Studies of plant root-associated microbiomes have revealed high diversity along with signature host species-specific and niche-specific associations. The functional implications (ecosystem, plant health) of these associations remain unexplained, however. We have sampled soil and roots of wheat and cucumber plants growing in identical soil conditions. The soil and plant-associated bacterial community composition was determined using 16S rRNA sequencing. In addition, large-scale metagenome and metatranscriptome sequencing was used to characterize community structure, functional potential and expressed physiological activity. A large database of approximately 2.4 million non-redundant ORFs was assembled from soil and root genomic DNA. The diversity of each habitat’s microbes varied widely between niches and between plant species. Based on metagenomic data, the functional characteristics of soil versus root bacteria deviate dramatically. Soil-to-root functional variations were particularly apparent in specific pathways including secretion systems, motility, ABC transporters, two-component systems, lipopolysaccharide metabolism and carbohydrate metabolism. In root-associated samples, the metagenomes were functionally similar between the different plant species, despite significant differences in community composition, suggesting the recruitment of root community was governed by a basic suite of genes, common to host-colonizing bacteria. Conversely, transcriptional profiles of root-associated communities were non-redundant. For example, high relative expression levels of nitric-oxide reductase genes characterized wheat root communities, while in cucumber root communities, expression of these genes was negligible. An opposite trend was found with respect to catalase and pectinases genes expression. These differences outline the structural as well as functional implication of host-microbe interactions that are crucial for plant growth, health and development.
