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Fermentation
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Application of Microbial Metabolism and Fermentation in Waste Management
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Application of Microbial Metabolism and Fermentation in Waste Management

A Special Issue of Fermentation (ISSN 2311-5637) belonging to the section "Industrial Fermentation".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 6639

Editor

Dr. Pengsong Li

E-Mail Website
Guest Editor
College of Environmental Science and Engineering, Beijing Forestry University, Beijing 100083, China
Interests: microbiome; synthetic biology; microbial CO2 conversion; biofuel; waste management
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The escalating challenge of waste generation necessitates innovative and sustainable management strategies that align with the principles of a circular economy. Microbial metabolism and fermentation processes present a powerful and versatile toolkit to address this challenge, transforming wastes from an environmental burden into valuable resources. This Special Issue, “Application of Microbial Metabolism and Fermentation in Waste Management,” aims to collate cutting-edge research that explores the pivotal role of microorganisms in waste management.

We invite contributions that delve into the microbial conversion of diverse organic wastes, such as municipal solid waste, agricultural residues, domestic sewage, and industrial effluents, into high-value products. Topics of interest include, but are not limited to, the production of biofuels (e.g., biogas, biohydrogen, bioethanol), platform chemicals, bioplastics, enzymes, and biofertilizers through anaerobic digestion, solid-state fermentation, and other novel bioprocesses. Studies focusing on the isolation and engineering of robust microbial consortia, the elucidation of metabolic pathways, the optimization of fermentation parameters for enhanced yield and efficiency, and the integration of these processes into sustainable waste management frameworks are highly encouraged. Research addressing the mitigation of greenhouse gas emissions and the bioremediation of hazardous contaminants using microbial systems is also welcome.

This Special Issue seeks to highlight advancements that bridge fundamental microbiology with practical engineering applications, offering solutions for waste reduction, energy recovery, and environmental protection. We welcome original research articles, reviews, and short communications that contribute to a deeper understanding and improved application of microbial fermentation technologies in creating a more sustainable future.

We look forward to receiving your innovative contributions.

Dr. Pengsong Li
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-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

  • waste management
  • microbial metabolism
  • aerobic composting
  • anaerobic digestion
  • biofuel
  • microbial fuel cell
  • microbial wastewater treatment
  • syngas fermentation

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Published Papers (5 papers)

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Research

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22 pages, 3517 KB  
Article
Valorization of Maize Lime-Cooking Wastewater Through Lipid and Carotenoid Production by Rhodotorula glutinis Yeast: An Approach Using Pulse Fed-Batch Culture and Techno-Economic Assessment
by Carolina Ramírez-Martínez, Gael Jesús Molina-Benítez, Mariana Franco-Morgado and Alberto Ordaz
Fermentation 2026, 12(6), 285; https://doi.org/10.3390/fermentation12060285 - 15 Jun 2026
Viewed by 657
Abstract
The increasing generation of agro-industrial residues like nejayote (maize lime-cooking wastewater from the maize nixtamalization process) poses significant environmental challenges in Mexico due to its elevated chemical oxygen demand (COD) and organic load. This study evaluates the physical separation of nejayote via membranes [...] Read more.
The increasing generation of agro-industrial residues like nejayote (maize lime-cooking wastewater from the maize nixtamalization process) poses significant environmental challenges in Mexico due to its elevated chemical oxygen demand (COD) and organic load. This study evaluates the physical separation of nejayote via membranes and its use as a low-cost substrate for producing lipids and carotenoids using Rhodotorula glutinis. A batch culture followed by pulse-feeding achieved a COD removal efficiency of 53.6% (0.22 g COD/(L h)) and a biomass concentration of 3.72 ± 0.45 g COD/L within 48 h. The yeast demonstrated a high specific metabolic efficiency, yielding 0.457 g of lipids and 0.0049 g of carotenoids per gram of biomass, with an oleaginous fraction of 46.21% in dry weight. Experimental data calibrated a process model in SuperPro Designer, simulating full-scale processes treating 100, 1000, and 10,000 m3 of nejayote per batch, producing up to 2137.11 MT of lipids and 22.90 MT of carotenoids annually. A techno-economic analysis estimated the investment, operating costs, and financial indicators for all scenarios. Strategies like evaporation and reverse osmosis to concentrate nejayote significantly improved profitability by reducing equipment size. Additionally, a circular economy approach was modeled, recovering process water and nutrient-rich side streams. These findings confirm that integrated physical and biological treatment, coupled with resource recovery, transforms this particularly agro-industrial residue into a technically robust and economically viable biorefinery feedstock, aligning industrial production with sustainable waste management. Full article
(This article belongs to the Special Issue Application of Microbial Metabolism and Fermentation in Waste Management)
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20 pages, 3519 KB  
Article
Valorizing Red Seaweed Spent Biomass into Reducing Sugars for β-Carotene Production by Rhodotorula paludigena
by Chatchol Kongsinkaew, Chutipol Tangsattayatithan, Supenya Chittapun, Parivat Phiphatbunyabhorn, Tunyaboon Laemthong, Mariena Ketudat-Cairns, Soisuda Pornpukdeewattana, Awanwee Petchkongkaew and Theppanya Charoenrat
Fermentation 2026, 12(5), 210; https://doi.org/10.3390/fermentation12050210 - 24 Apr 2026
Viewed by 1785
Abstract
Seaweed bioactive extraction generates de-extracted residual solids that remain carbohydrate-rich but are often underutilized. This study developed an integrated valorization route for Gracilaria fisheri spent biomass to produce fermentable sugars for β-carotene production by Rhodotorula paludigena CM33. Reducing sugar production was optimized using [...] Read more.
Seaweed bioactive extraction generates de-extracted residual solids that remain carbohydrate-rich but are often underutilized. This study developed an integrated valorization route for Gracilaria fisheri spent biomass to produce fermentable sugars for β-carotene production by Rhodotorula paludigena CM33. Reducing sugar production was optimized using response surface methodology (Box–Behnken design) by varying reaction time, sulfuric acid concentration, and biomass loading at 90 °C. The predicted optimum (47.39 min, 2.50% (w/v) H2SO4, and 7.13% (w/v) biomass) yielded 22.41 g/L reducing sugars and was validated experimentally at 22.22 ± 0.19 g/L, indicating that the model reliably predicted reducing sugar production. The optimized condition was scaled up in a 22 L bioreactor with sequential acid hydrolysis followed by enzyme-assisted hydrolysis, increasing reducing sugars from ~30 to ~40 g/L. FTIR and SEM analyses indicated progressive modification of the carbohydrate matrix across processing stages. Batch cultivation of R. paludigena on the hydrolysate showed that ammonium sulfate supplementation significantly increased biomass, whereas β-carotene titers were not significantly different. Repeated-batch operation on non-supplemented hydrolysate sustained production over four cycles with β-carotene titers of 13.75–17.27 mg/L, demonstrating the operational feasibility of the hydrolysate-based system. Overall, this work demonstrates a practical seaweed biorefinery approach to upgrade G. fisheri spent biomass into sugars and carotenoid-rich yeast biomass. Full article
(This article belongs to the Special Issue Application of Microbial Metabolism and Fermentation in Waste Management)
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16 pages, 2002 KB  
Article
Continuous Lactic Acid Fermentation of Actual Food Waste Slurry: Effects of Reaction Temperature and Hydraulic Retention Time
by Luxin Yang, Chuyun Zhao, Caiping Sun and Huan Li
Fermentation 2025, 11(12), 654; https://doi.org/10.3390/fermentation11120654 - 21 Nov 2025
Cited by 1 | Viewed by 1812
Abstract
Food waste (FW) valorization via lactic acid (LA) fermentation is a promising approach, yet most studies rely on surrogate substrates, limiting industrial applicability. This study investigated continuous LA fermentation of actual FW slurry from a Shenzhen treatment plant, focusing on the effects of [...] Read more.
Food waste (FW) valorization via lactic acid (LA) fermentation is a promising approach, yet most studies rely on surrogate substrates, limiting industrial applicability. This study investigated continuous LA fermentation of actual FW slurry from a Shenzhen treatment plant, focusing on the effects of hydraulic retention time (HRT: 1.33, 2.0, 3.0 days) and temperature (25, 30, 35, 40 °C) under open-culture conditions. Results showed that hydraulic retention time (HRT) and temperature jointly regulated fermentation performance and microbial communities. Short HRT (1.33 days) caused system instability with fluctuating LA concentrations, while extending the HRT to 2 days enhanced stability, achieving LA concentrations exceeding 14,000 mg/L across all temperatures. Further increasing the HRT to 3 days reduced LA yield and acidification rate, accompanied by acetic/propionic acid accumulation, especially at higher temperatures. Temperature affected the system’s hydrolysis rate, with higher temperatures promoting the hydrolysis of cellulose and hemicellulose. Metagenomic analysis revealed that Lactobacillaceae dominated (>90% of bacteria). The phosphoketolase pathway was the most abundant LA-producing route, and temperature and HRT affected carbohydrate-active enzyme profiles. Balancing efficiency and cost, an HRT of 2 days at 30–35 °C is recommended for industrial LA fermentation of actual FW. Full article
(This article belongs to the Special Issue Application of Microbial Metabolism and Fermentation in Waste Management)
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Review

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22 pages, 1728 KB  
Review
Photobiological Hydrogen Production in Cyanobacteria: Advances, Challenges, and Perspectives
by Wangruixue Tang, Zonghao Cheng, Weide Li, Pengsong Li, Ming Chen and Yujie Fu
Fermentation 2026, 12(6), 273; https://doi.org/10.3390/fermentation12060273 - 5 Jun 2026
Cited by 1 | Viewed by 1185
Abstract
Hydrogen molecules can serve as a promising clean energy supplier; conventional hydrogen production usually relies on fossil fuels and leads to intense greenhouse gas emissions. Significant emphasis has been placed on exploring sustainable and renewable hydrogen resources. Cyanobacteria can convert solar energy into [...] Read more.
Hydrogen molecules can serve as a promising clean energy supplier; conventional hydrogen production usually relies on fossil fuels and leads to intense greenhouse gas emissions. Significant emphasis has been placed on exploring sustainable and renewable hydrogen resources. Cyanobacteria can convert solar energy into hydrogen through oxygen-sensitive hydrogenases or nitrogenases. However, practical application remains severely constrained by oxygen-evolving photosynthesis, inefficient electron allocation, and the low metabolic priority of hydrogen production in cyanobacterial cells. In recent years, substantial progress has been achieved in understanding hydrogen metabolism and improving hydrogen production through physiological regulation, hydrogenase engineering, photosynthetic electron transport chain (PETC) reconstruction, metabolic engineering, and biohybrid systems. This review summarizes recent advances in cyanobacterial hydrogen production, with particular emphasis on hydrogen-producing pathways, key limiting factors, and current engineering strategies. Importantly, this review highlights that many currently reported strategies still provide only transient improvements because hydrogen production is constrained by system-level conflicts among photosynthesis, redox balance, carbon fixation, and cellular stability. In addition, emerging approaches including metagenomic resource mining, synthetic biology, AI-assisted engineering, biohybrid photoelectrochemical systems, and techno-economic optimization are discussed as potential directions for improving the efficiency, scalability, and practical feasibility of cyanobacterial hydrogen production technologies in the future. Full article
(This article belongs to the Special Issue Application of Microbial Metabolism and Fermentation in Waste Management)
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32 pages, 3253 KB  
Review
From Latin American Agro-Industrial Waste and CO2 to High-Value Bioproducts: Fermentation-Based Production Platforms for a Regional Bioeconomy
by José Rubén Morones-Ramírez
Fermentation 2026, 12(6), 268; https://doi.org/10.3390/fermentation12060268 - 30 May 2026
Viewed by 497
Abstract
This focused review examines fermentation and fermentation-integrated microbial platforms that convert two regionally relevant substrate classes, Latin American agro-industrial residues and concentrated CO2 streams, into high-value bioproducts. The review is not intended as a complete survey of all biomass valorization routes in [...] Read more.
This focused review examines fermentation and fermentation-integrated microbial platforms that convert two regionally relevant substrate classes, Latin American agro-industrial residues and concentrated CO2 streams, into high-value bioproducts. The review is not intended as a complete survey of all biomass valorization routes in Latin America. Instead, it evaluates platform–feedstock–product combinations with clear translational relevance for regional biorefineries, with emphasis on literature from 2020–2025 and on earlier benchmark studies only when they define current technical performance limits. Latin America and the Caribbean combine high-volume sugarcane, agave, coffee, citrus, banana, cacao, and tuber-processing residues with biogenic CO2 from ethanol fermentation and industrial point sources from cement, lime, and oil-and-gas operations. The technical opportunity is therefore not residue abundance alone, but the rational coupling of residue chemistry, CO2-source quality, locally isolated microbial strains, and process architectures that can be scaled under regional constraints. We compare phototrophic CO2-fixing modules based on cyanobacteria and microalgae, chemoautotrophic gas fermentation using Cupriavidus necator and related systems, heterotrophic yeast platforms including Rhodotorula spp. and Yarrowia lipolytica, and bacterial platforms for PHAs, bacterial cellulose, and organic acids. The core technical analysis focuses on substrate conditioning, hydrolysate inhibition, oxygen- and gas-transfer constraints, light delivery, C/N control, mixed-sugar utilization, metabolic engineering, reactor configuration, downstream processing, and quantitative reporting metrics. One fermentation-integrated laboratory case study—the Synechocystis sp. PCC 6803–Rhodotorula mucilaginosa UANL-001L CO2-to-carotenoid relay—and one explicitly defined non-fermentative boundary case on peel-extract-derived coating films are used to illustrate two different aspects of regional biorefinery design: dual-feedstock microbial conversion and low-CapEx product-fit decisions for agro-industrial residues. We conclude that Latin America’s strongest near-term position is in technically disciplined, product-specific biorefineries that integrate local feedstock chemistry with engineered or locally adapted chassis, rather than in generic biomass-to-product claims. Full article
(This article belongs to the Special Issue Application of Microbial Metabolism and Fermentation in Waste Management)
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