Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences the structure and complexity of microbial communities. We investigated the impact of conventional, no-till, and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harbored a much more complex fungal network with significantly higher connectivity than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. We also found a strong negative association (R 2 = 0.366; P < 0.0001) between agricultural intensification and root fungal network connectivity. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH, and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiome.

To test whether quantitative traits are under directional or homogenizing selection, it is common practice to compare population differentiation estimates at molecular markers (F ST ) and quantitative traits (Q ST ). If the trait is neutral and its determinism is additive, then theory predicts that Q ST ¼ F ST , while Q ST . F ST is predicted under directional selection for different local optima, and Q ST , F ST is predicted under homogenizing selection. However, nonadditive effects can alter these predictions. Here, we investigate the influence of dominance on the relation between Q ST and F ST for neutral traits. Using analytical results and computer simulations, we show that dominance generally deflates Q ST relative to F ST . Under inbreeding, the effect of dominance vanishes, and we show that for selfing species, a better estimate of Q ST is obtained from selfed families than from half-sib families. We also compare several sampling designs and find that it is always best to sample many populations (.20) with few families (five) rather than few populations with many families. Provided that estimates of Q ST are derived from individuals originating from many populations, we conclude that the pattern Q ST . F ST , and hence the inference of directional selection for different local optima, is robust to the effect of nonadditive gene actions.

Disentangling the mechanisms mediating the coexistence of habitat specialists and generalists has been a long-standing subject of investigation. However, the roles of species traits and environmental and spatial factors have not been assessed in a unifying theoretical framework. Theory suggests that specialist species are more competitive in natural communities. However, empirical work has shown that specialist species are declining worldwide due to habitat loss and fragmentation. We addressed the question of the coexistence of specialist and generalist species with a spatially explicit metacommunity model in continuous and heterogeneous environments. We characterized how species' dispersal abilities, the number of interacting species, environmental spatial autocorrelation, and disturbance impact community composition. Our results demonstrated that species' dispersal ability and the number of interacting species had a drastic influence on the composition of metacommunities. More specialized species coexisted when species had large dispersal abilities and when the number of interacting species was high. Disturbance selected against highly specialized species, whereas environmental spatial autocorrelation had a marginal impact. Interestingly, species richness and niche breadth were mainly positively correlated at the community scale but were negatively correlated at the metacommunity scale. Numerous diversely specialized species can thus coexist, but both species' intrinsic traits and environmental factors interact to shape the specialization signatures of communities at both the local and global scales.