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Wijaya J, Park J, Yang Y, Siddiqui SI, Oh S. A metagenome-derived artificial intelligence modeling framework advances the predictive diagnosis and interpretation of petroleum-polluted groundwater. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134513. [PMID: 38735183 DOI: 10.1016/j.jhazmat.2024.134513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/16/2024] [Accepted: 04/30/2024] [Indexed: 05/14/2024]
Abstract
Groundwater (GW) quality monitoring is vital for sustainable water resource management. The present study introduced a metagenome-derived machine learning (ML) model aimed at enhancing the predictive understanding and diagnostic interpretation of GW pollution associated with petroleum. In this framework, taxonomic and metabolic profiles derived from GW metagenomes were combined for use as the input dataset. By employing strategies that optimized data integration, model selection, and parameter tuning, we achieved a significant increase in diagnostic accuracy for petroleum-polluted GW. Explanatory artificial intelligence techniques identified petroleum degradation pathways and Rhodocyclaceae as strong predictors of a pollution diagnosis. Metagenomic analysis corroborated the presence of gene operons encoding aminobenzoate and xylene biodegradation within the de novo assembled genome of Rhodocyclaceae. Our genome-centric metagenomic analysis thus clarified the ecological interactions associated with microbiomes in breaking down petroleum contaminants, validating the ML-based diagnostic results. This metagenome-derived ML framework not only enhances the predictive diagnosis of petroleum pollution but also offers interpretable insights into the interaction between microbiomes and petroleum. The proposed ML framework demonstrates great promise for use as a science-based strategy for the on-site monitoring and remediation of GW pollution.
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Affiliation(s)
- Jonathan Wijaya
- Department of Civil Engineering, College of Engineering, Kyung Hee University, Yongin, Republic of Korea
| | - Joonhong Park
- Department of Civil and Environmental Engineering, Yonsei University, Seoul, Republic of Korea
| | - Yuyi Yang
- Key laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Sharf Ilahi Siddiqui
- Department of Chemistry, Ramjas College, University of Delhi, New Delhi 110007, India
| | - Seungdae Oh
- Department of Civil Engineering, College of Engineering, Kyung Hee University, Yongin, Republic of Korea.
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2
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Pang Z, Zhou H, Yang S, Wang Y, Xue Y, Feng S. Enhanced surfactant remediation of diesel-contaminated soil using O 3 nanobubbles. CHEMOSPHERE 2024; 356:141917. [PMID: 38588900 DOI: 10.1016/j.chemosphere.2024.141917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 03/09/2024] [Accepted: 04/04/2024] [Indexed: 04/10/2024]
Abstract
Currently, nanobubbles are widely discussed in environmental research due to their unique properties, including significant specific surface area, transfer efficiency, and free radical generation. In this study, O2 and O3 nanobubbles (diameters ranging from 0 to 500 nm) were combined with conventional surfactant technology to investigate their enhanced efficacy in removing diesel contaminants from soil. The impact of various factors such as surfactant concentration, temperature, and soil aging duration on pollutant removal rates was examined across different experimental approaches (stirring/flushing). Soil samples subjected to different treatments were characterized using TG-DTG and FTIR analysis, while GC/MS was employed to assess the degradation products of diesel constituents in the soil. The results indicated that the elution efficiencies of the three surfactants (SDS, SDBS, and TX-100) for diesel in soil correlated positively with concentration (0.3-1.4 CMC) and temperature (18-60 °C), and inversely with aging time (10-300 days), with the elution capacity was SDS > SDBS > TX-100. Mechanical stirring (500 rpm) and temperature variations (18-60 °C) did not affect the stability of the nanobubbles. Upon the introduction of O3 nanobubbles to the surfactant solution, there was a consistent increase in both the removal (degraded and removed) efficiency and rate of diesel under varying experimental conditions, resulting in an enhancement of removal rates by approximately 8-15%. FTIR spectroscopy showed that surfactants containing O3 nanobubbles mitigated the impact on the primary functional groups of soil organic matter. GC/MS analyses indicated that residual pollutants were predominantly alkanes, with degradation difficulty ranking as: alkanes < alkenes < cycloalkanes < aromatic compounds. TG-DTG coupled with GC/MS analysis demonstrated that O3 nanobubbles contributed to a reduction in surfactant residues. This study significantly advances our understanding of how nanobubbles facilitate and optimize surfactant-assisted remediation of contaminated soil, thereby advancing the precise application of nanobubble technology in soil remediation.
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Affiliation(s)
- Zhongzheng Pang
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China
| | - Huiping Zhou
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China.
| | - Songnan Yang
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China
| | - Yiqun Wang
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China
| | - Yingang Xue
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China
| | - Sheng Feng
- School of Environmental Science and Engineering, Changzhou University, Changzhou, 213164, China
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Antón-Herrero R, Chicca I, García-Delgado C, Crognale S, Lelli D, Gargarello RM, Herrero J, Fischer A, Thannberger L, Eymar E, Petruccioli M, D’Annibale A. Main Factors Determining the Scale-Up Effectiveness of Mycoremediation for the Decontamination of Aliphatic Hydrocarbons in Soil. J Fungi (Basel) 2023; 9:1205. [PMID: 38132804 PMCID: PMC10745009 DOI: 10.3390/jof9121205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Soil contamination constitutes a significant threat to the health of soil ecosystems in terms of complexity, toxicity, and recalcitrance. Among all contaminants, aliphatic petroleum hydrocarbons (APH) are of particular concern due to their abundance and persistence in the environment and the need of remediation technologies to ensure their removal in an environmentally, socially, and economically sustainable way. Soil remediation technologies presently available on the market to tackle soil contamination by petroleum hydrocarbons (PH) include landfilling, physical treatments (e.g., thermal desorption), chemical treatments (e.g., oxidation), and conventional bioremediation. The first two solutions are costly and energy-intensive approaches. Conversely, bioremediation of on-site excavated soil arranged in biopiles is a more sustainable procedure. Biopiles are engineered heaps able to stimulate microbial activity and enhance biodegradation, thus ensuring the removal of organic pollutants. This soil remediation technology is currently the most environmentally friendly solution available on the market, as it is less energy-intensive and has no detrimental impact on biological soil functions. However, its major limitation is its low removal efficiency, especially for long-chain hydrocarbons (LCH), compared to thermal desorption. Nevertheless, the use of fungi for remediation of environmental contaminants retains the benefits of bioremediation treatments, including low economic, social, and environmental costs, while attaining removal efficiencies similar to thermal desorption. Mycoremediation is a widely studied technology at lab scale, but there are few experiences at pilot scale. Several factors may reduce the overall efficiency of on-site mycoremediation biopiles (mycopiles), and the efficiency detected in the bench scale. These factors include the bioavailability of hydrocarbons, the selection of fungal species and bulking agents and their application rate, the interaction between the inoculated fungi and the indigenous microbiota, soil properties and nutrients, and other environmental factors (e.g., humidity, oxygen, and temperature). The identification of these factors at an early stage of biotreatability experiments would allow the application of this on-site technology to be refined and fine-tuned. This review brings together all mycoremediation work applied to aliphatic petroleum hydrocarbons (APH) and identifies the key factors in making mycoremediation effective. It also includes technological advances that reduce the effect of these factors, such as the structure of mycopiles, the application of surfactants, and the control of environmental factors.
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Affiliation(s)
- Rafael Antón-Herrero
- Department of Agricultural Chemistry and Food Science, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (R.A.-H.); (E.E.)
| | | | - Carlos García-Delgado
- Department of Geology and Geochemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Silvia Crognale
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
| | - Davide Lelli
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
| | - Romina Mariel Gargarello
- Water, Air and Soil Unit, Eurecat, Centre Tecnològic de Catalunya, 08242 Manresa, Spain; (R.M.G.); (J.H.)
| | - Jofre Herrero
- Water, Air and Soil Unit, Eurecat, Centre Tecnològic de Catalunya, 08242 Manresa, Spain; (R.M.G.); (J.H.)
| | | | | | - Enrique Eymar
- Department of Agricultural Chemistry and Food Science, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (R.A.-H.); (E.E.)
| | - Maurizio Petruccioli
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
| | - Alessandro D’Annibale
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
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Noszczyńska M, Pacwa-Płociniczak M, Bondarczuk K, Piotrowska-Seget Z. The microbial removal of bisphenols in aquatic microcosms and associated alteration in bacterial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:85292-85304. [PMID: 37386218 PMCID: PMC10404205 DOI: 10.1007/s11356-023-28305-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023]
Abstract
The concept of the study resulted from numerous concerns around bisphenol A (BPA) and bisphenol S (BPS) in aquatic environments. In this study, river water and sediment microcosms highly polluted with bisphenols and bioaugmented with two BPs-removing bacterial strains were constructed. The study aimed to determine the rate of high-concentrated BPA and BPS (BPs) removal from river water and sediment microniches, and the effect of water bioaugmentation with bacterial consortium on the removal rates of these pollutants. Moreover, the impact of introduced strains and exposure to BPs on the structural and functional composition of the autochthonous bacterial communities was elucidated. Our findings indicate that the removal activity of autochthonous bacteria was sufficient for effectively BPA elimination and reducing BPS content in the microcosms. The number of introduced bacterial cells decreased continuously until day 40, and on consecutive sampling days, no bioaugmented cells were detected. Sequencing analysis of the total 16S rRNA genes revealed that the community composition in bioaugmented microcosms amended with BPs differed significantly from those treated either with bacteria or BPs. A metagenomic analysis found an increase in the abundance of proteins responsible for xenobiotics removal in BPs-amended microcosms. This study provides new insights into the effects of bioaugmentation with a bacterial consortium on bacterial diversity and BPs removal in aquatic environments.
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Affiliation(s)
- Magdalena Noszczyńska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland.
| | - Magdalena Pacwa-Płociniczak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | - Kinga Bondarczuk
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Białystok, Poland
| | - Zofia Piotrowska-Seget
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
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Cauduro GP, Marmitt M, Ferraz M, Arend SN, Kern G, Modolo RCE, Leal AL, Valiati VH. Burkholderia vietnamiensis G4 as a biological agent in bioremediation processes of polycyclic aromatic hydrocarbons in sludge farms. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 195:116. [PMID: 36394643 DOI: 10.1007/s10661-022-10733-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are one of the main pollutants generated by the refining and use of oil. To search bioremediation alternatives for these compounds, mainly in situ, considering the biotic and abiotic variables that affect the contaminated sites is determinant for the success of bioremediation techniques. In this study, bioremediation strategies were evaluated in situ, including biostimulation and bioaugmentation for 16 priority PAHs present in activated sludge farms. B. vietnamiensis G4 was used as a biodegradation agent for bioaugmentation tests. The analyses occurred for 12 months, and temperature and humidity were measured to verify the effects of these factors on the biodegradation. We used the technique GC-MS to evaluate and quantify the degradation of PAHs over the time of the experiment. Of the four treatments applied, bioaugmentation with quarterly application proved to be the best strategy, showing the degradation of compounds of high (34.4% annual average) and low (21.9% annual average) molecular weight. A high degradation rate for high molecular weight compounds demonstrates that this technique can be successfully applied in bioremediation of areas with compounds considered toxic and stable in nature, contributing to the mitigation of impacts generated by PAHs.
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Affiliation(s)
- Guilherme Pinto Cauduro
- Laboratory of Genetics and Molecular Biology, Programa de Pós-Graduação Em Biologia, Universidade Do Vale Do Rio Dos Sinos (UNISINOS), Av. Unisinos 950, São Leopoldo, RS, 93022-750, Brazil
| | - Marcela Marmitt
- Laboratory of Genetics and Molecular Biology, Programa de Pós-Graduação Em Biologia, Universidade Do Vale Do Rio Dos Sinos (UNISINOS), Av. Unisinos 950, São Leopoldo, RS, 93022-750, Brazil
| | - Marlon Ferraz
- Laboratory of Fish Ecology, Programa de Pós-Graduação Em Biologia, Universidade Do Vale Do Rio Dos Sinos (UNISINOS), São Leopoldo, RS, Brazil
| | - Sabrina Nicole Arend
- Laboratory of Genetics and Molecular Biology, Programa de Pós-Graduação Em Biologia, Universidade Do Vale Do Rio Dos Sinos (UNISINOS), Av. Unisinos 950, São Leopoldo, RS, 93022-750, Brazil
| | - Gabriela Kern
- Laboratory of Genetics and Molecular Biology, Programa de Pós-Graduação Em Biologia, Universidade Do Vale Do Rio Dos Sinos (UNISINOS), Av. Unisinos 950, São Leopoldo, RS, 93022-750, Brazil
| | - Regina Célia Espinosa Modolo
- Programa de Pós-Graduação Em Engenharia Civil, Escola Politécnica, Universidade Do Vale Do Rio Dos Sinos (UNISINOS), São Leopoldo, RS, Brazil
| | - Ana Lusia Leal
- Superintendence for the Treatment of Wastewater, SITEL/CORSAN, Companhia Riograndense de Saneamento, Polo Petroquímico Do Sul, Triunfo, RS, Brazil
| | - Victor Hugo Valiati
- Laboratory of Genetics and Molecular Biology, Programa de Pós-Graduação Em Biologia, Universidade Do Vale Do Rio Dos Sinos (UNISINOS), Av. Unisinos 950, São Leopoldo, RS, 93022-750, Brazil.
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Li Y, Li C, Xin Y, Huang T, Liu J. Petroleum pollution affects soil chemistry and reshapes the diversity and networks of microbial communities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114129. [PMID: 36193589 DOI: 10.1016/j.ecoenv.2022.114129] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 05/25/2023]
Abstract
Soil is the bearing centre of terrestrial ecosystems. Oil pollution leads to changes in the physical and chemical properties of soil to varying degrees. Polluted soils form a unique microbial species composition, which provides rich materials for the bioremediation of oil-contaminated soil through biological enhancement. Understanding the microbial composition of petroleum-contaminated soil can provide a better biological method for soil remediation. Based on this, 16 S rRNA and ITS genetic markers were used to analyse the bacterial and fungal microbiota in petroleum-contaminated soil, and their physical and chemical properties (total organic carbon, alkaline hydrolysable nitrogen, total phosphorus, total potassium, available potassium, Cu, Zn, and Cd) were measured. It was found that petroleum pollution can significantly reduce the abundance and diversity of bacteria and fungi in the soil and significantly promote the relative abundance of Proteobacteria, Pseudomonas, Pseudoxanthomonas and Pseudoallescheria, which changed the dominant flora of bacteria and fungi and reshaped the co-occurrence network relationship between bacteria and fungi in oil-contaminated soil. The content of total organic carbon in petroleum-contaminated soil was significantly higher than that in uncontaminated soil, while the content of alkaline hydrolysable nitrogen and available potassium was significantly lower than that in uncontaminated soil, and the content of Cu significantly increased after pollution. Total organic carbon is the key driving factor that changes oil-contaminated soil microorganisms and plays a significant role in regulating the remodelling and composition of the microbial community in oil-contaminated soil. This study laid a solid theoretical foundation for the bioremediation of oil-contaminated soil.
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Affiliation(s)
- Yongquan Li
- School of Medicine, Northwest Minzu University, Lanzhou, China; Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, State Ethnic Affairs Commission, Lanzhou, China.
| | - Caili Li
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Ying Xin
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Tao Huang
- School of Medicine, Northwest Minzu University, Lanzhou, China
| | - Jin Liu
- School of Medicine, Northwest Minzu University, Lanzhou, China
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7
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Al-Kaabi N, Disi ZA, Al-Ghouti MA, Solling TI, Zouari N. Interaction between indigenous hydrocarbon-degrading bacteria in reconstituted mixtures for remediation of weathered oil in soil. BIOTECHNOLOGY REPORTS 2022; 36:e00767. [PMID: 36245697 PMCID: PMC9562452 DOI: 10.1016/j.btre.2022.e00767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/25/2022] [Accepted: 10/01/2022] [Indexed: 11/27/2022]
Abstract
It has been demonstrated that biostimulation is necessary to investigate the interactions between indigenous bacteria and establish an approach for the bioremediation of soils contaminated with weathered oil. This was achieved by adjusting the carbon (C)/nitrogen (N)/phosphorus (P) ratio to 100/10/1 combined with the application of 0.8 mL/kg Tween-80. In addition, three indigenous bacteria isolated from the same soil were introduced solely or combined concomitantly with stimulation. Removal of n-alkanes and the ratios of n-heptadecane to pristane and n-octadecane to phytane were taken to indicate their biodegradation performance over a period of 16 weeks. One strain of Pseudomonas aeruginosa D7S1 improved the efficiency of the process of stimulation. However, another Pseudomonas aeruginosa, D5D1, inhibited the overall process when combined with other bacteria. One strain of Bacillus licheniformis D1D2 did not affect the process significantly. The Fourier transform infrared analysis of the residual hydrocarbons supported the conclusions pertaining to the biodegradation processes when probing the modifications in densities and stretching. The indigenous bacteria cannot mutually benefit from their metabolisms for bioremediation if augmented artificially. However, the strain Pseudomonas. aeruginosa D7S1 was able to perform better alone than in a consortium of indigenous bacteria.
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Affiliation(s)
- Nasser Al-Kaabi
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, P.O. B 2713 Qatar,Corresponding author.
| | - Zulfa Al Disi
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, P.O. B 2713 Qatar
| | - Mohammad A. Al-Ghouti
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, P.O. B 2713 Qatar
| | - Theis Ivan Solling
- Center for Integrative Petroleum Research, KFUPM, Academic Loop Rd, Dhahran, 31261 KSA
| | - Nabil Zouari
- Environmental Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, P.O. B 2713 Qatar
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Ivshina I, Bazhutin G, Tyumina E. Rhodococcus strains as a good biotool for neutralizing pharmaceutical pollutants and obtaining therapeutically valuable products: Through the past into the future. Front Microbiol 2022; 13:967127. [PMID: 36246215 PMCID: PMC9557007 DOI: 10.3389/fmicb.2022.967127] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Active pharmaceutical ingredients present a substantial risk when they reach the environment and drinking water sources. As a new type of dangerous pollutants with high chemical resistance and pronounced biological effects, they accumulate everywhere, often in significant concentrations (μg/L) in ecological environments, food chains, organs of farm animals and humans, and cause an intense response from the aquatic and soil microbiota. Rhodococcus spp. (Actinomycetia class), which occupy a dominant position in polluted ecosystems, stand out among other microorganisms with the greatest variety of degradable pollutants and participate in natural attenuation, are considered as active agents with high transforming and degrading impacts on pharmaceutical compounds. Many representatives of rhodococci are promising as unique sources of specific transforming enzymes, quorum quenching tools, natural products and novel antimicrobials, biosurfactants and nanostructures. The review presents the latest knowledge and current trends regarding the use of Rhodococcus spp. in the processes of pharmaceutical pollutants’ biodegradation, as well as in the fields of biocatalysis and biotechnology for the production of targeted pharmaceutical products. The current literature sources presented in the review can be helpful in future research programs aimed at promoting Rhodococcus spp. as potential biodegraders and biotransformers to control pharmaceutical pollution in the environment.
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9
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Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives. ENVIRONMENTS 2022. [DOI: 10.3390/environments9040052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.
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Ubani O, Atagana HI, Selvarajan R, Ogola HJO. Unravelling the genetic and functional diversity of dominant bacterial communities involved in manure co-composting bioremediation of complex crude oil waste sludge. Heliyon 2022; 8:e08945. [PMID: 35243067 PMCID: PMC8857465 DOI: 10.1016/j.heliyon.2022.e08945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 01/07/2022] [Accepted: 02/09/2022] [Indexed: 01/07/2023] Open
Abstract
The present study aimed to characterize the bacterial community and functional diversity in co-composting microcosms of crude oil waste sludge amended with different animal manures, and to evaluate the scope for biostimulation based in situ bioremediation. Gas chromatography–mass spectrometry (GC–MS) analyses revealed enhanced attenuation (>90%) of the total polyaromatic hydrocarbons (PAHs); the manure amendments significantly enhancing (up to 30%) the degradation of high molecular weight (HMW) PAHs. Microbial community analysis showed the dominance (>99% of total sequences) of sequences affiliated to phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The core genera enriched were related to hydrocarbon metabolism (Pseudomonas, Delftia, Methylobacterium, Dietzia, Bacillus, Propionibacterium, Bradyrhizobium, Streptomyces, Achromobacter, Microbacterium and Sphingomonas). However, manure-treated samples exhibited high number and heterogeneity of unique operational taxonomic units (OTUs) with enrichment of additional hydrocarbon-degrading bacterial taxa (Proteiniphilum, unclassified Micrococcales, unclassified Lachnospiraceae, Sphingobium and Stenotrophomonas). Thirty-three culturable hydrocarbon-degrading microbes were isolated from the co-composting microcosms and mainly classified into Burkholderia, Sanguibacter, Pseudomonas, Bacillus, Rhodococcus, Lysinibacillus, Microbacterium, Brevibacterium, Geobacillus, Micrococcus, Arthrobacter, Cellulimicrobacterium, Streptomyces Dietzia,etc,. that was additionally affirmed with the presence of catechol 2,3-dioxygenase gene. Finally, enhanced in situ degradation of total (49%), LMW (>75%) and HMW PAHs (>35%) was achieved with an enriched bacterial consortium of these microbes. Overall, these findings suggests that co-composting treatment of crude oil sludge with animal manures selects for intrinsically diverse bacterial community, that could be a driving force behind accelerated bioremediation, and can be exploited for engineered remediation processes.
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Affiliation(s)
- Onyedikachi Ubani
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, University of South Africa, Florida Campus, Roodepoort, 1709, South Africa
- Corresponding author.
| | - Harrison I. Atagana
- Institute of Nanotechnology & Water Sustainability, College of Science, Engineering and Technology, University of South Africa, Florida Campus, Roodepoort, 1709, South Africa
| | - Ramganesh Selvarajan
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, University of South Africa, Florida Campus, Roodepoort, 1709, South Africa
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, 572000, Hainan Province, PR China
- PG Research Department of Microbiology, J.J College of Arts and Science (Autonomous), Sivapuram, Pudukkottai, 622 422, Tamil Nadu, India
| | - Henry JO. Ogola
- Department of Environmental Sciences, College of Agricultural and Environmental Sciences, University of South Africa, Florida Campus, Roodepoort, 1709, South Africa
- School of Agricultural and Food Sciences, Jaramogi Oginga Odinga University of Science and Technology, Bondo, P.O Box 210-40601, Kenya
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Simpson JB, Sekela JJ, Graboski AL, Borlandelli VB, Bivins MM, Barker NK, Sorgen AA, Mordant AL, Johnson RL, Bhatt AP, Fodor AA, Herring LE, Overkleeft H, Lee JR, Redinbo MR. Metagenomics combined with activity-based proteomics point to gut bacterial enzymes that reactivate mycophenolate. Gut Microbes 2022; 14:2107289. [PMID: 35953888 PMCID: PMC9377255 DOI: 10.1080/19490976.2022.2107289] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
Mycophenolate mofetil (MMF) is an important immunosuppressant prodrug prescribed to prevent organ transplant rejection and to treat autoimmune diseases. MMF usage, however, is limited by severe gastrointestinal toxicity that is observed in approximately 45% of MMF recipients. The active form of the drug, mycophenolic acid (MPA), undergoes extensive enterohepatic recirculation by bacterial β-glucuronidase (GUS) enzymes, which reactivate MPA from mycophenolate glucuronide (MPAG) within the gastrointestinal tract. GUS enzymes demonstrate distinct substrate preferences based on their structural features, and gut microbial GUS enzymes that reactivate MPA have not been identified. Here, we compare the fecal microbiomes of transplant recipients receiving MMF to healthy individuals using shotgun metagenomic sequencing. We find that neither microbial composition nor the presence of specific structural classes of GUS genes are sufficient to explain the differences in MPA reactivation measured between fecal samples from the two cohorts. We next employed a GUS-specific activity-based chemical probe and targeted metaproteomics to identify and quantify the GUS proteins present in the human fecal samples. The identification of specific GUS enzymes was improved by using the metagenomics data collected from the fecal samples. We found that the presence of GUS enzymes that bind the flavin mononucleotide (FMN) is significantly correlated with efficient MPA reactivation. Furthermore, structural analysis identified motifs unique to these FMN-binding GUS enzymes that provide molecular support for their ability to process this drug glucuronide. These results indicate that FMN-binding GUS enzymes may be responsible for reactivation of MPA and could be a driving force behind MPA-induced GI toxicity.
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Affiliation(s)
- Joshua B. Simpson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Josh J. Sekela
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda L. Graboski
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Valentina B. Borlandelli
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Marissa M. Bivins
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie K. Barker
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia A. Sorgen
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Angie L. Mordant
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca L. Johnson
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aadra P. Bhatt
- Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anthony A. Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Laura E. Herring
- UNC Proteomics Core Facility, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hermen Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - John R. Lee
- Department of Medicine, Division of Nephrology and Hypertension, New York, New York, USA
| | - Matthew. R. Redinbo
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, Department of Microbiology and Immunology, and the Institute for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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12
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Bodor A, Bounedjoum N, Feigl G, Duzs Á, Laczi K, Szilágyi Á, Rákhely G, Perei K. Exploitation of extracellular organic matter from Micrococcus luteus to enhance ex situ bioremediation of soils polluted with used lubricants. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:125996. [PMID: 33992922 DOI: 10.1016/j.jhazmat.2021.125996] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Chronic pollution by used lubricant oils (ULOs) poses a serious challenge to the environment. Under stress conditions, microorganisms, including potential degraders, can enter a viable but non-culturable (VBNC) state, complicating the bioremediation of ULO-polluted areas. Resuscitation-promoting factors (Rpfs) can reverse this transition and/or enhance the biodegradation performance of both native and augmented strains. Here, Rpf-containing extracellular organic matter (EOM) from Micrococcus luteus was used to enhance the ex situ ULO removal in biostimulated and bioaugmented (with Rhodococcus qingshengii KAG C, R. erythropolis PR4) soils. ULO bioconversion, microbial activity, and CFUs were significantly higher in EOM-treated soils compared to corresponding control soils. After 60 days, the initial ULO concentration (52,500 mg kg-1) was reduced by 37% and 45% with EOM-supplemented biostimulation and bioaugmentation, respectively. Based on high-throughput 16S rRNA analysis, the enhancement was attributable both to the reactivation of EOM-responsive hydrocarbonoclastic bacterial genera (e.g., Pseudomonas, Comamonas, Stenotrophomonas, Gordonia) and to the long-term positive effect of EOM on the degradative efficacy of the introduced rhodococci. Ecotoxicological responses revealed that reduced ULO concentration did not correlate with decreased soil toxicity. Our findings provide an insight into the applicability of EOM in bioremediation and its effects on the soil microbial activity and community composition.
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Affiliation(s)
- Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Feigl
- Department of Plant Biology, University of Szeged, Szeged, Hungary
| | - Ágnes Duzs
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary; Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary
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13
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Dutta K, Shityakov S, Khalifa I. New Trends in Bioremediation Technologies Toward Environment-Friendly Society: A Mini-Review. Front Bioeng Biotechnol 2021; 9:666858. [PMID: 34409018 PMCID: PMC8365754 DOI: 10.3389/fbioe.2021.666858] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/26/2021] [Indexed: 01/29/2023] Open
Abstract
Today's environmental balance has been compromised by the unreasonable and sometimes dangerous actions committed by humans to maintain their dominance over the Earth's natural resources. As a result, oceans are contaminated by the different types of plastic trash, crude oil coming from mismanagement of transporting ships spilling it in the water, and air pollution due to increasing production of greenhouse gases, such as CO2 and CH4 etc., into the atmosphere. The lands, agricultural fields, and groundwater are also contaminated by the infamous chemicals viz., polycyclic aromatic hydrocarbons, pyrethroids pesticides, bisphenol-A, and dioxanes. Therefore, bioremediation might function as a convenient alternative to restore a clean environment. However, at present, the majority of bioremediation reports are limited to the natural capabilities of microbial enzymes. Synthetic biology with uncompromised supervision of ethical standards could help to outsmart nature's engineering, such as the CETCH cycle for improved CO2 fixation. Additionally, a blend of synthetic biology with machine learning algorithms could expand the possibilities of bioengineering. This review summarized current state-of-the-art knowledge of the data-assisted enzyme redesigning to actively promote new research on important enzymes to ameliorate the environment.
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Affiliation(s)
- Kunal Dutta
- Department of Human Physiology, Vidyasagar University, Medinipur, India
| | - Sergey Shityakov
- Department of Chemoinformatics, Infochemistry Scientific Center, Saint Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University), Saint-Petersburg, Russia
| | - Ibrahim Khalifa
- Food Technology Department, Faculty of Agriculture, Benha University, Moshtohor, Egypt
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