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Role of Microorganisms in Remediating Contaminated Soils

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A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Environmental and Green Processes".

Deadline for manuscript submissions: closed (23 December 2022) | Viewed by 24555

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Special Issue Editors

Prof. Dr. Flavia De Nicola

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Guest Editor

Department of Sciences and Technologies, University of Sannio, Via F. De Sanctis SNC, 82100 Benevento, Italy
Interests: biomonitoring; ecotoxicology; bioaccumulation; environment; soil; polycyclic aromatic hydrocarbons; environmental impact assessment; heavy metals; lichens; environmental science; soil science; mass spectrometry; quantitation

Dr. Enrica Picariello

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Assistant Guest Editor

Department of Sciences and Technologies, University of Sannio, Via F. De Sanctis SNC, 82100 Benevento, Italy
Interests: terrestrial ecology; soil science; microbial ecology

Special Issue Information

Dear Colleagues,

Significant components of terrestrial ecosystems are being degraded as a result of human activities, including agricultural intensification, infrastructure expansion, soil and water pollution, and climate change. The contamination of soils with potentially toxic elements and organic compounds poses a risk to both environmental and human health.

Traditional remediation technologies heavily depend on chemical reagents and energy consumption, with huge social, economic, and environmental costs. Nature-based solutions offer great potential for application in the field of contaminated soil remediation.

Bioremediation utilizes microbial activity to remove contaminants in soil by delivering microrganisms capable of degrading contaminants, or by stimulating the native capability of microorganisms to degrade/transform contaminants, providing substrates or ameliorating the edaphic environment. The use of indigenous and exogeneous microorganisms in bioremediation processes can reduce the risks associated with contaminated soils. Since microbial degradation is one of the main processes by which contaminants are removed from soil, an understanding of the mechanisms involved is pivotal to enhance our knowledge of bioremediation, an advantageous, non-invasive, and cost-effective reclamation tool.

This Special Issue aims to create a discussion forum for scientists, policymakers (regulatory bodies, governmental agencies), and city managers regarding biological solutions in soil reclamation. It will provide an opportunity to share new studies and advancements in the bioremediation of contaminated soils (agricultural, industrial, urban) by different classes of pollutants. Relevant articles examining the role of microrganisms in processes that can lead to the remediation of degraded soil are welcome. Submissions on the monitoring and assessment of the efficiency of bioremediation in terms of target contaminants and soil toxixity, as well as the identification and selection of microorganisms useful in the restoration of contaminated soils, are also invited.

Prof. Dr. Flavia De Nicola
Dr. Enrica Picariello
Guest Editors

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Keywords

soil pollution
soil quality
bioremediation
biostimulation
bioaugmentation
natural attenuation
fungi
bacteria
enzymatic activities

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Published Papers (8 papers)

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Research

22 pages, 6835 KiB

Open AccessFeature PaperArticle

Treatment of Motor Oil-Contaminated Soil with Green Surfactant Using a Mobile Remediation System

by Israel Gonçalves Sales da Silva, Juliano Rodrigues Pappalardo, Nathália Maria Padilha da Rocha e Silva, Attilio Converti, Fabíola Carolina Gomes de Almeida and Leonie Asfora Sarubbo

Processes 2023, 11(4), 1081; https://doi.org/10.3390/pr11041081 - 3 Apr 2023

Cited by 2 | Viewed by 2410

Abstract

Leak of fuels and lubricants occurring during exploration, distribution, refining and storage operations is the major cause of environmental pollution due to petroderivatives dispersion. The quick use of a series of physicochemical and biological techniques is needed to drastically reduce the magnitude of damage provoked by these pollutants. Among them, soil washing proved to be an effective alternative to the remediation of hydrocarbon-polluted sites, mainly if combined with surfactant utilization. However, the direct use of surfactants can lead to problems related to the toxicity and dispersion of the resulting by-products, as the majority of marketed surfactants are produced from oil derivatives. In this context, green surfactants appear as a promising alternative to their synthetic counterpart. In the present study, two green surfactants, i.e., a chemically synthesized biobased surfactant and a Starmerella bombicola biosurfactant, were applied in soil decontamination tests using a concrete mixer-type Mobile Soil Remediation System (MSRS). The system was designed and developed with 3D printing based on bench-scale results. A commercial biosurfactant was formulated based on the microbial surfactant, which was compared with the biobased surfactant in various experimental conditions. A set of factorial designs combined with Response Surface Methodology was used to select the optimal conditions for pollutant removal using the prototype. The following variables were tested: Surfactant type, Surfactant volume, Surfactant dilution, Contaminant concentration, Soil type, Soil mass, Washing duration, Tank tilt angle, Mixing speed, and Type of basket. Under the optimized experimental condition, the commercial biosurfactant allowed to remove 92.4% of the motor oil adsorbed in the sand. These results demonstrate the possibility of using natural surfactants and the development of novel mechanical technologies to degrade hydrocarbons with economic earnings for oil industry. Full article

(This article belongs to the Special Issue Role of Microorganisms in Remediating Contaminated Soils)

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10 pages, 1144 KiB

Open AccessFeature PaperArticle

How Soil Microbial Communities from Industrial and Natural Ecosystems Respond to Contamination by Polycyclic Aromatic Hydrocarbons

by Enrica Picariello, Daniela Baldantoni and Flavia De Nicola

Processes 2023, 11(1), 130; https://doi.org/10.3390/pr11010130 - 1 Jan 2023

Cited by 2 | Viewed by 1771

Abstract

Soil microbial community plays a major role in removal of polycyclic aromatic hydrocarbons (PAHs) from soil, and bioremediation potentially offers an attractive and economic approach to the clean-up of polluted areas. To evaluate the contribution of different microbial groups in soil PAH degradation, enzymatic activity and phospholipid fatty acids (PLFAs) were analysed in a mesocosm trial in three different soils (two natural and one industrial) artificially contaminated with 3- and 5-rings PAHs. The Metabolic Activity Index (MAI) was applied to investigate the microbial community stability, in terms of resistance and resilience. Gram+ and Gram- bacteria were the predominant microbial groups in all soil types. In the first stage of incubation, fungi were predominant in the industrial soil, followed by mycorrhizae and actinomycetes, indicating their stimulation after PAH addition. In the two natural soils, several groups were predominant: actinomycetes in one, fungi and mycorrhizae in the other, indicating a different response of the two natural soils to PAH contamination. Regarding MAI calculated on the enzymatic activities, one natural soil showed a microbial community neither resistant nor resilient in respect to the other and to the industrial soil. Our results highlight that the microbial community changes its composition and then physiological functions according to the land use as a result of PAH addition. Full article

(This article belongs to the Special Issue Role of Microorganisms in Remediating Contaminated Soils)

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12 pages, 12399 KiB

Open AccessArticle

Studying Soil Ecology and Growth Conditions of Phellorinia herculeana, a Wild Edible Mushroom

by Rajendiran Oviya, Gunasekaran Sobanbabu, Palaniappan Anbazhagan, Natarajan Revathy, Palani Mahalakshmi, Karunakaran Manonmani, Petchimuthu Mareeswari, Ayyathurai Vijayasamundeeswari, Vellasamy Shanmugaiah, Sayaji Mehetre and Vellaisamy Ramamoorthy

Processes 2022, 10(9), 1797; https://doi.org/10.3390/pr10091797 - 7 Sep 2022

Cited by 2 | Viewed by 2559

Abstract

Phellorinia herculeana is an edible mushroom growing in nutritionally poor and desert soil. There has been little information available about its edaphic and culturing conditions for achieving the vigorous mycelial growth essential for its artificial cultivation, bioaugmentation and biodegradation in unfertile soil. Thus, the present study was conducted to assess its edaphic conditions and find a suitable culturing medium for obtaining maximum growth. It grows commonly in coastal soil with saline conditions, barren land soil unfit for cultivation, and desert soil. It forms a basidiocarp singly around xerophytic trees and annual plants and also in soil without vegetation. In addition to a well-developed pileus and stipe, it has a typical rhizoid that grows horizontally in soil. The rhizoid was thick at the base of the stipe and became thin into the mycelial strand. In our earlier study, we reported that its mycelial growth was very poor on nutrient-rich media containing simple sugar, for example, glucose. In the present study, we observed that cereal-grain-based agar media supported its mycelial growth and among the cereal-grain-based agar media, maize agar medium at the 5% level supported the maximum mycelial growth. Incorporation of glucose into the maize agar medium reduced its mycelial growth compared to its growth on maize agar medium without glucose. Its mycelial growth was at a maximum between 34 °C and 37 °C and at a pH between 7 and 8. Mass multiplication using sand-maize medium prepared at the ratio of 19:1 (sand: maize) supported the maximum mycelial growth. The results of this study would certainly pave a way for the scientific community to develop a protocol for its artificial cultivation and also for its mass multiplication, bioaugmentation and biodegradation in unfertile soil. Full article

(This article belongs to the Special Issue Role of Microorganisms in Remediating Contaminated Soils)

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19 pages, 1710 KiB

Open AccessArticle

Cadmium-Tolerant Bacteria in Cacao Farms from Antioquia, Colombia: Isolation, Characterization and Potential Use to Mitigate Cadmium Contamination

by Ruth Quiroga-Mateus, Santiago López-Zuleta, Eduardo Chávez and Daniel Bravo

Processes 2022, 10(8), 1457; https://doi.org/10.3390/pr10081457 - 26 Jul 2022

Cited by 5 | Viewed by 2566

Abstract

Bioremediation of farm soil is a technique that merits in-depth research. There are few studies related to the use of bioremediation to reduce cadmium (Cd) availability in soils used for cacao production. This study investigates (1) field bioprospection and strain characterization using techniques including isothermal microcalorimetry to select a group of cadmium-tolerant bacteria (CdtB) for potential use as bioremediators of cacao soils and (2) the application of bacterial inoculum to compare the immobilization of Cd under field conditions. Bioprospection was carried out in four cacao farms from the Antioquia district in Colombia. Culturable CdtB strains were isolated using CdCl₂ as a Cd source and identified using molecular techniques. The metabolic characterization of Cd immobilization was carried out using isothermal microcalorimetry with CdCl₂ amendments. Five cadmium-tolerant bacteria were isolated and characterized as Bacillus spp. The strain CdtB14 showed better growth and Cd immobilization ability (estimated through heat ratios) than any strain isolated thus far, suggesting potential for future use in bioproduct development. Furthermore, the application of two previously characterized CdtB strains with zeolite powder was performed in the same farms where the bioprospection process was carried out. The application of the preformulated inoculum resulted in a decrease of 0.30 + 0.1 mg kg⁻¹ of soil Cd in two out of the four assessed farms. The field results are preliminary and require data on the change in Cd in cacao beans to understand what this result means for Cd mitigation. This study is the first to combine bioprospecting and the performance of CdtB in laboratory and field experiments in cacao farms and shows the potential of bioremediation to mitigate Cd contamination in cacao. Full article

(This article belongs to the Special Issue Role of Microorganisms in Remediating Contaminated Soils)

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12 pages, 1511 KiB

Open AccessArticle

Optimization of Biofertilizer Formulation for Phosphorus Solubilizing by Pseudomonas fluorescens Ur21 via Response Surface Methodology

by Mohsen Barin, Farrokh Asadzadeh, Masoumeh Hosseini, Edith C. Hammer, Ramesh Raju Vetukuri and Roghayeh Vahedi

Processes 2022, 10(4), 650; https://doi.org/10.3390/pr10040650 - 27 Mar 2022

Cited by 10 | Viewed by 3415

Abstract

This study aimed to analyze and quantify the effect of different ratios of vermicompost, phosphate rock, and sulfur on P solubilization and release by Pseudomonas fluorescens Ur21, and to identify optimal levels of those variables for an efficient biofertilizer. Twenty experiments were defined by surface response methodology based on a central composite design (CCD), and the effects of various quantities of vermicompost, phosphate rock, and sulfur (encoded by −1, 0, or +1) on P solubilization was explored. The results show that the CCD model had high efficiency for predicting P solubilization (R² = 0.9035). The strongest effects of the included variables on the observed P solubilization were linear effects of sulfur and organic matter (vermicompost), a quadratic effect of phosphate rock, and an interactive effect of organic matter × phosphate rock. Statistical analysis of the coefficients in the CCD model revealed that vermicompost, vermicompost × phosphate rock, and phosphate rock × phosphate rock treatments increased P solubilization. The optimal predicted composition for maximal P solubilization by P. fluorescens Ur21 (at 1684.39 mg·kg⁻¹, with more than 90% of the added phosphate dissolved) was 58.8% vermicompost, 35.3% phosphate rock, and 5.8% sulfur. ANOVA analysis confirmed the model’s accuracy and validity in terms of F value (10.41), p value (<0.001), and non-significant lack of fit. Full article

(This article belongs to the Special Issue Role of Microorganisms in Remediating Contaminated Soils)

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14 pages, 1004 KiB

Open AccessArticle

Effect of Biochar and Microbial Inoculation on P, Fe, and Zn Bioavailability in a Calcareous Soil

by Roghayeh Vahedi, Mir Hassan Rasouli-Sadaghiani, Mohsen Barin and Ramesh Raju Vetukuri

Processes 2022, 10(2), 343; https://doi.org/10.3390/pr10020343 - 11 Feb 2022

Cited by 19 | Viewed by 2798

Abstract

To identify effective ways of increasing the yield of crops grown in nutrient-poor calcareous soils, the combined effects of biochar addition and inoculation with plant growth promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) on wheat growth and soil properties were investigated under rhizobox conditions. Measured soil properties included pH, electrical conductivity (EC), organic matter content (OM), the availability of P, Fe, and Zn in the rhizosphere, and the uptake of these elements by plants. Combined biochar addition and microbial inoculation were shown to significantly increase the concentration of available forms of P, Fe, and Zn in the soil when compared to non-biochar treatments. The highest soil pH (7.82) was observed following biochar addition without microbial inoculation. The EC following biochar addition and PGPR inoculation was significantly higher than the other treatments, and the soil OM content was highest when combining AMF inoculation with biochar addition. The available P content after AMF inoculation combined with biochar addition was 27.81% higher than the control conditions, and AMF inoculation increased Fe and Zn bioavailability by factors of 2.38 and 1.29, respectively, when combined with biochar addition relative to AMF inoculation alone. The simultaneous biochar addition and PGPR inoculation significantly increased P uptake by the plants. The highest shoot Fe and Zn uptake rates were observed after a simultaneous application of biochar and PGPR inoculation. Under these conditions, shoot uptake was higher than seen when combining biochar addition with AMF inoculation by factors of 1.64 and 1.21, respectively. In general, it can be concluded that combining inoculation with growth-promoting bacteria and biochar addition can effectively improve nutrient availability to plant and soil conditions. Full article

(This article belongs to the Special Issue Role of Microorganisms in Remediating Contaminated Soils)

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15 pages, 1125 KiB

Open AccessFeature PaperArticle

Harnessing the Potential of Symbiotic Endophytic Fungi and Plant Growth-Promoting Rhizobacteria to Enhance Soil Quality in Saline Soils

by Zahra Rouydel, Mohsen Barin, Mir Hassan Rasouli-Sadaghiani, Maryam Khezri, Ramesh Raju Vetukuri and Sandeep Kushwaha

Processes 2021, 9(10), 1810; https://doi.org/10.3390/pr9101810 - 12 Oct 2021

Cited by 5 | Viewed by 2469

Abstract

Soil salinity is one of the most important abiotic stresses limiting crop growth and production worldwide. Some microorganisms can improve the plants’ tolerance to salinity. For this purpose, a greenhouse experiment was performed to understand the influence of various microorganisms on soil biological indices and wheat growth under different saline conditions. The factors varied in the experiment were the microbial treatment (rhizobacteria, mycorrhizal fungi, endophytic fungus, and control) and salinity stress (0.5, 8, and 14 dS m⁻¹). Rhizobacteria were isolated from saline soils, but the fungi were prepared from a microbial bank. Overall, ten isolates were purified, and three with promising growth-promoting properties were identified using phenotypic and molecular methods. The selected isolates belonged to the genera Pseudomonas (P. aeruginosa Ur83 and P. fluorescens Ur67) and Stenotrophomonas (S. maltophilia Ur52). Soil quality indices were found to decrease with increasing salinity, but inoculation with microorganisms alleviated this decline. Inoculation with plant growth-promoting rhizobacteria (PGPRs) increased basal respiration, substrate-induced respiration, microbial biomass carbon, acid and alkaline phosphatase activities, and carbon availability by factors of 1.37, 1.27, 1.83, 3.07, 1.29, and 1.11, respectively. These results show that inoculation with symbiotic microorganisms can improve agricultural soil quality under saline conditions and may thus be valuable in agriculture. Full article

(This article belongs to the Special Issue Role of Microorganisms in Remediating Contaminated Soils)

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22 pages, 11109 KiB

Open AccessFeature PaperArticle

Application of Green Surfactants in the Remediation of Soils Contaminated by Hydrocarbons

by Israel Gonçalves Sales da Silva, Fabíola Carolina Gomes de Almeida, Nathália Maria Padilha da Rocha e Silva, Joaquim Teodoro Romão de Oliveira, Attilio Converti and Leonie Asfora Sarubbo

Processes 2021, 9(9), 1666; https://doi.org/10.3390/pr9091666 - 15 Sep 2021

Cited by 16 | Viewed by 4785

Abstract

Among the innovative technologies utilized for the treatment of contaminated soils, the use of green surfactants appears to be a biocompatible, efficient, and attractive alternative, since the cleaning processes that normally use synthetic surfactants as additives cause other problems due to toxicity and the accumulation of by-products. Three green surfactants, i.e., two biobased (biobased 1 and biobased 2) surfactants produced by chemical synthesis and a microbial surfactant produced from the yeast Starmerella bombicola ATCC 22214, were used as soil remediation agents and compared to a synthetic surfactant (Tween 80). The three surfactants were tested for their ability to emulsify, disperse, and remove different hydrophobic contaminants. The biosurfactant, which was able to reduce the water surface tension to 32.30 mN/m at a critical micelle concentration of 0.65 g/L, was then used to prepare a commercial formulation that showed lower toxicity to the tested environmental bioindicators and lower dispersion capacity than the biobased surfactants. All the green surfactants showed great emulsification capacity, especially against motor oil and petroleum. Therefore, their potential to remove motor oil adsorbed on different types of soils (sandy, silty, and clay soil and beach sand) was investigated either in kinetic (flasks) or static (packed columns) experiments. The commercial biosurfactant formulation showed excellent effectiveness in removing motor oil, especially from contaminated sandy soil (80.0 ± 0.46%) and beach sand (65.0 ± 0.14%) under static conditions, while, in the kinetic experiments, the commercial biosurfactant and the biobased 2 surfactant were able to remove motor oil from all the contaminated soils tested more effectively than the biobased 1 surfactant. Finally, the S. bombicola commercial biosurfactant was evaluated as a soil bioremediation agent. In degradation experiments carried out on motor oil-contaminated soils enriched with sugarcane molasses, oil degradation yield in the sandy soil reached almost 90% after 60 days in the presence of the commercial biosurfactant, while it did not exceed 20% in the presence of only S. bombicola cells. These results promise to contribute to the development of green technologies for the treatment of hydrophobic pollutants with economic gains for the oil industries. Full article

(This article belongs to the Special Issue Role of Microorganisms in Remediating Contaminated Soils)

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