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Fermentation
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10th Anniversary of Fermentation: Feature Papers in Section “Microbial...
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10th Anniversary of Fermentation: Feature Papers in Section “Microbial Metabolism, Physiology & Genetics”

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 3110

Special Issue Editors

Prof. Dr. Giovanni Vigliotta

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Guest Editor
Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, SA, Italy
Interests: energy metabolism; fermentation; molecular biology; antibiotics production; gene expression; growth control; food shelf life; bioremediation; water treatment; PGPB characterization
Prof. Dr. Rosanna Tofalo

E-Mail Website
Guest Editor
Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Via Balzarini 1, 64100 Teramo, Italy
Interests: wine yeast; saccharomyces cerevisiae; kluyveromyces marxianus; non-saccharomyces; yeast physiology; yeast flocculation; biofilm; biogenic amines
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

On the 10th anniversary of Fermentation, we are pleased to announce a Special Issue entitled “10th Anniversary of Fermentation: Feature Papers in Section “Microbial Metabolism, Physiology & Genetics”. Over the years, this section of Fermentation has addressed numerous interdisciplinary topics related to microorganisms and their biotechnological applications. It has contributed to the growth of the journal with the publication of numerous original articles on topics including the production of primary and secondary metabolites and the optimization of metabolic pathways for improving the yield and quality of products; responses to environmental stresses and changes in culture conditions, with particular attention to industrial growth conditions; development of genetically modified microorganisms for the production of bioactive compounds and sustainable materials, including the use of advanced CRISPR-Cas techniques and the synthesis of genetic circuits; the application of omics approaches (genomics, proteomics, and metabolomics) and bioinformatics systems for the global study of microbial functions and the discovery of new enzymes and metabolic pathways; the use of microorganisms for the production of biofuels, unicellular proteins, natural pigments and waste recycling for sustainability and bioproduction; studies of microorganisms in environmental applications such as bioremediation and agricultural production.

This Special Issue aims to provide further contributions to these topics through the interception, development, and integration of the most recent knowledge on the metabolic, genetic, and physiological fields of microbiology, with particular focus on the applicative use of microorganisms. We especially welcome contributions, both original research and reviews, that address emerging technologies, interdisciplinary approaches, and sustainable practices. The topics include all those cited above but are not limited to them. On this occasion, we would also like to receive contributions related to technological advances aimed at the study of uncultured microorganisms, a large and unexplored resource, which could open up new frontiers in the field of microbial biotechnology.

Prof. Dr. Giovanni Vigliotta
Prof. Dr. Rosanna Tofalo
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 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • fermentation
  • natural biocides
  • primary and secondary functional metabolites
  • antimicrobial peptides
  • pathogen control
  • antimicrobial resistance
  • genetic improvement of microorganisms
  • single-cell proteins
  • metabolic engineering
  • sustainable biotechnologies
  • green chemistry
  • enzymatic biotransformation
  • antimicrobial innovation
  • uncultured and unculturable microorganisms
  • chemicals and fuels for CO2 transformation
  • biomanufacturing technology
  • bioreactor technologies

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Published Papers (5 papers)

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Research

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13 pages, 4261 KiB  
Article
Involvement of the Methyltransferase CcLaeA in Regulating Laccase Production in Curvularia clavata J1
by Changyu Pi, Jinyang Li, Fangting Jiang, Jintong Zhang, Tongtong Bao, Shengguo Zhao and Guoshun Chen
Fermentation 2025, 11(4), 178; https://doi.org/10.3390/fermentation11040178 - 31 Mar 2025
Viewed by 305
Abstract
Laccases are synthesized by a diverse range of fungi. Nevertheless, despite the industrial significance of laccases, the regulatory mechanism governing laccase production has been relatively understudied. This research aims to explore the regulatory function of the methyltransferase CcLaeA in laccase biosynthesis using the [...] Read more.
Laccases are synthesized by a diverse range of fungi. Nevertheless, despite the industrial significance of laccases, the regulatory mechanism governing laccase production has been relatively understudied. This research aims to explore the regulatory function of the methyltransferase CcLaeA in laccase biosynthesis using the newly isolated fungal strain Curvularia clavata J1. Through CRISPR-Cas9-mediated gene disruption, the deletion of CclaeA led to a 1.5-fold increase in extracellular laccase activity in the ΔCclaeA mutant when compared to the wild-type strain. This finding indicates that CcLaeA functions as a transcriptional repressor of laccase biosynthesis. Transcriptomic analysis demonstrated that CcLaeA does not directly regulate the expression of laccase genes. Instead, it modulates genes associated with hydrolases and peptidases. This modulation potentially reduces the enzymatic degradation of laccase at the protein level. This study significantly enhances our understanding of fungal laccase regulation. By establishing a connection between the deletion of CclaeA and the improvement of enzyme stability and activity, this research offers practical insights for engineering fungal strains to optimize laccase yields for bioremediation and biofuel applications. Furthermore, the integration of targeted gene knockout with multi-omics validation sets up a methodological framework for investigating regulatory networks in non-model fungi. This framework is expected to accelerate the development of sustainable biocatalysts, thereby contributing to the advancement of biotechnology in various industrial sectors. Full article
(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in Section “Microbial Metabolism, Physiology & Genetics”)
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14 pages, 3149 KiB  
Article
Construction of Efficient Multienzyme Cascade Reactions for D-Tagatose Biosynthesis from D-Fructose
by Peiyu Miao, Qiang Wang, Kexin Ren, Tongtong Xu, Zigang Zhang, Runxin Hu, Meijuan Xu, Zhiming Rao and Xian Zhang
Fermentation 2025, 11(3), 139; https://doi.org/10.3390/fermentation11030139 - 12 Mar 2025
Viewed by 544
Abstract
D-tagatose is an ideal sucrose substitute with potential applications in food and healthcare. The combined catalysis of polyphosphate kinase (PPK), fructose kinase (FRK), D-tagatose-6-phosphate 3-differential anisomerase (FbaA) and phytase provides a low-cost and convenient pathway for the biosynthesis of D-tagatose from D-fructose; however, [...] Read more.
D-tagatose is an ideal sucrose substitute with potential applications in food and healthcare. The combined catalysis of polyphosphate kinase (PPK), fructose kinase (FRK), D-tagatose-6-phosphate 3-differential anisomerase (FbaA) and phytase provides a low-cost and convenient pathway for the biosynthesis of D-tagatose from D-fructose; however, there is still a problem of low catalytic efficiency that needs to be solved urgently. Therefore, this study enhanced the biosynthesis of D-tagatose by optimizing the expression levels of PPK, FRK and FbaA in a polycistronic system and knocking out the gene pfka of Escherichia coli. With 30 g/L D-fructose as a substrate, the conversion rate increased to 52%, which was the highest after 24 h. In addition, by constructing a multienzyme self-assembly system with SpyTag and SpyCatcher to improve the whole-cell catalytic ability, the conversion rate was further increased to 75%. Finally, through the fed-batch strategy, the optimal strain Ec-7 produced 68.1 g/L D-tagatose from 100 g/L D-fructose. The multienzyme cascade route reported herein provides an efficient and elegant innovative solution for the generation of D-tagatose. Full article
(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in Section “Microbial Metabolism, Physiology & Genetics”)
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18 pages, 1926 KiB  
Article
The Application of an Effective Microbial Fermentation Product as a Biostimulant in the Bioremediation of Soil Contaminated with Benzo[a]pyrene
by Xin Xie and Tangbing Cui
Fermentation 2025, 11(2), 76; https://doi.org/10.3390/fermentation11020076 - 4 Feb 2025
Viewed by 807
Abstract
The efficiency of polycyclic aromatic hydrocarbon (PAH) removal by indigenous microorganisms is often suboptimal, resulting in constraints on its practical application. To enhance the degradation efficiency of benzo[a]pyrene (B[a]P) in contaminated soil, an effective microbial fermented product (EMF) was employed as a biostimulant. [...] Read more.
The efficiency of polycyclic aromatic hydrocarbon (PAH) removal by indigenous microorganisms is often suboptimal, resulting in constraints on its practical application. To enhance the degradation efficiency of benzo[a]pyrene (B[a]P) in contaminated soil, an effective microbial fermented product (EMF) was employed as a biostimulant. Our findings demonstrated that when 1‱ or 1‰ (w/w) of the EMF was applied to the B[a]P-contaminated soil for 21 days, the biodegradation rates of the B[a]P were 59.37% and 100%, respectively, which is much higher than that by the natural attenuation (18.79%). The abundance of the 16S rDNA and PAH-RHDα GP genes were both significantly increased due to the applied EMF. Soil enzymatic activities were also affected, to different degrees, by the addition of the EMF. The diversity, composition, and functionality of the soil microbial community also changed to varying degrees. These results suggest that the use of the EMF to enhance the biodegradation of the B[a]P in soil may hold promise for the microbial remediation of PAH-contaminated soils. Full article
(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in Section “Microbial Metabolism, Physiology & Genetics”)
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12 pages, 4068 KiB  
Article
Fungal Biodegradation of Procyanidin in Submerged Fermentation
by Leidy Johana Valencia-Hernández, Jorge E. Wong-Paz, J. Alberto Ascacio-Valdés, Arely Prado-Barragan, Mónica L. Chávez-González and Cristóbal N. Aguilar
Fermentation 2025, 11(2), 75; https://doi.org/10.3390/fermentation11020075 - 3 Feb 2025
Viewed by 1292
Abstract
The coffee industry generates a large amount of waste that is difficult to treat due to its chemical composition, namely, the presence of caffeine and its derivatives, as well as recalcitrant molecules such as tannins (mainly condensed tannins or polymeric procyanidins), which make [...] Read more.
The coffee industry generates a large amount of waste that is difficult to treat due to its chemical composition, namely, the presence of caffeine and its derivatives, as well as recalcitrant molecules such as tannins (mainly condensed tannins or polymeric procyanidins), which make it an undervalued waste product. Procyanidins are compounds beneficial to human health and can be found in nature in fruit, grain, seeds, and beverages, among other foods. The zero-waste approach has allowed for the valorization of by-products from the food industry. Currently, coffee pulp is the target of research on extraction, purification, and alternative use. Research on the fungal degradation of procyanidins has emerged as an avenue for the efficient use of these by-products. In this study, the degradation and biotransformation of procyanidin is evaluated and comprises three steps: first, the extraction and partial purification of procyanidins from coffee pulp; second, the production of the potential procyanidin-degrading enzyme by submerged fermentation with Aspergillus niger GH1; third, enzymatic extracellular extract evaluation using a model system with commercial procyanidin C1. The biodegradation/biotransformation results reveal the formation of new compounds, including a final compound with an m/z of 289, possibly a monomeric molecule such as catechin or epicatechin. Identification of the compounds by HPLC-MS confirmed procyanidin C1 depletion under the described assay conditions, which could be used to understand biodegradation pathways proposed for future study. Furthermore, these results confirm that A. niger GH1 is able to degrade and biotransform procyanidin C1. Full article
(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in Section “Microbial Metabolism, Physiology & Genetics”)
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Review

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21 pages, 1128 KiB  
Review
Applications of Yeasts in Heavy Metal Remediation
by Qi Shao, Shihui Yan, Xin Sun, Hongming Chen, Yixiao Lu, Siqi Li, Yunjie Huang, Shimei Wang, Min Zhang and Zhen Li
Fermentation 2025, 11(5), 236; https://doi.org/10.3390/fermentation11050236 - 23 Apr 2025
Viewed by 286
Abstract
Yeasts have been extensively recognized as a type of model microorganism due to their facile cultivation, short growth cycle, and genetic stability. Different yeast strains, such as Saccharomyces cerevisiae and Rhodotorula mucilaginosa, have exhibited notable sorption capacities for heavy metals and metalloids. [...] Read more.
Yeasts have been extensively recognized as a type of model microorganism due to their facile cultivation, short growth cycle, and genetic stability. Different yeast strains, such as Saccharomyces cerevisiae and Rhodotorula mucilaginosa, have exhibited notable sorption capacities for heavy metals and metalloids. Yeast employs diverse pathways for detoxifying heavy metals via its cell walls, intracellular organelles, and extracellular polymeric substances (EPSs). The cell wall has many functional groups to adsorb metals, decreasing their concentrations in the environment. In intracellular regions, some proteins are capable of transporting metals into biological metabolic processes for detoxification. In extracellular regions, electrostatic as well as complexation mechanisms between protein in EPSs and heavy metals is well accepted. Meanwhile, mannose and glucose within EPSs are target sugars for complexation with metals. Many yeasts can hence work as excellent biomaterials for the bioremediation of metal pollution. Meanwhile, they can be combined with other materials to enhance remediation efficiency. This study reviews underlying mechanisms and cases of yeast-mediated metal detoxification, alongside highlighting yeasts’ industrial applications as bioremediation materials. Full article
(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in Section “Microbial Metabolism, Physiology & Genetics”)
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