Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

Abstract

words) 1Root-associated microbes play a key role in plant performance and productivity, making 2 them important players in agroecosystems. So far, very few studies have assessed the impact 3 of different farming systems on the root microbiota and it is still unclear whether agricultural 4 intensification influences network complexity of microbial communities. We investigated the 5 impact of conventional, no-till and organic farming on wheat root fungal communities using 6PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic 7 farming harboured a much more complex fungal network than conventional and no-till 8 farming systems. The abundance of keystone taxa was the highest under organic farming 9where agricultural intensification was the lowest. The occurrence of keystone taxa was best 10 explained by soil phosphorus levels, bulk density, pH and mycorrhizal colonization. The 11 majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants 12and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, 13 the abundance of mycorrhizal fungi in roots and soils was also significantly higher under 14 organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa 15 for agroecosystems, and we demonstrate that agricultural intensification reduces network 16 complexity and the abundance of keystone taxa in the root microbiota. 17

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

“…We found that all four fertilizer inputs induced speci c changes in the microbiome structure, a result that is similar to previous ndings tracking responses to different fertilization management regimes [71,72].…”

Tillage practices and residue management manipulate soil bacterial and fungal assembly and co-occurrence network patterns in maize agroecosystem

“…Since organic inputs provide a substantial supply of substrates and nutrients for soil microorganisms, previous studies indicated that organic inputs generally increased the complexity of soil microbial networks [33,35,36]. In contrast, we observed that residue retention simplified both soil bacterial and fungal co-occurrence networks in 2018.…”

“…Similarly, the application of rice straw generated more substantial bacterial network connectivity in residue retained soils [35]. In a recent study, Banerjee et al [36] compared no tillage, conventional and organic agricultural systems and observed a significantly higher complexity of fungal networks in organic systems, whereas they did not find a difference between no-till and conventional tillage systems. However, information on the manner in which microbial co-occurrence networks respond to tillage and residue management is still limited.…”

Molecular dialogue between arbuscular mycorrhizal fungi and the nonhost plant Arabidopsis thaliana switches from initial detection to antagonism

“…Twenty‐day‐old, in vitro ‐grown A. thaliana Col‐0 seedlings were transferred from liquid Hoagland medium (2.5 mM inorganic phosphate (Pi)) (Rodríguez‐Celma et al ., ) to 60 ml pots filled with soil from a field in the Reijerscamp nature reserve, the Netherlands (52°01′02.55″N, 5°77′99.83″E), where natural Arabidopsis populations grow as previously described (Berendsen et al ., ). Bulk soil pots were left unplanted.…”