Abstract
Interest in the study of the plant microbiome has grown dramatically over the last few decades. Plants harbor rich microbial communities that impact their phenotype in many
ways, including protection against pathogens. The study of functional traits of symbionts, like host range, and the genetic and ecological factors that drive their evolution, is fundamental to understanding plant-symbiont interactions. The existence of across-host fitness trade-offs is predicted to favor the evolution of specialism, but ecological factors like ecosystem heterogeneity can shift the balance in favor of generalism. Furthermore, symbiont-symbiont interactions affect plant-symbiont interactions and can modulate host range. In this work, data from 312 HTS libraries of 118 plants species from different communities in four ecologically distinct habitats in a heterogenous landscape were used to characterize the bacterial communities associated to plants and the effect ecological factors had on their functional traits. A list of more than 500 bacteria that have been found in plants was used to build a bacterial genome reference database for bacterial RNA sequence detection. Analysis of plant-bacteria and bacteria-virus bipartite networks allowed the characterization of their interactions and the identification of species likely to be involved in disease emergence. Plants hosted
characteristic bacterial communities in each habitat, with those of wild habitats being more diverse than those of cropland. Bacteria detected ranged from specialists to
generalists. Generalism was predominant at the landscape-level and in wild habitats, while specialism prevailed in cropland. The edge habitat included most of the plants,
bacteria, generalists, and interactions observed in the ecosystem, so it was proposed to act as a reservoir community of bacteria for the other habitats. The cropland habitat was the most simplified, with few bacteria and low connectivity, possibly as a result of human intervention. Nested and modular network architectures were found both at the landscape level and in every habitat. Modularity of the landscape network had a spatial component, with a strong role of the edge habitat in defining the modules, and a minor taxonomic component. Bacteria and viruses showed multiple non-random associations, most of them positive. The results obtained suggest that ecological changes brought
about by agriculture cause a simplification of bacterial communities that may lead to increased disease risk. The edge habitat, however, acts as a reservoir of bacterial
diversity and may initiate disease emergence. The relation found between habitat complexity and the predominance of specialism or generalism confirms theoretical predictions on host range evolution.
