Fungal and oomycete pathogen detection in the rhizosphere of organic tomatoes grown in cover crop-treated soils |
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| Institution: | 1. Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456, United States;2. Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691, United States;3. Department of Plant Science and Landscape Architecture, University of Maryland, Lower Eastern Shore Research and Education Center, Salisbury, MD 21801, United States;4. Department of Horticulture and Crop Science, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, OH 44691, United States;1. Division of Microbiology, Indian Agricultural Research Institute, New Delhi 110012, India;2. Department of Botany and Biotechnology, Arya PG College, Panipat 132103, India;1. Provincial Key Laboratory of Agrobiology, Institute of Agro-biotechnology, Jiangsu Academy of Agriculture Sciences, Nanjing 210014, China;2. Key Laboratory of Efficient Irrigation-Drainage and Agricultural Soil-Water Environment in Southern China, Ministry of Education, College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing 210098, China;3. Jiangsu Coast Development Group Co. Ltd., Nanjing 210003, China;1. Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China;2. College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China;1. Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal;2. Environmental Microbiology and Biotecnology Lab, Ecophysiology of Symbiotic Interactions Unit, Universidade Vila Velha (UVV), Boa Vista, Vila Velha, ES, 29102-770, Brazil;3. Soilvitae Lda., Tec Labs – Centro de Inovação Campus da Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal;4. Plant Physiology Lab, Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacazes, RJ, 28013-602, Brazil;5. Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (Nudiba), Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacazes, RJ, 28013-602, Brazil;6. Laboratory of Biochemistry and Physiology of Microorganisms, Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacazes, RJ, 28013-602, Brazil;1. INRA, UMR1355 Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France;2. University Nice Sophia Antipolis, ISA, UMR 1355, 06900 Sophia Antipolis, France;3. CNRS, UMR 7254, Institut Sophia Agrobiotech, F-06903 Sophia Antipolis, France |
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| Abstract: | Soil management practices, including the use of cover crops, affect soil and plant health through varied mechanisms. Impacts on microbial communities are known to be important, but are not well understood. Various techniques are used to measure the effect of treatments on microbial communities, but rarely are the results of more than one technique compared. This field study examined the impacts of a single-season application of cover crops on detection of pathogen species in the tomato crop rhizosphere. The study took place in Maryland, New York and Ohio (MD, NY and OH) in the summers of 2010 and 2011, with a total of 260 plots tested using both macroarray and T-RFLP analyses. The macroarray used in this study was specifically designed to detect thirty-one pathogens of solanaceous crops and had not previously been used for such a field study. The results of T-RFLP analysis, which is a common tool for examining microbial communities, were compared to the macroarray results and the limitations and benefits of each are presented. While not a quantitative measure, the macroarray was able to detect certain fungi with much greater sensitivity than T-RFLP. Our findings suggest that the results of PCR-based techniques used for microbial community studies should be compared to other methods to verify sensitivity. |
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| Keywords: | Cover crops Suppressive soils Microbial communities Soilborne pathogens Macroarray Terminal restriction fragment length polymorphisms |
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