Investigation of Miscanthus associated microbiome: effects of biotic and abiotic factors

Long-term sustainable production of biofuel feedstock crops like Miscanthus species requires minimum anthropogenic energy inputs as well as the maintenance of soil fertility. Beneficial microbes, such as nitrogen-fixing bacteria, contribute to plant yield and fitness, representing under-explored plant nutrient sources. Optimizing the positive interactions between Miscanthus species and associated bacteria has high potential to support sustainable crop production. Bacterial community functions are directly related to community structures, which rely on surrounding biotic and abiotic factors. Therefore, before Miscanthus-bacteria interactions can be optimized for better plant productivity, it is necessary to investigate the factors that regulate community assemblage of these microbes. The goal of this dissertation is to identify factors that significantly explain the Miscanthus-associated bacterial community variation. To achieve this goal, a combination of observational and experimental approaches was used. Miscanthus plants were collected from native, naturalized and cultivated habitats. These habitats represent a broad range of biotic and abiotic factors. Both Miscanthus endophytic compartment (rhizomes) and their surrounding rhizosphere soil were collected from each plant because both endophytes and rhizosphere bacteria are known to contribute to mutualistic plant-microbe interactions. Here, I accessed and compared both endophytic and rhizosphere bacterial communities, and evaluated whether plant genotypes and soil edaphic factors may influence them differently. As one of the most important beneficial bacteria groups, Miscanthus-associated diazotrophs assemblages were also examined in this work. I found endophytic and rhizosphere communities correlated differently with their surrounding environment. Overall, I found that endophytic communities were more likely to be genotype-specific than the rhizosphere bacteria while the rhizosphere communities tended to change when soil conditions changed. The effect of agricultural practices could be hard to maintain and not significantly change microbial communities. Therefore, the goal of optimizing rhizosphere communities by changing soil conditions cannot be achieved easily. Instead, Miscanthus-associated endophytes are relatively stable to environmental change, and I identified some key endophytic-enriched taxa were shared among Miscanthus sites at a global scale. Hence, facilitate beneficial taxa to colonize Miscanthus endophytic compartment during rhizome propagation or pre-treatment of Miscanthus seeds with beneficial strains may be effective strategies to enhance the mutualism between Miscanthus and bacteria. Even closely related Miscanthus genotypes tended to harbor very different endophytic N-fixing bacteria. On one hand, this result indicates the possibility of identifying plant genetic markers that control endophytic bacteria recruitment. On the other hand, the contribution of beneficial bacteria to Miscanthus must be evaluated on a genotype-by-genotype basis. I observed many highly similar bacteria taxa from sites located on different sides of the world, indicating plant-associated taxa might not be dispersal limited. However, the interconnections between bacteria species are context-depend. Miscanthus-associated bacterial taxa were much more tightly connected with each other in the native sites than in the naturalized sites. This result indicates that the presence of similar bacteria taxa does not necessarily lead to similar functions. Understanding the plant microbiome assemblage is simply the first step exploring the plant-bacteria interactions. This work contributes to our knowledge of the plant-associated microbiome, which provides guidance for optimizing Miscanthus-microbe interactions for the long-term sustainable cultivation of Miscanthus species