In order to understand how plants influence the assembly and diversity of soil and root endophyte microbial communities, we sampled species of two grass genera in their native range. We collected Brachypodium species and co-located Bromus spp. grasses and soils in Spain in May 2014. The grass species included Brachypodium distachyon and Brachypodium hybridum (formerly considered a polyploid cytotype of B. distachyon and now treated as a separate allotetraploid species), as well as Bromus tectorum and Bromus rubens. We sampled grass roots, rhizosphere soils containing roots (herein called ‘rhizosphere’), and surrounding bulk soil, in six locations within different Mediterranean mesic environments. From each sample we extracted whole meta-genomic DNA using MoBio kits (PowerPlant and PowerSoil PowerLyzer, as applicable). Sequence data was annotated against the greengenes database and analyzed using Quantitative Insights Into Microbial Ecology (QIIME).
Using Non-metric Multi-Dimensional Scaling (NMDS) and Analyses of Similarity (ANOSIM), we found that the microbial communities of the roots, rhizosphere, and bulk soils, are distinct. Within each plant genus, these sample groups share between 3.1% and 14.8% of microbial taxa, with bulk and rhizosphere soils being more similar than either is to samples of only roots. Analysis also showed that most locations had distinct soil and root microbial communities. In addition, while root endophyte microbial communities were distinct between Brachypodium spp. and Bromus spp., the rhizosphere and bulk soil communities overlapped. Further, there were almost twice as many overlapping microbial species between the rhizosphere and root communities in the Brachypodium samples as there were in the Bromus samples.
These findings lead to the initial conclusion that grass roots select from their surrounding rhizosphere communities, and that Brachypodium spp. roots may be less selective than Bromus spp. These findings also indicate that grass root endophyte communities are unique between plant genera, while nearby soil communities are not. This finding may help us identify beneficial or detrimental root endophytes, and ultimately help in the understanding of, and biocontrol for, these grasses, as both genera studied are invasive in California.