Cropping management in a livestock-pasture-crop integration modifies microbial communities, activity, and soil health score.

Understanding indicators of soil health is crucial for developing agricultural systems that are sustainable and climate resilient. Labile soil carbon (C), microbial properties, and nutrient status are all incorporated into the Haney Soil Health Tool with the goal of summarizing several indicators into one index. Monthly soil samples from an integrated crop-livestock system in Central Texas were collected from 2017 to 2019. Fields represented a range of management practices, including cover crops, no-till, rotational grazing, and a native prairie remnant. Soil samples were analyzed for total C, water-soluble C, macro- and micronutrient content and bioavailability, and phospholipid fatty acids (PLFAs). Microbial activity was determined via a 24-h CO2 incubation. Soil health score, C, and PLFAs were well correlated with each other. The greatest total PLFA (219.5 nmol g-1 soil) and organic C (54.3 g kg-1 soil) were found in the native prairie, and the lowest were found in the unfertilized continuous-corn system (60.5 nmol PLFAs g-1 soil and 24.0 g organic C kg-1 soil). Of all agroecosystems, the perennial grazing system (soil health score, 24.7) was most similar to the native prairie (soil health score, 27.4), having high soil C and a large microbial community. Of the row cropping systems, the no-till system approached the perennial systems better than the conventional till and unfertilized conventional till (soil health score, 11.1 vs. 8.0 and 5.3, respectively). This study highlights the value of perennial grass grazing in agroecosystems and appropriate best management practices. Expanding this analysis to other sites may provide additional insight.

Stronger fertilization effects on aboveground versus belowground plant properties across nine U.S. grasslands.

Increased nutrient inputs due to anthropogenic activity are expected to increase primary productivity across terrestrial ecosystems, but changes in allocation aboveground versus belowground with nutrient addition have different implications for soil carbon (C) storage. Thus, given that roots are major contributors to soil C storage, understanding belowground net primary productivity (BNPP) and biomass responses to changes in nutrient availability is essential to predicting carbon-climate feedbacks in the context of interacting global environmental changes. To address this knowledge gap, we tested whether a decade of nitrogen (N) and phosphorus (P) fertilization consistently influenced aboveground and belowground biomass and productivity at nine grassland sites spanning a wide range of climatic and edaphic conditions in the continental United States. Fertilization effects were strong aboveground, with both N and P addition stimulating aboveground biomass at nearly all sites (by 30% and 36%, respectively, on average). P addition consistently increased root production (by 15% on average), whereas other belowground responses to fertilization were more variable, ranging from positive to negative across sites. Site-specific responses to P were not predicted by the measured covariates. Atmospheric N deposition mediated the effect of N fertilization on root biomass and turnover. Specifically, atmospheric N deposition was positively correlated with root turnover rates, and this relationship was amplified with N addition. Nitrogen addition increased root biomass at sites with low N deposition but decreased it at sites with high N deposition. Overall, these results suggest that the effects of nutrient supply on belowground plant properties are context dependent, particularly with regard to background N supply rates, demonstrating that site conditions must be considered when predicting how grassland ecosystems will respond to increased nutrient loading from anthropogenic activity.

Indicators of water use efficiency across diverse agroecosystems and spatiotemporal scales.

Understanding the relationship between water and production within and across agroecosystems is essential for addressing several agricultural challenges of the 21st century: providing food, fuel, and fiber to a growing human population, reducing the environmental impacts of agricultural production, and adapting food systems to climate change. Of all human activities, agriculture has the highest demand for water globally. Therefore, increasing water use efficiency (WUE), or producing 'more crop per drop', has been a long-term goal of agricultural management, engineering, and crop breeding. WUE is a widely used term applied across a diverse array of spatial scales, spanning from the leaf to the globe, and over temporal scales ranging from seconds to months to years. The measurement, interpretation, and complexity of WUE varies enormously across these spatial and temporal scales, challenging comparisons within and across diverse agroecosystems. The goals of this review are to evaluate common indicators of WUE in agricultural production and assess tradeoffs when applying these indicators within and across agroecosystems amidst a changing climate. We examine three questions: (1) what are the uses and limitations of common WUE indicators, (2) how can WUE indicators be applied within and across agroecosystems, and (3) how can WUE indicators help adapt agriculture to climate change? Addressing these agricultural challenges will require land managers, producers, policy makers, researchers, and consumers to evaluate costs and benefits of practices and innovations of water use in agricultural production. Clearly defining and interpreting WUE in the most scale-appropriate way is crucial for advancing agroecosystem sustainability.

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.

Linking changes in species composition and biomass in a globally distributed grassland experiment.

Global change drivers, such as anthropogenic nutrient inputs, are increasing globally. Nutrient deposition simultaneously alters plant biodiversity, species composition and ecosystem processes like aboveground biomass production. These changes are underpinned by species extinction, colonisation and shifting relative abundance. Here, we use the Price equation to quantify and link the contributions of species that are lost, gained or that persist to change in aboveground biomass in 59 experimental grassland sites. Under ambient (control) conditions, compositional and biomass turnover was high, and losses (i.e. local extinctions) were balanced by gains (i.e. colonisation). Under fertilisation, the decline in species richness resulted from increased species loss and decreases in species gained. Biomass increase under fertilisation resulted mostly from species that persist and to a lesser extent from species gained. Drivers of ecological change can interact relatively independently with diversity, composition and ecosystem processes and functions such as aboveground biomass due to the individual contributions of species lost, gained or persisting.

The genetic basis for panicle trait variation in switchgrass (Panicum virgatum).

KEY MESSAGE: We investigate the genetic basis of panicle architecture in switchgrass in two mapping populations across a latitudinal gradient, and find many stable, repeatable genetic effects and limited genetic interactions with the environment. Grass species exhibit large diversity in panicle architecture influenced by genes, the environment, and their interaction. The genetic study of panicle architecture in perennial grasses is limited. In this study, we evaluate the genetic basis of panicle architecture including panicle length, primary branching number, and secondary branching number in an outcrossed switchgrass QTL population grown across ten field sites in the central USA through multi-environment mixed QTL analysis. We also evaluate genetic effects in a diversity panel of switchgrass grown at three of the ten field sites using genome-wide association (GWAS) and multivariate adaptive shrinkage. Furthermore, we search for candidate genes underlying panicle traits in both of these independent mapping populations. Overall, 18 QTL were detected in the QTL mapping population for the three panicle traits, and 146 unlinked genomic regions in the diversity panel affected one or more panicle trait. Twelve of the QTL exhibited consistent effects (i.e., no QTL by environment interactions or no QTL × E), and most (four of six) of the effects with QTL × E exhibited site-specific effects. Most (59.3%) significant partially linked diversity panel SNPs had significant effects in all panicle traits and all field sites and showed pervasive pleiotropy and limited environment interactions. Panicle QTL co-localized with significant SNPs found using GWAS, providing additional power to distinguish between true and false associations in the diversity panel.

A generalist-specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range.

Polyploidy results from whole-genome duplication and is a unique form of heritable variation with pronounced evolutionary implications. Different ploidy levels, or cytotypes, can exist within a single species, and such systems provide an opportunity to assess how ploidy variation alters phenotypic novelty, adaptability, and fitness, which can, in turn, drive the development of unique ecological niches that promote the coexistence of multiple cytotypes. Switchgrass, Panicum virgatum, is a widespread, perennial C4 grass in North America with multiple naturally occurring cytotypes, primarily tetraploids (4×) and octoploids (8×). Using a combination of genomic, quantitative genetic, landscape, and niche modeling approaches, we detect divergent levels of genetic admixture, evidence of niche differentiation, and differential environmental sensitivity between switchgrass cytotypes. Taken together, these findings support a generalist (8×)­specialist (4×) trade-off. Our results indicate that the 8× represent a unique combination of genetic variation that has allowed the expansion of switchgrass' ecological niche and thus putatively represents a valuable breeding resource.

Nutrient identity modifies the destabilising effects of eutrophication in grasslands.

Nutrient enrichment can simultaneously increase and destabilise plant biomass production, with co-limitation by multiple nutrients potentially intensifying these effects. Here, we test how factorial additions of nitrogen (N), phosphorus (P) and potassium with essential nutrients (K+) affect the stability (mean/standard deviation) of aboveground biomass in 34 grasslands over 7 years. Destabilisation with fertilisation was prevalent but was driven by single nutrients, not synergistic nutrient interactions. On average, N-based treatments increased mean biomass production by 21-51% but increased its standard deviation by 40-68% and so consistently reduced stability. Adding P increased interannual variability and reduced stability without altering mean biomass, while K+ had no general effects. Declines in stability were largest in the most nutrient-limited grasslands, or where nutrients reduced species richness or intensified species synchrony. We show that nutrients can differentially impact the stability of biomass production, with N and P in particular disproportionately increasing its interannual variability.

Soil carbon stocks in temperate grasslands differ strongly across sites but are insensitive to decade-long fertilization.

Enhancing soil carbon (C) storage has the potential to offset human-caused increases in atmospheric CO2 . Rising CO2 has occurred concurrently with increasing supply rates of biologically limiting nutrients such as nitrogen (N) and phosphorus (P). However, it is unclear how increased supplies of N and P will alter soil C sequestration, particularly in grasslands, which make up nearly a third of non-agricultural land worldwide. Here, we leverage a globally distributed nutrient addition experiment (the Nutrient Network) to examine how a decade of N and P fertilization (alone and in combination) influenced soil C and N stocks at nine grassland sites spanning the continental United States. We measured changes in bulk soil C and N stocks and in three soil C fractions (light and heavy particulate organic matter, and mineral-associated organic matter fractions). Nutrient amendment had variable effects on soil C and N pools that ranged from strongly positive to strongly negative, while soil C and N pool sizes varied by more than an order of magnitude across sites. Piecewise SEM clarified that small increases in plant C inputs with fertilization did not translate to greater soil C storage. Nevertheless, peak season aboveground plant biomass (but not root biomass or production) was strongly positively related to soil C storage at seven of the nine sites, and across all nine sites, soil C covaried with moisture index and soil mineralogy, regardless of fertilization. Overall, we show that site factors such as moisture index, plant productivity, soil texture, and mineralogy were key predictors of cross-site soil C, while nutrient amendment had weaker and site-specific effects on C sequestration. This suggests that prioritizing the protection of highly productive temperate grasslands is critical for reducing future greenhouse gas losses arising from land use change.

Soil properties as key predictors of global grassland production: Have we overlooked micronutrients?

Fertilisation experiments have demonstrated that nutrient availability is a key determinant of biomass production and carbon sequestration in grasslands. However, the influence of nutrients in explaining spatial variation in grassland biomass production has rarely been assessed. Using a global dataset comprising 72 sites on six continents, we investigated which of 16 soil factors that shape nutrient availability associate most strongly with variation in grassland aboveground biomass. Climate and N deposition were also considered. Based on theory-driven structural equation modelling, we found that soil micronutrients (particularly Zn and Fe) were important predictors of biomass and, together with soil physicochemical properties and C:N, they explained more unique variation (32%) than climate and N deposition (24%). However, the association between micronutrients and biomass was absent in grasslands limited by NP. These results highlight soil properties as key predictors of global grassland biomass production and point to serial co-limitation by NP and micronutrients.

Negative effects of nitrogen override positive effects of phosphorus on grassland legumes worldwide.

Anthropogenic nutrient enrichment is driving global biodiversity decline and modifying ecosystem functions. Theory suggests that plant functional types that fix atmospheric nitrogen have a competitive advantage in nitrogen-poor soils, but lose this advantage with increasing nitrogen supply. By contrast, the addition of phosphorus, potassium, and other nutrients may benefit such species in low-nutrient environments by enhancing their nitrogen-fixing capacity. We present a global-scale experiment confirming these predictions for nitrogen-fixing legumes (Fabaceae) across 45 grasslands on six continents. Nitrogen addition reduced legume cover, richness, and biomass, particularly in nitrogen-poor soils, while cover of non-nitrogen-fixing plants increased. The addition of phosphorous, potassium, and other nutrients enhanced legume abundance, but did not mitigate the negative effects of nitrogen addition. Increasing nitrogen supply thus has the potential to decrease the diversity and abundance of grassland legumes worldwide regardless of the availability of other nutrients, with consequences for biodiversity, food webs, ecosystem resilience, and genetic improvement of protein-rich agricultural plant species.

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

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.

Increasing effects of chronic nutrient enrichment on plant diversity loss and ecosystem productivity over time.

Human activities are enriching many of Earth's ecosystems with biologically limiting mineral nutrients such as nitrogen (N) and phosphorus (P). In grasslands, this enrichment generally reduces plant diversity and increases productivity. The widely demonstrated positive effect of diversity on productivity suggests a potential negative feedback, whereby nutrient-induced declines in diversity reduce the initial gains in productivity arising from nutrient enrichment. In addition, plant productivity and diversity can be inhibited by accumulations of dead biomass, which may be altered by nutrient enrichment. Over longer time frames, nutrient addition may increase soil fertility by increasing soil organic matter and nutrient pools. We examined the effects of 5-11 yr of nutrient addition at 47 grasslands in 12 countries. Nutrient enrichment increased aboveground live biomass and reduced plant diversity at nearly all sites, and these effects became stronger over time. We did not find evidence that nutrient-induced losses of diversity reduced the positive effects of nutrients on biomass; however, nutrient effects on live biomass increased more slowly at sites where litter was also increasing, regardless of plant diversity. This work suggests that short-term experiments may underestimate the long-term nutrient enrichment effects on global grassland ecosystems.

Effects of nitrogen fertilization and bioenergy crop species on central tendency and spatial heterogeneity of soil glycosidase activities.

Extracellular glycosidases in soil, produced by microorganisms, act as major agents for decomposing labile soil organic carbon (e.g., cellulose). Soil extracellular glycosidases are significantly affected by nitrogen (N) fertilization but fertilization effects on spatial distributions of soil glycosidases have not been well addressed. Whether the effects of N fertilization vary with bioenergy crop species also remains unclear. Based on a 3-year fertilization experiment in Middle Tennessee, USA, a total of 288 soil samples in topsoil (0-15 cm) were collected from two 15 m2 plots under three fertilization treatments in switchgrass (SG: Panicum virgatum L.) and gamagrass (GG: Tripsacum dactyloides L.) using a spatially explicit design. Four glycosidases, α-glucosidase (AG), ß-glucosidase (BG), ß-xylosidase (BX), cellobiohydrolase (CBH), and their sum associated with C acquisition (Cacq) were quantified. The three fertilization treatments were no N input (NN), low N input (LN: 84 kg N ha-1 year-1 in urea) and high N input (HN: 168 kg N ha-1 year-1 in urea). The descriptive and geostatistical approaches were used to evaluate their central tendency and spatial heterogeneity. Results showed significant interactive effects of N fertilization and crop type on BX such that LN and HN significantly enhanced BX by 14% and 44% in SG, respectively. The significant effect of crop type was identified and glycosidase activities were 15-39% higher in GG than those in SG except AG. Within-plot variances of glycosidases appeared higher in SG than GG but little differed with N fertilization due to large plot-plot variation. Spatial patterns were generally more evident in LN or HN plots than NN plots for BG in SG and CBH in GG. This study suggested that N fertilization elevated central tendency and spatial heterogeneity of glycosidase activities in surficial soil horizons and these effects however varied with crop and enzyme types. Future studies need to focus on specific enzyme in certain bioenergy cropland soil when N fertilization effect is evaluated.

General destabilizing effects of eutrophication on grassland productivity at multiple spatial scales.

Eutrophication is a widespread environmental change that usually reduces the stabilizing effect of plant diversity on productivity in local communities. Whether this effect is scale dependent remains to be elucidated. Here, we determine the relationship between plant diversity and temporal stability of productivity for 243 plant communities from 42 grasslands across the globe and quantify the effect of chronic fertilization on these relationships. Unfertilized local communities with more plant species exhibit greater asynchronous dynamics among species in response to natural environmental fluctuations, resulting in greater local stability (alpha stability). Moreover, neighborhood communities that have greater spatial variation in plant species composition within sites (higher beta diversity) have greater spatial asynchrony of productivity among communities, resulting in greater stability at the larger scale (gamma stability). Importantly, fertilization consistently weakens the contribution of plant diversity to both of these stabilizing mechanisms, thus diminishing the positive effect of biodiversity on stability at differing spatial scales. Our findings suggest that preserving grassland functional stability requires conservation of plant diversity within and among ecological communities.

Global impacts of fertilization and herbivore removal on soil net nitrogen mineralization are modulated by local climate and soil properties.

Soil nitrogen (N) availability is critical for grassland functioning. However, human activities have increased the supply of biologically limiting nutrients, and changed the density and identity of mammalian herbivores. These anthropogenic changes may alter net soil N mineralization (soil net Nmin ), that is, the net balance between N mineralization and immobilization, which could severely impact grassland structure and functioning. Yet, to date, little is known about how fertilization and herbivore removal individually, or jointly, affect soil net Nmin across a wide range of grasslands that vary in soil and climatic properties. Here we collected data from 22 grasslands on five continents, all part of a globally replicated experiment, to assess how fertilization and herbivore removal affected potential (laboratory-based) and realized (field-based) soil net Nmin . Herbivore removal in the absence of fertilization did not alter potential and realized soil net Nmin . However, fertilization alone and in combination with herbivore removal consistently increased potential soil net Nmin. Realized soil net Nmin , in contrast, significantly decreased in fertilized plots where herbivores were removed. Treatment effects on potential and realized soil net Nmin were contingent on site-specific soil and climatic properties. Fertilization effects on potential soil net Nmin were larger at sites with higher mean annual precipitation (MAP) and temperature of the wettest quarter (T.q.wet). Reciprocally, realized soil net Nmin declined most strongly with fertilization and herbivore removal at sites with lower MAP and higher T.q.wet. In summary, our findings show that anthropogenic nutrient enrichment, herbivore exclusion and alterations in future climatic conditions can negatively impact soil net Nmin across global grasslands under realistic field conditions. This is an important context-dependent knowledge for grassland management worldwide.

Author Correction: Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Geographic variation in the genetic basis of resistance to leaf rust between locally adapted ecotypes of the biofuel crop switchgrass (Panicum virgatum).

Local adaptation is an important process in plant evolution, which can be impacted by differential pathogen pressures along environmental gradients. However, the degree to which pathogen resistance loci vary in effect across space and time is incompletely described. To understand how the genetic architecture of resistance varies across time and geographic space, we quantified rust (Puccinia spp.) severity in switchgrass (Panicum virgatum) plantings at eight locations across the central USA for 3 yr and conducted quantitative trait locus (QTL) mapping for rust progression. We mapped several variable QTLs, but two large-effect QTLs which we have named Prr1 and Prr2 were consistently associated with rust severity in multiple sites and years, particularly in northern sites. By contrast, there were numerous small-effect QTLs at southern sites, indicating a genotype-by-environment interaction in rust resistance loci. Interestingly, Prr1 and Prr2 had a strong epistatic interaction, which also varied in the strength and direction of effect across space. Our results suggest that abiotic factors covarying with latitude interact with the genetic loci underlying plant resistance to control rust infection severity. Furthermore, our results indicate that segregating genetic variation in epistatically interacting loci may play a key role in determining response to infection across geographic space.