BayCEER Workshop 2022

Selection of the bacterial microbiome at the soil-root interface compared among varieties of Zea mays L.

Root-associated microbiomes are well known to affect fitness and performance of their hosts. Plants can harness this by promoting the formation of beneficial microbial communities. Microbes colonizing roots mainly originate from the surrounding soil. Species richness decreases and community composition changes towards the rhizosphere and endosphere due to selection by the plant. We hypothesize that different varieties of a widely used crop plant, Zea mays L., promote the formation of distinct microbial communities and ask how the influence of the plant differs between root associated compartments.

Using SSU rRNA amplicon sequencing, we investigated the bacterial community composition within multiple compartments of the soil-root interface for different varieties of Z. mays grown under field conditions. Furthermore, we compared two field sites with two different soil types, two sampling times and different sampling techniques for the rhizosphere soil.

Microbial communities were clearly distinguishable between field sites. At both sites, we observed marked differences between the compartments, with the root associated community (including endosphere and rhizoplane) being most different from the bulk soil community. Within this compartment, differences between plant varieties were readily detectable, with proteobacteria being particularly affected. The effects of sampling time and technique were comparably small or limited to specific microbial taxa.

These findings support the observation that plants actively shape the root associated microbial community. Environmental variables, probably especially edaphic properties, have large influence on the microbiome. Effects of variables with comparatively small impact such as plant variety are most likely to be found within the root compartment, since the influence of the plant is strongest there.