1
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Hussain B, Chen JS, Huang SW, Tsai IS, Rathod J, Hsu BM. Underpinning the ecological response of mixed chlorinated volatile organic compounds (CVOCs) associated with contaminated and bioremediated groundwaters: A potential nexus of microbial community structure and function for strategizing efficient bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122215. [PMID: 37473850 DOI: 10.1016/j.envpol.2023.122215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/22/2023]
Abstract
Understanding the structure, dynamics, and functionality of microbial communities is essential for developing sustainable and effective bioremediation strategies, particularly for sites contaminated with mixed chlorinated volatile organic compounds (CVOCs), which can make the biodegradation process more complex and challenging. In this study, 16S rRNA amplicon sequencing revealed a significant change in microbial distribution in response to CVOCs contamination. The loss of sensitive taxa such as Proteobacteria and Acidobacteriota was observed, while CVOCs-resistant taxa such as Campilobacterota were found significantly enriched in contaminated sites. Additionally, varying abundances of crucial enzymes involved in the sequential biodegradation of CVOCs were expressed depending on the contamination level. Association analysis revealed that specific genera such as Sulfurospirillum, Azospira, Trichlorobacter, Acidiphilium, and Magnetospririllum could relatively survive under higher levels of CVOC contamination, whereas pH, ORP and temperature had a negative influence in their abundance and distribution. However, Dechloromonas, Thiobacillus, Pseudarcicella, Hydrogenophaga, and Sulfuritalea showed a negative relationship with CVOC contamination, highlighting their sensitivity towards CVOC contamination. These findings provide valuable insights into the relationship among ecological responses, the groundwater bacterial community, and their functionality in response to mixed CVOC contamination, offering a fundamental basis for developing effective and sustainable bioremediation strategies for CVOC-contaminated groundwater systems.
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Affiliation(s)
- Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Shih-Wei Huang
- Institute of Environmental Toxin and Emerging Contaminant, Cheng Shiu University, Kaohsiung, Taiwan; Center for Environmental Toxin and Emerging Contaminant Research, Cheng Shiu University, Kaohsiung, Taiwan
| | - I-Sen Tsai
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Doctoral Program in Science, Technology, Environment and Mathematics, National Chung Cheng University, Chiayi, Taiwan
| | - Jagat Rathod
- Department of Environmental Biotechnology, Gujarat Biotechnology University, Near Gujarat International Finance and Tec (GIFT)-City, Gandhinagar, Gujarat, India
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan.
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2
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Cheng YH, Chang SC, Lai YL, Hu CC. Microbiome reengineering by four environmental factors for the rapid biodegradation of trichloroethylene. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 326:116658. [PMID: 36399881 DOI: 10.1016/j.jenvman.2022.116658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Trichloroethylene (TCE) was once a widely applied industrial solvent, but is now an infamous contaminant in groundwater. Although anaerobic reductive dechlorination is considered a greener remediation approach, the accumulation of toxic intermediates, such as vinyl chloride (VC), and a longer remediation period are highly concerning. Biostimulation and bioaugmentation have been developed to solve these problems. The former method may not be effective, and the latter may introduce foreign genes. Here, we propose a new approach by applying environmental stresses to reshape the indigenous microbiome. In this study, by using the Taguchi method, the effects of heating, pH, salinity, and desiccation were systematically examined. The optimum conditions were defined as 50 °C, pH 9, 3.50% salinity (w/v), and 21% volumetric water content (θW). The top performing group, G7, can complete the conversion of 11.81 mg/L TCE into ethene in 3.0 days with a 1.23% abundance of Dehalococcoides mccartyi 195 (Dhc 195). Redundancy analysis confirmed that temperature and salinity were the predominant factors in reorganizing the microbiomes. The microbiome structure and its effectiveness can last for at least 90 d. The repetitive selection conditions and sustainable degradation capability strongly supported that microbiome reengineering is feasible for the rapid bioremediation of TCE-contaminated environmental matrices.
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Affiliation(s)
- Yu-Hsuan Cheng
- Department of Environmental Engineering, National Chung Hsing University, No. 145, Xingda Road, Taichung, 40227, Taiwan
| | - Shu-Chi Chang
- Department of Environmental Engineering, National Chung Hsing University, No. 145, Xingda Road, Taichung, 40227, Taiwan.
| | - Yan-Lin Lai
- Graduate Institute of Biotechnology, National Chung Hsing University, No. 145, Xingda Road, Taichung, 40227, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, No. 145, Xingda Road, Taichung, 40227, Taiwan
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3
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Pal Y, Mayilraj S, Krishnamurthi S. Uncovering the structure and function of specialist bacterial lineages in environments routinely exposed to explosives. Lett Appl Microbiol 2022; 75:1433-1448. [PMID: 35972393 DOI: 10.1111/lam.13810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 07/30/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
Environmental contamination by hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine (RDX), and Octahydro-1, 3, 5, 7-tetranitro-1, 3, 5, 7-tetrazocine (HMX), the two most widely used compounds for military operations, is a long-standing problem at the manufacturing and decommissioning plants. Since explosives contamination has previously been shown to favour the growth of specific bacterial communities, the present study attempts to identify the specialist bacterial communities and their potential functional and metabolic roles by using amplicon targeted and whole-metagenome sequencing approaches (WMS) in samples collected from two distinct explosives manufacturing sites. We hypothesize that the community structure and functional attributes of bacterial population are substantially altered by the concentration of explosives and physicochemical conditions. The results highlight the predominance of Planctomycetes in contrast to previous reports from similar habitats. The detailed phylogenetic analysis revealed the presence of OTU's related to bacterial members known for their explosives degradation. Further, the functional and metabolic analyses highlighted the abundance of putative genes and unidentified taxa possibly associated with xenobiotic biodegradation. Our findings suggest that microbial species capable of utilizing explosives as a carbon, energy, or electron source are favoured by certain selective pressures based on the prevailing physicochemical and geographical conditions.
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Affiliation(s)
- Yash Pal
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh, -160036
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh, -160036.,Director of Research, Bentoli AgriNutrition, India Pvt Ltd., 3F2, Third Floor, Front Block, Metro Tower, Building No.115, Poonamallee, High Road, Chennai, - 600 084
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh, -160036
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4
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Hudari MSB, Richnow H, Vogt C, Nijenhuis I. Mini-review: effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: a review. FEMS Microbiol Ecol 2022; 98:6638985. [PMID: 35810002 DOI: 10.1093/femsec/fiac081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This mini-review intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural re-populations after exposure to high temperature.
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Affiliation(s)
- Mohammad Sufian Bin Hudari
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Hans Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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5
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Moroz OM, Hnatush SO, Yavorska HV, Zvir GI, Tarabas OV. Influence of potassium dichromate on the reduction of sulfur, nitrate and nitrite ions by bacteria Desulfuromonas sp. REGULATORY MECHANISMS IN BIOSYSTEMS 2022. [DOI: 10.15421/022220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
This article presents the regularities of reduction of sulfur, nitrate and nitrite ions by sulfur reducing bacteria Desulfuromonas sp., which were isolated from the water of the man-made Yavorivske Lake (Lviv Region, Ukraine), under the influence of potassium dichromate. This bacteria in the process of anaerobic respiration can use and reduce different electron acceptors, such as sulfur, nitrates, nitrites, oxidized forms of heavy metals, in particular, hexavalent chromium. Technogenically altered ecotopes are characterized by complex pollution, so several electron acceptors are available to bacteria at the same time. Strains of microorganisms isolated from such ecotopes are adapted to unfavourable conditions and therefore have high biotechnological potential. The purpose of this work was to investigate the regularities of elemental sulfur, nitrate or nitrite ion usage by sulfidogenic bacteria of Desulfuromonas genus in conditions of simultaneous presence in the medium of another electron acceptor – Cr(VI), to establish the succession of reduction of electron acceptors by strains of these bacteria and to evaluate the efficiency of their possible application in technologies of complex purification of the environment from metal compounds and other inorganic toxicants. Bacteria were grown under anaerobic conditions in Kravtsov-Sorokin medium without SO42– and without Mohr’s salt for 10 days. To study the efficiency of sulfur, nitrate or nitrite ions’ reduction at simultaneous presence in the medium of Cr(VI) bacteria were sown in media with elemental sulfur, NaNO3, NaNO2 or K2Cr2O7 to final S0, NO3–, NO2–or Cr(VI) concentration in the medium of 3.47 (concentration of SO42– in medium of standard composition) or 1.74, 3.47, 5.21, 6.94 and 10.41 mM. Biomass was determined by the turbidimetric method, and the concentrations of nitrate, nitrite, ammonium ions, hydrogen sulfide, Cr(VI), Cr(ІІІ) in cultural liquid were determined spectrophotometrically. It has been established that Cr(VI) inhibits the biomass accumulation and hydrogen sulfide production by bacteria of Desulfuromonas sp. after simultaneous addition into the medium of 3.47 mM S0 and 1.74–10.41 mM Cr(VI). In the medium with the same initial content (3.47 mM) of S0 and Cr(VI) bacteria produced Cr(III) at concentrations 3.3–3.4 times higher than that of hydrogen sulfide. It has been shown that K2Cr2O7 inhibits biomass accumulation, nitrate ions’ reduction and ammonium ions’ production by bacteria after simultaneous addition into the medium of 3.47 mM NO3– and 1.74–10.41 mM Cr(VI) or 1.74–10.41 mM NO3– and 3.47 mM Cr(VI). In the medium with the same initial content (3.47 mM) of NO3– and Cr(VI) bacteria reduced up to 1.2 times more nitrate ions than Cr(VI) with the production of ammonium ions at concentrations the same times higher than those of Cr(III). It has been established that K2Cr2O7 inhibits biomass accumulation, nitrite ions’ reduction and ammonium ions’ production by bacteria after simultaneous addition into the medium of 3.47 mM NO2– and 1.74–10.41 mM Cr(VI) or 1.74–10.41 mM NO2– and 3.47 mM Cr(VI). In the medium with the same initial content of (3.47 mM) NO2– and Cr(VI) the reduction of Cr(VI) by bacteria was only slightly, up to 1.1 times, lower than the reduction of nitrite ions, almost the same concentrations of trivalent chromium and ammonium ions were detected in the cultural liquid. The processes of nitrate and nitride reduction carried out by bacteria of Desulfuromonas genus were revealed to be less sensitive to the negative influence of sodium dichromate, as compared with the process of sulfur reduction, because in the media with the same initial content (3.47 mM) of NO3– or NO2– and Cr(VI) bacteria produced 1.1–1.2 times more NH4+ than Cr(III), but in the medium with the same initial content (3.47 mM) of S0 and Cr(VI) ) bacteria produced over than three times more Cr(III) than hydrogen sulfide. Our data allow us to conclude that bacteria of Desulfuromonas genus, the investigated strains of which are adapted to high concentrations (up to 10.41 mM) of inorganic toxicants, play an important role in the geochemical cycles of sulfur, nitrogen and chromium in aquatic environments that have been under anthropogenic influence.
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6
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Xie L, Yoshida N, Ishii S, Meng L. Isolation and Polyphasic Characterization of Desulfuromonas versatilis sp. Nov., an Electrogenic Bacteria Capable of Versatile Metabolism Isolated from a Graphene Oxide-Reducing Enrichment Culture. Microorganisms 2021; 9:1953. [PMID: 34576847 PMCID: PMC8465243 DOI: 10.3390/microorganisms9091953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 01/11/2023] Open
Abstract
In this study, a novel electrogenic bacterium denoted as strain NIT-T3 of the genus Desulfuromonas was isolated from a graphene-oxide-reducing enrichment culture that was originally obtained from a mixture of seawater and coastal sand. Strain NIT-T3 utilized hydrogen and various organic acids as electron donors and exhibited respiration using electrodes, ferric iron, nitrate, and elemental sulfur. The strain contained C16:1ω7c, C16:0, and C15:0 as major fatty acids and MK-8, 9, and 7 as the major respiratory quinones. Strain NIT-T3 contained four 16S rRNA genes and showed 95.7% similarity to Desulfuromonasmichiganensis BB1T, the closest relative. The genome was 4.7 Mbp in size and encoded 76 putative c-type cytochromes, which included 6 unique c-type cytochromes (<40% identity) compared to those in the database. Based on the physiological and genetic uniqueness, and wide metabolic capability, strain NIT-T3 is proposed as a type strain of 'Desulfuromonas versatilis' sp. nov.
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Affiliation(s)
- Li Xie
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya 466-8555, Aichi, Japan; (L.X.); (L.M.)
| | - Naoko Yoshida
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya 466-8555, Aichi, Japan; (L.X.); (L.M.)
| | - Shun’ichi Ishii
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Kanagawa, Japan;
| | - Lingyu Meng
- Department of Civil Engineering, Nagoya Institute of Technology (Nitech), Nagoya 466-8555, Aichi, Japan; (L.X.); (L.M.)
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7
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Wu B, Liu F, Fang W, Yang T, Chen GH, He Z, Wang S. Microbial sulfur metabolism and environmental implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 778:146085. [PMID: 33714092 DOI: 10.1016/j.scitotenv.2021.146085] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.
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Affiliation(s)
- Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Feifei Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Wenwen Fang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Tony Yang
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou 510006, China.
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8
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Liang Y, Lu Q, Liang Z, Liu X, Fang W, Liang D, Kuang J, Qiu R, He Z, Wang S. Substrate-dependent competition and cooperation relationships between Geobacter and Dehalococcoides for their organohalide respiration. ISME COMMUNICATIONS 2021; 1:23. [PMID: 37938613 PMCID: PMC9723705 DOI: 10.1038/s43705-021-00025-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 05/19/2023]
Abstract
Obligate and non-obligate organohalide-respiring bacteria (OHRB) play central roles in the geochemical cycling and environmental bioremediation of organohalides. Their coexistence and interactions may provide functional redundancy and community stability to assure organohalide respiration efficiency but, at the same time, complicate isolation and characterization of specific OHRB. Here, we employed a growth rate/yield tradeoff strategy to enrich and isolate a rare non-obligate tetrachloroethene (PCE)-respiring Geobacter from a Dehalococcoides-predominant microcosm, providing experimental evidence for the rate/yield tradeoff theory in population selection. Surprisingly, further physiological and genomic characterizations, together with co-culture experiments, revealed three unique interactions (i.e., free competition, conditional competition and syntrophic cooperation) between Geobacter and Dehalococcoides for their respiration of PCE and polychlorinated biphenyls (PCBs), depending on both the feeding electron donors (acetate/H2 vs. propionate) and electron acceptors (PCE vs. PCBs). This study provides the first insight into substrate-dependent interactions between obligate and non-obligate OHRB, as well as a new strategy to isolate fastidious microorganisms, for better understanding of the geochemical cycling and bioremediation of organohalides.
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Affiliation(s)
- Yongyi Liang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Qihong Lu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Zhiwei Liang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Xiaokun Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Wenwen Fang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Dawei Liang
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Space & Environment, Beihang University, Beijing, China
| | - Jialiang Kuang
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Rongliang Qiu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, China.
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9
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Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 2020; 70:5972-6016. [DOI: 10.1099/ijsem.0.004213] [Citation(s) in RCA: 696] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class
Deltaproteobacteria
comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum
Proteobacteria
, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class
Deltaproteobacteria
encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the
Oligoflexia
. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes
Deltaproteobacteria
and
Oligoflexia
in the phylum
Proteobacteria
. Instead, the great majority of currently recognized members of the class
Deltaproteobacteria
are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class
Oligoflexia
represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum
Thermodesulfobacteria
, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the
Thermodesulfobacteria
rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.
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Affiliation(s)
- David W Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Maria Chuvochina
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Claus Pelikan
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | | | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Alexander Loy
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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10
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Summer D, Schöftner P, Wimmer B, Pastar M, Kostic T, Sessitsch A, Gerzabek MH, Reichenauer TG. Synergistic effects of microbial anaerobic dechlorination of perchloroethene and nano zero-valent iron (nZVI) - A lysimeter experiment. N Biotechnol 2020; 57:34-44. [PMID: 32247067 DOI: 10.1016/j.nbt.2020.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 02/20/2020] [Accepted: 02/29/2020] [Indexed: 12/22/2022]
Abstract
Perchloroethene (PCE) is a hazardous and persistent groundwater pollutant. Both treatment with nanoscaled zero-valent iron (nZVI) and biological degradation by bacteria have downsides. Distribution of nZVI underground is difficult and a high percentage of injected nZVI is consumed by anaerobic corrosion, forming H2 rather than being available for PCE dechlorination. On the other hand, microbial PCE degradation can suffer from the absence of H2. This can cause the accumulation of the hazardous metabolites cis-1,2-dichloroethene (DCE) or vinylchloride (VC). The combination of chemical and biological PCE degradation is a promising approach to overcome the disadvantages of each method alone. In this lysimeter study, artificial aquifers were created to test the influence of nZVI on anaerobic microbial PCE dechlorination by a commercially available culture containing Dehalococcoides spp. under field-like conditions. The effect of the combined treatment was investigated with molasses as an additional electron source and after cessation of molasses addition. The combination of nZVI and the Dehalococcoides spp. containing culture led to a PCE discharge in the lysimeter outflow that was 4.7 times smaller than that with nZVI and 1.6 times smaller than with bacterial treatment. Moreover, fully dechlorinated end-products showed an 11-fold increase compared to nZVI and a 4.2-fold increase compared to the microbial culture. The addition of nZVI to the microbial culture also decreased the accumulation of hazardous metabolites by 1.7 (cis-DCE) and 1.2 fold (VC). The stimulatory effect of nZVI on microbial degradation was most obvious after the addition of molasses was stopped.
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Affiliation(s)
- Dorothea Summer
- Center of Health & Bioresources, Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln a.d. Donau, Austria.
| | - Philipp Schöftner
- Center of Health & Bioresources, Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln a.d. Donau, Austria.
| | - Bernhard Wimmer
- Quality Management, AIT Austrian Institute of Technology GmbH, 2444, Seibersdorf, Austria.
| | - Milica Pastar
- Center of Health & Bioresources, Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln a.d. Donau, Austria
| | - Tanja Kostic
- Center of Health & Bioresources, Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln a.d. Donau, Austria
| | - Angela Sessitsch
- Center of Health & Bioresources, Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln a.d. Donau, Austria
| | - Martin Hubert Gerzabek
- Department of Forestry and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, Peter-Jordan-Strasse 82, 1190, Vienna, Austria.
| | - Thomas Gerhard Reichenauer
- Center of Health & Bioresources, Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430, Tulln a.d. Donau, Austria.
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11
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Chen WY, Wu JH, Chu SC. Deciphering microbiomes in anaerobic reactors with superior trichloroethylene dechlorination performance at low pH conditions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 257:113567. [PMID: 31733964 DOI: 10.1016/j.envpol.2019.113567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/30/2019] [Accepted: 11/02/2019] [Indexed: 06/10/2023]
Abstract
Different pH conditions have been demonstrated to affect the activities of dechlorinating populations participating in the successive dechlorination of trichloroethylene to ethylene. However, the mechanism of the effect of pH conditions on the assembly of dechlorinating populations and their relations to the structure, function, and dynamics of the microbiome are unclear. In this study, we evaluated the effects of pH on microbiomes assembled in anaerobic trichloroethylene-dechlorinating reactors under neutral (pH 7.2), acidic (pH 6.2), and alkaline (pH 8.2) conditions. The results revealed that among the reactors, the acidic reactor had the highest efficiency for dechlorination without accumulation of dechlorinated metabolites, even at high loading rates. The results of high-throughput sequencing of the 16S rRNA gene indicated that the microbiomes in the 3 reactors underwent varied dynamic succession. The acidic reactor harbored a higher degree of complex microbes, dechlorinator diversity, and abundance of the Victoria subgroup of Dehalococcoides (1.2 ± 0.1 × 106 cell/mL), which were approximately 10-102-fold higher than those at neutral and alkaline conditions. The pH settings altered species-species connectivity and complexity of microbial interaction networks, with more commensal interactions in the dechlorinators of the acidic reactor. As predicted, abundances of several functional gene categories were in strong linearity with pH values, and the microbiome possessed significantly more abundant functions in the acidic reactor (P < 0.001), such as potentially stimulating hydrogen production, cobalamin synthesis, cobalt transport, transport and metabolism of amino acids and secondary metabolites, cell motility, and transcription. All results of microbiomic analyses consistently revealed the observed superior dechlorination process and suggested an association of the reductive dechlorination process with the pH-dependent microbiome. The results of this study provide a new insight into the trichloroethylene dechlorination with regards to pH, and they will be useful for improving bioremediation and management of trichloroethylene-contaminated sites.
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Affiliation(s)
- Wei-Yu Chen
- Department of Environmental Engineering, National Cheng Kung University, Taiwan
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Taiwan.
| | - Shun-Chieh Chu
- Environmental Forensic Department, Sustainable Environment Technology Division, Green Energy and Environment Research Labs (GEL), Industrial Technology Research Institute, Taiwan
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12
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Lin XQ, Li ZL, Zhu YY, Chen F, Liang B, Nan J, Wang AJ. Palladium/iron nanoparticles stimulate tetrabromobisphenol a microbial reductive debromination and further mineralization in sediment. ENVIRONMENT INTERNATIONAL 2020; 135:105353. [PMID: 31830727 DOI: 10.1016/j.envint.2019.105353] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
Tetrabromobisphenol A (TBBPA) has aroused serious pollution in surface sediment. To date, whether and how iron-based nanoparticles could stimulate TBBPA in situ anaerobic biodegradation in sediment remains poorly understood. In this study, the distinctly enhanced TBBPA degradation activity with the rate constant k improved 4.7 times by fed with Pd/Fe nanoparticles (0.412 g L-1 dosage, 0.5 wt% Pd loading) was observed. TBBPA degradation first went through reductive dehalogenation with bisphenol A (BPA) as the metabolites, and after the addition of Pd/Fe nanoparticles, BPA was further degraded to 4-(allene)phenol and 2,2-bis(4-hydroxyphenyl) propanoic acid via UPLC-QTOF-MS analysis, suggesting the complete detoxification potential. By the addition of Pd/Fe nanoparticles, the large amount of H2 production (560 times higher) and the significant inhibition of methane generation facilitated the metabolism of potential reductive dehalogenators (Desulfovibrio, Clostridium, etc.), demonstrated by their increased ecological abundance and the tighter cooperative interrelations between each other. Meanwhile, the addition of Pd/Fe nanoparticles largely promoted the ecological abundance of Fe(III) reducing and aromatics degrading bacteria (Bacillus, Cryptanaerobacter, etc.), resulting in BPA further degradation. The bacterial ecological network further revealed that the potential BPA degrading bacteria shared the more positive interactions with the potential dehalogenators in the presence of Pd/Fe nanoparticles. The study firstly revealed the addition of Pd/Fe nanoparticles obviously enhanced the respiratory metabolic activities and cooperative interrelations of reductive dehalogenators and BPA degraders, which gives suggestions for in situ remediation and detoxification of BFRs in contaminated sediment.
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Affiliation(s)
- Xiao-Qiu Lin
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090 China
| | - Zhi-Ling Li
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090 China.
| | - Ying-Ying Zhu
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090 China
| | - Fan Chen
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090 China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jun Nan
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090 China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090 China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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13
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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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14
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Chen F, Liang B, Li ZL, Yang JQ, Huang C, Lyu M, Yuan Y, Nan J, Wang AJ. Bioelectrochemical assisted dechlorination of tetrachloroethylene and 1,2-dichloroethane by acclimation of anaerobic sludge. CHEMOSPHERE 2019; 227:514-521. [PMID: 31004818 DOI: 10.1016/j.chemosphere.2019.04.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/06/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Volatile chlorinated hydrocarbons (VCHs) are often found as a type of persistent and ubiquitous contaminant in groundwater. The feasibility, characteristics and microbial mechanism of acclimation of biodiversity-rich inoculation source for bioelectrochemical stimulated VCH dechlorination remain poorly understood. Here, the superior bioelectrochemical catalytic activities were observed for tetrachloroethylene (0.26 mM d-1) and 1,2-dichloroethane (2.20 mM d-1) dechlorination in anaerobic sludge-acclimated biocathodes with an optimal potential of -0.5 V, averaging 1.60-2.71 times higher than those reported in previous works on biocathodes. When the cathode was applied as the sole electron donor for dechlorination, columbic efficiencies reached the values greater than 80%. Tetrachloroethylene dechlorination showed a metabolic pathway with cis-1,2-dichloroethene as the main product, whereas 1,2-dichloroethane was dechlorinated entirely to the nontoxic ethene. The cathodic biofilms were highly abundant with the dechlorination and electro-active genera, while significant bacterial consortium variation was observed in response to the different VCH types and changes in cathodic potential. Bacillus, Pseudomonas and Lactococcus were mostly enriched for tetrachloroethylene dechlorination, and pceA, tceA and omcX were highly expressed. Geobacter was the most predominant during 1,2-dichloroethane dechlorination with rdhA, tceA and omcX highly expressed. In addition, although the impact of cathodic potentials was weaker than that of VCH types, the lower cathodic potentials, the more abundant of the electrode respiring populations and the higher expression of extracellular electron transfer related gene. This study demonstrated the great potential of acclimation of anaerobic sludge by electrical stimulation for accelerating VCH remediations and gave insights into its working molecular mechanisms.
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Affiliation(s)
- Fan Chen
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Zhi-Ling Li
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Jia-Qi Yang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Cong Huang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Miao Lyu
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Ye Yuan
- School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, 224051, China
| | - Jun Nan
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Ai-Jie Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, 150090, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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15
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Lefevre E, Redfern L, Cooper EM, Stapleton HM, Gunsch CK. Acetate promotes microbial reductive debromination of tetrabromobisphenol A during the startup phase of anaerobic wastewater sludge bioreactors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 656:959-968. [PMID: 30625682 PMCID: PMC6481660 DOI: 10.1016/j.scitotenv.2018.11.403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 05/15/2023]
Abstract
The detection of increasing concentrations of tetrabromobisphenol A (TBBPA) in wastewater treatment plants is raising concerns as TBBPA has been identified as a potentially toxic flame retardant. The objectives of this study were to evaluate the effect of acetate biostimulation on TBBPA microbial reductive debromination, and the response of anaerobic sludge associated microbial communities repeatedly exposed to TBBPA. Results indicate that the bulk of the microbial community did not experience significant shifts as a result of TBBPA exposure, and that only a small fraction of the community responded to the presence of TBBPA. Taxa most likely responsible for TBBPA transformation affiliated to Clostridiales and the wastewater sludge group Blvii28. The biostimulating effect of acetate was only observed during reactor startup, when acetogenesis was likely not yet occurring. However, when acetate likely started to be microbially generated in the reactor, acetate addition resulted in a slight but significant inhibiting effect on TBBPA transformation. A significant increase of hydrogenotrophic methanogens in the TBBPA-spiked reactor overtime implies that TBBPA degraders were not in direct competition with methanogens for H2. These results strongly suggest that TBBPA degrading taxa might have been primarily using acetate as an electron donor for the reductive debromination of TBBPA.
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Affiliation(s)
- Emilie Lefevre
- Department of Civil and Environmental Engineering, Duke University, Hudson Hall, Durham, NC 27708, USA
| | - Lauren Redfern
- Department of Civil and Environmental Engineering, Duke University, Hudson Hall, Durham, NC 27708, USA
| | - Ellen M Cooper
- Nicholas School of the Environment, Duke University, 9 Circuit Drive, Durham, NC 27710, USA
| | - Heather M Stapleton
- Nicholas School of the Environment, Duke University, 9 Circuit Drive, Durham, NC 27710, USA
| | - Claudia K Gunsch
- Department of Civil and Environmental Engineering, Duke University, Hudson Hall, Durham, NC 27708, USA.
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16
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Türkowsky D, Jehmlich N, Diekert G, Adrian L, von Bergen M, Goris T. An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research. FEMS Microbiol Ecol 2019; 94:4830072. [PMID: 29390082 DOI: 10.1093/femsec/fiy013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/24/2018] [Indexed: 02/06/2023] Open
Abstract
Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide-respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different 'omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB. Despite the availability of a couple of proteomic and transcriptomic datasets dealing with OHRB, such approaches are currently not covered in reviews. Therefore, we here present an integrative and comparative overview of omics studies performed with the OHRB Sulfurospirillum multivorans, Dehalococcoides mccartyi, Desulfitobacterium spp. and Dehalobacter restrictus. Genes, transcripts, proteins and the regulatory and biochemical processes involved in OHR are discussed, and a comprehensive view on the unusual metabolism of D. mccartyi, which is one of the few bacteria possibly using a quinone-independent respiratory chain, is provided. Several 'omics'-derived theories on OHRB, e.g. the organohalide-respiratory chain, hydrogen metabolism, corrinoid biosynthesis or one-carbon metabolism are critically discussed on the basis of this integrative approach.
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Affiliation(s)
- Dominique Türkowsky
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
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17
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Wan J, Chen C, Chen J, Miao Q, Liu Y, Ye J, Chen K, Jin Y, Tang X, Shen C. Acceleration of perchloroethylene dechlorination by extracellular secretions from Microbacterium in a mixed culture containing Desulfitobacterium. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 245:651-657. [PMID: 30481679 DOI: 10.1016/j.envpol.2018.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/23/2018] [Accepted: 10/01/2018] [Indexed: 06/09/2023]
Abstract
The study was conducted to demonstrate the influence of extracellular secretions from Microbacterium on the reductive dechlorination of tetrachloroethene (PCE). A series of mixed cultures were established from a paddy soil sample. In the mixed cultures amended with extracellular secretions from Microbacterium, PCE was rapidly and completely converted into cis-1,2-dichloroethene (cis-DCE) and trans-1,2-dichloroethene (trans-DCE) within 40 days. The unamended mixed cultures showed weak signs of dechlorination after a pronounced lag phase, and trichloroethene (TCE) was accumulated as a major end product. This result means that amendment with extracellular secretions from Microbacterium shortened the lag phase, increased the dechlorination velocity and promoted the production of less-chlorinated chloroethene. The results were corroborated by defined subculture experiments, which proved that microorganisms from unamended mixed cultures could also be stimulated by extracellular secretions from Microbacterium. Desulfitobacterium was identified as the main dechlorinating population in all mixed cultures by direct PCR. Additionally, the 16S rRNA gene copies of Desulfitobacterium increased by one or two orders of magnitude with PCE dechlorination, which provided corroborative evidence for the identification result. The volatile fatty acids were monitored, and most interestingly, a close association between propionate oxidation and dechlorination was found, which has rarely been mentioned before. It was assumed that the oxidation of propionate provided hydrogen for dechlorination, while dechlorination facilitated the shift of the reaction toward propionate oxidation by reducing the partial pressure of hydrogen.
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Affiliation(s)
- Jixing Wan
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Chen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Department of Civil and Environmental Engineering, National University of Singapore, Singapore
| | - Jingwen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Qianyu Miao
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yindong Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Junxiang Ye
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Kezhen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yiying Jin
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xianjin Tang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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18
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Kawabe Y, Komai T. A Case Study of Natural Attenuation of Chlorinated Solvents Under Unstable Groundwater Conditions in Takahata, Japan. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2019; 102:280-286. [PMID: 30666385 DOI: 10.1007/s00128-019-02546-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/09/2019] [Indexed: 06/09/2023]
Abstract
The natural attenuation behavior of chlorinated solvents and their risks to human health at a contaminated groundwater site in Takahata, Japan, were investigated. It was found that volatile organic compound (VOC) concentrations gradually decreased via two attenuation mechanisms, namely dilution and biodegradation. It was estimated that the VOC concentrations will be below the Japanese limits within 30 years after stopping the active remediation in 2003, which suggests that there is a high possibility that monitored natural attenuation can be adopted as the clean-up method at this contaminated site. The risk levels of VOCs at the present time are much lower than those at the time when the contamination was discovered. Vinyl chloride still presents a risk in some wells, and there were occasional unexpected increases in the risk levels of tetrachloroethylene, trichloroethylene, and cis-1,2-dichloloethylene, which means that continuous monitoring of the groundwater is necessary for forecasting risk levels.
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Affiliation(s)
- Yoshishige Kawabe
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, 3058567, Japan.
| | - Takeshi Komai
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, 3058567, Japan
- Graduate School of Environmental Studies Tohoku University, 6-6-20, Aoba, Aramaki, Aoba-ku, Sendai, 9808579, Japan
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19
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Herrero J, Puigserver D, Nijenhuis I, Kuntze K, Carmona JM. Combined use of ISCR and biostimulation techniques in incomplete processes of reductive dehalogenation of chlorinated solvents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 648:819-829. [PMID: 30138882 DOI: 10.1016/j.scitotenv.2018.08.184] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/16/2018] [Accepted: 08/16/2018] [Indexed: 05/20/2023]
Affiliation(s)
- Jofre Herrero
- Department of Minerology, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona, Carrer Martí Franquès SN, Barcelona, Spain..
| | - Diana Puigserver
- Department of Minerology, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona, Carrer Martí Franquès SN, Barcelona, Spain
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry (ISOBIO), UFZ Centre for Environmental Research Leipzig-Halle, Permoserstr. 15, 04318 Leipzig, Germany
| | - Kevin Kuntze
- Department of Isotope Biogeochemistry (ISOBIO), UFZ Centre for Environmental Research Leipzig-Halle, Permoserstr. 15, 04318 Leipzig, Germany
| | - José M Carmona
- Department of Minerology, Petrology and Applied Geology, Faculty of Earth Sciences, University of Barcelona, Carrer Martí Franquès SN, Barcelona, Spain
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20
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Chen F, Li Z, Yang J, Liang B, Huang C, Cai W, Nan J, Wang A. Electron Fluxes in Biocathode Bioelectrochemical Systems Performing Dechlorination of Chlorinated Aliphatic Hydrocarbons. Front Microbiol 2018; 9:2306. [PMID: 30323798 PMCID: PMC6173060 DOI: 10.3389/fmicb.2018.02306] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/10/2018] [Indexed: 11/13/2022] Open
Abstract
Bioelectrochemical systems (BESs) are regarded as a promising approach for the enhanced dechlorination of chlorinated aliphatic hydrocarbons (CAHs). However, the electron distribution and transfer considering dechlorination, methanogenesis, and other bioprocesses in these systems are little understood. This study investigated the electron fluxes in biocathode BES performing dechlorination of three typical CAHs, 1,1,2,2-tetrachloroethene (PCE), 1,1,2-trichloroethene (TCE) and 1,2-dichloroethane (1,2-DCA). Anaerobic sludge was inoculated to cathode and biocathode was acclimated by the direct acclimation and selection. The constructed biocathode at −0.26 V had significantly higher dechlorination efficiency (E24h > 99.0%) than the opened circuit (E24h of 17.2–27.5%) and abiotic cathode (E24h of 5.5–10.8%), respectively. Cyclic voltammetry analysis demonstrated the enhanced cathodic current and the positive shift of onset potential in the cathodic biofilm. Under autotrophic conditions with electrons from the cathode as sole energy source (columbic efficiencies of 80.4–90.0%) and bicarbonate as sole carbon source, CAHs dechlorination efficiencies were still maintained at 85.0 ± 2.0%, 91.4 ± 1.8%, and 84.9 ± 3.1% for PCE, TCE, and 1,2-DCA, respectively. Cis-1,2-dichloroethene was the final product for PCE and TCE, while 1,2-DCA went through a different dechlorination pathway with the non-toxic ethene as the final metabolite. Methane was the main by-product of the heterotrophic biocathode, and methane production could be enhanced to some extent by electrochemical stimulation. The various electron fluxes originating from the cathode and oxidation of organic substrates might be responsible for the enhanced CAHs dechlorination, while methane generation and bacterial growth would probably reduce the fraction of electrons provided for CAH dechlorination. The study deals with the dechlorination and competitive bioprocesses in CAH-dechlorinating biocathodes with a focus on electron fluxes.
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Affiliation(s)
- Fan Chen
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Jiaqi Yang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Cong Huang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Weiwei Cai
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Jun Nan
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin, China.,Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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Němeček J, Steinová J, Špánek R, Pluhař T, Pokorný P, Najmanová P, Knytl V, Černík M. Thermally enhanced in situ bioremediation of groundwater contaminated with chlorinated solvents - A field test. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 622-623:743-755. [PMID: 29223901 DOI: 10.1016/j.scitotenv.2017.12.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/04/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
In situ bioremediation (ISB) using reductive dechlorination is a widely accepted but relatively slow approach compared to other technologies for the treatment of groundwater contaminated by chlorinated ethenes (CVOCs). Due to the known positive kinetic effect on microbial metabolism, thermal enhancement may be a viable means of accelerating ISB. We tested thermally enhanced ISB in aquifers situated in sandy saprolite and underlying fractured granite. The system comprised pumping, heating and subsequent injection of contaminated groundwater aiming at an aquifer temperature of 20-30°C. A fermentable substrate (whey) was injected in separate batches. The test was monitored using hydrochemical and molecular tools (qPCR and NGS). The addition of the substrate and increase in temperature resulted in a rapid increase in the abundance of reductive dechlorinators (e.g., Dehalococcoides mccartyi, Dehalobacter sp. and functional genes vcrA and bvcA) and a strong increase in CVOC degradation. On day 34, the CVOC concentrations decreased by 87% to 96% in groundwater from the wells most affected by the heating and substrate. On day 103, the CVOC concentrations were below the LOQ resulting in degradation half-lives of 5 to 6days. Neither an increase in biomarkers nor a distinct decrease in the CVOC concentrations was observed in a deep well affected by the heating but not by the substrate. NGS analysis detected Chloroflexi dechlorinating genera (Dehalogenimonas and GIF9 and MSBL5 clades) and other genera capable of anaerobic metabolic degradation of CVOCs. Of these, bacteria of the genera Acetobacterium, Desulfomonile, Geobacter, Sulfurospirillum, Methanosarcina and Methanobacterium were stimulated by the substrate and heating. In contrast, groundwater from the deep well (affected by heating only) hosted representatives of aerobic metabolic and aerobic cometabolic CVOC degraders. The test results document that heating of the treated aquifer significantly accelerated the treatment process but only in the case of an abundant substrate.
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Affiliation(s)
- Jan Němeček
- ENACON s.r.o., Krčská 16, CZ-140 00 Prague 4, Czech Republic; Technical University of Liberec, Studentská 2, CZ-461 17 Liberec, Czech Republic.
| | - Jana Steinová
- Technical University of Liberec, Studentská 2, CZ-461 17 Liberec, Czech Republic
| | - Roman Špánek
- Technical University of Liberec, Studentská 2, CZ-461 17 Liberec, Czech Republic
| | - Tomáš Pluhař
- Technical University of Liberec, Studentská 2, CZ-461 17 Liberec, Czech Republic
| | - Petr Pokorný
- ENACON s.r.o., Krčská 16, CZ-140 00 Prague 4, Czech Republic
| | - Petra Najmanová
- DEKONTA a.s., Volutová 2523, CZ-158 00 Prague 5, Czech Republic
| | - Vladislav Knytl
- DEKONTA a.s., Volutová 2523, CZ-158 00 Prague 5, Czech Republic
| | - Miroslav Černík
- Technical University of Liberec, Studentská 2, CZ-461 17 Liberec, Czech Republic
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22
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Atashgahi S, Häggblom MM, Smidt H. Organohalide respiration in pristine environments: implications for the natural halogen cycle. Environ Microbiol 2017; 20:934-948. [PMID: 29215190 DOI: 10.1111/1462-2920.14016] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/29/2017] [Accepted: 12/01/2017] [Indexed: 11/29/2022]
Abstract
Halogenated organic compounds, also termed organohalogens, were initially considered to be of almost exclusively anthropogenic origin. However, over 5000 naturally synthesized organohalogens are known today. This has also fuelled the hypothesis that the natural and ancient origin of organohalogens could have primed development of metabolic machineries for their degradation, especially in microorganisms. Among these, a special group of anaerobic microorganisms was discovered that could conserve energy by reducing organohalogens as terminal electron acceptor in a process termed organohalide respiration. Originally discovered in a quest for biodegradation of anthropogenic organohalogens, these organohalide-respiring bacteria (OHRB) were soon found to reside in pristine environments, such as the deep subseafloor and Arctic tundra soil with limited/no connections to anthropogenic activities. As such, accumulating evidence suggests an important role of OHRB in local natural halogen cycles, presumably taking advantage of natural organohalogens. In this minireview, we integrate current knowledge regarding the natural origin and occurrence of industrially important organohalogens and the evolution and spread of OHRB, and describe potential implications for natural halogen and carbon cycles.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
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Moreno-Medina CU, Poggi-Varaldo HM, Breton-Deval L, Rinderknecht-Seijas N. Effect of sudden addition of PCE and bioreactor coupling to ZVI filters on performance of fluidized bed bioreactors operated in simultaneous electron acceptor modes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:25534-25549. [PMID: 27498752 DOI: 10.1007/s11356-016-7275-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 07/18/2016] [Indexed: 06/06/2023]
Abstract
The present work evaluated the effects of (i) feeding a water contaminated with 80 mg/L PCE to bioreactors seeded with inoculum not acclimated to PCE, (ii) coupling ZVI side filters to bioreactors, and (iii) working in different biological regimes, i.e., simultaneous methanogenic aeration and simultaneous methanogenic-denitrifying regimes, on fluidized bed bioreactor performance. Simultaneous electron acceptors refer to the simultaneous presence of two compounds operating as final electron acceptors in the biological respiratory chain (e.g., use of either O2 or NO3- in combination with a methanogenic environment) in a bioreactor or environmental niche. Four lab-scale, mesophilic, fluidized bed bioreactors (bioreactors) were implemented. Two bioreactors were operated as simultaneous methanogenic-denitrifying (MD) units, whereas the other two were operated in partially aerated methanogenic (PAM) mode. In the first period, all bioreactors received a wastewater with 1 g chemical oxygen demand of methanol per liter (COD-methanol/L). In a second period, all the bioreactors received the wastewater plus 80 mg perchloroethylene (PCE)/L; at the start of period 2, one MD and one PAM were coupled to side sand-zero valent iron filters (ZVI). All bioreactors were inoculated with a microbial consortium not acclimated to PCE. In this work, the performance of the full period 1 and the first 60 days of period 2 is reported and discussed. The COD removal efficiency and the nitrate removal efficiency of the bioreactors essentially did not change between period 1 and period 2, i.e., upon PCE addition. On the contrary, specific methanogenic activity in PAM bioreactors (both with and without coupled ZVI filter) significantly decreased. This was consistent with a sharp fall of methane productivity in those bioreactors in period 2. During period 2, PCE removals in the range 86 to 97 % were generally observed; the highest removal corresponded to PAM bioreactors along with the highest dehalogenation efficiency (94 %). Principal component analysis as well as cluster analysis confirmed the trends mentioned above, i.e., the better performance of PAM over MD, and the unexpected no effect of the ZVI side filters on PCE removal and dehalogenation efficiencies. To the best of our knowledge, this is the first report on the combined treatment ZVI-biological of a water polluted with PCE, where the biological operation relied on simultaneous electron acceptors.
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Affiliation(s)
- C U Moreno-Medina
- Environmental Biotechnology and Renewable Energies R&D Group, Department of Biotechnology and Bioengineering, CINVESTAV del I.P.N, P.O. Box 14-740, Ciudad de Mexico, Mexico
| | - Hector M Poggi-Varaldo
- Environmental Biotechnology and Renewable Energies R&D Group, Department of Biotechnology and Bioengineering, CINVESTAV del I.P.N, P.O. Box 14-740, Ciudad de Mexico, Mexico.
| | - L Breton-Deval
- Environmental Biotechnology and Renewable Energies R&D Group, Department of Biotechnology and Bioengineering, CINVESTAV del I.P.N, P.O. Box 14-740, Ciudad de Mexico, Mexico
| | - N Rinderknecht-Seijas
- Escuela Superior de Ingeniería Química y Extractivas del I.P.N, Ciudad de Mexico, Mexico
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Xu Y, He Y, Tang X, Brookes PC, Xu J. Reconstruction of microbial community structures as evidences for soil redox coupled reductive dechlorination of PCP in a mangrove soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 596-597:147-157. [PMID: 28431359 DOI: 10.1016/j.scitotenv.2017.04.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/07/2017] [Accepted: 04/09/2017] [Indexed: 05/26/2023]
Abstract
The aim was to investigate the influence of pentachlorophenol (PCP) on the soil microbial communities and the coupled mechanism between PCP reductive dechlorination and soil redox under anaerobic condition. Accordingly, a slurry incubation experiment was carried out in which bacterial and archaeal communities were detected by MiSeq amplicon sequencing. The original microbial community balance was gradually disrupted and new microbial structure was reconstructed subsequently through self-regulation and acclimation during PCP transformation, coupling with the changes of soil biogeochemical redox dynamics. The phylum Bacteroidetes predominated during the earlier PCP dechlorination period and then was progressively replaced by Proteobacteria and Firmicutes groups when PCP was mostly transformed into 2,3,4,5-TeCP and 3,4,5-TCP. Heatmap and hierarchical cluster analysis revealed the Clostridium-like, Geobacter-like and Dehalococcoides-like organisms enriched concurrently during PCP reductive dechlorination processes. The relative abundance changes of the redox-active microorganisms, together with their relevance to the corresponding biogeochemical redox processes, showed that PCP dechlorination, Fe(III) and SO42- reduction, as well as methanogenesis were coupled terminal electron accepting processes. The combined analysis of the microbial function, the affinity for substrates (H2 and acetate) and the sensitivity for PCP toxicity by microorganisms might explain why electron transport chain has changed in soil biogeochemical redox process. Our study offers a comprehensive description of the impact of PCP on the soil microbial community structures, which could be very useful for understanding the regulation of soil nutrient and energy transfer during biogeochemical cycling processes in soils with significant inputs of exogenous pollutants.
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Affiliation(s)
- Yan Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China.
| | - Xianjin Tang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Philip C Brookes
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou 310058, China
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25
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Němeček J, Dolinová I, Macháčková J, Špánek R, Ševců A, Lederer T, Černík M. Stratification of chlorinated ethenes natural attenuation in an alluvial aquifer assessed by hydrochemical and biomolecular tools. CHEMOSPHERE 2017; 184:1157-1167. [PMID: 28672697 DOI: 10.1016/j.chemosphere.2017.06.100] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 06/07/2023]
Abstract
Biomolecular and hydrochemical tools were used to evaluate natural attenuation of chlorinated ethenes in a Quaternary alluvial aquifer located close to a historical source of large-scale tetrachloroethylene (PCE) contamination. Distinct stratification of redox zones was observed, despite the aquifer's small thickness (2.8 m). The uppermost zone of the target aquifer was characterised by oxygen- and nitrate-reducing conditions, with mixed iron- to sulphate-reducing conditions dominant in the lower zone, along with indications of methanogenesis. Natural attenuation of PCE was strongly influenced by redox heterogeneity, while higher levels of PCE degradation coincided with iron- to sulphate reducing conditions. Next generation sequencing of the middle and/or lower zones identified anaerobic bacteria (Firmicutes, Chloroflexi, Actinobacteria and Bacteroidetes) associated with reductive dechlorination. The relative abundance of dechlorinators (Dehalococcoides mccartyi, Dehalobacter sp.) identified by real-time PCR in soil from the lower levels supports the hypothesis that there is a significant potential for reductive dechlorination of PCE. Local conditions were insufficiently reducing for rapid complete dechlorination of PCE to harmless ethene. For reliable assessment of natural attenuation, or when designing monitoring or remedial systems, vertical stratification of key biological and hydrochemical markers should be analysed as standard, even in shallow aquifers.
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Affiliation(s)
- Jan Němeček
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic; ENACON s.r.o., Krčská 16, CZ-140 00, Prague 4, Czech Republic.
| | - Iva Dolinová
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic
| | - Jiřina Macháčková
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic
| | - Roman Špánek
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic
| | - Alena Ševců
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic
| | - Tomáš Lederer
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic
| | - Miroslav Černík
- Technical University of Liberec, Studentská 2, CZ-461 17, Liberec, Czech Republic
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Yang Y, Cápiro NL, Marcet TF, Yan J, Pennell KD, Löffler FE. Organohalide Respiration with Chlorinated Ethenes under Low pH Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:8579-8588. [PMID: 28665587 DOI: 10.1021/acs.est.7b01510] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bioremediation at chlorinated solvent sites often leads to groundwater acidification due to electron donor fermentation and enhanced dechlorination activity. The microbial reductive dechlorination process is robust at circumneutral pH, but activity declines at groundwater pH values below 6.0. Consistent with this observation, the activity of tetrachloroethene (PCE) dechlorinating cultures declined at pH 6.0 and was not sustained in pH 5.5 medium, with one notable exception. Sulfurospirillum multivorans dechlorinated PCE to cis-1,2-dichloroethene (cDCE) in pH 5.5 medium and maintained this activity upon repeated transfers. Microcosms established with soil and aquifer materials from five distinct locations dechlorinated PCE-to-ethene at pH 5.5 and pH 7.2. Dechlorination to ethene was maintained following repeated transfers at pH 7.2, but no ethene was produced at pH 5.5, and only the transfer cultures derived from the Axton Cross Superfund (ACS) microcosms sustained PCE dechlorination to cDCE as a final product. 16S rRNA gene amplicon sequencing of pH 7.2 and pH 5.5 ACS enrichments revealed distinct microbial communities, with the dominant dechlorinator being Dehalococcoides in pH 7.2 and Sulfurospirillum in pH 5.5 cultures. PCE-to-trichloroethene- (TCE-) and PCE-to-cDCE-dechlorinating isolates obtained from the ACS pH 5.5 enrichment shared 98.6%, and 98.5% 16S rRNA gene sequence similarities to Sulfurospirillum multivorans. These findings imply that sustained Dehalococcoides activity cannot be expected in low pH (i.e., ≤ 5.5) groundwater, and organohalide-respiring Sulfurospirillum spp. are key contributors to in situ PCE reductive dechlorination under low pH conditions.
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Affiliation(s)
| | - Natalie L Cápiro
- Department of Civil and Environmental Engineering, Tufts University , Medford, Massachusetts 02155, United States
| | - Tyler F Marcet
- Department of Civil and Environmental Engineering, Tufts University , Medford, Massachusetts 02155, United States
| | | | - Kurt D Pennell
- Department of Civil and Environmental Engineering, Tufts University , Medford, Massachusetts 02155, United States
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Ghattas AK, Fischer F, Wick A, Ternes TA. Anaerobic biodegradation of (emerging) organic contaminants in the aquatic environment. WATER RESEARCH 2017; 116:268-295. [PMID: 28347952 DOI: 10.1016/j.watres.2017.02.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 05/22/2023]
Abstract
Although strictly anaerobic conditions prevail in several environmental compartments, up to now, biodegradation studies with emerging organic contaminants (EOCs), such as pharmaceuticals and personal care products, have mainly focused on aerobic conditions. One of the reasons probably is the assumption that the aerobic degradation is more energetically favorable than degradation under strictly anaerobic conditions. Certain aerobically recalcitrant contaminants, however, are biodegraded under strictly anaerobic conditions and little is known about the organisms and enzymatic processes involved in their degradation. This review provides a comprehensive survey of characteristic anaerobic biotransformation reactions for a variety of well-studied, structurally rather simple contaminants (SMOCs) bearing one or a few different functional groups/structural moieties. Furthermore it summarizes anaerobic degradation studies of more complex contaminants with several functional groups (CMCs), in soil, sediment and wastewater treatment. While strictly anaerobic conditions are able to promote the transformation of several aerobically persistent contaminants, the variety of observed reactions is limited, with reductive dehalogenations and the cleavage of ether bonds being the most prevalent. Thus, it becomes clear that the transferability of degradation mechanisms deduced from culture studies of SMOCs to predict the degradation of CMCs, such as EOCs, in environmental matrices is hampered due the more complex chemical structure bearing different functional groups, different environmental conditions (e.g. matrix, redox, pH), the microbial community (e.g. adaptation, competition) and the low concentrations typical for EOCs.
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Affiliation(s)
- Ann-Kathrin Ghattas
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Ferdinand Fischer
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Arne Wick
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Thomas A Ternes
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany.
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Dolinová I, Štrojsová M, Černík M, Němeček J, Macháčková J, Ševců A. Microbial degradation of chloroethenes: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:13262-13283. [PMID: 28378313 DOI: 10.1007/s11356-017-8867-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/17/2017] [Indexed: 05/28/2023]
Abstract
Contamination by chloroethenes has a severe negative effect on both the environment and human health. This has prompted intensive remediation activity in recent years, along with research into the efficacy of natural microbial communities for degrading toxic chloroethenes into less harmful compounds. Microbial degradation of chloroethenes can take place either through anaerobic organohalide respiration, where chloroethenes serve as electron acceptors; anaerobic and aerobic metabolic degradation, where chloroethenes are used as electron donors; or anaerobic and aerobic co-metabolic degradation, with chloroethene degradation occurring as a by-product during microbial metabolism of other growth substrates, without energy or carbon benefit. Recent research has focused on optimising these natural processes to serve as effective bioremediation technologies, with particular emphasis on (a) the diversity and role of bacterial groups involved in dechlorination microbial processes, and (b) detection of bacterial enzymes and genes connected with dehalogenation activity. In this review, we summarise the different mechanisms of chloroethene bacterial degradation suitable for bioremediation and provide a list of dechlorinating bacteria. We also provide an up-to-date summary of primers available for detecting functional genes in anaerobic and aerobic bacteria degrading chloroethenes metabolically or co-metabolically.
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Affiliation(s)
- Iva Dolinová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Martina Štrojsová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Miroslav Černík
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Jan Němeček
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Jiřina Macháčková
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Alena Ševců
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
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29
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Kleindienst S, Higgins SA, Tsementzi D, Chen G, Konstantinidis KT, Mack EE, Löffler FE. 'Candidatus Dichloromethanomonas elyunquensis' gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family. Syst Appl Microbiol 2016; 40:150-159. [PMID: 28292625 DOI: 10.1016/j.syapm.2016.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
Abstract
Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. We describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively. Genome-aggregate average amino acid identities against Peptococcaceae members did not exceed 66%, suggesting that the DCM degrader does not affiliate with any described genus. Phylogenetic analysis of conserved single-copy functional genes supported that the DCM degrader represents a novel clade. Growth strictly depended on the presence of DCM, which was consumed at a rate of 160±3μmolL-1 d-1. The DCM degrader attained 5.25×107±1.0×107 cells per μmol DCM consumed. Fluorescence in situ hybridization revealed rod-shaped cells 4±0.8μm long and 0.4±0.1μm wide. Based on the unique phylogenetic, genomic, and physiological characteristics, we propose that the DCM degrader represents a new genus and species, 'Candidatus Dichloromethanomonas elyunquensis'.
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Affiliation(s)
- Sara Kleindienst
- 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, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA.
| | - Steven A Higgins
- 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, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Despina Tsementzi
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA
| | - Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Konstantinos T Konstantinidis
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA 30332, USA; School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - E Erin Mack
- Corporate Remediation Group, E. I. DuPont de Nemours and Company, Newark, DE 19714, USA
| | - Frank E Löffler
- 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, TN 37831, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA.
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Rasool K, Shahzad A, Lee DS. Exploring the potential of anaerobic sulfate reduction process in treating sulfonated diazo dye: Microbial community analysis using bar-coded pyrosequencing. JOURNAL OF HAZARDOUS MATERIALS 2016; 318:641-649. [PMID: 27475462 DOI: 10.1016/j.jhazmat.2016.07.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 07/04/2016] [Accepted: 07/20/2016] [Indexed: 06/06/2023]
Abstract
Anaerobic decolorization and biotransformation of azo dye was investigated in a sulfate-reducing environment. Batch reactor studies were performed with mixed cultures of anaerobic sulfate-reducing bacteria (SRBs) enriched from anaerobic digester sludge. Complete sulfate and color removal were achieved in batch experiments with different initial dye concentrations (50-2500mg/L) and 1000mg/L of sulfate. Induction of various oxidoreductive enzyme activities such as phenol oxidase, veratryl alcohol oxidase, lignin peroxidase, and azo reductase was studied to understand their involvement in dye metabolism under anoxic environment. The degradation of Cotton Red B was confirmed using high-performance liquid chromatography and gas chromatography-mass spectroscopy. Sulfidogenic sludge demonstrated excellent dye degradation and mineralization ability, producing aniline and 1,4-diamino benzene as metabolites. A barcoded 16S rRNA gene-pyrosequencing approach was used to assess the bacterial diversity in the sludge culture and a phylogenetic tree was constructed for sulfate-reducing bacteria.
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Affiliation(s)
- Kashif Rasool
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Qatar Foundation, PO Box 5825, Doha, Qatar
| | - Asif Shahzad
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - Dae Sung Lee
- Department of Environmental Engineering, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea.
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Puigserver D, Herrero J, Torres M, Cortés A, Nijenhuis I, Kuntze K, Parker BL, Carmona JM. Reductive dechlorination in recalcitrant sources of chloroethenes in the transition zone between aquifers and aquitards. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:18724-41. [PMID: 27314420 DOI: 10.1007/s11356-016-7068-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/09/2016] [Indexed: 05/20/2023]
Abstract
In the transition zone between aquifers and basal aquitards, the perchloroethene pools at an early time in their evolution are more recalcitrant than those elsewhere in the aquifer. The aim of this study is to demonstrate that the biodegradation of chloroethenes from aged pools (i.e., pools after decades of continuous groundwater flushing and dissolution) of perchloroethene is favored in the transition zone. A field site was selected where an aged pool exists at the bottom of a transition zone. Two boreholes were drilled to obtain sediment and groundwater samples to perform chemical, isotopic, molecular, and clone library analyses and microcosm experiments. The main results were as follows: (i) the transition zone is characterized by a high microbial richness; (ii) reductively dechlorinating microorganisms are present and partial reductive dechlorination coexists with denitrification, Fe and Mn reduction, and sulfate reduction; (iii) reductively dechlorinating microorganisms were also present in the zone of the aged pool; (v) the high concentrations of perchloroethene in this zone resulted in a decrease in microbial richness; (vi) however, the presence of fermenting microorganisms supplying electrons for the reductively dechlorinating microorganisms prevented the reductive dechlorination to be inhibited. These findings suggest that biostimulation and/or bioaugmentation could be applied to promote complete reductive dechlorination and to enhance the dissolution of more nonaqueous phase liquids (DNAPL).
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Affiliation(s)
- Diana Puigserver
- Department de Gequímica, Petrologia i Prospecció Geològica, Facultat de Geologia, Universitat de Barcelona, C/ Martí i Franquès, s/n, 08028, Barcelona, Spain
| | - Jofre Herrero
- Department de Gequímica, Petrologia i Prospecció Geològica, Facultat de Geologia, Universitat de Barcelona, C/ Martí i Franquès, s/n, 08028, Barcelona, Spain
| | - Mònica Torres
- Department de Gequímica, Petrologia i Prospecció Geològica, Facultat de Geologia, Universitat de Barcelona, C/ Martí i Franquès, s/n, 08028, Barcelona, Spain
| | - Amparo Cortés
- Departament de Productes Naturals, Biologia Vegetal i Edafologia, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII, s/n., 08028, Barcelona, Spain
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15., 04318, Leipzig, Germany
| | - Kevin Kuntze
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15., 04318, Leipzig, Germany
| | - Beth L Parker
- School of Engineering, University of Guelph, 50, Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - José M Carmona
- Department de Gequímica, Petrologia i Prospecció Geològica, Facultat de Geologia, Universitat de Barcelona, C/ Martí i Franquès, s/n, 08028, Barcelona, Spain.
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Badalamenti JP, Summers ZM, Chan CH, Gralnick JA, Bond DR. Isolation and Genomic Characterization of 'Desulfuromonas soudanensis WTL', a Metal- and Electrode-Respiring Bacterium from Anoxic Deep Subsurface Brine. Front Microbiol 2016; 7:913. [PMID: 27445996 PMCID: PMC4914508 DOI: 10.3389/fmicb.2016.00913] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/27/2016] [Indexed: 11/25/2022] Open
Abstract
Reaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, MN, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite organic carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes deposited in situ as bait, we electrochemically enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium, ‘Desulfuromonas soudanensis’ strain WTL, from an acetate-fed three-electrode bioreactor poised at +0.24 V (vs. standard hydrogen electrode). Cyclic voltammetry revealed that ‘D. soudanensis’ releases electrons at redox potentials approximately 100 mV more positive than the model freshwater surface isolate Geobacter sulfurreducens, suggesting that its extracellular respiration is tuned for higher potential electron acceptors. ‘D. soudanensis’ contains a 3,958,620-bp circular genome, assembled to completion using single-molecule real-time (SMRT) sequencing reads, which encodes a complete TCA cycle, 38 putative multiheme c-type cytochromes, one of which contains 69 heme-binding motifs, and a LuxI/LuxR quorum sensing cassette that produces an unidentified N-acyl homoserine lactone. Another cytochrome is predicted to lie within a putative prophage, suggesting that horizontal gene transfer plays a role in respiratory flexibility among metal reducers. Isolation of ‘D. soudanensis’ underscores the utility of electrode-based approaches for enriching rare metal reducers from a wide range of habitats.
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Affiliation(s)
| | - Zarath M Summers
- BioTechnology Institute, University of Minnesota - Twin Cities, Saint Paul MN, USA
| | - Chi Ho Chan
- BioTechnology Institute, University of Minnesota - Twin Cities, Saint Paul MN, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute, University of Minnesota - Twin Cities, Saint PaulMN, USA; Department of Microbiology, University of Minnesota - Twin Cities, MinneapolisMN, USA
| | - Daniel R Bond
- BioTechnology Institute, University of Minnesota - Twin Cities, Saint PaulMN, USA; Department of Microbiology, University of Minnesota - Twin Cities, MinneapolisMN, USA
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Liu CY, Cade-Menun BJ, Xu XH, Fan JL. Electron Donor Substances and Iron Oxides Stimulate Anaerobic Dechlorination of DDT in a Slurry System with Hydragric Acrisols. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:331-340. [PMID: 26828189 DOI: 10.2134/jeq2015.07.0406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The interactive effects between electron donor substances and iron (Fe) oxides have significant influence on electron transfer and the growth of Fe-reducing bacteria, which may affect the reductive dechlorination of 1,1,1-trichoro-2,2-bis(p-chlorophenyl)ethane (DDT) in soils. To evaluate the roles of volatile fatty acids and Fe(III) oxide in accelerating the reductive dechlorination of DDT in Hydragric Acrisols, a batch anaerobic incubation experiment was conducted in a slurry system with the following seven treatments: sterile soil, control (DDT-contaminated soil), lactic acid, propionic acid, goethite, lactic acid + goethite, and propionic acid + goethite. Results showed that after 20 d of incubation, DDT residues for these treatments decreased by 34, 65, 77, 81, 77, 90, and 92% of the initial quantities, respectively, with 1,1-dichloro-2,2-bis(4-chlorophenyl)-ethane as the dominant metabolite. The application of lactic acid had no significant effect on DDT dechlorination in the first 8 d while the methanogenesis rate increased quickly but accelerated DDT dechlorination after Day 8 while the methanogenesis rate decreased and Fe(II) contents increased. The application of propionic acid enhanced DDT dechlorination rates throughout the incubation. The amendment by goethite stimulated microbial reduction of Fe(III) oxides to generate Fe(II), which was an efficient electron donor, thus accelerating DDT dechlorination significantly in the early incubation period. A synergetic interaction that accelerated DDT dechlorination, either between lactic acid and goethite or between propionic acid and goethite, was obtained. The results will be of great significance to develop efficient in situ remediation technology of DDT-contaminated soil.
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Electrochemical and microbial monitoring of multi-generational electroactive biofilms formed from mangrove sediment. Bioelectrochemistry 2015; 106:125-32. [DOI: 10.1016/j.bioelechem.2015.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 04/24/2015] [Accepted: 05/04/2015] [Indexed: 12/30/2022]
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Cápiro NL, Löffler FE, Pennell KD. Spatial and temporal dynamics of organohalide-respiring bacteria in a heterogeneous PCE-DNAPL source zone. JOURNAL OF CONTAMINANT HYDROLOGY 2015; 182:78-90. [PMID: 26348832 DOI: 10.1016/j.jconhyd.2015.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/15/2015] [Accepted: 08/19/2015] [Indexed: 06/05/2023]
Abstract
Effective treatment of sites contaminated with dense non-aqueous phase liquids (DNAPLs) requires detailed understanding of the microbial community responses to changes in source zone strength and architecture. Changes in the spatial and temporal distributions of the organohalide-respiring Dehalococcoides mccartyi (Dhc) strains and Geobacter lovleyi strain SZ (GeoSZ) were examined in a heterogeneous tetrachloroethene- (PCE-) DNAPL source zone within a two-dimensional laboratory-scale aquifer flow cell. As part of a combined remedy approach, flushing with 2.3 pore volumes (PVs) of 4% (w/w) solution of the nonionic, biodegradable surfactant Tween® 80 removed 55% of the initial contaminant mass, and resulted in a PCE-DNAPL distribution that contained 51% discrete ganglia and 49% pools (ganglia-to-pool ratio of 1.06). Subsequent bioaugmentation with the PCE-to-ethene-dechlorinating consortium BDI-SZ resulted in cis-1,2-dichloroethene (cis-DCE) formation after 1 PV (ca. 7 days), while vinyl chloride (VC) and ethene were detected 10 PVs after bioaugmentation. Maximum ethene yields (ca. 90 μM) within DNAPL pool and ganglia regions coincided with the detection of the vcrA reductive dehalogenase (RDase) gene that exceeded the Dhc 16S rRNA genes by 2.0±1.3 and 4.0±1.7 fold in the pool and ganglia regions, respectively. Dhc and GeoSZ cell abundance increased by up to 4 orders-of-magnitude after 28 PVs of steady-state operation, with 1 to 2 orders-of-magnitude increases observed in close proximity to residual PCE-DNAPL. These observations suggest the involvement of these dechlorinators the in observed PCE dissolution enhancements of up to 2.3 and 6.0-fold within pool and ganglia regions, respectively. Analysis of the solid and aqueous samples at the conclusion of the experiment revealed that the highest VC (≥155 μM) and ethene (≥65 μM) concentrations were measured in zones where Dhc and GeoSZ were predominately attached to the solids. These findings demonstrate dynamic responses of organohalide-respiring bacteria in a heterogeneous DNAPL source zone, and emphasize the influence of source zone architecture on bioremediation performance.
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Affiliation(s)
- Natalie L Cápiro
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA 02155, United States.
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, United States; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 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, TN 37831, United States
| | - Kurt D Pennell
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA 02155, United States.
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Xu Y, He Y, Zhang Q, Xu J, Crowley D. Coupling between Pentachlorophenol Dechlorination and Soil Redox As Revealed by Stable Carbon Isotope, Microbial Community Structure, and Biogeochemical Data. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:5425-5433. [PMID: 25853431 DOI: 10.1021/es505040c] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Carbon isotopic analysis and molecular-based methods were used in conjunction with geochemical data sets to assess the dechlorination of pentachlorophenol (PCP) when coupled to biogeochemical processes in a mangrove soil having no prior history of anthropogenic contamination. The PCP underwent 96% dechlorination in soil amended with acetate, compared to 21% dehalogenation in control soil. Carbon isotope analysis of residual PCP demonstrated an obvious enrichment of 13C (εC, -3.01±0.1%). Molecular and statistical analyses demonstrated that PCP dechlorination and Fe(III) reduction were synergistically combined electron-accepting processes. Microbial community analysis further suggested that enhanced dechlorination of PCP during Fe(III) reduction was mediated by members of the multifunctional family of Geobacteraceae. In contrast, PCP significantly suppressed the growth of SO4(2-) reducers, which, in turn, facilitated the production of CH4 by diversion of electrons from SO4(2-) reduction to methanogenesis. The integrated data regarding stoichiometric alterations in this study gives direct evidence showing PCP, Fe(III), and SO4(2-) reduction, and CH4 production are coupled microbial processes during changes in soil redox.
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Affiliation(s)
- Yan Xu
- †Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Yan He
- †Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Qian Zhang
- †Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - Jianming Xu
- †Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, China
| | - David Crowley
- ‡Department of Environmental Sciences, University of California, Riverside, Riverside, California 92521, United States
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Renpenning J, Rapp I, Nijenhuis I. Substrate hydrophobicity and cell composition influence the extent of rate limitation and masking of isotope fractionation during microbial reductive dehalogenation of chlorinated ethenes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:4293-301. [PMID: 25734359 DOI: 10.1021/es506108j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This study investigated the effect of intracellular microscale mass transfer on microbial carbon isotope fractionation of tetrachloroethene (PCE) and trichloroethene (TCE). Significantly stronger isotope fractionation was observed for crude extracts vs intact cells of Sulfurospirillum multivorans, Geobacter lovleyi, Desulfuromonas michiganensis, Desulfitobacterium hafniense strain PCE-S, and Dehalobacter restrictus. Furthermore, carbon stable isotope fractionation was stronger for microorganisms with a Gram-positive cell envelope compared to those with a Gram-negative cell envelope. Significant differences were observed between model organisms in cellular sorption capacity for PCE (S. multivorans-K(d-PCE) = 0.42-0.51 L g(-1); D. hafniense-K(d-PCE) = 0.13 L g(-1)), as well as in envelope hydrophobicity (S. multivorans 33.0° to 72.2°; D. hafniense 59.1° to 60.8°) when previously cultivated with fumarate or PCE as electron acceptor, but not for TCE. Cell envelope properties and the tetrachloroethene reductive dehalogenase (PceA-RDase) localization did not result in significant effects on observed isotope fractionation of TCE. For PCE, however, systematic masking of isotope effects as a result of microscale mass transfer limitation at microbial membranes was observed, with carbon isotope enrichment factors of -2.2‰, -1.5 to -1.6‰, and -1.0‰ (CI95% < ± 0.2‰) for no membrane, hydrophilic outer membrane, and outer + cytoplasmic membrane, respectively. Conclusively, rate-limiting mass transfer barriers were (a) the outer membrane or cell wall and (b) the cytoplasmic membrane in case of a cytoplasmic location of the RDase enzyme. Overall, our results indicate that masking of isotope fractionation is determined by (1) hydrophobicity of the degraded compound, (2) properties of the cell envelope, and (3) the localization of the reacting enzyme.
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Affiliation(s)
- Julian Renpenning
- †Department for Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
| | - Insa Rapp
- †Department for Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
- ‡Department of Chemistry, Universität Duisburg-Essen, Universitätsstraße 2, 45141 Essen, Germany
| | - Ivonne Nijenhuis
- †Department for Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research - UFZ, Permoserstrasse 15, D-04318 Leipzig, Germany
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An TT, Picardal FW. Desulfuromonas carbonis sp. nov., an Fe(III)-, S0- and Mn(IV)-reducing bacterium isolated from an active coalbed methane gas well. Int J Syst Evol Microbiol 2015; 65:1686-1693. [PMID: 25736408 DOI: 10.1099/ijs.0.000159] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, mesophilic, obligately anaerobic, acetate-oxidizing, dissimilatory iron-, sulfur-, and manganese-reducing bacterium, designated strain ICBM(T), was obtained from an active, coalbed methane gas well in Indiana, USA. Strain ICBM(T) was a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium that was rich in c-type cytochromes and formed red colonies in solid medium. Strain ICBM(T) conserved energy to support growth from the oxidation of acetate, propionate, pyruvate, malate, fumarate, succinate and dl-lactate, concomitant with dissimilatory iron reduction. Strain ICBM(T) fermented fumarate yielding succinate and acetate. Strain ICBM(T) was able to grow in the temperature range of 10 °C to 37 °C, NaCl concentration range of 0 to 1.2 M, and pH range of 6.5 to 8.0. The physiological characteristics of strain ICBM(T) indicated that it belongs to the Desulfuromonas cluster. The G+C content of its genomic DNA was 61.2 mol%. The predominant cellular fatty acids were C16 : 0 (39.3%), C16 : 1ω7c and/or iso-C15 : 0 2-OH (36.6%). The closest cultured phylogenetic relative of strain ICBM(T) was Desulfuromonas michiganensis BB1(T) with only 95% 16S rRNA gene sequence similarity. This confirmed that strain ICBM(T) is affiliated with the genus Desulfuromonas . On the basis of phenotypic and genotypic differences between strain ICBM(T) and other taxa of the genus Desulfuromonas , strain ICBM(T) represents a novel species for which the name Desulfuromonas carbonis sp. nov. is proposed (type strain ICBM(T) = DSM 29759(T) = JCM 30471(T)). Strain ICBM(T) is the first Fe(III)-, S(0)-, and Mn(IV)-reducing bacterium that was isolated from a coal bed.
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Affiliation(s)
- Thuy T An
- School of Public and Environmental Affairs, Indiana University, MSB II, 702 N. Walnut Grove Ave, Bloomington, IN 47405-2204, USA
| | - Flynn W Picardal
- School of Public and Environmental Affairs, Indiana University, MSB II, 702 N. Walnut Grove Ave, Bloomington, IN 47405-2204, USA
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Wang ZJ, Liu QQ, Zhao LH, Du ZJ, Chen GJ. Bradymonas sediminis gen. nov., sp. nov., isolated from coastal sediment, and description of Bradymonadaceae fam. nov. and Bradymonadales ord. nov. Int J Syst Evol Microbiol 2015; 65:1542-1549. [PMID: 25713043 DOI: 10.1099/ijs.0.000135] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A novel Gram-stain-negative, rod-shaped, gliding, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated FA350(T), was isolated from coastal sediment from Xiaoshi Island, Weihai, China. Strain FA350(T) showed growth on modified nutrient agar supplemented with 0.1% d-(+)-trehalose and with distilled water replaced by seawater. Optimal growth occurred at 33 °C and pH 8.5 with 4% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FA350(T) belongs to a novel bacterial order in the class Deltaproteobacteria , and the most closely related type strains belong to the order Desulfuromonadales , with 85.1-85.6% 16S rRNA gene sequence similarity. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and two unknown phospholipids. Major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω10c and menaquinone MK-7 was the sole respiratory quinone. The DNA G+C content of strain FA350(T) was 60.3 mol%. The isolate and closely related environmental clones formed a novel order-level clade in the class Deltaproteobacteria . Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain FA350(T) may represent a novel order of the Deltaproteobacteria . Here, we propose the name Bradymonas sediminis gen. nov., sp. nov. to accommodate strain FA350(T). The type strain of Bradymonas sediminis is FA350(T) ( =DSM 28820(T) =CICC 10904(T)); Bradymonadales ord. nov. and Bradymonadaceae fam. nov. are also proposed to accommodate the novel taxon.
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Affiliation(s)
- Zong-Jie Wang
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Qian-Qian Liu
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Li-Hua Zhao
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.,College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
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Aulenta F, Fazi S, Majone M, Rossetti S. Electrically conductive magnetite particles enhance the kinetics and steer the composition of anaerobic TCE-dechlorinating cultures. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.09.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Karataş S, Hasar H, Taşkan E, Özkaya B, Şahinkaya E. Bio-reduction of tetrachloroethen using a H2-based membrane biofilm reactor and community fingerprinting. WATER RESEARCH 2014; 58:21-28. [PMID: 24731873 DOI: 10.1016/j.watres.2014.03.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/18/2014] [Accepted: 03/19/2014] [Indexed: 06/03/2023]
Abstract
Chlorinated ethenes in drinking water could be reductively dechlorinated to non-toxic ethene by using a hydrogen based membrane biofilm reactor (H2-MBfR) under denitrifying conditions as it provides an appropriate environment for dechlorinating bacteria in biofilm communities. This study evaluates the reductive dechlorination of perchloroethene (PCE) to non-toxic ethene (ETH) and comparative community analysis of the biofilm grown on the gas permeable membrane fibers. For these purposes, three H2-MBfRs receiving three different chlorinated ethenes (PCE, TCE and DCE) were operated under different hydraulic retention times (HRTs) and H2 pressures. Among these reactors, the H2-MBfR fed with PCE (H2-MBfR 1) accomplished a complete dechlorination, whereas cis-DCE accumulated in the TCE receiving H2-MBfR 2 and no dechlorination was detected in the DCE receiving H2-MBfR 3. The results showed that 95% of PCE dechlorinated to ETH together with over 99.8% dechlorination efficiency. Nitrate was the preferred electron acceptor as the most of electrons generated from H2 oxidation used for denitrification and dechlorination started under nitrate deficient conditions at increased H2 pressures. PCR-DGGE analysis showed that Dehalococcoides were present in autotrophic biofilm community dechlorinating PCE to ethene, and RDase genes analysis revealed that pceA, tceA, bvcA and vcrA, responsible for complete dechlorination step, were available in Dehalococcoides strains.
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Affiliation(s)
| | - Halil Hasar
- Fırat University, Faculty of Engineering, Department of Environmental Engineering, 23119 Elazığ, Turkey.
| | - Ergin Taşkan
- Fırat University, Faculty of Engineering, Department of Environmental Engineering, 23119 Elazığ, Turkey.
| | - Bestamin Özkaya
- Yıldız Technical University, Department of Environmental Engineering, İstanbul, Turkey.
| | - Erkan Şahinkaya
- Istanbul Medeniyet University, Department of Bioengineering, İstanbul, Turkey.
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42
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Lacroix E, Brovelli A, Maillard J, Rohrbach-Brandt E, Barry DA, Holliger C. Use of silicate minerals for long-term pH control during reductive dechlorination of high tetrachloroethene concentrations in continuous flow-through columns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 482-483:23-35. [PMID: 24636885 DOI: 10.1016/j.scitotenv.2014.02.099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 02/12/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
The long-term buffering potential of three silicate minerals (diopside, fayalite and forsterite) present as fine particles in porous quartz sand medium was evaluated in flow-through column experiments over a period of 6.5 months. The columns were operated with PCE concentrations close to saturation and inoculated with the organohalide-respiring consortium SDC-9™, which is able to completely dechlorinate PCE to ethene at high concentrations. In the absence of pH buffering agents, fermentation and organohalide respiration drove the pH close to 6.1, leading to severe inhibition of PCE dechlorination. Forsterite and fayalite were able to maintain the pH close to 7.5 and 6.5, respectively, and to sustain the production of VC and ethene. Diopside gradually lost its buffering capacity during the first 84 days due to the formation of a low reactive leached layer but dechlorination to cis-DCE was still achieved. Among the three minerals tested, forsterite was identified as the best buffering agent. Its presence led to the best PCE removal performance and the highest relative abundance of Dehalococcoides. This study showed that forsterite and fayalite are promising sources of long-term pH buffering for in situ bioremediation of source-zone PCE.
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Affiliation(s)
- Elsa Lacroix
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Ecological Engineering Laboratory, Lausanne, Switzerland; Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Laboratory for Environmental Biotechnology, Lausanne, Switzerland
| | - Alessandro Brovelli
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Ecological Engineering Laboratory, Lausanne, Switzerland
| | - Julien Maillard
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Laboratory for Environmental Biotechnology, Lausanne, Switzerland
| | - Emmanuelle Rohrbach-Brandt
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Laboratory for Environmental Biotechnology, Lausanne, Switzerland
| | - D A Barry
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Ecological Engineering Laboratory, Lausanne, Switzerland
| | - Christof Holliger
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Laboratory for Environmental Biotechnology, Lausanne, Switzerland.
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43
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Yu HY, Wang YK, Chen PC, Li FB, Chen MJ, Hu M. The effect of ammonium chloride and urea application on soil bacterial communities closely related to the reductive transformation of pentachlorophenol. JOURNAL OF HAZARDOUS MATERIALS 2014; 272:10-19. [PMID: 24662270 DOI: 10.1016/j.jhazmat.2014.02.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 10/08/2013] [Accepted: 02/24/2014] [Indexed: 06/03/2023]
Abstract
Pentachlorophenol (PCP) is widely distributed in the soil, and nitrogen fertilizer is extensively used in agricultural production. However, studies on the fate of organic contaminants as affected by nitrogen fertilizer application have been rare and superficial. The present study aimed to examine the effect of ammonium chloride (NH4Cl) and urea (CO(NH2)2) application on the reductive transformation of PCP in a paddy soil. The study showed that the addition of low concentrations of NH4Cl/CO(NH2)2 enhanced the transformation of PCP, while the addition of high concentrations of NH4Cl/CO(NH2)2 had the opposite effect. The variations in the abundance of soil microbes in response to NH4Cl/CO(NH2)2 addition showed that both NH4Cl and CO(NH2)2 had inhibitory effects on the growth of dissimilatory iron-reducing bacteria (DIRB) of the genus Comamonas. In contrast, for the genus Shewanella, low concentrations of NH4Cl inhibited growth, and high concentrations of NH4Cl enhanced growth, whereas all concentrations of CO(NH2)2 showed enhancement effects. In addition, consistent patterns of variation were found between the abundances of dechlorinating bacteria in the genus Dehalobacter and PCP transformation rates under NH4Cl/CO(NH2)2 addition. In conclusion, nitrogen application produced variations in the structure of the soil microbial community, especially in the abundance of dissimilatory iron-reducing bacteria and dechlorinating bacteria, which, in turn, affected PCP dechlorination.
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Affiliation(s)
- Huan-Yun Yu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, PR China
| | - Yong-kui Wang
- Environmental Science and Engineering College, Hubei Polytechic University, Huangshi 435003, Hubei, PR China
| | - Peng-cheng Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, PR China
| | - Fang-bai Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, PR China.
| | - Man-jia Chen
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, PR China
| | - Min Hu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou, PR China
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44
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Lacroix E, Brovelli A, Holliger C, Barry DA. Control of groundwater pH during bioremediation: improvement and validation of a geochemical model to assess the buffering potential of ground silicate minerals. JOURNAL OF CONTAMINANT HYDROLOGY 2014; 160:21-29. [PMID: 24589423 DOI: 10.1016/j.jconhyd.2014.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 06/03/2023]
Abstract
Accurate control of groundwater pH is of critical importance for in situ biological treatment of chlorinated solvents. The use of ground silicate minerals mixed with groundwater is an appealing buffering strategy as silicate minerals may act as long-term sources of alkalinity. In a previous study, we developed a geochemical model for evaluation of the pH buffering capacity of such minerals. The model included the main microbial processes driving groundwater acidification as well as mineral dissolution. In the present study, abiotic mineral dissolution experiments were conducted with five silicate minerals (andradite, diopside, fayalite, forsterite, nepheline). The goal of the study was to validate the model and to test the buffering capacity of the candidate minerals identified previously. These five minerals increased the pH from acidic to neutral and slightly basic values. The model was revised and improved to represent better the experimental observations. In particular, the experiments revealed the importance of secondary mineral precipitation on the buffering potential of silicates, a process not included in the original formulation. The main secondary phases likely to precipitate were identified through model calibration, as well as the degree of saturation at which they formed. The predictions of the revised geochemical model were in good agreement with the observations, with a correlation coefficient higher than 0.9 in most cases. This study confirmed the potential of silicates to act as pH control agents and showed the reliability of the geochemical model, which can be used as a design tool for field applications.
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Affiliation(s)
- Elsa Lacroix
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Ecological Engineering Laboratory, Station 2, 1015 Lausanne, Switzerland; Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Laboratory for Environmental Biotechnology, Station 6, 1015 Lausanne, Switzerland
| | - Alessandro Brovelli
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Ecological Engineering Laboratory, Station 2, 1015 Lausanne, Switzerland
| | - Christof Holliger
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Laboratory for Environmental Biotechnology, Station 6, 1015 Lausanne, Switzerland.
| | - D A Barry
- Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering (ENAC), Ecological Engineering Laboratory, Station 2, 1015 Lausanne, Switzerland
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45
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Use of silicate minerals for pH control during reductive dechlorination of chloroethenes in batch cultures of different microbial consortia. Appl Environ Microbiol 2014; 80:3858-67. [PMID: 24747895 DOI: 10.1128/aem.00493-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In chloroethene-contaminated sites undergoing in situ bioremediation, groundwater acidification is a frequent problem in the source zone, and buffering strategies have to be implemented to maintain the pH in the neutral range. An alternative to conventional soluble buffers is silicate mineral particles as a long-term source of alkalinity. In previous studies, the buffering potentials of these minerals have been evaluated based on abiotic dissolution tests and geochemical modeling. In the present study, the buffering potentials of four silicate minerals (andradite, diopside, fayalite, and forsterite) were tested in batch cultures amended with tetrachloroethene (PCE) and inoculated with different organohalide-respiring consortia. Another objective of this study was to determine the influence of pH on the different steps of PCE dechlorination. The consortia showed significant differences in sensitivities toward acidic pH for the different dechlorination steps. Molecular analysis indicated that Dehalococcoides spp. that were present in all consortia were the most pH-sensitive organohalide-respiring guild members compared to Sulfurospirillum spp. and Dehalobacter spp. In batch cultures with silicate mineral particles as pH-buffering agents, all four minerals tested were able to maintain the pH in the appropriate range for reductive dechlorination of chloroethenes. However, complete dechlorination to ethene was observed only with forsterite, diopside, and fayalite. Dissolution of andradite increased the redox potential and did not allow dechlorination. With forsterite, diopside, and fayalite, dechlorination to ethene was observed but at much lower rates for the last two dechlorination steps than with the positive control. This indicated an inhibition effect of silicate minerals and/or their dissolution products on reductive dechlorination of cis-dichloroethene and vinyl chloride. Hence, despite the proven pH-buffering potential of silicate minerals, compatibility with the bacterial community involved in in situ bioremediation has to be carefully evaluated prior to their use for pH control at a specific site.
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46
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Koenig JC, Groissmeier KD, Manefield MJ. Tolerance of anaerobic bacteria to chlorinated solvents. Microbes Environ 2014; 29:23-30. [PMID: 24441515 PMCID: PMC4041229 DOI: 10.1264/jsme2.me13113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 11/08/2013] [Indexed: 11/12/2022] Open
Abstract
The aim of this research was to evaluate the effects of four chlorinated aliphatic hydrocarbons (CAHs), perchloroethene (PCE), carbon tetrachloride (CT), chloroform (CF) and 1,2-dichloroethane (1,2-DCA), on the growth of eight anaerobic bacteria: four fermentative species (Escherichia coli, Klebsiella sp., Clostridium sp. and Paenibacillus sp.) and four respiring species (Pseudomonas aeruginosa, Geobacter sulfurreducens, Shewanella oneidensis and Desulfovibrio vulgaris). Effective concentrations of solvents which inhibited growth rates by 50% (EC50) were determined. The octanol-water partition coefficient or log Po/w of a CAH proved a generally satisfactory measure of its toxicity. Most species tolerated approximately 3-fold and 10-fold higher concentrations of the two relatively more polar CAHs CF and 1,2-DCA, respectively, than the two relatively less polar compounds PCE and CT. EC50 values correlated well with growth rates observed in solvent-free cultures, with fast-growing organisms displaying higher tolerance levels. Overall, fermentative bacteria were more tolerant to CAHs than respiring species, with iron- and sulfate-reducing bacteria in particular appearing highly sensitive to CAHs. These data extend the current understanding of the impact of CAHs on a range of anaerobic bacteria, which will benefit the field of bioremediation.
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Affiliation(s)
- Joanna C. Koenig
- Centre for Marine Bioinnovation, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Kathrin D. Groissmeier
- Helmholtz Institute of Groundwater Ecology, Ingolstaedter Landstrasse 1, D-85764, Neuherberg, Germany
| | - Mike J. Manefield
- Centre for Marine Bioinnovation, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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47
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Hamonts K, Ryngaert A, Smidt H, Springael D, Dejonghe W. Determinants of the microbial community structure of eutrophic, hyporheic river sediments polluted with chlorinated aliphatic hydrocarbons. FEMS Microbiol Ecol 2013; 87:715-32. [DOI: 10.1111/1574-6941.12260] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 10/29/2013] [Accepted: 11/15/2013] [Indexed: 01/15/2023] Open
Affiliation(s)
- Kelly Hamonts
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Mol Belgium
- Division Soil and Water Management; KU Leuven; Heverlee Belgium
| | - Annemie Ryngaert
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Mol Belgium
| | - Hauke Smidt
- Laboratory of Microbiology; Wageningen University; Wageningen The Netherlands
| | - Dirk Springael
- Division Soil and Water Management; KU Leuven; Heverlee Belgium
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Mol Belgium
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48
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Kim SJ, Park SJ, Cha IT, Min D, Kim JS, Chung WH, Chae JC, Jeon CO, Rhee SK. Metabolic versatility of toluene-degrading, iron-reducing bacteria in tidal flat sediment, characterized by stable isotope probing-based metagenomic analysis. Environ Microbiol 2013; 16:189-204. [DOI: 10.1111/1462-2920.12277] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 11/28/2022]
Affiliation(s)
- So-Jeong Kim
- Department of Microbiology; Chungbuk National University; Cheongju 361-763 Korea
| | - Soo-Je Park
- Department of Biology; Jeju National University; Jeju 690-756 Korea
| | - In-Tae Cha
- Department of Microbiology; Chungbuk National University; Cheongju 361-763 Korea
| | - Deullae Min
- Center for Gas Analysis; Korea Research Institute of Standards and Science; 267 Gajeong-ro, Yuseong-gu Daejeon 305-340 Korea
| | - Jin-Seog Kim
- Center for Gas Analysis; Korea Research Institute of Standards and Science; 267 Gajeong-ro, Yuseong-gu Daejeon 305-340 Korea
| | - Won-Hyung Chung
- Korean Bioinformation Center; Korean Research Institute of Bioscience and Bioengineering; Daejeon 305-806 Korea
| | - Jong-Chan Chae
- Division of Biotechnology; Chonbuk National University; Iksan 570-752 Korea
| | - Che Ok Jeon
- School of Biological Sciences; Chung-Ang University; Seoul 156-756 Korea
| | - Sung-Keun Rhee
- Department of Microbiology; Chungbuk National University; Cheongju 361-763 Korea
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49
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Kuder T, van Breukelen BM, Vanderford M, Philp P. 3D-CSIA: carbon, chlorine, and hydrogen isotope fractionation in transformation of TCE to ethene by a Dehalococcoides culture. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:9668-9677. [PMID: 23895211 DOI: 10.1021/es400463p] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Carbon (C), chlorine (Cl), and hydrogen (H) isotope effects were determined during dechlorination of TCE to ethene by a mixed Dehalococcoides (Dhc) culture. The C isotope effects for the dechlorination steps were consistent with data published in the past for reductive dechlorination (RD) by Dhc. The Cl effects (combined with an inverse H effect in TCE) suggested that dechlorination proceeded through nucleophilic reactions with cobalamin rather than by an electron transfer mechanism. Depletions of (37)Cl in daughter compounds, resulting from fractionation at positions away from the dechlorination center (secondary isotope effects), further support the nucleophilic dechlorination mechanism. Determination of C and Cl isotope ratios of the reactants and products in the reductive dechlorination chain offers a potential tool for differentiation of Dhc activity from alternative transformation mechanisms (e.g., aerobic degradation and reductive dechlorination proceeding via outer sphere mechanisms), in studies of in situ attenuation of chlorinated ethenes. Hydrogenation of the reaction products (DCE, VC, and ethene) showed a major preference for the (1)H isotope. Detection of depleted dechlorination products could provide a line of evidence in discrimination between alternative sources of TCE (e.g., evolution from DNAPL sources or from conversion of PCE).
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Affiliation(s)
- Tomasz Kuder
- School of Geology and Geophysics, University of Oklahoma , 100 E. Boyd Street, SEC 710, Norman, Oklahoma 73019, United States
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50
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Guan X, Liu F, Xie Y, Zhu L, Han B. Microbiota associated with the migration and transformation of chlorinated aliphatic hydrocarbons in groundwater. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2013; 35:535-549. [PMID: 23420483 DOI: 10.1007/s10653-013-9513-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 02/10/2013] [Indexed: 06/01/2023]
Abstract
Pollution of groundwater with chlorinated aliphatic hydrocarbons (CAHs) is a serious environmental problem which is threatening human health. Microorganisms are the major participants in degrading these contaminants. Here, groundwater contaminated for a decade with CAHs was investigated. Numerical simulation and field measurements were used to track and forecast the migration and transformation of the pollutants. The diversity, abundance, and possible activity of groundwater microbial communities at CAH-polluted sites were characterized by molecular approaches. The number of microorganisms was between 5.65E+05 and 1.49E+08 16S rRNA gene clone numbers per liter according to quantitative real-time PCR analysis. In 16S rRNA gene clone libraries constructed from samples along the groundwater flow, eight phyla were detected, and Proteobacteria were dominant (72.8 %). The microbial communities varied with the composition and concentration of pollutants. Meanwhile, toluene monooxygenases and methane monooxygenases capable of degradation of PCE and TCE were detected, demonstrating the major mechanism for PCE and TCE degradation and possibility for in situ remediation by addition of oxygen in this study.
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MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- China
- Environmental Monitoring
- Gas Chromatography-Mass Spectrometry
- Groundwater/chemistry
- Groundwater/microbiology
- Hydrocarbons, Chlorinated/analysis
- Hydrocarbons, Chlorinated/metabolism
- Molecular Sequence Data
- Phylogeny
- Polymerase Chain Reaction
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, RNA
- Water Pollutants, Chemical/analysis
- Water Pollutants, Chemical/metabolism
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Affiliation(s)
- Xiangyu Guan
- Beijing Key Laboratory of Water Resources and Environmental Engineering, School of Water Resources and Environment, China University of Geosciences, No.29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
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