Role of Microbes in the Remediation of Harmful Pollutants in Contaminated Ecosystems

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

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 9986

Special Issue Editors


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Guest Editor
Stazione Zoologica Anton Dohrn Napoli (SZN), 80121 Naples, Italy
Interests: marine microbial diversity and ecology; microbial-mediated bioremediation of marine ecosystems

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Guest Editor
Stazione Zoologica Anton Dohrn Napoli (SZN), 80121 Naples, Italy
Interests: phycoremediation; lipid biosynthesis in microalgae; microbial ecology; phytoplankton

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Guest Editor
Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
Interests: marine microbial ecology; biogeochemical cycles; bioremediation

Special Issue Information

Dear Colleagues,

Multiple anthropogenic activities contribute to the contamination and degradation of ecosystems, threatening good environmental status and human health, and calling for urgent, effective, and sustainable remediation solutions.

The chemical contamination of the ecosystems represents a major concern, leading to detrimental consequences at different levels of biological organization. However, the effects on the diversity and ecological function of microbial assemblages are still largely unknown, which limits our understanding of the impact of different types of contaminants on overall ecosystem functioning.

In addition, deepening our knowledge on the diversity and metabolic pathways of microbes inhabiting contaminated sites can unveil novel taxa (either as single strains or consortia) with biotechnological potential for the bioremediation of harmful pollutants. Indeed, bioremediation approaches based on the stimulation of useful autochthonous microbes (biostimulation) or the addition of useful microbes (bioaugmentation) are gaining increasing attention for their eco-compatibility and lower costs. For effective bioremediation, ideal microbes should be abundant and metabolically active in the natural system, resistant to mixed contaminations, easy to grow, and responsive to selective stimulation. However, frequent failures are observed due to unsuccessful increases in the abundance or activity of target microbes, or due to the low fitness of lab-grown microbes once released into the contaminated environment. It is thus important to improve our knowledge on the diversity and dynamics of natural microbial assemblages for optimizing bioremediation performance, especially in sites that show the co-presence of multiple contaminants.

This Special Issue calls for papers covering the following topics:

  • Next-generation sequencing studies on the diversity and function of microbes (including bacteria, archaea, microbial eukaryotes, and their viruses) in contaminated sites;
  • Studies on the potential of contaminants to act as drivers of microbial assemblage diversity and/or functioning in ecosystems, and the possible use of microbes as pollution bioindicators/biosensors;
  • Experimental studies on the effects of contamination on microbes and on the use of microbes for the bioremediation of contaminated ecosystems;
  • Microbial/microbiome engineering to boost the bioremediation of contaminated sites;
  • Understanding the mechanisms of microbial-mediated bioremediation and synergic interactions between different microbes that can enhance bioremediation yields;
  • Emerging pollutants and possible microbial-mediated bioremediation approaches for their removal/detoxification;
  • Microbial products useful for the bioremediation of contaminated sites (biosurfactants, siderophores, enzymes, metallothioneins, phytochelatins, EPS, etc.)
  • Studies covering aspects related to this Special Issue, even if not included above.

Dr. Eugenio Rastelli
Dr. Sergio Balzano
Prof. Dr. Antonio Dell'Anno
Guest Editors

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Keywords

  • bioremediation
  • bacteria
  • archaea
  • fungi
  • microalgae
  • viruses
  • petroleum hydrocarbons
  • heavy metals
  • emerging pollutants
  • experimental biostimulation and bioaugmentation
  • bioindicators and biosensors
  • microbial and microbiome engineering
  • biosurfactants
  • siderophores
  • hydrocarbon-degrading enzymes
  • metallothioneins
  • phytochelatins
  • exopolysaccharides

Published Papers (6 papers)

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Research

21 pages, 3847 KiB  
Article
Microbial and Monosaccharide Composition of Biofilms Developing on Sandy Loams from an Aquifer Contaminated with Liquid Radioactive Waste
by Tamara L. Babich, Nadezhda M. Popova, Diyana S. Sokolova, Andrei V. Perepelov, Alexey V. Safonov and Tamara N. Nazina
Microorganisms 2024, 12(2), 275; https://doi.org/10.3390/microorganisms12020275 - 28 Jan 2024
Viewed by 1084
Abstract
The development of microbial biofilms increases the survival of microorganisms in the extreme conditions of ecosystems contaminated with components of liquid radioactive waste (LRW) and may contribute to the successful bioremediation of groundwater. The purpose of this work was to compare the composition [...] Read more.
The development of microbial biofilms increases the survival of microorganisms in the extreme conditions of ecosystems contaminated with components of liquid radioactive waste (LRW) and may contribute to the successful bioremediation of groundwater. The purpose of this work was to compare the composition of the microorganisms and the exopolysaccharide matrix of the biofilms formed on sandy loams collected at the aquifer from a clean zone and from a zone with nitrate and radionuclide contamination. The aquifer is polluted from the nearby surface repository for liquid radioactive waste (Russia). The phylogenetic diversity of prokaryotes forming biofilms on the sandy loams’ surface was determined during 100 days using high-throughput sequencing of the V4 region of the 16S rRNA genes. Scanning electron microscopy was used to study the development of microbial biofilms on the sandy loams. The ratio of proteins and carbohydrates in the biofilms changed in the course of their development, and the diversity of monosaccharides decreased, depending on the contamination of the sites from which the rocks were selected. The presence of pollution affects biofilm formation and EPS composition along with the dominant taxa of microorganisms and their activity. Biofilms establish a concentration gradient of the pollutant and allow the microorganisms involved to effectively participate in the reduction of nitrate and sulfate; they decrease the risk of nitrite accumulation during denitrification and suppress the migration of radionuclides. These biofilms can serve as an important barrier in underground water sources, preventing the spread of pollution. Pure cultures of microorganisms capable of forming a polysaccharide matrix and reducing nitrate, chromate, uranyl, and pertechnetate ions were isolated from the biofilms, which confirmed the possibility of their participation in the bioremediation of the aquifer from nonradioactive waste components and the decrease in the radionuclides’ migration. Full article
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17 pages, 3756 KiB  
Article
Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan
by Olga Muter, Dita Gudrā, Gulzhan Daumova, Zhanat Idrisheva, Marzhan Rakhymberdina, Guntis Tabors, Baiba Dirnēna, Linda Dobkeviča, Olga Petrova, Baitak Apshikur, Megija Luņģe, Dāvids Fridmanis, Igor Denissov, Yerkebulan Bekishev, Raimonds Kasparinskis, Zarina Mukulysova and Stanislav Polezhayev
Microorganisms 2024, 12(2), 246; https://doi.org/10.3390/microorganisms12020246 - 24 Jan 2024
Viewed by 1056
Abstract
Heavy metal (HMe) pollution in regions with mining and metallurgy activities is known to be a serious environmental problem worldwide. Hydrological processes contribute to the dissemination of HMes (drainage, precipitation, flow rate). The aim of the present study is to investigate the microbial [...] Read more.
Heavy metal (HMe) pollution in regions with mining and metallurgy activities is known to be a serious environmental problem worldwide. Hydrological processes contribute to the dissemination of HMes (drainage, precipitation, flow rate). The aim of the present study is to investigate the microbial community structure in ten river sediments sampled in different regions of East Kazakhstan, which are contaminated with HMes. The overall degree of sediment contamination with HMes (Cr, Cu, Zn, Pb, and Cd) was assessed using the pollution index Zc, which ranged from 0.43 to 21.6, with the highest in Ridder City (Zc = 21.6) and Ust-Kamenogorsk City, 0.8 km below the dam of the hydroelectric power station (Zc = 19.6). The tested samples considerably differed in organic matter, total carbon, nitrogen, and phosphorus content, as well as in the abundance of HMe-related functional gene families and antibiotic resistance genes. Metagenomic analysis of benthic microorganisms showed the prevalence of Proteobacteria (88.84–97.61%) and Actinobacteria (1.21–5.98%) at the phylum level in all samples. At the class level, Actinobacteria (21.68–57.48%), Betaproteobacteria (19.38–41.17%), and Alphaproteobacteria (10.0–39.78%) were the most common among the classified reads. To the best of our knowledge, this is the first study on the metagenomic characteristics of benthic microbial communities exposed to chronic HMe pressure in different regions of East Kazakhstan. Full article
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17 pages, 2056 KiB  
Article
Effect of Lyoprotective Agents on the Preservation of Survival of a Bacillus cereus Strain PBG in the Freeze-Drying Process
by Diana Galeska Farfan Pajuelo, Milena Carpio Mamani, Gisela July Maraza Choque, Dina Mayumi Chachaque Callo and César Julio Cáceda Quiroz
Microorganisms 2023, 11(11), 2705; https://doi.org/10.3390/microorganisms11112705 - 4 Nov 2023
Viewed by 1403
Abstract
Lyophilization is a widely employed long-term preservation method in which the bacterial survival rate largely depends on the cryoprotectant used. Bacillus cereus strain PBC was selected for its ability to thrive in environments contaminated with arsenic, lead, and cadmium, tolerate 500 ppm of [...] Read more.
Lyophilization is a widely employed long-term preservation method in which the bacterial survival rate largely depends on the cryoprotectant used. Bacillus cereus strain PBC was selected for its ability to thrive in environments contaminated with arsenic, lead, and cadmium, tolerate 500 ppm of free cyanide, and the presence of genes such as ars, cad, ppa, dap, among others, associated with the bioremediation of toxic compounds and enterotoxins (nheA, nheB, nheC). Following lyophilization, the survival rates for Mannitol 2.5%, Mannitol 10%, and Glucose 1% were 98.02%, 97.12%, and 96.30%, respectively, with the rates being lower than 95% for other sugars. However, during storage, for the same sugars, the survival rates were 78.71%, 97.12%, and 99.97%, respectively. In the cake morphology, it was found that the lyophilized morphology showed no relationship with bacterial survival rate. The best cryoprotectant for the PBC strain was 1% glucose since it maintained constant and elevated bacterial growth rates during storage, ensuring that the unique characteristics of the bacterium were preserved over time. These findings hold significant implications for research as they report a new Bacillus cereus strain with the potential to be utilized in bioremediation processes. Full article
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13 pages, 2084 KiB  
Article
The Remediation of Dysprosium-Containing Effluents Using Cyanobacteria Spirulina platensis and Yeast Saccharomyces cerevisiae
by Inga Zinicovscaia, Nikita Yushin, Dmitrii Grozdov, Alexandra Peshkova, Konstantin Vergel and Elena Rodlovskaya
Microorganisms 2023, 11(8), 2009; https://doi.org/10.3390/microorganisms11082009 - 4 Aug 2023
Cited by 1 | Viewed by 955
Abstract
Dysprosium is one of the most critical rare earth elements for industry and technology. A comparative study was carried out to assess the biosorption capacity of cyanobacteria Spirulina platensis and yeast Saccharomyces cerevisiae toward dysprosium ions. The effect of experimental parameters such as [...] Read more.
Dysprosium is one of the most critical rare earth elements for industry and technology. A comparative study was carried out to assess the biosorption capacity of cyanobacteria Spirulina platensis and yeast Saccharomyces cerevisiae toward dysprosium ions. The effect of experimental parameters such as pH, dysprosium concentration, time of contact, and temperature on the biosorption capacity was evaluated. Biomass before and after dysprosium biosorption was analyzed using neutron activation analysis and Fourier-transform infrared spectroscopy. For both biosorbents, the process was quick and pH-dependent. The maximum removal of dysprosium using Spirulina platensis (50%) and Saccharomyces cerevisiae (68%) was attained at pH 3.0 during a one-hour experiment. The adsorption data for both biosorbents fitted well with the Langmuir isotherm model, whereas the kinetics of the process followed the pseudo-second-order and Elovich models. The maximum biosorption capacity of Spirulina platensis was 3.24 mg/g, and that of Saccharomyces cerevisiae was 5.84 mg/g. The thermodynamic parameters showed that dysprosium biosorption was a spontaneous process, exothermic for Saccharomyces cerevisiae and endothermic for Spirulina platensis. Biological sorbents can be considered an eco-friendly alternative to traditional technologies applied for dysprosium ion recovery from wastewater. Full article
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26 pages, 7834 KiB  
Article
Fe/S Redox-Coupled Mercury Transformation Mediated by Acidithiobacillus ferrooxidans ATCC 23270 under Aerobic and/or Anaerobic Conditions
by Yue Liu, Chenyun Gu, Hongchang Liu, Yuhang Zhou, Zhenyuan Nie, Yirong Wang, Lu Chen and Jinlan Xia
Microorganisms 2023, 11(4), 1028; https://doi.org/10.3390/microorganisms11041028 - 14 Apr 2023
Cited by 1 | Viewed by 1333
Abstract
Bioleaching processes or microbially mediated iron/sulfur redox processes in acid mine drainage (AMD) result in mineral dissolution and transformation, the release of mercury and other heavy metal ions, and changes in the occurrence forms and concentration of mercury. However, pertinent studies on these [...] Read more.
Bioleaching processes or microbially mediated iron/sulfur redox processes in acid mine drainage (AMD) result in mineral dissolution and transformation, the release of mercury and other heavy metal ions, and changes in the occurrence forms and concentration of mercury. However, pertinent studies on these processes are scarce. Therefore, in this work, the Fe/S redox-coupled mercury transformation mediated by Acidithiobacillus ferrooxidans ATCC 23270 under aerobic and/or anaerobic conditions was studied by combining analyses of solution behavior (pH, redox potential, and Fe/S/Hg ion concentrations), the surface morphology and elemental composition of the solid substrate residue, the Fe/S/Hg speciation transformation, and bacterial transcriptomics. It was found that: (1) the presence of Hg2+ significantly inhibited the apparent iron/sulfur redox process; (2) the addition of Hg2+ caused a significant change in the composition of bacterial surface compounds and elements such as C, N, S, and Fe; (3) Hg mainly occurred in the form of Hg0, HgS, and HgSO4 in the solid substrate residues; and (4) the expression of mercury-resistant genes was higher in earlier stages of growth than in the later stages of growth. The results indicate that the addition of Hg2+ significantly affected the iron/sulfur redox process mediated by A. ferrooxidans ATCC 23270 under aerobic, anaerobic, and coupled aerobic–anaerobic conditions, which further promoted Hg transformation. This work is of great significance for the treatment and remediation of mercury pollution in heavy metal-polluted areas. Full article
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14 pages, 1822 KiB  
Article
Characterization of Five Psychrotolerant Alcanivorax spp. Strains Isolated from Antarctica
by Simone Cappello, Ilaria Corsi, Sabrina Patania, Elisa Bergami, Maurizio Azzaro, Monique Mancuso, Maria Genovese, Alessia Lunetta and Gabriella Caruso
Microorganisms 2023, 11(1), 58; https://doi.org/10.3390/microorganisms11010058 - 24 Dec 2022
Cited by 2 | Viewed by 2975
Abstract
Five psychrotolerant Alcanivorax spp. strains were isolated from Antarctic coastal waters. Strains were screened for molecular and physiological properties and analyzed regarding their growth capacity. Partial 16S rDNA, alk-B1, and P450 gene sequencing was performed. Biolog EcoPlates and the API 20E [...] Read more.
Five psychrotolerant Alcanivorax spp. strains were isolated from Antarctic coastal waters. Strains were screened for molecular and physiological properties and analyzed regarding their growth capacity. Partial 16S rDNA, alk-B1, and P450 gene sequencing was performed. Biolog EcoPlates and the API 20E test were used to evaluate metabolic and biochemical profiles. Bacterial growth in sodium acetate was determined at 4, 15, 20, and 25 °C to evaluate the optimal temperature. Furthermore, the ability of each strain to grow in a hydrocarbon mixture at 4 and 25 °C was assayed. Biosurfactant production tests (drop-collapse and oil spreading) and emulsification activity tests (E24) were also performed. Concerning results of partial gene sequencing (16S rDNA, alk-B1, and P450), a high similarity of the isolates with the same genes isolated from other Alcanivorax spp. strains was observed. The metabolic profiles obtained by Biolog assays showed no significant differences in the isolates compared to the Alcanivorax borkumensis wild type. The results of biodegradative tests showed their capability to grow at different temperatures. All strains showed biosurfactant production and emulsification activity. Our findings underline the importance to proceed in the isolation and characterization of Antarctic hydrocarbon-degrading bacterial strains since their biotechnological and environmental applications could be useful even for pollution remediation in polar areas. Full article
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