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Yan M, Peng T, Zhao L, Li Q, Wu R, Wang Y, Wu Y, Teng Y, Xiang X, Zeng J, Lin X. The roles of organic amendments and plant treatments in soil polychlorinated biphenyl dissipation under oxic and sequential anoxic-oxic conditions. ENVIRONMENTAL RESEARCH 2024; 262:119943. [PMID: 39276835 DOI: 10.1016/j.envres.2024.119943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 08/29/2024] [Accepted: 09/05/2024] [Indexed: 09/17/2024]
Abstract
Understanding polychlorinated biphenyl (PCB) degradation in sequential anaerobic-aerobic remediation is crucial for effective remediation strategies. In this study, microcosm and greenhouse experiments were conducted to dissect the effects of organic amendments (carbon-based) and plant treatments (ryegrass) on soil PCB dissipation under oxic and sequential anoxic-oxic conditions. We analyzed the soil bacterial community in greenhouse experiments using high-throughput sequencing to explore plant-pollutant-microbe interactions. Microcosm results showed that organic amendments alone did not facilitate aerobic PCB removal, but significantly accelerated PCB dechlorination under anoxic conditions altering the profiles of PCB congeners. In standard greenhouses, plant treatments substantially increased PCB dissipation to 50.8 ± 3.9%, while organic amendments aided phytoremediation by promoting plant growth, increasing PCB removal to 65.9 ± 3.2%. In sequential anaerobic-aerobic greenhouses, plant growth was inhibited by flooding treatment while flooding stress was markedly alleviated by organic amendments. Plant treatments alone during sequential treatments did not lead to PCB dissipation; however, dissipation was significantly promoted following organic amendments, achieving a removal of 41.2 ± 5.7%. This PCB removal was primarily due to anaerobic dechlorination during flooding (27.8 ± 0.5% removal), rather than from plant growth stimulation in subsequent planting phase. Co-occurrence network and functional prediction analyses revealed that organic amendments recruited specific bacterial clusters with distinct functions under different conditions, especially stimulating plant-microbe interactions and xenobiotics biodegradation pathways in planted systems. The findings provide valuable guidance for the design of practical remediation strategies under various remedy scenarios, such as in arable or paddy fields.
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Affiliation(s)
- Meng Yan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing, 211135, PR China; Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, PR China
| | - Tingting Peng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing, 211135, PR China; Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, PR China
| | - Ling Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing, 211135, PR China
| | - Qigang Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing, 211135, PR China
| | - Ruini Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing, 211135, PR China
| | - Yiming Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing, 211135, PR China
| | - Yucheng Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing, 211135, PR China
| | - Ying Teng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing, 211135, PR China
| | - Xingjia Xiang
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, PR China.
| | - Jun Zeng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing, 211135, PR China.
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, No.298 Chuangyou Road, Nanjing, 211135, PR China
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Amirbekov A, Strojsova M, Nemecek J, Riha J, Hrabak P, Arias C, Sevcu A, Černík M. Biodiversity in wetland+ system: a passive solution for HCH dump effluents. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 88:3095-3109. [PMID: 38154796 PMCID: wst_2023_395 DOI: 10.2166/wst.2023.395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
The hexachlorocyclohexane isomers (HCH) are long-banned pesticides. Even though their use has been prohibited for decades, their presence in the environment is still reported worldwide. Wetland + is a registered trademark of the remedial treatment technology consisting of an aerobic sedimentary tank, a permeable reactive barrier, a biosorption system, and an aerobic wetland. This proven method combines a reductive treatment known from PRBs with the natural wetland self-cleaning processes. The average efficiency of the system is 96.8% for chlorobenzenes (ClB) and 81.7% for HCH, during the first 12 months of the system operation. The presence of the genes encoding enzymes involved in the degradation of the HCH compounds indicates that the removal of HCH and ClB occurs not only by chemical removal but also through aerobic and anaerobic combining biodegradation. Changes in abundance and the composition of the diatom community were found to be suitable indicators of the water quality and of the impact of the Wetland + operation on the water ecosystem. The system's annual operation exhibited a markedly higher number of diatom species in the closing profiles of the Ostrovský Creek, the Wetland + effluent recipient.
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Affiliation(s)
- Aday Amirbekov
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic E-mail:
| | - Martina Strojsova
- Faculty of Science, Humanities and Education, Technical University of Liberec, Trebízskeho 1244/2, Liberec 460 01, Czech Republic
| | - Jan Nemecek
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic
| | - Jakub Riha
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic
| | - Pavel Hrabak
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic
| | - Carlos Arias
- Department of Biology, Aquatic Biology, Ole Worms Allé 1, Aarhus University, Aarhus C 8000, Denmark; WATEC Aarhus University Centre for Water Technology, Aarhus University, Ole Worms Allé 3, Building 1171, Aarhus C 8000, Denmark
| | - Alena Sevcu
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic; Faculty of Science, Humanities and Education, Technical University of Liberec, Trebízskeho 1244/2, Liberec 460 01, Czech Republic
| | - Miroslav Černík
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Bendlova 7, Liberec 460 01, Czech Republic
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Chang J, Peng P, Farhan Ul-Haque M, Hira A, DiSpirito AA, Semrau JD. Inhibition of nitrous oxide reduction in forest soil microcosms by different forms of methanobactin. Environ Microbiol 2023; 25:2338-2350. [PMID: 37395163 DOI: 10.1111/1462-2920.16456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/14/2023] [Indexed: 07/04/2023]
Abstract
Copper plays a critical role in controlling greenhouse gas emissions as it is a key component of the particulate methane monooxygenase and nitrous oxide reductase. Some methanotrophs excrete methanobactin (MB) that has an extremely high copper affinity. As a result, MB may limit the ability of other microbes to gather copper, thereby decreasing their activity as well as impacting microbial community composition. Here, we show using forest soil microcosms that multiple forms of MB; MB from Methylosinus trichosporium OB3b (MB-OB3b) and MB from Methylocystis sp. strain SB2 (MB-SB2) increased nitrous oxide (N2 O) production as well caused significant shifts in microbial community composition. Such effects, however, were mediated by the amount of copper in the soils, with low-copper soil microcosms showing the strongest response to MB. Furthermore, MB-SB2 had a stronger effect, likely due to its higher affinity for copper. The presence of either form of MB also inhibited nitrite reduction and generally increased the presence of genes encoding for the iron-containing nitrite reductase (nirS) over the copper-dependent nitrite reductase (nirK). These data indicate the methanotrophic-mediated production of MB can significantly impact multiple steps of denitrification, as well as have broad effects on microbial community composition of forest soils.
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Affiliation(s)
- Jin Chang
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Peng Peng
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Abid Hira
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
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Xing Z, Chen S, Xu F, Su X, Gou F, Shi Y, Chen H, Xiang J, Li J, Zhao T. Quantitative analysis of TCE biodegradation pathway in landfill cover utilizing continuous monitoring, droplet digital PCR and multi-omics sequencing technology. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118509. [PMID: 37413727 DOI: 10.1016/j.jenvman.2023.118509] [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: 04/06/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/08/2023]
Abstract
The remediation of volatile chlorinated hydrocarbons in the quasi-vadose zone has become a significant challenge. We applied an integrated approach to assess the biodegradability of trichloroethylene to identify the biotransformation mechanism. The formation of the functional zone biochemical layer was assessed by analyzing the distribution of landfill gas, physical and chemical properties of cover soil, spatial-temporal variations of micro-ecology, biodegradability of landfill cover soil and distributional difference metabolic pathway. Real-time online monitoring showed that trichloroethylene continuously undergoes anaerobic dichlorination and simultaneous aerobic/anaerobic conversion-aerobic co-metabolic degradation on the vertical gradient of the landfill cover system and reduction in trans-1,2-dichloroethylene in the anoxic zone but not 1,1-dichloroethylene. PCR and diversity sequencing revealed the abundance and spatial distribution of known dichlorination-related genes within the landfill cover, with 6.61 ± 0.25 × 104-6.78 ± 0.09 × 106 and 1.17 ± 0.78 × 103-7.82 ± 0.07 × 105 copies per g/soil of pmoA and tceA, respectively. In addition, dominant bacteria and diversity were significantly linked with physicochemical factors, and Mesorhizobium, Pseudoxanthomonas and Gemmatimonas were responsible for biodegradation in the aerobic, anoxic and anaerobic zones. Metagenome sequencing identified 6 degradation pathways of trichloroethylene that may occur in the landfill cover; the main pathway was incomplete dechlorination accompanied by cometabolic degradation. These results indicate that the anoxic zone is important for trichloroethylene degradation.
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Affiliation(s)
- Zhilin Xing
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, China.
| | - Shangjie Chen
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Fuqing Xu
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Xia Su
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Fang Gou
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Yunchun Shi
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Hao Chen
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Jinxin Xiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Juan Li
- Chongqing Academy of Chinese Materia Medica, Chongqing, 400060, China
| | - Tiantao Zhao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, China.
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Li C, Xue C, Ouyang W, Liu M, Sun Y, Liu H. Identification and synergetic mechanism of TCE, H 2 and O 2 metabolic microorganisms in the joint H 2/O 2 system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163026. [PMID: 36965730 DOI: 10.1016/j.scitotenv.2023.163026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/19/2023] [Accepted: 03/19/2023] [Indexed: 05/17/2023]
Abstract
The sole H2 and O2 usually promote chlorinated hydrocarbons (CHCs) biotransformation by several mechanisms, including reductive dechlorination and aerobic oxidation. However, the mechanism of the CHCs transformation in joint H2 and O2 system (H2/O2 system) is still unclear. In this study, the degradation kinetics of trichloroethene (TCE) were investigated and DNA stable isotope probing (DNA-SIP) were used to explore the synergistic mechanism of functional microorganisms on TCE degradation under the condition of H2/O2 coexistence. In the H2/O2 microcosm, TCE was significantly removed by 13.00 μM within 40 days, much higher than N2, H2 and O2 microcosms, and 1,1-DCE was detected as an intermediate. DNA-SIP technology identified three anaerobic TCE metabolizers, five aerobic TCE metabolizers, nine hydrogen-oxidizing bacteria (HOB), some TCE metabolizers utilizing limited O2, and some anaerobic dechlorinating bacteria reductively using H2 to dechlorinate TCE. It is also confirmed for the first time that 3 OUTs belonging to Methyloversatilis and SH-PL14 can simultaneously utilize H2 and O2 as energy sources to grow and metabolize TCE or 1,1-DCE. HOB may provide carbon sources or electron acceptors or donors for TCE biotransformation. These findings confirm the coexistence of anaerobic and aerobic TCE metabolizers and degraders, which synergistically promoted the conversion of TCE in the joint H2/O2 system. Our results provide more information about the functional microbe resources and synergetic mechanisms for TCE degradation.
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Affiliation(s)
- Cui Li
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei 430078, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei 430078, PR China
| | - Chen Xue
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei 430078, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei 430078, PR China
| | - Weiwei Ouyang
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei 430078, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei 430078, PR China
| | - Minghui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei 430078, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei 430078, PR China
| | - Yingtao Sun
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, Guangdong 510640, PR China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hui Liu
- Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei 430078, PR China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei 430078, PR China.
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6
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Xu G, He J. Resilience of organohalide-detoxifying microbial community to oxygen stress in sewage sludge. WATER RESEARCH 2022; 224:119055. [PMID: 36126627 DOI: 10.1016/j.watres.2022.119055] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/20/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Organohalide pollutants are prevalent in the environment, causing harms to wildlife and human. Organohalide-respiring bacteria (OHRB) could detoxify these pollutants in anaerobic environments, but the most competent OHRB (i.e., Dehalococcoides) is susceptible to oxygen. This study reports exceptional resistance and resilience of sewage sludge microbial communities to oxygen stress for attenuation of structurally distinct organohalide pollutants, including tetrachloroethene, tetrabromobisphenol A, and polybrominated diphenyl ethers. The dehalogenation rate constant of these organohalide pollutants in oxygen-exposed sludge microcosms was maintained as 74-120% as that in the control without oxygen exposure. Subsequent top-down experiments clarified that sludge flocs and non-OHRB contributed to alleviating oxygen stress on OHRB. In the dehalogenating microcosms, multiple OHRB (Dehahlococcoides, Dehalogenimonas, and Sulfurospirillum) harboring distinct reductive dehalogenase genes (pceA, pteA, tceA, vcrA, and bdeA) collaborated to detoxify organohalide pollutants but responded differentially to oxygen stress. Comprehensive microbial community analyses (taxonomy, diversity, and structure) demonstrated certain resilience of the sludge-derived dehalogenating microbial communities to oxygen stress. Additionally, microbial co-occurrence networks were intensified by oxygen stress in most microcosms, as a possible stress mitigation strategy. Altogether the mechanistic and ecological findings in this study contribute to remediation of organohalide-contaminated sites encountering oxygen disturbance.
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Affiliation(s)
- Guofang Xu
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore; NUS Graduate School - Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, 119077, Singapore
| | - Jianzhong He
- Department of Civil and Environmental Engineering, National University of Singapore, 117576, Singapore; NUS Graduate School - Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, 119077, Singapore.
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7
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Li C, Chen R, Liu H, Huang Y, Yu J, Ouyang W, Xue C. Response of chlorinated hydrocarbon transformation and microbial community structure in an aquifer to joint H 2 and O 2. RSC Adv 2022; 12:23252-23262. [PMID: 36090448 PMCID: PMC9380535 DOI: 10.1039/d2ra04185e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/10/2022] [Indexed: 11/21/2022] Open
Abstract
Hydrogen (H2) and oxygen (O2) are critical electron donors and acceptors to promote the anaerobic and aerobic microbial transformation of chlorinated hydrocarbons (CHCs), respectively. Electrochemical technology can effectively supply H2 and O2 directly to an aquifer. However, the response of CHC transformation and microbial community structure to joint H2 and O2 are still unclear. In this work, microcosms containing different combinations of H2 and O2 were constructed with natural sediments and nine mixed CHCs. The joint H2 and O2 microcosm (H2/O2 microcosm) significantly promoted the biotransformation of trichloroethylene (TCE), trans-dichloroethene (tDCE) and chloroform (CF). Illumina sequencing analyses suggested that a particular microbial community was formed in the H2/O2 microcosm. The specific microbial species included Methyloversatilis, Dechloromonas, Sediminibacterium, Pseudomonas, Acinetobacter, Curvibacter, Comamonas and Acidovorax, and the relative abundance of the tceA, phe and soxB genes synchronously increased. These results suggested that some specific microbes are potential CHC converters using H2 and O2 as energy sources, and aerobic and anaerobic transformations exist simultaneously in the H2/O2 microcosm. It provides a theoretical basis for establishing efficient green remediation technologies for CHC contaminated aquifers.
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Affiliation(s)
- Cui Li
- School of Environmental Studies, China University of Geosciences Wuhan Hubei 430078 PR China
| | - Rong Chen
- School of Environmental and Biological Engineering, Wuhan Technology and Business University Wuhan Hubei 430065 PR China
| | - Hui Liu
- School of Environmental Studies, China University of Geosciences Wuhan Hubei 430078 PR China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences Wuhan Hubei 430078 PR China
| | - Yao Huang
- School of Environmental Studies, China University of Geosciences Wuhan Hubei 430078 PR China
| | - Jintao Yu
- School of Environmental Studies, China University of Geosciences Wuhan Hubei 430078 PR China
| | - Weiwei Ouyang
- School of Environmental Studies, China University of Geosciences Wuhan Hubei 430078 PR China
| | - Chen Xue
- School of Environmental Studies, China University of Geosciences Wuhan Hubei 430078 PR China
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8
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Richards PM, Ewald JM, Zhao W, Rectanus H, Fan D, Durant N, Pound M, Mattes TE. Natural Biodegradation of Vinyl Chloride and cis-Dichloroethene in Aerobic and Suboxic Conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:56154-56167. [PMID: 35322370 DOI: 10.1007/s11356-022-19755-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Chlorinated ethene (CE) groundwater contamination is commonly treated through anaerobic biodegradation (i.e., reductive dechlorination) either as part of an engineered system or through natural attenuation. Aerobic biodegradation has also been recognized as a potentially significant pathway for the removal of the lower CEs cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC). However, the role of aerobic biodegradation under low oxygen conditions typical of contaminated groundwater is unclear. Bacteria capable of aerobic VC biodegradation appear to be common in the environment, while aerobic biodegradation of cDCE is less common and little is known regarding the organisms responsible. In this study, we investigate the role of aerobic cDCE and VC biodegradation in a mixed contaminant plume (including CEs, BTEX, and ketones) at Naval Air Station North Island, Installation Restoration Site 9. Sediment and groundwater collected from the plume source area, mid-plume, and shoreline were used to prepare microcosms under fully aerobic (8 mg/L dissolved oxygen (DO)) and suboxic (< 1 mg/L DO) conditions. In the shoreline microcosms, VC and cDCE were rapidly degraded under suboxic conditions (100% and 77% removal in < 62 days). In the suboxic VC microcosms, biodegradation was associated with a > 5 order of magnitude increase in the abundance of functional gene etnE, part of the aerobic VC utilization pathway. VC and cDCE were degraded more slowly under fully aerobic conditions (74% and 30% removal) in 110 days. High-throughput 16S rRNA and etnE sequencing suggest the presence of novel VC- and cDCE-degrading bacteria. These results suggest that natural aerobic biodegradation of cDCE and VC is occurring at the site and provide new evidence that low (< 1 mg/L) DO levels play a significant role in natural attenuation of cDCE and VC.
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Affiliation(s)
- Patrick M Richards
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Jessica M Ewald
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Weilun Zhao
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Heather Rectanus
- Geosyntec Consultants, Inc, 10211 Wincopin Circle, 4th Floor, Columbia, MD, 21044, USA
| | - Dimin Fan
- Geosyntec Consultants, Inc, 10211 Wincopin Circle, 4th Floor, Columbia, MD, 21044, USA
| | - Neal Durant
- Geosyntec Consultants, Inc, 10211 Wincopin Circle, 4th Floor, Columbia, MD, 21044, USA
| | - Michael Pound
- Naval Facilities Engineering Systems Command (NAVFAC) Southwest, 750 Pacific Hwy, San Diego, CA, 92132, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA.
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9
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Zhang C, Atashgahi S, Bosma TNP, Peng P, Smidt H. Organohalide respiration potential in marine sediments from Aarhus Bay. FEMS Microbiol Ecol 2022; 98:fiac073. [PMID: 35689665 PMCID: PMC9303371 DOI: 10.1093/femsec/fiac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/09/2022] [Accepted: 06/08/2022] [Indexed: 11/14/2022] Open
Abstract
Organohalide respiration (OHR), catalysed by reductive dehalogenases (RDases), plays an important role in halogen cycling. Natural organohalides and putative RDase-encoding genes have been reported in Aarhus Bay sediments, however, OHR has not been experimentally verified. Here we show that sediments of Aarhus Bay can dehalogenate a range of organohalides, and different organohalides differentially affected microbial community compositions. PCE-dechlorinating cultures were further examined by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing. Known organohalide-respiring bacteria (OHRB) including Dehalococcoides, Dehalobacter and Desulfitobacterium decreased in abundance during transfers and serial dilutions, suggesting the importance of yet uncharacterized OHRB in these cultures. Switching from PCE to 2,6-DBP led to its complete debromination to phenol in cultures with and without sulfate. 2,6-DBP debrominating cultures differed in microbial composition from PCE-dechlorinating cultures. Desulfobacterota genera recently verified to include OHRB, including Desulfovibrio and Desulfuromusa, were enriched in all microcosms, whereas Halodesulfovibrio was only enriched in cultures without sulfate. Hydrogen and methane were detected in cultures without sulfate. Hydrogen likely served as electron donor for OHR and methanogenesis. This study shows that OHR can occur in marine environments mediated by yet unknown OHRB, suggesting their role in natural halogen cycling.
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Affiliation(s)
- Chen Zhang
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tom N P Bosma
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peng Peng
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109-2125, United States
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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10
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Ghezzi D, Filippini M, Cappelletti M, Firrincieli A, Zannoni D, Gargini A, Fedi S. Molecular characterization of microbial communities in a peat-rich aquifer system contaminated with chlorinated aliphatic compounds. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:23017-23035. [PMID: 33438126 DOI: 10.1007/s11356-020-12236-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
In an aquifer-aquitard system in the subsoil of the city of Ferrara (Emilia-Romagna region, northern Italy) highly contaminated with chlorinated aliphatic toxic organics such as trichloroethylene (TCE) and tetrachloroethylene (PCE), a strong microbial-dependent dechlorination activity takes place during migration of contaminants through shallow organic-rich layers with peat intercalations. The in situ microbial degradation of chlorinated ethenes, formerly inferred by the utilization of contaminant concentration profiles and Compound-Specific Isotope Analysis (CSIA), was here assessed using Illumina sequencing of V4 hypervariable region of 16S rRNA gene and by clone library analysis of dehalogenase metabolic genes. Taxon-specific investigation of the microbial communities catalyzing the chlorination process revealed the presence of not only dehalogenating genera such as Dehalococcoides and Dehalobacter but also of numerous other groups of non-dehalogenating bacteria and archaea thriving on diverse metabolisms such as hydrolysis and fermentation of complex organic matter, acidogenesis, acetogenesis, and methanogenesis, which can indirectly support the reductive dechlorination process. Besides, the diversity of genes encoding some reductive dehalogenases was also analyzed. Geochemical and 16S rRNA and RDH gene analyses, as a whole, provided insights into the microbial community complexity and the distribution of potential dechlorinators. Based on the data obtained, a possible network of metabolic interactions has been hypothesized to obtain an effective reductive dechlorination process.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
- Laboratory of NanoBiotechnology, IRCSS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136, Bologna, Italy
| | - Maria Filippini
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, via Zamboni 67, 40126, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
| | - Alessandro Gargini
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, via Zamboni 67, 40126, Bologna, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
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11
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Jin D, Zhang F, Shi Y, Kong X, Xie Y, Du X, Li Y, Zhang R. Diversity of bacteria and archaea in the groundwater contaminated by chlorinated solvents undergoing natural attenuation. ENVIRONMENTAL RESEARCH 2020; 185:109457. [PMID: 32247910 DOI: 10.1016/j.envres.2020.109457] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 03/27/2020] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Chlorinated solvents (CS)-contaminated groundwater poses serious risks to the environment and public health. Microorganisms play a vital role in efficient remediation of CS. In this study, the microbial community (bacterial and archaeal) composition of three CS-contaminated groundwater wells located at an abandoned chemical factory which covers three orders of magnitude in concentration (0.02-16.15 mg/L) were investigated via 16S rRNA gene high-throughput sequencing. The results indicated that Proteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal groups at the phylum level in groundwater, respectively. The major bacterial genera (Flavobacterium sp., Mycobacterium sp. and unclassified Parcubacteria taxa, etc.) and archaeal genera (Thaumarchaeota Group C3, Miscellaneous Crenarchaeotic Group and Miscellaneous Euryarchaeotic Group, etc.) might be involved in the dechlorination processes. In addition, Pearson's correlation analyses showed that alpha diversity of the bacterial community was not significantly correlated with CS concentration, while alpha diversity of archaeal community greatly decreased with the increased contamination of CS. Moreover, partial Mantel test indicated that oxidation-reduction potential, dissolved oxygen, temperature and methane concentration were major drivers of bacterial and archaeal community composition, whereas CS concentration had no significant impact, indicating that both indigenous bacterial and archaeal community compositions are capable of withstanding elevated CS contamination. This study improves our understanding of how the natural microbial community responds to high CS-contaminated groundwater.
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Affiliation(s)
- Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fengsong Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yi Shi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xiao Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunfeng Xie
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Xiaoming Du
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yanxia Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Ruiyong Zhang
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, 30655, Germany
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12
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Metagenomic- and Cultivation-Based Exploration of Anaerobic Chloroform Biotransformation in Hypersaline Sediments as Natural Source of Chloromethanes. Microorganisms 2020; 8:microorganisms8050665. [PMID: 32370295 PMCID: PMC7284496 DOI: 10.3390/microorganisms8050665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/22/2020] [Accepted: 04/29/2020] [Indexed: 01/23/2023] Open
Abstract
Chloroform (CF) is an environmental contaminant that can be naturally formed in various environments ranging from forest soils to salt lakes. Here we investigated CF removal potential in sediments obtained from hypersaline lakes in Western Australia. Reductive dechlorination of CF to dichloromethane (DCM) was observed in enrichment cultures derived from sediments of Lake Strawbridge, which has been reported as a natural source of CF. No CF removal was observed in abiotic control cultures without artificial electron donors, indicating biotic CF dechlorination in the enrichment cultures. Increasing vitamin B12 concentration from 0.04 to 4 µM in enrichment cultures enhanced CF removal and reduced DCM formation. In cultures amended with 4 µM vitamin B12 and 13C labelled CF, formation of 13CO2 was detected. Known organohalide-respiring bacteria and reductive dehalogenase genes were neither detected using quantitative PCR nor metagenomic analysis of the enrichment cultures. Rather, members of the order Clostridiales, known to co-metabolically transform CF to DCM and CO2, were detected. Accordingly, metagenome-assembled genomes of Clostridiales encoded enzymatic repertoires for the Wood-Ljungdahl pathway and cobalamin biosynthesis, which are known to be involved in fortuitous and nonspecific CF transformation. This study indicates that hypersaline lake microbiomes may act as a filter to reduce CF emission to the atmosphere.
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13
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Chow SJ, Lorah MM, Wadhawan AR, Durant ND, Bouwer EJ. Sequential biodegradation of 1,2,4-trichlorobenzene at oxic-anoxic groundwater interfaces in model laboratory columns. JOURNAL OF CONTAMINANT HYDROLOGY 2020; 231:103639. [PMID: 32283437 DOI: 10.7281/t1/i3ilxo] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 05/24/2023]
Abstract
Halogenated organic solvents such as chlorobenzenes (CBs) are frequent groundwater contaminants due to legacy spills. When contaminated anaerobic groundwater discharges into surface water through wetlands and other transition zones, aeration can occur from various physical and biological processes at shallow depths, resulting in oxic-anoxic interfaces (OAIs). This study investigated the potential for 1,2,4-trichlorobenzene (1,2,4-TCB) biodegradation at OAIs. A novel upflow column system was developed to create stable anaerobic and aerobic zones, simulating a natural groundwater OAI. Two columns containing (1) sand and (2) a mixture of wetland sediment and sand were operated continuously for 295 days with varied doses of 0.14-1.4 mM sodium lactate (NaLac) as a model electron donor. Both column matrices supported anaerobic reductive dechlorination and aerobic degradation of 1,2,4-TCB spatially separated between anaerobic and aerobic zones. Reductive dechlorination produced a mixture of di- and monochlorobenzene daughter products, with estimated zero-order dechlorination rates up to 31.3 μM/h. Aerobic CB degradation, limited by available dissolved oxygen, occurred for 1,2,4-TCB and all dechlorinated daughter products. Initial reductive dechlorination did not enhance the overall observed extent or rate of subsequent aerobic CB degradation. Increasing NaLac dose increased the extent of reductive dechlorination, but suppressed aerobic CB degradation at 1.4 mM NaLac due to increased oxygen demand. 16S-rRNA sequencing of biofilm microbial communities revealed strong stratification of functional anaerobic and aerobic organisms between redox zones including the sole putative reductive dechlorinator detected in the columns, Dehalobacter. The sediment mixture column supported enhanced reductive dechlorination compared to the sand column at all tested NaLac doses and growth of Dehalobacter populations up to 4.1 × 108 copies/g (51% relative abundance), highlighting the potential benefit of sediments in reductive dechlorination processes. Results from these model systems suggest both substantial anaerobic and aerobic CB degradation can co-occur along the OAI at contaminated sites where bioavailable electron donors and oxygen are both present.
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Affiliation(s)
- Steven J Chow
- Department of Environmental Health and Engineering, Johns Hopkins University, Address: 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Michelle M Lorah
- U.S. Geological Survey, MD-DE-DC Water Science Center, Address: 5522 Research Park Drive, Baltimore, MD 21228, United States.
| | - Amar R Wadhawan
- Arcadis U.S. Inc., Address: 7550 Teague Road Suite 210, Hanover, MD 21076, United States
| | - Neal D Durant
- Geosyntec Consultants, Address: 10211 Wincopin Cir Floor 4, Columbia, MD 21044, United States
| | - Edward J Bouwer
- Department of Environmental Health and Engineering, Johns Hopkins University, Address: 3400 North Charles Street, Baltimore, MD 21218, United States
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14
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Chow SJ, Lorah MM, Wadhawan AR, Durant ND, Bouwer EJ. Sequential biodegradation of 1,2,4-trichlorobenzene at oxic-anoxic groundwater interfaces in model laboratory columns. JOURNAL OF CONTAMINANT HYDROLOGY 2020; 231:103639. [PMID: 32283437 PMCID: PMC7217665 DOI: 10.1016/j.jconhyd.2020.103639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/16/2020] [Accepted: 03/23/2020] [Indexed: 05/09/2023]
Abstract
Halogenated organic solvents such as chlorobenzenes (CBs) are frequent groundwater contaminants due to legacy spills. When contaminated anaerobic groundwater discharges into surface water through wetlands and other transition zones, aeration can occur from various physical and biological processes at shallow depths, resulting in oxic-anoxic interfaces (OAIs). This study investigated the potential for 1,2,4-trichlorobenzene (1,2,4-TCB) biodegradation at OAIs. A novel upflow column system was developed to create stable anaerobic and aerobic zones, simulating a natural groundwater OAI. Two columns containing (1) sand and (2) a mixture of wetland sediment and sand were operated continuously for 295 days with varied doses of 0.14-1.4 mM sodium lactate (NaLac) as a model electron donor. Both column matrices supported anaerobic reductive dechlorination and aerobic degradation of 1,2,4-TCB spatially separated between anaerobic and aerobic zones. Reductive dechlorination produced a mixture of di- and monochlorobenzene daughter products, with estimated zero-order dechlorination rates up to 31.3 μM/h. Aerobic CB degradation, limited by available dissolved oxygen, occurred for 1,2,4-TCB and all dechlorinated daughter products. Initial reductive dechlorination did not enhance the overall observed extent or rate of subsequent aerobic CB degradation. Increasing NaLac dose increased the extent of reductive dechlorination, but suppressed aerobic CB degradation at 1.4 mM NaLac due to increased oxygen demand. 16S-rRNA sequencing of biofilm microbial communities revealed strong stratification of functional anaerobic and aerobic organisms between redox zones including the sole putative reductive dechlorinator detected in the columns, Dehalobacter. The sediment mixture column supported enhanced reductive dechlorination compared to the sand column at all tested NaLac doses and growth of Dehalobacter populations up to 4.1 × 108 copies/g (51% relative abundance), highlighting the potential benefit of sediments in reductive dechlorination processes. Results from these model systems suggest both substantial anaerobic and aerobic CB degradation can co-occur along the OAI at contaminated sites where bioavailable electron donors and oxygen are both present.
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Affiliation(s)
- Steven J Chow
- Department of Environmental Health and Engineering, Johns Hopkins University, Address: 3400 North Charles Street, Baltimore, MD 21218, United States
| | - Michelle M Lorah
- U.S. Geological Survey, MD-DE-DC Water Science Center, Address: 5522 Research Park Drive, Baltimore, MD 21228, United States.
| | - Amar R Wadhawan
- Arcadis U.S. Inc., Address: 7550 Teague Road Suite 210, Hanover, MD 21076, United States
| | - Neal D Durant
- Geosyntec Consultants, Address: 10211 Wincopin Cir Floor 4, Columbia, MD 21044, United States
| | - Edward J Bouwer
- Department of Environmental Health and Engineering, Johns Hopkins University, Address: 3400 North Charles Street, Baltimore, MD 21218, United States
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15
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Hydrochemical Conditions for Aerobic/Anaerobic Biodegradation of Chlorinated Ethenes—A Multi-Site Assessment. WATER 2020. [DOI: 10.3390/w12020322] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A stall of cis-1,2-DCE and vinyl chloride (VC) is frequently observed during bioremediation of groundwater chloroethenes via reductive dechlorination. These chloroethenes may be oxidised by aerobic methanotrophs or ethenotrophs co-metabolically and/or metabolically. We assessed the potential for such oxidation at 12 sites (49 groundwater samples) using hydrochemical and molecular biological tools. Both ethenotroph (etnC and etnE) and methanotroph (mmoX and pmoA) functional genes were identified in 90% of samples, while reductive dehalogenase functional genes (vcrA and bvcA) were identified in 82%. All functional genes were simultaneously detected in 78% of samples, in actively biostimulated sites in 88% of samples. Correlation analysis revealed that cis-1,2-DCE concentration was positively correlated with vcrA, etnC and etnE, while VC concentration was correlated with etnC, etnE, vcrA and bvcA. However, feature selection based on random forest classification indicated a significant relationship for the vcrA in relation to cis-1,2-DCE, and vcrA, bvcA and etnE for VC and no prove of relationship between cis-1,2-DCE or VC and the methanotroph functional genes. Analysis of hydrochemical parameters indicated that aerobic oxidation of chloroethenes by ethenotrophs may take place under a range of redox conditions of aquifers and coincide with high ethene and VC concentrations.
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16
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Richards PM, Liang Y, Johnson RL, Mattes TE. Cryogenic soil coring reveals coexistence of aerobic and anaerobic vinyl chloride degrading bacteria in a chlorinated ethene contaminated aquifer. WATER RESEARCH 2019; 157:281-291. [PMID: 30959331 DOI: 10.1016/j.watres.2019.03.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/04/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
Vinyl chloride (VC) is a common groundwater contaminant and known human carcinogen. Three major bacterial guilds are known to participate in VC biodegradation: aerobic etheneotrophs and methanotrophs, and anaerobic organohalide-respiring VC-dechlorinators. We investigated the spatial relationships between functional genes representing these three groups of bacteria (as determined by qPCR) with chlorinated ethene concentrations in a surficial aquifer at a contaminated site. We used cryogenic soil coring to collect high-resolution aquifer sediment samples and to preserve sample geochemistry and nucleic acids under field conditions. All samples appeared to be anaerobic (i.e., contained little to no dissolved oxygen). VC biodegradation associated functional genes from etheneotrophs (etnC and/or etnE), methanotrophs (mmoX and/or pmoA), and anaerobic VC-dechlorinators (bvcA and/or vcrA) coexisted in 48% of the samples. Transcripts of etnC/etnE and bvcA/vcrA were quantified in contemporaneous groundwater samples, indicating co-located gene expression. Functional genes from etheneotrophs and anaerobic VC-dechlorinators were correlated to VC concentrations in the lower surficial aquifer (p < 0.05). Methanotroph functional genes were not correlated to VC concentrations. Cryogenic soil coring proved to be a powerful tool for capturing high-spatial resolution trends in geochemical and nucleic acid data in aquifer sediments. We conclude that both aerobic etheneotrophs and anaerobic VC-dechlorinators may play a significant role in VC biodegradation in aquifers that have little dissolved oxygen.
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Affiliation(s)
- Patrick M Richards
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Yi Liang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Richard L Johnson
- OHSU-PSU School of Public Health, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA.
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17
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Bratkič A, Klun K, Gao Y. Mercury speciation in various aquatic systems using passive sampling technique of diffusive gradients in thin-film. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 663:297-306. [PMID: 30711596 DOI: 10.1016/j.scitotenv.2019.01.241] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/19/2019] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
Mercury (Hg) is one of the primary health concerns in natural and urbanised environments due to past and present natural and anthropogenic emissions. Its environmental cycle is driven by redox reactions, microbial metabolism and organic matter (OM) interactions, which may all lead to formation of bioaccumulative organic Hg species; methylmercury (MeHg), with damaging consequences for human and ecosystem health. Hence, Hg lability and bioavailability has been the focus of many investigations and assessed with a variety of chemical proxies in order to improve understanding of the conditions that lead to enhanced bioavailability of Hg and its species. We investigated Hg labile species with Diffusive Gradient in Thin-film technique (DGT) in the water column and sediment of Zenne River (Brussels, Belgium) and Gulf of Trieste (North Adriatic). They represent two contemporary important Hg-impacted areas; the former by anthropogenic urban pollution, and the latter by historic pollution from Hg mining. Hg speciation of labile inorganic and methylmercury in these two environments was not yet investigated using DGT technique. The results show labile Hg species changing with season in the water column of Zenne River, while the sediments are the source of bioavailable MeHg to the water column that is transported further creating a halo effect in the region. Values of labile Hg species for water column and sediments in Gulf of Trieste differ from previous research, highlighting the need for more investigation into Hg bioavailability. MeHg/THg ratios were compared to other sampling methods for labile Hg species.
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Affiliation(s)
- Arne Bratkič
- Analytical, Environmental and Geochemistry, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Katja Klun
- Marine Biology Station, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia
| | - Yue Gao
- Analytical, Environmental and Geochemistry, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
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18
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Liu X, Wu Y, Wilson FP, Yu K, Lintner C, Cupples AM, Mattes TE. Integrated methodological approach reveals microbial diversity and functions in aerobic groundwater microcosms adapted to vinyl chloride. FEMS Microbiol Ecol 2018; 94:5045312. [DOI: 10.1093/femsec/fiy124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/25/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Xikun Liu
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Yang Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Nanshan District, Shenzhen 518055, China
| | - Fernanda P Wilson
- Department of Civil and Environmental Engineering, Engineering Building, 428 S. Shaw Lane, Room 3546, East Lansing, MI 48824, USA
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Nanshan District, Shenzhen 518055, China
| | - Carly Lintner
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Engineering Building, 428 S. Shaw Lane, Room 3546, East Lansing, MI 48824, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
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19
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Weatherill JJ, Atashgahi S, Schneidewind U, Krause S, Ullah S, Cassidy N, Rivett MO. Natural attenuation of chlorinated ethenes in hyporheic zones: A review of key biogeochemical processes and in-situ transformation potential. WATER RESEARCH 2018; 128:362-382. [PMID: 29126033 DOI: 10.1016/j.watres.2017.10.059] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 10/12/2017] [Accepted: 10/28/2017] [Indexed: 06/07/2023]
Abstract
Chlorinated ethenes (CEs) are legacy contaminants whose chemical footprint is expected to persist in aquifers around the world for many decades to come. These organohalides have been reported in river systems with concerning prevalence and are thought to be significant chemical stressors in urban water ecosystems. The aquifer-river interface (known as the hyporheic zone) is a critical pathway for CE discharge to surface water bodies in groundwater baseflow. This pore water system may represent a natural bioreactor where anoxic and oxic biotransformation process act in synergy to reduce or even eliminate contaminant fluxes to surface water. Here, we critically review current process understanding of anaerobic CE respiration in the competitive framework of hyporheic zone biogeochemical cycling fuelled by in-situ fermentation of natural organic matter. We conceptualise anoxic-oxic interface development for metabolic and co-metabolic mineralisation by a range of aerobic bacteria with a focus on vinyl chloride degradation pathways. The superimposition of microbial metabolic processes occurring in sediment biofilms and bulk solute transport delivering reactants produces a scale dependence in contaminant transformation rates. Process interpretation is often confounded by the natural geological heterogeneity typical of most riverbed environments. We discuss insights from recent field experience of CE plumes discharging to surface water and present a range of practical monitoring technologies which address this inherent complexity at different spatial scales. Future research must address key dynamics which link supply of limiting reactants, residence times and microbial ecophysiology to better understand the natural attenuation capacity of hyporheic systems.
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Affiliation(s)
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Uwe Schneidewind
- Department of Engineering Geology and Hydrogeology, RWTH Aachen University, Aachen, Germany
| | - Stefan Krause
- School of Geography, Earth and Environmental Science, University of Birmingham, UK
| | - Sami Ullah
- School of Geography, Earth and Environmental Science, University of Birmingham, UK
| | | | - Michael O Rivett
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, UK; GroundH(2)O Plus Ltd., Quinton, Birmingham, UK
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20
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Liang Y, Liu X, Singletary MA, Wang K, Mattes TE. Relationships between the Abundance and Expression of Functional Genes from Vinyl Chloride (VC)-Degrading Bacteria and Geochemical Parameters at VC-Contaminated Sites. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:12164-12174. [PMID: 28981261 DOI: 10.1021/acs.est.7b03521] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bioremediation of vinyl chloride (VC) contamination in groundwater could be mediated by three major bacterial guilds: anaerobic VC-dechlorinators, methanotrophs, and ethene-oxidizing bacteria (etheneotrophs) via metabolic or cometabolic pathways. We collected 95 groundwater samples across 6 chlorinated ethene-contaminated sites and searched for relationships among VC biodegradation gene abundance and expression and site geochemical parameters (e.g., VC concentrations). Functional genes from the three major VC-degrading bacterial guilds were present in 99% and expressed in 59% of the samples. Etheneotroph and methanotroph functional gene abundances ranged from 102 to 109 genes per liter of groundwater among the samples with VC reductive dehalogenase gene (bvcA and vcrA) abundances reaching 108 genes per liter of groundwater. Etheneotroph functional genes (etnC and etnE) and VC reductive dehalogenase genes (bvcA and vcrA) were strongly related to VC concentrations (p < 0.001). Methanotroph functional genes (mmoX and pmoA) were not related to VC concentration (p > 0.05). Samples from sites with bulk VC attenuation rates >0.08 year-1 contained higher levels of etheneotroph and anaerobic VC-dechlorinator functional genes and transcripts than those with bulk VC attenuation rates <0.004 year-1. We conclude that both etheneotrophs and anaerobic VC-dechlorinators have the potential to simultaneously contribute to VC biodegradation at these sites.
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Affiliation(s)
| | | | - Michael A Singletary
- NAVFAC Southeast, EV3 Environmental Restoration Building 135, Naval Air Station Jacksonville, Florida 32508, United States
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21
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Concurrent Haloalkanoate Degradation and Chlorate Reduction by Pseudomonas chloritidismutans AW-1 T. Appl Environ Microbiol 2017; 83:AEM.00325-17. [PMID: 28411224 DOI: 10.1128/aem.00325-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/09/2017] [Indexed: 11/20/2022] Open
Abstract
Haloalkanoates are environmental pollutants that can be degraded aerobically by microorganisms producing hydrolytic dehalogenases. However, there is a lack of information about the anaerobic degradation of haloalkanoates. Genome analysis of Pseudomonas chloritidismutans AW-1T, a facultative anaerobic chlorate-reducing bacterium, showed the presence of two putative haloacid dehalogenase genes, the l-DEX gene and dehI, encoding an l-2-haloacid dehalogenase (l-DEX) and a halocarboxylic acid dehydrogenase (DehI), respectively. Hence, we studied the concurrent degradation of haloalkanoates and chlorate as a yet-unexplored trait of strain AW-1T The deduced amino acid sequences of l-DEX and DehI revealed 33 to 37% and 26 to 86% identities with biochemically/structurally characterized l-DEX and the d- and dl-2-haloacid dehalogenase enzymes, respectively. Physiological experiments confirmed that strain AW-1T can grow on chloroacetate, bromoacetate, and both l- and d-α-halogenated propionates with chlorate as an electron acceptor. Interestingly, growth and haloalkanoate degradation were generally faster with chlorate as an electron acceptor than with oxygen as an electron acceptor. In line with this, analyses of l-DEX and DehI dehalogenase activities using cell-free extract (CFE) of strain AW-1T grown on dl-2-chloropropionate under chlorate-reducing conditions showed up to 3.5-fold higher dehalogenase activity than the CFE obtained from AW-1T cells grown on dl-2-chloropropionate under aerobic conditions. Reverse transcription-quantitative PCR showed that the l-DEX gene was expressed constitutively independently of the electron donor (haloalkanoates or acetate) or acceptor (chlorate or oxygen), whereas the expression of dehI was induced by haloalkanoates. Concurrent degradation of organic and inorganic halogenated compounds by strain AW-1T represents a unique metabolic capacity in a single bacterium, providing a new piece of the puzzle of the microbial halogen cycle.IMPORTANCE Halogenated organic and inorganic compounds are important environmental pollutants that have carcinogenic and genotoxic effects on both animals and humans. Previous research studied the degradation of organic and inorganic halogenated compounds separately but not concurrently. This study shows concurrent degradation of halogenated alkanoates and chlorate as an electron donor and acceptor, respectively, coupled to growth in a single bacterium, Pseudomonas chloritidismutans AW-1T Hence, besides biogenesis of molecular oxygen from chlorate reduction enabling a distinctive placement of strain AW-1T between aerobic and anaerobic microorganisms, we can now add another unique metabolic potential of this bacterium to the roster. The degradation of different halogenated compounds under anoxic conditions by a single bacterium is also of interest for the natural halogen cycle in different aquatic and terrestrial ecosystems where ample natural production of halogenated compounds has been documented.
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Liang Y, Cook LJ, Mattes TE. Temporal abundance and activity trends of vinyl chloride (VC)-degrading bacteria in a dilute VC plume at Naval Air Station Oceana. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:13760-13774. [PMID: 28401391 DOI: 10.1007/s11356-017-8948-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
Assessment and monitoring of microbial community dynamics is useful when tracking the progress of vinyl chloride (VC) bioremediation strategies, particularly in dilute plumes where apparent VC attenuation rates are low. In a long-term field study, the abundance and the activity of microbial VC degraders were tracked in three monitoring wells (MW05, MW25, and MW19) along a dilute VC plume at Naval Air Station (NAS) Oceana. High-throughput sequencing of partial 16S ribosomal RNA (rRNA) genes and transcripts revealed diverse groundwater microbial communities and showed that methanotrophs and anaerobic respirers (e.g., methanogens, sulfate reducers, and iron reducers) were among the most active and abundant guilds. Quantitative PCR analysis showed that among bacterial guilds with a potential to contribute to VC biodegradation, methanotrophs were the most abundant and active microbial group. Ethene-oxidizing bacterial populations were less abundant and relatively inactive compared to methanotrophs. In MW19, expression of functional genes associated with both aerobic VC oxidation and anaerobic VC reduction was observed. Overall, our results reveal that the groundwater community contains various active bacterial guilds previously associated with metabolic and cometabolic VC degradation processes either under aerobic and anaerobic conditions that might have contributed to the slowly decreasing VC concentrations at the NAS Oceana site over the 6-year study period.
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Affiliation(s)
- Yi Liang
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA
| | - Laura J Cook
- CH2M 5701 Cleveland Street Suite 200, Virginia Beach, VA, 23462, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, University of Iowa, 4105 Seamans Center, Iowa City, IA, 52242, USA.
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Lu Y, Ramiro-Garcia J, Vandermeeren P, Herrmann S, Cichocka D, Springael D, Atashgahi S, Smidt H. Dechlorination of three tetrachlorobenzene isomers by contaminated harbor sludge-derived enrichment cultures follows thermodynamically favorable reactions. Appl Microbiol Biotechnol 2017; 101:2589-2601. [PMID: 27909745 PMCID: PMC5320011 DOI: 10.1007/s00253-016-8004-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 01/27/2023]
Abstract
Dechlorination patterns of three tetrachlorobenzene isomers, 1,2,3,4-, 1,2,3,5-, and 1,2,4,5-TeCB, were studied in anoxic microcosms derived from contaminated harbor sludge. The removal of doubly, singly, and un-flanked chlorine atoms was noted in 1,2,3,4- and 1,2,3,5-TeCB fed microcosms, whereas only singly flanked chlorine was removed in 1,2,4,5-TeCB microcosms. The thermodynamically more favorable reactions were selectively followed by the enriched cultures with di- and/or mono-chlorobenzene as the main end products of the reductive dechlorination of all three isomers. Based on quantitative PCR analysis targeting 16S rRNA genes of known organohalide-respiring bacteria, the growth of Dehalococcoides was found to be associated with the reductive dechlorination of all three isomers, while growth of Dehalobacter, another known TeCB dechlorinator, was only observed in one 1,2,3,5-TeCB enriched microcosm among biological triplicates. Numbers of Desulfitobacterium and Geobacter as facultative dechlorinators were rather stable suggesting that they were not (directly) involved in the observed TeCB dechlorination. Bacterial community profiling suggested bacteria belonging to the phylum Bacteroidetes and the order Clostridiales as well as sulfate-reducing members of the class Deltaproteobacteria as putative stimulating guilds that provide electron donor and/or organic cofactors to fastidious dechlorinators. Our results provide a better understanding of thermodynamically preferred TeCB dechlorinating pathways in harbor environments and microbial guilds enriched and active in anoxic TeCB dechlorinating microcosms.
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Affiliation(s)
- Yue Lu
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- College of Environmental Science and Engineering, Hunan University, Changsha, People's Republic of China
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | | | - Steffi Herrmann
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Danuta Cichocka
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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Atashgahi S, Lu Y, Ramiro-Garcia J, Peng P, Maphosa F, Sipkema D, Dejonghe W, Smidt H, Springael D. Geochemical Parameters and Reductive Dechlorination Determine Aerobic Cometabolic vs Aerobic Metabolic Vinyl Chloride Biodegradation at Oxic/Anoxic Interface of Hyporheic Zones. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:1626-1634. [PMID: 28004913 DOI: 10.1021/acs.est.6b05041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hyporheic zones mediate vinyl chloride (VC) biodegradation in groundwater discharging into surface waters. At the oxic/anoxic interface (OAI) of hyporheic zones subjected to redox oscillations, VC is degraded via coexisting aerobic ethenotrophic and anaerobic reductive dechlorination pathways. However, the identity of aerobic VC degradation pathways (cometabolic vs metabolic) and their interactions with reductive dechlorination in relation to riverbed sediment geochemistry remain ill-defined. We addressed this using microcosms containing OAI sediments incubated under fluctuating oxic/anoxic atmosphere. Under oxic atmosphere, aerobic metabolic VC oxidation was absent in sediments with high total organic carbon (TOC) and VC was reductively dechlorinated to ethene. Ethene was oxidized by ethenotrophs that can degrade VC cometabolically. Contrastingly, VC was metabolically oxidized by ethenotrophs in low-TOC sediments with low reductive dechlorination potential. Accordingly, enrichment and isolation of metabolic VC-oxidizing ethenotrophs was successful only from the low-TOC sediment. Sequence analysis of etnE genes from the microcosms as well phylogenetic typing of the isolates showed that ethenotrophs in the sediments were facultative anaerobic Proteobacteria capable of coping with OAI-associated redox fluctuations. Our results suggest that local sediment heterogeneity supports/selects divergent VC degradation processes at the OAI and that high reductive dechlorination potential suppresses development of aerobic metabolic VC oxidation potential.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
- KU Leuven , Division of Soil and Water Management, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
| | - Yue Lu
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peng Peng
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Farai Maphosa
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Springael
- KU Leuven , Division of Soil and Water Management, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
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Atashgahi S, Lu Y, Zheng Y, Saccenti E, Suarez-Diez M, Ramiro-Garcia J, Eisenmann H, Elsner M, J.M. Stams A, Springael D, Dejonghe W, Smidt H. Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol. Environ Microbiol 2016; 19:968-981. [DOI: 10.1111/1462-2920.13531] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/12/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Siavash Atashgahi
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Boeretang 200, 2400 Mol Belgium
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - Yue Lu
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Ying Zheng
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | | | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München-National Research Center for Environmental Health; Ingolstädter Landstrasse 1 Neuherberg D-85764 Germany
| | - Alfons J.M. Stams
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Centre of Biological Engineering; University of Minho; Braga Portugal
| | - Dirk Springael
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Boeretang 200, 2400 Mol Belgium
| | - Hauke Smidt
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
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Lee J, Im J, Kim U, Löffler FE. A Data Mining Approach to Predict In Situ Detoxification Potential of Chlorinated Ethenes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:5181-5188. [PMID: 27116079 DOI: 10.1021/acs.est.5b05090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Despite advances in physicochemical remediation technologies, in situ bioremediation treatment based on Dehalococcoides mccartyi (Dhc) reductive dechlorination activity remains a cornerstone approach to remedy sites impacted with chlorinated ethenes. Selecting the best remedial strategy is challenging due to uncertainties and complexity associated with biological and geochemical factors influencing Dhc activity. Guidelines based on measurable biogeochemical parameters have been proposed, but contemporary efforts fall short of meaningfully integrating the available information. Extensive groundwater monitoring data sets have been collected for decades, but have not been systematically analyzed and used for developing tools to guide decision-making. In the present study, geochemical and microbial data sets collected from 35 wells at five contaminated sites were used to demonstrate that a data mining prediction model using the classification and regression tree (CART) algorithm can provide improved predictive understanding of a site's reductive dechlorination potential. The CART model successfully predicted the 3-month-ahead reductive dechlorination potential with 75.8% and 69.5% true positive rate (i.e., sensitivity) for the training set and the test set, respectively. The machine learning algorithm ranked parameters by relative importance for assessing in situ reductive dechlorination potential. The abundance of Dhc 16S rRNA genes, CH4, Fe(2+), NO3(-), NO2(-), and SO4(2-) concentrations, total organic carbon (TOC) amounts, and oxidation-reduction potential (ORP) displayed significant correlations (p < 0.01) with dechlorination potential, with NO3(-), NO2(-), and Fe(2+) concentrations exhibiting precedence over other parameters. Contrary to prior efforts, the power of data mining approaches lies in the ability to discern synergetic effects between multiple parameters that affect reductive dechlorination activity. Overall, these findings demonstrate that data mining techniques (e.g., machine learning algorithms) effectively utilize groundwater monitoring data to derive predictive understanding of contaminant degradation, and thus have great potential for improving decision-making tools. A major need for realizing the predictive capabilities of data mining approaches is a curated, open-access, up-to-date and comprehensive collection of biogeochemical groundwater monitoring data.
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Affiliation(s)
- Jaejin Lee
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Jeongdae Im
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Ungtae Kim
- Department of Civil and Environmental Engineering, Cleveland State University , Cleveland, Ohio 44115, United States
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee , Knoxville, Tennessee 37996, United States
- Center for Environmental Biotechnology, University of Tennessee , Knoxville, Tennessee 37996, United States
- Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division , Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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27
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Epoxyalkane:Coenzyme M Transferase Gene Diversity and Distribution in Groundwater Samples from Chlorinated-Ethene-Contaminated Sites. Appl Environ Microbiol 2016; 82:3269-3279. [PMID: 27016563 DOI: 10.1128/aem.00673-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/17/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Epoxyalkane:coenzyme M transferase (EaCoMT) plays a critical role in the aerobic biodegradation and assimilation of alkenes, including ethene, propene, and the toxic chloroethene vinyl chloride (VC). To improve our understanding of the diversity and distribution of EaCoMT genes in the environment, novel EaCoMT-specific terminal-restriction fragment length polymorphism (T-RFLP) and nested-PCR methods were developed and applied to groundwater samples from six different contaminated sites. T-RFLP analysis revealed 192 different EaCoMT T-RFs. Using clone libraries, we retrieved 139 EaCoMT gene sequences from these samples. Phylogenetic analysis revealed that a majority of the sequences (78.4%) grouped with EaCoMT genes found in VC- and ethene-assimilating Mycobacterium strains and Nocardioides sp. strain JS614. The four most-abundant T-RFs were also matched with EaCoMT clone sequences related to Mycobacterium and Nocardioides strains. The remaining EaCoMT sequences clustered within two emergent EaCoMT gene subgroups represented by sequences found in propene-assimilating Gordonia rubripertincta strain B-276 and Xanthobacter autotrophicus strain Py2. EaCoMT gene abundance was positively correlated with VC and ethene concentrations at the sites studied. IMPORTANCE The EaCoMT gene plays a critical role in assimilation of short-chain alkenes, such as ethene, VC, and propene. An improved understanding of EaCoMT gene diversity and distribution is significant to the field of bioremediation in several ways. The expansion of the EaCoMT gene database and identification of incorrectly annotated EaCoMT genes currently in the database will facilitate improved design of environmental molecular diagnostic tools and high-throughput sequencing approaches for future bioremediation studies. Our results further suggest that potentially significant aerobic VC degraders in the environment are not well represented in pure culture. Future research should aim to isolate and characterize aerobic VC-degrading bacteria from these underrepresented groups.
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Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river. Sci Rep 2015; 5:17284. [PMID: 26607034 PMCID: PMC4660315 DOI: 10.1038/srep17284] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/28/2015] [Indexed: 01/18/2023] Open
Abstract
The impact of the installation of a technologically advanced wastewater treatment plant (WWTP) on the benthic microbial community of a vinyl chloride (VC) impacted eutrophic river was examined two years before, and three and four years after installation of the WWTP. Reduced dissolved organic carbon and increased dissolved oxygen concentrations in surface water and reduced total organic carbon and total nitrogen content in the sediment were recorded in the post-WWTP samples. Pyrosequencing of bacterial 16S rRNA gene fragments in sediment cores showed reduced relative abundance of heterotrophs and fermenters such as Chloroflexi and Firmicutes in more oxic and nutrient poor post-WWTP sediments. Similarly, quantitative PCR analysis showed 1–3 orders of magnitude reduction in phylogenetic and functional genes of sulphate reducers, denitrifiers, ammonium oxidizers, methanogens and VC-respiring Dehalococcoides mccartyi. In contrast, members of Proteobacteria adapted to nutrient-poor conditions were enriched in post-WWTP samples. This transition in the trophic state of the hyporheic sediments reduced but did not abolish the VC respiration potential in the post-WWTP sediments as an important hyporheic sediment function. Our results highlight effective nutrient load reduction and parallel microbial ecological state restoration of a human-stressed urban river as a result of installation of a WWTP.
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29
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Mattes TE, Jin YO, Livermore J, Pearl M, Liu X. Abundance and activity of vinyl chloride (VC)-oxidizing bacteria in a dilute groundwater VC plume biostimulated with oxygen and ethene. Appl Microbiol Biotechnol 2015; 99:9267-76. [DOI: 10.1007/s00253-015-6771-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 06/08/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022]
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Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing. Appl Microbiol Biotechnol 2015; 99:7735-43. [DOI: 10.1007/s00253-015-6606-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/09/2015] [Accepted: 04/12/2015] [Indexed: 10/23/2022]
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Sutton NB, Atashgahi S, van der Wal J, Wijn G, Grotenhuis T, Smidt H, Rijnaarts HHM. Microbial dynamics during and after in situ chemical oxidation of chlorinated solvents. GROUND WATER 2015; 53:261-270. [PMID: 24898385 DOI: 10.1111/gwat.12209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 03/13/2014] [Indexed: 06/03/2023]
Abstract
In situ chemical oxidation (ISCO) followed by a bioremediation step is increasingly being considered as an effective biphasic technology. Information on the impact of chemical oxidants on organohalide respiring bacteria (OHRB), however, is largely lacking. Therefore, we used quantitative PCR (qPCR) to monitor the abundance of OHRB (Dehalococcoides mccartyi, Dehalobacter, Geobacter, and Desulfitobacterium) and reductive dehalogenase genes (rdh; tceA, vcrA, and bvcA) at a field location contaminated with chlorinated solvents prior to and following treatment with sodium persulfate. Natural attenuation of the contaminants tetrachloroethene (PCE) and trichloroethene (TCE) observed prior to ISCO was confirmed by the distribution of OHRB and rdh genes. In wells impacted by persulfate treatment, a 1 to 3 order of magnitude reduction in the abundances of OHRB and complete absence of rdh genes was observed 21 days after ISCO. Groundwater acidification (pH<3) and increase in the oxidation reduction potential (>500 mV) due to persulfate treatment were significant and contributed to disruption of the microbial community. In wells only mildly impacted by persulfate, a slight stimulation of the microbial community was observed, with more than 1 order of magnitude increase in the abundance of Geobacter and Desulfitobacterium 36 days after ISCO. After six months, regeneration of the OHRB community occurred, however, neither D. mccartyi nor any rdh genes were observed, indicating extended disruption of biological natural attenuation (NA) capacity following persulfate treatment. For full restoration of biological NA activity, additional time may prove sufficient; otherwise addition electron donor amendment or bioaugmentation may be required.
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Affiliation(s)
- Nora B Sutton
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
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Schneidewind U, Haest PJ, Atashgahi S, Maphosa F, Hamonts K, Maesen M, Calderer M, Seuntjens P, Smidt H, Springael D, Dejonghe W. Kinetics of dechlorination by Dehalococcoides mccartyi using different carbon sources. JOURNAL OF CONTAMINANT HYDROLOGY 2014; 157:25-36. [PMID: 24275111 DOI: 10.1016/j.jconhyd.2013.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 10/05/2013] [Accepted: 10/18/2013] [Indexed: 06/02/2023]
Abstract
Stimulated anaerobic dechlorination is generally considered a valuable step for the remediation of aquifers polluted with chlorinated ethenes (CEs). Correct simulation and prediction of this process in situ, however, require good knowledge of the associated biological reactions. The aim of this study was to evaluate the dechlorination reaction in an aquifer contaminated with trichloroethene (TCE) and its daughter products, discharging into the Zenne River. Different carbon sources were used in batch cultures and these were related to the dechlorination reaction, together with the monitored biomarkers. Appropriate kinetic formulations were assessed. Reductive dechlorination of TCE took place only when external carbon sources were added to microcosms, and occurred concomitant with a pronounced increase in the Dehalococcoides mccartyi cell count as determined by 16S rRNA gene-targeted qPCR. This indicates that native dechlorinating bacteria are present in the aquifer of the Zenne site and that the oligotrophic nature of the aquifer prevents a complete degradation to ethene. The type of carbon source, the cell number of D. mccartyi or the reductive dehalogenase genes, however, did not unequivocally explain the observed differences in degradation rates or the extent of dechlorination. Neither first-order, Michaelis-Menten nor Monod kinetics could perfectly simulate the dechlorination reactions in TCE spiked microcosms. A sensitivity analysis indicated that the inclusion of donor limitation would not significantly enhance the simulations without a clear process understanding. Results point to the role of the supporting microbial community but it remains to be verified how the complexity of the microbial (inter)actions should be represented in a model framework.
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Affiliation(s)
- Uwe Schneidewind
- Flemish Institute for Technological Research (VITO), Environmental Modeling Unit, Boeretang 200, 2400 Mol, Belgium; Ghent University, Department of Soil Management, Coupure Links 653, 9000 Ghent, Belgium
| | - Pieter Jan Haest
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
| | - Siavash Atashgahi
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium; Wageningen University, Laboratory of Microbiology, 6703 HB Wageningen, The Netherlands; KU Leuven, Division Soil and Water Management, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Farai Maphosa
- Wageningen University, Laboratory of Microbiology, 6703 HB Wageningen, The Netherlands
| | - Kelly Hamonts
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
| | - Miranda Maesen
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
| | - Montse Calderer
- Manresa Technology Centre - CTM, Environmental Technology Area, Av. Bases de Manresa, 08242 Manresa, Spain
| | - Piet Seuntjens
- Flemish Institute for Technological Research (VITO), Environmental Modeling Unit, Boeretang 200, 2400 Mol, Belgium; Ghent University, Department of Soil Management, Coupure Links 653, 9000 Ghent, Belgium; University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Hauke Smidt
- Wageningen University, Laboratory of Microbiology, 6703 HB Wageningen, The Netherlands
| | - Dirk Springael
- KU Leuven, Division Soil and Water Management, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium.
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Evaluation of solid polymeric organic materials for use in bioreactive sediment capping to stimulate the degradation of chlorinated aliphatic hydrocarbons. Appl Microbiol Biotechnol 2013; 98:2255-66. [DOI: 10.1007/s00253-013-5138-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 07/15/2013] [Accepted: 07/17/2013] [Indexed: 10/26/2022]
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