Introduction
Plants have evolved alongside microbes for millions of years and have formed intricate relationships with soil microbial communities via their root systems. Soil microbial community composition is shaped by soil abiotic conditions and varying soil types contain microbiomes with distinct taxonomic distributions (Fierer 2017; Hartman & Tringe 2019). Plant host genetics also drive the assembly of rhizosphere and endosphere microbial communities (Jones et al. 2019; Trivedi et al. 2020), and crop varieties or natural ecotypes (or genotypes) grown in a common environment can differ in root and rhizosphere community structure (Bowsher et al. 2020; Li et al. 2018; Perez-Jaramillò et al. 2017; Wagner et al. 2016). To some degree, the root microbiome can be thought of as an extended phenotype of the plant. Plant-soil-microbiome relationships can influence plant traits and there is strong evidence that microbes can yield positive effects on plant performance directly or indirectly by impacting plant functional traits (Egamberdieva et al. 2017; Lau & Lennon 2012; Wagner et al. 2014) or negatively as pathogens. Plant root associated microbiomes impact root traits, can increase nutrient acquisition, provide indirect impacts on shoot traits (such as increasing shoot biomass) and promote tolerance to abiotic and biotic stress (Friesen et al. 2011; Mendes et al.2013; Santhanam et al. 2015; Sukumar et al. 2013). In synthetic community research, growing the same genotype in the presence or absence of differing sets of selected microbiomes produces a wide range of plant trait modulation (De Souza et al. 2020; Vorholt et al. 2017). Given the growing evidence of microbial effects on plant growth and development, it’s possible that plant microbial interactions also play a role in the process of local adaptation, where plant populations diverge and exhibit different niche characteristics and habitat preferences (Petipas et al. 2021).
Many plant species are composed of highly varied ecotypes across their range, each of which may show a high degree of trait divergence. Quantitative traits can be profoundly influenced by environmental factors and the degree to which these factors influence plant traits can vary widely across genotypes. These types of interactions are termed genotype-by-environment interaction (GxE; Des Marais et al. 2013). Many studies focus on local adaptation and GxE in response to changing habitats or conditions (Leimu & Fischer 2008; Midolo & Wellstein 2020), however, the relative contribution of abiotic and biotic factors in driving GxE is often unclear (Runquist et al. 2020). Plants encounter diverse biotic factors including competition, herbivory, pathogens and an array of microbial communities (Bischoff et al. 2006; Järemo et al. 1999), but little is known about how specific interactions between plants and microbial communities contribute to adaptation. Numerous quantitative trait loci (QTL) mapping studies have explored the genetic architecture of GxE in natural and crop populations for a number of abiotic factors and this approach has become widely utilized to study plant responses to abiotic stress and to understand plant trait plasticity (Des Marais et al. 2016; Vij & Tyagi 2007). Far less is known about the influence of biotic factors, especially microbiomes. Additional experimental studies exploring the impact of microbial communities are critically needed to fully elucidate aspects of plant-microbe interactions and local adaptation.
Panicum hallii is a diploid, C4, self-fertilizing, North American native perennial bunch grass that occurs across a large geographical range with diverse habitats and climate. There are two naturally occurring ecotypes of P. hallii that are classified as separate varieties: an upland xeric ecotype, P. hallii var. hallii(hereafter referred to as hallii ) and a lowland mesic ecotype,P. hallii var. filipes (hereafter referred to asfilipes ). These ecotypes display trait divergence in a similar direction and magnitude to other perennial grass species with upland and lowland ecotypes, a pattern which is thought to be driven by adaptive evolution along precipitation gradients across a species range (Gray et al. 2014; Khasanova et al. 2019; Lowry et al. 2014). Many observations have shown that both ecotypes of P. hallii display a large degree of plasticity in several shoot traits in response to changes in abiotic factors including light (Weng et al. 2019) and precipitation (Lovell et al. 2018), yet these differences are minor in comparison to the differences inherent between the ecotypes. Compared to abiotic factors, little is known about the importance or relative contribution of biotic environmental variation, especially soil microbiota, in shaping plant shoot and root traits in the P. hallii system and plants in general.
Here, we conducted a quantitative genetic experiment to examine the impact of soil microbiomes and host genetics on root and shoot traits. A recombinant inbred population (RIL) derived from a cross between the upland and lowland ecotypes of P. hallii allowed us to identify plant genomic regions contributing to microbial-mediated traits. To overcome the limitations of synthetic community approaches and the complexity of natural soils, we took a hybrid approach of inoculating sterilized soils with naturally derived microbial communities in a greenhouse setting. Specifically, we sought to answer four questions: 1) Does the native soil microbiome drive plasticity in P. halliiabove- and below-ground traits? 2) Are microbiome effects general, or specifically related to the location of origin of the microbiome? 3) DoP. hallii ecotypes exhibit GxE in response to variable soil microbiomes? And, 4) Can we map genetic effects and their interactions with the microbiome to the genome? Overall, our experiment demonstrates the impact of living soil microbiomes on the quantitative genetic architecture of both root and shoot traits in P. hallii and highlights the potential importance of microbiomes in local adaptation.