Soil microbiome is more heterogeneous in organic than in conventional farming system

Manoeli Lupatini, Gerard W. Korthals, Mattias de Hollander, Thierry K.S. Janssens, Eiko E. Kuramae*

*Corresponding author for this work

    Research output: Contribution to JournalArticleAcademicpeer-review

    Abstract

    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.

    Original languageEnglish
    Article number2064
    JournalFrontiers in Microbiology
    Volume7
    Issue numberJAN
    DOIs
    Publication statusPublished - 4 Jan 2017

    Funding

    The authors acknowledge Johnny Visser and colleagues of Vredepeel experimental farm, Leonardo Pitombo for the soil sampling, Agata Pijl and Victor Carrion for laboratory assistance. This study was funded by BE-BASIC Foundation (F08.002.05) and The Netherlands Organization for Scientific Research (NWO) and FAPESP grant number 729.004.003. The scholarship to the first author was granted by FAPERGS/CAPES (Research Agency of the State of Rio Grande do Sul/Brazilian Federal Agency for Support and Evaluation of Graduate Education within the Ministry of Education of Brazil). Publication number 6214 of the Netherlands Institute of Ecology, NIOO-KNAW.

    FundersFunder number
    Research Agency of the State of Rio Grande do Sul/Brazilian Federal Agency for Support and Evaluation of Graduate Education6214
    Nederlands Instituut voor Ecologie
    Fundação de Amparo à Pesquisa do Estado de São Paulo729.004.003
    Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
    Nederlandse Organisatie voor Wetenschappelijk Onderzoek
    Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul
    BE-Basic FoundationF08.002.05

      Keywords

      • 16S rRNA
      • Agro-ecosystem
      • Bioindicator
      • Microbial diversity
      • Microbial ecology
      • Soil health treatment
      • Soil-borne pathogen
      • Sustainability

      Fingerprint

      Dive into the research topics of 'Soil microbiome is more heterogeneous in organic than in conventional farming system'. Together they form a unique fingerprint.

      Cite this