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Łomża P, Krucoń T, Tabernacka A. Potential of Microbial Communities to Perform Dehalogenation Processes in Natural and Anthropogenically Modified Environments-A Metagenomic Study. Microorganisms 2023; 11:1702. [PMID: 37512875 PMCID: PMC10385969 DOI: 10.3390/microorganisms11071702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Halogenated organic compounds (HOCs) pose a serious problem for the environment. Many are highly toxic and accumulate both in soil and in organisms. Their biological transformation takes place by dehalogenation, in which the halogen substituents are detached from the carbon in the organic compound by enzymes produced by microorganisms. This increases the compounds' water solubility and bioavailability, reduces toxicity, and allows the resulting compound to become more susceptible to biodegradation. The microbial halogen cycle in soil is an important part of global dehalogenation processes. The aim of the study was to examine the potential of microbial communities inhabiting natural and anthropogenically modified environments to carry out the dehalogenation process. The potential of microorganisms was assessed by analyzing the metagenomes from a natural environment (forest soils) and from environments subjected to anthropopression (agricultural soil and sludge from wastewater treatment plants). Thirteen genes encoding enzymes with dehalogenase activity were identified in the metagenomes of both environments, among which, 2-haloacid dehalogenase and catechol 2,3-dioxygenase were the most abundant genes. Comparative analysis, based on comparing taxonomy, identified genes, total halogens content and content of DDT derivatives, demonstrated the ability of microorganisms to transform HOCs in both environments, indicating the presence of these compounds in the environment for a long period of time and the adaptive need to develop mechanisms for their detoxification. Metagenome analyses and comparative analyses indicate the genetic potential of microorganisms of both environments to carry out dehalogenation processes, including dehalogenation of anthropogenic HOCs.
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Affiliation(s)
- Pola Łomża
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
| | - Tomasz Krucoń
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, 1 Miecznikowa Street, 02-089 Warsaw, Poland
| | - Agnieszka Tabernacka
- Department of Biology, Faculty of Building Services, Hydro and Environmental Engineering, Warsaw University of Technology, 20 Nowowiejska Street, 00-653 Warsaw, Poland
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Cheng YH, Chang SC, Lai YL, Hu CC. Microbiome reengineering by four environmental factors for the rapid biodegradation of trichloroethylene. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 326:116658. [PMID: 36399881 DOI: 10.1016/j.jenvman.2022.116658] [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: 06/04/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Trichloroethylene (TCE) was once a widely applied industrial solvent, but is now an infamous contaminant in groundwater. Although anaerobic reductive dechlorination is considered a greener remediation approach, the accumulation of toxic intermediates, such as vinyl chloride (VC), and a longer remediation period are highly concerning. Biostimulation and bioaugmentation have been developed to solve these problems. The former method may not be effective, and the latter may introduce foreign genes. Here, we propose a new approach by applying environmental stresses to reshape the indigenous microbiome. In this study, by using the Taguchi method, the effects of heating, pH, salinity, and desiccation were systematically examined. The optimum conditions were defined as 50 °C, pH 9, 3.50% salinity (w/v), and 21% volumetric water content (θW). The top performing group, G7, can complete the conversion of 11.81 mg/L TCE into ethene in 3.0 days with a 1.23% abundance of Dehalococcoides mccartyi 195 (Dhc 195). Redundancy analysis confirmed that temperature and salinity were the predominant factors in reorganizing the microbiomes. The microbiome structure and its effectiveness can last for at least 90 d. The repetitive selection conditions and sustainable degradation capability strongly supported that microbiome reengineering is feasible for the rapid bioremediation of TCE-contaminated environmental matrices.
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Affiliation(s)
- Yu-Hsuan Cheng
- Department of Environmental Engineering, National Chung Hsing University, No. 145, Xingda Road, Taichung, 40227, Taiwan
| | - Shu-Chi Chang
- Department of Environmental Engineering, National Chung Hsing University, No. 145, Xingda Road, Taichung, 40227, Taiwan.
| | - Yan-Lin Lai
- Graduate Institute of Biotechnology, National Chung Hsing University, No. 145, Xingda Road, Taichung, 40227, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, No. 145, Xingda Road, Taichung, 40227, Taiwan
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Kjellerup BV, Nijenhuis I, Rossetti S. Editorial: Thematic issue on anaerobic biological dehalogenation. FEMS Microbiol Ecol 2022; 98:6780077. [PMID: 36308759 DOI: 10.1093/femsec/fiac108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 07/13/2022] [Accepted: 09/09/2022] [Indexed: 01/21/2023] Open
Affiliation(s)
- Birthe Veno Kjellerup
- A. James Clark School of Engineering, University of Maryland at College Park, 1147 Glenn L. Martin Hall, College Park, MD 20742, United States
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), via Salaria km 29300, 00015 Monterotondo (RM), Italy
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Rossi MM, Alfano S, Amanat N, Andreini F, Lorini L, Martinelli A, Petrangeli Papini M. A Polyhydroxybutyrate (PHB)-Biochar Reactor for the Adsorption and Biodegradation of Trichloroethylene: Design and Startup Phase. Bioengineering (Basel) 2022; 9:bioengineering9050192. [PMID: 35621470 PMCID: PMC9137886 DOI: 10.3390/bioengineering9050192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/26/2022] [Accepted: 04/25/2022] [Indexed: 11/16/2022] Open
Abstract
In this work, polyhydroxy butyrate (PHB) and biochar from pine wood (PWB) are used in a mini-pilot scale biological reactor (11.3 L of geometric volume) for trichloroethylene (TCE) removal (80 mgTCE/day and 6 L/day of flow rate). The PHB-biochar reactor was realized with two sequential reactive areas to simulate a multi-reactive permeable barrier. The PHB acts as an electron donor source in the first “fermentative” area. First, the thermogravimetric (TGA) and differential scanning calorimetry (DSC) analyses were performed. The PHB-powder and pellets have different purity (96% and 93% w/w) and thermal properties. These characteristics may affect the biodegradability of the biopolymer. In the second reactive zone, the PWB works as a Dehalococcoides support and adsorption material since its affinity for chlorinated compounds and the positive effect of the “coupled adsorption and biodegradation” process has been already verified. A specific dechlorinating enriched culture has been inoculated in the PWB zone to realize a coupled adsorption and biodegradation process. Organic acids were revealed since the beginning of the test, and during the monitoring period the reductive dichlorination anaerobic pathway was observed in the first zone; no chlorinated compounds were detected in the effluent thanks to the PWB adsorption capacity.
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Affiliation(s)
- Marta M. Rossi
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (S.A.); (N.A.); (L.L.); (A.M.); (M.P.P.)
- Correspondence:
| | - Sara Alfano
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (S.A.); (N.A.); (L.L.); (A.M.); (M.P.P.)
| | - Neda Amanat
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (S.A.); (N.A.); (L.L.); (A.M.); (M.P.P.)
| | | | - Laura Lorini
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (S.A.); (N.A.); (L.L.); (A.M.); (M.P.P.)
| | - Andrea Martinelli
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (S.A.); (N.A.); (L.L.); (A.M.); (M.P.P.)
| | - Marco Petrangeli Papini
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (S.A.); (N.A.); (L.L.); (A.M.); (M.P.P.)
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Rossi MM, Matturro B, Amanat N, Rossetti S, Petrangeli Papini M. Coupled Adsorption and Biodegradation of Trichloroethylene on Biochar from Pine Wood Wastes: A Combined Approach for a Sustainable Bioremediation Strategy. Microorganisms 2022; 10:microorganisms10010101. [PMID: 35056550 PMCID: PMC8779034 DOI: 10.3390/microorganisms10010101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/29/2021] [Accepted: 12/31/2021] [Indexed: 12/24/2022] Open
Abstract
Towards chlorinated solvents, the effectiveness of the remediation strategy can be improved by combining a biological approach (e.g., anaerobic reductive dechlorination) with chemical/physical treatments (e.g., adsorption). A coupled adsorption and biodegradation (CAB) process for trichloroethylene (TCE) removal is proposed in a biofilm-biochar reactor (BBR) to assess whether biochar from pine wood (PWB) can support a dechlorinating biofilm by combining the TCE (100 µM) adsorption. The BBR operated for eight months in parallel with a biofilm reactor (BR)-no PWB (biological process alone), and with an abiotic biochar reactor (ABR)-no dechlorinating biofilm (only an adsorption mechanism). Two flow rates were investigated. Compared to the BR, which resulted in a TCE removal of 86.9 ± 11.9% and 78.73 ± 19.79%, the BBR demonstrated that PWB effectively adsorbs TCE and slows down the release of its intermediates. The elimination of TCE was quantitative, with 99.61 ± 0.79% and 99.87 ± 0.51% TCE removal. Interestingly, the biomarker of the reductive dechlorination process, Dehalococcoides mccartyi, was found in the BRR (9.2 × 105 16S rRNA gene copies/g), together with the specific genes tceA, bvcA, and vcrA (8.16 × 106, 1.28 × 105, and 8.01 × 103 gene copies/g, respectively). This study suggests the feasibility of biochar to support the reductive dechlorination of D. mccartyi, opening new frontiers for field-scale applications.
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Affiliation(s)
- Marta M. Rossi
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (N.A.); (M.P.P.)
- Correspondence:
| | - Bruna Matturro
- Water Research Institute (IRSA—CNR), Via Salaria km 29.300, 00015 Monterotondo, Italy; (B.M.); (S.R.)
| | - Neda Amanat
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (N.A.); (M.P.P.)
| | - Simona Rossetti
- Water Research Institute (IRSA—CNR), Via Salaria km 29.300, 00015 Monterotondo, Italy; (B.M.); (S.R.)
| | - Marco Petrangeli Papini
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (N.A.); (M.P.P.)
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Differentiating closely affiliated Dehalococcoides lineages by a novel genetic marker identified via computational pangenome analysis. Appl Environ Microbiol 2021; 88:e0218121. [PMID: 34910572 DOI: 10.1128/aem.02181-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As a group, Dehalococcoides dehalogenate a wide range of organohalide pollutants but the range of organohalide compounds that can be utilized for reductive dehalogenation differs among the Dehalococcoides strains. Dehalococcoides lineages cannot be reliably disambiguated in mixed communities using typical phylogenetic markers, which often confounds bioremediation efforts. Here, we describe a computational approach to identify Dehalococcoides genetic markers with improved discriminatory resolution. Screening core genes from the Dehalococcoides pangenome for degree of similarity and frequency of 100% identity found a candidate genetic marker encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function. This gene exhibits the fewest completely identical amino acid sequences and among the lowest average amino acid sequence identity in the core pangenome. Primers targeting BNR could effectively discriminate between 40 available BNR sequences (in silico) and 10 different Dehalococcoides isolates (in vitro). Amplicon sequencing of BNR fragments generated from 22 subsurface soil samples revealed a total of 109 amplicon sequence variants, suggesting a high diversity of Dehalococcoides distributed in environment. Therefore, the BNR gene can serve as an alternative genetic marker to differentiate strains of Dehalococcoides in complicated microbial communities. Importance The challenge of discriminating between phylogenetically similar but functionally distinct bacterial lineages is particularly relevant to the development of technologies seeking to exploit the metabolic or physiological characteristics of specific members of bacterial genera. A computational approach was developed to expedite screening of potential genetic markers among phylogenetically affiliated bacteria. Using this approach, a gene encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function was selected and evaluated as a genetic marker to differentiate strains of Dehalococcoides, an environmentally relevant genus of bacteria whose members can transform and detoxify a range of halogenated organic solvents and persistent organic pollutants, in complex microbial communities to demonstrate the validity of the approach. Moreover, many apparently phylogenetically distinct, currently uncharacterized Dehalococcoides were detected in environmental samples derived from contaminated sites.
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