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

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 36134

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Dr. Mariusz Cycoń

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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
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Dear Colleagues,

Soil microorganisms perform many vital processes and participate in the maintenance of soil health and quality. They play a crucial role in organic matter turnover, nutrients release, and stabilization of the soil structure and ensure soil fertility. The homeostasis of soil may be disturbed by organic and inorganic contaminants including pesticide, heavy metals, toxic hydrocarbons, antibiotics, etc. The antimicrobial activity of these chemicals in soil may differentially inhibit the growth of soil microorganisms and thus influence the soil microbial community composition, which may result in alterations of the ecological functionality of the soil. The fast response and sensitivity of microorganisms to contaminants contribute to the fact that microbial parameters are thought to be useful indicators for the assessment of soil fertility and quality status.

In this context, this Special Issue of Microorganisms welcomes researchers all over the world to contribute with original articles, as well as reviews addressing the latest knowledge about:

the impact of contaminants on the community structure as well as the genetic and functional diversity of soil microorganisms;
the specific markers and methods for studying the effect of contaminants on soil microorganisms;
the use of molecular tools for monitoring the changes in microbial communities of contaminated soils;
the fate and activity of microorganisms involved in the degradation of contaminants; and

the bioremediation of contaminated soils by inoculating of specific microorganisms and their ecological behavior including the survival dynamics and the interaction with indigenous microorganisms

Dr. Mariusz Cycoń
Guest Editor

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Keywords

soil contamination
microbial activity
microbial diversity
microbial community structure
bioremediation of environment
bioaugmentation
behavior of inoculated microorganisms

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Microorganisms in the Polluted Soil 2.0 in Microorganisms (2 articles)

Published Papers (8 papers)

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Research

16 pages, 5754 KiB

Open AccessArticle

Microbial Succession under Freeze–Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil

by Hugo Emiliano de Jesus, Renato S. Carreira, Simone S. M. Paiva, Carlos Massone, Alex Enrich-Prast, Raquel S. Peixoto, Jorge L. Mazza Rodrigues, Charles K. Lee, Craig Cary and Alexandre S. Rosado

Microorganisms 2021, 9(3), 609; https://doi.org/10.3390/microorganisms9030609 - 16 Mar 2021

Cited by 6 | Viewed by 3314

Abstract

The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes. Full article

(This article belongs to the Special Issue Microorganisms in The Polluted Soil)

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20 pages, 3530 KiB

Open AccessArticle

Bioremediation by Cupriavidus metallidurans Strain MSR33 of Mercury-Polluted Agricultural Soil in a Rotary Drum Bioreactor and Its Effects on Nitrogen Cycle Microorganisms

by Guillermo Bravo, Paulina Vega-Celedón, Juan Carlos Gentina and Michael Seeger

Microorganisms 2020, 8(12), 1952; https://doi.org/10.3390/microorganisms8121952 - 9 Dec 2020

Cited by 25 | Viewed by 4586

Abstract

Nitrogen cycle microorganisms are essential in agricultural soils and may be affected by mercury pollution. The aims of this study are to evaluate the bioremediation of mercury-polluted agricultural soil using Cupriavidus metallidurans MSR33 in a rotary drum bioreactor (RDB) and to characterize the effects of mercury pollution and bioremediation on nitrogen cycle microorganisms. An agricultural soil was contaminated with mercury (II) (20–30 ppm) and subjected to bioremediation using strain MSR33 in a custom-made RDB. The effects of mercury and bioremediation on nitrogen cycle microorganisms were studied by qPCR. Bioremediation in the RDB removed 82% mercury. MSR33 cell concentrations, thioglycolate, and mercury concentrations influence mercury removal. Mercury pollution strongly decreased nitrogen-fixing and nitrifying bacterial communities in agricultural soils. Notably, after soil bioremediation process nitrogen-fixing and nitrifying bacteria significantly increased. Diverse mercury-tolerant strains were isolated from the bioremediated soil. The isolates Glutamicibacter sp. SB1a, Brevundimonas sp. SB3b, and Ochrobactrum sp. SB4b possessed the merG gene associated with the plasmid pTP6, suggesting the horizontal transfer of this plasmid to native gram-positive and gram-negative bacteria. Bioremediation by strain MSR33 in an RDB is an attractive and innovative technology for the clean-up of mercury-polluted agricultural soils and the recovery of nitrogen cycle microbial communities. Full article

(This article belongs to the Special Issue Microorganisms in The Polluted Soil)

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16 pages, 4005 KiB

Open AccessArticle

Application of Erythromycin and/or Raoultella sp. Strain MC3 Alters the Metabolic Activity of Soil Microbial Communities as Revealed by the Community Level Physiological Profiling Approach

by Mariusz Cycoń, Anna Markowicz, Tomasz J. Wąsik and Zofia Piotrowska-Seget

Microorganisms 2020, 8(12), 1860; https://doi.org/10.3390/microorganisms8121860 - 25 Nov 2020

Cited by 2 | Viewed by 2296

Abstract

Erythromycin (EM), a macrolide antibiotic, by influencing the biodiversity of microorganisms, might change the catabolic activity of the entire soil microbial community. Hence, the goal of this study was to determine the metabolic biodiversity in soil treated with EM (1 and 10 mg/kg soil) using the community-level physiological profiling (CLPP) method during a 90-day experiment. In addition, the effect of soil inoculation with antibiotic-resistant Raoultella sp. strain MC3 on CLPP was evaluated. The resistance and resilience concept as well as multifactorial analysis of data was exploited to interpret the outcomes obtained. EM negatively affected the metabolic microbial activity, as indicated by the values of the CLPP indices, i.e., microbial activity expressed as the average well-color development (AWCD), substrate richness (R), the Shannon–Wiener (H) and evenness (E) indices and the AWCD values for the six groups of carbon substrate present in EcoPlates until 15 days. The introduction of strain MC3 into soil increased the degradative activity of soil microorganisms in comparison with non-inoculated control. In contrast, at the consecutive sampling days, an increase in the values of the CLPP parameters was observed, especially for EM-10 + MC3-treated soil. Considering the average values of the resistance index for all of the measurement days, the resistance of the CLPP indices and the AWCD values for carbon substrate groups were categorized as follows: E > H > R > AWCD and polymers > amino acids > carbohydrates > miscellaneous > amines > carboxylic acids. The obtained results suggest a low level of resistance of soil microorganisms to EM and/or strain MC3 at the beginning of the exposure time, but the microbial community exhibited the ability to recover its initial decrease in catabolic activity over the experimental period. Despite the short-term effects, the balance of the soil ecosystem may be disturbed. Full article

(This article belongs to the Special Issue Microorganisms in The Polluted Soil)

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17 pages, 1610 KiB

Open AccessArticle

Effect of Co-contamination by PAHs and Heavy Metals on Bacterial Communities of Diesel Contaminated Soils of South Shetland Islands, Antarctica

by Alejandro Gran-Scheuch, Javiera Ramos-Zuñiga, Edwar Fuentes, Denisse Bravo and José M. Pérez-Donoso

Microorganisms 2020, 8(11), 1749; https://doi.org/10.3390/microorganisms8111749 - 7 Nov 2020

Cited by 36 | Viewed by 4153

Abstract

Diesel oil is the main source of energy used in Antarctica. Since diesel is composed of toxic compounds such as polycyclic aromatic hydrocarbons (PAHs) and heavy metals, it represents a constant threat to the organisms inhabiting this continent. In the present study, we characterized the chemical and biological parameters of diesel-exposed soils obtained from King George Island in Antarctica. Contaminated soils present PAH concentrations 1000 times higher than non-exposed soils. Some contaminated soil samples also exhibited high concentrations of cadmium and lead. A 16S metagenome analysis revealed the effect of co-contamination on bacterial communities. An increase in the relative abundance of bacteria known as PAH degraders or metal resistant was determined in co-contaminated soils. Accordingly, the soil containing higher amounts of PAHs exhibited increased dehydrogenase activity than control soils, suggesting that the microorganisms present can metabolize diesel. The inhibitory effect on soil metabolism produced by cadmium was lower in diesel-contaminated soils. Moreover, diesel-contaminated soils contain higher amounts of cultivable heterotrophic, cadmium-tolerant, and PAH-degrading bacteria than control soils. Obtained results indicate that diesel contamination at King George island has affected microbial communities, favoring the presence of microorganisms capable of utilizing PAHs as a carbon source, even in the presence of heavy metals. Full article

(This article belongs to the Special Issue Microorganisms in The Polluted Soil)

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17 pages, 3352 KiB

Open AccessArticle

Quorum Quenching in a Novel Acinetobacter sp. XN-10 Bacterial Strain against Pectobacterium carotovorum subsp. carotovorum

by Wenping Zhang, Qingqing Luo, Yiyin Zhang, Xinghui Fan, Tian Ye, Sandhya Mishra, Pankaj Bhatt, Lianhui Zhang and Shaohua Chen

Microorganisms 2020, 8(8), 1100; https://doi.org/10.3390/microorganisms8081100 - 23 Jul 2020

Cited by 24 | Viewed by 3758

Abstract

Quorum sensing (QS) is a cell density-dependent mechanism that regulates the expression of specific genes in microbial cells. Quorum quenching (QQ) is a promising strategy for attenuating pathogenicity by interfering with the QS system of pathogens. N-Acyl-homoserine lactones (AHLs) act as signaling molecules in many Gram-negative bacterial pathogens and have received wide attention. In this study, a novel, efficient AHL-degrading bacterium, Acinetobacter sp. strain XN-10, was isolated from agricultural contaminated soil and evaluated for its degradation efficiency and potential use against QS-mediated pathogens. Strain XN-10 could effectively degrade N-(3-oxohexanoyl)-L-homoserine lactone (OHHL), N-hexanoyl-L-homoserine lactone (C6HSL), N-(3-oxododecanoyl)-L-homoserine lactone (3OC12HSL), and N-(3-oxooctanoyl)-L-homoserine lactone (3OC8HSL), which all belong to the AHL family. Analysis of AHL metabolic products by gas chromatography–mass spectrometry (GC-MS) led to the identification of N-cyclohexyl-propanamide, and pentanoic acid, 4-methyl, methyl ester as the main intermediate metabolites, revealing that AHL could be degraded by hydrolysis and dehydroxylation. All intermediates were transitory and faded away without any non-cleavable metabolites at the end of the experiment. Furthermore, strain XN-10 significantly attenuated the pathogenicity of Pectobacterium carotovorum subsp. carotovorum (Pcc) to suppress tissue maceration in carrots, potatoes, and Chinese cabbage. Taken together, our results shed light on the QQ mechanism of a novel AHL-degrading bacterial isolate, and they provide useful information which show potential for biocontrol of infectious diseases caused by AHL-dependent bacterial pathogens. Full article

(This article belongs to the Special Issue Microorganisms in The Polluted Soil)

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18 pages, 2025 KiB

Open AccessArticle

Construction of a Tetracycline Degrading Bacterial Consortium and Its Application Evaluation in Laboratory-Scale Soil Remediation

by Xueling Wu, Yichao Gu, Xiaoyan Wu, Xiangyu Zhou, Han Zhou, Charles Amanze, Li Shen and Weimin Zeng

Microorganisms 2020, 8(2), 292; https://doi.org/10.3390/microorganisms8020292 - 20 Feb 2020

Cited by 32 | Viewed by 4574

Abstract

As an environmental pollutant, tetracycline (TC) can persist in the soil for years and damage the ecosystem. So far, many methods have been developed to handle the TC contamination. Microbial remediation, which involves the use of microbes to biodegrade the pollutant, is considered cost-efficient and more suitable for practical application in soil. This study isolated several strains from TC-contaminated soil and constructed a TC-degrading bacterial consortium containing Raoultella sp. XY-1 and Pandoraea sp. XY-2, which exhibited better growth and improved TC degradation efficiency compared with single strain (81.72% TC was biodegraded within 12 days in Lysogeny broth (LB) medium). Subsequently, lab-scale soil remediation was conducted to evaluate its effectiveness in different soils and the environmental effects it brought. Results indicated that the most efficient TC degradation was recorded at 30 °C and in soil sample Y which had relatively low initial TC concentration (around 35 mg/kg): TC concentration decreased by 43.72% within 65 days. Soil properties were affected, for instance, at 30 °C, the pH value of soil sample Y increased to near neutral, and soil moisture content (SMC) of both soils declined. Analysis of bacterial communities at the phylum level showed that Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi were the four dominant phyla, and the relative abundance of Proteobacteria significantly increased in both soils after bioremediation. Further analysis of bacterial communities at the genus level revealed that Raoultella sp. XY-1 successfully proliferated in soil, while Pandoraea sp. XY-2 was undetectable. Moreover, bacteria associated with nitrogen cycling, biodegradation of organic pollutants, soil biochemical reactions, and plant growth were affected, causing the decline in soil bacterial diversity. Variations in the relative abundance of tetracycline resistance genes (TRGs) and mobile gene elements (MGEs) were investigated, the results obtained indicated that tetD, tetG, tetX, intI1, tnpA-04, and tnpA-05 had higher relative abundance in original soils, and the relative abundance of most TRGs and MGEs declined after the microbial remediation. Network analysis indicated that tnpA may dominate the transfer of TRGs, and Massilia, Alkanibacter, Rhizomicrobium, Xanthomonadales, Acidobacteriaceae, and Xanthomonadaceae were possible hosts of TRGs or MGEs. This study comprehensively evaluated the effectiveness and the ecological effects of the TC-degrading bacterial consortium in soil environment. Full article

(This article belongs to the Special Issue Microorganisms in The Polluted Soil)

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14 pages, 2512 KiB

Open AccessArticle

Enhanced Cypermethrin Degradation Kinetics and Metabolic Pathway in Bacillus thuringiensis Strain SG4

by Pankaj Bhatt, Yaohua Huang, Wenping Zhang, Anita Sharma and Shaohua Chen

Microorganisms 2020, 8(2), 223; https://doi.org/10.3390/microorganisms8020223 - 7 Feb 2020

Cited by 108 | Viewed by 6031

Abstract

Cypermethrin is popularly used as an insecticide in households and agricultural fields, resulting in serious environmental contamination. Rapid and effective techniques that minimize or remove insecticidal residues from the environment are urgently required. However, the currently available cypermethrin-degrading bacterial strains are suboptimal. We aimed to characterize the kinetics and metabolic pathway of highly efficient cypermethrin-degrading Bacillus thuringiensis strain SG4. Strain SG4 effectively degraded cypermethrin under different conditions. The maximum degradation was observed at 32 °C, pH 7.0, and a shaking speed of 110 rpm, and about 80% of the initial dose of cypermethrin (50 mg·L⁻¹) was degraded in minimal salt medium within 15 days. SG4 cells immobilized with sodium alginate provided a higher degradation rate (85.0%) and lower half-life (t_1/2) of 5.3 days compared to the 52.9 days of the control. Bioaugmentation of cypermethrin-contaminated soil slurry with strain SG4 significantly enhanced its biodegradation (83.3%). Analysis of the degradation products led to identification of nine metabolites of cypermethrin, which revealed that cypermethrin could be degraded first by cleavage of its ester bond, followed by degradation of the benzene ring, and subsequent metabolism. A new degradation pathway for cypermethrin was proposed based on analysis of the metabolites. We investigated the active role of B. thuringiensis strain SG4 in cypermethrin degradation under various conditions that could be applied in large-scale pollutant treatment. Full article

(This article belongs to the Special Issue Microorganisms in The Polluted Soil)

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11 pages, 2235 KiB

Open AccessArticle

Cupriavidus sp. HN-2, a Novel Quorum Quenching Bacterial Isolate, is a Potent Biocontrol Agent Against Xanthomonas campestris pv. campestris

by Tian Ye, Tian Zhou, Qiting Li, Xudan Xu, Xinghui Fan, Lianhui Zhang and Shaohua Chen

Microorganisms 2020, 8(1), 45; https://doi.org/10.3390/microorganisms8010045 - 25 Dec 2019

Cited by 26 | Viewed by 4613

Abstract

Diffusible signal factor (DSF) represents a family of widely conserved quorum sensing (QS) signals involved in the regulation of virulence factor production in many Gram-negative bacterial pathogens. Quorum quenching, which disrupts QS either by degradation of QS signals or interference of signal generation or perception, is a promising strategy for prevention and control of QS-mediated bacterial infections. In this study, a novel DSF-degrading strain, HN-2, was isolated from contaminated soil and identified as Cupriavidus sp. The isolate exhibited superior DSF degradation activity and completely degraded 2 mmol·L^–1 of DSF within 24 h. Analysis of the degradation products of DSF by gas chromatography–mass spectrometry led to the identification of trans-2-decenoic acid methyl ester as the main intermediate product, suggesting that DSF could be degraded by oxidation and hydroxylation. Moreover, this study presents for the first time, evidence that Cupriavidus sp. can reduce the black rot disease caused by Xanthomonas campestris pv. campestris (Xcc). Application of the HN-2 strain as a biocontrol agent could substantially reduce the disease severity. These findings reveal the biochemical basis of a highly efficient DSF-degrading bacterial isolate and present a useful agent for controlling infectious diseases caused by DSF-dependent bacterial pathogens. Full article

(This article belongs to the Special Issue Microorganisms in The Polluted Soil)

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