Gene-by-environment interactions in plants: Molecular mechanisms, environmental drivers, and adaptive plasticity.

Plants demonstrate a broad range of responses to environmental shifts. One of the most remarkable responses is plasticity, which is the ability of a single plant genotype to produce different phenotypes in response to environmental stimuli. As with all traits, the ability of plasticity to evolve depends on the presence of underlying genetic diversity within a population. A common approach for evaluating the role of genetic variation in driving differences in plasticity has been to study genotype-by-environment interactions (G × E). G × E occurs when genotypes produce different phenotypic trait values in response to different environments. In this review, we highlight progress and promising methods for identifying the key environmental and genetic drivers of G × E. Specifically, methodological advances in using algorithmic and multivariate approaches to understand key environmental drivers combined with new genomic innovations can greatly increase our understanding about molecular responses to environmental stimuli. These developing approaches can be applied to proliferating common garden networks that capture broad natural environmental gradients to unravel the underlying mechanisms of G × E. An increased understanding of G × E can be used to enhance the resilience and productivity of agronomic systems.

Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress.

We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.

Plant physical defenses contribute to a latitudinal gradient in resistance to insect herbivory within a widespread perennial grass.

PREMISE: Herbivore pressure can vary across the range of a species, resulting in different defensive strategies. If herbivory is greater at lower latitudes, plants may be better defended there, potentially driving a latitudinal gradient in defense. However, relationships that manifest across the entire range of a species may be confounded by differences within genetic subpopulations, which may obscure the drivers of these latitudinal gradients. METHODS: We grew plants of the widespread perennial grass Panicum virgatum in a common garden that included genotypes from three genetic subpopulations spanning an 18.5° latitudinal gradient. We then assessed defensive strategies of these plants by measuring two physical resistance traits-leaf mass per area (LMA) and leaf ash, a proxy for silica-and multiple measures of herbivory by caterpillars of the generalist herbivore fall armyworm (Spodoptera frugiperda). RESULTS: Across all genetic subpopulations, low-latitude plants experienced less herbivory than high-latitude plants. Within genetic subpopulations, however, this relationship was inconsistent-the most widely distributed and phenotypically variable subpopulation (Atlantic) exhibited more consistent latitudinal trends than either of the other two subpopulations. The two physical resistance traits, LMA and leaf ash, were both highly heritable and positively associated with resistance to different measures of herbivory across all subpopulations, indicating their importance in defense against herbivores. Again, however, these relationships were inconsistent within subpopulations. CONCLUSIONS: Defensive gradients that occur across the entire species range may not arise within localized subpopulations. Thus, identifying the drivers of latitudinal gradients in herbivory defense may depend on adequately sampling the diversity within a species.

Genetically correlated leaf tensile and morphological traits are driven by growing season length in a widespread perennial grass.

PREMISE: Leaf tensile resistance, a leaf's ability to withstand pulling forces, is an important determinant of plant ecological strategies. One potential driver of leaf tensile resistance is growing season length. When growing seasons are long, strong leaves, which often require more time and resources to construct than weak leaves, may be more advantageous than when growing seasons are short. Growing season length and other ecological conditions may also impact the morphological traits that underlie leaf tensile resistance. METHODS: To understand variation in leaf tensile resistance, we measured size-dependent leaf strength and size-independent leaf toughness in diverse genotypes of the widespread perennial grass Panicum virgatum (switchgrass) in a common garden. We then used quantitative genetic approaches to estimate the heritability of leaf tensile resistance and whether there were genetic correlations between leaf tensile resistance and other morphological traits. RESULTS: Leaf tensile resistance was positively associated with aboveground biomass (a proxy for fitness). Moreover, both measures of leaf tensile resistance exhibited high heritability and were positively genetically correlated with leaf lamina thickness and leaf mass per area (LMA). Leaf tensile resistance also increased with the growing season length in the habitat of origin, and this effect was mediated by both LMA and leaf thickness. CONCLUSIONS: Differences in growing season length may promote selection for different leaf lifespans and may explain existing variation in leaf tensile resistance in P. virgatum. In addition, the high heritability of leaf tensile resistance suggests that P. virgatum will be able to respond to climate change as growing seasons lengthen.

Multiple constraints cause positive and negative feedbacks limiting grassland soil CO2 efflux under CO2 enrichment.

Terrestrial ecosystems are increasingly enriched with resources such as atmospheric CO2 that limit ecosystem processes. The consequences for ecosystem carbon cycling depend on the feedbacks from other limiting resources and plant community change, which remain poorly understood for soil CO2 efflux, JCO2, a primary carbon flux from the biosphere to the atmosphere. We applied a unique CO2 enrichment gradient (250 to 500 µL L-1) for eight years to grassland plant communities on soils from different landscape positions. We identified the trajectory of JCO2 responses and feedbacks from other resources, plant diversity [effective species richness, exp(H)], and community change (plant species turnover). We found linear increases in JCO2 on an alluvial sandy loam and a lowland clay soil, and an asymptotic increase on an upland silty clay soil. Structural equation modeling identified CO2 as the dominant limitation on JCO2 on the clay soil. In contrast with theory predicting limitation from a single limiting factor, the linear JCO2 response on the sandy loam was reinforced by positive feedbacks from aboveground net primary productivity and exp(H), while the asymptotic JCO2 response on the silty clay arose from a net negative feedback among exp(H), species turnover, and soil water potential. These findings support a multiple resource limitation view of the effects of global change drivers on grassland ecosystem carbon cycling and highlight a crucial role for positive or negative feedbacks between limiting resources and plant community structure. Incorporating these feedbacks will improve models of terrestrial carbon sequestration and ecosystem services.

Seed size variation impacts local adaptation and life-history strategies in a perennial grass.

Seed mass is an ecologically important trait that often differs considerably among ecotypes. Yet, because few studies examine the impacts of seed mass on adult life-history traits, its role in local adaptation is unclear. In this study, using accessions of Panicum hallii that spanned the two major ecotypes, we examined whether covariation between seed mass, seedling and reproductive traits impacts ecotypic divergence and local adaptation. The perennial grass P. hallii has two distinct ecotypes-a large-seeded upland ecotype adapted to xeric environments and a small-seeded lowland ecotype adapted to mesic environments. In the greenhouse, seed mass varied greatly across P. hallii genotypes in a manner consistent with ecotypic divergence. Seed mass covaried significantly with several seedling and reproductive traits. At field sites representing the habitats of the two ecotypes, seed mass had different impacts on seedling and adult recruitment: selection favoured large seeds in upland habitat and small seeds in lowland habitat, which was consistent with local adaptation. By demonstrating the central role of seed mass in ecotypic differences in P. hallii and its importance to seedling and adult recruitment under field conditions, these studies show that early life-history traits can promote local adaptation and potentially explain ecotype formation.

Legacies of precipitation influence primary production in Panicum virgatum.

Precipitation is a key driver of primary production worldwide, but primary production does not always track year-to-year variation in precipitation linearly. Instead, plant responses to changes in precipitation may exhibit time lags, or legacies of past precipitation. Legacies can be driven by multiple mechanisms, including persistent changes in plant physiological and morphological traits and changes to the physical environment, such as plant access to soil water. We used three precipitation manipulation experiments in central Texas, USA to evaluate the magnitude, duration, and potential mechanisms driving precipitation legacies on aboveground primary production of the perennial C4 grass, Panicum virgatum. Specifically, we performed a rainout shelter study, where eight genotypes grew under different precipitation regimes; a transplant study, where plants that had previously grown in a rainout shelter under different precipitation regimes were moved to a common environment; and a mesocosm study, where the effect of swapping precipitation regime was examined with a single genotype. Across these experiments, plants previously grown under wet conditions generally performed better than expected when exposed to drought. Panicum virgatum exhibited stronger productivity legacies of past wet years on current-year responses to drought than of past dry years on current-year responses to wet conditions. Additionally, previous year tiller counts, a proxy for meristem availability, were important in determining legacy effects on aboveground production. As climate changes and precipitation extremes-both dry and wet-become more common, these results suggest that populations of P. virgatum may become less resilient.

Nutrients and consumers impact tree colonization differently from performance in a successional old field.

Successful colonization and growth of trees within herbaceous communities may result from different interactions with the herbaceous community. First, colonizing trees compete against larger, established herbs, while subsequent growth occurs among similarly sized or smaller herbs. This shift from colonization to growth may lead three drivers of community dynamics-nutrients, consumers, and herbaceous diversity-to differentially affect tree colonization and, later, tree performance. Initially, these drivers should favor larger, established herbs, reducing tree colonization. Later, when established trees can better compete with herbs, these drivers should benefit trees and increase their performance. In a 4-year study in a southeastern US old field, we added nutrients to, excluded aboveground consumers from, and manipulated initial richness of, the herbaceous community, and then allowed trees to naturally colonize these communities (from intact seedbanks or as seed rain) and grow. Nutrients and consumers had opposing effects on tree colonization and performance: adding nutrients and excluding consumers reduced tree colonization rate, but later increased the size of established trees (height, basal diameter). Adding nutrients and excluding consumers also restricted tree colonization to earlier years of study, which partially explained the effect of nutrient addition on plant size. Together, this shows differing impacts of nutrients and consumers: factors that initially limited tree colonization also resulted in larger established trees. This suggests that succession of grasslands that are either eutrophied or have diminished consumer pressure may experience lags and pulses in woody encroachment, leading to an extended period of herbaceous dominance followed by accelerated woody growth.

Eutrophication, biodiversity loss, and species invasions modify the relationship between host and parasite richness during host community assembly.

Host and parasite richness are generally positively correlated, but the stability of this relationship in response to global change remains poorly understood. Rapidly changing biotic and abiotic conditions can alter host community assembly, which in turn, can alter parasite transmission. Consequently, if the relationship between host and parasite richness is sensitive to parasite transmission, then changes in host composition under various global change scenarios could strengthen or weaken the relationship between host and parasite richness. To test the hypothesis that host community assembly can alter the relationship between host and parasite richness in response to global change, we experimentally crossed host diversity (biodiversity loss) and resource supply to hosts (eutrophication), then allowed communities to assemble. As previously shown, initial host diversity and resource supply determined the trajectory of host community assembly, altering post-assembly host species richness, richness-independent host phylogenetic diversity, and colonization by exotic host species. Overall, host richness predicted parasite richness, and as predicted, this effect was moderated by exotic abundance-communities dominated by exotic species exhibited a stronger positive relationship between post-assembly host and parasite richness. Ultimately, these results suggest that, by modulating parasite transmission, community assembly can modify the relationship between host and parasite richness. These results thus provide a novel mechanism to explain how global environmental change can generate contingencies in a fundamental ecological relationship-the positive relationship between host and parasite richness.

Herbivores and nutrients control grassland plant diversity via light limitation.

Human alterations to nutrient cycles and herbivore communities are affecting global biodiversity dramatically. Ecological theory predicts these changes should be strongly counteractive: nutrient addition drives plant species loss through intensified competition for light, whereas herbivores prevent competitive exclusion by increasing ground-level light, particularly in productive systems. Here we use experimental data spanning a globally relevant range of conditions to test the hypothesis that herbaceous plant species losses caused by eutrophication may be offset by increased light availability due to herbivory. This experiment, replicated in 40 grasslands on 6 continents, demonstrates that nutrients and herbivores can serve as counteracting forces to control local plant diversity through light limitation, independent of site productivity, soil nitrogen, herbivore type and climate. Nutrient addition consistently reduced local diversity through light limitation, and herbivory rescued diversity at sites where it alleviated light limitation. Thus, species loss from anthropogenic eutrophication can be ameliorated in grasslands where herbivory increases ground-level light.

Past is prologue: host community assembly and the risk of infectious disease over time.

Infectious disease risk is often influenced by host diversity, but the causes are unresolved. Changes in diversity are associated with changes in community structure, particularly during community assembly; therefore, by incorporating change over time, host community assembly may provide a framework to resolve causation. In turn, community assembly can be driven by many processes, including resource enrichment. To test the hypothesis that community assembly causally links host diversity to future disease, we experimentally manipulated host diversity and resource supply to hosts, then allowed communities to assemble for 2 years (surveyed 2012-2014). Initially, host diversity increased disease. Subsequently, host diversity did not directly alter disease. However, host diversity determined the trajectory of host community assembly, altering colonisation by exotic host species and richness-independent host phylogenetic diversity, which together reversed the initial increase in disease. Ultimately, incorporating the temporal dimension of community assembly revealed novel mechanisms linking host diversity to future disease.

A growth-defense trade-off is general across native and exotic grasses.

High-resource environments typically favor quick-growing, poorly defended plants, while resource-poor environments typically favor slow-growing, well-defended plants. The prevailing hypothesis explaining this pattern states that, as resource availability increases, well-defended, slow-growing species are replaced by poorly defended, fast-growing species. A second hypothesis states that greater resource availability increases allocation to growth at the expense of defense, within species. Regardless of mechanism, if exotic species are released from enemies relative to natives, shifts in allocation to growth and defense both within and among species could differ by geographic provenance. To test whether resource availability alters growth or defense, within and among species, and whether any such effects differ between natives and exotics, we manipulated soil nutrient supply and access of aboveground insect herbivores and fungal pathogens under field conditions to individuals of six native and six exotic grass species that co-occurred in a North Carolina old field. The prevailing hypothesis' prediction-that species-level enemy impact increases with species' nutrient responsiveness-was confirmed. Moreover, this relationship did not differ between native and exotic species. The second hypothesis' prediction-that individual-level enemy impact increases with nutrient supply, after accounting for species-level variation in performance-was not supported. Together, these results support the idea, across native and exotic species, that plant species turnover is the primary mechanism underlying effects of nutrient enrichment on allocation to growth and defense in plant communities.

A multivariate test of disease risk reveals conditions leading to disease amplification.

Theory predicts that increasing biodiversity will dilute the risk of infectious diseases under certain conditions and will amplify disease risk under others. Yet, few empirical studies demonstrate amplification. This contrast may occur because few studies have considered the multivariate nature of disease risk, which includes richness and abundance of parasites with different transmission modes. By combining a multivariate statistical model developed for biodiversity-ecosystem-multifunctionality with an extensive field manipulation of host (plant) richness, composition and resource supply to hosts, we reveal that (i) host richness alone could not explain most changes in disease risk, and (ii) shifting host composition allowed disease amplification, depending on parasite transmission mode. Specifically, as predicted from theory, the effect of host diversity on parasite abundance differed for microbes (more density-dependent transmission) and insects (more frequency-dependent transmission). Host diversity did not influence microbial parasite abundance, but nearly doubled insect parasite abundance, and this amplification effect was attributable to variation in host composition. Parasite richness was reduced by resource addition, but only in species-rich host communities. Overall, this study demonstrates that multiple drivers, related to both host community and parasite characteristics, can influence disease risk. Furthermore, it provides a framework for evaluating multivariate disease risk in other systems.

Effects of native diversity, soil nutrients, and natural enemies on exotic invasion in experimental plant communities.

Many factors can promote exotic plant success. Three of these factors-greater pressure from natural enemies on natives, increased soil nutrient supply, and low native species richness-may interact during invasions. To test for independent and interactive effects of these drivers, we planted herbaceous perennial communities at two levels of native richness (monocultures and five-species polycultures). We then factorially manipulated soil nutrient supply and access to these communities by aboveground foliar enemies (fungal pathogens and insect herbivores), and allowed natural colonization to proceed for four years. We predicted that nutrient addition would increase exotic success, while enemy exclusion and increasing native richness would reduce exotic success. Additionally, we expected that enemy exclusion would reduce the benefits of nutrient addition to exotic species most in species-poor communities, and that this effect would be weaker in species-rich communities. In total, we found no evidence that nutrient supply, enemy access, and native richness interacted to influence exotic success. Furthermore, native richness had no effect on exotic success. Instead, nutrient addition increased, and enemy exclusion decreased, exotic success independently. As predicted, enemy exclusion reduced exotic success, primarily by slowing the decline in abundance of planted native species. Together, these results demonstrate that multiple drivers of exotic success can act independently within a single system.

Joint effects of nutrient addition and enemy exclusion on exotic plant success.

Worldwide, ecosystems are increasingly dominated by exotic plant species, a shift hypothesized to result from numerous ecological factors. Two of these, increased resource availability and enemy release, may act in concert to increase exotic success in plant communities (Resource-Enemy Release Hypothesis, R-ERH). To test this, we manipulated the availability of soil nutrients and access of vertebrate herbivores, insect herbivores, and fungal pathogens to intact grassland communities containing both native and exotic species. Our results supported both conditions necessary for R-ERH. First, exotics were less damaged than natives, experiencing less foliar damage (insect herbivory and fungal disease) than native species, particularly in communities where soil nutrients were added. Second, fertilization increased foliar damage on native species, but not exotic species. As well as fulfilling both conditions for R-ERH, these results demonstrate the importance of considering the effects of resource availability when testing for enemy release. When both conditions are fulfilled, R-ERH predicts that increasing resource availability will increase exotic abundance only in the presence of enemies. Our results fully supported this prediction for vertebrate herbivores: fertilization increased exotic cover only in communities exposed to vertebrate herbivores. Additionally, the prediction was partially supported for insect herbivores and fungal pathogens, excluding these enemies reduced exotic cover as predicted, but inconsistent with R-ERH, this effect occurred only in unfertilized communities. These results highlight the need to consider the influence of multiple enemy guilds on community processes like exotic plant invasions. Moreover, this study experimentally demonstrates that resource availability and natural enemies can jointly influence exotic success in plant communities.

Effects of soil nitrogen availability and native grass diversity on exotic forb dominance.

Exotic plants are often most successful in high resource environments. By drawing down available resources, species-rich communities may be able to reduce exotic success when resource supply is elevated. We tested the prediction that exotic success would be greatest in species-poor communities when nitrogen availability is high. We also tested two underlying assumptions of this prediction: species-rich communities draw down soil nitrogen availability more than species-poor communities following fertilization and exotic success increases when soil nitrogen availability is high. In a restored grassland where native grass diversity was manipulated (one, three, or five-species) seven years earlier to form a gradient in species richness, we manipulated nitrogen availability directly via fertilization, and indirectly via burning. We then examined the success of the exotic forb Galium verum L. Contrary to our prediction, diversity and nutrient treatments did not jointly influence exotic success. Instead, one-time fertilization increased exotic biomass in the first year of the study. This likely occurred because the effect of nutrient treatments on nitrogen availability was independent of diversity treatment. Thus, we found no evidence that species-rich communities are better able to reduce exotic biomass when nitrogen is added than are species-poor communities. This suggests that in some systems, the effects of increasing species richness can be overwhelmed by the effects of nutrient addition that promote exotic success.

The role of drought- and disturbance-mediated competition in shaping community responses to varied environments.

By altering the strength of intra- and interspecific competition, droughts may reshape plant communities. Furthermore, species may respond differently to drought when other influences, such as herbivory, are considered. To explore this relationship, we conducted a greenhouse experiment measuring responses to inter- and intraspecific competition for two grasses, Schedonorus arundinaceus and Paspalum dilatatum, while varying water availability and simulating herbivory via clipping. We then parameterized population growth models to examine the long-term outcome of competition under these conditions. Under drought, S. arundinaceus was less water stressed than P. dilatatum, which exhibited severe water stress; clipping alleviated this stress, increasing the competitive ability of P. dilatatum relative to S. arundinaceus. Although P. dilatatum competed weakly under drought, clipping reduced water stress in P. dilatatum, thereby enhancing its ability to compete with S. arundinaceus under drought. Supporting these observations, population growth models predicted that P. dilatatum would exclude S. arundinaceus when clipped under drought, while S. arundinaceus would exclude P. dilatatum when unclipped under drought. When the modeled environment varied temporally, environmental variation promoted niche differences that, though insufficient to maintain stable coexistence, prevented unconditional competitive exclusion by promoting priority effects. Our results suggest that it is important to consider how species respond not just to stable, but also to variable, environments. When species differ in their responses to drought, competition, and simulated herbivory, stable environments may promote competitive exclusion, while fluctuating environments may promote coexistence. These interactions are critical to understanding how species will respond to global change.

Physiological Responses of C4 Perennial Bioenergy Grasses to Climate Change: Causes, Consequences, and Constraints.

C4 perennial bioenergy grasses are an economically and ecologically important group whose responses to climate change will be important to the future bioeconomy. These grasses are highly productive and frequently possess large geographic ranges and broad environmental tolerances, which may contribute to the evolution of ecotypes that differ in physiological acclimation capacity and the evolution of distinct functional strategies. C4 perennial bioenergy grasses are predicted to thrive under climate change-C4 photosynthesis likely evolved to enhance photosynthetic efficiency under stressful conditions of low [CO2], high temperature, and drought-although few studies have examined how these species will respond to combined stresses or to extremes of temperature and precipitation. Important targets for C4 perennial bioenergy production in a changing world, such as sustainability and resilience, can benefit from combining knowledge of C4 physiology with recent advances in crop improvement, especially genomic selection.

Do invasive species perform better in their new ranges?

A fundamental assumption in invasion biology is that most invasive species exhibit enhanced performance in their introduced range relative to their home ranges. This idea has given rise to numerous hypotheses explaining "invasion success" by virtue of altered ecological and evolutionary pressures. There are surprisingly few data, however, testing the underlying assumption that the performance of introduced populations, including organism size, reproductive output, and abundance, is enhanced in their introduced compared to their native range. Here, we combined data from published studies to test this hypothesis for 26 plant and 27 animal species that are considered to be invasive. On average, individuals of these 53 species were indeed larger, more fecund, and more abundant in their introduced ranges. The overall mean, however, belied significant variability among species, as roughly half of the investigated species (N=27) performed similarly when compared to conspecific populations in their native range. Thus, although some invasive species are performing better in their new ranges, the pattern is not universal, and just as many are performing largely the same across ranges.

Disease decreases variation in host community structure in an old-field grassland.

Disease may drive variation in host community structure by modifying the interplay of deterministic and stochastic processes that shape communities. For instance, deterministic processes like ecological selection can benefit species less impacted by disease. When communities have higher levels of disease and disease consistently selects for certain host species, this can reduce variation in host community composition. On the other hand, when host communities are less impacted by disease and selection is weaker, stochastic processes (e.g., drift, dispersal) may play a bigger role in host community structure, which can increase variation among communities. While effects of disease on host community structure have been quantified in field experiments, few have addressed the role of disease in modulating variation in structure among host communities. To address this, we conducted a field experiment spanning three years, using a tractable system: foliar fungal pathogens in an old-field grassland community dominated by the grass Lolium arundinaceum, tall fescue. We reduced foliar fungal disease burden in replicate host communities (experimental plots in intact vegetation) in three fungicide regimens that varied in the seasonal duration of fungicide treatment and included a fungicide-free control. We measured host diversity, biomass, and variation in community structure among replicate communities. Disease reduction generally decreased plant richness and increased aboveground biomass relative to communities experiencing ambient levels of disease. These changes in richness and aboveground biomass were consistent across years despite changes in structure of the plant communities over the experiment's three years. Importantly, disease reduction amplified host community variation, suggesting that disease diminished the degree to which host communities were structured by stochastic processes. These results of experimental disease reduction both highlight the potential importance of stochastic processes in plant communities and reveal the potential for disease to regulate variation in host community structure.