Role of Microbes in the Remediation of Pollutants in the Environment

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

Deadline for manuscript submissions: 15 June 2025 | Viewed by 11854

Special Issue Editors


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Guest Editor
College of Environment and Ecology, Chongqing University, Chongqing 100875, China
Interests: environmental microbiology

E-Mail Website
Guest Editor
School of Biology, Food, and Environment, Hefei University, Hefei 230601, China
Interests: environmental pollution control and remediation technology

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 limit 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 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 other aspects related to this Special Issue, even if not included in the list above.

Dr. Lilan Zhang
Dr. Xiaowei Liu
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
  • hydrocarbon-degrading enzymes

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Published Papers (7 papers)

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Research

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17 pages, 2340 KiB  
Article
Characterizing the Contaminant-Adhesion of a Dibenzofuran Degrader Rhodococcus sp.
by Yu Chen, Qingquan Wei, Xudi Wang, Yanan Wu, Changai Fu, Xu Wang, Hangzhou Xu and Li Li
Microorganisms 2025, 13(1), 93; https://doi.org/10.3390/microorganisms13010093 - 6 Jan 2025
Viewed by 798
Abstract
The adhesion between dibenzofuran (DF) and degrading bacteria is the first step of DF biodegradation and affects the efficient degradation of DF. However, their efficient adhesion mechanism at the molecular level remains unclear. Therefore, this study first examined the adhesive behaviors and molecular [...] Read more.
The adhesion between dibenzofuran (DF) and degrading bacteria is the first step of DF biodegradation and affects the efficient degradation of DF. However, their efficient adhesion mechanism at the molecular level remains unclear. Therefore, this study first examined the adhesive behaviors and molecular mechanisms of Rhodococcus sp. strain p52 upon exposure to DF. The results showed that the adhesion between strain p52 and DF is mediated by extracellular polymeric substances (EPSs). Compared with sodium acetate as a carbon source, the percentages of glucose and proteins related to electron transfer, toxin–antitoxin, and stress responses were elevated, which were analyzed by polysaccharide composition and proteomics, and the contents of extracellular polysaccharides and proteins were increased. Moreover, biofilm analysis suggested an increase in EPS content, and the change in components increased biofilm yield and promoted loose and porous aggregation between the bacteria; this aggregation caused an increase in the specific surface area in contact with DF. The surface characteristics analysis indicated that the production of EPS reduced the absolute value of the zeta potential and increased the hydrophobicity of strain p52, which was beneficial for the adhesion of strain p52 and DF. These findings help us to enhance the understanding of the adhesion mechanisms and bioremediation of polycyclic aromatic hydrocarbons by degrading bacteria. Full article
(This article belongs to the Special Issue Role of Microbes in the Remediation of Pollutants in the Environment)
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21 pages, 6428 KiB  
Article
UV-C Exposure Enhanced the Cd2+ Adsorption Capability of the Radiation-Resistant Strain Sphingomonas sp. M1-B02
by Yunshi Li, Haoyuan Niu, Shuang Li, Ming Yue and Gaosen Zhang
Microorganisms 2024, 12(12), 2620; https://doi.org/10.3390/microorganisms12122620 - 18 Dec 2024
Viewed by 1117
Abstract
Microbial adsorption is a cost-effective and environmentally friendly remediation method for heavy metal pollution. The adsorption mechanism of cadmium (Cd) by bacteria inhabiting extreme environments is largely unexplored. This study describes the biosorption of Cd2+ by Sphingomonas sp. M1-B02, which was isolated [...] Read more.
Microbial adsorption is a cost-effective and environmentally friendly remediation method for heavy metal pollution. The adsorption mechanism of cadmium (Cd) by bacteria inhabiting extreme environments is largely unexplored. This study describes the biosorption of Cd2+ by Sphingomonas sp. M1-B02, which was isolated from the moraine on the north slope of Mount Everest and has a good potential for biosorption. The difference in Cd2+ adsorption of the strain after UV irradiation stimulation indicated that the adsorption reached 68.90% in 24 h, but the adsorption after UV irradiation increased to 80.56%. The genome of strain M1-B02 contained antioxidant genes such as mutL, recA, recO, and heavy metal repair genes such as RS14805, apaG, chrA. Hydroxyl, nitro, and etceteras bonds on the bacterial surface were involved in Cd2+ adsorption through complexation reactions. The metabolites of the strains were significantly different after 24 h of Cd2+ stress, with pyocyanin, L-proline, hypoxanthine, etc., being downregulated and presumably involved in Cd2+ biosorption and upregulated after UV-C irradiation, which may explain the increase in Cd2+ adsorption capacity of the strain after UV-C irradiation, while the strain improved the metabolism of the antioxidant metabolite carnosine, indirectly increasing the adsorption capacity of the strains for Cd2+. Full article
(This article belongs to the Special Issue Role of Microbes in the Remediation of Pollutants in the Environment)
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17 pages, 10197 KiB  
Article
Factors and Mechanisms Affecting Arsenic Migration in Cultivated Soils Irrigated with Contained Arsenic Brackish Groundwater
by Wenjing Dai, Rongguang Shi, Xiaodong Li, Zhiqi Zhao, Zihan Xia, Dongli Li, Yan Li, Gaoyang Cui and Shiyuan Ding
Microorganisms 2024, 12(12), 2385; https://doi.org/10.3390/microorganisms12122385 - 21 Nov 2024
Cited by 1 | Viewed by 1120
Abstract
Contained arsenic (As) and unsafe brackish groundwater irrigation can lead to serious As pollution and increase the ecological risk in cultivated soils. However, little is known about how Fe oxides and microbes affect As migration during soil irrigation processes involving arsenic-contaminated brackish groundwater. [...] Read more.
Contained arsenic (As) and unsafe brackish groundwater irrigation can lead to serious As pollution and increase the ecological risk in cultivated soils. However, little is known about how Fe oxides and microbes affect As migration during soil irrigation processes involving arsenic-contaminated brackish groundwater. In this study, the samples (porewater and soil) were collected through the dynamic soil column experiments to explore the As migration process and its effect factors during soil irrigation. The results showed that the As concentration in porewater samples from the topsoil was enriched compared to that in the subsoil, and the main solid As fractions were strongly adsorbed or bound to amorphous and crystalline Fe oxides. The aqueous As concentration and the solid As fractions indicated that reductive dissolution and desorption from amorphous Fe oxides were the primary mechanisms of As release at the topsoil and subsoil, respectively. Meanwhile, Sphingomonas_sp., Microvirga_ossetica and Acidobacteriota_bacterium were the dominant microbes affecting As biotransformation by arsenate reductase gene (arsC) expression. Accompanied by the Eh and competitive ions concentration change, amorphous Fe oxide dissolution increased to facilitate the As release, and the changes in the microbial community structure related to As reduction may have enhanced As mobilization in soils irrigated by As-containing brackish groundwater. Full article
(This article belongs to the Special Issue Role of Microbes in the Remediation of Pollutants in the Environment)
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17 pages, 3705 KiB  
Article
The Marine-Origin Exopolysaccharide-Producing Bacteria Micrococcus Antarcticus HZ Inhibits Pb Uptake in Pakchoi (Brassica chinensis L.) and Affects Rhizosphere Microbial Communities
by Nan Liu, Gangrui Zhang, Longyu Fang, Rui Geng, Shengbo Shi, Jinghua Li, Wei Wang, Mingchun Lin, Junfeng Chen, Yanru Si, Zeyun Zhou, Baoli Shan, Maoyu Men, Qisheng Fan, Chengze Wang, Chaoqun Zhang and Lujiang Hao
Microorganisms 2024, 12(10), 2002; https://doi.org/10.3390/microorganisms12102002 - 1 Oct 2024
Viewed by 1202
Abstract
Exopolysaccharides (EPSs) produced by microorganisms play an important role in biotolerance and reducing heavy metal (HM) contamination by limiting the migration of HMs into plants. However, research on the application of EPS-producing marine bacteria for soil heavy metal remediation remains limited, particularly regarding [...] Read more.
Exopolysaccharides (EPSs) produced by microorganisms play an important role in biotolerance and reducing heavy metal (HM) contamination by limiting the migration of HMs into plants. However, research on the application of EPS-producing marine bacteria for soil heavy metal remediation remains limited, particularly regarding their mechanisms of HM immobilization in soil and impact on plant growth. In this study, the EPS-producing marine bacterium Micrococcus antarcticus HZ was investigated for its ability to immobilize Pb and produce EPSs in soil filtrate. The effects on the growth quality and biomass of pakchoi (Brassica chinensis L.), as well as bacterial communities in inter-root soil contaminated with Pb, were also investigated. The results indicated that HZ could reduce the Pb concentration in the soil filtrate, achieving a removal rate of 43.25–63.5%. The EPS content and pH levels increased in the presence of Pb. Pot experiments showed that adding HZ significantly increased the biomass of pakchoi (9.45–14.69%), vitamin C (Vc) (9.69–12.92%), and soluble protein content (22.58–49.7%). HZ reduced the Pb content in the roots (17.52–47.48%) and leaves (edible tissues) (43.82–52.83%) of pakchoi. HZ increased soil enzyme activities (alkaline phosphatase, dehydrogenase, and urease), and the contents of ammonium nitrogen and nitrate nitrogen. Additionally, HZ also increased the relative abundance of beneficial bacteria (e.g., Proteobacteria, Cyanobacteria, and Chlorobacteria) in the inter-root soil, which have prophylactic and heavy-metal fixation functions. In summary, HZ reduces effective Pb content in edible tissues, roots, and inter-root soil by regulating inter-root soil microbial community structure, increasing soil pH, nitrogen content, and soil enzyme activity, and altering dominant phylum abundance. Full article
(This article belongs to the Special Issue Role of Microbes in the Remediation of Pollutants in the Environment)
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15 pages, 3844 KiB  
Article
Distribution and Characterization of Quaternary Ammonium Biocides Resistant Bacteria in Different Soils, in South-Western China
by Ziyi Guo, Cunli Qin and Lilan Zhang
Microorganisms 2024, 12(8), 1742; https://doi.org/10.3390/microorganisms12081742 - 22 Aug 2024
Cited by 5 | Viewed by 1722
Abstract
Quaternary ammonium compounds (QACs) are active ingredients in hundreds of disinfectants for controlling the epidemic of infectious diseases like SARS-CoV-2 (COVID-19), and are also widely used in shale gas exploitation. The occurrence of QAC-resistant bacteria in the environment could enlarge the risk of [...] Read more.
Quaternary ammonium compounds (QACs) are active ingredients in hundreds of disinfectants for controlling the epidemic of infectious diseases like SARS-CoV-2 (COVID-19), and are also widely used in shale gas exploitation. The occurrence of QAC-resistant bacteria in the environment could enlarge the risk of sterilization failure, which is not fully understood. In this study, QAC-resistant bacteria were enumerated and characterized in 25 soils collected from shale gas exploitation areas. Total counts of QAC-resistant bacteria ranged from 6.81 × 103 to 4.48 × 105 cfu/g, accounting for 1.59% to 29.13% of the total bacteria. In total, 29 strains were further purified and identified as Lysinibacillus, Bacillus, and Klebsiella genus. There, bacteria covering many pathogenic bacteria showed different QACs tolerance with MIC (minimum inhibition concentration) varying from 4 mg/L to 64 mg/L and almost 58.6% of isolates have not previously been found to tolerate QACs. Meanwhile, the QAC-resistant strains in the produced water of shale gas were also identified. Phylogenetic trees showed that the resistant species in soil and produced water are distinctly different. That is the first time the distribution and characterization of QAC-resistant bacteria in the soil environment has been analyzed. Full article
(This article belongs to the Special Issue Role of Microbes in the Remediation of Pollutants in the Environment)
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Review

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17 pages, 676 KiB  
Review
The Strategies Microalgae Adopt to Counteract the Toxic Effect of Heavy Metals
by Xin-Yue Yang, Yu-Xin Wei, Yan-Qiu Su, Zhong-Wei Zhang, Xiao-Yan Tang, Yang-Er Chen, Ming Yuan and Shu Yuan
Microorganisms 2025, 13(5), 989; https://doi.org/10.3390/microorganisms13050989 - 25 Apr 2025
Viewed by 193
Abstract
Besides biomass production, some microalgae have been used to treat wastewater contamination. However, in general, high concentrations of heavy metals significantly inhibit algal growth. We thus need to find ways to promote the resistance of microalgae to heavy metals, increase their growth rate [...] Read more.
Besides biomass production, some microalgae have been used to treat wastewater contamination. However, in general, high concentrations of heavy metals significantly inhibit algal growth. We thus need to find ways to promote the resistance of microalgae to heavy metals, increase their growth rate under stress, and achieve coupling of heavy metal removal and biomass production simultaneously. In this review, mechanisms for removal of heavy metals by microalgae are proposed. Effects of exogenous chemical additives (dissolved organic matters, formaldehyde, sulphate, phosphate, nitric oxide donors, etc.) on algal biosorption to heavy metals are summarized. Genetic manipulation and microalgal strain selection strategies are also introduced, especially for the acid-tolerant strains with high biosorption efficiencies to Cr(VI) and Cd2+ at low pH conditions. Recent advances in (semi)continuous heavy-metal-bioremediation and biomass-production coupled system with immobilized microalgae, as well as challenges and solutions to the commercialization and industrialization of the coupled system were discussed. Full article
(This article belongs to the Special Issue Role of Microbes in the Remediation of Pollutants in the Environment)
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25 pages, 1066 KiB  
Review
Bioremediation of Polycyclic Aromatic Hydrocarbons by Means of Bacteria and Bacterial Enzymes
by Anastasiia T. Davletgildeeva and Nikita A. Kuznetsov
Microorganisms 2024, 12(9), 1814; https://doi.org/10.3390/microorganisms12091814 - 2 Sep 2024
Cited by 8 | Viewed by 3560
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread, persistent, and toxic environmental pollutants. Many anthropogenic and some natural factors contribute to the spread and accumulation of PAHs in aquatic and soil systems. The effective and environmentally friendly remediation of these chemical compounds is an important [...] Read more.
Polycyclic aromatic hydrocarbons (PAHs) are widespread, persistent, and toxic environmental pollutants. Many anthropogenic and some natural factors contribute to the spread and accumulation of PAHs in aquatic and soil systems. The effective and environmentally friendly remediation of these chemical compounds is an important and challenging problem that has kept scientists busy over the last few decades. This review briefly summarizes data on the main sources of PAHs, their toxicity to living organisms, and physical and chemical approaches to the remediation of PAHs. The basic idea behind existing approaches to the bioremediation of PAHs is outlined with an emphasis on a detailed description of the use of bacterial strains as individual isolates, consortia, or cell-free enzymatic agents. Full article
(This article belongs to the Special Issue Role of Microbes in the Remediation of Pollutants in the Environment)
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