Organic management shapes AM fungal community structure and function, partially mitigating the negative effects of conventional agriculture
Arbuscular mycorrhizal (AM) fungi are important plant symbionts that provide plants with nutrients and water as well as support plant defences against pests and disease. Consequently, they present a promising alternative to using environmentally damaging and costly fertilisers and pesticides in agricultural systems. However, our limited understanding of how agricultural practices impact AM fungal diversity and functions is a key impediment to using them effectively in agriculture.We assessed how organic and conventional agricultural management systems shaped AM fungal communities. We also investigated how AM fungal communities derived from these agricultural management systems affected crop biomass and development. Six soil samples from five organically and five conventionally managed agricultural sites were used to cultivate Sorghum bicolor. Plant growth, plant nutrient concentrations, and AM fungal colonisation rates were analysed alongside DNA metabarcoding of community composition.We observed that soil from conventional agricultural fields resulted in a pronounced reduction in sorghum biomass (-53.6%) and a significant delay in flowering compared to the non-mycorrhizal plants. Sorghum biomass was also reduced with soil from the organic system, but to a lesser extent (-30%) and without a delay in flowering. Organic systems were associated with a large proportion of AM fungal taxa (50.5% of VTs) not found in conventional systems, including Diversispora (r2 = 0.09, p < 0.001), Archaeospora (r2 = 0.07, p < 0.001) and Glmous (r2 = 0.25, p < 0.001) spp., but also shared a large proportion of taxa with conventional systems (42.3% of VTs). Conventional systems had relatively few unique taxa (7.2% of VTs).Our results suggest that conventional agricultural practices selected against AM fungi that were, in this context, more beneficial for host plants. In contrast, organic management practices mitigate this negative effect, likely due to the presence of specific key AM fungal taxa. However, this mitigation is only partial, as less beneficial AM fungal taxa still persist, probably due to abiotic factors associated with agricultural management and the sensitivity of AM fungi to these factors. This persistence explains why the effect is not entirely eradicated.