Bacterial communities of the rhizosphere explained by spatial structure and sampling grain

In this study, we sampled from three depths within the rhizosphere of Salvia lyrata to ask: How does bacterial richness and relative abundance compare between discrete rhizosphere depths and a combined rhizosphere sample from the same plant? Further we ask, how does bacterial richness, the raw number of reads, and relative abundance in reads compare between differences in sampling grain? To achieve this, we utilized two types of pooling methods to examine the impact of sampling grain. These were pooling rhizosphere soil depths prior to DNA extraction (in vitro) and combining community data tables post sequencing and processing (in silico). We expand on previous published research by illustrating that small-scale spatial heterogeneity of rhizosphere microbiomes can be captured using high resolution 16S rRNA gene sequencing. Further, not only does bacterial richness and relative abundance differ based on the spatial extent, or depth, sampled within the rhizosphere, but they also differ greatly based on fine versus coarse grain sampling methods.