Fig. 6

Experimental design. a Soil domestication study: rhizospheres and endospheres of rice plants grown in two domesticated and two uncultivated soils were 16S rRNA gene profiled to understand how soil cultivation history affects root microbiome assembly. Additionally, unplanted bulk soils were sampled to characterize the inherent compositional differences between soil types. Both planted and unplanted potted soils were kept under submergence in a controlled greenhouse setting. b Native plant study: rhizospheres and endospheres of rice (Oryza sativa), mudplantain (Heteranthera limosa), sedge (Cypeus iria), and redstem (Ammania coccinea) were 16S rRNA gene profiled to explore differences between a monoculture crop and native plant species grown in the same flooded rice paddy. Additionally, bulk soil samples were collected to understand the compositional relationship of their associated communities to those acquired by the conspecific plant (rice) and the other hosts. c Seedling vigor study: rice plants were grown in a common substrate treated with microbial inocula derived from domesticated, uncultivated, or intermediate soils in order to analyze the effect of soil microbiomes with distinct cultivation histories on plant growth. As a control, plants were grown in substrate treated with corresponding sterilized inocula in order to account for any residual abiotic variation. Additionally, the endospheres of a subset of plants were 16S rRNA gene profiled to assess community structure. In all panels, tables under each graphic represent the number of replicates sequenced for each treatment/sample type combination. BS, RS, and ES stand for bulk soil, rhizosphere, and endosphere communities, respectively; ES1 and ES2 represent endosphere communities collected from the first or second seedling vigor experiment, respectively. In all cases, NA stands for not applicable