Secondary Metabolism of Microorganisms, 3rd Edition

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

Deadline for manuscript submissions: 15 January 2025 | Viewed by 5319

Special Issue Editors


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Guest Editor
1. Instituto de Biotecnología de León (INBIOTEC), León, Spain
2. Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Campus de Vegazana, Universidad de León, 24071 León, Spain
Interests: fungal secondary metabolism; molecular biology; biotechnology; genetic engineering; omics
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Guest Editor
Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain
Interests: secondary metabolites; microorganisms; proteomics; plastics; actinobacteria; fungi; carotenoids; steroids; immunosuppressors; antibiotics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issues, "Secondary Metabolism of Microorganisms" and “Secondary Metabolism of Microorganisms 2.0”.

Microbial secondary metabolism represents a very interesting research field. On the one hand, secondary metabolism is considered nonessential for microbial growth and development, but it results in the biosynthesis of an impressive array of compounds relevant for: (i) human and animal health (e.g., antibiotics, receptor antagonists and agonists, and immunosuppressants), (ii) food and feed (e.g., pigments), (iii) agriculture (e.g., pheromones and plant protectants), and (iv) farming (e.g., toxins). This industrially relevant group of compounds is produced by certain taxonomic clades of organisms such as bacteria, mainly Actinobacteria, and fungi. Since metabolite formation is usually repressed during the logarithmic phase of growth and boosted along the stationary growth phase, a regulatory fine-tuning of nutrients (e.g., phosphate and nitrogen), precursors, and energy molecules is needed. The understanding of this strictly controlled process opens the door to synthetic biology to redirect metabolic pathways, avoiding nutrient sinks and by-product generation.

On the other hand, secondary metabolism plays a significant ecological role in the communication among different microorganisms in nature. At present, mixed fermentation or co-cultivation is a trending method to study, understand, and harness microbial competition and communication when the appropriate physiological conditions are provided.

This Special Issue of Microorganisms invites researchers to contribute research articles, reviews, and opinions addressing the latest knowledge on the secondary metabolism of microorganisms, including molecular biology, omics, synthetic biology, industrial microbiology, genome editing, metabolite production, downstream processing, gene control and regulation, etc., both in fundamental research and its applications. This Special Issue is divided into three blocks: i) microbial secondary metabolites; ii) the regulation of secondary metabolism; and iii) communication between microbial communities. Manuscripts covering these areas of knowledge, and others related to microbial secondary metabolism, are of interest for this Special Issue.

Dr. Carlos García-Estrada
Dr. Carlos Barreiro
Guest Editors

Manuscript Submission Information

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Related Special Issue

Published Papers (5 papers)

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Research

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14 pages, 2512 KiB  
Article
An Overview of Lsr2 Repressor Effect in Streptomyces spp. Secondary Metabolism
by Lorena Cuervo, Mónica G. Malmierca and Carlos Olano
Microorganisms 2024, 12(11), 2317; https://doi.org/10.3390/microorganisms12112317 - 14 Nov 2024
Viewed by 467
Abstract
The genus Streptomyces is one of the largest producers of secondary metabolites with bioactive properties of interest. However, many of the genes involved in synthesizing these compounds are silenced under laboratory conditions. One of the strategies used to activate these metabolic pathways is [...] Read more.
The genus Streptomyces is one of the largest producers of secondary metabolites with bioactive properties of interest. However, many of the genes involved in synthesizing these compounds are silenced under laboratory conditions. One of the strategies used to activate these metabolic pathways is the elimination of repressor genes, which prevent the transcription of other genes. In this work, the lsr2 gene has been selected for study since it is a repressor with a preference for binding to AT-rich regions, which makes it exert its effect especially on those horizontally transferred gene sequences that have a very different GC content to the core Streptomyces spp. genome. Therefore, the effects of the deletion of this gene are observed, and, in addition, a mapping of the potential binding sites of Lsr2 in Streptomyces spp. genomes is proposed. As a result of this gene knockout, the production of various secondary metabolites is overproduced and/or activated, which suggests that the study of this regulator can be interesting in the field of natural product discovery. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms, 3rd Edition)
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16 pages, 2977 KiB  
Article
Isolation and Identification of Indole Alkaloids from Aspergillus amstelodami BSX001 and Optimization of Ultrasound-Assisted Extraction of Neoechinulin A
by Shuyao Li, Xiaobo Liu, Qiuya Gu and Xiaobin Yu
Microorganisms 2024, 12(5), 864; https://doi.org/10.3390/microorganisms12050864 - 26 Apr 2024
Cited by 1 | Viewed by 1147
Abstract
This study aimed to investigate the alkaloid secondary metabolites of Aspergillus amstelodami BSX001, a fungus isolated from Anhua dark tea, and to improve the extraction yield of the active ingredients by optimizing the extraction process. The structural characterization of the compounds was investigated [...] Read more.
This study aimed to investigate the alkaloid secondary metabolites of Aspergillus amstelodami BSX001, a fungus isolated from Anhua dark tea, and to improve the extraction yield of the active ingredients by optimizing the extraction process. The structural characterization of the compounds was investigated using mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. The antioxidant activity of echinulin-related alkaloids was evaluated by determining the total reducing power and DPPH radical scavenging capacity. The extraction process of the compound with optimum activity was optimized by a single-factor test and response surface methodology (RSM) combined with Box–Behnken design (BBD). The optimized result was validated. Finally, a new alkaloid 8-hydroxyechinulin (1), and four known alkaloids, variecolorin G (2), echinulin (3), neoechinulin A (4), and eurocristatine (5), were isolated. Echinulin-related compounds 1, 3, and 4 possessed certain antioxidant activities, with IC50 values of 0.587 mg/mL, 1.628 mg/mL, and 0.219 mg/mL, respectively, against DPPH radicals. Their total reducing power at a concentration of 0.5 mg/mL was 0.29 mmol/L, 0.17 mmol/L, and 4.25 mmol/L. The extraction process of neoechinulin A was optimized with the optimum extraction parameters of 72.76% methanol volume fraction, 25 mL/g solid–liquid ratio, and 50.8 °C soaking temperature. Under these conditions, the extraction yield of neoechinulin A was up to 1.500 mg/g. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms, 3rd Edition)
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14 pages, 1541 KiB  
Article
Harnessing the Biocontrol Potential of Bradyrhizobium japonicum FCBP-SB-406 to Manage Charcoal Rot of Soybean with Increased Yield Response for the Development of Sustainable Agriculture
by Umar Khalid, Zill-e-Huma Aftab, Tehmina Anjum, Najat A. Bokhari, Waheed Akram and Waheed Anwar
Microorganisms 2024, 12(2), 304; https://doi.org/10.3390/microorganisms12020304 - 31 Jan 2024
Viewed by 1349
Abstract
Plant growth-promoting bacteria (PGPRs) have the potential to act as biofertilizers and biopesticides. This study was planned to explore indigenously isolated PGPRs as a potential candidate to control charcoal rot that affects various crops including soybean. Among the four different tested species of [...] Read more.
Plant growth-promoting bacteria (PGPRs) have the potential to act as biofertilizers and biopesticides. This study was planned to explore indigenously isolated PGPRs as a potential candidate to control charcoal rot that affects various crops including soybean. Among the four different tested species of PGPRs, Bradyrhizobium japonicum (FCBP-SB-406) showed significant potential to enhance growth and control soil borne pathogens such as Macrophomina phaseolina. Bacillus subtilis (FCBP-SB-324) followed next. Bradyrhizobium japonicum (FCBP-SB-406) reduced disease severity up to 81.25% in comparison to the control. The strain showed a strong fertilizing effect as a highly significant increase in biomass and other agronomic parameters was recorded in plants grown in its presence. The same was supported by the Pearson’s correlation and principal component analysis. A decrease in disease incidence and severity may be due to the induced resistance imparted by the bacterium. This resulted in significant increments in quantities of defense enzymes, including catalase, peroxidase (PO), polyphenol oxidase (PPO), phenylalanine ammonia lyase (PAL) and superoxide dismutase (SOD). A significant production of proteases, catalases and hydrogen cyanide by B. japonicum (FCBP-SB-406) can also be associated to mycoparasitism. The establishment of PGPRs in treated soils also showed positive effects on soil health. Total metabolite profiling of treated plants in comparison to the control showed the upregulation of many flavonoids, isoflavonoids and amino acids. Many of these compounds have been well reported with antimicrobial activities. Bradyrhizobium japonicum (FCBP-SB-406) can be employed for the production of a potential formulation to support sustainable agriculture by reducing the input of synthetic pesticides and fertilizers. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms, 3rd Edition)
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12 pages, 1637 KiB  
Article
Secondary Metabolites from the Nematode-Trapping Fungus Dactylellina haptotyla YMF1.03409
by Hongmei Lei, Guangke Zhang, Peiji Zhao and Guohong Li
Microorganisms 2023, 11(11), 2693; https://doi.org/10.3390/microorganisms11112693 - 3 Nov 2023
Cited by 1 | Viewed by 1153
Abstract
As a representative nematode-trapping fungus, Dactylellina haptotyla can capture and kill nematodes by producing traps, known as adhesive knobs. In this paper, the strain of D. haptotyla YMF1.03409 was studied by means of medium screening, fermentation, and purification and identification of crude extracts. [...] Read more.
As a representative nematode-trapping fungus, Dactylellina haptotyla can capture and kill nematodes by producing traps, known as adhesive knobs. In this paper, the strain of D. haptotyla YMF1.03409 was studied by means of medium screening, fermentation, and purification and identification of crude extracts. Eighteen compounds were obtained from D. haptotyla YMF1.03409, including two new metabolites, nosporins C (1) and D (2). The known metabolites were identified to be 3-chloro-4-methoxybenzaldehyde (3), 3-chloro-4-methoxybenzoic acid (4), 2-chloro-1-methoxy-4-(methoxymethyl)benzene (5), 3-hydroxy-3-methyloxindole (6), nicotinic acid (7), succinic acid (8), 3,4-dihydroxybutanoic acid (9), 5′-O-methyladenosine (10), uridine (11), 2′-deoxyuridine (12), thymidine (13), 3-(phenylmethyl)-2,5-morpholinedione (14), methyl-β-D-glucopyranoside (15), 1,2-benzenedicarboxylic acid bis(2-methyl heptyl) ester (16), β-sitosterol (17), and 3β,6α-diol-stigmastane (18). The bioactive assay showed that these compounds had no obvious nematicidal activity against the nematodes Meloidogyne incognita and Panagrellus redivivus. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms, 3rd Edition)
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Review

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13 pages, 2655 KiB  
Review
Indolizidines from Actinomycetes: An Overview of Producers, Biosynthesis and Bioactivities
by Janina Krause
Microorganisms 2024, 12(7), 1445; https://doi.org/10.3390/microorganisms12071445 - 16 Jul 2024
Viewed by 668
Abstract
Indolizidines have long been recognized for their valuable bioactivities, their common feature being a bicyclic structure connected via a nitrogen atom. Traditionally, plants have been identified as the primary producers. However, recent discoveries have revealed that certain bacterial strains belonging to the genus [...] Read more.
Indolizidines have long been recognized for their valuable bioactivities, their common feature being a bicyclic structure connected via a nitrogen atom. Traditionally, plants have been identified as the primary producers. However, recent discoveries have revealed that certain bacterial strains belonging to the genus of actinomycetes also possess the ability to synthesize various indolizidine-based compounds. Among these strains, Streptomyces sp. HNA39, Saccharopolyspora sp. RL78, and Streptomyces NCIB 11649 have been identified as producers of cyclizidines, characterized by their distinctive cyclopropyl moiety. Additionally, Streptomyces griseus OS-3601 synthesizes a unique class of indolizidine derivatives known as iminimycins, distinguished by their rare imine-cation structure. Protoplast fusion of a Streptomyces griseus strain with Streptomyces tenjimariensis resulted in a new indolizidine named indolizomycin. This review aims to provide an overview of known bacterial indolizidine producers, summarize current knowledge regarding the biosynthesis of cyclizidines and iminimycins, and assess their respective bioactivities. Full article
(This article belongs to the Special Issue Secondary Metabolism of Microorganisms, 3rd Edition)
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