Relative contribution of genetics, environments, and GxE interactions on Maize Stalk Endophyte

Plant-associated microbes can benefit their host plant by supplying vital nutrients, manipulating hormone levels, and producing secondary metabolites. There has been great interest in harnessing these interactions to improve agriculture; however, most microbes that show early promise fail to translate to field settings. Although there are likely several reasons for this, one key aspect is that the interactions between plants and microbes likely vary across different host genetics and different environments. However, the degree to which this happens is largely unknown. To understand the environmental context of plant-microbe interaction, we sampled stalks from 20 specific maize hybrids across 12 locations in 2019. After quantifying the bacterial endophyte community in each sample, we determined the relative contribution of host genotype, environment, and gene-by-environment (GxE) interactions in determining the makeup of these communities. We find large effects of both the environment and GxE on the overall community composition and also on individual taxa. Host genotype, meanwhile, had little to no consistent effects across environments, and these patterns hold for predicted metabolic pathways. Connecting the microbial community with environmental factors identified soil pH as a major correlate of the endophyte community, with soil potassium and cumulative rainfall also affecting it. These results are among the first to look at the contribution of genetics, environments, and GxE interactions to maize endophytes. Our results indicate that while host genetics does affect the stalk community, its effects are wholly dependent on interactions with the environment. The environment thus appears to be the major factor shaping these endophyte communities, with genetics playing a modulating role. Given that GxE interactions are still significant, however, prediction of how these communities will behave in novel hosts and/or environments could be extremely difficult.