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Microorganisms
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Microorganisms: A Way Forward for Sustainable Development?
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Microorganisms: A Way Forward for Sustainable Development?

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

Deadline for manuscript submissions: 31 May 2025 | Viewed by 10463

Special Issue Editor

Dr. Akhilesh Kumar Chaurasia

E-Mail Website
Guest Editor
School of Medicine, Department of Molecular Cell Biology, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
Interests: microbial biotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The increasing cost of food, feeds, fuel, and fertilizers (4F) has created significant challenges in the 21th century. Climate change and geopolitical situations have further accentuated this problem to an alarming level where futuristic technology involving microbial biotechnology will play a key role in solving these problems and creating a sustainable circular bioeconomy. Microorganisms have already been exemplified to play a crucial role in the circular economy by creating biomass for food, feed, fuel and biofertilizer. Furthermore, microbes help to break down organic waste and persistent chemicals and convert it into valuable resources such as biogas, biofertilizers, and bio-based chemicals. However, the use of high-value microbials is often limited to the lab and/or pilot scale due to their limited efficiency or difficulties associated with obtaining regulatory approval. Microbial biotechnology and genetic engineering using cutting-edge technology can increase efficiency and enable the use of microbial potentials at an industrial scale to solve the crisis of 4F. This Special Issue of ‘Microrganisms’ focuses on 4F using wild-type or genetically engineered microbes to achieve a sustainable solution for 4F and create a circular economy.

You may choose our Joint Special Issue in Applied Microbiology.

Dr. Akhilesh Kumar Chaurasia
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 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. 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

  • microorganisms
  • microbial biotechnology
  • sustainability
  • genetically engineered microbes

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Published Papers (6 papers)

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Research

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22 pages, 4160 KiB  
Article
Eco-Friendly Biomass Production and Identification of Active Compounds of Paenibacillus polymyxa EB.KN35 with Potent Anti-Fusarium oxysporum Effect
by Van Anh Ngo, Anh Dzung Nguyen, San-Lang Wang, Tu Quy Phan, Thi Ha Trang Tran, Dinh Sy Nguyen and Van Bon Nguyen
Microorganisms 2025, 13(4), 800; https://doi.org/10.3390/microorganisms13040800 - 31 Mar 2025
Viewed by 252
Abstract
Fusarium oxysporum is a fungal plant pathogen for over 100 agricultural crop species. There are strategies for managing Fusarium wilt, including antagonistic bacteria that offer a promising and sustainable effect. In this work, among the various endophytic bacterial strains, Paenibacillus polymyxa EB.KN35 was selected [...] Read more.
Fusarium oxysporum is a fungal plant pathogen for over 100 agricultural crop species. There are strategies for managing Fusarium wilt, including antagonistic bacteria that offer a promising and sustainable effect. In this work, among the various endophytic bacterial strains, Paenibacillus polymyxa EB.KN35 was selected as the best antifungal strain against F. oxysporum. For eco-friendly biomass production of this bacterium, some agricultural byproducts were tested for cultivation, and a soybean processing byproduct (SPBP) was found to be a suitable C/N source for P. polymyxa EB.KN35 fermentation. The utilization of a 14 L bioreactor system for P. polymyxa EB.KN35 fermentation achieved a high biomass productivity (3.46 × 1011 CFU/mL) in a short time (8 h). In bioactive compound analysis, EB.KN35 was found to be secreting several plant growth-promoting compounds such as GA3, IAA, kinetin, and zeatin (via HPLC) and eleven volatile compounds (via GC–MS). The docking study indicated that some volatile compounds (1, 2, 4, and 9) may play a significant role in inhibiting F. oxysporum. The study results highlight the potential for reusing a soybean processing byproduct as a C/N source for the bioproduction of P. polymyxa EB.KN35 with potential use as a biocontrol agent and biofertilizer. Full article
(This article belongs to the Special Issue Microorganisms: A Way Forward for Sustainable Development?)
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12 pages, 1079 KiB  
Article
d-Xylitol Production from Sugar Beet Press Pulp Hydrolysate with Engineered Aspergillus niger
by Melanie Knesebeck, Marcel Rüllke, Veronika Schönrock, J. Philipp Benz and Dirk Weuster-Botz
Microorganisms 2024, 12(12), 2489; https://doi.org/10.3390/microorganisms12122489 - 3 Dec 2024
Viewed by 987
Abstract
d-Xylitol is a low-calorie and anti-cariogenic sweetener suitable for diabetic patients, making it a valuable ingredient in various health-related applications. In this study, we investigated the production of d-xylitol from l-arabinose derived from sugar beet press pulp (SBPP) hydrolysate using [...] Read more.
d-Xylitol is a low-calorie and anti-cariogenic sweetener suitable for diabetic patients, making it a valuable ingredient in various health-related applications. In this study, we investigated the production of d-xylitol from l-arabinose derived from sugar beet press pulp (SBPP) hydrolysate using an engineered Aspergillus niger strain. Initial batch studies applying stirred tank bioreactors demonstrated d-xylitol production of 4.6 g L−1 with a yield of 0.37 g d-xylitol g−1 l-arabinose with a synthetic medium. Subsequently, the conversion of enzymatically produced and clarified SBPP hydrolysate was studied. We found that pre-treatment of the enzymatic hydrolysate with activated carbon was essential to remove inhibitory components. Moreover, an automated aeration switch-off was implemented based on the CO2 signal of the off-gas analyzer of the stirred tank bioreactor to prevent d-xylitol degradation after l-arabinose depletion. This resulted in a final d-xylitol concentration of 4.3 g L−1 with an improved yield of 0.43 g d-xylitol g−1 l-arabinose. The feasibility of utilizing the agricultural residue SBPP for d-xylitol production was successfully demonstrated with engineered A. niger. Full article
(This article belongs to the Special Issue Microorganisms: A Way Forward for Sustainable Development?)
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16 pages, 4800 KiB  
Article
Response Surface Methodology-Based Optimization of the Chitinolytic Activity of Burkholderia contaminans Strain 614 Exerting Biological Control against Phytopathogenic Fungi
by Imen Ben Slimene Debez, Hayet Houmani, Henda Mahmoudi, Khaoula Mkadmini, Pedro Garcia-Caparros, Ahmed Debez, Olfa Tabbene, Naceur Djébali and Maria-Camino Urdaci
Microorganisms 2024, 12(8), 1580; https://doi.org/10.3390/microorganisms12081580 - 2 Aug 2024
Viewed by 1117
Abstract
As part of the development of alternative and environmentally friendly control against phytopathogenic fungi, Burkholderia cepacia could be a useful species notably via the generation of hydrolytic enzymes like chitinases, which can act as a biological control agent. Here, a Burkholderia contaminans S614 [...] Read more.
As part of the development of alternative and environmentally friendly control against phytopathogenic fungi, Burkholderia cepacia could be a useful species notably via the generation of hydrolytic enzymes like chitinases, which can act as a biological control agent. Here, a Burkholderia contaminans S614 strain exhibiting chitinase activity was isolated from a soil in southern Tunisia. Then, response surface methodology (RSM) with a central composite design (CCD) was used to assess the impact of five factors (colloidal chitin, magnesium sulfate, dipotassium phosphate, yeast extract, and ammonium sulfate) on chitinase activity. B. contaminans strain 614 growing in the optimized medium showed up to a 3-fold higher chitinase activity. This enzyme was identified as beta-N-acetylhexosaminidase (90.1 kDa) based on its peptide sequences, which showed high similarity to those of Burkholderia lata strain 383. Furthermore, this chitinase significantly inhibited the growth of two phytopathogenic fungi: Botrytis cinerea M5 and Phoma medicaginis Ph8. Interestingly, a crude enzyme from strain S614 was effective in reducing P. medicaginis damage on detached leaves of Medicago truncatula. Overall, our data provide strong arguments for the agricultural and biotechnological potential of strain S614 in the context of developing biocontrol approaches. Full article
(This article belongs to the Special Issue Microorganisms: A Way Forward for Sustainable Development?)
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11 pages, 712 KiB  
Article
Insights into Effects of Combined Capric and Lauric Acid on Rumen Bacterial Composition
by Mariana Vadroňová, Adam Šťovíček, Alena Výborná, Yvona Tyrolová, Denisa Tichá and Miroslav Joch
Microorganisms 2024, 12(6), 1085; https://doi.org/10.3390/microorganisms12061085 - 27 May 2024
Viewed by 1344
Abstract
This study used next-generation sequencing to assess the impact of combined capric acid (C10) and lauric acid (C12) on the ruminal bacterial composition. Eight Holstein cows were randomly assigned to two groups using a cross-over design. The cows were fed two silage-based diets [...] Read more.
This study used next-generation sequencing to assess the impact of combined capric acid (C10) and lauric acid (C12) on the ruminal bacterial composition. Eight Holstein cows were randomly assigned to two groups using a cross-over design. The cows were fed two silage-based diets with the addition of either 100 g of stearic acid per cow per day (control), or 50 g of capric acid and 50 g of lauric acid per cow per day (C10 + C12). On day 18, 250 mL of rumen fluid was collected from each cow, and DNA was isolated, amplified, and sequenced. Treatment did not alter bacterial diversity indices, the relative abundance of archaea, nor the fiber-degrading microorganisms, except for a decrease in Fibrobacter (from 2.9% to 0.7%; p = 0.04). The relative abundance of Prevotellaceae decreased (from 39.9% to 29.6%; p = 0.009), which is notable because some members help to efficiently utilize ammonia by releasing it slowly into the rumen. Furthermore, the relative abundance of Clostridia increased (from 28.4% to 41.5%; p = 0.008), which may have aided the increased ammonia–nitrogen levels in the rumen, as this class contains hyperammonia-producing members. Our study reveals alterations in bacterial abundances with implications for rumen ammonia levels, offering insights into potential strategies for modulating rumen fermentation processes and methane production in ruminant livestock. Full article
(This article belongs to the Special Issue Microorganisms: A Way Forward for Sustainable Development?)
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Review

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17 pages, 2385 KiB  
Review
Recent Trends in the Production and Recovery of Bioplastics Using Polyhydroxyalkanoates Copolymers
by Andrés García, Claudia Aguirre, Andrés Pérez, Sofía S. Bahamonde, Viviana Urtuvia, Alvaro Díaz-Barrera and Carlos Peña
Microorganisms 2024, 12(11), 2135; https://doi.org/10.3390/microorganisms12112135 - 24 Oct 2024
Cited by 2 | Viewed by 2078
Abstract
Polyhydroxyalkanoates (PHAs) are polyesters synthesized as a carbon and energy reserve material by a wide number of bacteria. These polymers are characterized by their thermoplastic properties similar to those of plastics derived from the petrochemical industry, such as polyethylene and polypropylene. PHAs are [...] Read more.
Polyhydroxyalkanoates (PHAs) are polyesters synthesized as a carbon and energy reserve material by a wide number of bacteria. These polymers are characterized by their thermoplastic properties similar to those of plastics derived from the petrochemical industry, such as polyethylene and polypropylene. PHAs are widely used in the medical field and have the potential to be used in other applications due to their biocompatibility and biodegradability. Among PHAs, P(3HB-co-3HV) copolymers are thermo-elastomeric polyesters that are typically soft and flexible with low to no crystallinity, which can expand the range of applications of these bioplastics. Several bacterial species, such as Cupriavidus necator, Azotobacter vinelandii, Halomonas sp. and Bacillus megaterium, have been successfully used for P(3HB-co-3HV) production, both in batch and fed-batch cultures using different low-cost substrates, such as vegetable and fruit waste. Nevertheless, in recent years, several fermentation strategies using other microbial models, such as methanotrophic bacterial strains as well as halophilic bacteria, have been developed in order to improve PHA production in cultivation conditions that are easily implemented on a large scale. This review aims to summarize the recent trends in the production and recovery of PHA copolymers by fermentation, including different cultivation modalities, low-cost raw materials, as well as downstream strategies that have recently been developed with the purpose of producing copolymers, such as P(3HB-co-3HV), with suitable mechanical properties for applications in the biomedical field. Full article
(This article belongs to the Special Issue Microorganisms: A Way Forward for Sustainable Development?)
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12 pages, 1580 KiB  
Review
Response of Escherichia coli to Acid Stress: Mechanisms and Applications—A Narrative Review
by Zepeng Li, Zhaosong Huang and Pengfei Gu
Microorganisms 2024, 12(9), 1774; https://doi.org/10.3390/microorganisms12091774 - 28 Aug 2024
Cited by 3 | Viewed by 3773
Abstract
Change in pH in growth conditions is the primary stress for most neutralophilic bacteria, including model microorganism Escherichia coli. However, different survival capacities under acid stress in different bacteria are ubiquitous. Research on different acid-tolerance mechanisms in microorganisms is important for the [...] Read more.
Change in pH in growth conditions is the primary stress for most neutralophilic bacteria, including model microorganism Escherichia coli. However, different survival capacities under acid stress in different bacteria are ubiquitous. Research on different acid-tolerance mechanisms in microorganisms is important for the field of combating harmful gut bacteria and promoting fermentation performance of industrial strains. Therefore, this study aimed to carry out a narrative review of acid-stress response mechanism of E. coli discovered so far, including six AR systems, cell membrane protection, and macromolecular repair. In addition, the application of acid-tolerant E. coli in industry was illustrated, such as production of industrial organic acid and developing bioprocessing for industrial wastes. Identifying these aspects will open the opportunity for discussing development aspects for subsequent research of acid-tolerant mechanisms and application in E. coli. Full article
(This article belongs to the Special Issue Microorganisms: A Way Forward for Sustainable Development?)
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