Root-associated microbiome of plants altered in cell wall features - growth chamber samples

The plant-associated microbiome is shaped by a complex interaction between plant genotype and environment. It was hypothesized that the composition of the plant cell wall is one important factor structuring the root microbial communities. To experimentally test this hypothesis we used transgenic lines of Coyote tobacco plants (Nicotiana attenuata) silenced in different genes relevant for the cell wall composition or chemistry, namely cinnamyl alcohol dehydrogenase (irCAD), pectin methyl esterase (irPME), xyloglucan endotransglucosylation (irXTH), rapid alkalinization factor (irRALF) and plants altered in ethylene perception (35S-etr1). The lines were grown in a growth chamber in soil from the plant's native habitat in Utah, USA. We characterized the root-associated microbiome by amplicon sequencing and analyzed the metabolome of the same samples.