Root-associated microbiome of Nicotiana attenuata altered in cell wall features
The plant-associdated 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 cell wall composition, namely cinnamyl alcohol dehydrogenase (irCAD), pectin methyl esterase (irPME), xyloglucan endotransglucosylation (irXTH), and plants altered in ethylene perception (35S-etr1). The lines were grown in two different environments, in a growth chamber and in 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. Based on alpha- and beta-diversity parameters the root-associated microbiome of plants grown under controlled conditions was clearly distinct among the genotypes. The microbiomes of empty vector controls clustered separately from all other lines, while irPME and 35Setr1 as well as irXTH and irCAD root-associated microbiomes formed distinct clusters. The root metabolome pattern matched with the microbiome pattern.  In contrast, roots of field-grown plants showed only a few bacterial taxa to be significantly enriched in specific genotyes, while diversity parameters were not different among the lines. At the metabolite level only plants altered in lignin biosynthesis (irCAD) clustered separately from the other genotypes. Based on these results we conclude that under controlled conditions cell wall biosynthesis metabolism is an important driver of the microbiome assembly, but in complex environments the impact of the genotype on root microbiota is less important.