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van der Waals MJ, Thornton SF, Rolfe SA, Rock L, Smith JWN, Bosma TNP, Gerritse J. Potential of stable isotope analysis to deduce anaerobic biodegradation of ethyl tert-butyl ether (ETBE) and tert-butyl alcohol (TBA) in groundwater: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:16150-16163. [PMID: 38319419 PMCID: PMC10894111 DOI: 10.1007/s11356-024-32109-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Understanding anaerobic biodegradation of ether oxygenates beyond MTBE in groundwater is important, given that it is replaced by ETBE as a gasoline additive in several regions. The lack of studies demonstrating anaerobic biodegradation of ETBE, and its product TBA, reflects the relative resistance of ethers and alcohols with a tertiary carbon atom to enzymatic attack under anoxic conditions. Anaerobic ETBE- or TBA-degrading microorganisms have not been characterized. Only one field study suggested anaerobic ETBE biodegradation. Anaerobic (co)metabolism of ETBE or TBA was reported in anoxic microcosms, indicating their biodegradation potential in anoxic groundwater systems. Non-isotopic methods, such as the detection of contaminant loss, metabolites, or ETBE- and TBA-degrading bacteria are not sufficiently sensitive to track anaerobic biodegradation in situ. Compound- and position-specific stable isotope analysis provides a means to study MTBE biodegradation, but isotopic fractionation of ETBE has only been studied with a few aerobic bacteria (εC -0.7 to -1.7‰, εH -11 to -73‰) and at one anoxic field site (δ2H-ETBE +14‰). Similarly, stable carbon isotope enrichment (δ13C-TBA +6.5‰) indicated TBA biodegradation at an anoxic field site. CSIA and PSIA are promising methods to detect anaerobic ETBE and TBA biodegradation but need to be investigated further to assess their full potential at field scale.
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Affiliation(s)
- Marcelle J van der Waals
- Unit Subsurface and Groundwater Systems, Deltares, Daltonlaan 600, Utrecht, 3484 BK, The Netherlands
- Present address: KWR Water Research Institute, Groningenhaven 7, 3433 PE, Nieuwegein, The Netherlands
| | - Steven F Thornton
- Department of Civil and Structural Engineering, University of Sheffield, Mappin St, Sheffield, S1 3JD, UK
| | - Stephen A Rolfe
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Luc Rock
- Shell Global Solutions International BV, Carel van Bylandtlaan 30, The Hague, 2596 HR, The Netherlands
- Present address: Shell Global Solutions (Canada) Inc, 4000 - 500 Centre Street SE, Calgary, AB, T2G 1A6, Canada
| | - Jonathan W N Smith
- Shell Global Solutions (UK) Ltd, Shell Centre, York Road, London, SE1 7NA, UK
| | - Tom N P Bosma
- Unit Subsurface and Groundwater Systems, Deltares, Daltonlaan 600, Utrecht, 3484 BK, The Netherlands
| | - Jan Gerritse
- Unit Subsurface and Groundwater Systems, Deltares, Daltonlaan 600, Utrecht, 3484 BK, The Netherlands.
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Hirakata Y, Mei R, Morinaga K, Katayama T, Tamaki H, Meng XY, Watari T, Yamaguchi T, Hatamoto M, Nobu MK. Identification and cultivation of anaerobic bacterial scavengers of dead cells. THE ISME JOURNAL 2023; 17:2279-2289. [PMID: 37872273 PMCID: PMC10689501 DOI: 10.1038/s41396-023-01538-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/25/2023]
Abstract
The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle.
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Affiliation(s)
- Yuga Hirakata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan.
| | - Ran Mei
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Kana Morinaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Taiki Katayama
- Geomicrobiology Research Group, Research Institute for Geo-Resources and Environment, Geological Survey of Japan (GSJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
- Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan.
- 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, Japan.
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Sun Y, Yin M, Zheng D, Wang T, Zhao X, Luo C, Li J, Liu Y, Xu S, Deng S, Wang X, Zhang D. Different acetonitrile degraders and degrading genes between anaerobic ammonium oxidation and sequencing batch reactor as revealed by stable isotope probing and magnetic-nanoparticle mediated isolation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143588. [PMID: 33218816 DOI: 10.1016/j.scitotenv.2020.143588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 06/11/2023]
Abstract
Microbial degraders play crucial roles in wastewater treatment processes, but their use is limited as most microbes are yet unculturable. Stable isotope probing (SIP) is a cultivation-independent technique identifying functional-yet-uncultivable microbes in ambient environment, but is unsatisfactory for substrates with low assimilation rate owing to the low isotope incorporation into DNA. In this study, we used acetonitrile as the target low-assimilation chemical in many wastewater treatment plants and attempted to identify the active acetonitrile degraders in the activated sludge, via DNA-SIP and magnetic-nanoparticle mediated isolation (MMI) which is another cultivation-independent approach without the requirement of substrate labeling. The two approaches identified different active acetonitrile degraders in a 3-day short-term anaerobic ammonium oxidation (ANAMMOX). MMI enriched significantly more acetonitrile-degraders than SIP, showing the advantages in identifying the active degraders for low-assimilation substrates. Sequencing batch reactor (SBR, 30-day degradation) helped in more incorporation of 15N-labeled acetonitrile into the active degraders, thus the same acetonitrile-degraders and acetonitrile-degrading genes were identified by SIP and MMI. Different acetonitrile degraders between ANAMMOX and SBR were attributed to the distinct hydrological conditions. Our study for the first time explored the succession of acetonitrile-degraders in wastewater and identified the active acetonitrile-degraders which could be further enriched for enhancing acetonitrile degradation performance. These findings provide new insights into the acetonitrile metabolic process in wastewater treatment plants and offer suggestive conclusions for selecting appropriate treatment strategy in wastewater management.
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Affiliation(s)
- Yujiao Sun
- College of Water Science, Beijing Normal University, Beijing 100875, China
| | - Meng Yin
- College of Water Science, Beijing Normal University, Beijing 100875, China
| | - Danyang Zheng
- College of Water Science, Beijing Normal University, Beijing 100875, China
| | - Tiandai Wang
- College of Water Science, Beijing Normal University, Beijing 100875, China
| | - Xiaohui Zhao
- College of Water Science, Beijing Normal University, Beijing 100875, China
| | - Chunling Luo
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Jibing Li
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yueqiao Liu
- College of Water Science, Beijing Normal University, Beijing 100875, China
| | - Shangwei Xu
- College of Water Science, Beijing Normal University, Beijing 100875, China
| | - Songqiang Deng
- Research Institute for Environmental Innovation (Tsinghua-Suzhou), Suzhou 215163, China
| | - Xinzi Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China.
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Chen J, Tong T, Jiang X, Xie S. Biodegradation of sulfonamides in both oxic and anoxic zones of vertical flow constructed wetland and the potential degraders. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:115040. [PMID: 32593905 DOI: 10.1016/j.envpol.2020.115040] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/06/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
The pollution of wastewater with antibiotics and antibiotics resistance genes has attracted public concerns about ecosystem and global health. Swine wastewater can contain high concentrations of antibiotics, especially sulfonamides, even after full-scale wastewater treatment. In this study, mesocosm-scale vertical flow constructed wetlands (VF-CWs) were applied to abate nutrients and antibiotics in swine wastewater containing sulfonamides. VF-CWs performed well in the removal of both nutrients and antibiotics. Sulfonamides did not influence total organic carbon (TOC) and total phosphorus (TP) removal, and even slightly enhanced NH4+-N removal. High removal efficiencies (26.42-84.05%) were achieved for sulfadiazine (SDZ), sulfamethoxazole (SMX) and sulfamethazine (SMZ). Together with lab-scale sorption and biodegradation experiments, microbial degradation was found to be the most important removal mechanism for sulfonamides in VF-CWs. Sulfonamides addition increased bacterial alpha-diversity and changed microbial community structure. Moreover, antibiotics promoted antibiotic-resistant or -degrading bacteria. Bacillus, Geobacter and other seven genera were correlated with sulfonamides reduction under either aerobic or anaerobic condition. In summary, VF-CW is a suitable alternative for swine wastewater treatment, and biodegradation plays the key role in sulfonamides abatement. Main findings of the work. This was the first work to combine bacterial community analysis with microcosm experiments to uncover the major removal mechanism of sulfonamides in constructed wetlands.
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Affiliation(s)
- Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Tianli Tong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Xinshu Jiang
- State Key Joint Laboratory of Environment Simulation and Pollution Control (SKJLESPC), Beijing Key Laboratory for Emerging Organic Contaminants Control (BKLEOC), School of Environment, POPs Research Center, Tsinghua University, Beijing, 100084, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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Thornton SF, Nicholls HCG, Rolfe SA, Mallinson HEH, Spence MJ. Biodegradation and fate of ethyl tert-butyl ether (ETBE) in soil and groundwater: A review. JOURNAL OF HAZARDOUS MATERIALS 2020; 391:122046. [PMID: 32145642 DOI: 10.1016/j.jhazmat.2020.122046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/07/2019] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
This review summarises the current state of knowledge on the biodegradation and fate of the gasoline ether oxygenate ethyl tert-butyl ether (ETBE) in soil and groundwater. Microorganisms have been identified in soil and groundwater with the ability to degrade ETBE aerobically as a carbon and energy source, or via cometabolism using alkanes as growth substrates. Aerobic biodegradation of ETBE initially occurs via hydroxylation of the ethoxy carbon by a monooxygenase enzyme, with subsequent formation of intermediates which include acetaldehyde, tert-butyl acetate (TBAc), tert-butyl alcohol (TBA), 2-hydroxy-2-methyl-1-propanol (MHP) and 2-hydroxyisobutyric acid (2-HIBA). Slow cell growth and low biomass yields on ETBE are believed to result from the ether structure and slow degradation kinetics, with potential limitations on ETBE metabolism. Genes known to facilitate transformation of ETBE include ethB (within the ethRABCD cluster), encoding a cytochrome P450 monooxygenase, and alkB-encoding alkane hydroxylases. Other genes have been identified in microorganisms but their activity and specificity towards ETBE remains poorly characterised. Microorganisms and pathways supporting anaerobic biodegradation of ETBE have not been identified, although this potential has been demonstrated in limited field and laboratory studies. The presence of co-contaminants (other ether oxygenates, hydrocarbons and organic compounds) in soil and groundwater may limit aerobic biodegradation of ETBE by preferential metabolism and consumption of available dissolved oxygen or enhance ETBE biodegradation through cometabolism. Both ETBE-degrading microorganisms and alkane-oxidising bacteria have been characterised, with potential for use in bioaugmentation and biostimulation of ETBE degradation in groundwater.
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Affiliation(s)
- S F Thornton
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - H C G Nicholls
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - S A Rolfe
- Dept of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Sheffield S10 2TN, UK
| | - H E H Mallinson
- Groundwater Protection and Restoration Group, Dept of Civil and Structural Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - M J Spence
- Concawe, Environmental Science for European Refining, Boulevard du Souverain 165, 1160 Brussels, Belgium
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Jiang B, Jin N, Xing Y, Su Y, Zhang D. Unraveling uncultivable pesticide degraders via stable isotope probing (SIP). Crit Rev Biotechnol 2018; 38:1025-1048. [DOI: 10.1080/07388551.2018.1427697] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Naifu Jin
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Yuping Su
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
- School of Environment, Tsinghua University, Beijing, PR China
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7
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Fischer A, Manefield M, Bombach P. Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies. Curr Opin Biotechnol 2016; 41:99-107. [PMID: 27314918 DOI: 10.1016/j.copbio.2016.04.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/15/2016] [Accepted: 04/29/2016] [Indexed: 11/25/2022]
Abstract
Stable isotope tools are increasingly applied for in-depth evaluation of biodegradation of organic pollutants at contaminated field sites. They can be divided into three methods i) determination of changes in natural abundance of stable isotopes using compound-specific stable isotope analysis (CSIA), ii) detection of incorporation of stable-isotope label from a stable-isotope labelled target compound into degradation and/or mineralisation products and iii) determination of stable-isotope label incorporation into biomarkers using stable isotope probing (SIP). Stable isotope tools have been applied as key monitoring tools for multiple-line-of-evidence-approaches (MLEA) for sensitive evaluation of pollutant biodegradation. This review highlights the application of CSIA, SIP and MLEA including stable isotope tools for assessing natural and stimulated biodegradation of organic pollutants in field studies dealing with soil and groundwater contaminations.
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Affiliation(s)
- Anko Fischer
- Isodetect GmbH, Deutscher Platz 5b, 04103 Leipzig, Germany.
| | - Mike Manefield
- Micronovo Py Ltd, 18 Mason St, Maroubra, NSW, 2035, Australia
| | - Petra Bombach
- Isodetect GmbH, Deutscher Platz 5b, 04103 Leipzig, Germany
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8
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Cupples AM. Contaminant-Degrading Microorganisms Identified Using Stable Isotope Probing. Chem Eng Technol 2016. [DOI: 10.1002/ceat.201500479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Liu T, Ahn H, Sun W, McGuinness LR, Kerkhof LJ, Häggblom MM. Identification of a Ruminococcaceae Species as the Methyl tert-Butyl Ether (MTBE) Degrading Bacterium in a Methanogenic Consortium. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:1455-1464. [PMID: 26727046 DOI: 10.1021/acs.est.5b04731] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The widespread use of methyl tert-butyl ether (MTBE) has caused major contamination of groundwater sources and is a concern due to its taste and odor problems, as well as its toxicity. MTBE can be degraded anaerobically which makes bioremediation of contaminated aquifers a potential solution. Nevertheless, the organisms and mechanisms that are responsible for anaerobic MTBE degradation are still unknown. The aim of our research was to identify the organisms actively degrading MTBE. For this purpose we characterized an anaerobic methanogenic culture enriched with MTBE as the sole carbon source from the New Jersey Arthur Kill intertidal strait sediment. The cultures were analyzed using stable isotope probing (SIP) combined with terminal restriction fragment length polymorphism (T-RFLP), high-throughput sequencing and clone library analysis of bacterial 16S rRNA genes. The sequence data indicated that phylotypes belonging to the Ruminococcaceae in the Firmicutes were predominant in the methanogenic cultures. SIP experiments also showed sequential incorporation of the (13)C labeled MTBE by the bacterial community with a bacterium most closely related to Saccharofermentans acetigenes identified as the bacterium active in O-demethylation of MTBE. Identification of the microorganisms responsible for the activity will help us better understand anaerobic MTBE degradation processes in the field and determine biomarkers for monitoring natural attenuation.
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Affiliation(s)
- Tong Liu
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Hyeri Ahn
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Weimin Sun
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Lora R McGuinness
- Department of Marine and Coastal Science, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Lee J Kerkhof
- Department of Marine and Coastal Science, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, New Jersey 08901, United States
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