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Biochemical and Molecular Aspects of Bioremediation of Soils with Organic Pollutants by Microorganisms

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (20 April 2025) | Viewed by 4022

Special Issue Editor

Dr. Mariusz Cycoń

E-Mail Website
Guest Editor
Department of Microbiology and Virology, School of Pharmacy with the Division of Laboratory Medicine, Medical University of Silesia, Sosnowiec, Poland
Interests: environmental microbiology and biotechnology; biodegradation of organic pollutants; bioremediation of contaminated soils; microbial infection; antibiotics; drug resistance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The widespread and continuous use of pharmaceuticals (e.g., antibiotics, non-steroidal anti-inflammatory drugs, etc.), petroleum, pesticides, and other organic compounds is a major problem as they pollute soils and affect non-target organisms. Since the abovementioned compounds may not degrade immediately after introduction into soil and because their large residues have been detected in the environment, there is an urgent need to remediate polluted soils. Various remediation techniques have been developed for this purpose; however, bioremediation, which involves microorganisms, has emerged as the most advantageous method for cleaning up contaminated soils. However, it is important to understand the molecular aspects of bioremediation processes in which microorganisms participate regarding contaminated soils. Molecular methods can provide us with a valuable set of unique tools to study microbial communities, the functional capabilities of particular environments, and specific microorganisms degrading pollutants involved in the bioremediation processes. Moreover, molecular methods offer the possibility of monitoring the fate and abundance of inoculants, as well as the expression of genes encoding enzymes involved in the degradation of toxic pollutants.

This Special Issue of the International Journal of Molecular Sciences welcomes researchers all over the world to contribute original articles and reviews addressing the latest knowledge about the degradation potential of indigenous soil microorganisms in relation to organic pollutants, the use of molecular tools for monitoring the changes in microbial communities of contaminated soils, and the expression of genes encoding enzymes involved in the degradation of toxic pollutants, as well as the specific markers and molecular tools for monitoring the effectiveness of soil bioremediation.

Dr. Mariusz Cycoń
Guest Editor

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Keywords

  • bioremediation
  • soil pollution
  • organic pollutants
  • microorganisms
  • microbial communities
  • gene expression
  • enzyme degradation
  • molecular tools
  • indigenous soil microorganisms
  • contaminated soils

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Published Papers (4 papers)

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Research

13 pages, 2397 KiB  
Communication
Impact of Tire-Derived Microplastics on Microbiological Activity of Aerobic Granular Sludge
by Weronika Irena Mądzielewska, Piotr Jachimowicz, Job Oliver Otieno and Agnieszka Cydzik-Kwiatkowska
Int. J. Mol. Sci. 2025, 26(9), 4136; https://doi.org/10.3390/ijms26094136 - 27 Apr 2025
Viewed by 177
Abstract
In recent years, there has been an increase in the emission of tire wear particle (TWP) microplastics from wastewater treatment plants into the environment. The aim of this study was to determine the effect of TWPs in wastewater flowing into a biological reactor [...] Read more.
In recent years, there has been an increase in the emission of tire wear particle (TWP) microplastics from wastewater treatment plants into the environment. The aim of this study was to determine the effect of TWPs in wastewater flowing into a biological reactor on the transcription of the 16S rRNA gene and the key genes responsible for nitrogen metabolism, amoA, nirK and nosZ, in aerobic granular sludge. The laboratory experiment was carried out in sequencing aerobic granular sludge reactors operated in an 8 h cycle into which TWP microplastics were introduced with municipal wastewater at a dose of 50–500 mg TWPs/L. The ammonia removal rate and the production of oxidized forms of nitrogen increased with the TWP dose. Gene transcript abundance analysis showed that the presence of rubber and substances leached from it promoted the activity of ammonium-oxidizing bacteria (160% increase), while the transcription of genes related to denitrification conversions was negatively affected. The activity of nitrite reductase gradually decreased with increasing TWP concentration in wastewater (decreased by 33% at 500 mg TWPs/L), while nitric oxide reductase activity was significantly inhibited even at the lowest TWP dose (decreased by 58% at 500 mg TWPs/L). The data obtained indicate that further studies are needed on the mechanisms of the effects of TWPs on the activities of the most important groups of microorganisms in wastewater treatment to minimize the negative effects of TWPs on biological wastewater treatment. Full article
(This article belongs to the Special Issue Biochemical and Molecular Aspects of Bioremediation of Soils with Organic Pollutants by Microorganisms)
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25 pages, 7057 KiB  
Article
Enhanced Dissipation of Non-Steroidal Anti-Inflammatory Drugs (NSAIDs) in Soil by the Bioaugmentation with Newly Isolated Strain Acinetobacter johnsonii MC5
by Mariusz Cycoń, Agnieszka Żmijowska and Magdalena Klim
Int. J. Mol. Sci. 2025, 26(1), 190; https://doi.org/10.3390/ijms26010190 - 29 Dec 2024
Viewed by 679
Abstract
The presented study investigated the possibility of using the Acinetobacter johnsonii MC5 strain, isolated from raw sewage by the enrichment culture method, in the bioremediation of soil contaminated with selected NSAIDs, i.e., ibuprofen (IBF), diclofenac (DCF), and naproxen (NPX), using the bioaugmentation technique. [...] Read more.
The presented study investigated the possibility of using the Acinetobacter johnsonii MC5 strain, isolated from raw sewage by the enrichment culture method, in the bioremediation of soil contaminated with selected NSAIDs, i.e., ibuprofen (IBF), diclofenac (DCF), and naproxen (NPX), using the bioaugmentation technique. The degradation potential of A. johnsonii MC5 was first evaluated using a mineral salt medium containing drugs as the only sources of carbon and energy. The results show that the strain MC5 was capable of utilizing the tested compounds in medium, indicating that the drugs might be metabolically degraded. IBF and NPX were degraded with a similar rate and DT50 values were determined to be approximately 5 days, while the degradation process for DCF was slower, and the DT50 value was about 5 times higher (22.7 days) compared to those calculated for IBF and NPX. Bioaugmentation of non-sterile soil with A. johnsonii MC5 increased the rate of disappearance of the tested drugs, and DT50 values decreased 5.4-, 3.6-, or 6.5-fold for IBF, DCF, or NPX, respectively, in comparison with the values obtained for the soil with indigenous microorganisms only. The obtained results suggest that A. johnsonii MC5 may have potential for use in bioremediation of NSAID-contaminated soils; however, detailed studies are needed before using this strain in such process on a larger scale. Full article
(This article belongs to the Special Issue Biochemical and Molecular Aspects of Bioremediation of Soils with Organic Pollutants by Microorganisms)
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17 pages, 1837 KiB  
Article
A Study of the Community Relationships Between Methanotrophs and Their Satellites Using Constraint-Based Modeling Approach
by Maryam A. Esembaeva, Mikhail A. Kulyashov, Fedor A. Kolpakov and Ilya R. Akberdin
Int. J. Mol. Sci. 2024, 25(22), 12469; https://doi.org/10.3390/ijms252212469 - 20 Nov 2024
Viewed by 1149
Abstract
Biotechnology continues to drive innovation in the production of pharmaceuticals, biofuels, and other valuable compounds, leveraging the power of microbial systems for enhanced yield and sustainability. Genome-scale metabolic (GSM) modeling has become an essential approach in this field, which enables a guide for [...] Read more.
Biotechnology continues to drive innovation in the production of pharmaceuticals, biofuels, and other valuable compounds, leveraging the power of microbial systems for enhanced yield and sustainability. Genome-scale metabolic (GSM) modeling has become an essential approach in this field, which enables a guide for targeting genetic modifications and the optimization of metabolic pathways for various industrial applications. While single-species GSM models have traditionally been employed to optimize strains like Escherichia coli and Lactococcus lactis, the integration of these models into community-based approaches is gaining momentum. Herein, we present a pipeline for community metabolic modeling with a user-friendly GUI, applying it to analyze interactions between Methylococcus capsulatus, a biotechnologically important methanotroph, and Escherichia coli W3110 under oxygen- and nitrogen-limited conditions. We constructed models with unmodified and homoserine-producing E. coli strains using the pipeline implemented in the original BioUML platform. The E. coli strain primarily utilized acetate from M. capsulatus under oxygen limitation. However, homoserine produced by E. coli significantly reduced acetate secretion and the community growth rate. This homoserine was taken up by M. capsulatus, converted to threonine, and further exchanged as amino acids. In nitrogen-limited modeling conditions, nitrate and ammonium exchanges supported the nitrogen needs, while carbon metabolism shifted to fumarate and malate, enhancing E. coli TCA cycle activity in both cases, with and without modifications. The presence of homoserine altered cross-feeding dynamics, boosting amino acid exchanges and increasing pyruvate availability for M. capsulatus. These findings suggest that homoserine production by E. coli optimizes resource use and has potential for enhancing microbial consortia productivity. Full article
(This article belongs to the Special Issue Biochemical and Molecular Aspects of Bioremediation of Soils with Organic Pollutants by Microorganisms)
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22 pages, 5295 KiB  
Article
Response of Soil Microbiota, Enzymes, and Plants to the Fungicide Azoxystrobin
by Małgorzata Baćmaga, Jadwiga Wyszkowska and Jan Kucharski
Int. J. Mol. Sci. 2024, 25(15), 8104; https://doi.org/10.3390/ijms25158104 - 25 Jul 2024
Cited by 5 | Viewed by 1269
Abstract
The present study was aimed at assessing the impact of azoxystrobin—a fungicide commonly used in plant protection against pathogens (Amistar 250 SC)—on the soil microbiota and enzymes, as well as plant growth and development. The laboratory experiment was conducted in three analytical terms [...] Read more.
The present study was aimed at assessing the impact of azoxystrobin—a fungicide commonly used in plant protection against pathogens (Amistar 250 SC)—on the soil microbiota and enzymes, as well as plant growth and development. The laboratory experiment was conducted in three analytical terms (30, 60, and 90 days) on sandy clay (pH—7.0). Azoxystrobin was applied to soil in doses of 0.00 (C), 0.110 (F) and 32.92 (P) mg kg−1 d.m. of soil. Its 0.110 mg kg−1 dose stimulated the proliferation of organotrophic bacteria and actinobacteria but inhibited that of fungi. It also contributed to an increase in the colony development index (CD) and a decrease in the ecophysiological diversity index (EP) of all analyzed groups of microorganisms. Azoxystrobin applied at 32.92 mg kg−1 reduced the number and EP of microorganisms and increased their CD. PP952051.1 Bacillus mycoides strain (P), PP952052.1 Prestia megaterium strain (P) bacteria, as well as PP952052.1 Kreatinophyton terreum isolate (P) fungi were identified in the soil contaminated with azoxystrobin, all of which may exhibit resistance to its effects. The azoxystrobin dose of 0.110 mg kg−1 stimulated the activity of all enzymes, whereas its 32.92 mg kg−1 dose inhibited activities of dehydrogenases, alkaline phosphatase, acid phosphatase, and urease and stimulated the activity of catalase. The analyzed fungicide added to the soil at both 0.110 and 32.92 mg kg−1 doses inhibited seed germination and elongation of shoots of Lepidium sativum L., Sinapsis alba L., and Sorgum saccharatum L. Full article
(This article belongs to the Special Issue Biochemical and Molecular Aspects of Bioremediation of Soils with Organic Pollutants by Microorganisms)
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