Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons

Abstract

It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence.

The effects of heating, rhizosphere, and depth on root litter decomposition are mediated by soil moisture

“…Moreover, while the rhizosphere had no statistically significant effect on total litter recovery, we recovered a greater fraction of the applied litter in the root fraction of planted compared to unplanted plots, which counter-intuitively indicates greater comminution of roots into bulk soil in the absence of the plant rhizosphere. This observation may be tied to greater soil moisture levels in unplanted plots leading to higher soil activity of the fauna responsible for comminution, or to differences in the microbial or macrofaunal communities in the planted and unplanted plots (e.g., Brandt et al 2006;Bird et al 2011;Shi et al 2015). Populations of soil macrofauna, which are key to litter comminution, can be reduced during dry conditions (Lindberg et al 2002).…”

Variation of the Bacterial Communities in the Rhizosphere of Three Species of the Genus Tagetes (Marigold) Over Time

“…Nevertheless, recent works have shown that changes in the microbial communities of the rhizosphere could be related with habitat filtering or intraspecific competition. For example, Shi et al (2015) analyze the changes in microbial rhizosphere communities of the annual grass Avena fatua in two growing sessions and found that in spite of the different starting communities in both seasons, the successional patterns were similar and the final communities were very similar. On the other hand, Yuan et al (2016) analyzed the rhizosphere of the seepweed Suaeda salsa and found that both phylogenetic clustering (abiotic factors) and overdispersion (biotic factors) are involved in the high tolerance to salinity in this plant species.…”

Microbial community assembly differs by mineral type in the rhizosphere

“…In order to determine whether the bacteria that we identified as successful mineral colonizers 393 were simply the same subset of soil bacteria that were successful in the Avena sp. rhizosphere, 394 we compared our results to those of (Shi et al, 2015), which studied the same soil and Avena 395 .…”

“…http://dx.doi.org/10.1101/128850 doi: bioRxiv preprint first posted online fatua (a close relative of Avena barbata). Of the OTUs that were significantly enriched in the 396 mineral samples, only 8% (kaolinite) to 18% (heavy fraction) were also identified as members of 397 the dynamic rhizosphere (Shi et al, 2015) (Supplementary Figures 15 and 16). One notable 398 difference is the Firmicutes phylum, which contains important mineral colonizers, but not 399 notable rhizosphere responders.…”

“…http://dx.doi.org/10.1101/128850 doi: bioRxiv preprint first posted online Apr. 20, 2017; on a previous experiment, where Avena fatua (a close relative of Avena barbata) was grown in 287 the same soil as this experiment, and bulk and rhizosphere soils were sampled and analyzed over 288 two growing seasons to determine members of the "dynamic rhizosphere" (Shi et al, 2015). 289…”