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Sustainable Bioprocesses for Valorization of Food Industry Waste: Microbial and...
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Sustainable Bioprocesses for Valorization of Food Industry Waste: Microbial and Enzymatic Innovations and Reactor Design

A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Biological Processes and Systems".

Deadline for manuscript submissions: 31 August 2026 | Viewed by 2922

Special Issue Editors

Dr. Pedro Fernandes

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Guest Editor
1. BioRG—Bioengineering and Sustainability Research Group, Faculty of Engineering, Universidade Lusófona, Campo Grande 376, 1749-024 Lisbon, Portugal
2. iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico (IST), Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
3. Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
Interests: biocatalysis; bioreactors; bioprocess engineering
Special Issues, Collections and Topics in MDPI journals
Dr. Carla C. C. R. de Carvalho

E-Mail Website
Guest Editor
iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
Interests: bacterial adaptation; marine biotechnology; biocatalysis; bioreactors; bioprocess engineering
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

According to FAO, approximately a third of all food produced for human consumption is lost or wasted. In the European Union alone, it is estimated that 132 kg of food waste per inhabitant are generated annually. Innovative strategies for the valorization of this waste for nutrient recovery, as an example, is thus paramount. This Special Issue focuses on cutting-edge biotechnological solutions that harness microbial and enzymatic processes to convert waste streams into valuable products, promoting circular economy principles. Key areas to be addressed include the following:

  • Microbial and Enzymatic Innovations: Exploration of novel microbial strains, enzymatic catalysts, and metabolic engineering approaches that enhance the efficiency of product recovery and bioconversion processes.
  • Bioreactor Design: Advances in reactor configurations, optimization strategies, and process control mechanisms that improve scalability and performance at industrial level.
  • Sustainability and Environmental Impact: Assessing the ecological benefits, economic feasibility, and lifecycle analyses of these bioprocesses in achieving a sustainable food sector.

By integrating bioprocess engineering, microbiology, and enzyme technology, this Special Issue aims to provide transformative insights into waste valorization strategies that support global sustainability goals, with interest for researchers, industry professionals, and policymakers.

Dr. Pedro Fernandes
Dr. Carla C. C. R. de Carvalho
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-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Processes is an international peer-reviewed open access semimonthly 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 2400 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

  • sustainable bioprocesses
  • bioprocess engineering
  • microbial and enzymatic processes
  • waste valorization strategies
  • valuable products
  • reactor design

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Published Papers (4 papers)

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Research

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11 pages, 933 KB  
Article
Evaluation of Edible Pleurotus ostreatus for Cellulase Production by Submerged Fermentation Using Bench-Scale Bioreactor
by Olimpio C. Escosteguy, Dinalva Schein, Gustavo N. Pezzini and Marcio A. Mazutti
Processes 2026, 14(6), 990; https://doi.org/10.3390/pr14060990 - 20 Mar 2026
Viewed by 272
Abstract
Industries seek microorganisms capable of producing all types of cellulases, using low-cost substrate and under adequate process conditions, especially through submerged fermentation. Pleurotus ostreatus “L123” was evaluated as a potential microorganism for cellulase production, assaying total cellulolytic activity (FPase). Fermentation was carried out [...] Read more.
Industries seek microorganisms capable of producing all types of cellulases, using low-cost substrate and under adequate process conditions, especially through submerged fermentation. Pleurotus ostreatus “L123” was evaluated as a potential microorganism for cellulase production, assaying total cellulolytic activity (FPase). Fermentation was carried out using a 14L bioreactor, inoculated with 10% (v/v) grown on potato dextrose broth for 4 days. Fermentation media was composed of defatted rice bran (50 g/L), glucose (5 g/L), corn steep liquor (5 g/L) and chloramphenicol (0.25 g/L). Aeration and agitation effects on enzymatic activity were evaluated using a central composite design (CCD) for FPase after 5 days of fermentation. The obtained model was statistically significant, with the interaction of both parameters also being significant and presenting a negative effect. Membrane ultrafiltration (150 kDa MWCO) led to an approximately 3-fold increase in specific activity of permeate (0.6441 vs. 0.2043 FPU/mg of protein), with retention of around 80% of protein content while maintaining enzymatic activity of permeate similar to unfiltered broth (0.0932 vs. 0.0923 FPU/mL). The maximum value obtained experimentally was 0.1444 FPU/mL, which is significantly lower in comparison to commercially used strains and consequently unfeasible for industrial use at current state. However, after further improvements and optimization, Pleurotus ostreatus “L123” can become an alternative for in situ cellulase production through submerged fermentation. Full article
(This article belongs to the Special Issue Sustainable Bioprocesses for Valorization of Food Industry Waste: Microbial and Enzymatic Innovations and Reactor Design)
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18 pages, 3120 KB  
Article
Use of Demerara and VHP Sugars Combined with Various Nitrogen Sources for Enhanced Fructosyltransferase Production in Aspergillus oryzae IPT-301
by Amanda P. S. Cavini, Mariana F. M. Cardoso, Ana Carolina Vieira, Marta Filipa Simões, Alex Fernando de Almeida, Maria L. A. N. Teixeira, Sergio A. V. Morales, Alfredo E. Maiorano, Rafael F. Perna and Cristiane A. Ottoni
Processes 2026, 14(5), 840; https://doi.org/10.3390/pr14050840 - 5 Mar 2026
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Abstract
This study investigated the effect of low-cost carbon and nitrogen sources on fructosyltransferase (FTase) production by Aspergillus oryzae IPT-301, aiming to optimize the enzymatic synthesis of fructooligosaccharides (FOS), prebiotic compounds valued for their bifidogenic effects. FTase is a key enzyme in transfructosylation, the [...] Read more.
This study investigated the effect of low-cost carbon and nitrogen sources on fructosyltransferase (FTase) production by Aspergillus oryzae IPT-301, aiming to optimize the enzymatic synthesis of fructooligosaccharides (FOS), prebiotic compounds valued for their bifidogenic effects. FTase is a key enzyme in transfructosylation, the central step in FOS production. To reduce production costs, Very High Polarization (VHP) and Demerara (DM) sugars were evaluated as carbon sources, while sodium nitrate (NaNO3), ammonium sulfate (NH4)2SO4, and urea were tested as nitrogen sources. FTase production, both extracellular and intracellular, was conducted under submerged fermentation at 30 °C and 200 rpm for 72 h. DM sugar outperformed VHP, increasing extracellular and intracellular transfructosylation activity (AT) by 2.3-fold and 2.1-fold, respectively. Among nitrogen sources, NaNO3 was most effective in DM-containing media, yielding 1.6–2.0 times higher extracellular AT and up to 4.7 times greater intracellular activity compared to other nitrogen sources. These findings suggest that the combination of DM sugar and NaNO3 significantly enhances FTase yield, providing a cost-effective strategy for industrial-scale FOS production. Full article
(This article belongs to the Special Issue Sustainable Bioprocesses for Valorization of Food Industry Waste: Microbial and Enzymatic Innovations and Reactor Design)
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11 pages, 669 KB  
Article
Valorization of Fatty Acid by Catalytic Sugar Derivatization: Lipase Versus Layered Double Hydroxide
by Alan José Corrêa Manso, Ana Gabriela R. A. Soares, Gabriel F. S. Silva, Mayllon S. Oliveira, Gizele C. F. Sant’Ana, Luiz F. B. Malta, Ivana L. M. Ferreira and Jaqueline D. Senra
Processes 2026, 14(4), 584; https://doi.org/10.3390/pr14040584 - 7 Feb 2026
Viewed by 378
Abstract
Sugar fatty acid esters represent promising scaffolds for technological applications. These compounds are low-cost and allow rapid modulation of their properties. In this study, we have shown that lipase obtained from solid fermentation from Aspergillus niger (hydrolytic activity of 8.32 × 106 [...] Read more.
Sugar fatty acid esters represent promising scaffolds for technological applications. These compounds are low-cost and allow rapid modulation of their properties. In this study, we have shown that lipase obtained from solid fermentation from Aspergillus niger (hydrolytic activity of 8.32 × 106 U/g) can promote a selective route towards the 2,5-dissubstituted D-mannitol laurate. Indeed, the lipase hydrolytic activity allowed the yield of 80% in DMF (P.A.) at 55 °C and 6 h. Finally, Mg/Al layered double hydroxides (LDH) were compared towards the selectivity of the expected dissubstituted product. The data obtained through the comparative analysis allows establishing some variables such as solvent (DMF), temperature (55 °C) and solvent dehydration degree for obtaining these molecules for future application studies in supramolecular gelation systems. Full article
(This article belongs to the Special Issue Sustainable Bioprocesses for Valorization of Food Industry Waste: Microbial and Enzymatic Innovations and Reactor Design)
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Review

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23 pages, 2706 KB  
Review
Sustainable Production of Alternative Proteins from Basidiomycetes: Valorization of Mycelial and Fruiting Body Biomass
by Amanda Rubia de Figueiredo Trindade, Isadora de Brito Hilario, Ederson Aparecido Gimenes da Rocha, Leonardo Antônio da Rosa Borges dos Santos, Cristina Giatti Marques de Souza, Marina Proença Dantas, Bruna Mayara Roldão Ferreira, Rúbia Carvalho Gomes Corrêa, Natália Ueda Yamaguchi, Adelar Bracht and Rosane Marina Peralta
Processes 2025, 13(11), 3746; https://doi.org/10.3390/pr13113746 - 20 Nov 2025
Cited by 1 | Viewed by 1363
Abstract
Global population growth, climate change, and the environmental impact of livestock production have accelerated the search for sustainable and efficient protein sources. Fruiting bodies (mushrooms) and mycelial biomass have emerged as promising alternatives due to their high nutritional quality, low ecological footprint, and [...] Read more.
Global population growth, climate change, and the environmental impact of livestock production have accelerated the search for sustainable and efficient protein sources. Fruiting bodies (mushrooms) and mycelial biomass have emerged as promising alternatives due to their high nutritional quality, low ecological footprint, and compatibility with circular bioeconomy principles. This review highlights the nutritional, biotechnological, and environmental aspects of fungal proteins obtained from both fruiting bodies and mycelial biomass of Basidiomycetes. Emphasis is placed on amino acid composition, protein digestibility, and advances in cultivation and fermentation systems for large-scale production. Submerged and solid-state fermentation processes are analyzed in terms of scalability, resource efficiency, and integration with agro-industrial residues for sustainable bioprocessing. Comparative analyses reveal that mycelial biomass production achieves high protein yields with significantly reduced land, water, and energy requirements compared to conventional protein sources. Emerging fungal species such as Schizophyllum commune and Auricularia polytricha demonstrate strong potential for producing protein-rich mycelia applicable to functional and plant-based foods. Finally, the review discusses current technological innovations, regulatory frameworks, and market perspectives that position fungal biomass as a strategic component in the ongoing global protein transition. Full article
(This article belongs to the Special Issue Sustainable Bioprocesses for Valorization of Food Industry Waste: Microbial and Enzymatic Innovations and Reactor Design)
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