Rhizosphere bacterial communities explained by spatial structure and sampling grain

Background/Question/Methods: With rapid advancement in molecular technology, the grain at which we can assess large scale ecological patterns and processes has become refined to the microbial community level. However, a finer scale in measuring microbiomes from a perspective relative to the microbe is needed to realistically portray microbiome community assembly and microbial recruitment to host tissue over time. Here, I examined community membership and structure of three fine grain bacterial microbiomes dependent on the sampling position along the root length with a pooled sample describing the whole rhizosphere of Salvia lyrata. I additionally tested the hypothesis that because of increased microbial recruitment to the root tip due to secondary metabolite root exudation, bacterial communities sampled from the deepest point along the root will have more variability in community membership than other fine grain sampling locations. Using sterile field techniques, I sampled soil at 0 to 1cm, 1 to 2.5cm, and 2.5 to 4cm depths within the rhizosphere of S. lyrata (N=30) to represent microbiomes as a proxy for position along the root length. All microbial communities were characterized by using the Illumina MiSeq protocol for 16S rRNA library prep and sequencing.

Results/Conclusions: I have shown that community membership and structure of microbiomes made at a finer grain scale differ significantly when compared to the whole rhizosphere microbiome of S. lyrata. I also observed that microbiomes were less diverse and abundance at the root tip due to increased microbial competition for carbon in comparison to other positions along the root. The observed community differences are dependent on minute biological processes, such as secondary exudate secretion from the root tip, rather than seasonal weather patterns that affect the microbiome within the rhizosphere as a whole. In summary, to further elucidate how host specific microbiomes assemble and influence plant host survival over their lifetime, the scale at which bacterial communities are sampled should be reflective of processes that occur within the rhizosphere versus generalized community sampling.