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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.

Societal Impact Statement Infestation by the parasitic weed Striga is a major cause of cereal crop production losses on smallholder farms in Africa. Essential plant nutrients play an important indirect role in parasite seed germination, the first prerequisite for successful parasitism. Here, we demonstrate that increasing the nutrient availability for the host plant can also impede Striga development beyond its germination, independent of the resistance levels of the sorghum host. This insight provides additional support for crop protection recommendations to Striga‐affected farmers. Growing a resistant crop variety combined with adequate levels of fertilisers should be the backbone of defence against this parasitic weed. Summary Striga hermonthica is a widespread parasitic weed in sub‐Saharan Africa and an important biotic constraint to sorghum production. Resistant varieties and fertilisers are crucial components of integrated Striga management. N and P fertilisers reduce the production of host‐plant strigolactones, known as Striga germination stimulants, and thereby reduce infection. Whether essential plant nutrients affect the parasite–host interaction beyond Striga germination is unknown. We conducted mini‐rhizotron assays to investigate the effects of macronutrient and micronutrient availability on post‐germination Striga development. Four sorghum genotypes (Framida, IS10978, N13, IS9830) covering the complete array of known mechanisms of post‐attachment resistance were compared with susceptible genotype Ochuti. Plants were infected with pre‐germinated Striga seeds and subjected to four nutrient treatment levels: (1) 25% of the optimal concentration of Long Ashton solution for cereals; (2) 25% macronutrient and optimal micronutrient concentration; (3) optimal macronutrient and 25% micronutrient concentration; and (4) optimal macronutrient and micronutrient concentrations. Compared with the 25% base nutrient level, treatments supplemented with macronutrients reduced the number of viable vascular connections established by pre‐germinated Striga seedlings as well as the total parasite biomass on the sorghum root system. Macronutrient treatment effects were observed across sorghum genotypes, independent of the presence and type of post‐attachment resistance, but appeared to specifically improve mechanical resistance, hypersensitive and incompatibility responses before Striga reaches the host‐root xylem. This study demonstrates, for the first time, that nutrient availability drives Striga parasitism beyond the germination stages. Increased availability of nutrients, in particular macronutrients, enhances host‐plant resistance in post‐attachment stages, reinforcing the importance of current fertiliser recommendations. Infestation by the parasitic weed Striga is a major cause of cereal crop production losses on smallholder farms in Africa. Essential plant nutrients play an important indirect role in parasite seed germination, the first prerequisite for successful parasitism. Here, we demonstrate that increasing the nutrient availability for the host plant can also impede Striga development beyond its germination, independent of the resistance levels of the sorghum host. This insight provides additional support for crop protection recommendations for Striga‐affected farmers. Growing a resistant crop variety combined with adequate levels of fertilisers should be the backbone of defence against this parasitic weed.

On upland soils in tropical Africa, common production constraints of rice and maize on smallholder farms are poor soil fertility—resulting from soil erosion and nutrient depletion—and infestation by witchweeds ( Striga spp.). In Madagascar where these crops are often grown in rotation, combining legume cover crops with no-till and crop residue mulching—labelled conservation agriculture (CA)—may address these problems. Previously, it was shown that CA practices contribute to steep reductions in Striga asiatica infection. In the current study, a 4-year field experiment was conducted to test, for the first time, the hypothesis that CA practices also contribute to crop yield and soil improvements under Striga- infested conditions. The conventional mono-crop rice–maize rotation practice, involving seasonal tillage and crop residue removal, was compared to three rice–maize rotation systems following CA practices, each with a different legume cover crop option: (1) two short-cycle annual species, cowpea ( Vigna unguiculata ) and mucuna ( Mucuna pruriens ); (2) a long-cycle annual, ricebean ( Vigna umbellata ); and (3) a perennial, stylosanthes ( S. guianensis ). Rice yields, as well as yield variability, generally increased by changing from the conventional to a CA practice, and maize yields were variable and low in particular under the CA practices. CA practices significantly reduced soil displacement by rainwater runoff and increased soil nitrogen and pH levels (0–20 cm depth), in particular with stylosanthes as cover crop, but did not result in a significant change in soil organic carbon concentration. Rice yields correlated negatively with Striga asiatica plant numbers in years with moderate infection levels. This is the first study that shows mixed outcomes from CA practices in tropical cereal rotation systems on degraded, Striga -infested soils, and subsequent entry points for system improvements. Suggested improvements include judicious cover crop management, complementary fertilizer applications and selection of competitive, resistant and adapted crop varieties.

To test whether quantitative traits are under directional or homogenizing selection, it is common practice to compare population differentiation estimates at molecular markers (FST) and quantitative traits (QST). If the trait is neutral and its determinism is additive, then theory predicts that QST = FST, while QST > FST is predicted under directional selection for different local optima, and QST < FST is predicted under homogenizing selection. However, nonadditive effects can alter these predictions. Here, we investigate the influence of dominance on the relation between QST and FST for neutral traits. Using analytical results and computer simulations, we show that dominance generally deflates QST relative to FST. Under inbreeding, the effect of dominance vanishes, and we show that for selfing species, a better estimate of QST 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 QST are derived from individuals originating from many populations, we conclude that the pattern QST > FST, and hence the inference of directional selection for different local optima, is robust to the effect of nonadditive gene actions.

Societal Impact Statement The global success and expansion of a small pool of major crops, including rice, wheat and maize, risks homogenising global agriculture. Focusing on the agriculturally diverse Ethiopian Highlands, this study tested whether farm diversity tends to be lower among farmers who grow more introduced crops. Surprisingly, it was found that farmers have successfully integrated introduced crops, resulting in more diverse and heterogenous farms without negatively impacting indigenous crop diversity. This is encouraging because diverse farms, comprising indigenous agricultural systems supplemented by introduced crops, may help address global challenges such as food insecurity. Summary The global expansion of a handful of major crops risks eroding indigenous crop diversity and homogenising agroecosystems, with significant consequences for sustainable and resilient food systems. Here, we investigate the farm‐scale impact of introduced crops on indigenous agroecosystems. We surveyed 1369 subsistence farms stratified across climate gradients in the Ethiopian Highlands, a hotspot of agrobiodiversity, to characterise the richness and cultivated area of the 83 edible crops they contained. We further categorise these crops as being indigenous to Ethiopia, or introduced across three different eras. We apply non‐metric multidimensional scaling and mixed effects modelling to characterise agroecosystem composition across farms with different proportions of introduced crops. Crops from different periods do not differ significantly in frequency or abundance across farms. Among geographically matched pairs of farms, those with higher proportions of modern introduced crops had significantly higher overall crop richness. Furthermore, farms with a high proportion of modern introduced crops showed higher heterogeneity in crop composition. An analysis of socio‐economic drivers indicated that poverty is negatively associated with the cultivated area of introduced crops. In our Ethiopian case study, global patterns of major crop expansion are not necessarily associated with agrobiodiversity loss at the farm scale or higher homogeneity across indigenous agricultural systems. Importantly, socioeconomic factors may influence farmers' propensity to adopt novel species, suggesting targets for agricultural extension policies. Given the rapid climatic, economic and demographic changes impacting global food systems and the threats to food security these entail, robust indigenous agricultural systems enriched with diverse introduced crops may help maintain resilience. እንደሩዝ፣ ስንዴና በቆሎ ያሉ ጥቂት ሰብሎች በሥፋት መሠራጨታቸው፣ የግብርና ምርት ብዝሃነትን በአለምዓቀፍ ደረጃ ሥጋት ላይ የሚጥል ነው። ይህ ጥናት፤ ብዝሃ ምርት በሚሰጠው የኢትዮጵያ ደጋማ አካባቢዎች ግብርና ላይ ተመርኩዞ፣ አገር በቀል ያልሆኑ ሰብሎችን በብዛት በሚያበቅሉ አርሶአደሮች መካከል ‘የምርት ብዝሃነት ቀንሶ ይሆን?’ በሚል ምርምር አከናውኗል። በውጤቱም፣ አርሶአደሮች ከውጭ የገቡትን ሰብሎች ከአገር በቀሎቹ ሰብሎች ጋር አጣምረው የተለያዩ ሰብሎችን በማብቀል ብዝሃ ምርታማነታቸውን በአስደናቂ ሁኔታ አሳይተው ውጤታማ ሊሆኑ መቻላቸው ተስተውሏል። ከውጭ የገቡት ሰብሎችም የአገር በቀል ሰብሎች ላይ አሉታዊ ተፅዕኖ እንዳላሳደሩ ጥናቱ አረጋግጧል። ከውጭ በሚገቡ ሰብሎች የሚታገዙ አገር በቀል ሰብሎችን የማብቀል ብዝሃ ምርት የግብርና ሥርአት፣ እንደ የምግብ እጥረት ያሉ አለም አቀፍ ተግዳሮቶችን ለመመከት ስለሚያስችል ሊበረታታ ይገባል።. El éxito y la expansión global de una pequeña selección de cultivos mayores como el arroz, trigo y maiz, amenazan con homogenizar los sistemas agrícolas globales. Con enfoque en las tierras altas de Etiopía, cuya diversidad agrícola es alta, este estudio examina si la diversidad en granjas tiende a ser menor entre productores que cultivan un mayor número de cultivos introducidos. Sorprendentemente, encontramos que los productores de esta zona han integrado exitosamente los cultivos introducidos, lo cual resulta en granjas más diversas y heterogéneas, sin impactos negativos sobre la diversidad de cultivos nativos. Esto es prometedor, ya que las granjas diversas que mantienen sistemas agrícolas locales que a la vez son suplementados por cultivos introducidos, pueden ayudar a responder a retos globales como la inseguridad alimentaria. Le succès et l’expansion mondiale d’une poignée de cultures majeures, telles que le riz, le maïs et le blé, menacent d’homogénéiser les systèmes agricoles mondiaux. En se concentrant sur les hautes terres éthiopiennes, où la diversité agricole est élevée, cette étude examine si la diversité cultivée dans les fermes a tendance à être plus faible chez les agriculteurs qui cultivent un plus grand nombre de cultures introduites. Etonnamment, nous avons constaté que les agriculteurs de cette région ont intégré les cultures introduites avec succès, ce qui a donné lieu à des exploitations plus diversifiées et hétérogènes, sans impact négatif sur la diversité des cultures indigènes. Ceci est prometteur, car des exploitations diversifiées qui maintiennent des systèmes agricoles locaux, tout en étant complétées par des cultures introduites, peuvent aider à répondre aux défis mondiaux tels que l’insécurité alimentaire. The global success and expansion of a small pool of major crops, including rice, wheat and maize, risks homogenising global agriculture. Focusing on the agriculturally diverse Ethiopian Highlands, this study tested whether farm diversity tends to be lower among farmers who grow more introduced crops. Surprisingly, it was found that farmers have successfully integrated introduced crops, resulting in more diverse and heterogenous farms without negatively impacting indigenous crop diversity. This is encouraging because diverse farms, comprising indigenous agricultural systems supplemented by introduced crops, may help address global challenges such as food insecurity.

Interspecific competition, life history traits, environmental heterogeneity and spatial structure as well as disturbance are known to impact the successful dispersal strategies in metacommunities. However, studies on the direction of impact of those factors on dispersal have yielded contradictory results and often considered only few competing dispersal strategies at the same time. We used a unifying modeling approach to contrast the combined effects of species traits (adult survival, specialization), environmental heterogeneity and structure (spatial autocorrelation, habitat availability) and disturbance on the selected, maintained and coexisting dispersal strategies in heterogeneous metacommunities. Using a negative exponential dispersal kernel, we allowed for variation of both species dispersal distance and dispersal rate. We showed that strong disturbance promotes species with high dispersal abilities, while low local adult survival and habitat availability select against them. Spatial autocorrelation favors species with higher dispersal ability when adult survival and disturbance rate are low, and selects against them in the opposite situation. Interestingly, several dispersal strategies coexist when disturbance and adult survival act in opposition, as for example when strong disturbance regime favors species with high dispersal abilities while low adult survival selects species with low dispersal. Our results unify apparently contradictory previous results and demonstrate that spatial structure, disturbance and adult survival determine the success and diversity of coexisting dispersal strategies in competing metacommunities.

Ecological strategies are integral to understanding species survival in different environments. However, how habitat specialisation is involved in such strategies is not fully understood, particularly in heterogeneous and disturbed environments. Here, we studied the trait associations between specialisation, dispersal ability, competitiveness, reproductive investment and survival rate in a spatially explicit metacommunity model under various disturbance rates. Though no unique trait values were associated with specialisation, relationships were uncovered depending on environmental factors. We found strong trait associations mainly for generalist species, while specialist species exhibited a larger range of trait combinations. Trait associations were driven first by the disturbance rate and second by species’ dispersal ability and generation overlap. With disturbance, low dispersal ability was strongly selected against, for specialists as well as for generalists. Our results demonstrate that habitat specialisation is critical for the emergence of trait strategies in metacommunities and that disturbance in interaction with dispersal ability limits not only the range of trait values but also the type of possible trait associations.

Aims Cover crops play an important role in soil fertility as they can accumulate large amounts of nutrients. This study aimed at understanding the nutrient uptake capacity of a wide range of cover crops and at assessing the relevance of acquisition strategies. Methods A field experiment was conducted to characterize 20 species in terms of leaf and root traits. Plant traits were related to nutrient concentration and shoot biomass production with a redundancy analysis. Acquisition strategies were identified using a cluster analysis. Results Root systems varied greatly among cover crop species. Five nutrient acquisition strategies were delineated. Significant amounts of nutrients (about 120 kg ha⁻¹ of nitrogen, 30 kg ha⁻¹ of phosphorus and 190 kg ha⁻¹ of potassium) were accumulated by the species in a short period. Nutrient acquisition strategies related to high accumulations of nutrients consisted in either high shoot biomass and root mass and dense tissues, or high nutrient concentrations and root length densities. Species with high root length densities showed lower C/N ratios. Conclusions The same amounts of nutrients were accumulated by groups with different acquisition strategies. However, their nutrient concentrations offer different perspectives in terms of nutrient release for the subsequent crop and nutrient cycling improvement.

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.

Host plant defence mechanisms (resistance and tolerance) and plant nutrition are two of the most widely proposed components for the control of hemiparasitic weeds of the genus Striga in tropical cereal production systems. Neither of the two components alone is effective enough to prevent parasitism and concomitant crop losses. This review explores the potential of improved plant nutrition, being the chemical constituent of soil fertility, to fortify the expression of plant inherent resistance and tolerance against Striga. Beyond reviewing advances in parasitic plant research, we assess relevant insights from phytopathology and plant physiology in the broader sense to identify opportunities and knowledge gaps and to develop the way forward regarding research and development of combining genetics and plant nutrition for the durable control of Striga.