Distinct soil microbial diversity under long-term organic and conventional farming
Open accessAbstract
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.
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Recent rapid developments in soil biology have prompted the feasibility of indicators based on genotypic and phenotypic community diversity.
“Recent rapid developments in soil biology have prompted the feasibility of indicators based on genotypic and phenotypic community diversity (Hartmann et al., 2015; Kumari et al., 2017; Nielsen and Winding, 2002; Ritz et al., 2009).”
From Soil quality – A critical review (2018) · cites this paper as Hartmann et al., 2015
The Introduction (page unavailable) says advances in high-throughput DNA sequencing enable more detailed assessment of soil microbial communities, and the Methods describe an analysis to identify indicator taxa. These passages support the feasibility of DNA-based community indicators, but our copy does not establish indicators based on phenotypic community diversity. (LLM, conf=0.85)
Experimental — accuracy not yet measuredLasiosphaeriaceae has been indicated as responsive to organic soil management.
“The latter family has been indicated by Hartmann et al. (2015) as responsive to organic soil management.”
From The hidden potential of saprotrophic fungi in arable soil: Patterns of short-term stimulation by organic amendments (2020) · cites this paper as Hartmann et al. (2015)
The Discussion (Management-sensitive microbial taxa; page unavailable) identifies Lasiosphaeriaceae as a cluster associated with farmyard-manure (FYM) systems. The Methods (The DOK long-term experiment; page unavailable) specifies that those systems included both organic farms and a conventional farm, so the finding is about FYM-based management rather than organic management specifically. (LLM, conf=0.88)
Experimental — accuracy not yet measured
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- Authors
- Hartmann, M., Frey, B., Mayer, J., Mäder, P., & Widmer, F.
- Affiliations
- Swiss Federal Institute for Forest, Snow and Landscape Research (CH)
- Agroscope (CH)
- Department of Soil Sciences, Research Institute of Organic Agriculture , Frick, Switzerland
- Corresponding author
- Hartmann, Martin
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-10-31
- Volume
- 9
- Issue
- 5
- Pages
- 1177-1194
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- PMC
- PMC4409162
- OpenAlex
- W2062307117
- Cited by
- 1,496
- References
- 91
- Citations by year
- 2026: 169 · 2025: 146 · 2024: 156 · 2023: 154 · 2022: 164 · 2021: 188 · 2020: 171 · 2019: 138 · 2018: 93 · 2017: 63 · 2016: 38 · 2015: 15 · 2014: 1
- FWCI
- 55.02
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- The ISME Journal (publishedVersion, cc-by-nc-sa)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Repository for Publications and Research Data (ETH Zurich) (publishedVersion, cc-by-nc-sa)
- DORA WSL (Swiss Federal Institute for Forest, Snow and Landscape Research) (submittedVersion, cc-by-nc-sa)
- ETH Zürich Research Collection
- Funders
- National Science Foundation
- University of Southern California
- McGill University
- University of Glasgow
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Sveriges Lantbruksuniversitet
- Bundesamt für Landwirtschaft
- Agroscope
- Forschungsinstitut für biologischen Landbau
- Topics
- Life Sciences › Agricultural and Biological Sciences › Soil Science › Soil Carbon and Nitrogen Dynamics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
- Keywords
- soil microbial diversity, organic farming, conventional farming, soil microbiome, long-term field experiment, organic fertilizer, integrated fertilization, crop protection, pesticide use, manure, compost, bacterial community structure, fungal community structure, microbial guilds, low-input agriculture
- MeSH terms
- Agriculture, Bacteria, Fertilizers, Fungi, Manure, Minerals, Soil, Soil Microbiology, Sequence Analysis, DNA, Ecosystem, Computational Biology, Biodiversity, Organic Agriculture
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