There is an urgent need to address challenges with environmental degradation and climate change in our agricultural landscapes, and the solution may lie with soil microbes. The soil microbes living in close association with plant roots, in the rhizosphere, play a central role in nutrient cycling, carbon sequestration, and plant growth and, therefore have significant promise for agriculture. Compared to annual crops, perennial cropping systems, such as those used for cellulosic bioenergy, do more for addressing carbon sequestration and soil health. However, to harness the benefits of microbes in these systems, we need to first understand the primary factors impacting their assembly. Many studies show microbial assembly is largely mediated by the plant host, but these studies often focus on isolated plants, and do not consider how neighboring plant interactions may also alter microbiome assembly. Furthermore, for soil biology to be an agricultural solution it is also essential that their benefits are clear and align with farmers' management goals. Studies show that farmers value soil biology and soil health more broadly, but how this guides their management decisions is unknown. To this end, in my dissertation, I use microbial ecology (Chapters 1-3) and social science (Chapter 4), to investigate how plant-microbial interactions and farmer perspectives can be harnessed for sustainable agriculture.In my first three chapters I examine how switchgrass (Panicum virgatum L.), a candidate bioenergy crop, mediates the assembly of its root and rhizosphere microbiome, considering two factors: genotype and neighborhood context. In Chapter 1 I asked if, like plant species, plant genotypes also associate with distinct microbiomes. Using an established field experiment with twelve mature switchgrass cultivars, I found that genotypes have subtle, though significant effects on their rhizosphere microbiomes, and that root traits contribute to this variation. Next, in Chapters 2 and 3, I asked if and how a host plant's microbiome changes with different neighbor plants. To do this, I used two different greenhouse experiments where a focal switchgrass plant was neighbored by different species. In Chapter 2, I show that neighbor identity explains 21% of the variation in the focal plant's rhizosphere community. Changes in the focal plant's root exudates, as well as spillover of microbes from a larger, more competitive neighbor, contributed to the microbiome shifts. In Chapter 3, I disentangle the relative role of microbial spillover versus the host plant in mediating the previously observed neighborhood effects by using specialized plant growth systems called rhizoboxes with root barriers. Here, neighbor identity altered the root microbiomes, but not rhizosphere communities, which also did not differ among the plant species. These results suggest that the host plant does play a role in mediating neighborhood effects in the roots, but shifts in the rhizosphere depend upon each neighbor species harboring a distinct microbiome in the first place. My first three chapters show that there is not one switchgrass microbiome, and that microbial assembly is influenced by plant genotype and neighborhood context. Both factors should be considered as we seek to understand plant-microbial studies in natural settings.Finally, in Chapter Four, I ask how farmers perceive, evaluate, and understand soil health. Using surveys and interviews I found that Michigan farmers have a complex understanding of soil health, and that soil biology is a top consideration, but that it is challenging for farmers to link this knowledge to management decisions. The interviews also revealed several salient research and outreach opportunities that could help farmers more intentionally fit soil health into their management decisions, such as identifying faster-responding indicators of soil biological health or discussing soil health in terms that resonate with farmers' mental models. Altogether, my dissertation shows how mechanistic studies and farmer perspectives each provide novel insights for the potential role of soil biology in sustainable agriculture.
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