The transition toward sustainable agriculture requires rethinking cropping systems in the light of less intensive and chemically reliant practices. Weed management is one of the target practices to evolve cropping systems with decreased impact on the environment. While softened management will lead to increased weeds/crops coexistence, it is of importance to assess the relative benefits and drawbacks of new practices. Among the potential drawbacks of weeds/crops coexistence, disease risk may increase if weeds are hosting pathogens. In this study, we assessed the potential of weeds for hosting pathogenic generalist fungi known to translate into disease in crops. We first describe prevalence in fields after harvest and relate prevalence to species characteristics and communities. Then, we directly test the idea that weeds serve as inoculums sources during cropping with a natural experiment. This study highlights variation in host skill among feral weeds for Colletotrichum species, including potential congeneric sub-specialization on different weeds within communities. Last, prevalence within fields was more correlated to focal crop inoculation rates compared to local weed load, but there was a significant correlation effect with prevalence on weeds in the vicinity of fields, suggesting that weeds are mediating disease levels at the local scale, too. Results pointed to the importance of weed host skill in disease risk yet open the door to the potential control of pathogens via targeted weed management.

Landscape effects might impede or increase spore dispersal and disease risk for crops, as trees and hedges buffer winds and can behave as spore traps, therefore limiting diffusion of fungi, or, on the contrary, behave as disease relay once vegetation is infected and become inoculum sources. In this study, we investigated weekly prevalence of the pathogenic fungus Colletotrichum gloeosporioides on guava tree leaves, differentiating impacts of leaf height on tree, age, and location within leaf. We first estimated differences in prevalence for each covariate, and then related infection rates to weather effects during the year. Our results highlighted a great variance of prevalence among individual trees, and a lower contamination of tree tops, as well as a tendency for greater odds of infection in tips of young leaves compared to older ones. Last, we show evidence that individual tree contaminations are associated with different disease dynamics: early and dispersal-based, late and growth-based, as well as with intermediate dynamic ranges. Pathogen infection dynamics will thus be greatly impacted by cover characteristics at local scale, and tree cover should not be perceived as homogeneously driving disease levels.

Crop pathogenic fungi may originate from reservoir pools including wild vegetation surrounding fields, and it is thus important to characterize any potential source of pathogens. We therefore investigated natural vegetation’s potential for hosting a widespread pathogenic group, Colletotrichum gloeosporioides species complex. We stratified sampling in different forest environments and natural vegetation strata to determine whether the fungi were found preferentially in specific niches and areas. We found that the fungi complex was fairly broadly distributed in the wild flora, with high prevalence in every study environment and stratum. Some significant variation in prevalence nevertheless occurred and was possibly associated with fungal growth conditions (more humid areas had greater prevalence levels while drier places had slightly lower presence). Results also highlighted potential differences in disease effects of strains between strata components of study flora, suggesting that while natural vegetation is a highly probable source of inoculums for local crops nearby, differences in aggressiveness between vegetation strata might also lead to differential impact on cultivated crops.

The Green Revolution was foundational to modern agriculture and relied heavily on both genetics and elite cultivars improved for yield, and environmental control of field conditions (till, irrigation, fertilizers and weeds, pathogen and pest control via biocides). While the Green Revolution was a keystone in achieving food security in the face of an increasing global population, it also translated into a diverse array of issues pertaining to environmental degradation and deforestation (Carter et al., 2017), overuse of synthetic chemicals (Schreinemachers & Tipraqsa, 2012), carbon dioxide or greenhouse gas effects (Stavi & Lal, 2013) and negative impacts on both agrodiversity and biodiversity (Dudley & Alexander, 2017). Current trends in agricultural developments are thus focused on mitigating these negative impacts while trying to improve yield and maintain food security.Avenues of research towards more sustainable agricultural systems are numerous and often revolve around the greatest weaknesses of the Green Revolution: targeting ecological interactions for improved productivity and increased resilience, even at landscape levels (Petit et al., 2020). Indeed, favourable prospects for the use of such interactions are documented throughout the literature (Gaba et al., 2015). They typically involve many levels, from soil-based interactions involving soil microbiota (e.g., Nkongolo & Narendrula-Kotha, 2020), tripartite soil-plant interactions (namely intercropping, e.g., Tilman, 2020) and biomass cycling and increased soil health and fertilization (Espie & Ridgway, 2020). They may also rely on crop diversity as a way to control disease spread