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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 (31 March 2022) | Viewed by 41199

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Prof. Dr. Giovanni Vallini

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Department of Biotechnology, University of Verona, Strada Le Grazie 15 – Ca’ Vignal, 37134 Verona, Italy
Interests: microbial biodegradations and biotransformations; microbial interactions with metals/metalloids; plant-assisted bioremediation
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Dr. Silvia Lampis

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Dear Colleagues,

The Merriam-Webster Dictionary of the English Language tells us that the term “bioremediation”, meaning the cleanup of contaminated environmental matrices such as soils, sediments, and groundwater, as well as waste from a variety of human activities, containing pollutants that pose environmental and health risks, by means of the use of microorganisms (e.g., bacteria and fungi) able to break down the unwanted substances, appeared in the scientific literature for the first time in 1986. Since then, the study of microbial degradative capabilities in view of their possible exploitation in environmental reclamation protocols—both in situ and ex situ—has had a burst, witnessed by the rich literature available today in this field, although bioremediation is still not a widely diffuse practice in full-scale applications. Nevertheless, microbial bioremediation can be seen today as an effective and inexpensive biotechnological strategy providing an alternative to energivorous and labor-intensive physico-chemical options to remove noxious contaminants from polluted contexts or to prevent toxic waste release into the environment. Bioremediation processes are typically the result of synergic interrelations of complex microbial consortia acting through parallel or sequential catabolic reactions. Although traditional culture-dependent approaches can provide key information on the metabolic traits and the functional activity of axenic cultures of microbial strains isolated from contaminated sites, only the recent development of metagenomic methods supported by high-throughput DNA sequencing technology has given information hitherto unknown regarding the microbial communities as a whole and has also allowed us to obtain an in-depth understanding of the metabolic capabilities of the indigenous microbes, adapted to the actual environmental conditions prevailing at specific sites to be remediated.

In light of the picture outlined above, this Special Issue of Microorganisms aims to collect the results of the most recent studies concerning microbial bioremediation, falling within the following sub-themes: A) New insights into the in vitro biodegradation of recalcitrant contaminants such as polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), alkylphenol polyethoxylates (APEOs), and polyfluoroalkyl substances (PFASs) by bacterial and fungal strains; B) Depictions of in situ bioremediation dynamics as revealed by metagenomic studies at specific contaminated sites; C) The functioning of innovative microbially catalyzed processes for ex situ treatments of polluted environmental matrices.

Considering the interest aroused by the launch of a special issue on "Microbial Bioremediation" and the numerous requests received from scientists involved in studies dealing with different aspects of microbial catalysis aimed at environmental decontamination, decidedly consistent with the subject of this special issue of Microorganisms, it is deemed appropriate extend the deadline for the submission of contributions to March 31, 2022.

Prof. Dr. Giovanni Vallini
Prof. Dr. Silvia Lampis
Guest Editors

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Keywords

APEOs
bacterial degraders
bioremediation
culture-dependent protocols
fungal degradation patterns
metagenomic approaches
microbial degradation
PAHs
PCBs
PFASs
refractory organic pollutants

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Published Papers (9 papers)

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Research

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17 pages, 2652 KiB

Open AccessArticle

Great Abilities of Shinella zoogloeoides Strain from a Landfarming Soil for Crude Oil Degradation and a Synergy Model for Alginate-Bead-Entrapped Consortium Efficiency

by Emerance Jessica Claire D’Assise Goma-Tchimbakala, Ilaria Pietrini, Federica Dal Bello, Joseph Goma-Tchimbakala, Stefano Lo Russo and Stefano Paolo Corgnati

Microorganisms 2022, 10(7), 1361; https://doi.org/10.3390/microorganisms10071361 - 6 Jul 2022

Cited by 7 | Viewed by 3074

Abstract

Oil contamination is of great concern worldwide and needs to be properly addressed. The present work aimed to contribute to the development of bacterial consortia for oil recovery. We investigated the community structure of a landfarming-treated soil (LF2) by metagenomics to unravel the presence of hydrocarbon degraders. Moreover, we isolated Shinella zoogloeoides LFG9 and Bacillus swezeyi LFS15 from LF2 and combined them with Pseudomonas guguanensis SGPP2 isolated from an auto mechanic workshop soil to form the mixed consortium COG1. Bacterial isolates were tested for biosurfactant production. Additionally, the bioremediation potential of COG1 was studied as free and entrapped consortia by gas chromatography-mass spectrometry, in comparison to the single strains. Results revealed the presence of Actinobacteria (66.11%), Proteobacteria (32.21%), Gammaproteobacteria (5.39%), Actinomycetales (65.15%), Burkholderiales (13.92%), and Mycobacterium (32.22%) taxa, indicating the presence of hydrocarbon degraders in soil LF2. All three isolated strains were biosurfactant producers capable of degrading crude oil components within 14 days. However, Shinella zoogloeoides LFG9 performed best and was retained as candidate for further bioremediation investigation. In addition, COG1 performed better when immobilized, with entrapment effectiveness manifested by increased fatty acids and aromatic compound degradation. Attempt to improve crude oil biodegradation by adding surfactants failed as sodium dodecyl sulfate restrained the immobilized consortium performance. Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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17 pages, 2844 KiB

Open AccessArticle

Gradual Enhancement of the Assemblage Stability of the Reed Rhizosphere Microbiome with Recovery Time

by Fuchao Zheng, Xiaoming Mou, Jinghua Zhang, Tiange Zhang, Lu Xia, Shenglai Yin, Lingye Wu, Xin Leng, Shuqing An and Dehua Zhao

Microorganisms 2022, 10(5), 937; https://doi.org/10.3390/microorganisms10050937 - 29 Apr 2022

Cited by 6 | Viewed by 2740

Abstract

Rhizoplane microbes are considered proxies for evaluating the assemblage stability of the rhizosphere in wetland ecosystems due to their roles in plant growth and ecosystem health. However, our knowledge of how microbial assemblage stability is promoted in the reed rhizosphere of wetlands undergoing recovery is limited. We investigated the assemblage stability, diversity, abundance, co-occurrence patterns, and functional characteristics of reed rhizosphere microbes in restored wetlands. The results indicated that assemblage stability significantly increased with recovery time and that the microbial assemblages were capable of resisting seasonal fluctuations after more than 20 years of restoration. The number of bacterial indicators was greater in the restoration groups with longer restoration periods. Most bacterial indicators appeared in the 30-year restoration group. However, the core taxa and keystone species of module 2 exhibited greater abundance within longer recovery periods and were well organized, with rich and diverse functions that enhanced microbial assemblage stability. Our study provides insight into the connection between the rhizosphere microbiome and recovery period and presents a useful theoretical basis for the empirical management of wetland ecosystems. Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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22 pages, 5306 KiB

Open AccessArticle

Cupriavidus metallidurans CH34 Possesses Aromatic Catabolic Versatility and Degrades Benzene in the Presence of Mercury and Cadmium

by Pablo Alviz-Gazitua, Roberto E. Durán, Felipe A. Millacura, Franco Cárdenas, Luis A. Rojas and Michael Seeger

Microorganisms 2022, 10(2), 484; https://doi.org/10.3390/microorganisms10020484 - 21 Feb 2022

Cited by 10 | Viewed by 3883

Abstract

Heavy metal co-contamination in crude oil-polluted environments may inhibit microbial bioremediation of hydrocarbons. The model heavy metal-resistant bacterium Cupriavidus metallidurans CH34 possesses cadmium and mercury resistance, as well as genes related to the catabolism of hazardous BTEX aromatic hydrocarbons. The aims of this study were to analyze the aromatic catabolic potential of C. metallidurans CH34 and to determine the functionality of the predicted benzene catabolic pathway and the influence of cadmium and mercury on benzene degradation. Three chromosome-encoded bacterial multicomponent monooxygenases (BMMs) are involved in benzene catabolic pathways. Growth assessment, intermediates identification, and gene expression analysis indicate the functionality of the benzene catabolic pathway. Strain CH34 degraded benzene via phenol and 2-hydroxymuconic semialdehyde. Transcriptional analyses revealed a transition from the expression of catechol 2,3-dioxygenase (tomB) in the early exponential phase to catechol 1,2-dioxygenase (catA1 and catA2) in the late exponential phase. The minimum inhibitory concentration to Hg (II) and Cd (II) was significantly lower in the presence of benzene, demonstrating the effect of co-contamination on bacterial growth. Notably, this study showed that C. metallidurans CH34 degraded benzene in the presence of Hg (II) or Cd (II). Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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19 pages, 6122 KiB

Open AccessArticle

Bioremediation of Petroleum Hydrocarbons in Seawater: Prospects of Using Lyophilized Native Hydrocarbon-Degrading Bacteria

by Rafaela Perdigão, C. Marisa R. Almeida, Catarina Magalhães, Sandra Ramos, Ana L. Carolas, Bruno S. Ferreira, Maria F. Carvalho and Ana P. Mucha

Microorganisms 2021, 9(11), 2285; https://doi.org/10.3390/microorganisms9112285 - 3 Nov 2021

Cited by 18 | Viewed by 5402

Abstract

This work aimed to develop a bioremediation product of lyophilized native bacteria to respond to marine oil spills. Three oil-degrading bacterial strains (two strains of Rhodococcus erythropolis and one Pseudomonas sp.), isolated from the NW Portuguese coast, were selected for lyophilization after biomass growth optimization (tested with alternative carbon sources). Results indicated that the bacterial strains remained viable after the lyophilization process, without losing their biodegradation potential. The biomass/petroleum ratio was optimized, and the bioremediation efficiency of the lyophilized bacterial consortium was tested in microcosms with natural seawater and petroleum. An acceleration of the natural oil degradation process was observed, with an increased abundance of oil-degraders after 24 h, an emulsion of the oil/water layer after 7 days, and an increased removal of total petroleum hydrocarbons (47%) after 15 days. This study provides an insight into the formulation and optimization of lyophilized bacterial agents for application in autochthonous oil bioremediation. Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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15 pages, 1743 KiB

Open AccessArticle

Combining Culture-Dependent and Independent Approaches for the Optimization of Epoxiconazole and Fludioxonil-Degrading Bacterial Consortia

by Diogo A. M. Alexandrino, Ana P. Mucha, Maria Paola Tomasino, C. Marisa R. Almeida and Maria F. Carvalho

Microorganisms 2021, 9(10), 2109; https://doi.org/10.3390/microorganisms9102109 - 7 Oct 2021

Cited by 8 | Viewed by 2266

Abstract

Epoxiconazole (EPO) and fludioxonil (FLU) are two widely used fluorinated pesticides known to be highly persistent and with high ecotoxicological potential, turning them into pollutants of concern. This work aimed to optimize two degrading bacterial consortia, previously obtained from an agricultural soil through enrichment with EPO and FLU, by characterizing the contribution of their corresponding bacterial isolates to the biodegradation of these pesticides using both culture-dependent and independent methodologies. Results showed that a co-culture of the strains Hydrogenophaga eletricum 5AE and Methylobacillus sp. 8AE was the most efficient in biodegrading EPO, being able to defluorinate ca. 80% of this pesticide in 28 days. This catabolic performance is likely the result of a commensalistic cooperation, in which H. eletricum may be the defluorinating strain and Methylobacillus sp. may assume an accessory, yet pivotal, catabolic role. Furthermore, 16S rRNA metabarcoding analysis revealed that these strains represent a minority in their original consortium, showing that the biodegradation of EPO can be driven by less abundant phylotypes in the community. On the other hand, none of the tested combinations of bacterial strains showed potential to biodegrade FLU, indicating that the key degrading strains were not successfully isolated from the original enrichment culture. Overall, this work shows, for the first time, the direct involvement of two bacterial species, namely H. eletricum and Methylobacillus sp., in the biodegradation of EPO, while also offering insight on how they might cooperate to accomplish this process. Moreover, the importance of adequate culture-dependent approaches in the engineering of microbial consortia for bioremediation purposes is also emphasized. Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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13 pages, 2385 KiB

Open AccessArticle

Removal of Phenols in Table Olive Processing Wastewater by Using a Mixed Inoculum of Candida boidinii and Bacillus pumilus: Effects of Inoculation Dynamics, Temperature, pH, and Effluent Age on the Abatement Efficiency

by Daniela Campaniello, Barbara Speranza, Clelia Altieri, Milena Sinigaglia, Antonio Bevilacqua and Maria Rosaria Corbo

Microorganisms 2021, 9(8), 1783; https://doi.org/10.3390/microorganisms9081783 - 23 Aug 2021

Cited by 1 | Viewed by 2374

Abstract

The main goal of this paper was to assess the ability of a combination of Candida boidinii and Bacillus pumilus to remove phenol in table olive processing water, as a function of some variables, like temperature, pH, a dilution of waste and the order of inoculation of the two microorganisms. At this purpose C. boidinii and B. pumilus were sequentially inoculated in two types of table olive processing water (fresh wastewater, FTOPW and wastewater stored for 3 months-aged wastewater, ATOPW). pH (6 and 9), temperature (10 and 35 °C) and dilution ratio (0, 1:1) were combined through a 2^k fractional design. Data were modeled using two different approaches: Multifactorial Analysis of Variance (MANOVA) and multiple regression. A higher removal yield was achieved by inoculating B. pumilus prior to the yeast (192 vs. 127 mg/L); moreover, an increased efficiency was gained at 35 °C (mean removal of 200 mg/L). The use of two statistic approach suggested a different weight of variables; temperature was a global variable, that is a factor able to affect the yield of the process in all conditions. On the other hand, an alkaline pH could increase the removal of phenol at 10 °C (25–43%). Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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14 pages, 1899 KiB

Open AccessArticle

Isolation and Characterization of Novel Bacteria Capable of Degrading 1,4-Dioxane in the Presence of Diverse Co-Occurring Compounds

by Tanmoy Roy Tusher, Takuya Shimizu, Chihiro Inoue and Mei-Fang Chien

Microorganisms 2021, 9(5), 887; https://doi.org/10.3390/microorganisms9050887 - 21 Apr 2021

Cited by 21 | Viewed by 3786

Abstract

Biodegradation is found to be a promising, cost-effective and eco-friendly option for the treatment of industrial wastewater contaminated by 1,4-dioxane (1,4-D), a highly stable synthetic chemical and probable human carcinogen. This study aimed to isolate, identify, and characterize metabolic 1,4-D-degrading bacteria from a stable 1,4-D-degrading microbial consortium. Three bacterial strains (designated as strains TS28, TS32, and TS43) capable of degrading 1,4-D as a sole carbon and energy source were isolated and identified as Gram-positive Pseudonocardia sp. (TS28) and Gram-negative Dokdonella sp. (TS32) and Afipia sp. (TS43). This study, for the first time, confirmed that the genus Dokdonella is involved in the biodegradation of 1,4-D. The results reveal that all of the isolated strains possess inducible 1,4-D-degrading enzymes and also confirm the presence of a gene encoding tetrahydrofuran/dioxane monooxygenase (thmA/dxmA) belonging to group 5 soluble di-iron monooxygenases (SDIMOs) in both genomic and plasmid DNA of each of the strains, which is possibly responsible for the initial oxidation of 1,4-D. Moreover, the isolated strains showed a broad substrate range and are capable of degrading 1,4-D in the presence of additional substrates, including easy-to-degrade compounds, 1,4-D biodegradation intermediates, structural analogs, and co-contaminants of 1,4-D. This indicates the potential of the isolated strains, especially strain TS32, in removing 1,4-D from contaminated industrial wastewater containing additional organic load. Additionally, the results will help to improve our understanding of how multiple 1,4-D-degraders stably co-exist and interact in the consortium, relying on a single carbon source (1,4-D) in order to develop an efficient biological 1,4-D treatment system. Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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Review

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13 pages, 696 KiB

Open AccessReview

Azospirillum spp. from Plant Growth-Promoting Bacteria to Their Use in Bioremediation

by María Antonia Cruz-Hernández, Alberto Mendoza-Herrera, Virgilio Bocanegra-García and Gildardo Rivera

Microorganisms 2022, 10(5), 1057; https://doi.org/10.3390/microorganisms10051057 - 20 May 2022

Cited by 32 | Viewed by 6151

Abstract

Xenobiotic contamination, a worldwide environmental concern, poses risks for humans, animals, microbe health, and agriculture. Hydrocarbons and heavy metals top the list of toxins that represent a risk to nature. This review deals with the study of Azospirillum sp., widely reported as plant growth-promoting bacteria in various cultures. However, its adaptation properties in adverse environments make it a good candidate for studying remediation processes in environments polluted with hydrocarbons and heavy metals. This review includes studies that address its properties as a plant growth promoter, its genomics, and that evaluate its potential use in the remediation of hydrocarbons and heavy metals. Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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16 pages, 3174 KiB

Open AccessReview

Bacterial Biosorbents, an Efficient Heavy Metals Green Clean-Up Strategy: Prospects, Challenges, and Opportunities

by Van Hong Thi Pham, Jaisoo Kim, Soonwoong Chang and Woojin Chung

Microorganisms 2022, 10(3), 610; https://doi.org/10.3390/microorganisms10030610 - 13 Mar 2022

Cited by 83 | Viewed by 9083

Abstract

Rapid industrialization has led to the pollution of soil and water by various types of contaminants. Heavy metals (HMs) are considered the most reactive toxic contaminants, even at low concentrations, which cause health problems through accumulation in the food chain and water. Remediation using conventional methods, including physical and chemical techniques, is a costly treatment process and generates toxic by-products, which may negatively affect the surrounding environment. Therefore, biosorption has attracted significant research interest in the recent decades. In contrast to existing methods, bacterial biomass offers a potential alternative for recovering toxic/persistent HMs from the environment through different mechanisms for metal ion uptake. This review provides an outlook of the advantages and disadvantages of the current bioremediation technologies and describes bacterial groups, especially extremophiles with biosorbent potential for heavy metal removal with relevant examples and perspectives. Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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