation of waste activated sludge (WAS) and rubberwood hydrolysates (RWHs). Among all the pretreatments, SL and laccase co-pretreatment markedly increased soluble bioavailable substrates (carbohydrates and proteins) by inducing EPS catabolism and WAS disintegration, and obtained the highest VFAs yield of 7049.43 mg/L. The proportion of VFA composition can be controlled by modifying the types and amounts of added bioenzymes. Under SL and laccase co-pretreatment conditions, RWHs were more efficiently converted into VFAs due to the higher activity of WAS, resulting in lower cellulose (3.41%) and lignin (0.66%) content in the fermentation broth. Compared with other pretreatments, SL and laccase co-pretreatment enhanced the enrichment of the functional microorganisms, including anaerobic fermentation bacteria (Firmicutes, Bacteroidota, and Proteobacteria) and reducing bacteria (Acinerobacter and Ahniella). Therefore, the combination pretreatments might be a promising solution for strengthening VFA accumulation in the WAS and RWH co-fermentation. Full article
(This article belongs to the Special Issue The Future of Fermentation Technology in the Biorefining Process: 3rd Edition)
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25 pages, 7385 KB  
Article
Anaerobic Digestion of Food Waste and Granular Inoculum: Study on Temperature Effect and Substrate-to-Inoculum Ratio on Biogas Production
by Madalina Ivanovici, Gabriela-Alina Dumitrel, Vasile Daniel Gherman, Teodor Todinca, Ana-Maria Pana and Valentin Laurentiu Ordodi
Fermentation 2025, 11(6), 348; https://doi.org/10.3390/fermentation11060348 - 15 Jun 2025
Cited by 1 | Viewed by 3161
Abstract
The development of food waste anaerobic digestion (AD) is a contemporary research topic addressed in the scientific community to meet the requirements of food waste valorization and proper substrate configuration for an efficient AD process. In this study, multiple AD experiments were performed [...] Read more.
The development of food waste anaerobic digestion (AD) is a contemporary research topic addressed in the scientific community to meet the requirements of food waste valorization and proper substrate configuration for an efficient AD process. In this study, multiple AD experiments were performed on food waste together with industrial inoculum using laboratory-scale bioreactors. Food waste consisted mainly of fruits and vegetables (80.9%) and boiled rice (19.1%). The effect of operating temperature (33 °C, 37 °C, 41 °C, 45 °C) and the ratio between food waste mixture and inoculum-FIR (1:1, 3:2 and 2:1, w/w) on the production and composition of biogas, and the conversion yield for CH4 and organic carbon, were investigated. The best results were obtained at an FIR of 2:1 and a temperature of 37 °C, with a total biogas production of 468.59 NL h−1 kg−1VSadded (51% v/v CH4 conc.) and a conversion yield of 36.42% for CH4. A modified Gompertz model was applied on the accumulated CH4 and biogas to evaluate the process performance. The model parameters were investigated in conjunction with the physico-chemical characteristics of the substrate, inoculum taxonomic profile, pH measurements, and TG-DTA analysis. The conducted analyses emphasized the susceptibility of the selected substrate towards easy degradation and improved biotransformation reactions when temperature and FIR were increased. Full article
(This article belongs to the Special Issue The Future of Fermentation Technology in the Biorefining Process: 3rd Edition)
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Review

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20 pages, 3126 KB  
Review
Integrated Pretreatment and Microbial Matching for PHA Production from Lignocellulosic Agro-Forestry Residues
by Dongna Li, Shanshan Liu, Qiang Wang, Xiaojun Ma and Jianing Li
Fermentation 2025, 11(10), 563; https://doi.org/10.3390/fermentation11100563 - 29 Sep 2025
Viewed by 1376
Abstract
Lignocellulosic agro-forestry residues (LARs), such as rice straw, sugarcane bagasse, and wood wastes, are abundant and low-cost feedstocks for polyhydroxyalkanoate (PHA) bioplastics. However, their complex cellulose–hemicellulose–lignin matrix requires integrated valorization strategies. This review presents a dual-framework approach: “pretreatment–co-substrate compatibility” and “pretreatment–microbial platform matching”, [...] Read more.
Lignocellulosic agro-forestry residues (LARs), such as rice straw, sugarcane bagasse, and wood wastes, are abundant and low-cost feedstocks for polyhydroxyalkanoate (PHA) bioplastics. However, their complex cellulose–hemicellulose–lignin matrix requires integrated valorization strategies. This review presents a dual-framework approach: “pretreatment–co-substrate compatibility” and “pretreatment–microbial platform matching”, to align advanced pretreatment methods (including deacetylation–microwave integration, deep eutectic solvents, and non-sterilized lignin recovery) with engineered or extremophilic microbial hosts. A “metabolic interaction” perspective on co-substrate fermentation, encompassing dynamic carbon flux allocation, synthetic consortia cooperation, and one-pot process coupling, is used to elevate PHA titers and tailor copolymer composition. In addition, we synthesize comprehensive kinetic analyses from the literature that elucidate microbial growth, substrate consumption, and dynamic carbon flux allocation under feast–famine conditions, thereby informing process optimization and scalability. Microbial platforms are reclassified as broad-substrate, process-compatible, or product-customized categories to emphasize adaptive evolution, CRISPR-guided precision design, and consortia engineering. Finally, next-generation techno-economic analyses, embracing multi-product integration, regional adaptation, and carbon-efficiency metrics, are surveyed to chart viable paths for scaling LAR-to-PHA into circular bioeconomy manufacturing. Full article
(This article belongs to the Special Issue The Future of Fermentation Technology in the Biorefining Process: 3rd Edition)
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19 pages, 1361 KB  
Review
Sugarcane Bagasse: A Sustainable Feedstock for Biorefinery Portfolios in South Africa
by Lindile Nhleko and Patrick T. Sekoai
Fermentation 2025, 11(9), 489; https://doi.org/10.3390/fermentation11090489 - 22 Aug 2025
Viewed by 2247
Abstract
Rising global populations, infrastructural development, and rapid urbanization have heightened the reliance on a linear economy, resulting in severe environmental and human impacts. This crisis has triggered an urgent quest for sustainable and ecologically benign innovations, as outlined in the United Nations’ Sustainable [...] Read more.
Rising global populations, infrastructural development, and rapid urbanization have heightened the reliance on a linear economy, resulting in severe environmental and human impacts. This crisis has triggered an urgent quest for sustainable and ecologically benign innovations, as outlined in the United Nations’ Sustainable Development Goals (SDGs). This review investigates the potential of sugarcane bagasse (SCB) as a promising feedstock for advancing circular bioeconomy initiatives in South Africa. It shows how this copious bioresource can be utilized to enhance the country’s biobased value chains by producing bio-commodities, such as biofuels and platform chemicals. The review also identifies the driving forces behind the circular bioeconomy model within the South African sugarcane industry. To achieve the circular bioeconomy, it outlines essential technological prerequisites, including critical pretreatment strategies and emerging bio-innovations necessary for the effective valorization of SCB. Furthermore, it showcases the R&D and commercial strides that have been achieved in South Africa. Finally, the study covers techno-economic studies that corroborate the economic viability of this domain. In conclusion, harnessing SCB not only presents a viable biorefinery pathway towards sustainable economic growth but also contributes to environmental preservation and social well-being, aligning with global sustainability imperatives. The successful integration of these innovative approaches could play a pivotal role in transforming the South African sugarcane industry into a continental leader in circular bioeconomy innovations. Full article
(This article belongs to the Special Issue The Future of Fermentation Technology in the Biorefining Process: 3rd Edition)
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