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Guo S, Geisen S, Mo Y, Yan X, Huang R, Liu H, Gao Z, Tao C, Deng X, Xiong W, Shen Q, Kowalchuk GA, Li R. Predatory protists impact plant performance by promoting plant growth-promoting rhizobacterial consortia. THE ISME JOURNAL 2024; 18:wrae180. [PMID: 39312488 PMCID: PMC11459550 DOI: 10.1093/ismejo/wrae180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/22/2024] [Accepted: 09/20/2024] [Indexed: 09/25/2024]
Abstract
Plant performance is impacted by rhizosphere bacteria. These bacteria are subjected to both bottom-up control by root exudates as well as top-down control by predators, particularly protists. Protists stimulate plant growth-promoting microbes resulting in improved plant performance. However, knowledge of the mechanisms that determine the interconnections within such tripartite protist-bacteria-plant interactions remains limited. We conducted experiments examining the effects of different densities of the predatory protist Cercomonas lenta on rhizosphere bacterial communities, specifically zooming on interactions between Cercomonas lenta and key bacterial taxa, as well as interactions among key bacterial taxa. We tracked rhizosphere bacterial community composition, potential microbial interactions, and plant performance. We found that Cercomonas lenta inoculation led to an average increase in plant biomass of 92.0%. This effect was linked to an increase in plant growth-promoting rhizobacteria (Pseudomonas and Sphingomonas) and a decrease in bacteria (Chitinophaga) that negatively impact on plant growth-promoting rhizobacteria. We also found evidence for cooperative enhancements in biofilm formation within the plant growth-promoting rhizobacterial consortium. Cercomonas lenta enhanced a plant growth-promoting rhizobacterial consortium colonization by promoting its cooperative biofilm formation in the rhizosphere, leading to a 14.5% increase in phosphate solubilization that benefits plant growth. Taken together, we provide mechanistic insights into how the predatory protist Cercomonas lenta impacts plant growth, namely by stimulating plant beneficial microbes and enhancing their interactive activities such as biofilm formation. Predatory protists may therefore represent promising biological agents that can contribute to sustainable agricultural practices by promoting interactions between the plant and its microbiome.
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Affiliation(s)
- Sai Guo
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Provice 210095, P. R. China
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen 6700 AA, the Netherlands
| | - Yani Mo
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Provice 210095, P. R. China
| | - Xinyue Yan
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Provice 210095, P. R. China
| | - Ruoling Huang
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Provice 210095, P. R. China
| | - Hongjun Liu
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Provice 210095, P. R. China
| | - Zhilei Gao
- Department of Research and Innovation, EUROstyle BV, Ecomunitypark 1, Oosterwolde 8431 SM, the Netherlands
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Chengyuan Tao
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Provice 210095, P. R. China
| | - Xuhui Deng
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Provice 210095, P. R. China
| | - Wu Xiong
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Provice 210095, P. R. China
| | - Qirong Shen
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Provice 210095, P. R. China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht 3584 CH, the Netherlands
| | - Rong Li
- The Sanya Institute of the Nanjing Agricultural University, Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Provice 210095, P. R. China
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Song Y, Sun L, Wang H, Zhang S, Fan K, Mao Y, Zhang J, Han X, Chen H, Xu Y, Sun K, Ding Z, Wang Y. Enzymatic fermentation of rapeseed cake significantly improved the soil environment of tea rhizosphere. BMC Microbiol 2023; 23:250. [PMID: 37679671 PMCID: PMC10483718 DOI: 10.1186/s12866-023-02995-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Rapeseed cake is an important agricultural waste. After enzymatic fermentation, rapeseed cake not only has specific microbial diversity but also contains a lot of fatty acids, organic acids, amino acids and their derivatives, which has potential value as a high-quality organic fertilizer. However, the effects of fermented rapeseed cake on tea rhizosphere microorganisms and soil metabolites have not been reported. In this study, we aimed to elucidate the effect of enzymatic rapeseed cake fertilizer on the soil of tea tree, and to reveal the correlation between rhizosphere soil microorganisms and nutrients/metabolites. RESULTS The results showed that: (1) The application of enzymatic rapeseed cake increased the contents of soil organic matter (OM), total nitrogen (TN), total phosphorus (TP), available nitrogen (AN), and available phosphorus (AP); increased the activities of soil urease (S-UE), soil catalase (S-CAT), soil acid phosphatase (S-ACP) and soil sucrase (S-SC); (2) The application of enzymatic rapeseed cake increased the relative abundance of beneficial rhizosphere microorganisms such as Chaetomium, Inocybe, Pseudoxanthomonas, Pseudomonas, Sphingomonas, and Stenotrophomonas; (3) The application of enzymatic rapeseed cake increased the contents of sugar, organic acid, and fatty acid in soil, and the key metabolic pathways were concentrated in sugar and fatty acid metabolisms; (4) The application of enzymatic rapeseed cake promoted the metabolism of sugar, organic acid, and fatty acid in soil by key rhizosphere microorganisms; enzymes and microorganisms jointly regulated the metabolic pathways of sugar and fatty acids in soil. CONCLUSIONS Enzymatic rapeseed cake fertilizer improved the nutrient status and microbial structure of tea rhizosphere soil, which was beneficial for enhancing soil productivity in tea plantations. These findings provide new insights into the use of enzymatic rapeseed cake as an efficient organic fertilizer and expand its potential for application in tea plantations.
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Affiliation(s)
- Yujie Song
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Litao Sun
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Huan Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shuning Zhang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Kai Fan
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yilin Mao
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Zhang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiao Han
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hao Chen
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yang Xu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Kangwei Sun
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhaotang Ding
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China.
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Wang P, Cao J, Mao L, Zhu L, Zhang Y, Zhang L, Jiang H, Zheng Y, Liu X. Effect of H 3PO 4-modified biochar on the fate of atrazine and remediation of bacterial community in atrazine-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158278. [PMID: 36029817 DOI: 10.1016/j.scitotenv.2022.158278] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
The application of chemically modified biochar is a promising strategy for the remediation of contaminated (e.g., pesticides) soil. In this study, H3PO4 was used to modify peanut shell to improve the remediation performance of biochar. Surface area (980.19 m2/g), pore volume (0.12 cm3/g), and the functional groups (OH, CO, and phosphorus-containing groups) on the biochar were increased by H3PO4 treatment. The sorption experimental data were well fitted by Freundlich model, while the sorption affinity (Kf) of H3PO4 modified biochar (PBC) for atrazine was 128 times greater than that of the untreated biochar (BC) in the aquatic systems. The Kf values of PBC-amended soil to atrazine were increased by 13.57 times than that of single soil. The strong sorption of PBC on atrazine delayed the degradation of atrazine in soil, and the residual percentage of atrazine in soil and soil-PBC mixture were 4.90% and 71.44% at the end of 60-day incubation, with the degradation half-life increased from 13.3 to 121.6 d. The analysis of high-throughput sequencing results showed that atrazine reduced the diversity of soil microbial community, but the abundance of microorganisms with degradation function increased and became dominant species. The addition of PBC in soil accelerated the microbial remediation of atrazine stress, which may promote the soil nitrogen cycle. Therefore, amendment of atrazine contaminated soil with PBC can reduce the environmental risk of atrazine and benefit the soil microbial ecology.
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Affiliation(s)
- Pingping Wang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Junli Cao
- Shanxi Center for Testing of Functional Agro-Products, Shanxi Agricultural University, Taiyuan 030031, China
| | - Liangang Mao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lizhen Zhu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yanning Zhang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lan Zhang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongyun Jiang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yongquan Zheng
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Xingang Liu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Shen J, Luo Y, Tao Q, White PJ, Sun G, Li M, Luo J, He Y, Li B, Li Q, Xu Q, Cai Y, Li H, Wang C. The exacerbation of soil acidification correlates with structural and functional succession of the soil microbiome upon agricultural intensification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154524. [PMID: 35288138 DOI: 10.1016/j.scitotenv.2022.154524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Agricultural intensification driven by land-use changes has caused continuous and cumulative soil acidification (SA) throughout the global agroecosystem. Microorganisms mediate acid-generating reactions; however, the microbial mechanisms responsible for exacerbating SA feedback remain largely unknown. To determine the microbial community composition and putative function associated with SA, we conducted a metagenomic analysis of soils across a chronosequence that has elapsed since the conversion of rice-wheat (RW) to rice-vegetable (RV) rotations. Compared to RW rotations, soil pH decreased by 0.50 and 1.56 units (p < 0.05) in response to 10-year and 20-year RV rotations, respectively. Additionally, acid saturation ratios were increased by 7.3% and 36.2% (p < 0.05), respectively. The loss of microbial beta-diversity was a key element that contributed to the exacerbation of SA in the RV. Notably, the 20-year RV-enriched microbial taxa were more hydrogen (H+)-, aluminium (Al3+)-, and nitrate nitrogen (NO3--N) -dependent and contained more genera exhibiting dehydrogenation functions than did RW-enriched taxa. "M00115, M00151, M00417, and M00004" and "M00531 and M00135" that are the "proton-pumping" and "proton-consuming" gene modules, respectively, were linked to the massive recruitment of acid-dependent biomarkers in 20-year RV soils, particularly Rhodanobacter, Gemmatirosa, Sphingomonas, and Streptomyces. Collectively, soils in long-term RV rotations were highly acidified and acid-sensitive, as the enrichment of microbial dehydrogenation genes allowing for soil buffering capacity is more vulnerable to H+ loading and consequently promotes the colonization of more acid-tolerant and acidogenic microbes, and ultimately provide new clues for researchers to elucidate the interaction between SA and the soil microbiome.
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Affiliation(s)
- Jie Shen
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Youlin Luo
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Philip J White
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Geng Sun
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Meng Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Jipeng Luo
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuting He
- Chengdu Popularization of Agricultural Technique Station, Chengdu 610041, China
| | - Bing Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiquan Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang Xu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Cai
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Huanxiu Li
- Fruit and Vegetable Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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Li J, Ou Y, Zhang Y, Guo S, Li S, Guo C, Dang Z, Cao Z, Feng J, Sun J. Viability and distribution of bacteria immobilized on Sawdust@silica: The removal mechanism of phenanthrene in soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 198:110649. [PMID: 32325259 DOI: 10.1016/j.ecoenv.2020.110649] [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: 02/06/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
Immobilized cells (ICs) have been widely used to enhance the remediation of organic-contaminated soil (e.g., polycyclic aromatic hydrocarbons, PAHs). Once ICs are added to the heterogeneous soil, degradation hotspots are immediately formed near the carrier, leaving the remaining soil lack of degrading bacteria. Therefore, it remains unclear how ICs efficiently utilize PAHs in soil. In this study, the viability of Silica-IC (Cells@Sawdust@Silica) and the distribution of inoculated ICs and phenanthrene (Phe) in a slurry system (soil to water ratio 1:2) were investigated to explore the removal mechanism of PAHs by the ICs. Results showed that the Silica-IC maintained (i) good reproductive ability (displayed by the growth curve in soil and water phase), (ii) excellent stability, which was identified by the ratio of colony forming units in the soil phase to the water phase, the difference between the colony number and the DNA copies, and characteristics of the biomaterial observed by the FESEM, and (iii) high metabolic activity (the removal percentages of Phe in soil by the ICs were more than 95% after 48 h). Finally, the possible pathways for the ICs to efficiently utilize Phe in soil are proposed based on the distribution and correlation of Phe and ICs between the soil and water phase. The adsorption-degradation process was dominant, i.e., the enhanced degradation occurred between the ICs and carrier-adsorbed Phe. This study provided new insights on developing a bio-material for efficient bio-remediation of PAHs-contaminated soil.
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Affiliation(s)
- Jinghua Li
- School of Environment, Henan Normal University, Xinxiang, Henan, 453007, PR China; Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Province, Xinxiang, Henan, 453007, PR China; School of Environment and Energy, South China University of Technology, The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, Guangzhou, 510006, PR China
| | - Yiwen Ou
- School of Environment, Henan Normal University, Xinxiang, Henan, 453007, PR China
| | - Yanshi Zhang
- School of Environment, Henan Normal University, Xinxiang, Henan, 453007, PR China
| | - Shuli Guo
- School of Environment, Henan Normal University, Xinxiang, Henan, 453007, PR China
| | - Shaohua Li
- School of Environment, Henan Normal University, Xinxiang, Henan, 453007, PR China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, Guangzhou, 510006, PR China.
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, Guangzhou, 510006, PR China
| | - Zhiguo Cao
- School of Environment, Henan Normal University, Xinxiang, Henan, 453007, PR China; Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Province, Xinxiang, Henan, 453007, PR China
| | - Jinglan Feng
- School of Environment, Henan Normal University, Xinxiang, Henan, 453007, PR China; Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Province, Xinxiang, Henan, 453007, PR China
| | - Jianhui Sun
- School of Environment, Henan Normal University, Xinxiang, Henan, 453007, PR China; Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, International Joint Laboratory on Key Techniques in Water Treatment, Henan Province, Xinxiang, Henan, 453007, PR China
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Asemoloye MD, Ahmad R, Jonathan SG. Synergistic rhizosphere degradation of γ-hexachlorocyclohexane (lindane) through the combinatorial plant-fungal action. PLoS One 2017; 12:e0183373. [PMID: 28859100 PMCID: PMC5578508 DOI: 10.1371/journal.pone.0183373] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/02/2017] [Indexed: 11/19/2022] Open
Abstract
Fungi are usually involved in degradation/deterioration of many anthropogenic wastes due to their verse enzyme secretions and adaptive capabilities. In this study, five dominant fungal strains were isolated from an aged lindane polluted site, they were all mixed (100 mg each) together with pent mushroom compost (SMC) and applied to lindane polluted soil (5 kg) at 10, 20, 30, 40% and control 0% (soil with no treatment), these were used to grow M. maximus Jacq for 3 months. To establish lindane degradation, deductions such as Degradation rate (K1), Half-life (t1/2) and Degradation efficiency (DE) were made based on the analyzed lindane concentrations before and after the experiment. We also tested the presence and expressions of phosphoesterases (mpd and opd-A) and catechol 1,2-dioxygenases (efk2 and efk4) genes in the strains. The stains were identified as Aspergillus niger (KY693970); Talaromyces atroroseus (KY488464), Talaromyces purpurogenus (KY488468), Yarrowia lipolytica (KY488469) and Aspergillus flavus (KY693973) through morphological and molecular methods. Combined rhizospheric action of M. maximus and fungi speed up lindane degradation rate, initially detected lindane concentration of 45 mg/kg was reduced to 11.26, 9.34 and 11.23 mg/kg in 20, 30 and 40% treatments respectively making 79.76, 85.93 and 88.67% degradation efficiencies. K1 of 1.29 was recorded in control while higher K1 of 1.60, 1.96 and 2.18 /day were recorded in 20, 30 and 40% treatments respectively. The best t1/2 of 0.32 and 0.35 /day were recorded in 40 and 30% compared to control (0.54 /day). All the strains were also affirmed to possess the tested genes; opd was overexpressed in all the strains except KY693973 while mpd was overexpressed in KY693970, KY488464 but moderately expressed in KY488468, KY488469 and KY693973. However, efk genes were under-expressed in most of the strains except KY488469 and KY693973 which showed moderate expression of efk4. This work suggests that the synergistic association of the identified rhizospheric fungi and M. maximus roots could be used to remove lindane in soil at a limited time period and this combination could be used at large scale.
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Affiliation(s)
- Michael Dare Asemoloye
- Food and Environmental Mycology/Biotechnology Unit, Department of Botany, University of Ibadan, Ibadan, Nigeria
| | - Rafiq Ahmad
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Segun Gbolagade Jonathan
- Food and Environmental Mycology/Biotechnology Unit, Department of Botany, University of Ibadan, Ibadan, Nigeria
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Wang F, Dörfler U, Jiang X, Schroll R. Predicting isoproturon long-term mineralization from short-term experiment: Can this be a suitable approach? CHEMOSPHERE 2016; 144:312-318. [PMID: 26366929 DOI: 10.1016/j.chemosphere.2015.08.086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 08/25/2015] [Accepted: 08/30/2015] [Indexed: 06/05/2023]
Abstract
A worldwide used pesticide - isoproturon (IPU) - was selected to test whether short-term experiments can be used to predict long-term mineralization of IPU in soil. IPU-mineralization was measured for 39 and 265 days in four different agricultural soils with a low mineralization dynamic. Additionally, in one soil IPU dissipation, formation and dissipation of metabolites, formation of non-extractable residues (NER) and (14)C-microbial biomass from (14)C-IPU were monitored for 39 and 265 days. The data from short-term and long-term experiments were used for model fitting. The long-term dynamics of IPU mineralization were considerably overestimated by the short-term experiments in two soils with neutral pH, while in two other soils with low pH and lower mineralization, the long-term mineralization of IPU could be sufficiently predicted. Additional investigations in one of the soils with neutral pH showed that dissipation of IPU and metabolites could be correctly predicted by the short-term experiment. However, the formation of NER and (14)C-microbial biomass were remarkably overestimated by the short-term experiment. Further, it could be shown that the released NER and (14)C-microbial biomass were the main contributors of (14)CO2 formation at later incubation stages. Taken together, our results indicate that in soils with neutral pH short-term experiments were inadequate to predict the long-term mineralization of IPU.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Research Unit Microbe-Plant Interactions, 85764 Neuherberg, Germany
| | - Ulrike Dörfler
- Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Research Unit Microbe-Plant Interactions, 85764 Neuherberg, Germany
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Reiner Schroll
- Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Research Unit Microbe-Plant Interactions, 85764 Neuherberg, Germany.
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Characterization of para-Nitrophenol-Degrading Bacterial Communities in River Water by Using Functional Markers and Stable Isotope Probing. Appl Environ Microbiol 2015. [PMID: 26209677 DOI: 10.1128/aem.01794-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Microbial degradation is a major determinant of the fate of pollutants in the environment. para-Nitrophenol (PNP) is an EPA-listed priority pollutant with a wide environmental distribution, but little is known about the microorganisms that degrade it in the environment. We studied the diversity of active PNP-degrading bacterial populations in river water using a novel functional marker approach coupled with [(13)C6]PNP stable isotope probing (SIP). Culturing together with culture-independent terminal restriction fragment length polymorphism analysis of 16S rRNA gene amplicons identified Pseudomonas syringae to be the major driver of PNP degradation in river water microcosms. This was confirmed by SIP-pyrosequencing of amplified 16S rRNA. Similarly, functional gene analysis showed that degradation followed the Gram-negative bacterial pathway and involved pnpA from Pseudomonas spp. However, analysis of maleylacetate reductase (encoded by mar), an enzyme common to late stages of both Gram-negative and Gram-positive bacterial PNP degradation pathways, identified a diverse assemblage of bacteria associated with PNP degradation, suggesting that mar has limited use as a specific marker of PNP biodegradation. Both the pnpA and mar genes were detected in a PNP-degrading isolate, P. syringae AKHD2, which was isolated from river water. Our results suggest that PNP-degrading cultures of Pseudomonas spp. are representative of environmental PNP-degrading populations.
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Draft Genome Sequence of Isoproturon-Mineralizing Sphingomonas sp. SRS2, Isolated from an Agricultural Field in the United Kingdom. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00569-15. [PMID: 26021936 PMCID: PMC4447921 DOI: 10.1128/genomea.00569-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sphingomonas sp. SRS2 was the first described pure strain that is capable of mineralizing the phenylurea herbicide isoproturon and some of its related compounds. This strain has been studied thoroughly and shows potential for bioremediation purposes. We present the draft genome sequence of this bacterium, which will aid future studies.
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Dechesne A, Badawi N, Aamand J, Smets BF. Fine scale spatial variability of microbial pesticide degradation in soil: scales, controlling factors, and implications. Front Microbiol 2014; 5:667. [PMID: 25538691 PMCID: PMC4257087 DOI: 10.3389/fmicb.2014.00667] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/17/2014] [Indexed: 11/16/2022] Open
Abstract
Pesticide biodegradation is a soil microbial function of critical importance for modern agriculture and its environmental impact. While it was once assumed that this activity was homogeneously distributed at the field scale, mounting evidence indicates that this is rarely the case. Here, we critically examine the literature on spatial variability of pesticide biodegradation in agricultural soil. We discuss the motivations, methods, and main findings of the primary literature. We found significant diversity in the approaches used to describe and quantify spatial heterogeneity, which complicates inter-studies comparisons. However, it is clear that the presence and activity of pesticide degraders is often highly spatially variable with coefficients of variation often exceeding 50% and frequently displays non-random spatial patterns. A few controlling factors have tentatively been identified across pesticide classes: they include some soil characteristics (pH) and some agricultural management practices (pesticide application, tillage), while other potential controlling factors have more conflicting effects depending on the site or the pesticide. Evidence demonstrating the importance of spatial heterogeneity on the fate of pesticides in soil has been difficult to obtain but modeling and experimental systems that do not include soil's full complexity reveal that this heterogeneity must be considered to improve prediction of pesticide biodegradation rates or of leaching risks. Overall, studying the spatial heterogeneity of pesticide biodegradation is a relatively new field at the interface of agronomy, microbial ecology, and geosciences and a wealth of novel data is being collected from these different disciplinary perspectives. We make suggestions on possible avenues to take full advantage of these investigations for a better understanding and prediction of the fate of pesticides in soil.
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Affiliation(s)
- Arnaud Dechesne
- Department of Environmental Engineering, Technical University of DenmarkLyngby, Denmark
| | - Nora Badawi
- Department of Geochemistry, Geological Survey of Denmark and GreenlandCopenhagen, Denmark
| | - Jens Aamand
- Department of Geochemistry, Geological Survey of Denmark and GreenlandCopenhagen, Denmark
| | - Barth F. Smets
- Department of Environmental Engineering, Technical University of DenmarkLyngby, Denmark
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Liliensiek AK, Thakuria D, Clipson N, Talukdar NC. Linking phylogeny to abundant ribotypes of community fingerprints: an exercise on the phylotypic responses to plant species, fertilisation and Lolium perenne ingression. SPRINGERPLUS 2013; 2:522. [PMID: 24255830 PMCID: PMC3824697 DOI: 10.1186/2193-1801-2-522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 07/26/2013] [Indexed: 11/16/2022]
Abstract
The present study explores the potential of directly linking phylogenetic identities obtained by cloning and sequencing of ITS sequences to dominant ribotypes of molecular community fingerprints to give further insight into dominant members of the communities in three Irish grassland soils. The ten most abundant bacterial ribotypes of untreated bare soils of three grassland microcosms were chosen to represent the "baseline community" of the respective soil. Identities on phylum and order level were assigned to these ribotypes on a weighted basis, by matching sequence homologies of cloned ITS sequences with ribotypes of the same fragment lengths ±5 bp. Results showed that ribotypes were represented by the phyla Acidobacteria, Actinobacteria, Proteobacteria, and Firmicutes and the distribution of the ribotype and phylotype communities was shown to be highly site-specific. Furthermore the response of dominant bacterial phylotypes to plant species composition, fertilisation and Lolium perenne ingression was investigated within a larger microcosm study (Microb Ecol 63:509-521).
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Affiliation(s)
- Ann-Kathrin Liliensiek
- />School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4 Ireland
- />Department of Aquatic Chemistry, Federal Institute of Hydrology, Am Mainzer Tor 1, Koblenz, 56068 Germany
| | - Dwipendra Thakuria
- />School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4 Ireland
| | - Nicholas Clipson
- />School of Biology and Environmental Sciences, University College Dublin, Belfield, Dublin 4 Ireland
| | - Narayan C Talukdar
- />Department of Biotechnology, Institute of Bioresources and Sustainable Development, Microbial Resources Division, GOI, Imphal, Manipur India
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12
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Bers K, De Mot R, Springael D. In situresponse of the linuron degradation potential to linuron application in an agricultural field. FEMS Microbiol Ecol 2013; 85:403-16. [DOI: 10.1111/1574-6941.12129] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 03/25/2013] [Accepted: 04/01/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Karolien Bers
- Division of Soil and Water Management; KU Leuven; Leuven Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics; KU Leuven; Leuven Belgium
| | - Dirk Springael
- Division of Soil and Water Management; KU Leuven; Leuven Belgium
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13
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Murakami Y, Otsuka S, Senoo K. Abundance and community structure of sphingomonads in leaf residues and nearby bulk soil. Microbes Environ 2011; 25:183-9. [PMID: 21576871 DOI: 10.1264/jsme2.me10114] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We examined the abundance and community structure of sphingomonads in the decaying leaf residues of eight plant species as well as the nearby soil, by 16S rRNA gene-based real-time PCR and denaturing gradient gel electrophoresis. In the leaf residues, the sphingomonads generally accumulated to high levels, comprising approximately 15% of the total bacteria, and formed a community structure related to sampling locations. At least within the time period studied, their abundance in leaf residues changed, but their community structure was basically maintained. In soil, sphingomonads made up only 1.7% of total bacteria on average. The community structure of sphingomonads differed between the leaf residues and bulk soil, among plant plots, and among samples collected at different times. The results show that particular sphingomonad populations accumulate in leaf residues compared to the surrounding bulk soil under field conditions.
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Affiliation(s)
- Yuta Murakami
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan
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Karpouzas DG, Singh BK. Application of fingerprinting molecular methods in bioremediation studies. Methods Mol Biol 2010; 599:69-88. [PMID: 19882280 DOI: 10.1007/978-1-60761-439-5_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Bioremediation has been identified as a beneficial and effective strategy for the removal of recalcitrant environmental contaminants. Bioaugmentation of polluted environments with exogenous degrading microorganisms constitutes a major strategy of bioremediation. However, the ecological role of these strains and their impact on the endogenous microbial community of the micro-ecosystems where they are released should be known. Fingerprinting PCR-based methods, like denaturating gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (TRFLP), could be used in studies exploring the ecology of pollutant-degrading microorganisms and their effects on the structure of the soil microbial community. This chapter provides a brief outline of the technical details involved in the application of DGGE and TRFLP fingerprinting in soil microbial ecology, with particular reference to bioremediation studies.
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Yamamoto S, Otsuka S, Murakami Y, Nishiyama M, Senoo K. Genetic diversity of gamma-hexachlorocyclohexane-degrading sphingomonads isolated from a single experimental field. Lett Appl Microbiol 2009; 49:472-7. [DOI: 10.1111/j.1472-765x.2009.02691.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Juhler RK, Henriksen TH, Ernstsen V, Vinther FP, Rosenberg P. Impact of basic soil parameters on pesticide disappearance investigated by multivariate partial least square regression and statistics. JOURNAL OF ENVIRONMENTAL QUALITY 2008; 37:1719-32. [PMID: 18689733 DOI: 10.2134/jeq2006.0230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Dissipation time is a key parameter when studying and modeling the environmental fate of pesticides. This study was conducted to characterize the variability of pesticide disappearance in soil and to identify possible controlling parameters related to intrinsic soil properties and microbiology. Multivariate data analysis was used to study spatial variability in three horizons from 24 sandy soil profiles. The time for 50% disappearance (DT(50)) was characterized for two herbicides, metribuzin (MBZ) and MCPA, and methyltriazine amine (MTA; transformation product of metsulfuron-methyl, tribenuron-methyl, thifensulfuron-methyl, and chlorsulfuron). Normal and log-normal distributions were compared for DT(50) and soil properties and descriptive statistics were calculated. Conformity with log-transformed distributions was observed and assuming normality of the DT(50) data would cause 5 to 35% overestimation. Mean DT(50) were: MCPA 9.5, MBZ 168, and MTA 127. Significant effect of soil depth on DT(50) was shown for MCPA and MBZ, with low values in deeper horizons. Simple linear correlation for combinations of MCPA, MTA, pH, and total organic carbon (TOC) was observed. Using partial least squares regression (PLS) 71 to 85% of the total DT(50) variance was explained. A specific predictor variable could not be identified as the controlling components differed within horizons and compounds. For MCPA the overall important predictor variables were microbiology and TOC, whereas for MTA and MBZ it was inorganic variables (Al, Fe, cation exchange capacity, base saturation percent, and pH) and microbiology. The study indicates that PLS generated input data can improve pesticide fate modeling and reduce the uncertainty in dissipation estimation.
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Affiliation(s)
- R K Juhler
- Geological Survey of Denmark and Greenland, GEUS, Øster Voldgade 10, DK-1350 Copenhagen K, Denmark.
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Baxter J, Cummings SP. The degradation of the herbicide bromoxynil and its impact on bacterial diversity in a top soil. J Appl Microbiol 2008; 104:1605-16. [PMID: 18217937 DOI: 10.1111/j.1365-2672.2007.03709.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To study how repeated applications of an herbicide bromoxynil to a soil, mimicking the regime used in the field, affected the degradation of the compound and whether such affects were reflected by changes in the indigenous bacterial community present. METHODS AND RESULTS Bromoxynil degradation was monitored in soil microcosms using HPLC. Its impact on the bacterial community was determined using denaturing gradient gel electrophoresis (DGGE) and quantitative PCR of five bacterial taxa (Pseudomonads, Actinobacteria, alpha-Proteobacteria, Acidobacteria and nitrifying bacteria). Three applications of 10 mg kg(-1) of bromoxynil at 28-day intervals resulted in rapid degradation, the time for removal of 50% of the compound decreasing from 6.4 days on the first application to 4.9 days by the third. Bacterial population profiles showed significant similarity throughout the experiment. With the addition of 50 mg kg(-1) bromoxynil to soil, the degradation was preceded by a lag phase and the time for 50% of the compound to be degraded increased from 7 days to 28 days by the third application. The bacterial population showed significant differences 7 days after the final application of bromoxynil that correlated with an inhibition of degradation during the same period. CONCLUSIONS These analyses highlighted that the addition of bromoxynil gave rise to significant shifts in the community diversity and its structure as measured by four abundant taxa, when compared with the control microcosm. These changes persisted even after bromoxynil had been degraded. SIGNIFICANCE AND IMPACT OF THE STUDY Here we show that bromoxynil can exert an inhibitory effect on the bacterial population that results in decreased rates of degradation and increased persistence of the compound. In addition, we demonstrate that molecular approaches can identify statistically significant changes in microbial communities that occur in conjunction with changes in the rate of degradation of the compound in the soil.
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Affiliation(s)
- J Baxter
- School of Applied Sciences, University of Northumbria, Newcastle-upon-Tyne, UK
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Fenlon KA, Jones KC, Semple KT. Development of microbial degradation of cypermethrin and diazinon in organically and conventionally managed soils. ACTA ACUST UNITED AC 2007; 9:510-5. [PMID: 17554421 DOI: 10.1039/b700668c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The behaviour of pesticides in the soil is a complex issue and is controlled by the physical, chemical and biological properties of the soil. The ability of microorganisms to degrade pesticides is not only controlled by the bioavailability of a chemical but also by their capacity to develop the ability to utilise available chemicals. The development of catabolism in the indigenous soil microflora of four organically and one conventionally managed soils was investigated for two pesticides: cypermethrin and diazinon. Soils were amended with cypermethrin and diazinon and aged for 0, 2, 4, 6, 8, and 14 weeks and, at each time point, mineralisation of freshly added 14C-cypermethrin or 14C-diazinon was measured by trapping 14CO2. In general, contact times between the soil and the pesticide resulted in a reduction in the lag phase (the period of time before mineralisation exceeded 5% of the added activity), followed by increases in the extent of mineralisation. Cypermethrin was mineralised significantly in all soils; whereas, diazinon was only appreciably mineralised in two of the soils, most notably in the organic soil from Redesdale. Statistical analysis showed pH and organic matter content of the soil had a significant effect on the extent of mineralisation (P< or = 0.05) of the cypermethrin in the soils.
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Affiliation(s)
- Katie A Fenlon
- Department of Environmental Science, Faculty of Science and Technology, Lancaster University, Lancaster, UK LA1 4YQ
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