Local adaptation and genetic divergence in the dominant grass Andropogon gerardii across the Great Plains’ rainfall gradient

Doctor of PhilosophyDepartment of BiologyLoretta C JohnsonMany prior studies have uncovered evidence for local adaptation using reciprocal transplant experiments. However, these studies are rarely conducted for a long enough time to observe succession and competitive dynamics in a community context, limiting inferences for long-lived species. Furthermore, most studies lack comprehensive investigation with only few responses or measurements included, and lack integrative studies combining both ecology and genomics. Here, we report on a long-term experiment focused on Andropogon gerardii, the dominant grass of the North American Great Plains tallgrass ecosystem. Our approach used a reciprocal garden platform in which four reciprocal garden sites were planted with three regional ecotypes of Andropogon gerardii, using dry, mesic, and wet ecotypes originating from western KS to Illinois that span 500–1,200 mm rainfall/year. We focus on this foundation grass that comprises 80% of tallgrass prairie biomass, is a major forage grass for cattle, and is widely used in restoration. First, we aimed to assess genetically based local adaptation of A. gerardii ecotypes in realistic competitive settings. We addressed the following questions: 1) Do ecotypes display local adaptation to regional climate when planted in realistic ecological communities? 2) Does adaptive genetic variation underlie divergent phenotypes? 3) Do we see evidence of local adaptation if the plants are exposed to competition among ecotypes of A. gerardii in mixed ecotype plots? 4) Is local adaptation related to climate gradients? We demonstrate local adaptation and differentiation of ecotypes in wet and dry environments. Surprisingly, the apparent generalist mesic ecotype performed comparably under all rainfall conditions. Ecotype performance was underpinned by differences in neutral diversity and candidate genes corroborating strong differences among ecotypes. Ecotype differentiation was related to climate, primarily rainfall. Second, we used the reciprocal gardens in plants growing singly without competition to detect genetic and environmental plasticity effects on phenotypic variation and combined with genetic analyses. The goal was to evaluate the extent to which A. gerardii ecotypes differ across spatially varying climatic regions, thus potentially signaling local specialization, i.e., genetic differentiation and adaptation of ecotypes to precipitation. Here we addressed the following questions: 1) Are A. gerardii ecotypes locally adapted to environment across the precipitation gradient? 2) What is the relative role of genetic constraints and plasticity in controlling phenotypic differences? 3) How will different ecotypes of A. gerardii respond under different climatic conditions, especially precipitation, when planted in home environment and reciprocally transplanted into foreign environments? 4) What are the underlying genetic bases for these traits? 5) How are genotypes and phenotypes structured by climate? Surprisingly, we did not detect consistent local adaptation. Rather, we detected co-gradient variation primarily for most vegetative responses. All ecotypes were stunted in western KS. Eastward, the wet ecotype was increasingly robust relative to other ecotypes. In contrast, fitness showed evidence for local adaptation in wet and dry ecotypes with wet and mesic ecotypes producing little seed in western KS. Earlier flowering time in the dry ecotype suggests adaptation to end of season drought. The wet ecotype was robust, tall with high biomass, and wide leaves putatively adapted for the highly competitive, light-limited Eastern Great Plains. We detected genetic differentiation and outlier genes associated with primarily precipitation. We identified candidate gene GA1 for which allele frequency associated with plant height. Sourcing of climate adapted ecotypes should be considered for restoration. Finally, we aimed to determine to what extent this ecologically-important prairie grass, big bluestem, responds to environmental change, both ecologically and transcriptionally through expression of genes. Here we aimed to answer: 1) Do bluestem ecotypes growing across a longitudinal precipitation gradient transcribe a different suite of genes or show differential expression levels of the same genes in response to environment? 2) Is the local ecotype of big bluestem more transcriptionally responsive in its home environment? and 3) How does an ecologically important grass respond ecologically and at the level of its transcriptome to a drier or wetter environment at the margin of its range? Without long-term studies, wrong conclusions would have been reached based on insufficient data. Ultimately, restoring and conserving prairies with climate-matched ecotypes is critical to future ecology, conservation, and sustainability of these vital grasslands under climate change

Genetic and environmental influences on stomates of big bluestem (Andropogon gerardii)

Big bluestem (Andropogon gerardii) is a dominant C4 prairie grass that has wide distribution and several genetically distinct ecotypes. Many of the ecotypic adaptations are related to water availability in the native environment. Stomates facilitate photosynthetic gas exchange and regulate water loss from the plant. As such, stomatal size and density represent possible adaptations to conserve water. We hypothesized drought-tolerant ecotypes of big bluestem would have fewer or smaller stomates compared to more mesic ecotypes. Five ecotypes of big bluestem were planted in four common gardens from western Kansas to southern Illinois, USA to determine genetic and environmental influences on stomates. Leaves of all ecotypes of A. gerardii were largely hypostomatous and genetics was a greater influence than environment for stomatal size and density. The drought-tolerant Sand bluestem had larger stomates on abaxial surfaces of leaves, but a lower density compared to most other ecotypes. The most mesic Illinois ecotype and the Kaw cultivar had the greatest density of stomates on abaxial surfaces of leaves. Sand Bluestem had a greater density of stomates on adaxial surfaces of leaves compared to all other ecotypes. Gas exchange measures followed patterns of stomate distribution, where abaxial CO2 uptake rates were greater than adaxial CO2 uptake rates, although differences between leaf surfaces was more pronounced in stomatal density than in CO2 uptake. There were minor differences in size and density of stomates among sites that corresponded with precipitation, although these differences were minor, illustrating the genetic underpinnings of stomates in big bluestem. There is a genetic predisposition for drought-tolerant ecotypes to have fewer stomates, illustrating an evolutionary adaptation to drought tolerance in an important prairie species

Local adaptation, genetic divergence, and experimental selection in a foundation grass across the US Great Plains’ climate gradient

Many prior studies have uncovered evidence for local adaptation using reciprocal transplant experiments. However, these studies are rarely conducted for a long enough time to observe succession and competitive dynamics in a community context, limiting inferences for long-lived species. Furthermore, the genetic basis of local adaptation and genetic associations with climate has rarely been identified. Here, we report on a long-term (6-year) experiment conducted under natural conditions focused on Andropogon gerardii, the dominant grass of the North American Great Plains tallgrass ecosystem. We focus on this foundation grass that comprises 80% of tallgrass prairie biomass and is widely used in 20,000 km 2 of restoration. Specifically, we asked the following questions: (a) Whether ecotypes are locally adapted to regional climate in realistic ecological communities. (b) Does adaptive genetic variation underpin divergent phenotypes across the climate gradient? (c) Is there evidence of local adaptation if the plants are exposed to competition among ecotypes in mixed ecotype plots? Finally, (d) are local adaptation and genetic divergence related to climate? Reciprocal gardens were planted with 3 regional ecotypes (originating from dry, mesic, wet climate sources) of Andropogon gerardii across a precipitation gradient (500–1,200 mm/year) in the US Great Plains. We demonstrate local adaptation and differentiation of ecotypes in wet and dry environments. Surprisingly, the apparent generalist mesic ecotype performed comparably under all rainfall conditions. Ecotype performance was underpinned by differences in neutral diversity and candidate genes corroborating strong differences among ecotypes. Ecotype differentiation was related to climate, primarily rainfall. Without long-term studies, wrong conclusions would have been reached based on the first two years. Further, restoring prairies with climate-matched ecotypes is critical to future ecology, conservation, and sustainability under climate change

Adaptive genetic potential and plasticity of trait variation in the foundation prairie grass Andropogon gerardii across the US Great Plains’ climate gradient: Implications for climate change and restoration

Plant response to climate depends on a species’ adaptive potential. To address this, we used reciprocal gardens to detect genetic and environmental plasticity effects on phenotypic variation and combined with genetic analyses. Four reciprocal garden sites were planted with three regional ecotypes of Andropogon gerardii, a dominant Great Plains prairie grass, using dry, mesic, and wet ecotypes originating from western KS to Illinois that span 500–1,200 mm rainfall/year. We aimed to answer: (a) What is the relative role of genetic constraints and phenotypic plasticity in controlling phenotypes? (b) When planted in the homesite, is there a trait syndrome for each ecotype? (c) How are genotypes and phenotypes structured by climate? and (d) What are implications of these results for response to climate change and use of ecotypes for restoration? Surprisingly, we did not detect consistent local adaptation. Rather, we detected co-gradient variation primarily for most vegetative responses. All ecotypes were stunted in western KS. Eastward, the wet ecotype was increasingly robust relative to other ecotypes. In contrast, fitness showed evidence for local adaptation in wet and dry ecotypes with wet and mesic ecotypes producing little seed in western KS. Earlier flowering time in the dry ecotype suggests adaptation to end of season drought. Considering ecotype traits in homesite, the dry ecotype was characterized by reduced canopy area and diameter, short plants, and low vegetative biomass and putatively adapted to water limitation. The wet ecotype was robust, tall with high biomass, and wide leaves putatively adapted for the highly competitive, light-limited Eastern Great Plains. Ecotype differentiation was supported by random forest classification and PCA. We detected genetic differentiation and outlier genes associated with primarily precipitation. We identified candidate gene GA1 for which allele frequency associated with plant height. Sourcing of climate adapted ecotypes should be considered for restoration

Pseudomonas cultivated from Andropogon gerardii rhizosphere show functional potential for promoting plant host growth and drought resilience

Abstract Background Climate change will result in more frequent droughts that can impact soil-inhabiting microbiomes (rhizobiomes) in the agriculturally vital North American perennial grasslands. Rhizobiomes have contributed to enhancing drought resilience and stress resistance properties in plant hosts. In the predicted events of more future droughts, how the changing rhizobiome under environmental stress can impact the plant host resilience needs to be deciphered. There is also an urgent need to identify and recover candidate microorganisms along with their functions, involved in enhancing plant resilience, enabling the successful development of synthetic communities. Results In this study, we used the combination of cultivation and high-resolution genomic sequencing of bacterial communities recovered from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. Phylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified a bacterial genome of interest – MAG-Pseudomonas. Further metabolic pathway and pangenome analyses recovered genes and pathways related to stress responses including ACC deaminase; nitrogen transformation including assimilatory nitrate reductase in MAG-Pseudomonas, which might be associated with enhanced drought tolerance and growth for Andropogon gerardii. Conclusions Our data indicated that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant host’s growth during stressful conditions. Our study also suggested the nitrogen transformation potential of MAG-Pseudomonas that could impact Andropogon gerardii growth in a positive way. The cultivation of MAG-Pseudomonas sets the foundation to construct a successful synthetic community for Andropogon gerardii. To conclude, stress resilience mediated through genes ACC deaminase, nitrogen transformation potential through assimilatory nitrate reductase in MAG-Pseudomonas could place this microorganism as an important candidate of the rhizobiome aiding the plant host resilience under environmental stress. This study, therefore, provided insights into the MAG-Pseudomonas and its potential to optimize plant productivity under ever-changing climatic patterns, especially in frequent drought conditions

Tallgrass prairie phylogeny and functional traits along a longitudinal gradient

Community phylogeny, functional traits of grassland species, and model building data and code for GLMMs and GLMs which can be used to access grassland biodiversity.  </p

Additional file 1: Table S1. of Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii

Number of high quality reads by ecotype and population for 454 and HiSeq platforms. Figure S1. Workflow diagram of transcriptome assembly pipeline. Figure S2. Cumulative length of sequences and number of sequences for various k-mer values, 454 data, and the combined 454 and HiSeq data. Figure S3. N values for various k-mers and MIRA 454 and MIRA clustered assemblies. Figure S4. Ortholog hit ratio for final MIRA clustered assembly. OHR is the length of the BLASTX hit region divided by the length of the protein, in our case using the S. bicolor database. OHR is an estimate of the percent of the full length protein sequence represented in the assembly. An OHR of 1 indicates a potential full length transcript. (DOCX 230 kb

Bacterial but Not Fungal Rhizosphere Community Composition Differ among Perennial Grass Ecotypes under Abiotic Environmental Stress

Environmental change, especially frequent droughts, is predicted to detrimentally impact the North American perennial grasslands. Consistent dry spells will affect plant communities as well as their associated rhizobiomes, possibly altering the plant host performance under environmental stress. Therefore, there is a need to understand the impact of drought on the rhizobiome, and how the rhizobiome may modulate host performance and ameliorate its response to drought stress. In this study, we analyzed bacterial and fungal communities in the rhizospheres of three ecotypes (dry, mesic, and wet) of dominant prairie grass, Andropogon gerardii. The ecotypes were established in 2010 in a common garden design and grown for a decade under persistent dry conditions at the arid margin of the species’ range in Colby, Kansas. The experiment aimed to answer whether and to what extent do the different ecotypes maintain or recruit distinct rhizobiomes after 10 years in an arid climate. In order to answer this question, we screened the bacterial and fungal rhizobiome profiles of the ecotypes under the arid conditions of western Kansas as a surrogate for future climate environmental stress using 16S rRNA and ITS2 metabarcoding sequencing. Under these conditions, bacterial communities differed compositionally among the A. gerardii ecotypes, whereas the fungal communities did not. The ecotypes were instrumental in driving the differences among bacterial rhizobiomes, as the ecotypes maintained distinct bacterial rhizobiomes even after 10 years at the edge of the host species range. This study will aid us to optimize plant productivity through the use of different ecotypes under future abiotic environmental stress, especially drought

Ecotypes of an ecologically dominant prairie grass (\u3ci\u3eAndropogon gerardii\u3c/i\u3e) exhibit genetic divergence across the U.S. Midwest grasslands’ environmental gradient

Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation by distance (IBD) vs. isolation by environment (IBE) on ecotype divergence, (iii) identify outlier loci under selection and (iv) assess the association between outlier loci and climate. Using two primer sets, we genotyped 378 plants at 384 polymorphic AFLP loci across regional ecotypes from central and eastern Kansas and Illinois. Neighbour-joining tree and PCoA revealed strong genetic differentiation between Kansas and Illinois ecotypes, which was better explained by IBE than IBD. We found high genetic variability within prairies (80%) and even fragmented Illinois prairies, surprisingly, contained high within-prairie genetic diversity (92%). Using BAYENV2, 14 topranked outlier loci among ecotypes were associated with temperature and precipitation variables. Six of seven BAYESCAN FST outliers were in common with BAYENV2 outliers. High genetic diversity may enable big bluestem populations to better withstand changing climates; however, population divergence supports the use of local ecotypes in grassland restoration. Knowledge of genetic variation in this ecological dominant and other grassland species will be critical to understanding grassland response and restoration challenges in the face of a changing climate

Data from: Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands environmental gradient

Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study the nature of population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation-by-distance (IBD) vs. isolation-by-environment (IBE) on ecotype divergence, (iii) identify outlier loci under selection, and (iv) assess the association between outlier loci and climate. Using two primer sets, we genotyped 378 plants at 384 polymorphic AFLP loci across regional ecotypes from central and eastern Kansas, and Illinois. Neighbor-joining tree and PCA revealed strong genetic differentiation between Kansas and Illinois ecotypes, which was better explained by IBE than IBD. High genetic variability within prairies was found (80%) and even fragmented Illinois prairies, surprisingly, contain high within-prairie genetic diversity (92%). Using Bayenv2, we identified 14 top-ranked outlier loci among ecotypes to be associated with temperature and precipitation variables. Six of seven BayeScan FST-outliers were also found in common with Bayenv2 outliers. High genetic diversity may enable big bluestem populations to better withstand changing climates; however, population divergence supports the use of local ecotypes in grassland restoration. Knowledge of genetic variation in this ecological dominant and other grassland species will be critical to understanding grassland response and restoration challenges in the face of a changing climate