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Aldas-Vargas A, Kers JG, Smidt H, Rijnaarts HHM, Sutton NB. Bioaugmentation has temporary effect on anaerobic pesticide biodegradation in simulated groundwater systems. Biodegradation 2024; 35:281-297. [PMID: 37439919 PMCID: PMC10951022 DOI: 10.1007/s10532-023-10039-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/30/2023] [Indexed: 07/14/2023]
Abstract
Groundwater is the most important source for drinking water in The Netherlands. Groundwater quality is threatened by the presence of pesticides, and biodegradation is a natural process that can contribute to pesticide removal. Groundwater conditions are oligotrophic and thus biodegradation can be limited by the presence and development of microbial communities capable of biodegrading pesticides. For that reason, bioremediation technologies such as bioaugmentation (BA) can help to enhance pesticide biodegradation. We studied the effect of BA using enriched mixed inocula in two column bioreactors that simulate groundwater systems at naturally occurring redox conditions (iron and sulfate-reducing conditions). Columns were operated for around 800 days, and two BA inoculations (BA1 and BA2) were conducted in each column. Inocula were enriched from different wastewater treatment plants (WWTPs) under different redox-conditions. We observed a temporary effect of BA1, reaching 100% removal efficiency of the pesticide 2,4-D after 100 days in both columns. In the iron-reducing column, 2,4-D removal was in general higher than under sulfate-reducing conditions demonstrating the influence of redox conditions on overall biodegradation. We observed a temporary shift in microbial communities after BA1 that is relatable to the increase in 2,4-D removal efficiency. After BA2 under sulfate-reducing conditions, 2,4-D removal efficiency decreased, but no change in the column microbial communities was observed. The present study demonstrates that BA with a mixed inoculum can be a valuable technique for improving biodegradation in anoxic groundwater systems at different redox-conditions.
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Affiliation(s)
- Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Jannigje G Kers
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH, Wageningen, The Netherlands
| | - Huub H M Rijnaarts
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands.
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2
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Vogel AL, Thompson KJ, Straub D, Musat F, Gutierrez T, Kleindienst S. Genetic redundancy in the naphthalene-degradation pathway of Cycloclasticus pugetii strain PS-1 enables response to varying substrate concentrations. FEMS Microbiol Ecol 2024; 100:fiae060. [PMID: 38614960 PMCID: PMC11099662 DOI: 10.1093/femsec/fiae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 04/15/2024] Open
Abstract
Polycyclic aromatic hydrocarbon (PAH) contamination in marine environments range from low-diffusive inputs to high loads. The influence of PAH concentration on the expression of functional genes [e.g. those encoding ring-hydroxylating dioxygenases (RHDs)] has been overlooked in PAH biodegradation studies. However, understanding marker-gene expression under different PAH loads can help to monitor and predict bioremediation efficiency. Here, we followed the expression (via RNA sequencing) of Cycloclasticus pugetii strain PS-1 in cell suspension experiments under different naphthalene (100 and 30 mg L-1) concentrations. We identified genes encoding previously uncharacterized RHD subunits, termed rhdPS1α and rhdPS1β, that were highly transcribed in response to naphthalene-degradation activity. Additionally, we identified six RHD subunit-encoding genes that responded to naphthalene exposure. By contrast, four RHD subunit genes were PAH-independently expressed and three other RHD subunit genes responded to naphthalene starvation. Cycloclasticus spp. could, therefore, use genetic redundancy in key PAH-degradation genes to react to varying PAH loads. This genetic redundancy may restrict the monitoring of environmental hydrocarbon-degradation activity using single-gene expression. For Cycloclasticus pugetii strain PS-1, however, the newly identified rhdPS1α and rhdPS1β genes might be potential target genes to monitor its environmental naphthalene-degradation activity.
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Affiliation(s)
- Anjela L Vogel
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Katharine J Thompson
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Daniel Straub
- Eberhard Karls University of Tübingen, Quantitative Biology Center (QBiC), Auf der Morgenstelle 10, Tübingen 72076, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Florin Musat
- Aarhus University, Department of Biology, Section for Microbiology, Ny Munkegade 116, Aarhus C 8000, Denmark
- Babeş-Bolyai University, Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Str. Republicii nr 44, Cluj-Napoca 400015, Romania
| | - Tony Gutierrez
- Heriot-Watt University, Institute of Mechanical Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Edinburgh EH14 4AS, UK
| | - Sara Kleindienst
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
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3
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Vogel AL, Thompson KJ, Straub D, App CB, Gutierrez T, Löffler FE, Kleindienst S. Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation. Front Microbiol 2023; 14:1185619. [PMID: 37455737 PMCID: PMC10338962 DOI: 10.3389/fmicb.2023.1185619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 07/18/2023] Open
Abstract
Microbial degradation of petroleum hydrocarbons is a crucial process for the clean-up of oil-contaminated environments. Cycloclasticus spp. are well-known polycyclic aromatic hydrocarbon (PAH) degraders that possess PAH-degradation marker genes including rhd3α, rhd2α, and pahE. However, it remains unknown if the expression of these genes can serve as an indicator for active PAH degradation. Here, we determined transcript-to-gene (TtG) ratios with (reverse transcription) qPCR in cultures of Cycloclasticus pugetii strain PS-1 grown with naphthalene, phenanthrene, a mixture of these PAHs, or alternate substrates (i.e., no PAHs). Mean TtG ratios of 1.99 × 10-2, 1.80 × 10-3, and 3.20 × 10-3 for rhd3α, rhd2α, and pahE, respectively, were measured in the presence or absence of PAHs. The TtG values suggested that marker-gene expression is independent of PAH degradation. Measurement of TtG ratios in Arctic seawater microcosms amended with water-accommodated crude oil fractions, and incubated under in situ temperature conditions (i.e., 1.5°C), only detected Cycloclasticus spp. rhd2α genes and transcripts (mean TtG ratio of 4.15 × 10-1). The other marker genes-rhd3α and pahE-were not detected, suggesting that not all Cycloclasticus spp. carry these genes and a broader yet-to-be-identified repertoire of PAH-degradation genes exists. The results indicate that the expression of PAH marker genes may not correlate with PAH-degradation activity, and transcription data should be interpreted cautiously.
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Affiliation(s)
- Anjela L. Vogel
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, Germany
| | - Katharine J. Thompson
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, Germany
| | - Daniel Straub
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Constantin B. App
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Tony Gutierrez
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom
| | - Frank E. Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States
| | - Sara Kleindienst
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, Germany
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4
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Vogel AL, Thompson KJ, Kleindienst S, Zarfl C. Dosage concentration and pulsing frequency affect the degradation efficiency in simulated bacterial polycyclic aromatic hydrocarbon-degrading cultures. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:59813-59825. [PMID: 37016250 PMCID: PMC10163121 DOI: 10.1007/s11356-023-26546-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/15/2023] [Indexed: 05/08/2023]
Abstract
A major source of anthropogenic polycyclic aromatic hydrocarbon (PAH) inputs into marine environments are diffuse emissions which result in low PAH concentrations in the ocean water, posing a potential threat for the affected ecosystems. However, the remediation of low-dosage PAH contaminations through microbial processes remains largely unknown. Here, we developed a process-based numerical model to simulate batch cultures receiving repeated low-dosage naphthalene pulses compared to the conventionally used one-time high-dosage. Pulsing frequency as well as dosage concentration had a large impact on the degradation efficiency. After 10 days, 99.7%, 97.2%, 86.6%, or 83.5% of the 145 mg L-1 naphthalene was degraded when given as a one-time high-dosage or in 2, 5, or 10 repeated low-concentration dosages equally spaced throughout the experiment, respectively. If the simulation was altered, giving the system that received 10 pulses time to recover to 99.7%, pulsing patterns affected the degradation of naphthalene. When pulsing 10 days at once per day, naphthalene accumulated following each pulse and if the degradation was allowed to continue until the recovered state was reached, the incubation time was prolonged to 17 days with a generation time of 3.81 days. If a full recovery was conditional before the next pulse was added, the scenario elongated to 55 days and generation time increased to 14.15 days. This indicates that dissolution kinetics dominate biodegradation kinetics, and the biomass concentration of PAH-degrading bacteria alone is not a sufficient indicator for quantifying active biodegradation. Applying those findings to the environment, a one-time input of a high dosage is potentially degraded faster than repeated low-dosage PAH pollution and repeated low-dosage input could lead to PAH accumulation in vulnerable pristine environments. Further research on the overlooked field of chronic low-dosage PAH contamination is necessary.
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Affiliation(s)
- Anjela L Vogel
- Department of Geosciences, Eberhard Karls University of Tübingen, Schnarrenbergstr. 94-96, 72076, Tübingen, Germany.
| | - Katharine J Thompson
- Department of Geosciences, Eberhard Karls University of Tübingen, Schnarrenbergstr. 94-96, 72076, Tübingen, Germany
| | - Sara Kleindienst
- Department of Geosciences, Eberhard Karls University of Tübingen, Schnarrenbergstr. 94-96, 72076, Tübingen, Germany
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, Germany
| | - Christiane Zarfl
- Department of Geosciences, Eberhard Karls University of Tübingen, Schnarrenbergstr. 94-96, 72076, Tübingen, Germany
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5
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Aldas-Vargas A, Poursat BAJ, Sutton NB. Potential and limitations for monitoring of pesticide biodegradation at trace concentrations in water and soil. World J Microbiol Biotechnol 2022; 38:240. [PMID: 36261779 PMCID: PMC9581840 DOI: 10.1007/s11274-022-03426-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022]
Abstract
Pesticides application on agricultural fields results in pesticides being released into the environment, reaching soil, surface water and groundwater. Pesticides fate and transformation in the environment depend on environmental conditions as well as physical, chemical and biological degradation processes. Monitoring pesticides biodegradation in the environment is challenging, considering that traditional indicators, such as changes in pesticides concentration or identification of pesticide metabolites, are not suitable for many pesticides in anaerobic environments. Furthermore, those indicators cannot distinguish between biotic and abiotic pesticide degradation processes. For that reason, the use of molecular tools is important to monitor pesticide biodegradation-related genes or microorganisms in the environment. The development of targeted molecular (e.g., qPCR) tools, although laborious, allowed biodegradation monitoring by targeting the presence and expression of known catabolic genes of popular pesticides. Explorative molecular tools (i.e., metagenomics & metatranscriptomics), while requiring extensive data analysis, proved to have potential for screening the biodegradation potential and activity of more than one compound at the time. The application of molecular tools developed in laboratory and validated under controlled environments, face challenges when applied in the field due to the heterogeneity in pesticides distribution as well as natural environmental differences. However, for monitoring pesticides biodegradation in the field, the use of molecular tools combined with metadata is an important tool for understanding fate and transformation of the different pesticides present in the environment.
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Affiliation(s)
- Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Baptiste A J Poursat
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands.
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6
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Schwarz E, Khurana S, Chakrawal A, Chavez Rodriguez L, Wirsching J, Streck T, Manzoni S, Thullner M, Pagel H. Spatial Control of Microbial Pesticide Degradation in Soil: A Model-Based Scenario Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14427-14438. [PMID: 36166755 PMCID: PMC9583605 DOI: 10.1021/acs.est.2c03397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/12/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Microbial pesticide degraders are heterogeneously distributed in soil. Their spatial aggregation at the millimeter scale reduces the frequency of degrader-pesticide encounter and can introduce transport limitations to pesticide degradation. We simulated reactive pesticide transport in soil to investigate the fate of the widely used herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) in response to differently aggregated distributions of degrading microbes. Four scenarios were defined covering millimeter scale heterogeneity from homogeneous (pseudo-1D) to extremely heterogeneous degrader distributions and two precipitation scenarios with either continuous light rain or heavy rain events. Leaching from subsoils did not occur in any scenario. Within the topsoil, increasing spatial heterogeneity of microbial degraders reduced macroscopic degradation rates, increased MCPA leaching, and prolonged the persistence of residual MCPA. In heterogeneous scenarios, pesticide degradation was limited by the spatial separation of degrader and pesticide, which was quantified by the spatial covariance between MCPA and degraders. Heavy rain events temporarily lifted these transport constraints in heterogeneous scenarios and increased degradation rates. Our results indicate that the mild millimeter scale spatial heterogeneity of degraders typical for arable topsoil will have negligible consequences for the fate of MCPA, but strong clustering of degraders can delay pesticide degradation.
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Affiliation(s)
- Erik Schwarz
- Department
of Physical Geography, Stockholm University, 10691 Stockholm, Sweden
- Bolin
Centre for Climate Research, Stockholm University, 10691 Stockholm, Sweden
- Institute
of Soil Science and Land Evaluation, Biogeophysics, University of Hohenheim, 70599 Stuttgart, Germany
| | - Swamini Khurana
- Department
of Physical Geography, Stockholm University, 10691 Stockholm, Sweden
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research (UFZ), 04318 Leipzig, Germany
| | - Arjun Chakrawal
- Department
of Physical Geography, Stockholm University, 10691 Stockholm, Sweden
- Bolin
Centre for Climate Research, Stockholm University, 10691 Stockholm, Sweden
| | - Luciana Chavez Rodriguez
- Institute
of Soil Science and Land Evaluation, Biogeophysics, University of Hohenheim, 70599 Stuttgart, Germany
- Department
of Ecology and Evolutionary Biology, University
of California Irvine, Irvine, California 92697, United States
| | - Johannes Wirsching
- Institute
of Soil Science and Land Evaluation, Soil Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Thilo Streck
- Institute
of Soil Science and Land Evaluation, Biogeophysics, University of Hohenheim, 70599 Stuttgart, Germany
| | - Stefano Manzoni
- Department
of Physical Geography, Stockholm University, 10691 Stockholm, Sweden
- Bolin
Centre for Climate Research, Stockholm University, 10691 Stockholm, Sweden
| | - Martin Thullner
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research (UFZ), 04318 Leipzig, Germany
- Federal
Institute for Geosciences and Natural Resources (BGR), 30655 Hannover, Germany
| | - Holger Pagel
- Institute
of Soil Science and Land Evaluation, Biogeophysics, University of Hohenheim, 70599 Stuttgart, Germany
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7
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White AM, Nault ME, McMahon KD, Remucal CK. Synthesizing Laboratory and Field Experiments to Quantify Dominant Transformation Mechanisms of 2,4-Dichlorophenoxyacetic Acid (2,4-D) in Aquatic Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10838-10848. [PMID: 35856571 DOI: 10.1021/acs.est.2c03132] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Laboratory studies used to assess the environmental fate of organic chemicals such as pesticides fail to replicate environmental conditions, resulting in large errors in predicted transformation rates. We combine laboratory and field data to identify the dominant loss processes of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) in lakes for the first time. Microbial and photochemical degradation are individually assessed using laboratory-based microcosms and irradiation studies, respectively. Field campaigns are conducted in six lakes to quantify 2,4-D loss following large-scale herbicide treatments. Irradiation studies show that 2,4-D undergoes direct photodegradation, but modeling efforts demonstrated that this process is negligible under environmental conditions. Microcosms constructed using field inocula show that sediment microbial communities are responsible for degradation of 2,4-D in lakes. Attempts to quantify transformation products are unsuccessful in both laboratory and field studies, suggesting that their persistence is not a major concern. The synthesis of laboratory and field experiments is used to demonstrate best practices in designing laboratory persistence studies and in using those results to mechanistically predict contaminant fate in complex aquatic environments.
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Affiliation(s)
- Amber M White
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Michelle E Nault
- Wisconsin Department of Natural Resources Madison, Bureau of Water Quality, Madison, Wisconsin 53707, United States
| | - Katherine D McMahon
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Bacteriology, University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - Christina K Remucal
- Environmental Chemistry and Technology Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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8
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Wang J, Poursat BAJ, Feng J, de Ridder D, Zhang C, van der Wal A, Sutton NB. Exploring organic micropollutant biodegradation under dynamic substrate loading in rapid sand filters. WATER RESEARCH 2022; 221:118832. [PMID: 35949068 DOI: 10.1016/j.watres.2022.118832] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Microbial removal of trace organic micropollutants (OMPs) from drinking water sources remains challenging. Nitrifying and heterotrophic bacteria in rapid sand filters (RSFs) are capable of biodegrading OMPs while growing on ammonia and dissolved organic matter (DOM). The loading patterns of ammonia and DOM may therefore affect microbial activities as well as OMP biodegradation. So far, there is very limited information on the effect of substrate loading on OMP biodegradation at environmentally relevant concentrations (∼ 1 µg/L) in RSFs. We investigated the biodegradation rates of 16 OMPs at various substrate loading rates and/or empty bed contact times (EBCT). The presence of DOM improved the biodegradation of paracetamol (41.8%) by functioning as supplementary carbon source for the heterotrophic degrader, while hindering the biodegradation of 2,4-D, mecoprop and benzotriazole due to substrate competition. Lower loading ratios of DOM/benzotriazole benefited benzotriazole biodegradation by reducing substrate competition. Higher ammonia loading rates enhanced benzotriazole removal by stimulating nitrification-based co-metabolism. However, stimulating nitrification inhibited heterotrophic activity, which in turn inhibited the biodegradation of paracetamol, 2,4-D and mecoprop. A longer EBCT promoted metformin biodegradation as it is a slowly biodegradable compound, but suppressed the biodegradation of paracetamol and benzotriazole due to limited substrate supply. Therefore, the optimal substrate loading pattern is contingent on the type of OMP, which can be chosen based on the priority compounds in practice. The overall results contribute to understanding OMP biodegradation mechanisms at trace concentrations and offer a step towards enhancing microbial removal of OMPs from drinking water by optimally using RSFs.
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Affiliation(s)
- Jinsong Wang
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Baptiste A J Poursat
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Jiahao Feng
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - David de Ridder
- Evides Water Company N.V., Schaardijk 150, 3063 NH Rotterdam, The Netherlands
| | - Chen Zhang
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700 EH Wageningen, The Netherlands
| | - Albert van der Wal
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands; Evides Water Company N.V., Schaardijk 150, 3063 NH Rotterdam, The Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands.
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9
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Gorodylova N, Michel C, Seron A, Joulian C, Delorme F, Bresch S, Garreau C, Giovannelli F, Michel K. Modified zeolite-supported biofilm in service of pesticide biodegradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:45296-45316. [PMID: 33864216 DOI: 10.1007/s11356-021-13876-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
The development of biofilms on modified natural zeolites was investigated with purpose to obtain biocomposites with biodegradation activity towards pesticides MCPA (2-methyl-4-chlorophenoxyacetic acid) and glyphosate (N-(phosphonomethyl)glycine) for potential application in bioaugmentation of polluted agricultural soils. Microbial communities were selected from agricultural pesticide-contaminated soil/water samples and enriched on the basis of their ability to biodegrade the pesticides. In order to enhance affinity of microbial communities to the support material, the natural mineral zeolite was modified by nontoxic environmentally friendly cations (Li+, Na+, K+, NH4+, H+, Mg2+, Ca2+, Fe3+) by methods preserving its structure and characterised using powder XRD, surface area measurement and chemical composition analysis. Kinetics of pesticide degradation by the biocomposites was studied in liquid media. Results showed that according to zeolite modifications, the microbial activity and biodiversity changed. The best biodegradation rate of MCPA and glyphosate reached 0.12-0.13 mg/h with half-life of 16-18 h, which is considerably quicker than observed in natural environment. However, in some cases, biodegradation activity towards pesticides was lost which was connected to unfavourable zeolite modification and accumulation of toxic metabolites. High-throughput sequencing on the 16S rRNA genes of the biofilm communities highlighted the selection of bacteria genera known to metabolise MCPA (Aminobacter, Cupriavidus, Novosphingobium, Pseudomonas, Rhodococcus, Sphingobium and Sphingopyxis) and glyphosate (Pseudomonas). Altogether, results suggested that zeolites do not only have a passive role of biofilm support but also have protective and nutrient-supportive functions that consequently increase biodiversity of the pesticide degraders growing in the biofilm and influence the pesticide biodegradation rate.
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Affiliation(s)
- Nataliia Gorodylova
- Division of Water, Environment, Process and Analyses (DEPA), BRGM, The French Geological Survey, 3 Avenue Claude Guillemin, 45100, Orléans, France.
- CNRS, INSA CVL, GREMAN UMR 7347, IUT de Blois, GREMAN, University of Tours, 15 Rue de la Chocolaterie, 41029, Blois, France.
- University of Pardubice, Studentska 95, 53210, Pardubice, Czech Republic.
| | - Caroline Michel
- Division of Water, Environment, Process and Analyses (DEPA), BRGM, The French Geological Survey, 3 Avenue Claude Guillemin, 45100, Orléans, France
| | - Alain Seron
- Division of Water, Environment, Process and Analyses (DEPA), BRGM, The French Geological Survey, 3 Avenue Claude Guillemin, 45100, Orléans, France
| | - Catherine Joulian
- Division of Water, Environment, Process and Analyses (DEPA), BRGM, The French Geological Survey, 3 Avenue Claude Guillemin, 45100, Orléans, France
| | - Fabian Delorme
- CNRS, INSA CVL, GREMAN UMR 7347, IUT de Blois, GREMAN, University of Tours, 15 Rue de la Chocolaterie, 41029, Blois, France
| | - Sophie Bresch
- CDHR Centre-Val-de-Loire, 620 Rue de Cornay, Saint-Cyr-en-Val, 45590, France
| | | | - Fabien Giovannelli
- CNRS, INSA CVL, GREMAN UMR 7347, IUT de Blois, GREMAN, University of Tours, 15 Rue de la Chocolaterie, 41029, Blois, France
| | - Karine Michel
- Division of Water, Environment, Process and Analyses (DEPA), BRGM, The French Geological Survey, 3 Avenue Claude Guillemin, 45100, Orléans, France
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10
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Carles L, Martin-Laurent F, Devers M, Spor A, Rouard N, Beguet J, Besse-Hoggan P, Batisson I. Potential of preventive bioremediation to reduce environmental contamination by pesticides in an agricultural context: A case study with the herbicide 2,4-D. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:125740. [PMID: 33848793 DOI: 10.1016/j.jhazmat.2021.125740] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/01/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
One of the major problems with pesticides is linked to the non-negligible proportion of the sprayed active ingredient that does not reach its intended target and contaminates environmental compartments. Here, we have implemented and provided new insights to the preventive bioremediation process based on the simultaneous application of the pesticide with pesticide-degrading microorganisms to reduce the risk of leaching into the environment. This study pioneers such a practice, in an actual farming context. The 2,4-dichlorophenoxyacetic acid herbicide (2,4-D) and one of its bacterial mineralizing-strains (Cupriavidus necator JMP134) were used as models. The 2,4-D biodegradation was studied in soil microcosms planted with sensitive (mustard) and insensitive (wheat) plants. Simultaneous application of a 2,4-D commercial formulation (DAM®) at agricultural recommended doses with 105 cells.g-1 dw of soil of the JMP134 strain considerably accelerated mineralization of the herbicide since its persistence was reduced threefold for soil supplemented with the mineralizing bacterium without reducing the herbicide efficiency. Furthermore, the inoculation of the Cupriavidus necator strain did not significantly affect the α- and β-diversity of the bacterial community. By tackling the contamination immediately at source, the preventive bioremediation process proves to be an effective and promising way to reduce environmental contamination by agricultural pesticides.
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Affiliation(s)
- Louis Carles
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement (LMGE), F-63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Sigma Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France.
| | - Fabrice Martin-Laurent
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Marion Devers
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Aymé Spor
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Nadine Rouard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Jérémie Beguet
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ., Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Pascale Besse-Hoggan
- Université Clermont Auvergne, CNRS, Sigma Clermont, Institut de Chimie de Clermont-Ferrand (ICCF), F-63000 Clermont-Ferrand, France
| | - Isabelle Batisson
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement (LMGE), F-63000 Clermont-Ferrand, France
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11
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Störiko A, Pagel H, Mellage A, Cirpka OA. Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models? Front Microbiol 2021; 12:684146. [PMID: 34220770 PMCID: PMC8250433 DOI: 10.3389/fmicb.2021.684146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Environmental omics and molecular-biological data have been proposed to yield improved quantitative predictions of biogeochemical processes. The abundances of functional genes and transcripts relate to the number of cells and activity of microorganisms. However, whether molecular-biological data can be quantitatively linked to reaction rates remains an open question. We present an enzyme-based denitrification model that simulates concentrations of transcription factors, functional-gene transcripts, enzymes, and solutes. We calibrated the model using experimental data from a well-controlled batch experiment with the denitrifier Paracoccous denitrificans. The model accurately predicts denitrification rates and measured transcript dynamics. The relationship between simulated transcript concentrations and reaction rates exhibits strong non-linearity and hysteresis related to the faster dynamics of gene transcription and substrate consumption, relative to enzyme production and decay. Hence, assuming a unique relationship between transcript-to-gene ratios and reaction rates, as frequently suggested, may be an erroneous simplification. Comparing model results of our enzyme-based model to those of a classical Monod-type model reveals that both formulations perform equally well with respect to nitrogen species, indicating only a low benefit of integrating molecular-biological data for estimating denitrification rates. Nonetheless, the enzyme-based model is a valuable tool to improve our mechanistic understanding of the relationship between biomolecular quantities and reaction rates. Furthermore, our results highlight that both enzyme kinetics (i.e., substrate limitation and inhibition) and gene expression or enzyme dynamics are important controls on denitrification rates.
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Affiliation(s)
- Anna Störiko
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Holger Pagel
- Biogeophysics, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Adrian Mellage
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Olaf A. Cirpka
- Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
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12
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Michel C, Baran N, André L, Charron M, Joulian C. Side Effects of Pesticides and Metabolites in Groundwater: Impact on Denitrification. Front Microbiol 2021; 12:662727. [PMID: 34054765 PMCID: PMC8155494 DOI: 10.3389/fmicb.2021.662727] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/30/2021] [Indexed: 01/16/2023] Open
Abstract
The impact of two pesticides (S-metolachlor and propiconazole) and their respective main metabolites (ESA-metolachlor and 1,2,4-triazole) on bacterial denitrification in groundwater was studied. For this, the denitrification activity and the bacterial diversity of a microbial community sampled from a nitrate-contaminated groundwater were monitored during 20 days in lab experiments in the presence or absence of pesticides or metabolites at 2 or 10 μg/L. The kinetics of nitrate reduction along with nitrite and N2O production all suggested that S-metolachlor had no or only little impact, whereas its metabolite ESA-metolachlor inhibited denitrification by 65% at 10 μg/L. Propiconazole and 1,2,4-triazole also inhibited denitrification at both concentrations, but to a lesser extent (29–38%) than ESA-metolachlor. When inhibition occurred, pesticides affected the reduction of nitrate into nitrite step. However, no significant differences were detected on the abundance of nitrate reductase narG and napA genes, suggesting an impact of pesticides/metabolites at the protein level rather than on denitrifying bacteria abundance. 16S rRNA gene Illumina sequencing indicated no major modification of bacterial diversity in the presence or absence of pesticides/metabolites, except for ESA-metolachlor and propiconazole at 10 μg/L that tended to increase or decrease Shannon and InvSimpson indices, respectively. General growth parameters suggested no impact of pesticides, except for propiconazole at 10 μg/L that partially inhibited acetate uptake and induced a decrease in microbial biomass. In conclusion, pesticides and metabolites can have side effects at environmental concentrations on microbial denitrification in groundwater and may thus affect ecosystem services based on microbial activities.
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Affiliation(s)
- Caroline Michel
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
| | - Nicole Baran
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
| | - Laurent André
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France.,Université d'Orléans, CNRS, BRGM, UMR 7327 Institut des Sciences de la Terre d'Orléans, Orléans, France
| | - Mickael Charron
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
| | - Catherine Joulian
- BRGM, DEPA (Direction de l'Eau, de l'Environnement, des Procédés et Analyses), Orléans, France
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13
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Rahman I, Mujahid A, Palombo EA, Müller M. A functional gene-array analysis of microbial communities settling on microplastics in a peat-draining environment. MARINE POLLUTION BULLETIN 2021; 166:112226. [PMID: 33711605 DOI: 10.1016/j.marpolbul.2021.112226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Concerns about microplastic (MP) pollution arise from the rafting potential of these durable particles which potentially propagate harmful chemicals and bacteria across wide spatial gradients. While many studies have been conducted in the marine environment, knowledge of MPs in coastal and freshwater systems is limited. For this study, we exposed two MPs (polyethylene terephthalate and polylactic acid) to the undisturbed peat-draining Maludam River in Malaysia, for 6 months. The microbial communities on these MPs and the surrounding water were sequenced by MiSeq, while the genetic responses of these communities were assessed by GeoChip 5.0S. Microbial communities were dominated by the phyla Proteobacteria, Acidobacteria and Actinobacteria. Metabolic processes involved with carbon, nitrogen, sulfur, metal homeostasis, organic remediation and virulence had significantly different gene expression among the communities on MPs and in the surrounding water. Our study is the first to look at changes in gene expression of whole plastisphere communities.
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Affiliation(s)
- Ishraq Rahman
- Faculty of Engineering, Computing and Science, Swinburne University of Technology, Sarawak Campus, 93350 Kuching, Sarawak, Malaysia; International University of Business, Agriculture and Technology (IUBAT), Uttara, Dhaka 1230, Bangladesh
| | - Aazani Mujahid
- Faculty of Resource Science & Technology, University Malaysia Sarawak, 94300, Sarawak, Malaysia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Moritz Müller
- Faculty of Engineering, Computing and Science, Swinburne University of Technology, Sarawak Campus, 93350 Kuching, Sarawak, Malaysia.
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14
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Chavez Rodriguez L, Ingalls B, Schwarz E, Streck T, Uksa M, Pagel H. Gene-Centric Model Approaches for Accurate Prediction of Pesticide Biodegradation in Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:13638-13650. [PMID: 33064475 DOI: 10.1021/acs.est.0c03315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pesticides are widely used in agriculture despite their negative impact on ecosystems and human health. Biogeochemical modeling facilitates the mechanistic understanding of microbial controls on pesticide turnover in soils. We propose to inform models of coupled microbial dynamics and pesticide turnover with measurements of the abundance and expression of functional genes. To assess the advantages of informing models with genetic data, we developed a novel "gene-centric" model and compared model variants of differing structural complexity against a standard biomass-based model. The models were calibrated and validated using data from two batch experiments in which the degradation of the pesticides dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxyacetic acid (MCPA) were observed in soil. When calibrating against data on pesticide mineralization, the gene-centric and biomass-based models performed equally well. However, accounting for pesticide-triggered gene regulation allows improved performance in capturing microbial dynamics and in predicting pesticide mineralization. This novel modeling approach also reveals a hysteretic relationship between pesticide degradation rates and gene expression, implying that the biodegradation performance in soils cannot be directly assessed by measuring the expression of functional genes. Our gene-centric model provides an effective approach for exploiting molecular biology data to simulate pesticide degradation in soils.
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Affiliation(s)
- Luciana Chavez Rodriguez
- Institute of Soil Science and Land Evaluation, Biogeophysics Section, University of Hohenheim, Stuttgart, Germany
| | - Brian Ingalls
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada
| | - Erik Schwarz
- Institute of Soil Science and Land Evaluation, Biogeophysics Section, University of Hohenheim, Stuttgart, Germany
| | - Thilo Streck
- Institute of Soil Science and Land Evaluation, Biogeophysics Section, University of Hohenheim, Stuttgart, Germany
| | - Marie Uksa
- Institute of Soil Science and Land Evaluation, Soil Biology Section, University of Hohenheim, Stuttgart, Germany
| | - Holger Pagel
- Institute of Soil Science and Land Evaluation, Biogeophysics Section, University of Hohenheim, Stuttgart, Germany
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15
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Aguilar-Rangel EJ, Prado BL, Vásquez-Murrieta MS, Los Santos PED, Siebe C, Falcón LI, Santillán J, Alcántara-Hernández RJ. Temporal analysis of the microbial communities in a nitrate-contaminated aquifer and the co-occurrence of anammox, n-damo and nitrous-oxide reducing bacteria. JOURNAL OF CONTAMINANT HYDROLOGY 2020; 234:103657. [PMID: 32777591 DOI: 10.1016/j.jconhyd.2020.103657] [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: 01/08/2020] [Revised: 04/13/2020] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
Groundwater-N pollution derives from agricultural and urban activities, and compromises water quality in shallow aquifers, putting human and environmental health at risk. Nonetheless, subsurface microbiota can transform dissolved inorganic nitrogen into N2. In this study, we surveyed the microbial community of a shallow aquifer by sampling one well, one piezometer and a spring within an agricultural area that receives N-inputs of more than 700 kg/ha per year through irrigation with wastewater. The survey was conducted during a year with a 16S rRNA next-gen approach. In parallel, we quantified the number of gene copies and transcripts related to anaerobic ammonium oxidation (anammox, hzo), nitrite-dependent anaerobic methane oxidation (n-damo, nod and pmoA) and nitrous oxide reduction (last step of denitrification, nosZ), during the dry and rainy seasons. Our results showed that the groundwater samples had 17.7 to 22.5 mg/L of NO3--N. The bacterial and archaeal community structure was distinctive at each site, and it remained relatively stable over time. We verified the co-occurrence of N-transforming bacteria, which was correlated with the concentration of NO2-/NO3- and ORP/DO values (DO: ~3.0 mg/L). Our analyses suggest that these conditions may allow the presence of nitrifying microorganisms which can couple with anammox, n-damo and denitrifying bacteria in interrelated biogeochemical pathways. Gene density (as the number of gene copies per litre) was lower in the rainy season than in the dry season, possibly due to dilution by rainwater infiltration. Yet, the numbers of hzo gene copies here found were similar to those reported in oceanic oxygen minimum zones and in a carbonate-rock aquifer. The transcript sequences showed that Candidatus Brocadia spp. (anammox), Candidatus Methylomirabilis spp. (n-damo) and autotrophic denitrifying Betaproteobacteria coexist in the groundwater environment, with the potential to attenuate the concentration of dissolved inorganic nitrogen by reducing it to N2 rather than N2O; delivering thus, an important ecosystem service to remove contaminants.
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Affiliation(s)
- Eduardo J Aguilar-Rangel
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - Blanca L Prado
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - María Soledad Vásquez-Murrieta
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Del. Miguel Hidalgo, 11340 Ciudad de México, Mexico
| | - Paulina Estrada-de Los Santos
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Del. Miguel Hidalgo, 11340 Ciudad de México, Mexico
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - Luisa I Falcón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Yucatán, Mexico
| | - Jazmín Santillán
- Posgrado en Ciencias de la Tierra, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - Rocío J Alcántara-Hernández
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico.
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16
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Storck V, Gallego S, Vasileiadis S, Hussain S, Béguet J, Rouard N, Baguelin C, Perruchon C, Devers-Lamrani M, Karpouzas DG, Martin-Laurent F. Insights into the Function and Horizontal Transfer of Isoproturon Degradation Genes ( pdmAB) in a Biobed System. Appl Environ Microbiol 2020; 86:e00474-20. [PMID: 32414799 PMCID: PMC7357488 DOI: 10.1128/aem.00474-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/30/2020] [Indexed: 01/10/2023] Open
Abstract
Biobeds, designed to minimize pesticide point source contamination, rely mainly on biodegradation processes. We studied the interactions of a biobed microbial community with the herbicide isoproturon (IPU) to explore the role of the pdmA gene, encoding the large subunit of an N-demethylase responsible for the initial demethylation of IPU, via quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR) and the effect of IPU on the diversity of the total bacterial community and its active fraction through amplicon sequencing of DNA and RNA, respectively. We further investigated the localization and dispersal mechanisms of pdmAB in the biobed packing material by measuring the abundance of the plasmid pSH (harboring pdmAB) of the IPU-degrading Sphingomonas sp. strain SH (previously isolated from the soil used in the biobed) compared with the abundance of the pdmA gene and metagenomic fosmid library screening. pdmA abundance and expression increased concomitantly with IPU mineralization, verifying its major role in IPU transformation in the biobed system. DNA- and RNA-based 16S rRNA gene sequencing analysis showed no effects on bacterial diversity. The pdmAB-harboring plasmid pSH showed a consistently lower abundance than pdmA, suggesting the localization of pdmAB in replicons other than pSH. Metagenomic analysis identified four pdmAB-carrying fosmids. In three of these fosmids, the pdmAB genes were organized in a well-conserved operon carried by sphingomonad plasmids with low synteny with pSH, while the fourth fosmid contained an incomplete pdmAB cassette localized in a genomic fragment of a Rhodanobacter strain. Further analysis suggested a potentially crucial role of IS6 and IS256 in the transposition and activation of the pdmAB operon.IMPORTANCE Our study provides novel insights into the interactions of IPU with the bacterial community of biobed systems, reinforces the assumption of a transposable nature of IPU-degrading genes, and verifies that on-farm biobed systems are hot spots for the evolution of pesticide catabolic traits.
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Affiliation(s)
- Veronika Storck
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Sara Gallego
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Sotirios Vasileiadis
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, Larisa, Greece
| | - Sabir Hussain
- Department of Environmental Sciences and Engineering, Government College, University of Faisalabad, Faisalabad, Pakistan
| | - Jérémie Béguet
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Nadine Rouard
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Céline Baguelin
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, Larisa, Greece
- Hydreka Enoveo, Lyon, France
| | - Chiara Perruchon
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, Larisa, Greece
| | - Marion Devers-Lamrani
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis, Larisa, Greece
| | - Fabrice Martin-Laurent
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
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17
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Schostag MD, Albers CN, Jacobsen CS, Priemé A. Low Turnover of Soil Bacterial rRNA at Low Temperatures. Front Microbiol 2020; 11:962. [PMID: 32523564 PMCID: PMC7261852 DOI: 10.3389/fmicb.2020.00962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/22/2020] [Indexed: 12/02/2022] Open
Abstract
Ribosomal RNA (rRNA) is used widely to investigate potentially active microorganisms in environmental samples, including soil microorganisms and other microbial communities that are subjected to pronounced seasonal variation in temperature. This raises a question about the turnover of intracellular microbial rRNA at environmentally relevant temperatures. We analyzed the turnover at four temperatures of RNA isolated from soil bacteria amended with 14C-labeled uridine. We found that the half-life of recently produced RNA increased from 4.0 days at 20°C to 15.8 days at 4°C, and 215 days at −4°C, while no degradation was detected at −18°C during a 1-year period. We discuss the implications of the strong temperature dependency of rRNA turnover for interpretation of microbiome data based on rRNA isolated from environmental samples.
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Affiliation(s)
- Morten Dencker Schostag
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Christian Nyrop Albers
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, Denmark.,Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Carsten Suhr Jacobsen
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, Denmark.,Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Anders Priemé
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
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18
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Monteiro DA, Fonseca EDS, Rodrigues RDAR, da Silva JJN, da Silva EP, Balieiro FDC, Alves BJR, Rachid CTCDC. Structural and functional shifts of soil prokaryotic community due to Eucalyptus plantation and rotation phase. Sci Rep 2020; 10:9075. [PMID: 32493970 PMCID: PMC7270125 DOI: 10.1038/s41598-020-66004-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/27/2020] [Indexed: 11/09/2022] Open
Abstract
Agriculture, forestry and other land uses are currently the second highest source of anthropogenic greenhouse gases (GHGs) emissions. In soil, these gases derive from microbial activity, during carbon (C) and nitrogen (N) cycling. To investigate how Eucalyptus land use and growth period impact the microbial community, GHG fluxes and inorganic N levels, and if there is a link among these variables, we monitored three adjacent areas for 9 months: a recently planted Eucalyptus area, fully developed Eucalyptus forest (final of rotation) and native forest. We assessed the microbial community using 16S rRNA gene sequencing and qPCR of key genes involved in C and N cycles. No considerable differences in GHG flux were evident among the areas, but logging considerably increased inorganic N levels. Eucalyptus areas displayed richer and more diverse communities, with selection for specific groups. Land use influenced communities more extensively than the time of sampling or growth phase, although all were significant modulators. Several microbial groups and genes shifted temporally, and inorganic N levels shaped several of these changes. No correlations among microbial groups or genes and GHG were found, suggesting no link among these variables in this short-rotation Eucalyptus study.
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Affiliation(s)
- Douglas Alfradique Monteiro
- LABEM - Laboratory of Biotechnology and Microbial Ecology, Institute of Microbiology Paulo de Góes, Department of General Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eduardo da Silva Fonseca
- LABEM - Laboratory of Biotechnology and Microbial Ecology, Institute of Microbiology Paulo de Góes, Department of General Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | | | - Caio Tavora Coelho da Costa Rachid
- LABEM - Laboratory of Biotechnology and Microbial Ecology, Institute of Microbiology Paulo de Góes, Department of General Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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19
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Cao Y, Yu M, Dong G, Chen B, Zhang B. Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation. Molecules 2020; 25:molecules25030706. [PMID: 32041334 PMCID: PMC7037809 DOI: 10.3390/molecules25030706] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022] Open
Abstract
Biodegradation of contaminants is extremely complicated due to unpredictable microbial behaviors. Monitoring of microbial biodegradation drives us to determine (1) the amounts of specific degrading microbes, (2) the abundance, and (3) expression level of relevant functional genes. To this endeavor, the cultivation independent polymerase chain reaction (PCR)-based monitoring technique develops from endpoint PCR, real-time quantitative PCR, and then into novel digital PCR. In this review, we introduce these three categories of PCR techniques and summarize the timely applications of digital PCR and its superiorities than qPCR for biodegradation monitoring. Digital PCR technique, emerging as the most accurately absolute quantification method, can serve as the most promising and robust tool for monitoring of microbial biodegradation.
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Affiliation(s)
| | | | | | - Bing Chen
- Correspondence: (B.C.); (B.Z.); Tel.: +1-709-864-8958 (B.C.); +1-709-864-3301 (B.Z.)
| | - Baiyu Zhang
- Correspondence: (B.C.); (B.Z.); Tel.: +1-709-864-8958 (B.C.); +1-709-864-3301 (B.Z.)
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Sharma PK, Sharma V, Sharma S, Bhatia G, Singh K, Sharma R. Comparative metatranscriptome analysis revealed broad response of microbial communities in two soil types, agriculture versus organic soil. J Genet Eng Biotechnol 2019; 17:6. [PMID: 31659568 PMCID: PMC6821142 DOI: 10.1186/s43141-019-0006-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 09/05/2019] [Indexed: 01/11/2023]
Abstract
BACKGROUND Studying expression of genes by direct sequencing and analysis of metatranscriptomes at a particular time and space can disclose structural and functional insights about microbial communities. The present study reports comparative analysis of metatranscriptome from two distinct soil ecosystems referred as M1 (agriculture soil) and O1 (organic soil). RESULTS Analysis of sequencing reads revealed Proteobacteria as major dominant phyla in both soil types. The order of the top 3 abundant phyla in M1 sample was Proteobacteria > Ascomycota > Firmicutes, whereas in sample O1, the order was Proteobacteria > Cyanobacteria > Actinobacteria. Analysis of differentially expressed genes demonstrated high expression of transcripts related to copper-binding proteins, proteins involved in electron carrier activity, DNA integration, endonuclease activity, MFS transportation, and other uncharacterized proteins in M1 compared to O1. Of the particular interests, several transcripts related to nitrification, ammonification, stress response, and alternate carbon fixation pathways were highly expressed in M1. In-depth analysis of the sequencing data revealed that transcripts of archaeal origin had high expression in M1 compared to O1 indicating the active role of Archaea in metal- and pesticide-contaminated environment. In addition, transcripts encoding 4-hydroxyphenylpyruvate dioxygenase, glyoxalase/bleomycin resistance protein/dioxygenase, metapyrocatechase, and ring hydroxylating dioxygenases of aromatic hydrocarbon degradation pathways had high expression in M1. Altogether, this study provided important insights about the transcripts and pathways upregulating in the presence of pesticides and herbicides. CONCLUSION Altogether, this study claims a high expression of microbial transcripts in two ecosystems with a wide range of functions. It further provided clue about several molecular markers which could be a strong indicator of metal and pesticide contamination in soils. Interestingly, our study revealed that Archaea are playing a significant role in nitrification process as compared to bacteria in metal- and pesticide-contaminated soil. In particular, high expression of transcripts related to aromatic hydrocarbon degradation in M1 soil indicates their important role in biodegradation of pollutants, and therefore, further investigation is needed.
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Affiliation(s)
| | - Vinay Sharma
- Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab 140407 India
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), Miyapur, Hyderabad, Telangana 500 049 India
| | - Garima Bhatia
- Department of Biotechnology, Panjab University, Chandigarh, 160014 India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, 160014 India
| | - Rohit Sharma
- Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab 140407 India
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Luo Y, Atashgahi S, Rijnaarts HHM, Comans RNJ, Sutton NB. Influence of different redox conditions and dissolved organic matter on pesticide biodegradation in simulated groundwater systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 677:692-699. [PMID: 31071671 DOI: 10.1016/j.scitotenv.2019.04.128] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Insights into the influence of redox conditions, that is the availability of electron acceptors, and dissolved organic matter (DOM) on pesticide biodegradation in groundwater are key to understanding the environmental fate of pesticides in natural groundwater systems. Here, the influence of redox conditions and supplemental DOM addition on biodegradation of pesticides, 2,4-dichlorophenoxyacetic acid (2,4-D), 2,6-dichlorobenzamide (BAM), mecoprop-p (MCPP) and bentazone, was tested in microcosm and subsequent column experiments. Pesticide degradation, functional genes and changes in specific fractions and quantity of DOM were systematically quantified. In aerobic microcosm experiments, the highest 2,4-D degradation rate was obtained with the presence of more assimilable DOM. In column experiments, minimal pesticide degradation (≤33.77%) in any anaerobic redox conditions was observed in the absence of DOM. However, in the presence of DOM, 2,4-D biodegradation was considerably enhanced under nitrate-reducing conditions (from 23.5 ± 10.2% to 82.3 ± 11.6%) and in a column without external electron acceptor amendment (from -6.3 ± 12.6% to 31.1 ± 36.3%). Observed preferential depletion of the fulvic acid fraction of DOM provides indications for specific functional DOM properties. The qPCR results show an increase in microbial biomass and functional genes (tfdA) in liquid phase after DOM addition. The results of this work provide insights into the interplays among DOM, redox geochemistry, and pesticide biodegradation, and show the potential of a novel approach - DOM addition to groundwater systems - for in situ biostimulation technology to remove pesticides from groundwater systems.
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Affiliation(s)
- Yujia Luo
- Sub-department of Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Huub H M Rijnaarts
- Sub-department of Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Rob N J Comans
- Department of Soil Quality, Wageningen University, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Nora B Sutton
- Sub-department of Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands.
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Svenningsen NB, Damgaard M, Rasmussen M, Pérez-Pantoja D, Nybroe O, Nicolaisen MH. Cupriavidus pinatubonensis AEO106 deals with copper-induced oxidative stress before engaging in biodegradation of the herbicide 4-chloro-2-methylphenoxyacetic acid. BMC Microbiol 2017; 17:211. [PMID: 29084513 PMCID: PMC5663122 DOI: 10.1186/s12866-017-1119-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/19/2017] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Microbial degradation of phenoxy acid (PA) herbicides in agricultural soils is important to minimize herbicide leaching to groundwater reservoirs. Degradation may, however, be hampered by exposure of the degrader bacteria to toxic metals as copper (Cu) in the soil environment. Exposure to Cu leads to accumulation of intracellular reactive oxygen species (ROS) in some bacteria, but it is not known how Cu-derived ROS and an ensuing oxidative stress affect the degradation of PA herbicides. Based on the previously proposed paradigm that bacteria deal with environmental stress before they engage in biodegradation, we studied how the degradation of the PA herbicide 2-methyl-4-chlorophenoxyacetic acid (MCPA) by the model PA degrader Cupriavidus pinatubonensis AEO106 was affected by Cu exposure. RESULTS Exposure of C. pinatubonensis in batch culture to sublethal concentrations of Cu increased accumulation of ROS measured by the oxidant sensing probe 2,7-dichlorodihydrofluorescein diacetate and flow cytometry, and resulted in upregulation of a gene encoding a protein belong to the Ohr/OsmC protein family. The ohr/osmC gene was also highly induced by H2O2 exposure suggesting that it is involved in the oxidative stress response in C. pinatubonensis. The increased ROS accumulation and increased expression of the oxidative stress defense coincided with a delay in the catabolic performance, since both expression of the catabolic tfdA gene and MCPA mineralization were delayed compared to unexposed control cells. CONCLUSIONS The current study suggests that Cu-induced ROS accumulation in C. pinatubonensis activates a stress response involving the product of the ohr/osmC gene. Further, the stress response is launched before induction of the catabolic tfdA gene and mineralization occurs.
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Affiliation(s)
- Nanna Bygvraa Svenningsen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Mette Damgaard
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Maria Rasmussen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, San Joaquín, Santiago, Chile
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark
| | - Mette Haubjerg Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Denmark.
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Rousidou C, Karaiskos D, Myti D, Karanasios E, Karas PA, Tourna M, Tzortzakakis EA, Karpouzas DG. Distribution and function of carbamate hydrolase genescehAandmcdin soils: the distinct role of soil pH. FEMS Microbiol Ecol 2016; 93:fiw219. [DOI: 10.1093/femsec/fiw219] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2016] [Indexed: 11/13/2022] Open
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Application of biodegradation in mitigating and remediating pesticide contamination of freshwater resources: state of the art and challenges for optimization. Appl Microbiol Biotechnol 2016; 100:7361-76. [DOI: 10.1007/s00253-016-7709-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/26/2016] [Accepted: 06/27/2016] [Indexed: 10/21/2022]
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Functional Redundancy of Linuron Degradation in Microbial Communities in Agricultural Soil and Biopurification Systems. Appl Environ Microbiol 2016; 82:2843-2853. [PMID: 26944844 DOI: 10.1128/aem.04018-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/28/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The abundance of libA, encoding a hydrolase that initiates linuron degradation in the linuron-metabolizing Variovorax sp. strain SRS16, was previously found to correlate well with linuron mineralization, but not in all tested environments. Recently, an alternative linuron hydrolase, HylA, was identified in Variovorax sp. strain WDL1, a strain that initiates linuron degradation in a linuron-mineralizing commensal bacterial consortium. The discovery of alternative linuron hydrolases poses questions about the respective contribution and competitive character of hylA- and libA-carrying bacteria as well as the role of linuron-mineralizing consortia versus single strains in linuron-exposed settings. Therefore, dynamics of hylA as well as dcaQ as a marker for downstream catabolic functions involved in linuron mineralization, in response to linuron treatment in agricultural soil and on-farm biopurification systems (BPS), were compared with previously reported libA dynamics. The results suggest that (i) organisms containing either libA or hylA contribute simultaneously to linuron biodegradation in the same environment, albeit to various extents, (ii) environmental linuron mineralization depends on multispecies bacterial food webs, and (iii) initiation of linuron mineralization can be governed by currently unidentified enzymes. IMPORTANCE A limited set of different isofunctional catabolic gene functions is known for the bacterial degradation of the phenylurea herbicide linuron, but the role of this redundancy in linuron degradation in environmental settings is not known. In this study, the simultaneous involvement of bacteria carrying one of two isofunctional linuron hydrolysis genes in the degradation of linuron was shown in agricultural soil and on-farm biopurification systems, as was the involvement of other bacterial populations that mineralize the downstream metabolites of linuron hydrolysis. This study illustrates the importance of the synergistic metabolism of pesticides in environmental settings.
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Saleh O, Pagel H, Enowashu E, Devers M, Martin-Laurent F, Streck T, Kandeler E, Poll C. Evidence for the importance of litter as a co-substrate for MCPA dissipation in an agricultural soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:4164-4175. [PMID: 25943518 DOI: 10.1007/s11356-015-4633-1] [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: 01/30/2015] [Accepted: 04/28/2015] [Indexed: 06/04/2023]
Abstract
Environmental controls of 2-methyl-4-chlorophenoxyacetic acid (MCPA) degradation are poorly understood. We investigated whether microbial MCPA degraders are stimulated by (maize) litter and whether this process depends on concentrations of MCPA and litter. In a microcosm experiment, different amounts of litter (0, 10 and 20 g kg(-1)) were added to soils exposed to three levels of the herbicide (0, 5 and 30 mg kg(-1)). The treated soils were incubated at 20 °C for 6 weeks, and samples were taken after 1, 3 and 6 weeks of incubation. In soils with 5 mg kg(-1) MCPA, about 50 % of the MCPA was dissipated within 1 week of the incubation. Almost complete dissipation of the herbicide had occurred by the end of the incubation with no differences between the three litter amendments. At the higher concentration (30 mg kg(-1)), MCPA endured longer in the soil, with only 31 % of the initial amount being removed at the end of the experiment in the absence of litter. Litter addition greatly increased the dissipation rate with 70 and 80 % of the herbicide being dissipated in the 10 and 20 g kg(-1) litter treatments, respectively. Signs of toxic effects of MCPA on soil bacteria were observed from related phospholipid fatty acid (PLFA) analyses, while fungi showed higher tolerance to the increased MCPA levels. The abundance of bacterial tfdA genes in soil increased with the co-occurrence of litter and high MCPA concentration, indicating the importance of substrate availability in fostering MCPA-degrading bacteria and thereby improving the potential for removal of MCPA in the environment.
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Affiliation(s)
- Omar Saleh
- Institute of Soil Science and Land Evaluation, Soil Biology, University of Hohenheim, Emil-Wolff-Str. 27, D-70593, Stuttgart, Germany
- Department of Biology and Biochemistry, Birzeit University, P.O. Box 14, Birzeit, West Bank, Palestine
| | - Holger Pagel
- Institute of Soil Science and Land Evaluation, Biogeophysics, University of Hohenheim, Emil-Wolff-Str. 27, D-70593, Stuttgart, Germany
| | - Esther Enowashu
- Institute of Soil Science and Land Evaluation, Soil Biology, University of Hohenheim, Emil-Wolff-Str. 27, D-70593, Stuttgart, Germany
| | - Marion Devers
- INRA, UMR 1347 Agroécologie, 17 Rue Sully, BP 8 6510, F-21065, Dijon, Cedex, France
| | | | - Thilo Streck
- Institute of Soil Science and Land Evaluation, Biogeophysics, University of Hohenheim, Emil-Wolff-Str. 27, D-70593, Stuttgart, Germany
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation, Soil Biology, University of Hohenheim, Emil-Wolff-Str. 27, D-70593, Stuttgart, Germany
| | - Christian Poll
- Institute of Soil Science and Land Evaluation, Soil Biology, University of Hohenheim, Emil-Wolff-Str. 27, D-70593, Stuttgart, Germany.
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Paszko T, Muszyński P, Materska M, Bojanowska M, Kostecka M, Jackowska I. Adsorption and degradation of phenoxyalkanoic acid herbicides in soils: A review. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2016; 35:271-86. [PMID: 26292078 DOI: 10.1002/etc.3212] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 05/04/2015] [Accepted: 08/14/2015] [Indexed: 05/23/2023]
Abstract
The primary aim of the present review on phenoxyalkanoic acid herbicides-2-(2,4-dichlorophenoxy) acetic acid (2,4-D), 2-(4-chloro-2-methylphenoxy) acetic acid (MCPA), (2R)-2-(2,4-dichlorophenoxy) propanoic acid (dichlorprop-P), (2R)-2-(4-chloro-2-methylphenoxy) propanoic acid (mecoprop-P), 4-(2,4-dichlorophenoxy) butanoic acid (2,4-DB), and 4-(4-chloro-2-methylphenoxy) butanoic acid (MCPB)-was to compare the extent of their adsorption in soils and degradation rates to assess their potential for groundwater contamination. The authors found that adsorption decreased in the sequence of 2,4-DB > 2,4-D > MCPA > dichlorprop-P > mecoprop-P. Herbicides are predominantly adsorbed as anions-on organic matter and through a water-bridging mechanism with adsorbed Fe cations-and their neutral forms are adsorbed mainly on organic matter. Adsorption of anions of 2,4-D, MCPA, dichlorprop-P, and mecoprop-P is inversely correlated with their lipophilicity values, and modeling of adsorption of the compounds based on this relationship is possible. The predominant dissipation mechanism of herbicides in soils is bacterial degradation. The contribution of other mechanisms, such as degradation by fungi, photodegradation, or volatilization from soils, is much smaller. The rate of bacterial degradation decreased in the following order: 2,4-D > MCPA > mecoprop-P > dichlorprop-P. It was found that 2,4-D and MCPA have the lowest potential for leaching into groundwater and that mecoprop-P and dichlorprop-P have slightly higher potential. Because of limited data on adsorption and degradation of 2,4-DB and MCPB, estimation of their leaching potential was not possible.
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Affiliation(s)
- Tadeusz Paszko
- Department of Chemistry, University of Life Sciences, Lublin, Poland
| | - Paweł Muszyński
- Department of Chemistry, University of Life Sciences, Lublin, Poland
| | | | - Monika Bojanowska
- Department of Chemistry, University of Life Sciences, Lublin, Poland
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Feld L, Hjelmsø MH, Nielsen MS, Jacobsen AD, Rønn R, Ekelund F, Krogh PH, Strobel BW, Jacobsen CS. Pesticide Side Effects in an Agricultural Soil Ecosystem as Measured by amoA Expression Quantification and Bacterial Diversity Changes. PLoS One 2015; 10:e0126080. [PMID: 25938467 PMCID: PMC4418756 DOI: 10.1371/journal.pone.0126080] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 03/29/2015] [Indexed: 11/26/2022] Open
Abstract
Background and Methods Assessing the effects of pesticide hazards on microbiological processes in the soil is currently based on analyses that provide limited insight into the ongoing processes. This study proposes a more comprehensive approach. The side effects of pesticides may appear as changes in the expression of specific microbial genes or as changes in diversity. To assess the impact of pesticides on gene expression, we focused on the amoA gene, which is involved in ammonia oxidation. We prepared soil microcosms and exposed them to dazomet, mancozeb or no pesticide. We hypothesized that the amount of amoA transcript decreases upon pesticide application, and to test this hypothesis, we used reverse-transcription qPCR. We also hypothesized that bacterial diversity is affected by pesticides. This hypothesis was investigated via 454 sequencing and diversity analysis of the 16S ribosomal RNA and RNA genes, representing the active and total soil bacterial communities, respectively. Results and Conclusion Treatment with dazomet reduced both the bacterial and archaeal amoA transcript numbers by more than two log units and produced long-term effects for more than 28 days. Mancozeb also inhibited the numbers of amoA transcripts, but only transiently. The bacterial and archaeal amoA transcripts were both sensitive bioindicators of pesticide side effects. Additionally, the numbers of bacterial amoA transcripts correlated with nitrate production in N-amended microcosms. Dazomet reduced the total bacterial numbers by one log unit, but the population size was restored after twelve days. The diversity of the active soil bacteria also seemed to be re-established after twelve days. However, the total bacterial diversity as reflected in the 16S ribosomal RNA gene sequences was largely dominated by Firmicutes and Proteobacteria at day twelve, likely reflecting a halt in the growth of early opportunists and the re-establishment of a more diverse population. We observed no effects of mancozeb on diversity.
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Affiliation(s)
- Louise Feld
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
- * E-mail:
| | - Mathis Hjort Hjelmsø
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
| | - Morten Schostag Nielsen
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
| | - Anne Dorthe Jacobsen
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
| | - Regin Rønn
- University of Copenhagen, Department of Biology, Section of Terrestrial Ecology, Copenhagen, Denmark
| | - Flemming Ekelund
- University of Copenhagen, Department of Biology, Section of Terrestrial Ecology, Copenhagen, Denmark
| | - Paul Henning Krogh
- University of Aarhus, Department of Bioscience, Section of Soil Fauna Ecology and Ecotoxicology, Silkeborg, Denmark
| | - Bjarne Westergaard Strobel
- University of Copenhagen, Department of Plant and Environmental Sciences, Section of Environmental Chemistry and Physics, Frederiksberg, Denmark
| | - Carsten Suhr Jacobsen
- Geological Survey of Denmark and Greenland (GEUS), Department of Geochemistry, Copenhagen, Denmark
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Han L, Liu Y, Li C, Zhao D. Cloning, expression, characterization and mutational analysis of the tfdA gene from Cupriavidus campinensis BJ71. World J Microbiol Biotechnol 2015; 31:1021-30. [PMID: 25850533 DOI: 10.1007/s11274-015-1852-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
Abstract
2,4-Dichlorophenoxyacetic acid (2,4-D)/α-ketoglutarate (α-KG) dioxygenase (TfdA) is an Fe(II)-dependent enzyme that catalyzes the first step in degradation of the herbicide 2,4-D. Previous studies focused on the tfdA gene in Ralstonia eutropha JMP134 isolated in Australia. In this study, a new tfdA gene was cloned from Cupriavidus campinensis BJ71, an effective degrading bacteria from China, based on the iCOnsensus-DEgenerate Hybrid Oligonucleotide Primers (iCODEHOPs) protocol, combined with high-efficiency Thermal Asymmetric Interlaced PCR (hiTAIL-PCR). The open reading frame of 861 bp encoded a putative 287 amino acid protein with a theoretical molecular mass of 32.32 kDa. The gene was overexpressed in Escherichia coli BL21 (DE3) and the purified TfdA showed optimal activity at pH 6.75 and 30 °C. This enzyme was more thermostable and it could use 3-hydrocinnamic acid as substrate, with a similar enzyme activity compared with 2,4-D. TfdA and its variants were created as maltose-binding protein (MBP) tagged fusion proteins to examine the roles of putative substrate-binding residues. The MBP-N110A, MBP-V198A and MBP-R207K proteins showed decreased k cat and increased Km, and MBP-R278A was inactive, suggesting these residues may affect 2,4-D binding or catalysis.
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Affiliation(s)
- Lizhen Han
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guiyang, 550025, China,
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Coleman NV. Primers: Functional Genes for Aerobic Chlorinated Hydrocarbon-Degrading Microbes. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_91] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Impaired reduction of N2O to N2 in acid soils is due to a posttranscriptional interference with the expression of nosZ. mBio 2014; 5:e01383-14. [PMID: 24961695 PMCID: PMC4073493 DOI: 10.1128/mbio.01383-14] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accumulating empirical evidence over the last 60 years has shown that the reduction of N2O to N2 is impaired by low soil pH, suggesting that liming of acid soils may reduce N2O emissions. This option has not gained much momentum in global change research, however, possibly due to limited understanding of why low pH interferes with N2O reductase. We hypothesized that the reason is that denitrifying organisms in soils are unable to assemble functional N2O reductase (N2OR) at low pH, as shown to be the case for the model strain Paracoccus denitrificans. We tested this by experiments with bacteria extracted from soils by density gradient centrifugation. The soils were sampled from a long-term liming experiment (soil pH 4.0, 6.1, and 8.0). The cells were incubated (stirred batches, He atmosphere) at pH levels ranging from 5.7 to 7.6, while gas kinetics (NO, N2O, and N2) and abundances of relevant denitrification genes (nirS, nirK, and nosZ) and their transcripts were monitored. Cells from the most acidic soil (pH 4.0) were unable to reduce N2O at any pH. These results warrant a closer inspection of denitrification communities of very acidic soils. Cells from the neutral soils were unable to produce functional N2OR at pH values of ≤6.1, despite significant transcription of the nosZ gene. The N2OR expressed successfully at pH 7.0, however, was functional over the entire pH range tested (5.7 to 7.6). These observations lend strong support to our hypothesis: low soil pH diminishes/prevents reduction of N2O, primarily by precluding a successful assembly of functional N2O reductase. Impaired N2O reduction in acid soils was first observed ~60 years ago, and the phenomenon has been rediscovered several times since then. The practical implication would be that the emissions of N2O from cropped soils could be controlled by soil pH management, but this option has largely been ignored till now. One reason for this could be that the mechanisms involved have remained obscure. Here, we provide compelling evidence that the primary reason is that low pH interferes with the making of the enzyme N2O reductase rather than the function of the enzyme if properly assembled. The implications are important for understanding how pH controls the kinetics of N2O and N2 production by denitrification. The improved understanding provides credibility for soil pH management as a way to mitigate N2O emissions.
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16S rRNA gene phylogeny and tfdA gene analysis of 2,4-D-degrading bacteria isolated in China. World J Microbiol Biotechnol 2014; 30:2567-76. [PMID: 24898178 DOI: 10.1007/s11274-014-1680-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/27/2014] [Indexed: 10/25/2022]
Abstract
Twenty-two 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterial isolates were collected from agricultural soils at three sites in China. Sequence analysis of the 16S rRNA genes indicated that the isolates were phylogenetically grouped into four categories: Ochrobactrum anthropi, in the Alpha- class of the phylum Proteobacteria (3 out of 22 isolates), Cupriavidus sp., of the Betaproteobacteria (3 out of 22), Pseudomonas sp. and Stenotrophomonas sp., which are Gammaproteobacteria (7 out of 22), and Bacillus sp., of the phylum Firmicutes (9 out of 22). Primers were designed to amplify the conserved domain of tfdA, which is known to be involved in the degradation of 2,4-D. Results showed that the tfdA genes of all 22 strains were most similar to that of Cupriavidus necator JMP134, which belongs to the 2,4-D/α-ketoglutarate dioxygenase TfdA protein family, indicating that the JMP134-type tfdA gene is likely to be almost universal among the 2,4-D-degrading bacteria isolated from China. Degradation abilities of these 22 strains were investigated in assays using 2,4-D as the sole source of carbon and energy. Thirteen strains degraded >60 % of the available 2,4-D (500 mg l(-1)) over a 1-week incubation period, while a further nine Bacillus sp. strains degraded 50-81 % of the available 2,4-D. None of these nine strains degraded other selected herbicides, such as mecoprop, 2-methyl-4-chlorophenoxyacetic acid, quizalofop, and fluroxypyr. This is the first report of 2,4-D-degradation by Bacilli.
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Jacobsen CS, Hjelmsø MH. Agricultural soils, pesticides and microbial diversity. Curr Opin Biotechnol 2014; 27:15-20. [DOI: 10.1016/j.copbio.2013.09.003] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/05/2013] [Accepted: 09/09/2013] [Indexed: 11/28/2022]
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Uchida Y, Wang Y, Akiyama H, Nakajima Y, Hayatsu M. Expression of denitrification genes in response to a waterlogging event in a Fluvisol and its relationship with large nitrous oxide pulses. FEMS Microbiol Ecol 2014; 88:407-23. [PMID: 24592962 DOI: 10.1111/1574-6941.12309] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/11/2014] [Accepted: 02/18/2014] [Indexed: 11/30/2022] Open
Abstract
The contributions of large N2 O pulses following waterlogging to the annual cumulative N2 O productions were significant in a Fluvisol. To uncover the mechanisms underlying these large N2 O pulses, a Fluvisol sampled from an agricultural field in Japan was subjected to waterlogging during incubation. Larger N2 O emissions were observed in intact soil cores when compared to emissions from sieved soils, indicating the importance of soil properties. The most important factor controlling the magnitude of the N2 O pulses after waterlogging was the soil moisture prior to waterlogging. The major pathway for N2 O production was denitrification. Quantitative PCR and quantitative RT-PCR analyses showed that the denitrification genes (nirS, nirK, and nosZ) correlated with N2 O emissions at the mRNA level but not at the DNA level. The change in denitrification gene mRNA levels was more prominent in the 0- to 1-cm soil compared with the 1- to 3-cm soil. Water-soluble and hot-water-soluble carbon contents also showed the highest amount in the 0- to 1-cm soil. These indicate that there was a strong variation in soil microbial properties over very small changes in soil depth, and this variation is important in determining the magnitude of N2 O emissions.
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Affiliation(s)
- Yoshitaka Uchida
- Task Force for Innovation in Life, Resources and Environment Sciences, Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
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Zabaloy MC, Gómez MA. Isolation and characterization of indigenous 2,4-D herbicide degrading bacteria from an agricultural soil in proximity of Sauce Grande River, Argentina. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0731-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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López-Guerrero MG, Ormeño-Orrillo E, Rosenblueth M, Martinez-Romero J, Martïnez-Romero E. Buffet hypothesis for microbial nutrition at the rhizosphere. FRONTIERS IN PLANT SCIENCE 2013; 4:188. [PMID: 23785373 PMCID: PMC3682122 DOI: 10.3389/fpls.2013.00188] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/23/2013] [Indexed: 05/31/2023]
Abstract
An emphasis is made on the diversity of nutrients that rhizosphere bacteria may encounter derived from roots, soil, decaying organic matter, seeds, or the microbial community. This nutrient diversity may be considered analogous to a buffet and is contrasting to the hypothesis of oligotrophy at the rhizosphere. Different rhizosphere bacteria may have preferences for some substrates and this would allow a complex community to be established at the rhizosphere. To profit from diverse nutrients, root-associated bacteria should have large degrading capabilities and many transporters (seemingly inducible) that may be encoded in a significant proportion of the large genomes that root-associated bacteria have. Rhizosphere microbes may have a tendency to evolve toward generalists. We propose that many genes with unknown function may encode enzymes that participate in degrading diverse rhizosphere substrates. Knowledge of bacterial genes required for nutrition at the rhizosphere will help to make better use of bacteria as plant-growth promoters in agriculture.
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Affiliation(s)
| | | | | | | | - Esperanza Martïnez-Romero
- *Correspondence: Esperanza Martínez-Romero, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad SN, Cuernavaca, Morelos CP 62210, Mexico e-mail: ,
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Ditterich F, Poll C, Pagel H, Babin D, Smalla K, Horn MA, Streck T, Kandeler E. Succession of bacterial and fungal 4-chloro-2-methylphenoxyacetic acid degraders at the soil-litter interface. FEMS Microbiol Ecol 2013; 86:85-100. [DOI: 10.1111/1574-6941.12131] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 03/20/2013] [Accepted: 04/03/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Franziska Ditterich
- Institute of Soil Science and Land Evaluation; Soil Biology Section; University of Hohenheim; Stuttgart; Germany
| | - Christian Poll
- Institute of Soil Science and Land Evaluation; Soil Biology Section; University of Hohenheim; Stuttgart; Germany
| | - Holger Pagel
- Institute of Soil Science and Land Evaluation; Biogeophysics Section; University of Hohenheim; Stuttgart; Germany
| | - Doreen Babin
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | - Kornelia Smalla
- Julius Kühn-Institut; Federal Research Centre for Cultivated Plants; Institute for Epidemiology and Pathogen Diagnostics; Braunschweig; Germany
| | - Marcus A. Horn
- Department of Ecological Microbiology; University of Bayreuth; Bayreuth; Germany
| | - Thilo Streck
- Institute of Soil Science and Land Evaluation; Biogeophysics Section; University of Hohenheim; Stuttgart; Germany
| | - Ellen Kandeler
- Institute of Soil Science and Land Evaluation; Soil Biology Section; University of Hohenheim; Stuttgart; Germany
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Batıoğlu-Pazarbaşı M, Milosevic N, Malaguerra F, Binning PJ, Albrechtsen HJ, Bjerg PL, Aamand J. Discharge of landfill leachate to streambed sediments impacts the mineralization potential of phenoxy acid herbicides depending on the initial abundance of tfdA gene classes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2013; 176:275-83. [PMID: 23454590 DOI: 10.1016/j.envpol.2013.01.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 01/29/2013] [Accepted: 01/31/2013] [Indexed: 05/23/2023]
Abstract
To understand the role of abundance of tfdA gene classes belonging to β- and γ-proteobacteria on phenoxy acid herbicide degradation, streambed sediments were sampled around three seepage meters (SMs) installed in a landfill-impacted groundwater-surface water interface. Highest herbicide mass discharge to SM3, and lower herbicide mass discharges to SM1 and SM2 were determined due to groundwater discharge rates and herbicide concentrations. SM1-sediment with the lowest abundance of tfdA gene classes had the slowest mineralization, whereas SM2- and SM3-sediments with more abundant tfdA genes had faster mineralization. The observed difference in mineralization rates between discharge zones was simulated by a Monod-based kinetic model, which confirmed the role of abundance of tfdA gene classes. This study suggests presence of specific degraders adapted to slow growth rate and high yield strategy due to long-term herbicide exposure; and thus groundwater-surface water interface could act as a natural biological filter and protect stream water quality.
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Affiliation(s)
- Meriç Batıoğlu-Pazarbaşı
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, DK-1350 Copenhagen K, Denmark.
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Badawi N, Johnsen AR, Sørensen J, Aamand J. Centimeter-scale spatial variability in 2-methyl-4-chlorophenoxyacetic Acid mineralization increases with depth in agricultural soil. JOURNAL OF ENVIRONMENTAL QUALITY 2013; 42:683-689. [PMID: 23673934 DOI: 10.2134/jeq2012.0397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Mineralization of organic chemicals in soil is typically studied using large homogenized samples, but little is known about the small-scale spatial distribution of mineralization potential. We studied centimeter-scale spatial distribution of 2-methyl-4-chlorophenoxyacetic acid (MCPA) mineralization activity at different depths (8-115 cm) in a Danish agricultural soil profile using a 96-well microplate C-radiorespirometric method for small-volume samples. The heterotrophic microbial population and specific MCPA degraders decreased 10- to 100-fold from the plow layer to a depth of 115 cm. MCPA was mineralized in all samples in the plow layer, but only about 60% in the transition zone immediately below the plow layer showed mineralization; at greater depth even fewer samples showed mineralization. A patchy spatial distribution of mineralization activity was observed from right below the plow layer and in the subsoil, with a few clearly defined active zones surrounded by areas devoid of mineralization activity. Due to the patchy distribution of mineralization activity at the centimeter scale just beneath the plow layer, MCPA and presumably other weakly sorbing pesticides might be at risk of leaching to the groundwater if transported from the plow layer into the subsoil.
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40
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Bælum J, Chambon JC, Scheutz C, Binning PJ, Laier T, Bjerg PL, Jacobsen CS. A conceptual model linking functional gene expression and reductive dechlorination rates of chlorinated ethenes in clay rich groundwater sediment. WATER RESEARCH 2013; 47:2467-78. [PMID: 23490098 DOI: 10.1016/j.watres.2013.02.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/06/2013] [Accepted: 02/08/2013] [Indexed: 05/26/2023]
Abstract
We used current knowledge of cellular processes involved in reductive dechlorination to develop a conceptual model to describe the regulatory system of dechlorination at the cell level; the model links bacterial growth and substrate consumption to the abundance of messenger RNA of functional genes involved in the dechlorination process. The applicability of the model was tested on a treatability study of biostimulated and bioaugmented microcosms. Using quantitative real time PCR, high-resolution expression profiles of the functional reductive dehalogenase genes bvcA and vcrA were obtained during two consecutive dechlorination events of trichlorethene, cis-dichlorethene and vinyl chloride. Up-regulation of the bvcA (for the biostimulated microcosms) and vcrA (for the bioaugmented microcosms) gene expression fitted well with high rates of dechlorination of vinyl chloride, while no known transcripts could be measured during trichloroethene and cis-dichlorethene dechlorination. Maximum concentrations of 2.1 and 1.7 transcripts per gene of the bvcA and vcrA genes, respectively, were measured at the same time points as maximum dechlorination rates were observed. The developed model compared well with the experimental data for both biostimulated and bioaugmented microcosms under non-steady state conditions and was supported by results from a recently published study under steady state conditions.
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Affiliation(s)
- Jacob Bælum
- The Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, DK-1350 Copenhagen, Denmark
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41
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Chambon JC, Bjerg PL, Scheutz C, Baelum J, Jakobsen R, Binning PJ. Review of reactive kinetic models describing reductive dechlorination of chlorinated ethenes in soil and groundwater. Biotechnol Bioeng 2012; 110:1-23. [DOI: 10.1002/bit.24714] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 08/13/2012] [Accepted: 08/16/2012] [Indexed: 11/08/2022]
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42
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Estimating the biodegradation of pesticide in soils by monitoring pesticide-degrading gene expression. Biodegradation 2012; 24:203-13. [PMID: 22991035 DOI: 10.1007/s10532-012-9574-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 07/09/2012] [Indexed: 10/28/2022]
Abstract
Assessing in situ microbial abilities of soils to degrade pesticides is of great interest giving insight in soil filtering capability, which is a key ecosystem function limiting pollution of groundwater. Quantification of pesticide-degrading gene expression by reverse transcription quantitative PCR (RT-qPCR) was tested as a suitable indicator to monitor pesticide biodegradation performances in soil. RNA extraction protocol was optimized to enhance the yield and quality of RNA recovered from soil samples to perform RT-qPCR assays. As a model, the activity of atrazine-degrading communities was monitored using RT-qPCRs to estimate the level of expression of atzD in five agricultural soils showing different atrazine mineralization abilities. Interestingly, the relative abundance of atzD mRNA copy numbers was positively correlated to the maximum rate and to the maximal amount of atrazine mineralized. Our findings indicate that the quantification of pesticide-degrading gene expression may be suitable to assess biodegradation performance in soil and monitor natural attenuation of pesticide.
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Modeling of phenoxy acid herbicide mineralization and growth of microbial degraders in 15 soils monitored by quantitative real-time PCR of the functional tfdA gene. Appl Environ Microbiol 2012; 78:5305-12. [PMID: 22635998 DOI: 10.1128/aem.00990-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mineralization potentials, rates, and kinetics of the three phenoxy acid (PA) herbicides, 2,4-dichlorophenoxyacetic acid (2,4-D), 4-chloro-2-methylphenoxyacetic acid (MCPA), and 2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP), were investigated and compared in 15 soils collected from five continents. The mineralization patterns were fitted by zero/linear or exponential growth forms of the three-half-order models and by logarithmic (log), first-order, or zero-order kinetic models. Prior and subsequent to the mineralization event, tfdA genes were quantified using real-time PCR to estimate the genetic potential for degrading PA in the soils. In 25 of the 45 mineralization scenarios, ∼60% mineralization was observed within 118 days. Elevated concentrations of tfdA in the range 1 × 10(5) to 5 × 10(7) gene copies g(-1) of soil were observed in soils where mineralization could be described by using growth-linked kinetic models. A clear trend was observed that the mineralization rates of the three PAs occurred in the order 2,4-D > MCPA > MCPP, and a correlation was observed between rapid mineralization and soils exposed to PA previously. Finally, for 2,4-D mineralization, all seven mineralization patterns which were best fitted by the exponential model yielded a higher tfdA gene potential after mineralization had occurred than the three mineralization patterns best fitted by the Lin model.
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44
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Monard C, Mchergui C, Nunan N, Martin-Laurent F, Vieublé-Gonod L. Impact of soil matric potential on the fine-scale spatial distribution and activity of specific microbial degrader communities. FEMS Microbiol Ecol 2012; 81:673-83. [PMID: 22531018 DOI: 10.1111/j.1574-6941.2012.01398.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 04/19/2012] [Accepted: 04/19/2012] [Indexed: 11/29/2022] Open
Abstract
The impact of the soil matric potential on the relationship between the relative abundance of degraders and their activity and on the spatial distribution of both at fine scales was determined to understand the role of environmental conditions in the degradation of organic substrates. The mineralization of (13) C-glucose and (13) C-2,4-dichlorophenoxyacetic acid (2,4-D) was measured at different matric potentials (-0.001, -0.01 and -0.316 MPa) in 6 × 6 × 6 mm(3) cubes excised from soil cores. At the end of the incubation, total bacterial and 2,4-D degrader abundances were determined by quantifying the 16S rRNA and the tfdA genes, respectively. The mineralization of 2,4-D was more sensitive to changes in matric potential than was that of glucose. The amount and spatial structure of 2,4-D mineralization decreased with matric potential, whilst the spatial variability increased. On the other hand, the spatial variation of glucose mineralization was less affected by changes in matric potential. The relationship between the relative abundance of 2,4-D degraders and 2,4-D mineralization was significantly affected by matric potential: the relative abundance of tfdA needed to be higher to reach a given level of 2,4-D mineralization in dryer than in moister conditions. The data show how microbial interactions with their microhabitat can have an impact on soil processes at larger scales.
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Affiliation(s)
- Cécile Monard
- INRA, UMR 1091 Environnement et Grandes Cultures, Bâtiment EGER, Thiverval Grignon, France
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45
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Microbial degradation of 2,4-dichlorophenoxyacetic acid on the Greenland ice sheet. Appl Environ Microbiol 2012; 78:5070-6. [PMID: 22582066 DOI: 10.1128/aem.00400-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Greenland ice sheet (GrIS) receives organic carbon (OC) of anthropogenic origin, including pesticides, from the atmosphere and/or local sources, and the fate of these compounds in the ice is currently unknown. The ability of supraglacial heterotrophic microbes to mineralize different types of OC is likely a significant factor determining the fate of anthropogenic OC on the ice sheet. Here we determine the potential of the microbial community from the surface of the GrIS to mineralize the widely used herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). Surface ice cores were collected and incubated for up to 529 days in microcosms simulating in situ conditions. Mineralization of side chain- and ring-labeled [(14)C]2,4-D was measured in the samples, and quantitative PCR targeting the tfdA genes in total DNA extracted from the ice after the experiment was performed. We show that the supraglacial microbial community on the GrIS contains microbes that are capable of degrading 2,4-D and that they are likely present in very low numbers. They can mineralize 2,4-D at a rate of up to 1 nmol per m(2) per day, equivalent to ∼26 ng C m(-2) day(-1). Thus, the GrIS should not be considered a mere reservoir of all atmospheric contaminants, as it is likely that some deposited compounds will be removed from the system via biodegradation processes before their potential release due to the accelerated melting of the ice sheet.
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46
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Dynamics of the linuron hydrolase libA gene pool size in response to linuron application and environmental perturbations in agricultural soil and on-farm biopurification systems. Appl Environ Microbiol 2012; 78:2783-9. [PMID: 22307296 DOI: 10.1128/aem.06991-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
libA, a gene encoding a novel type of linuron hydrolase, was recently identified in the linuron-mineralizing Variovorax sp. strain SRS16. In order to assess the contribution of libA to linuron degradation in environmental settings, libA abundance was monitored in response to the application of linuron and to environmental perturbations in agricultural soil microcosms and microcosms simulating the matrix of on-farm biopurification systems. libA numbers were measured by real-time PCR and linked to reported data of Variovorax community composition and linuron mineralization capacity. In the soil microcosms and one biopurification system setup, libA numbers responded to the application of linuron and environmental changes in congruency with the modulation of linuron mineralization capacity and the occurrence of a particular Variovorax phylotype (phylotype A). However, in another biopurification system setup, no such correlations were found. Our data suggest that in the simulated environmental settings, the occurrence of libA can be linked to the linuron mineralization capacity and that libA is primarily hosted by Variovorax phylotype A strains. However, the results also suggest that, apart from libA, other, as-yet-unknown isofunctional genes play an important role in linuron mineralization in the environment.
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47
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Batıoğlu-Pazarbaşı M, Baelum J, Johnsen AR, Sørensen SR, Albrechtsen HJ, Aamand J. Centimetre-scale vertical variability of phenoxy acid herbicide mineralization potential in aquifer sediment relates to the abundance of tfdA genes. FEMS Microbiol Ecol 2012; 80:331-41. [DOI: 10.1111/j.1574-6941.2012.01300.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
| | - Jacob Baelum
- Department of Geochemistry; Geological Survey of Denmark and Greenland (GEUS); Copenhagen K; Denmark
| | - Anders R. Johnsen
- Department of Geochemistry; Geological Survey of Denmark and Greenland (GEUS); Copenhagen K; Denmark
| | - Sebastian R. Sørensen
- Department of Geochemistry; Geological Survey of Denmark and Greenland (GEUS); Copenhagen K; Denmark
| | - Hans-Jørgen Albrechtsen
- DTU Environment; Department of Environmental Engineering; Technical University of Denmark; Kgs. Lyngby; Denmark
| | - Jens Aamand
- Department of Geochemistry; Geological Survey of Denmark and Greenland (GEUS); Copenhagen K; Denmark
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Wang Y, Morimoto S, Ogawa N, Fujii T. A survey of the cellular responses in Pseudomonas putida KT2440 growing in sterilized soil by microarray analysis. FEMS Microbiol Ecol 2011; 78:220-32. [DOI: 10.1111/j.1574-6941.2011.01146.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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49
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Effect of soil clay content on RNA isolation and on detection and quantification of bacterial gene transcripts in soil by quantitative reverse transcription-PCR. Appl Environ Microbiol 2011; 77:6249-52. [PMID: 21724880 DOI: 10.1128/aem.00055-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we evaluated the effect of soil clay content on RNA isolation and on quantitative reverse transcription-PCR (qRT-PCR) quantification of microbial gene transcripts. The amount of clay significantly altered RNA isolation yields and qRT-PCR analyses. Recommendations are made for quantifying microbial gene transcripts in soil samples varying in clay content.
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50
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DeCoste NJ, Gadkar VJ, Filion M. Verticillium dahliae alters Pseudomonas spp. populations and HCN gene expression in the rhizosphere of strawberry. Can J Microbiol 2011; 56:906-15. [PMID: 21076481 DOI: 10.1139/w10-080] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The production of hydrogen cyanide (HCN) by beneficial root-associated bacteria is an important mechanism for the biological control of plant pathogens. However, little is known about the biotic factors affecting HCN gene expression in the rhizosphere of plants. In this study, real-time reverse transcription PCR (qRT-PCR) assays were developed to investigate the effect of the plant pathogen Verticillium dahliae on hcnC (encoding for HCN biosynthesis) gene expression in Pseudomonas sp. LBUM300. Strawberry plants were inoculated with Pseudomonas sp. LBUM300 and (or) V. dahliae and grown in pots filled with nonsterilized field soil. RNA was extracted from rhizosphere soil sampled at 0, 15, 30, and 45 days following inoculation with V. dahliae and used for qRT-PCR analyses. Populations of V. dahliae and Pseudomonas sp. LBUM300 were also monitored using a culture-independent qPCR approach. hcnC expression was detected at all sampling dates. The presence of V. dahliae had a significant stimulation effect on hcnC gene expression and also increased the population of Pseudomonas sp. LBUM300. However, the V. dahliae population was not altered by the presence of Pseudomonas sp. LBUM300. To our knowledge, this study is the first to evaluate the effect of a plant pathogen on HCN gene expression in the rhizosphere soil.
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Affiliation(s)
- Nadine J DeCoste
- Université de Moncton, Department of Biology, Moncton, NB E1A 3E9, Canada
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