Host selection shapes Miscanthus microbiome assembly and network complexity

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Niuniu Ji, Di Liang and Angela Kent, DOE Center for Advanced Bioenergy & Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, Angela Kent, Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, Angela Kent, University of Illinois at Urbana-Champaign

Background/Question/Methods
Plants are inhabited by diverse microbes in every compartment, including root, stem, leaf, flower, and fruit. The plant microbiome contributes functions to support host health and productivity. Harnessing the plant microbiome is increasingly considered as a viable approach to improve the sustainability of crop production. One of the prerequisites for the development of such effective technologies is to improve the fundamental understanding of ecological processes that govern microbiome assembly. Miscanthus is a genus of perennial rhizomatous C4 grass originating from East Asia with great capacity for adapting to various climates and soil conditions for production as a bioenergy feedstock. Miscanthus provides microorganisms with multiple microhabitats (e.g. rhizosphere and endophytic compartments). However, little work has been done to evaluate microbiome assembly along the soil-plant continuum. Identifying the extent to which host genotypes and edaphic factors influence assembly or function of the host-associated microbiome could provide us with novel methods to manage and understand the plant microbiome. DNA sequencing was used to characterize bacterial and fungal assemblages from endophyte and rhizosphere soil samples in two species: Miscanthus sinensis and Miscanthus floridulus collected from diverse habitats across Taiwan, to test the effect of host and environment on rhizosphere and endophyte microbiome.
Results/Conclusions
From natural Miscanthus populations sampled across diverse soil environments, we found the relative importance of host genotype and edaphic factors for assembly of the Miscanthus microbiome shifted between rhizosphere soil and endophytic compartment. The endophyte bacterial and fungal assembly were mainly affected by host genetics (bacteria, R2 = 0.988, p = 0.002; fungi, R2 = 0.618, p = 0.001). In contrast, composition of the rhizosphere bacteria was determined by soil factors (pH, R2 = 0.238, p = 0.001; soil moisture, R2 = 0.012, p = 0.001; Total N, R2= 0.043, p = 0.001). We also found the microbial diversity and network complexity decreased with increasing host effect. These data suggest host selection is stronger for the endophytic microbiome. In addition, rhizosphere bacterial communities were enriched for functions involved in biogeochemical cycling processes, while endophyte bacterial communities were enriched for biosynthesis functions. Rhizosphere fungal communities were primarily saprotrophs, plant pathogens, and parasites, while endophyte fungal communities were mainly assigned to endophyte and plant pathogen guilds. Results of this study have implications for future crop management and bioenergy feedstock development.