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Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial...

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Autores principales: Lupatini, Manoeli, Korthals, Gerard W., de Hollander, Mattias, Janssens, Thierry K. S., Kuramae, Eiko E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209367/
https://www.ncbi.nlm.nih.gov/pubmed/28101080
http://dx.doi.org/10.3389/fmicb.2016.02064
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author Lupatini, Manoeli
Korthals, Gerard W.
de Hollander, Mattias
Janssens, Thierry K. S.
Kuramae, Eiko E.
author_facet Lupatini, Manoeli
Korthals, Gerard W.
de Hollander, Mattias
Janssens, Thierry K. S.
Kuramae, Eiko E.
author_sort Lupatini, Manoeli
collection PubMed
description Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms.
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spelling pubmed-52093672017-01-18 Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System Lupatini, Manoeli Korthals, Gerard W. de Hollander, Mattias Janssens, Thierry K. S. Kuramae, Eiko E. Front Microbiol Microbiology Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms. Frontiers Media S.A. 2017-01-04 /pmc/articles/PMC5209367/ /pubmed/28101080 http://dx.doi.org/10.3389/fmicb.2016.02064 Text en Copyright © 2017 Lupatini, Korthals, de Hollander, Janssens and Kuramae. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Lupatini, Manoeli
Korthals, Gerard W.
de Hollander, Mattias
Janssens, Thierry K. S.
Kuramae, Eiko E.
Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System
title Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System
title_full Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System
title_fullStr Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System
title_full_unstemmed Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System
title_short Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System
title_sort soil microbiome is more heterogeneous in organic than in conventional farming system
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209367/
https://www.ncbi.nlm.nih.gov/pubmed/28101080
http://dx.doi.org/10.3389/fmicb.2016.02064
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