Seven Arabidopsis Midwestern accessions in HPG1 were grown in two locations, Warren Woods and the Michigan Research and Extension Center, for two successive years and sampled monthly during the growing seasons over the span of two years. The aim was to collect samples for bacterial microbiome analysis using 16S rRNA from all developmental stages of the plants to understand how the microbiome changes in space and time.
Figure 1. PCoA showing separation of bacteria from soil, roots, and rosettes (colors) and location (shapes).
We find that the phyllosphere and rhizosphere communities have distinct compositions compared to each other and to the surrounding soil (Figure 1 above). Figure 2 (below) shows the networks constructed for each developmental stage in the roots at two different sites. The taxa richness, and thus the number of members in the network, increased as plant development progressed. An increase in community diversity at later stages can be seen as the number of different types of bacteria represented increases.
Figure 2. Bacterial networks sampled from A. thaliana roots by developmental stage. WW vegetative not sampled.
Bacterial networks also show more modularity in their structure as plant development progresses. Relative to random networks of the same size, networks from later developmental stages in both tissues were more modular than the networks from earlier developmental stages. There is more analysis that can be done on the modules present in the plant and soil networks to determine what variables in the data (microbe relatedness, site, or year) can best explain the patterns in community structure.
Previous studies on plant microbial networks identified sets of fungal or bacterial taxa as “hubs” because they were exceptionally well connected in inferred interaction networks. It is posited that this small set of microbes has outsized influence on phyllosphere and rhizosphere communities through interactions. However, in this dataset we find that the bacteria identified as hubs based on their connections in the network varied across plant development in both the phyllosphere and rhizosphere. This suggests the influence of a hub microbe may not be predictable across different tissues and developmental stages in plants.