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Fermentation
Special Issues
Microbial Upcycling of Organic Waste to Biofuels and Biochemicals
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Microbial Upcycling of Organic Waste to Biofuels and Biochemicals

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

Deadline for manuscript submissions: 30 September 2026 | Viewed by 6435

Editors

Dr. Le Zhang

E-Mail Website
Guest Editor
Biomass Energy Engineering Center, Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
Interests: biomass energy engineering; waste-to-resource technologies; environmental microbial technologies
Special Issues, Collections and Topics in MDPI journals
Dr. Rouf Ahmad Dar

E-Mail Website
Guest Editor
Biomass Energy Engineering Centre, Department of Resources and Environment, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
Interests: anaerobic digestion; microbial management of organic wastes; biofuels; lignocellulolytic enzyme production

Special Issue Information

Dear Colleagues,

The management of organic wastes is currently a critical challenge globally. Of specific interest is food waste, agricultural waste, horticultural waste, animal manure, waste-activated sludge, wastewater, algal residues, and other industrial organic residues. Meanwhile, abundant renewable energy and resources remain unharnessed in such organic wastes. Therefore, to overcome the challenge, a large number of studies on microbial fermentation technologies have been conducted to convert various organic wastes to biofuels and biochemicals. For instance, anaerobic digestion of organic wastes can be performed for the production of methane-rich biogas. Acidogenic fermentation of organic wastes can be conducted for the production of carboxylic acids. Fermentation of oleaginous yeast can be carried out for the production of microbial lipids. Additionally, biohydrogen can be obtained through dark fermentation of organic wastes, and polypeptide can be produced from the fermentation of certain pure strains. These studies and related field-scale tests have contributed a lot to improving the sustainability of a circular economy.

To further enhance the process efficiency, studies on some enhancing strategies, such as feedstock pretreatment, microbial bio-augmentation, and supplementation of additives in fermentation bioreactors, have been conducted with promising findings, but the efficiency requires further confirmation in larger-scale fermentation systems. To make the fermentation systems more practical, lifecycle assessment and cost–benefit analysis have been performed to analyze the economic feasibility. The post-treatment of the fermentation liquid also requires more investigation to find the appropriate approaches that can reduce its environmental impacts and treatment cost.

In the global context of circular economy, this Special Issue aims to encourage and advance the research of microbial fermentation technologies for the conversion of various organic wastes into biofuels and biochemicals.

Dr. Le Zhang
Dr. Rouf Ahmad Dar
Guest Editors

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-anonymized 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

  • fermentation
  • organic wastes
  • biochemicals
  • biofuels
  • bioenergy
  • biogas
  • biohydrogen
  • anaerobic digestion
  • acidogenic fermentation
  • dark fermentation

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Published Papers (2 papers)

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Review

41 pages, 3378 KB  
Review
Current Trends of Cellulosic Ethanol Technology from the Perspective of Industrial Development
by Gabrielly Karla Silva Santos, Carlos Eduardo de Farias Silva, Brígida Maria Villar da Gama, Josimayra Almeida Medeiros, Mathieu Brulé, Albanise Enide da Silva, Renata Maria Rosas Garcia Almeida, Daniele Vital Vich, Rafail Isemin, Xianhua Guo and Ana Karla de Souza Abud
Fermentation 2026, 12(1), 48; https://doi.org/10.3390/fermentation12010048 - 14 Jan 2026
Cited by 3 | Viewed by 2911
Abstract
Driven by the energy transition within the framework of the United Nations Framework Convention on Climate Change, second-generation (2G) ethanol stands out as a technical and sustainable alternative to fossil fuels. Although first-generation ethanol, produced from saccharine and starchy feedstocks, represents an advance [...] Read more.
Driven by the energy transition within the framework of the United Nations Framework Convention on Climate Change, second-generation (2G) ethanol stands out as a technical and sustainable alternative to fossil fuels. Although first-generation ethanol, produced from saccharine and starchy feedstocks, represents an advance in mitigating emissions, its expansion is limited by competition with areas destined for food production. In this context, 2G ethanol, obtained from residual lignocellulosic biomass, emerges as a strategic route for diversifying and expanding the renewable energy matrix. Thus, this work discusses the current state of 2G ethanol technology based on the gradual growth in production and the consolidation of this route over the last few years. Industrial second-generation ethanol plants operating around the world demonstrate the high potential of agricultural waste as a raw material, particularly corn straw in the United States, which offers a lower cost and significant yield in the production of this biofuel. Similarly, in Brazil, sugarcane by-products, especially bagasse and straw, are consolidating as the main sources for 2G ethanol, integrated into the biorefinery concept and the valorization of by-products obtained during the 2G ethanol production process. However, despite the wide availability of lignocellulosic biomass and its high productive potential, the consolidation of 2G ethanol is still conditioned by technical and economic challenges, especially the high costs associated with pretreatment stages and enzymatic cocktails, as well as the formation of inhibitory compounds that compromise the efficiency of the process. Genetic engineering plays a particularly important role in the development of microorganisms to produce more efficient enzymatic cocktails and to ferment hexoses and pentoses (C6 and C5 sugars) into ethanol. In this scenario, not only are technological limitations important but also public policies and tax incentives, combined with the integration of the biorefinery concept and the valorization of (by)products, which prove fundamental to reducing costs, increasing process efficiency, and ensuring the economic viability and sustainability of second-generation ethanol. Full article
(This article belongs to the Special Issue Microbial Upcycling of Organic Waste to Biofuels and Biochemicals)
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28 pages, 1337 KB  
Review
Recent Advances in Microbial Bioconversion as an Approach to Boost Hydroxytyrosol Recovery from Olive Mill Wastewater
by Irene Maria Zingale, Anna Elisabetta Maccarronello, Claudia Carbone, Cinzia Lucia Randazzo, Teresa Musumeci and Cinzia Caggia
Fermentation 2025, 11(8), 477; https://doi.org/10.3390/fermentation11080477 - 20 Aug 2025
Cited by 2 | Viewed by 2982
Abstract
Olive mill wastewater (OMWW) is a highly complex matrix derived from olive oil extraction, containing phenolic compounds, lipids, minerals, and organic acids. Hydroxytyrosol (HT), an outstanding antioxidant and health-promoting phenolic compound, has garnered significant interest as a natural preservative and functional ingredient. Enzymatic [...] Read more.
Olive mill wastewater (OMWW) is a highly complex matrix derived from olive oil extraction, containing phenolic compounds, lipids, minerals, and organic acids. Hydroxytyrosol (HT), an outstanding antioxidant and health-promoting phenolic compound, has garnered significant interest as a natural preservative and functional ingredient. Enzymatic hydrolysis, utilizing purified enzymes to cleave glycosidic or ester bonds, and microbial bioconversion, employing whole microorganisms with their intrinsic enzymes and metabolic pathways, are effective biotechnological strategies for fostering the release of HT from its conjugated forms. These approaches offer great potential for the sustainable recovery of HT from OMWW, contributing to the valorization of this environmentally impactful agro-industrial by-product. Processed OMWW can lead to clean-label HT-enriched foods and beverages, capitalizing on by-product valorization and improving food safety and quality. In this review, the most important aspects of the chemistry, technology, and microbiology of OMWW were explored in depth. Recent trends and findings in terms of both enzymatic and microbial bioconversion processes are critically discussed, including spontaneous and driven fermentation, using selected microbial strains. These approaches are presented as economically viable options for obtaining HT-enriched OMWW for applications in the food and nutraceutical sectors. The selected topics aim to provide the reader with a solid background while inspiring and facilitating future research and innovation. Full article
(This article belongs to the Special Issue Microbial Upcycling of Organic Waste to Biofuels and Biochemicals)
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