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Chen C, Xu G, Rogers MJ, He J. Metabolic Synergy of Dehalococcoides Populations Leading to Greater Reductive Dechlorination of Polychlorinated Biphenyls. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2384-2392. [PMID: 38266236 DOI: 10.1021/acs.est.3c08473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Polychlorinated biphenyls (PCBs) are dioxin-like pollutants that cause persistent harm to life. Organohalide-respiring bacteria (OHRB) can detoxify PCBs via reductive dechlorination, but individual OHRB are potent in dechlorinating only specific PCB congeners, restricting the extent of PCB dechlorination. Moreover, the low biomass of OHRB frequently leads to the slow natural attenuation of PCBs at contaminated sites. Here we constructed defined microbial consortia comprising various combinations of PCB-dechlorinating Dehalococcoides strains (CG1, CG4, and CG5) to successfully enhance PCB dechlorination. Specifically, the defined consortia consisting of strains CG1 and CG4 removed 0.28-0.44 and 0.23-0.25 more chlorine per PCB from Aroclor1260 and Aroclor1254, respectively, compared to individual strains, which was attributed to the emergence of new PCB dechlorination pathways in defined consortia. Notably, different Dehalococcoides populations exhibited similar growth when cocultivated, but temporal differences in the expression of PCB reductive dehalogenase genes indicated their metabolic synergy. Bioaugmentation with individual strains (CG1, CG4, and CG5) or defined consortia led to greater PCB dechlorination in wetland sediments, and augmentation with the consortium comprising strains CG1 and CG4 resulted in the greatest PCB dechlorination. These findings collectively suggest that simultaneous application of multiple Dehalococcoides strains, which catalyze complementary dechlorination pathways, is an effective strategy to accelerate PCB dechlorination.
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Affiliation(s)
- Chen Chen
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Matthew James Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
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Chen C, Xu G, He J. Substrate-dependent strategies to mitigate sulfate inhibition on microbial reductive dechlorination of polychlorinated biphenyls. CHEMOSPHERE 2023; 342:140063. [PMID: 37673179 DOI: 10.1016/j.chemosphere.2023.140063] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/30/2023] [Accepted: 09/02/2023] [Indexed: 09/08/2023]
Abstract
Sulfate widely co-exists with polychlorinated biphenyls (PCBs) at various concentrations in the subsurface environment. Previous studies have suggested that sulfate often hampers microbial degradation of aliphatic chlorinated solvents such as chloroethenes. However, the impact of sulfate on microbial reductive dechlorination of aromatic PCBs and the underlying mechanisms have received limited attention. Likewise, strategies to mitigate such inhibition remain scarce. Here we found that the mechanisms and mitigation strategies of sulfate inhibition on PCB dechlorination were substrate-dependent. Under electron donor-limiting conditions, even a low concentration of sulfate (2 mM) resulted in a decreased PCB dechlorination rate by 88.7% in a co-culture comprising Dehalococcoides mccartyi CG1 and the sulfate-reducing bacterium Desulfovibrio desulfuricans F1, an inhibition which was attributed to the competition for electron donor between sulfate reduction and PCB dechlorination. As expected, re-amendment of 5 mM lactate effectively re-initiated PCB dechlorination. However, in the presence of a higher concentration of sulfate (5 mM), the PCB dechlorination rate in the co-culture was 77.7% lower than in the control, even with excessive electron donor supply. This inhibition was linked to high concentration of sulfide (∼5 mM) produced from sulfate reduction, as suggested by high availability of electron donor, recovery of dechlorination activity after removal of sulfide, and negligible influence of sulfate on PCB dechlorination in the axenic culture of D. mccartyi CG1. Indeed, sulfide (>5 mM) was found to directly suppress expression of PCB-dechlorinating reductive dehalogenase gene. The highest transcriptional level of pcbA1 was 2.9 ± 0.3 transcripts·cell-1 in the presence of ∼5 mM sulfide, which was increased to 37.4 ± 5.0 transcripts·cell-1 when sulfide was removed. Under this scenario, introduction of ferrous salts (5 mM) efficiently alleviated sulfide inhibition on PCB dechlorination. Interestingly, the augmentation of methanogens in the co-culture was also effective in mitigating sulfide inhibition on PCB dechlorination, offering a new approach to protect Dehalococcoides under sulfide stress. Collectively, these findings deepen our understanding of the influence of sulfate on microbial reductive dechlorination of PCBs and contribute to developing appropriate strategies based on geochemical conditions to alleviate sulfate inhibition during bioremediation of PCB-contaminated sites.
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Affiliation(s)
- Chen Chen
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
| | - Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore.
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Xu G, Zhao S, Chen C, Zhang N, He J. Alleviating Chlorinated Alkane Inhibition on Dehalococcoides to Achieve Detoxification of Chlorinated Aliphatic Cocontaminants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:15112-15122. [PMID: 37772791 DOI: 10.1021/acs.est.3c04535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Cocontamination by multiple chlorinated solvents is a prevalent issue in groundwater, presenting a formidable challenge for effective remediation. Despite the recognition of this issue, a comprehensive assessment of microbial detoxification processes involving chloroethenes and associated cocontaminants, along with the underpinning microbiome, remains absent. Moreover, strategies to mitigate the inhibitory effects of cocontaminants have not been reported. Here, we revealed that chloroform exhibited the most potent inhibitory effects, followed by 1,1,1-trichloroethane and 1,1,2-trichloroethane, on dechlorination of dichloroethenes (DCEs) in Dehalococcoides-containing consortia. The observed inhibition could be attributed to suppression of biosynthesis and enzymatic activity of reductive dehalogenases and growth of Dehalococcoides. Notably, cocontaminants more profoundly inhibited Dehalococcoides populations harboring the vcrA gene than those possessing the tceA gene, thereby explaining the accumulation of vinyl chloride under cocontaminant stress. Nonetheless, we successfully ameliorated cocontaminant inhibition by augmentation with Desulfitobacterium sp. strain PR owing to its ability to attenuate cocontaminants, resulting in concurrent detoxification of DCEs, trichloroethanes, and chloroform. Microbial community analyses demonstrated obvious alterations in taxonomic composition, structure, and assembly of the dechlorinating microbiome in the presence of cocontaminants, and introduction of strain PR reshaped the dechlorinating microbiome to be similar to its original state in the absence of cocontaminants. Altogether, these findings contribute to developing bioremediation technologies to clean up challenging sites polluted with multiple chlorinated solvents.
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Affiliation(s)
- Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Chen Chen
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Ning Zhang
- College of Chemical Engineering and Pharmacy, Henan University of Science and Technology, Luoyang, Henan 471003, China
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore 117576, Singapore
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Xu G, Zhao X, Zhao S, Rogers MJ, He J. Salinity determines performance, functional populations, and microbial ecology in consortia attenuating organohalide pollutants. THE ISME JOURNAL 2023; 17:660-670. [PMID: 36765150 PMCID: PMC10119321 DOI: 10.1038/s41396-023-01377-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023]
Abstract
Organohalide pollutants are prevalent in coastal regions due to extensive intervention by anthropogenic activities, threatening public health and ecosystems. Gradients in salinity are a natural feature of coasts, but their impacts on the environmental fate of organohalides and the underlying microbial communities remain poorly understood. Here we report the effects of salinity on microbial reductive dechlorination of tetrachloroethene (PCE) and polychlorinated biphenyls (PCBs) in consortia derived from distinct environments (freshwater and marine sediments). Marine-derived microcosms exhibited higher halotolerance during PCE and PCB dechlorination, and a halotolerant dechlorinating culture was enriched from these microcosms. The organohalide-respiring bacteria (OHRB) responsible for PCE and PCB dechlorination in marine microcosms shifted from Dehalococcoides to Dehalobium when salinity increased. Broadly, lower microbial diversity, simpler co-occurrence networks, and more deterministic microbial community assemblages were observed under higher salinity. Separately, we observed that inhibition of dechlorination by high salinity could be attributed to suppressed viability of Dehalococcoides rather than reduced provision of substrates by syntrophic microorganisms. Additionally, the high activity of PCE dechlorinating reductive dehalogenases (RDases) in in vitro tests under high salinity suggests that high salinity likely disrupted cellular components other than RDases in Dehalococcoides. Genomic analyses indicated that the capability of Dehalobium to perform dehalogenation under high salinity was likely owing to the presence of genes associated with halotolerance in its genomes. Collectively, these mechanistic and ecological insights contribute to understanding the fate and bioremediation of organohalide pollutants in environments with changing salinity.
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Affiliation(s)
- Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, 117576, Singapore
- NUS Graduate School - Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, Singapore, 119077, Singapore
| | - Xuejie Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, 117576, Singapore
| | - Siyan Zhao
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, 117576, Singapore
| | - Matthew J Rogers
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, 117576, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, 117576, Singapore.
- NUS Graduate School - Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, Singapore, 119077, Singapore.
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Dutta N, Usman M, Ashraf MA, Luo G, Zhang S. A critical review of recent advances in the bio-remediation of chlorinated substances by microbial dechlorinators. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2022.100359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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Dehalogenation of Chlorinated Ethenes to Ethene by a Novel Isolate, " Candidatus Dehalogenimonas etheniformans". Appl Environ Microbiol 2022; 88:e0044322. [PMID: 35674428 DOI: 10.1128/aem.00443-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Dehalococcoides mccartyi strains harboring vinyl chloride (VC) reductive dehalogenase (RDase) genes are keystone bacteria for VC detoxification in groundwater aquifers, and bioremediation monitoring regimens focus on D. mccartyi biomarkers. We isolated a novel anaerobic bacterium, "Candidatus Dehalogenimonas etheniformans" strain GP, capable of respiratory dechlorination of VC to ethene. This bacterium couples formate and hydrogen (H2) oxidation to the reduction of trichloro-ethene (TCE), all dichloroethene (DCE) isomers, and VC with acetate as the carbon source. Cultures that received formate and H2 consumed the two electron donors concomitantly at similar rates. A 16S rRNA gene-targeted quantitative PCR (qPCR) assay measured growth yields of (1.2 ± 0.2) × 108 and (1.9 ± 0.2) × 108 cells per μmol of VC dechlorinated in cultures with H2 or formate as electron donor, respectively. About 1.5-fold higher cell numbers were measured with qPCR targeting cerA, a single-copy gene encoding a putative VC RDase. A VC dechlorination rate of 215 ± 40 μmol L-1 day-1 was measured at 30°C, with about 25% of this activity occurring at 15°C. Increasing NaCl concentrations progressively impacted VC dechlorination rates, and dechlorination ceased at 15 g NaCl L-1. During growth with TCE, all DCE isomers were intermediates. Tetrachloroethene was not dechlorinated and inhibited dechlorination of other chlorinated ethenes. Carbon monoxide formed and accumulated as a metabolic by-product in dechlorinating cultures and impacted reductive dechlorination activity. The isolation of a new Dehalogenimonas species able to effectively dechlorinate toxic chlorinated ethenes to benign ethene expands our understanding of the reductive dechlorination process, with implications for bioremediation and environmental monitoring. IMPORTANCE Chlorinated ethenes are risk drivers at many contaminated sites, and current bioremediation efforts focus on organohalide-respiring Dehalococcoides mccartyi strains to achieve detoxification. We isolated and characterized the first non-Dehalococcoides bacterium, "Candidatus Dehalogenimonas etheniformans" strain GP, capable of metabolic reductive dechlorination of TCE, all DCE isomers, and VC to environmentally benign ethene. In addition to hydrogen, the new isolate utilizes formate as electron donor for reductive dechlorination, providing opportunities for more effective electron donor delivery to the contaminated subsurface. The discovery that a broader microbial diversity can achieve detoxification of toxic chlorinated ethenes in anoxic aquifers illustrates the potential of naturally occurring microbes for biotechnological applications.
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Haluska AA, Finneran KT. Increasing electron donor concentration does not accelerate complete microbial reductive dechlorination in contaminated sediment with native organic carbon. Biodegradation 2021; 32:577-593. [PMID: 34081242 DOI: 10.1007/s10532-021-09953-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 05/22/2021] [Indexed: 11/26/2022]
Abstract
Experiments with Fe(III)-rich, chloroethene-contaminated sediment demonstrated that trichloroethylene (TCE) and vinyl chloride (VC) were completely reduced to ethene regardless of whether electron donor(s) were added at 1 × stoichiometry or 10 × stoichiometry relative to all-electron acceptors. Unamended controls uniformly reduced TCE to ethene with a mean time to complete dechlorination (operationally defined as the presence of stoichiometric ethene production) of 79 days. Adding 1 × and 10 × acetate hindered the rate and extent of TCE and VC reduction relative to unamended controls, with several only partially reduced when the experiments were terminated. Adding high molecular mass (soybean oil derivative) substrates did not increase microbial reductive dechlorination relative to unamended incubations, and in many cases, hindered microbial dechlorination in favor of methanogenesis. The mean time to complete dechlorination was comparable between low (× 1) and high (× 10) electron donor concentration for all lipid-based electron donors tested. Those tested included Newman Zone® Standard without sodium lactate (96 vs. 75 days, respectively), CAP 18 ME (85 vs. 94 days, respectively), EOS 598B42 (68 vs. 72 days, respectively), and acetate (134 vs. 125 days, respectively). These data suggest that the addition of an electron donor does not always increase the rate and extent of reductive dechlorination but will increase costs. In particular, increasing the concentration of electron donors higher than the stoichiometric demand only decreased complete microbial reductive dechlorination, which is the opposite of most standard "more time and more electrons" approaches. These data argue that site-specific electron donor demands must be evaluated, and in some cases, a monitored natural attenuation (MNA) approach is most favorable.
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Affiliation(s)
- Alexander Arthur Haluska
- Environmental Engineering and Earth Sciences, Clemson University, 312 Biosystems Research Complex, 105 Collings Street, Clemson, SC, 29634, USA
- Center for Applied Geoscience, Geological Institute, University of Tϋbingen, Hölderlinstrße 12, 72070, Tübingen, Germany
| | - Kevin T Finneran
- Environmental Engineering and Earth Sciences, Clemson University, 312 Biosystems Research Complex, 105 Collings Street, Clemson, SC, 29634, USA.
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Sánchez-Andrea I, Guedes IA, Hornung B, Boeren S, Lawson CE, Sousa DZ, Bar-Even A, Claassens NJ, Stams AJM. The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans. Nat Commun 2020; 11:5090. [PMID: 33037220 PMCID: PMC7547702 DOI: 10.1038/s41467-020-18906-7] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 09/14/2020] [Indexed: 12/30/2022] Open
Abstract
Six CO2 fixation pathways are known to operate in photoautotrophic and chemoautotrophic microorganisms. Here, we describe chemolithoautotrophic growth of the sulphate-reducing bacterium Desulfovibrio desulfuricans (strain G11) with hydrogen and sulphate as energy substrates. Genomic, transcriptomic, proteomic and metabolomic analyses reveal that D. desulfuricans assimilates CO2 via the reductive glycine pathway, a seventh CO2 fixation pathway. In this pathway, CO2 is first reduced to formate, which is reduced and condensed with a second CO2 to generate glycine. Glycine is further reduced in D. desulfuricans by glycine reductase to acetyl-P, and then to acetyl-CoA, which is condensed with another CO2 to form pyruvate. Ammonia is involved in the operation of the pathway, which is reflected in the dependence of the autotrophic growth rate on the ammonia concentration. Our study demonstrates microbial autotrophic growth fully supported by this highly ATP-efficient CO2 fixation pathway.
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Affiliation(s)
- Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Iame Alves Guedes
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Bastian Hornung
- Leids Universitair Medisch Centrum (LUMC), Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Xiao Z, Jiang W, Chen D, Xu Y. Bioremediation of typical chlorinated hydrocarbons by microbial reductive dechlorination and its key players: A review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 202:110925. [PMID: 32800212 DOI: 10.1016/j.ecoenv.2020.110925] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Chlorinated hydrocarbon contamination in soils and groundwater has a severe negative impact on the human health. Microbial reductive dechlorination is a major degradation pathway of chlorinated hydrocarbon in anaerobic subsurface environments, has been extensively studied. Recent progress on the diversity of the reductive dechlorinators and the key enzymes of chlororespiration has been well reviewed. Here, we present a thorough overview of the studies related to bioremediation of chloroethenes and polychlorinated biphenyls based on enhanced in situ reductive dechlorination. The major part of this review is to provide an up-to-date summary of functional microorganisms which are either detected during in situ biostimulation or applied in bioaugmentation strategies. The applied biostimulants and corresponding reductive dechlorination products are also summarized and the future research needs are finally discussed.
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Affiliation(s)
- Zhixing Xiao
- College of Urban Construction, Nanjing Tech University, Nanjing, 211816, PR China
| | - Wei Jiang
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, PR China
| | - Dan Chen
- College of Urban Construction, Nanjing Tech University, Nanjing, 211816, PR China
| | - Yan Xu
- Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 210096, PR China.
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