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Lin F, Mao Y, Zhao F, Idris AL, Liu Q, Zou S, Guan X, Huang T. Towards Sustainable Green Adjuvants for Microbial Pesticides: Recent Progress, Upcoming Challenges, and Future Perspectives. Microorganisms 2023; 11:microorganisms11020364. [PMID: 36838328 PMCID: PMC9965284 DOI: 10.3390/microorganisms11020364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Microbial pesticides can be significantly improved by adjuvants. At present, microbial pesticide formulations are mainly wettable powders and suspension concentrations, which are usually produced with adjuvants such as surfactants, carriers, protective agents, and nutritional adjuvants. Surfactants can improve the tension between liquid pesticides and crop surfaces, resulting in stronger permeability and wettability of the formulations. Carriers are inert components of loaded or diluted pesticides, which can control the release of active components at appropriate times. Protective agents are able to help microorganisms to resist in adverse environments. Nutritional adjuvants are used to provide nutrients for microorganisms in microbial pesticides. Most of the adjuvants used in microbial pesticides still refer to those of chemical pesticides. However, some adjuvants may have harmful effects on non-target organisms and ecological environments. Herein, in order to promote research and improvement of microbial pesticides, the types of microbial pesticide formulations were briefly reviewed, and research progress of adjuvants and their applications in microbial pesticides were highlighted, the challenges and the future perspectives towards sustainable green adjuvants of microbial pesticides were also discussed in this review.
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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: 11] [Impact Index Per Article: 5.5] [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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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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Southwell RV, Hilton SL, Pearson JM, Hand LH, Bending GD. Inclusion of seasonal variation in river system microbial communities and phototroph activity increases environmental relevance of laboratory chemical persistence tests. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139070. [PMID: 32464572 PMCID: PMC7298614 DOI: 10.1016/j.scitotenv.2020.139070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/22/2020] [Accepted: 04/26/2020] [Indexed: 04/15/2023]
Abstract
Regulatory tests assess crop protection product environmental fate and toxicity before approval for commercial use. Although globally applied laboratory tests can assess biodegradation, they lack environmental complexity. Microbial communities are subject to temporal and spatial variation, but there is little consideration of these microbial dynamics in the laboratory. Here, we investigated seasonal variation in the microbial composition of water and sediment from a UK river across a two-year time course and determined its effect on the outcome of water-sediment (OECD 308) and water-only (OECD 309) biodegradation tests, using the fungicide isopyrazam. These OECD tests are performed under dark conditions, so test systems incubated under non-UV light:dark cycles were also included to determine the impact on both inoculum characteristics and biodegradation. Isopyrazam degradation was faster when incubated under non-UV light at all collection times in water-sediment microcosms, suggesting that phototrophic communities can metabolise isopyrazam throughout the year. Degradation rate varied seasonally between inoculum collection times only in microcosms incubated in the light, but isopyrazam mineralisation to 14CO2 varied seasonally under both light and dark conditions, suggesting that heterotrophic communities may also play a role in degradation. Bacterial and phototroph communities varied across time, but there was no clear link between water or sediment microbial composition and variation in degradation rate. During the test period, inoculum microbial community composition changed, particularly in non-UV light incubated microcosms. Overall, we show that regulatory test outcome is not influenced by temporal variation in microbial community structure; however, biodegradation rates from higher tier studies with improved environmental realism, e.g. through addition of non-UV light, may be more variable. These data suggest that standardised OECD tests can provide a conservative estimate of pesticide persistence end points and that additional tests including non-UV light could help bridge the gap between standard tests and field studies.
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Affiliation(s)
- Rebecca V Southwell
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK; Product Safety, Jealott's Hill International Research Centre, Syngenta, Bracknell, Berkshire RG4 6EY, UK.
| | - Sally L Hilton
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK
| | - Jonathan M Pearson
- School of Engineering, Library Road, University of Warwick, Coventry CV4 7AL, UK
| | - Laurence H Hand
- Product Safety, Jealott's Hill International Research Centre, Syngenta, Bracknell, Berkshire RG4 6EY, UK
| | - Gary D Bending
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, UK
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5
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König S, Vogel HJ, Harms H, Worrich A. Physical, Chemical and Biological Effects on Soil Bacterial Dynamics in Microscale Models. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00053] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile. Appl Environ Microbiol 2019; 85:AEM.02658-18. [PMID: 30658975 PMCID: PMC6414393 DOI: 10.1128/aem.02658-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/21/2018] [Indexed: 11/29/2022] Open
Abstract
The ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil compartments and that most are dominated by a few dispersing taxa. Importantly, an increase in shared dispersers among the preferential flow paths of the clay till suggests that active dispersal plays a role in the successful colonization of these habitats. This study assessed the dispersal of five bacterial communities from contrasting compartments along a fractured clay till depth profile comprising plow layer soil, preferential flow paths (biopores and the tectonic fractures below), and matrix sediments, down to 350 cm below the surface. A recently developed expansion of the porous surface model (PSM) was used to capture bacterial communities dispersing under controlled hydration conditions on a soil-like surface. All five communities contained bacteria capable of active dispersal under relatively low hydration conditions (−3.1 kPa). Further testing of the plow layer community revealed active dispersal even at matric potentials of −6.3 to −8.4 kPa, previously thought to be too dry for dispersal on the PSM. Using 16S rRNA gene amplicon sequencing, the dispersing communities were found to be less diverse than their corresponding total communities. The dominant dispersers in most compartments belonged to the genus Pseudomonas and, in the plow layer soil, to Rahnella as well. An exception to this was the dispersing community in the matrix at 350 cm below the surface, which was dominated by Pantoea. Hydrologically connected compartments shared proportionally more dispersing than nondispersing amplicon sequence variants (ASVs), suggesting that active dispersal is important for colonizing these compartments. These results highlight the importance of including soil profile heterogeneity when assessing the role of active dispersal and contribute to discerning the importance of active dispersal in the soil environment. IMPORTANCE The ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil compartments and that most are dominated by a few dispersing taxa. Importantly, an increase in shared dispersers among the preferential flow paths of the clay till suggests that active dispersal plays a role in the successful colonization of these habitats.
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Hage‐Ahmed K, Rosner K, Steinkellner S. Arbuscular mycorrhizal fungi and their response to pesticides. PEST MANAGEMENT SCIENCE 2019; 75:583-590. [PMID: 30255557 PMCID: PMC6587947 DOI: 10.1002/ps.5220] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 05/19/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) form symbioses with the majority of plant species and can provide multiple benefits to the host plant. In agro-ecosystems, the abundance and community structure of AMF are affected by agricultural management practices. This review describes and discusses current knowledge on the effects of inorganic and organic chemical pesticides on AMF in the conflicting area between agricultural use and environmental concerns. Variable effects have been reported following chemical pesticide use, ranging from neutral to positive and negative. Moreover, a species-specific reaction has been documented. The reported effects of pesticides on arbuscular mycorrhizal symbiosis are very diverse, and even when the same substance is investigated, the results are often contradictory. These effects depend on many parameters, such as the active substance, the mode of action, the mode of application and the dosage. In the field, determinants such as the physico-chemical behavior of the active substances, the soil type and other soil microorganisms contribute to the fate of pesticides and thus the amount of active substances to which AMF are exposed. This review highlights that the fate of AMF following pesticide use needs to be addressed in a broader agro-ecosystem context. © 2018 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Karin Hage‐Ahmed
- Division of Plant Protection, Department of Crop SciencesUniversity of Natural Resources and Life Sciences ViennaTullnAustria
| | - Kathrin Rosner
- Division of Plant Protection, Department of Crop SciencesUniversity of Natural Resources and Life Sciences ViennaTullnAustria
| | - Siegrid Steinkellner
- Division of Plant Protection, Department of Crop SciencesUniversity of Natural Resources and Life Sciences ViennaTullnAustria
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Singh DP, Prabha R, Gupta VK, Verma MK. Metatranscriptome Analysis Deciphers Multifunctional Genes and Enzymes Linked With the Degradation of Aromatic Compounds and Pesticides in the Wheat Rhizosphere. Front Microbiol 2018; 9:1331. [PMID: 30034370 PMCID: PMC6043799 DOI: 10.3389/fmicb.2018.01331] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/31/2018] [Indexed: 11/19/2022] Open
Abstract
Agricultural soils are becoming contaminated with synthetic chemicals like polyaromatic compounds, petroleum hydrocarbons, polychlorinated biphenyls (PCBs), phenols, herbicides, insecticides and fungicides due to excessive dependency of crop production systems on the chemical inputs. Microbial degradation of organic pollutants in the agricultural soils is a continuous process due to the metabolic multifunctionalities and enzymatic capabilities of the soil associated communities. The plant rhizosphere with its complex microbial inhabitants and their multiple functions, is amongst the most live and dynamic component of agricultural soils. We analyzed the metatranscriptome data of 20 wheat rhizosphere samples to decipher the taxonomic microbial communities and their multifunctionalities linked with the degradation of organic soil contaminants. The analysis revealed a total of 21 different metabolic pathways for the degradation of aromatic compounds and 06 for the xenobiotics degradation. Taxonomic annotation of wheat rhizosphere revealed bacteria, especially the Proteobacteria, actinobacteria, firmicutes, bacteroidetes, and cyanobacteria, which are shown to be linked with the degradation of aromatic compounds as the dominant communities. Abundance of the transcripts related to the degradation of aromatic amin compounds, carbazoles, benzoates, naphthalene, ketoadipate pathway, phenols, biphenyls and xenobiotics indicated abundant degradation capabilities in the soils. The results highlighted a potentially dominant role of crop rhizosphere associated microbial communities in the remediation of contaminant aromatic compounds.
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Affiliation(s)
- Dhananjaya P. Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Ratna Prabha
- Department of Bio-Medical Engineering and Bio-Informatics, Chhattisgarh Swami Vivekanand Technical University, Bhilai, India
| | - Vijai K. Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
| | - Mukesh K. Verma
- Department of Bio-Medical Engineering and Bio-Informatics, Chhattisgarh Swami Vivekanand Technical University, Bhilai, India
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Novel Method Reveals a Narrow Phylogenetic Distribution of Bacterial Dispersers in Environmental Communities Exposed to Low-Hydration Conditions. Appl Environ Microbiol 2018; 84:AEM.02857-17. [PMID: 29374034 DOI: 10.1128/aem.02857-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 01/14/2018] [Indexed: 12/20/2022] Open
Abstract
In this study, we developed a method that provides profiles of community-level surface dispersal from environmental samples under controlled hydration conditions and enables us to isolate and uncover the diversity of the fastest bacterial dispersers. The method expands on the porous surface model (PSM), previously used to monitor the dispersal of individual bacterial strains in liquid films at the surface of a porous ceramic disc. The novel procedure targets complex communities and captures the dispersed bacteria on a solid medium for growth and detection. The method was first validated by distinguishing motile Pseudomonas putida and Flavobacterium johnsoniae strains from their nonmotile mutants. Applying the method to soil and lake water bacterial communities showed that community-scale dispersal declined as conditions became drier. However, for both communities, dispersal was detected even under low-hydration conditions (matric potential, -3.1 kPa) previously proven too dry for P. putida strain KT2440 motility. We were then able to specifically recover and characterize the fastest dispersers from the inoculated communities. For both soil and lake samples, 16S rRNA gene amplicon sequencing revealed that the fastest dispersers were substantially less diverse than the total communities. The dispersing fraction of the soil microbial community was dominated by Pseudomonas species cells, which increased in abundance under low-hydration conditions, while the dispersing fraction of the lake community was dominated by Aeromonas species cells and, under wet conditions (-0.5 kPa), also by Exiguobacterium species cells. The results gained in this study bring us a step closer to assessing the dispersal ability within complex communities under environmentally relevant conditions.IMPORTANCE Dispersal is a key process of bacterial community assembly, and yet, very few attempts have been made to assess bacterial dispersal at the community level, as the focus has previously been on pure-culture studies. A crucial factor for dispersal in habitats where hydration conditions vary, such as soils, is the thickness of the liquid films surrounding solid surfaces, but little is known about how the ability to disperse in such films varies within bacterial communities. Therefore, we developed a method to profile community dispersal and identify fast dispersers on a rough surface resembling soil surfaces. Our results suggest that within the motile fraction of a bacterial community, only a minority of the bacterial types are able to disperse in the thinnest liquid films. During dry periods, these efficient dispersers can gain a significant fitness advantage through their ability to colonize new habitats ahead of the rest of the community.
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Bedmar F, Gimenez D, Costa JL, Daniel PE. Persistence of acetochlor, atrazine, and S-metolachlor in surface and subsurface horizons of 2 typic argiudolls under no-tillage. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2017; 36:3065-3073. [PMID: 28577318 DOI: 10.1002/etc.3874] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/13/2017] [Accepted: 06/02/2017] [Indexed: 06/07/2023]
Abstract
Variations in soil properties with depth strongly influence the degradation and persistence of herbicides, underlining the importance of studying these processes in soil horizons with distinctively different properties. The persistence of the herbicides acetochlor, atrazine, and S-metolachlor was measured in samples of the A, B, and C horizons of 2 Typic Argiudolls from Argentina under no-till management. The soils studied differed in soil organic carbon (OC) content, pH, particle size distribution, and structure. Quantification of herbicides in soil was done through high-performance liquid chromatography with diode array detector. There were interactions of herbicide × horizon (p < 0.01) that resulted in degradation rates (k) of all herbicides decreasing, and their corresponding dissipation half-life (DT50) values increasing, with soil depth. Herbicide persistence across all soils and horizons ranged from 15 to 73 d for acetochlor, 13 to 29 d for atrazine, and 82 to 141 d for S-metolachlor, which had significantly (p < 0.01) greater persistence than atrazine and acetochlor. The DT50 values of herbicides were negatively correlated with the contents of OC (correlation coefficients ranging from -0.496 to -0.773), phosphorus (-0.427 to -0.564), and nitrogen-nitrate (-0.507 to -0.662), and with microbial activity (-0.454 to -0.687) and the adsorption coefficient (-0.530 to -0.595); DT50s were positively correlated with pH (0.366 to 0.648). Adsorption was likely the most influential process in determining persistence of these herbicides in surface and subsurface horizons. The present study can potentially improve the prediction of the fate of acetochlor, atrazine, and S-metolachlor in soils because it includes much needed information on the degradation of the herbicides in subsurface horizons. Environ Toxicol Chem 2017;36:3065-3073. © 2017 SETAC.
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Affiliation(s)
- Francisco Bedmar
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Buenos Aires, Argentina
| | - Daniel Gimenez
- Department of Environmental Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - José Luis Costa
- Instituto Nacional de Tecnología Agropecuaria (INTA), Balcarce, Buenos Aires, Argentina
| | - Peter E Daniel
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Buenos Aires, Argentina
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Tecon R, Or D. Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol Rev 2017; 41:599-623. [PMID: 28961933 PMCID: PMC5812502 DOI: 10.1093/femsre/fux039] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 07/10/2017] [Indexed: 12/13/2022] Open
Abstract
Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.
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Affiliation(s)
- Robin Tecon
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Dani Or
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
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12
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Lerch TZ, Chenu C, Dignac MF, Barriuso E, Mariotti A. Biofilm vs. Planktonic Lifestyle: Consequences for Pesticide 2,4-D Metabolism by Cupriavidus necator JMP134. Front Microbiol 2017; 8:904. [PMID: 28588567 PMCID: PMC5440565 DOI: 10.3389/fmicb.2017.00904] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/03/2017] [Indexed: 01/01/2023] Open
Abstract
The development of bacterial biofilms in natural environments may alter important functions, such as pollutant bioremediation by modifying both the degraders' physiology and/or interactions within the matrix. The present study focuses on the influence of biofilm formation on the metabolism of a pesticide, 2,4-dichlorophenoxyacetic acid (2,4-D), by Cupriavidus necator JMP134. Pure cultures were established in a liquid medium with 2,4-D as a sole carbon source with or without sand grains for 10 days. Bacterial numbers and 2,4-D concentrations in solution were followed by spectrophotometry, the respiration rate by gas chromatography and the surface colonization by electron microscopy. In addition, isotopic techniques coupled with Fatty Acid Methyl Ester (FAME) profiling were used to determine possible metabolic changes. After only 3 days, approximately 80% of the cells were attached to the sand grains and microscopy images showed that the porous medium was totally clogged by the development of a biofilm. After 10 days, there was 25% less 2,4-D in the solution in samples with sand than in control samples. This difference was due to (1) a higher (+8%) mineralization of 2,4-D by sessile bacteria and (2) a retention (15%) of 2,4-D in the biofilm matrix. Besides, the amount of carbohydrates, presumably constituting the biofilm polysaccharides, increased by 63%. Compound-specific isotope analysis revealed that the FAME isotopic signature was less affected by the biofilm lifestyle than was the FAME composition. These results suggest that sessile bacteria differ more in their anabolism than in their catabolism compared to their planktonic counterparts. This study stresses the importance of considering interactions between microorganisms and their habitat when studying pollutant dynamics in porous media.
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Affiliation(s)
- Thomas Z Lerch
- UMR IEES-Paris, Institute of Ecology and Environmental Sciences of Paris, (Centre National de la Recherche Scientifique, UPMC, Institut National de la Recherche Agronomique, UPEC, IRD, Université Paris Diderot)Créteil, France
| | - Claire Chenu
- UMR ECOSYS, Écologie Fonctionnelle et Écotoxicologie des Agroécosystèmes (Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay)Thiverval-Grignon, France
| | - Marie F Dignac
- UMR ECOSYS, Écologie Fonctionnelle et Écotoxicologie des Agroécosystèmes (Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay)Thiverval-Grignon, France
| | - Enrique Barriuso
- UMR ECOSYS, Écologie Fonctionnelle et Écotoxicologie des Agroécosystèmes (Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay)Thiverval-Grignon, France
| | - André Mariotti
- UMR IEES-Paris, Institute of Ecology and Environmental Sciences of Paris, (Centre National de la Recherche Scientifique, UPMC, Institut National de la Recherche Agronomique, UPEC, IRD, Université Paris Diderot)Créteil, France
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13
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Reedich LM, Millican MD, Koch PL. Temperature Impacts on Soil Microbial Communities and Potential Implications for the Biodegradation of Turfgrass Pesticides. JOURNAL OF ENVIRONMENTAL QUALITY 2017; 46:490-497. [PMID: 28724094 DOI: 10.2134/jeq2017.02.0067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Maintaining healthy turfgrass often results in the use of pesticides to manage weed, insect, and disease pests. To identify and understand potential nontarget impacts of pesticide usage while still maintaining attractive and functional turfgrass sites, it is important to improve our understanding of how pesticides degrade in various environments throughout the growing season. Temperature heavily influences microbial community composition and activity, and the microbial community often heavily influences pesticide degradation in soil ecosystems. Pesticide transformation products generated through the action of soil microbial degradation networks can vary in their toxicity, with the potential result that a pesticide applied in the spring at 10°C could produce different transformation products with different toxicological impacts than the sample pesticide applied to the same site at 22°C. The objective of this review is to examine past research surrounding soil microbial activity related to pesticide degradation and provide a foundation for how the soil microbiome interacts with pesticides and how seasonal temperature variations may influence those interactions.
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Bouhajja E, Agathos SN, George IF. Metagenomics: Probing pollutant fate in natural and engineered ecosystems. Biotechnol Adv 2016; 34:1413-1426. [PMID: 27825829 DOI: 10.1016/j.biotechadv.2016.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 10/01/2016] [Accepted: 10/12/2016] [Indexed: 12/23/2022]
Abstract
Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field. In this review, we survey the main steps of metagenomics applied to environments contaminated with organic compounds or heavy metals. We emphasize technical solutions proposed to overcome encountered obstacles. We then compare two metagenomic approaches, i.e. library-based targeted metagenomics and direct sequencing of metagenomes. In the former, environmental DNA is cloned inside a host, and then clones of interest are selected based on (i) their expression of biodegradative functions or (ii) sequence homology with probes and primers designed from relevant, already known sequences. The highest score for the discovery of novel genes and degradation pathways has been achieved so far by functional screening of large clone libraries. On the other hand, direct sequencing of metagenomes without a cloning step has been more often applied to polluted environments for characterization of the taxonomic and functional composition of microbial communities and their dynamics. In this case, the analysis has focused on 16S rRNA genes and marker genes of biodegradation. Advances in next generation sequencing and in bioinformatic analysis of sequencing data have opened up new opportunities for assessing the potential of biodegradation by microbes, but annotation of collected genes is still hampered by a limited number of available reference sequences in databases. Although metagenomics is still facing technical and computational challenges, our review of the recent literature highlights its value as an aid to efficiently monitor the clean-up of contaminated environments and develop successful strategies to mitigate the impact of pollutants on ecosystems.
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Affiliation(s)
- Emna Bouhajja
- Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium
| | - Spiros N Agathos
- Laboratoire de Génie Biologique, Earth and Life Institute, Université Catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348 Louvain-la-Neuve, Belgium; School of Life Sciences and Biotechnology, Yachay Tech University, 100119 San Miguel de Urcuquí, Ecuador
| | - Isabelle F George
- Université Libre de Bruxelles, Laboratoire d'Ecologie des Systèmes Aquatiques, Campus de la Plaine CP 221, Boulevard du Triomphe, 1050 Brussels, Belgium.
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15
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Kurt Z, Mack EE, Spain JC. Natural Attenuation of Nonvolatile Contaminants in the Capillary Fringe. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:10172-10178. [PMID: 27523982 DOI: 10.1021/acs.est.6b02525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
When anoxic polluted groundwater encounters the overlying vadose zone an oxic/anoxic interface is created, often near the capillary fringe. Biodegradation of volatile contaminants in the capillary fringe can prevent vapor migration. In contrast, the biodegradation of nonvolatile contaminants in the vadose zone has received comparatively little attention. Nonvolatile compounds do not cause vapor intrusion, but they still move with the groundwater and are major contaminants. Aniline (AN) and diphenylamine (DPA) are examples of toxic nonvolatile contaminants found often at dye and munitions manufacturing sites. In this study, we tested the hypothesis that bacteria can aerobically biodegrade AN and DPA in the capillary fringe and decrease the contaminant concentrations in the anoxic plume beneath the vadose zone. Laboratory multiport columns that represented the unsaturated zone were used to evaluate degradation of AN or DPA in contaminated water. The biodegradation fluxes of the contaminants were estimated to be 113 ± 26 mg AN·m(-2)·h(-1) and 76 ± 18 mg DPA·m(-2)·h(-1) in the presence of bacteria known to degrade AN and DPA. Oxygen and contaminant profiles along with enumeration of bacterial populations indicated that most of the biodegradation took place within the lower part of the capillary fringe. The results indicate that bacteria capable of contaminant biodegradation in the capillary fringe can create a sink for nonvolatile contaminants.
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Affiliation(s)
- Zohre Kurt
- School of Civil and Environmental Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0512, United States
- Institute of Scientific Research and High Technology Services , Calle Pullpn, Panamá, Panama
| | - E Erin Mack
- DuPont, Corporate Remediation Group, P.O. Box 6101, Glasgow 300, Newark, Delaware 19714-6101, United States
| | - Jim C Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0512, United States
- Center for Environmental Diagnostics and Bioremediation, University of West Florida , Pensacola, Florida 32514-5751, United States
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Worrich A, König S, Banitz T, Centler F, Frank K, Thullner M, Harms H, Miltner A, Wick LY, Kästner M. Bacterial Dispersal Promotes Biodegradation in Heterogeneous Systems Exposed to Osmotic Stress. Front Microbiol 2016; 7:1214. [PMID: 27536297 PMCID: PMC4971104 DOI: 10.3389/fmicb.2016.01214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/21/2016] [Indexed: 11/13/2022] Open
Abstract
Contaminant biodegradation in soils is hampered by the heterogeneous distribution of degrading communities colonizing isolated microenvironments as a result of the soil architecture. Over the last years, soil salinization was recognized as an additional problem especially in arid and semiarid ecosystems as it drastically reduces the activity and motility of bacteria. Here, we studied the importance of different spatial processes for benzoate biodegradation at an environmentally relevant range of osmotic potentials (ΔΨo) using model ecosystems exhibiting a heterogeneous distribution of the soil-borne bacterium Pseudomonas putida KT2440. Three systematically manipulated scenarios allowed us to cover the effects of (i) substrate diffusion, (ii) substrate diffusion and autonomous bacterial dispersal, and (iii) substrate diffusion and autonomous as well as mediated bacterial dispersal along glass fiber networks mimicking fungal hyphae. To quantify the relative importance of the different spatial processes, we compared these heterogeneous scenarios to a reference value obtained for each ΔΨo by means of a quasi-optimal scenario in which degraders were ab initio homogeneously distributed. Substrate diffusion as the sole spatial process was insufficient to counteract the disadvantage due to spatial degrader heterogeneity at ΔΨo ranging from 0 to -1 MPa. In this scenario, only 13.8-21.3% of the quasi-optimal biodegradation performance could be achieved. In the same range of ΔΨo values, substrate diffusion in combination with bacterial dispersal allowed between 68.6 and 36.2% of the performance showing a clear downwards trend with decreasing ΔΨo. At -1.5 MPa, however, this scenario performed worse than the diffusion scenario, possibly as a result of energetic disadvantages associated with flagellum synthesis and emerging requirements to exceed a critical population density to resist osmotic stress. Network-mediated bacterial dispersal kept biodegradation almost consistently high with an average of 70.7 ± 7.8%, regardless of the strength of the osmotic stress. We propose that especially fungal network-mediated bacterial dispersal is a key process to achieve high functionality of heterogeneous microbial ecosystems also at reduced osmotic potentials. Thus, mechanical stress by, for example, soil homogenization should be kept low in order to preserve fungal network integrity.
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Affiliation(s)
- Anja Worrich
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental MicrobiologyLeipzig, Germany; UFZ - Helmholtz Centre for Environmental Research, Department of Environmental BiotechnologyLeipzig, Germany
| | - Sara König
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental MicrobiologyLeipzig, Germany; UFZ - Helmholtz Centre for Environmental Research, Department of Ecological ModellingLeipzig, Germany
| | - Thomas Banitz
- UFZ - Helmholtz Centre for Environmental Research, Department of Ecological Modelling Leipzig, Germany
| | - Florian Centler
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology Leipzig, Germany
| | - Karin Frank
- UFZ - Helmholtz Centre for Environmental Research, Department of Ecological ModellingLeipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany; Institute for Environmental Systems Research, University of OsnabrückOsnabrück, Germany
| | - Martin Thullner
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology Leipzig, Germany
| | - Hauke Harms
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental MicrobiologyLeipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Anja Miltner
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology Leipzig, Germany
| | - Lukas Y Wick
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology Leipzig, Germany
| | - Matthias Kästner
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Biotechnology Leipzig, Germany
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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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18
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Otto S, Banitz T, Thullner M, Harms H, Wick LY. Effects of Facilitated Bacterial Dispersal on the Degradation and Emission of a Desorbing Contaminant. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6320-6326. [PMID: 27195517 DOI: 10.1021/acs.est.6b00567] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The quantitative relationship between a compound's availability for biological removal and ecotoxicity is a key issue for retrospective risk assessment and remediation approaches. Here, we investigated the impact of facilitated bacterial dispersal at a model soil-atmosphere interface on the release, degradation, and outgassing of a semivolatile contaminant. We designed a laboratory microcosm with passive dosing of phenanthrene (PHE) to a model soil-atmosphere interface (agar surface) in the presence and absence of glass fibers known to facilitate the dispersal of PHE-degrading Pseudomonas fluorescens LP6a. We observed that glass fibers (used as a model to mimic a fungal hyphal network) resulted in (i) increased bacterial surface coverage, (ii) effective degradation of matrix-bound PHE, and (iii) substantially reduced PHE emission to locations beyond the contamination zone even at low bacterial surface coverage. Our data suggest that bacterial dispersal networks such as mycelia promote the optimized spatial arrangement of microbial populations to allow for effective contaminant degradation and reduction of potential hazard to organisms beyond a contaminated zone.
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Affiliation(s)
| | | | | | - Hauke Harms
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Deutscher Platz 5e, 04103 Leipzig, Germany
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Mycelium-Like Networks Increase Bacterial Dispersal, Growth, and Biodegradation in a Model Ecosystem at Various Water Potentials. Appl Environ Microbiol 2016; 82:2902-2908. [PMID: 26944849 DOI: 10.1128/aem.03901-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/02/2016] [Indexed: 11/20/2022] Open
Abstract
Fungal mycelia serve as effective dispersal networks for bacteria in water-unsaturated environments, thereby allowing bacteria to maintain important functions, such as biodegradation. However, poor knowledge exists on the effects of dispersal networks at various osmotic (Ψo) and matric (Ψm) potentials, which contribute to the water potential mainly in terrestrial soil environments. Here we studied the effects of artificial mycelium-like dispersal networks on bacterial dispersal dynamics and subsequent effects on growth and benzoate biodegradation at ΔΨo and ΔΨm values between 0 and -1.5 MPa. In a multiple-microcosm approach, we used a green fluorescent protein (GFP)-tagged derivative of the soil bacterium Pseudomonas putida KT2440 as a model organism and sodium benzoate as a representative of polar aromatic contaminants. We found that decreasing ΔΨo and ΔΨm values slowed bacterial dispersal in the system, leading to decelerated growth and benzoate degradation. In contrast, dispersal networks facilitated bacterial movement at ΔΨo and ΔΨm values between 0 and -0.5 MPa and thus improved the absolute biodegradation performance by up to 52 and 119% for ΔΨo and ΔΨm, respectively. This strong functional interrelationship was further emphasized by a high positive correlation between population dispersal, population growth, and degradation. We propose that dispersal networks may sustain the functionality of microbial ecosystems at low osmotic and matric potentials.
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