Abstract
Conversion of natural ecosystems into agricultural land may strongly affect the soil microbiome and the functioning of the soil ecosystem. Alternative farming systems, such as organic farming, have therefore been advocated to reduce this impact, yet the outcomes of different agricultural management regimes often remain ambiguous and their evaluations mostly lack a proper more natural benchmark. We used high-throughput amplicon sequencing, linear models, redundancy analyses, and co-occurrence network analyses to investigate the effect of organic and integrated pest management (IPM) on soil fungal and bacterial communities in both the crop and drive rows of apple orchards in Belgium, and we included semi-natural grasslands as a benchmark. Fungi were strongly influenced by agricultural management, with lower diversity indices and distinct communities in IPM compared to organic orchards, whereas IPM orchards had a higher AMF abundance and the most complex and connected fungal communities. Bacterial diversity indices, community composition, and functional groups were less affected by management, with only a higher network connectivity and abundance of keystone taxa in organic drive rows. On the other hand, none of the agricultural soil microbiomes matched the complexity and connectedness of our semi-natural benchmark, demonstrating that even more nature-friendly agricultural management practices strongly affect the soil microbiome and highlighting the essential role of (semi-)natural systems as a harbor of robust and functionally diverse fungal and bacterial communities.
Highlights
Soils and their associated biodiversity play a crucial role in providing a wide range of ecosystem services in terrestrial ecosystems (Barrios, 2007; De Vries et al, 2013; van der Heijden and Wagg, 2013; Bardgett and Van Der Putten, 2014)
Bacterial operational taxonomical units (OTUs) richness was not significantly affected by management or location in the management model, but bacterial 1D and phylogenetic diversity (PD) were significantly higher in crop rows compared to drive rows
In the land use models, fungal OTU richness was significantly lower in grasslands compared to organic orchards (p = 0.015), whereas grasslands and organic orchards both did not significantly differ in fungal OTU richness compared to integrated pest management (IPM) orchards (Figure 1A; Supplementary Table S1)
Summary
Soils and their associated biodiversity play a crucial role in providing a wide range of ecosystem services in terrestrial ecosystems (Barrios, 2007; De Vries et al, 2013; van der Heijden and Wagg, 2013; Bardgett and Van Der Putten, 2014). Organic farming is a booming sector with 72.3 million ha of organic farmland as of 2019, increasing more than 5-fold since 1999 (Schlatter et al, 2021) This indicates the need for a thorough comparison of soil microbiomes between organic and conventional farming systems, and between farming systems and a benchmark of natural or semi-natural land. Organic farms generally harbor distinct microbial communities compared to conventional farms (Hartmann et al, 2015; Wang et al, 2016; Lupatini et al, 2017; Jurburg et al, 2020), some studies did not find differences in bacterial community composition (Pershina et al, 2015; Hendgen et al, 2018). On the other hand, Jurburg et al (2020) did not find differences in microbial richness between conventional and organic farms, while others found inconsistent responses of fungal and bacterial diversity (Hendgen et al, 2018; Lupatini et al, 2018; Finn et al, 2021)
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