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Legumes and rhizobial bacteria are, perhaps, the first example of humans using beneficial microbes to increase agricultural yields. In symbiosis with legumes, rhizobia live inside plant organs called nodules and provide plant accessible nitrogen in exchange for carbon resources. While there is massive scientific and industry interest in leveraging plant-microbe relationships to reduce inputs and increase crop resilience (Busbyet al., 2017; Tojuet al., 2018), there are many barriers to widespread implementation, including a failure of inoculants to survive and compete in agricultural soils (Thieset al., 1991; Chibebaet al., 2017; Kaminskyet al., 2019) and the repeated loss of mutualistic benefits over time (Klingeret al., 2016). These barriers may stem from the rapid evolution of microbes and the facultative nature of this mutualism. Rhizobia do not always live in symbiosis with plants, and the majority of the population at any given time lives in the soil or root rhizosphere (Denison & Kiers, 2004; Pooleet al., 2018).Likewise, because the symbiosis is re-established each generation, microbes are exposed to seasonal variation of abiotic factors and a diversity of biotic partners (Heath & Stinchcombe, 2014; Burghardt, 2020). Most agricultural rhizobial research remains centered on plant benefits, but decades of evolutionary theory and data indicate that both sides must benefit for the relationship to persist. Here I aim to 1) identify the genetic determinants of legume x rhizobial interactions, 2) measure the sensitivity of rhizobial-legume interactions to abiotic and biotic environmental variation, and 3) establish methodologies to measure ecological and evolutionary processes in agricultural fields. By focusing on the rapid evolutionary potential and ecological complexity of the rhizobia life cycle, my research program aims to generate the foundational knowledge necessary to flip the script and manage legume-rhizobial mutualisms for long-term sustainability and resilience to environmental stressors.Objective1: Identify legume/rhizobia genes underlying genome x genome interactions and mutualism success by conducting Select & Resequence (S&R) experiments using three types of host genetic variation:Medicago truncatula symbiosis mutantsMedicago truncatula HapMap GWAS panelMedicago sativa public and commercial testvarietiesA panel of Medicago HapMap speciesObjective2: Assess the environment-dependence (abiotic and biotic) of legume-rhizobia interactions measured in terms of rhizobial strain fitness, root and nodule traits, nitrous-oxide production, and legume productivityConduct S&Rexperiments that manipulate key environmental variations (e.g., temperature, salt, moisture, and pH)Collect a time course of Medicago root exudates in response to environmental stresses and across plant developmental stages (e.g., N or P limitation). Here, I will test the extent to which different root exudates shift rhizobial strain competition.Assess the effect of adding additional microbial community members (e.g., AMF, Bacillus, nematodes) on strain competition outcomes in nodulesObjective3: Translate the S&Rmethodology and nodule phenotyping to agricultural fields to measure how host genetic variation, seasonal variation, and crop-rotation systems influence rhizobial strain success and evolutionary dynamicsUse the Penn State Universityalfalfa varietal trial to 1) measure rhizobial allele frequencies, root and nodule phenotypes across seasons and years and 2) create a bacterial strain collection from local Medicago rhizosphere and nodule samplesAssess rhizobial partner-cycling between legume cover crops and legume cash crops in a long-term cover-crop mixture experiment at Pennsylvania State University Rock Creek Experimental Station

Burghardt, Li, T.
Pennsylvania State University
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