Ecological and evolutionary approaches to improving crop variety mixtures

The root of plant-plant interactions: Belowground special cocktails

Plants interact with each other via a multitude of processes among which belowground communication facilitated by specialized metabolites plays an important but overlooked role. Until now, the exact targets, modes of action, and resulting phenotypes that these metabolites induce in neighboring plants have remained largely unknown. Moreover, positive interactions driven by the release of root exudates are prevalent in both natural field conditions and controlled laboratory environments. In particular, intraspecific positive interactions suggest a genotypic recognition mechanism in addition to non-self perception in plant roots. This review concentrates on recent discoveries regarding how plants interact with one another through belowground signals in intra- and interspecific mixtures. Furthermore, we elaborate on how an enhanced understanding of these interactions can propel the field of agroecology forward.

Discrimination of relatedness drives rice flowering and reproduction in cultivar mixtures

The improvement of performance and yield in both cultivar and species mixtures has been well established. Despite the clear benefits of crop mixtures to agriculture, identifying the critical mechanisms behind performance increases are largely lacking. We experimentally demonstrated that the benefits of rice cultivar mixtures were linked to relatedness-mediated intraspecific neighbour recognition and discrimination under both field and controlled conditions. We then tested biochemical mechanisms of responses in incubation experiments involving the addition of root exudates and a root-secreted signal, (-)-loliolide, followed by transcriptome analysis. We found that closely related cultivar mixtures increased grain yields by modifying root behaviour and accelerating flowering over distantly related mixtures. Importantly, these responses were accompanied by altered concentration of signalling (-)-loliolide that affected rice transcriptome profiling, directly regulating root growth and flowering gene expression. These findings suggest that beneficial crop combinations may be generated a-priori by manipulating neighbour genetic relatedness in rice cultivar mixtures and that root-secreted (-)-loliolide functions as a key mediator of genetic relatedness interactions. The ability of relatedness discrimination to regulate rice flowering and yield raises an intriguing possibility to increase crop production.

Factors Influencing the Emergence of Heterogeneous Populations of Common Bean (Phaseolus vulgaris L.) and Their Potential for Intercropping

The common bean is an important legume valued for its protein-rich seeds and its ability to fix nitrogen, making it a key element of crop rotation. In conventional agriculture, the emphasis is on uniformity and genetic purity to optimize crop performance and maximize yields. This is due to both the legal obligations to register varieties and the challenges of implementing breeding programs to create genetically diverse varieties. This paper focuses on the factors that influence the occurrence of heterogeneous common bean populations. The main factors contributing to this diversity have been described, including local adaptations, variable weather conditions, different pollinator species, and intricate interactions between genes controlling seed coat colour. We also discuss the benefits of intercropping common beans for organic farming systems, highlighting the improvement in resistance to diseases, and adverse environmental conditions. This paper contributes to a better understanding of common bean seed heterogeneity and the legal obligation to use heterogeneous populations.

The push-pull intercrop Desmodium does not repel, but intercepts and kills pests

Over two decades ago, an intercropping strategy was developed that received critical acclaim for synergizing food security with ecosystem resilience in smallholder farming. The push-pull strategy reportedly suppresses lepidopteran pests in maize through a combination of a repellent intercrop (push), commonly Desmodium spp., and an attractive, border crop (pull). Key in the system is the intercrop's constitutive release of volatile terpenoids that repel herbivores. However, the earlier described volatile terpenoids were not detectable in the headspace of Desmodium, and only minimally upon herbivory. This was independent of soil type, microbiome composition, and whether collections were made in the laboratory or in the field. Furthermore, in oviposition choice tests in a wind tunnel, maize with or without an odor background of Desmodium was equally attractive for the invasive pest Spodoptera frugiperda. In search of an alternative mechanism, we found that neonate larvae strongly preferred Desmodium over maize. However, their development stagnated and no larva survived. In addition, older larvae were frequently seen impaled and immobilized by the dense network of silica-fortified, non-glandular trichomes. Thus, our data suggest that Desmodium may act through intercepting and decimating dispersing larval offspring rather than adult deterrence. As a hallmark of sustainable pest control, maize-Desmodium push-pull intercropping has inspired countless efforts to emulate stimulo-deterrent diversion in other cropping systems. However, detailed knowledge of the actual mechanisms is required to rationally improve the strategy, and translate the concept to other cropping systems.

Chemically Mediated Plant-Plant Interactions: Allelopathy and Allelobiosis

Plant-plant interactions are a central driver for plant coexistence and community assembly. Chemically mediated plant-plant interactions are represented by allelopathy and allelobiosis. Both allelopathy and allelobiosis are achieved through specialized metabolites (allelochemicals or signaling chemicals) produced and released from neighboring plants. Allelopathy exerts mostly negative effects on the establishment and growth of neighboring plants by allelochemicals, while allelobiosis provides plant neighbor detection and identity recognition mediated by signaling chemicals. Therefore, plants can chemically affect the performance of neighboring plants through the allelopathy and allelobiosis that frequently occur in plant-plant intra-specific and inter-specific interactions. Allelopathy and allelobiosis are two probably inseparable processes that occur together in plant-plant chemical interactions. Here, we comprehensively review allelopathy and allelobiosis in plant-plant interactions, including allelopathy and allelochemicals and their application for sustainable agriculture and forestry, allelobiosis and plant identity recognition, chemically mediated root-soil interactions and plant-soil feedback, and biosynthesis and the molecular mechanisms of allelochemicals and signaling chemicals. Altogether, these efforts provide the recent advancements in the wide field of allelopathy and allelobiosis, and new insights into the chemically mediated plant-plant interactions.

The Influence of External Parameters on the Ripeness of Pumpkins

Growing pumpkins in controlled environments, such as greenhouses, has become increasingly important due to the potential to optimise yield and quality. However, achieving optimal environmental conditions for pumpkin cultivation requires precise monitoring and control, which can be facilitated by modern sensor technologies. The objective of this study was to determine the optimal placement of sensors to determine the influence of external parameters on the maturity of pumpkins. The greenhouse used in the study consisted of a plastic film for growing pumpkins. Five different sensors labeled from A1 to A5 measured the air temperature, humidity, soil temperature, soil humidity, and illumination at five different locations. We used two methods, error-based sensor placement and entropy-based sensor placement, to evaluate optimisation. We selected A3 sensor locations where the monitored data were close to the reference value, i.e., the average data of all measurement locations and parameters. Using this method, we selected sensor positions to monitor the influence of external parameters on the maturity of pumpkins. These methods enable the determination of optimal sensor locations to represent the entire facility environment and detect areas with significant environmental disparities. Our study provides an accurate measurement of the internal environment of a greenhouse and properly selects the base installation locations of sensors in the pumpkin greenhouse.

Double gains: Boosting crop productivity and reducing carbon footprints through maize-legume intercropping in the Yellow River Delta, China

The increasing demand for environmentally friendly agricultural practices has driven the need for diversified crop cultivation to optimize crop productivity while minimizing carbon footprints (CFs). However, the impacts of crop diversification on crop production and environmental benefits are still poorly understood. In this study, conducted at two sites in the Yellow River Delta, China, we investigated the effects of legume intercropping, specifically maize/soybean (M/S) and maize/peanut (M/P) systems, on crop productivity, economic return, ecosystem economic budget (NEEB), CF, and carbon sustainability index (CSI) in comparison to conventional monocrops. Crops were grown in replicated field plots and fertilized in their strips according to common practice for monocrops. Compared to the expected averages of monocrops, maize/legume intercropping demonstrated higher crop yields, with M/S achieving a 37% and 43% increase at the two sites, respectively, and M/P achieving an 11% and 20% increase. The higher overyielding in M/S was attributed to stronger selection effects, i.e., interspecific facilitation. However, the complementarity effects induced by the competitive dominance of maize were similar in both intercropping systems. Additionally, M/S exhibited greater potential for improving net revenues compared to M/P. Life cycle assessments revealed lower CFs in the intercropping systems compared to monocultures. M/S reduced CFs per unit of area by 26.8% at both sites, CFs per unit of maize equivalent energy yield by 25% and 33%, and CFs per unit of revenue by 20% and 25% at the two sites, respectively. M/P also resulted in reduced CFs, albeit to a lesser extent. Intercropping enhanced the CSI, with the highest values observed in the M/S system. However, both intercropping systems showed limited effects on soil C sequestration. Overall, our results highlight that maize/legume intercropping is a feasible approach to enhance crop productivity while reducing CFs. The M/S system outperformed the M/P system in terms of crop yields, economic benefits, and CF reduction. However, the intercropping systems showed limited effects on SOC storage. This study provides important implications for sustainable agriculture by appropriate crop diversification.

Upland rice varietal mixtures in Madagascar: evaluating the effects of varietal interaction on crop performance

Introduction

Rice plays a critical role in human livelihoods and food security. However, its cultivation requires inputs that are not accessible to all farming communities and can have negative effects on ecosystems. simultaneously, ecological research demonstrates that biodiversity management within fields contributes to ecosystem functioning.

Methods

This study aims to evaluate the mixture effect of four functionally distinct rice varieties in terms of characteristics and agronomic performance and their spatial arrangement on the upland rice performance in the highlands of Madagascar. The study was conducted during the 2021-2022 rainfall season at two close sites in Madagascar. Both site differ from each other's in soil properties and soil fertility management. The experimental design at each site included three modalities: i) plot composition, i.e., pure stand or binary mixture; ii) the balance between the varieties within a mixture; iii) and for the balanced mixture (50% of each variety), the spatial arrangement, i.e., row or checkerboard patterns. Data were collected on yields (grain and biomass), and resistance to Striga asiatica infestation, Pyricularia oryzea and bacterial leaf blight (BLB) caused by Xanthomonas oryzae-pv from each plot.

Results and discussion

Varietal mixtures produced significantly higher grain and biomass yields, and significantly lower incidence of Pyricularia oryzea compared to pure stands. No significant differences were observed for BLB and striga infestation. These effects were influenced by site fertility, the less fertilized site showed stronger mixture effects with greater gains in grain yield (60%) and biomass yield (42%). The most unbalanced repartition (75% and 25% of each variety) showed the greatest mixture effect for grain yield at both sites, with a strong impact of the varietal identity within the plot. The mixture was most effective when EARLY_MUTANT_IAC_165 constituted 75% of the density associated with other varieties at 25% density. The assessment of the net effect ratio of disease, an index evaluating the mixture effect in disease reduction, indicated improved disease resistance in mixtures, regardless of site conditions. Our study in limited environments suggests that varietal mixtures can enhance rice productivity, especially in low-input situations. Further research is needed to understand the ecological mechanisms behind the positive mixture effect.

Fostering temporal crop diversification to reduce pesticide use

Temporal crop diversification could reduce pesticide use by increasing the proportion of crops with low pesticide use (dilution effects) or enhancing the regulation of pests, weeds and diseases (regulation effects). Here, we use the French National DEPHY Network to compare pesticide use between 16 main crops (dilution effect) and to assess whether temporal crop taxonomic and functional diversification, as implemented in commercial farms specialized in arable field crops, could explain variability in total pesticide use within 16 main crops (regulation effect). The analyses are based on 14,556 crop observations belonging to 1334 contrasted cropping systems spanning the diversity of French climatic regions. We find that cropping systems with high temporal crop diversity generally include crops with low pesticide use. For several crops, total pesticide use is reduced under higher temporal crop functional diversity, temporal crop taxonomic diversity, or both. Higher cover crop frequency increases total pesticide use through an increase in herbicide use. Further studies are required to identify crop sequences that maximize regulation and dilution effects while achieving other facets of cropping system multiperformance.

Increased Conidia Production and Germination In Vitro Correlate with Virulence Enhancement in Fusarium oxysporum f. sp. cucumerinum

Cucumber plants commonly suffer from Fusarium wilt disease, which is caused by Fusarium oxysporum f. sp. cucumerinum (Foc). Although resistant cultivars assist with Fusarium wilt disease control, enhancement of the virulence of Foc has been identified after monoculture of wilt-resistant cultivars. To investigate the biological characteristics that contribute to the virulence evolution of Foc, a wildtype strain foc-3b (WT) and its virulence-enhanced variant Ra-4 (InVir) were compared in terms of their growth, reproduction, stress tolerance, and colonization in cucumber plants. The InVir strain showed similar culture characteristics on PDA media to the WT strain but produced significantly more conidia (>two fold), with a distinctly higher germination rate (>four fold) than the WT strain. The colony diameter of the InVir strain increased faster than the WT strain on PDA plates; however, the mycelia dry weight of the InVir was significantly lower (<70%) than that of the WT harvested from PDB. The InVir strain exhibited a significant increase in tolerance to osmolality (1 M NaCl, 1 M KCl, etc.). The GFP-labeled InVir strain propagated in the cucumber vascular faster than the WT strain. These results suggest that increased conidia production and germination in vitro may correlate with virulence enhancement in Fusarium oxysporum f. sp. cucumerinum. This study will provide an insight into its virulence evolution and help us understand the mechanisms underlying the evolutionary biology of F. oxysporum.

A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvense L.) accessions

Introduction

Roots have a central role in plant resource capture and are the interface between the plant and the soil that affect multiple ecosystem processes. Field pennycress (Thlaspi arvense L.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich seeds (30-35% oil) amenable to biofuel production and as a protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand plastic responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity.

Methods

Using a root imaging and analysis pipeline, the 4D architecture of the pennycress root system was characterized under four nitrate regimes, ranging from zero to high nitrate concentrations. These measurements were taken at four time points (days 5, 9, 13, and 17 after sowing).

Results

Significant nitrate condition response and genotype interactions were identified for many root traits, with the greatest impact observed on lateral root traits. In trace nitrate conditions, a greater lateral root count, length, density, and a steeper lateral root angle was observed compared to high nitrate conditions. Additionally, genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density.

Discussion

These findings illustrate root trait variance among pennycress accessions. These traits could serve as targets for breeding programs aimed at developing improved cover crops that are responsive to nitrate, leading to enhanced productivity, resilience, and ecosystem service.

Single-gene resolution of diversity-driven overyielding in plant genotype mixtures

In plant communities, diversity often increases productivity and functioning, but the specific underlying drivers are difficult to identify. Most ecological theories attribute positive diversity effects to complementary niches occupied by different species or genotypes. However, the specific nature of niche complementarity often remains unclear, including how it is expressed in terms of trait differences between plants. Here, we use a gene-centred approach to study positive diversity effects in mixtures of natural Arabidopsis thaliana genotypes. Using two orthogonal genetic mapping approaches, we find that between-plant allelic differences at the AtSUC8 locus are strongly associated with mixture overyielding. AtSUC8 encodes a proton-sucrose symporter and is expressed in root tissues. Genetic variation in AtSUC8 affects the biochemical activities of protein variants and natural variation at this locus is associated with different sensitivities of root growth to changes in substrate pH. We thus speculate that - in the particular case studied here - evolutionary divergence along an edaphic gradient resulted in the niche complementarity between genotypes that now drives overyielding in mixtures. Identifying genes important for ecosystem functioning may ultimately allow linking ecological processes to evolutionary drivers, help identify traits underlying positive diversity effects, and facilitate the development of high-performance crop variety mixtures.

The proportion of resistant hosts in mixtures should be biased towards the resistance with the lowest breaking cost

Current agricultural practices facilitate emergence and spread of plant diseases through the wide use of monocultures. Host mixtures are a promising alternative for sustainable plant disease control. Their effectiveness can be partly explained by priming-induced cross-protection among plants. Priming occurs when plants are challenged with non-infective pathogen genotypes, resulting in increased resistance to subsequent infections by infective pathogen genotypes. We developed an epidemiological model to explore how mixing two distinct resistant varieties can reduce disease prevalence. We considered a pathogen population composed of three genotypes infecting either one or both varieties. We found that host mixtures should not contain an equal proportion of resistant plants, but a biased ratio (e.g. 80 : 20) to minimize disease prevalence. Counter-intuitively, the optimal ratio of resistant varieties should contain a lower proportion of the costliest resistance for the pathogen to break. This benefit is amplified by priming. This strategy also prevents the invasion of pathogens breaking all resistances.

Evaluation of Cowpea Landraces under a Mediterranean Climate

Cowpea (Vigna unguiculata (L.) Walp.) yield is strongly influenced by environmental conditions. Average seed yield can decrease to a great extent when drought conditions occur, especially when they prevail during flowering and seed filling periods. Identifying genotypes presenting yield stability is one of the most important breeding goals. Local varieties or crop landraces are genetic resources that, despite exhibiting intermediate yield production capacity, present high yield stability in low-input cropping systems. The objective of this study was therefore to evaluate five selected cowpea landraces originated from different Greek islands under Mediterranean climatic conditions. A complete randomized block design with four replications was used during three consecutive cropping seasons. Many phenological and agronomic traits studied showed statistically significant genotype × experimental year interaction, while there was a strong experimental year effect. Among the landraces studied, local population VG23 from Kythira Island was the most productive under the experimental climatic and soil conditions, while local population VG2 from Lemnos Island was characterized by low seed productivity. Conclusively, our study showed that VG23 landrace is a promising genetic material to be used for seed yield improvement.

The socio-economic challenges of managing pathogen evolution in agriculture

Genetic resistance forms the foundation of infectious disease management in crops. However, rapid pathogen evolution is causing the breakdown of resistance and threatening disease control. Recent research efforts have identified strategies for resistance gene deployment that aim to disrupt pathogen adaptation and prevent breakdown. To date, there has been limited practical uptake of such strategies. In this paper, we focus on the socio-economic challenges associated with translating applied evolutionary research into scientifically informed management strategies to control pathogen adaptation. We develop a conceptual framework for the economic valuation of resistance and demonstrate that in addition to various direct benefits, resistance delivers considerable indirect and non-market value to farmers and society. Incentives for stakeholders to engage in stewardship strategies are complicated by the uncertain timeframes associated with evolutionary processes, difficulties in assigning ownership rights to genetic resources and lack of governance. These interacting biological, socio-economic and institutional complexities suggest that resistance breakdown should be viewed as a wicked problem, with often conflicting imperatives among stakeholders and no simple cause or solution. Promoting the uptake of scientific research outcomes that address complex issues in sustainable crop disease management will require a mix of education, incentives, legislation and social change. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.

Climate service driven adaptation may alleviate the impacts of climate change in agriculture

Building a resilient and sustainable agricultural sector requires the development and implementation of tailored climate change adaptation strategies. By focusing on durum wheat (Triticum turgidum subsp. durum) in the Euro-Mediterranean region, we estimate the benefits of adapting through seasonal cultivar-selection supported by an idealised agro-climate service based on seasonal climate forecasts. The cost of inaction in terms of mean yield losses, in 2021–2040, ranges from −7.8% to −5.8% associated with a 7% to 12% increase in interannual variability. Supporting cultivar choices at local scale may alleviate these impacts and even turn them into gains, from 0.4% to 5.3%, as soon as the performance of the agro-climate service increases. However, adaptation advantages on mean yield may come with doubling the estimated increase in the interannual yield variability.

Tritrophic defenses as a central pivot of low-emission, pest-suppressive farming systems

The ongoing COVID-19 pandemic has spotlighted the intricate connections between human and planetary health. Given that pesticide-centered crop protection degrades ecological resilience and (in-)directly harms human health, the adoption of ecologically sound, biodiversity-driven alternatives is imperative. In this Synthesis paper, we illuminate how ecological forces can be manipulated to bolster 'tritrophic defenses' against crop pests, pathogens, and weeds. Three distinct, yet mutually compatible approaches (habitat-mediated, breeding-dependent, and epigenetic tactics) can be deployed at different organizational levels, that is, from an individual seed to entire farming landscapes. Biodiversity can be harnessed for crop protection through ecological infrastructures, diversification tactics, and reconstituted soil health. Crop diversification is ideally guided by interorganismal interplay and plant-soil feedbacks, entailing resistant cultivars, rotation schemes, or multicrop arrangements. Rewarding opportunities also exist to prime plants for enhanced immunity or indirect defenses. As tritrophic defenses spawn multiple societal cobenefits, they could become core features of healthy, climate-resilient, and low-carbon food systems.

Advancing the science and practice of ecological nutrient management for smallholder farmers

Soil degradation is widespread in smallholder agrarian communities across the globe where limited resource farmers struggle to overcome poverty and malnutrition. This review lays out the scientific basis and practical management options for an ecologically based approach to sustainably managing soil fertility, with particular attention to smallholder subsistence systems. We seek to change the trajectory of development programs that continue to promote inorganic fertilizers and other high input strategies to resource constrained smallholders, despite ample evidence that this approach is falling short of food security goals and contributing to resource degradation. Ecological nutrient management (ENM) is an agroecological approach to managing the biogeochemical cycles that govern soil ecosystem services and soil fertility. The portfolio of ENM strategies extends beyond reliance on inorganic fertilizers and is guided by the following five principles: (1) Build soil organic matter and other nutrient reserves. (2) Minimize the size of N and P pools that are the most susceptible to loss. (3) Maximize agroecosystem capacity to use soluble, inorganic N and P. (4) Use functional and phylogenetic biodiversity to minimize bare fallows and maximize presence of growing plants. (5) Construct agroecosystem and field scale mass balances to track net nutrient flows over multiple growing seasons. Strategic increases in spatial and temporal plant species diversity is a core ENM tactic that expands agroecosystem multifunctionality to meet smallholder priorities beyond soil restoration and crop yields. Examples of ENM practices include the use of functionally designed polycultures, diversified rotations, reduced fallow periods, increased reliance on legumes, integrated crop-livestock production, and use of variety of soil amendments. These practices foster soil organic matter accrual and restoration of soil function, both of which underpin agroecosystem resilience. When ENM is first implemented, short-term yield outcomes are variable; however, over the long-term, management systems that employ ENM can increase yields, yield stability, profitability and food security. ENM rests on a solid foundation of ecosystem and biogeochemical science, and despite the many barriers imposed by current agricultural policies, successful ENM systems are being promoted by some development actors and used by smallholder farmers, with promising results.

Plant biodiversity promotes sustainable agriculture directly and via belowground effects

While the positive relationship between plant biodiversity and ecosystem functioning (BEF) is well established, the extent to which this is mediated via belowground microbial processes is poorly understood. Growing evidence suggests that plant community structure influences soil microbial diversity, which in turn promotes functions desired for sustainable agriculture. Here, we outline the 'plant-directed' and soil microbe-mediated mechanisms expected to promote positive BEF. We identify how this knowledge can be utilized in plant diversification schemes to maximize ecosystem functioning in agroecosystems, which are typically species poor and sensitive to biotic and abiotic stressors. In the face of resource overexploitation and global change, bridging the gaps between biodiversity science and agricultural practices is crucial to meet food security in the Anthropocene.

Harnessing belowground processes for sustainable intensification of agricultural systems

Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant-microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.

Host mixtures for plant disease control: benefits from pathogen selection and immune priming

Multiline and cultivar mixtures are highly effective methods for agroecological plant disease control. Priming‐induced cross protection, occurring when plants are challenged by avirulent pathogen genotypes and resulting in increased resistance to subsequent infection by virulent ones, is one critical key to their lasting performance against polymorphic pathogen populations. Strikingly, this mechanism was until recently absent from mathematical models aiming at designing optimal host mixtures. We developed an epidemiological model to explore the effect of host mixtures composed of variable numbers of single‐resistance cultivars on the equilibrium prevalence of the disease caused by pathogen populations polymorphic for virulence complexity. This model shows that a relatively large amount of resistance genes must be deployed to achieve low disease prevalence, as pathogen competition in mixtures tends to select for intermediate virulence complexity. By contrast, priming significantly reduces the number of plant genotypes needed to drop disease prevalence below an acceptable threshold. Given the limited availability of resistance genes in cultivars, this mechanism of plant immunity should be assessed when designing host mixtures.

Dynamics of Pathogenic Fungi in Field Hedges: Vegetation Cover Is Differentially Impacted by Weather

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.

Genetic diversity and disease: The past, present, and future of an old idea

Why do infectious diseases erupt in some host populations and not others? This question has spawned independent fields of research in evolution, ecology, public health, agriculture, and conservation. In the search for environmental and genetic factors that predict variation in parasitism, one hypothesis stands out for its generality and longevity: genetically homogeneous host populations are more likely to experience severe parasitism than genetically diverse populations. In this perspective piece, I draw on overlapping ideas from evolutionary biology, agriculture, and conservation to capture the far-reaching implications of the link between genetic diversity and disease. I first summarize the development of this hypothesis and the results of experimental tests. Given the convincing support for the protective effect of genetic diversity, I then address the following questions: (1) Where has this idea been put to use, in a basic and applied sense, and how can we better use genetic diversity to limit disease spread? (2) What new hypotheses does the established disease-diversity relationship compel us to test? I conclude that monitoring, preserving, and augmenting genetic diversity is one of our most promising evolutionarily informed strategies for buffering wild, domesticated, and human populations against future outbreaks.

Optimizing Plant Disease Management in Agricultural Ecosystems Through Rational In-Crop Diversification

Biodiversity plays multifaceted roles in societal development and ecological sustainability. In agricultural ecosystems, using biodiversity to mitigate plant diseases has received renewed attention in recent years but our knowledge of the best ways of using biodiversity to control plant diseases is still incomplete. In term of in-crop diversification, it is not clear how genetic diversity per se in host populations interacts with identifiable resistance and other functional traits of component genotypes to mitigate disease epidemics and what is the best way of structuring mixture populations. In this study, we created a series of host populations by mixing different numbers of potato varieties showing different late blight resistance levels in different proportions. The amount of naturally occurring late blight disease in the mixture populations was recorded weekly during the potato growing seasons. The percentage of disease reduction (PDR) in the mixture populations was calculated by comparing their observed late blight levels relative to that expected when they were planted in pure stands. We found that PDR in the mixtures increased as the number of varieties and the difference in host resistance (DHR) between the component varieties increased. However, the level of host resistance in the potato varieties had little impact on PDR. In mixtures involving two varieties, the optimum proportion of component varieties for the best PDR depended on their DHR, with an increasing skewness to one of the component varieties as the DHR between the component varieties increased. These results indicate that mixing crop varieties can significantly reduce disease epidemics in the field. To achieve the best disease mitigation, growers should include as many varieties as possible in mixtures or, if only two component mixtures are possible, increase DHR among the component varieties.

Differentiation of endospheric microbiota in ancient and modern wheat cultivar roots

Modern plant breeding and agrosystems artificialization could have altered plants' ability to filter and recruit beneficial microorganisms in its microbiota. Thus, compared to modern cultivars, we hypothesized that root-endosphere microbiota in modern wheat cultivars are less resistant to colonization by fungi and bacteria and thus more susceptible to also recruit more pathogens. We used an in-field experimental design including six wheat varieties (three ancient vs. three modern) grown in monoculture and in mixture (three replicates each). Endospheric microbiota of wheat roots were analyzed on four individuals sampled randomly in each plot. Composition-based clustering of sequences was then characterized from amplicon mass-sequencing. We show that the bacterial and fungal microbiota composition in wheat roots differed between ancient and modern wheat cultivar categories. However, the responses observed varied with the group considered. Modern cultivars harbored higher richness of bacterial and fungal pathogens than ancient cultivars. Both cultivar types displayed specific indicator species. A synergistic effect was identified in mixtures of modern cultivars with a higher root endospheric mycobiota richness than expected from a null model. The present study shows the effect of plant breeding on the microbiota associated plant roots. The results call for making a diagnosis of the cultivar's endospheric-microbiota composition. These new results also suggest the importance of a holobiont-vision while considering plant selection in crops and call for better integration of symbiosis in the development of next-generation agricultural practices.

Breeding Beyond Monoculture: Putting the "Intercrop" Into Crops

Intercropping is both a well-established and yet novel agricultural practice, depending on one's perspective. Such perspectives are principally governed by geographic location and whether monocultural practices predominate. Given the negative environmental effects of monoculture agriculture (loss of biodiversity, reliance on non-renewable inputs, soil degradation, etc.), there has been a renewed interest in cropping systems that can reduce the impact of modern agriculture while maintaining (or even increasing) yields. Intercropping is one of the most promising practices in this regard, yet faces a multitude of challenges if it is to compete with and ultimately replace the prevailing monocultural norm. These challenges include the necessity for more complex agricultural designs in space and time, bespoke machinery, and adapted crop cultivars. Plant breeding for monocultures has focused on maximizing yield in single-species stands, leading to highly productive yet specialized genotypes. However, indications suggest that these genotypes are not the best adapted to intercropping systems. Re-designing breeding programs to accommodate inter-specific interactions and compatibilities, with potentially multiple different intercropping partners, is certainly challenging, but recent technological advances offer novel solutions. We identify a number of such technology-driven directions, either ideotype-driven (i.e., "trait-based" breeding) or quantitative genetics-driven (i.e., "product-based" breeding). For ideotype breeding, plant growth modeling can help predict plant traits that affect both inter- and intraspecific interactions and their influence on crop performance. Quantitative breeding approaches, on the other hand, estimate breeding values of component crops without necessarily understanding the underlying mechanisms. We argue that a combined approach, for example, integrating plant growth modeling with genomic-assisted selection and indirect genetic effects, may offer the best chance to bridge the gap between current monoculture breeding programs and the more integrated and diverse breeding programs of the future.