Long-Term Maize-Legume Intercropping Shifts Structure and Composition of Soil Microbiome with Potential Impacts on Ecosystem Services and Food Safety

Purpose: Push-pull is an intercropping technology that rapidly spreads among Sub-Saharan smallholder farmers. It intercrops maize with Desmodium to fight off stem borers, eliminate parasitic weeds, and improve soil fertility and yields. The above-ground components of push-pull cropping have been well investigated. However, impact on and from the soil microbiome and its role in diverse ecosystem benefits are unknown. Here we describe the soil microbiome associated with push-pull and compare it with maize monoculture.Methods: Soil samples from long-term maize-desmodium intercropping and maize monoculture plots were analysed using 16S and ITS metagenomics.Results: Maize-desmodium intercropping caused a strong divergence in fungal microbiome, which was more diverse and species rich than monoculture plots. Zooming into genera revealed that intercropping enhanced fungal genera linked to important ecosystem services. These include mycorrhizal and endophytic groups such as Edenia, Acrocalyma and Colletotrichum, saprophytic and decomposer fungi like Pithya and Cristinia and fungi with biocontrol properties, for instance, Talaromyces, Penicillin, Clonostachys and Trichoderma. Fungal genera enriched in monoculture plots were few, and were functionally linked to plant diseases (for example Didymella, Curvularia and Parastagonospora), and human pathogenic taxa (Exserohilum, Curvularia and Aspergillus). Although separating well, bacterial microbiomes did not, except in a few genera, differ between treatments. Conclusion: Maize-desmodium intercropping diversifies fungal microbiomes and favors taxa that are associated with important ecosystem services, including plant health, productivity and food safety. Further studies should increase the resolution of shifts noted above, experimentally ascertain the inferred functions, and translate this knowledge to improve cropping systems.

Root-endophytic fungi cause morphological and functional differences in Scots pine roots in contrast to ectomycorrhizal fungi

Endophytic fungi and ectomycorrhizal fungi co-exist in the mycorrhizal root tips of boreal forest trees. However, very little is known about the functional role they play in their host’s biology. The activity of enzymes responsible for important biochemical processes is used to determine the functional role of root-associated mycorrhizal fungi. However, enzyme activity is never studied in the presence of endophytic fungi in-planta. The aims of this study were to investigate the effect of Scots pine (Pinus sylvestris L.) root-isolated fungal endophytes on the host plant root morphology, to determine their functional effects using host root-excreted enzyme activity measurements, and to compare them with roots colonized by decomposer and ectomycorrhizal fungal strains and noncolonised Scots pine root tips. Our results show that endophytic fungi did not damage the pine roots in contrast to the decomposer fungi. The endophytic fungi penetrated the cortical cells of the host plant. The roots colonised by endophytic fungi produce different exo-enzymes compared with those produced by roots colonized by other fungal groups or noncolonized control root tips. Our results indicate that endophytic fungi are clearly a distinctive ecological group of fungi that have functional traits different from those of ectomycorrhizal and decomposer fungi.