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Soil Biology and Biochemistry
Vol. 103, 2016, Pages: 327–336

Organic farming induces changes in soil microbiota that affect agro-ecosystem functions

Giuliano Bonanomi, Francesca De Filippis, Gaspare Cesarano, Antonietta La Storia, Danilo Ercolini, Felice Scala

Department of Agricultural Sciences, University of Naples Federico II, via Università 100, Portici, 80055, Naples, Italy.


Cultivation of vegetables under plastic tunnels is a steadily growing farming system in the agricultural sector but raises concerns about its environmental sustainability. The aim of the present work was to assess the impact of organic farming, compared to conventional cultivation, on agro-ecosystem functions and soil microbial communities. Two farms that practiced organic cultivation for 10 and 20 years were compared with one conventional farm, all with cultivations under plastic tunnel. Soil functions were assessed with multi-species bioassays on plant growth and organic matter decomposition, and microbial communities were characterized by high-throughput sequencing of bacterial and eukaryotic rRNA gene markers. Plant growth and organic matter decomposition were higher in organic compared to conventionally management soils. Agronomical practices showed a significant effect on microbial diversity and composition. Soil bacterial diversity was lower in both organic farms than in the conventional farm. Soil eukaryotic diversity was slightly higher in the 10-year organic farm but lower in the 20-year organic farm compared to the conventional farm. At phylum level, Acidobacteria, Firmicutes, and TM7 were higher, while Planctomycetes, Verrucomicrobia, and Actinobacteria were lower in organic-farmed soils compared to conventional farm. Noteworthy, Metazoa raised from 0.1% of eukarya relative abundance in conventional-farmed to 20.9% in 20 year organic-farmed soil. Correlation analysis between microbial OTUs relative abundance and ecosystem functions suggest that eukarya play a major role, compared to bacteria, in controlling plant growth and organic carbon cycling. Integration of microbial diversity data with plant growth and decomposition of organic matter decomposition allowed us to provide a linkage between agricultural management, microbial community composition, and soil functionality.

Graphical abstract

Keywords: Soil microbiota; Beneficial microbes; Soilborne pathogens; Earthworms; Crop yield; Soil organic carbon.

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