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Microorganisms
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Resource Utilization of Microorganisms: Fermentation and Biosynthesis
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Resource Utilization of Microorganisms: Fermentation and Biosynthesis

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: 30 June 2026 | Viewed by 5457

Special Issue Editor

Prof. Dr. Shoushuai Feng

E-Mail Website
Guest Editor
The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214000, China
Interests: bioprocess; fermentation; bioleaching; extremophiles; physiological and metabolic mechanisms; acidophiles
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microorganisms serve as pivotal biocatalysts in sustainable biomanufacturing, driving innovations in resource efficiency and economic viability. This Special Issue explores cutting-edge advances in microbial resource utilization, fermentation optimization, synthetic biology, and sustainability utilization to enhance biosynthesis pathways for high-value products. This Special Issue focuses on maximizing the resource potential of industrial microorganisms through integrated approaches in fermentation and biosynthesis. Studies on fermentation process engineering, covering nutrient formulation, bioreactor operations, and environmental control will be featured. Additionally, we seek papers exploring advances in strain improvement using synthetic biology tools for producing enzymes, therapeutics, and natural compounds, including metabolic engineering, chassis cell design, heterologous expression systems, and cell-free biosynthesis. Research on circular bioeconomy strategies, such as microbial waste recycling and clean production technologies, is also welcomed. 

This Special Issue is dedicated to all aspects of “Resource Utilization of Microorganisms: Fermentation and Biosynthesis” research, with special emphasis on the following topics:

  1. Fermentation Process Optimization
  • Engineering of nutrient regimes, bioreactor design, environmental parameters, and scale-up strategies for yield enhancement. 
  1. Molecular-Level Strain Improvement
  • Metabolic engineering, synthetic biology, and heterologous expression systems (enzymes/proteins/natural products); chassis cell design; directed evolution; and cell-free biosynthesis. 
  1. Sustainability utilization
  • Microbial recycling of industrial effluents/residues via circular fermentation and clean production technologies. 

Prof. Dr. Shoushuai Feng
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. Microorganisms 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 2700 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

  • industrial microorganisms resources
  • microbial physiological traits
  • fermentation optimization
  • synthetic biology
  • sustainability application

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Published Papers (6 papers)

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Research

Jump to: Review

24 pages, 5263 KB  
Article
Post-Transcriptional Regulatory Mechanism Based on CsrA and rpoS in Extremophile Sulfur Oxidizer Acidithiobacillus caldus
by Yiwen Zhu, Panyan Chen, Hailin Yang, Yanjun Tong and Shoushuai Feng
Microorganisms 2026, 14(3), 724; https://doi.org/10.3390/microorganisms14030724 - 23 Mar 2026
Viewed by 377
Abstract
Acidithiobacillus caldus is perpetually exposed to multiple extreme environmental stresses. CsrA, functioning as a post-transcriptional regulator of physiological metabolism, acts as a differential modulator, facilitating more economical and efficient adaptation to extreme environments. The csrA expression recombinant strain was constructed in A. caldus [...] Read more.
Acidithiobacillus caldus is perpetually exposed to multiple extreme environmental stresses. CsrA, functioning as a post-transcriptional regulator of physiological metabolism, acts as a differential modulator, facilitating more economical and efficient adaptation to extreme environments. The csrA expression recombinant strain was constructed in A. caldus MTH-04 by conjugative transfer technology pJD215. Physiological characterization revealed enhanced acid tolerance, significantly elongated flagella, elevated extracellular secretion, and altered biofilm composition. Notably, intracellular concentrations of free glutamate and aspartate increased to 24.18 mg/L and 16.07 mg/L, respectively. The secondary structure of CsrA protein was determined in vitro through circular dichroism spectroscopy and size-exclusion chromatography. Electrophoretic Mobility Shift Assay (EMSA) successfully demonstrated in vitro binding activity of CsrA to the rpoS leader mRNA. CsrA suppresses rpoS mRNA translation by competing with ribosomes for binding sites, thereby negatively regulating rpoS expression. Critical binding sites were further validated through site-directed mutagenesis. Through EMSA, RT-qPCR and the translation reporter system, it was also found that CsrA has a dual regulatory function for nearby flagella- and motility-related gene clusters (flgC, 07035, motD, 15040), which also implies the global regulatory role of CsrA. In summary, a potential overall post-transcriptional regulatory mechanism based on CsrA and rpoS by extremophile A. caldus was proposed. Finally, the efficiency of bioleaching application by csrA overexpression strain was improved by 20.81%. Full article
(This article belongs to the Special Issue Resource Utilization of Microorganisms: Fermentation and Biosynthesis)
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15 pages, 2112 KB  
Article
Enhancing Synthesis Efficiency in Microbial 1,5-Pentanediol Production Through Transcriptomics-Informed Metabolic Engineering of Escherichia coli
by Hongyu Deng, Fei Meng, Yihao Sun, Yang Song, Chunhui Zhao, Xiaonan Wang, Yan Zhang, Ruiming Wang and Ning Chen
Microorganisms 2026, 14(3), 715; https://doi.org/10.3390/microorganisms14030715 - 22 Mar 2026
Viewed by 426
Abstract
The microbial production of 1,5-pentanediol (1,5-PDO), a versatile platform chemical with extensive industrial applications, remains limited by suboptimal fermentation titers and incomplete understanding of metabolic bottlenecks. To address these challenges, this study employed comparative transcriptomics to systematically identify novel genetic targets capable of [...] Read more.
The microbial production of 1,5-pentanediol (1,5-PDO), a versatile platform chemical with extensive industrial applications, remains limited by suboptimal fermentation titers and incomplete understanding of metabolic bottlenecks. To address these challenges, this study employed comparative transcriptomics to systematically identify novel genetic targets capable of enhancing 1,5-PDO biosynthesis in engineered Escherichia coli. Transcriptomic profiling of the 1,5-PDO-producing strain relative to the parental E. coli W3110, conducted at both exponential (24 h) and stationary (96 h) growth phases, revealed 1384 significantly differentially expressed genes, including 851 upregulated and 533 downregulated genes. From these, 20 candidate metabolic genes associated with 1,5-PDO synthesis were selected for functional validation through plasmid-based overexpression or CRISPR interference (CRISPRi)-mediated repression. Reverse engineering confirmed that overexpression of fecA (encoding an iron(III)-citrate transporter) and deletion of gadA (encoding glutamate decarboxylase) significantly enhanced 1,5-PDO production. Subsequent chromosomal integration of fecA at the neutral ilvG locus and deletion of gadA generated the optimized strain S7, which achieved a 1,5-PDO titer of 1.7 g/L in shake flask cultures, representing a 13.3% increase over the parental strain, with a concomitant 50% improvement in glucose yield (0.18 mol/mol). In fed-batch fermentation at the 5 L bioreactor scale, strain S7 attained a titer of 12.45 g/L and a glucose yield of 0.26 mol/mol, marking a 15.6% enhancement in carbon conversion efficiency relative to the parental strain (0.225 mol/mol), while concurrently improving biomass accumulation by 7.6%. These findings demonstrate that transcriptomics-guided reverse engineering constitutes an effective strategy for elucidating nonobvious metabolic determinants and optimizing microbial cell factories for efficient 1,5-PDO production. The identification of fecA and gadA as beneficial targets provides valuable insights into the metabolic rewiring underlying enhanced 1,5-PDO biosynthesis and establishes a foundation for further strain improvement through systems metabolic engineering. Full article
(This article belongs to the Special Issue Resource Utilization of Microorganisms: Fermentation and Biosynthesis)
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16 pages, 2662 KB  
Article
Effects of Silage Inoculants on the Quality and Microbial Community of Whole-Plant Corn Silage Under Different Fertilization Treatments
by Deli Dong, Gulinigeer Ainizirehong, Maierhaba Aihemaiti, Xin Huang, Yang Li, Huaibing Yao, Yuanyuan Yan, Min Hou and Weidong Cui
Microorganisms 2026, 14(1), 65; https://doi.org/10.3390/microorganisms14010065 - 27 Dec 2025
Viewed by 699
Abstract
The purpose of this study is to investigate the effects of silage inoculants (FJ) and natural fermentation (CK) on the quality and microbial community of whole-plant corn silage under different fertilization treatments, including conventional fertilization (CK), liquid microbial inoculant and conventional fertilization (JJ), [...] Read more.
The purpose of this study is to investigate the effects of silage inoculants (FJ) and natural fermentation (CK) on the quality and microbial community of whole-plant corn silage under different fertilization treatments, including conventional fertilization (CK), liquid microbial inoculant and conventional fertilization (JJ), and microbial organic fertilizer and conventional fertilization (YJ). After 30 days of room-temperature fermentation, parameters including pH, LA, CP, starch, ADF, NDF, and the microbial community were determined. The results showed that after 30 days of ensiling, silage inoculants significantly affected the nutritional components and fermentation parameters of whole-plant corn silage under different fertilization treatments. Furthermore, the two factors (silage inoculants and different fertilization treatments) exhibited a significant interaction effect. Simple effects analysis revealed that the significant interaction was mainly driven by a more pronounced differential effect of fertilization treatments on the nutritional indicators (starch, CP, ADF, and NDF) under silage inoculant (FJ) addition than under natural fermentation (CK) (p < 0.05). Among all silage treatments, the silage inoculants + microbial solution drip irrigation and conventional fertilization (FJJJ) group exhibited relatively superior silage quality. Specifically, the FJJJ group had the lowest contents of pH, ADF, and NDF, along with the highest contents of lactic acid (LA) and ether extract (EE). The addition of silage inoculants under different fertilization treatments consistently increased the abundance and reinforced the dominance of Lactobacillus in the microbial community. This effect was most pronounced in the FJJJ group, which showed the highest relative abundance. In contrast, the relative abundance of genera such as Pantoea, Acinetobacter, Klebsiella, and Pseudomonas decreased significantly. In summary, appropriate fertilization treatments combined with the addition of silage inoculants contribute to enhancing the quality of whole-plant corn silage and improve the fermentation microbial community of the silage. These findings provide a theoretical basis for producing high-quality corn silage. Full article
(This article belongs to the Special Issue Resource Utilization of Microorganisms: Fermentation and Biosynthesis)
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17 pages, 2360 KB  
Article
Harvest Stage Dictates the Nutritive Value of Sorghum Stalk Silage by Shaping Its Fermentation Profile and Microbial Composition
by Xiaoqiang Zhao, Ruiyi Liu, Jing Wang, Yawei Zhang, Shuo Zhang, Wenbin Bai, Qingshan Liu and Yuanqing Zhang
Microorganisms 2025, 13(9), 2131; https://doi.org/10.3390/microorganisms13092131 - 11 Sep 2025
Cited by 1 | Viewed by 944
Abstract
The present experiment aimed to investigate the effects of harvest stages on the fermentation quality and nutritional value of sorghum stalk silage. Sorghum stalks were harvested at the three stages (milk, dough, and ripe), chopped, and ensiled for 60 d. Each treatment had [...] Read more.
The present experiment aimed to investigate the effects of harvest stages on the fermentation quality and nutritional value of sorghum stalk silage. Sorghum stalks were harvested at the three stages (milk, dough, and ripe), chopped, and ensiled for 60 d. Each treatment had five replicates, and the silages were evaluated for fermentation quality, nutritional composition, in vitro rumen fermentation characteristics, and bacterial community profiles. The results showed that the crude protein, neutral detergent fiber, and acid detergent fiber contents decreased significantly with harvest maturity (p < 0.05). Consequently, silage from the ripe stage possessed the highest dry matter, relative feed value, and total digestible nutrients (p < 0.05). In vitro rumen fermentation indicated that the ripe stage silage exhibited the greatest gas production, and the lowest concentrations of ruminal ammonia–nitrogen (p < 0.05). Microbial analysis revealed a shift from dominant epiphytic Proteobacteria to fermentative Firmicutes post-ensiling, with the ripe stage community co-dominated by Lactobacillus and Leuconostoc, in contrast to the milk stage’s enrichment with Klebsiella. In conclusion, harvesting sorghum at the ripe stage is the optimal strategy as it establishes a beneficial microbial community, resulting in silage with superior nutritional value and rumen fermentation efficiency. Full article
(This article belongs to the Special Issue Resource Utilization of Microorganisms: Fermentation and Biosynthesis)
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28 pages, 9356 KB  
Article
Integrated Microbiome–Metabolome Analysis and Functional Strain Validation Reveal Key Biochemical Transformations During Pu-erh Tea Pile Fermentation
by Mengkai Hu, Huimin Zhang, Leisa Han, Wenfang Zhang, Xinhui Xing, Yi Wang, Shujian Ou, Yan Liu, Xiangfei Li and Zhenglian Xue
Microorganisms 2025, 13(8), 1857; https://doi.org/10.3390/microorganisms13081857 - 8 Aug 2025
Cited by 3 | Viewed by 1532
Abstract
Fermentation plays a pivotal role in shaping the flavor and overall quality of Pu-erh tea, a microbially fermented dark tea. Here, we monitored physicochemical properties, chemical constituents, and microbial succession at 15 fermentation time points. Amplicon sequencing identified Staphylococcus, Bacillus, Kocuria [...] Read more.
Fermentation plays a pivotal role in shaping the flavor and overall quality of Pu-erh tea, a microbially fermented dark tea. Here, we monitored physicochemical properties, chemical constituents, and microbial succession at 15 fermentation time points. Amplicon sequencing identified Staphylococcus, Bacillus, Kocuria, Aspergillus, Blastobotrys, Thermomyces, and Rasamsonia as dominant genera, with prokaryotic communities showing greater richness and diversity than eukaryotic ones. Beta diversity and clustering analyses revealed stable microbial structures during late fermentation stages. Non-targeted metabolomics detected 347 metabolites, including 56 significantly differential compounds enriched in caffeine metabolism and unsaturated fatty acid biosynthesis. Fermentation phases exhibited distinct metabolic patterns, with volatile aroma compounds (2-acetyl-1-pyrroline, 2,5-dimethylpyrazine) and health-beneficial fatty acids (linoleic acid, arachidonic acid) accumulating in later stages. OPLS-DA and KEGG PATHWAY analyses confirmed significant shifts in metabolite profiles relevant to flavor and biofunctionality. RDA revealed strong correlations between microbial taxa, environmental parameters, and representative metabolites. To functionally verify microbial contributions, 17 bacterial and 10 fungal strains were isolated. Six representative strains, mainly Bacillus and Aspergillus, exhibited high enzymatic activity on macromolecules, confirming their roles in polysaccharide and protein degradation. This integrative multi-omics investigation provides mechanistic insights into Pu-erh tea fermentation and offers a scientific basis for microbial community optimization in tea processing. Full article
(This article belongs to the Special Issue Resource Utilization of Microorganisms: Fermentation and Biosynthesis)
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Review

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19 pages, 5101 KB  
Review
Revealing Microbial Siderophores: From Genes to Applications
by Jionglin Cai, Yuting Fang, Xia Liu, Mark Owusu Adjei and Ben Fan
Microorganisms 2026, 14(2), 393; https://doi.org/10.3390/microorganisms14020393 - 6 Feb 2026
Cited by 2 | Viewed by 883
Abstract
Iron is an essential micronutrient for nearly all microorganisms, yet its bioavailability is severely limited in most environments. To overcome this restriction, microorganisms produce siderophores, high-affinity iron-chelating molecules that play pivotal roles in microbial iron homeostasis, interspecies competition, and host–pathogen interactions. Despite extensive [...] Read more.
Iron is an essential micronutrient for nearly all microorganisms, yet its bioavailability is severely limited in most environments. To overcome this restriction, microorganisms produce siderophores, high-affinity iron-chelating molecules that play pivotal roles in microbial iron homeostasis, interspecies competition, and host–pathogen interactions. Despite extensive research, current understanding of siderophore biosynthetic and regulatory diversity remains largely limited to specific models, with comprehensive cross-taxonomic frameworks only beginning to emerge. This review systematically integrates recent advances in the genetic and biochemical foundations of microbial siderophore production, focusing on the two major biosynthetic pathways: nonribosomal peptide synthetase (NRPS)-dependent and NRPS-independent synthetase (NIS). We further elaborate on the diverse transport systems in Gram-negative and Gram-positive bacteria, as well as fungi, alongside the iron-responsive regulators (e.g., Fur) and gene clusters that coordinate iron uptake and utilization. Beyond physiological mechanisms, we discuss how these insights inform emerging applications of siderophores across multiple fields: in medicine, enabling “Trojan horse” antimicrobial strategies; in agriculture, enhancing plant iron uptake and serving as biocontrol agents; in environmental remediation, facilitating heavy-metal detoxification; and in biosensing, acting as selective probes for metals and pathogens. By bridging fundamental mechanisms with practical applications, this review aims to provide an integrative perspective for future exploration of microbial iron homeostasis and its biotechnological potential. Full article
(This article belongs to the Special Issue Resource Utilization of Microorganisms: Fermentation and Biosynthesis)
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