Distinct soil microbial diversity under long-term organic and conventional farming

By Martin Hartmann, B. Frey, J. Mayer, P. Mäder, F. Widmer. The ISME Journal, 2014

1,278 citations recorded by the source corpus.

Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms.

Subfields: Ecology, Soil Science

View Paper: https://www.semanticscholar.org/paper/b12c78ac60269387e3d820fb946e62d7206fd8f7

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Citations in the corpus

Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies (2017, background): “…of soils subjected to different agricultural management practices for two decades, revealed that systems not receiving manure harbored a dispersed and functionally versatile community, characterized by oligotrophic organisms adapted to nutrient-limited environments (Hartmann et al., 2015).”
Understanding and exploiting plant beneficial microbes (2017, background): “Current Opinion in Plant Biology 2017, 38:155–163 community that in turn can be deeply impacted by agricultural practices [62,63].”
Making Conventional Agriculture Environmentally Friendly: Moving beyond the Glorification of Organic Agriculture and the Demonization of Conventional Agriculture (2018, background): “• Organic farming fosters healthy soil [23] and soil microbiota [24] facilitating the availability of nutrients to plants [25].”
Long-term and legacy effects of manure application on soil microbial community composition (2018, background): “By contrast, organic fertilizers (including manures) usually have positive effects on soil microbial communities (Chinnadurai et al. 2014; Francioli et al. 2016; Hartmann et al. 2015).”
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming (2018, background): “The association of Firmicutes OTUs to organic plots that receive manure fertilizer was found earlier [36].”
The Role of Soil Microorganisms in Plant Mineral Nutrition—Current Knowledge and Future Directions (2017, background): “The work of Hartmann et al. (2015) examines bacterial 16S and fungal ITS2 sequences in a long-term field experiment comparing organic with conventional farming systems, showing correlations between taxon abundance and fertilization regime, with the bacterial Firmicutes phylum and several fungal…”