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Microorganisms
Special Issues
Microbial Metabolism and Application in Biodegradation
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Microbial Metabolism and Application in Biodegradation

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

Deadline for manuscript submissions: 31 August 2025 | Viewed by 3715

Special Issue Editor

Dr. Ronnie Lubbers

E-Mail Website
Guest Editor
Molecular Microbiology and Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
Interests: bioremediation; utilization of renewable resources; carbon and nitrogen metabolism; aromatic compounds; microbial plastic degradation; lignin; pollutants
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial metabolism is fundamental to biodegradation, the process by which microorganisms break down complex organic compounds into simpler forms. This metabolic activity holds immense importance across various domains, particularly in environmental remediation. By harnessing microbial metabolic capabilities, biodegradation offers a sustainable and cost-effective solution for mitigating pollution and restoring ecosystems. Microbes play a crucial role in cleaning up pollutants, such as oil spills, industrial waste, and agricultural runoff, transforming them into less harmful substances. This process aids in environmental cleanup efforts, safeguarding ecosystems and human health.

Microbial metabolism is integral to biodegradation processes with diverse applications spanning environmental remediation, waste management, bioenergy production, pharmaceuticals, biotechnology, and agriculture. Understanding and harnessing microbial metabolic pathways offer innovative solutions for addressing environmental challenges and advancing sustainable development goals.

This Special Issue covers a broad spectrum of topics including but not limited to the following:

  • Advancements in microbial biodegradation technologies
    • Novel strains, metabolic pathways, and enzyme and gene discovery
    • Metabolic pathway induction and regulation
  • Microbial metabolic engineering for bioproduct synthesis
    • Microbial synthesis of biofuels, biopolymers, and biochemicals
    • High-value chemical synthesis
    • Secondary metabolic pathways, novel molecules, and bioactive compound discovery
  • Bioremediation approaches for emerging contaminants in soil, water, and air
    • Degradation of microplastics, PFAS, organic pollutants, and pharmaceuticals
    • Bioremediation strategies

Dr. Ronnie Lubbers
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

  • bioremediation
  • utilization of renewable resources
  • carbon and nitrogen metabolism
  • aromatic compounds
  • microbial plastic degradation
  • lignin
  • pollutants

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (6 papers)

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Research

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20 pages, 4462 KiB  
Article
Immobilization of Acinetobacter sp. A-1 and Applicability in Removal of Difenoconazole from Water–Sediment Systems
by Feiyu Chen, Liping Wang, Yi Zhou, Jingyi Sui, Tianyue Wang, Jia Yang, Xiuming Cui, Ye Yang and Wenping Zhang
Microorganisms 2025, 13(4), 802; https://doi.org/10.3390/microorganisms13040802 - 1 Apr 2025
Viewed by 260
Abstract
Difenoconazole, as a systemic triazole fungicide, is a broad-spectrum, highly effective agent that has been widely used for controlling fungal diseases in 46 different crops (or crop categories), including rice, wheat, and corn. Due to the improper use of difenoconazole, concerns about its [...] Read more.
Difenoconazole, as a systemic triazole fungicide, is a broad-spectrum, highly effective agent that has been widely used for controlling fungal diseases in 46 different crops (or crop categories), including rice, wheat, and corn. Due to the improper use of difenoconazole, concerns about its environmental residues and toxicity to non-target organisms have drawn significant attention from researchers. In response to this issue, this study aimed to isolate microbial strains capable of degrading difenoconazole from the environment. A novel difenoconazole-degrading strain, Acinetobacter sp. A-1, was screened and identified, demonstrating the ability to degrade 62.43% of 50 mg/L difenoconazole within seven days. Further optimization of the degradation conditions was conducted using single-factor experiments and response surface methodology experiments. The results showed that the optimal degradation conditions for strain A-1 were a difenoconazole concentration of 55.71 mg/L, a pH of 6.94, and an inoculation volume of 1.97%, achieving a degradation rate of 79.30%. Finally, strain A-1 was immobilized using sodium alginate, and its stability and bioremediation efficiency were evaluated. The results indicated that the immobilized strain A-1 exhibited high stability and significantly reduced the half-life of difenoconazole in the water–sediment contamination system. In the sterilized water–sediment system, the degradation rate of difenoconazole by the immobilized strain A-1 reached 65.26%. Overall, this study suggests that Acinetobacter sp. A-1 is a promising candidate for difenoconazole degradation, and immobilization technology can effectively enhance its removal efficiency in water–sediment systems. Full article
(This article belongs to the Special Issue Microbial Metabolism and Application in Biodegradation)
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16 pages, 1870 KiB  
Article
Seasonal Variations of Community Structure and Functional Genes of Synechococcus in the Subtropical Coastal Waters: Insights from FACS and High-Throughput Sequencing
by Zhenzhen Song, Ting Zhang, Yantao Liang, Andrew Mcminn, Min Wang, Nianzhi Jiao and Tingwei Luo
Microorganisms 2025, 13(4), 764; https://doi.org/10.3390/microorganisms13040764 - 27 Mar 2025
Viewed by 282
Abstract
Synechococcus plays a pivotal role in the marine biogeochemical cycle. Advances in isolation techniques and high-throughput sequencing have expanded our understanding of the diversity of the Synechococcus community. However, their genomic diversity, functional dynamics and seasonal variations in the coastal waters are still [...] Read more.
Synechococcus plays a pivotal role in the marine biogeochemical cycle. Advances in isolation techniques and high-throughput sequencing have expanded our understanding of the diversity of the Synechococcus community. However, their genomic diversity, functional dynamics and seasonal variations in the coastal waters are still not well known. Here, seawater samples were collected seasonally (March, June, August, December) from three stations in the coastal waters of Xiamen. Using fluorescence-activated cell sorting (FACS), we isolated 1000 Synechococcus cells per sample and performed ITS amplicon sequencing and metagenomic sequencing to analyze the seasonal variations in community structure and functional genes of Synechococcus. Firstly, we conducted a comparative analysis of in situ data and FACS data from three sampling sites in August. FACS samples revealed low-abundance Synechococcus strains underdetected by in situ samples. In addition, 24 clades representing Synechococcus subclusters S5.1, S5.2, and S5.3 were detected from three in situ samples and twelve FACS samples, suggesting the high diversity of Synechococcus in the coastal waters of Xiamen. Furthermore, the Synechococcus community displayed pronounced seasonal variations, and temperature significantly influenced the variations in Synechococcus community composition. Additionally, Synechococcus populations exhibit seasonal functional dynamics, with enhanced metabolic activity in summer characterized by higher numbers of functional genes associated with metabolic pathways compared to winter samples. Altogether, this study underscored the significance of FACS and high-throughput sequencing to reveal the diversity and functional dynamics of Synechococcus. Full article
(This article belongs to the Special Issue Microbial Metabolism and Application in Biodegradation)
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21 pages, 2801 KiB  
Article
Characterization of Glyphosate Resistance and Degradation Profile of Caballeronia zhejiangensis CEIB S4-3 and Genes Involved in Its Degradation
by Manuel Isaac Morales-Olivares, María Luisa Castrejón-Godínez, Patricia Mussali-Galante, Efraín Tovar-Sánchez, Hugo Albeiro Saldarriaga-Noreña and Alexis Rodríguez
Microorganisms 2025, 13(3), 651; https://doi.org/10.3390/microorganisms13030651 - 13 Mar 2025
Viewed by 661
Abstract
Herbicides are the most employed pesticides in agriculture worldwide; among them, glyphosate is the most successful herbicide molecule in history. The extensive use of glyphosate has been related to environmental pollution and toxic effects on non-target organisms. Effective remediation and treatment alternatives must [...] Read more.
Herbicides are the most employed pesticides in agriculture worldwide; among them, glyphosate is the most successful herbicide molecule in history. The extensive use of glyphosate has been related to environmental pollution and toxic effects on non-target organisms. Effective remediation and treatment alternatives must be developed to reduce the environmental presence of glyphosate and its adverse effects. Bioremediation using microorganisms has been proposed as a feasible alternative for treating glyphosate pollution; due to this, identifying and characterizing microorganisms capable of biodegrading glyphosate is a key environmental task for the bioremediation of polluted sites by this herbicide. This study characterized the glyphosate resistance profile and degradation capacity of the bacterial strain Caballeronia zhejiangensis CEIB S4-3. According to the results of the bacterial growth inhibition assays on agar plates, C. zhejiangensis CEIB S4-3 can resist exposure to high concentrations of glyphosate, up to 1600 mg/L in glyphosate-based herbicide (GBH) formulation, and 12,000 mg/L of the analytical-grade molecule. In the inhibition assay in liquid media, C. zhejiangensis CEIB S4-3 resisted glyphosate exposure to all concentrations evaluated (25–400 mg/L). After 48 h exposure, GBH caused important bacterial growth inhibition (>80%) at concentrations between 100 and 400 mg/L, while exposure to analytical-grade glyphosate caused bacterial growth inhibitions below 15% in all tested concentrations. Finally, this bacterial strain was capable of degrading 60% of the glyphosate supplemented to culture media (50 mg/L), when used as the sole carbon source, in twelve hours; moreover, C. zhejiangensis CEIB S4-3 can also degrade the primary glyphosate degradation metabolite aminomethylphosphonic acid (AMPA). Genomic analysis revealed the presence of genes associated with the two reported metabolic pathways for glyphosate degradation, the sarcosine and AMPA pathways. This is the first report on the glyphosate degradation capacity and the genes related to its metabolism in a Caballeronia genus strain. The results from this investigation demonstrate that C. zhejiangensis CEIB S4-3 exhibits significant potential for glyphosate biodegradation, suggesting its applicability in bioremediation strategies targeting this contaminant. Full article
(This article belongs to the Special Issue Microbial Metabolism and Application in Biodegradation)
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21 pages, 2975 KiB  
Article
Diversity and Distribution of Hydrocarbon-Degrading Genes in the Cold Seeps from the Mediterranean and Caspian Seas
by Yogita Warkhade, Laura G. Schaerer, Isaac Bigcraft, Terry C. Hazen and Stephen M. Techtmann
Microorganisms 2025, 13(2), 222; https://doi.org/10.3390/microorganisms13020222 - 21 Jan 2025
Viewed by 752
Abstract
Marine cold seeps are unique ecological niches characterized by the emergence of hydrocarbons, including methane, which fosters diverse microbial communities. This study investigates the diversity and distribution of hydrocarbon-degrading genes and organisms in sediments from the Caspian and Mediterranean Seas, utilizing 16S rRNA [...] Read more.
Marine cold seeps are unique ecological niches characterized by the emergence of hydrocarbons, including methane, which fosters diverse microbial communities. This study investigates the diversity and distribution of hydrocarbon-degrading genes and organisms in sediments from the Caspian and Mediterranean Seas, utilizing 16S rRNA and metagenomic sequencing to elucidate microbial community structure and functional potential. Our findings reveal distinct differences in hydrocarbon degrading gene profiles between the two seas, with pathways for aerobic and anaerobic hydrocarbon degradation co-existing in sediments from both basins. Aerobic pathways predominate in the surface sediments of the Mediterranean Sea, while anaerobic pathways are favored in the surface sediments of the anoxic Caspian Sea. Additionally, sediment depths significantly influence microbial diversity, with variations in gene abundance and community composition observed at different depths. Aerobic hydrocarbon-degrading genes decrease in diversity with depth in the Mediterranean Sea, whereas the diversity of aerobic hydrocarbon-degrading genes increases with depth in the Caspian Sea. These results enhance our understanding of microbial ecology in cold seep environments and have implications for bioremediation practices targeting hydrocarbon pollutants in marine ecosystems. Full article
(This article belongs to the Special Issue Microbial Metabolism and Application in Biodegradation)
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18 pages, 17896 KiB  
Article
Biodegradation of Phenol at High Initial Concentration by Rhodococcus opacus 3D Strain: Biochemical and Genetic Aspects
by Tatiana O. Anokhina, Tatiana Z. Esikova, Valentina N. Polivtseva, Nataliya E. Suzina and Inna P. Solyanikova
Microorganisms 2025, 13(1), 205; https://doi.org/10.3390/microorganisms13010205 - 18 Jan 2025
Viewed by 998
Abstract
Phenolic compounds are an extensive group of natural and anthropogenic organic substances of the aromatic series containing one or more hydroxyl groups. The main sources of phenols entering the environment are waste from metallurgy and coke plants, enterprises of the leather, furniture, and [...] Read more.
Phenolic compounds are an extensive group of natural and anthropogenic organic substances of the aromatic series containing one or more hydroxyl groups. The main sources of phenols entering the environment are waste from metallurgy and coke plants, enterprises of the leather, furniture, and pulp and paper industries, as well as wastewater from the production of phenol–formaldehyde resins, adhesives, plastics, and pesticides. Among this group of compounds, phenol is the most common environmental pollutant. One of the cheapest and most effective ways to combat phenol pollution is biological purification. However, the inability of bacteria to decompose high concentrations of phenol is a significant limitation. Due to the uncoupling of oxidative phosphorylation, phenol concentrations above 1 g/L are toxic and inhibit cell growth. This article presents data on the biodegradative potential of Rhodococcus opacus strain 3D. This strain is capable of decomposing a wide range of toxicants, including phenol. In the present study, cell growth with phenol, growth after rest, growth of immobilized cells before and after rest, phase contrast, and scanning microscopy of immobilized cells on fiber were studied in detail. The free-living and immobilized cells can decompose phenol concentrations up to 1.5 g/L and 2.5 g/L, respectively. The decomposition of the toxicant was catalyzed by the enzymes catechol 1,2-dioxygenase and cis,cis-muconate cycloisomerase. The role of protocatechuate 3,4-dioxygenase in biodegradative processes is discussed. In this work, it is shown that the immobilized cells can be stored for a long time (up to 2 years) without significant loss of their degradation activity. An assessment of the induction of genes potentially involved in this process was taken. Based on our investigation, we can conclude that this strain can be considered an effective destructor that is capable of degrading phenol at high concentrations, increases its biodegradative potential during immobilization, and retains this ability for a long storage time. Therefore, the strain can be used in biotechnology for the purification of aqueous samples at high concentrations from phenolic contamination. Full article
(This article belongs to the Special Issue Microbial Metabolism and Application in Biodegradation)
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Review

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25 pages, 2388 KiB  
Review
Lignin-Degrading Enzymes and the Potential of Pseudomonas putida as a Cell Factory for Lignin Degradation and Valorization
by Qing Zhou, Annabel Fransen and Han de Winde
Microorganisms 2025, 13(4), 935; https://doi.org/10.3390/microorganisms13040935 - 18 Apr 2025
Viewed by 391
Abstract
Efficient utilization of lignin, a complex polymer in plant cell walls, is one of the key strategies for developing a green and sustainable bioeconomy. However, bioconversion of lignin poses a significant challenge due to its recalcitrant nature. Microorganisms, particularly fungi and bacteria, play [...] Read more.
Efficient utilization of lignin, a complex polymer in plant cell walls, is one of the key strategies for developing a green and sustainable bioeconomy. However, bioconversion of lignin poses a significant challenge due to its recalcitrant nature. Microorganisms, particularly fungi and bacteria, play a crucial role in lignin biodegradation, using various enzymatic pathways. Among bacteria, Pseudomonas putida is considered a promising host for lignin degradation and valorization, due to its robust and flexible metabolism and its tolerance to many noxious and toxic compounds. This review explores the various mechanisms of lignin breakdown by microorganisms, with a focus on P. putida’s metabolic versatility and genetic engineering potential. By leveraging advanced genetic tools and metabolic pathway optimization, P. putida can be engineered to efficiently convert lignin into valuable bioproducts, offering sustainable solutions for lignin valorization in industrial applications. Full article
(This article belongs to the Special Issue Microbial Metabolism and Application in Biodegradation)
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