Nitrogen Availability Modulates the Host Control of the Barley Rhizosphere Microbiota

Microbial communities thriving in the root-soil interface, the rhizosphere microbiota, are a potential resource of functions related to plant nutrition and health. However, their deployment in agriculture is impaired by the limited knowledge of the mechanisms regulating plant-microbiota interactions. I hypothesize that the barley genotype shapes the rhizosphere microbiota to support plant growth in soils with limited nutrient supply.

With the aim to investigate the role of the microbiota in plant Nitrogen (N) availability, two wild barley genotypes (Hordeum vulgare subp. spontaneum) from Israel and a domesticated cultivar (H. vulgare subp. vulgare) were grown in controlled greenhouse conditions. Soil was amended with three N fertilizer levels (100, 25 and 0%, respectively) of ammonia and nitrate, while keeping the other nutrients to an optimum level. At early stem elongation rhizosphere was collected and aboveground biomass measured. An Illumina MiSeq protocol and bioinformatic approaches were used to produce 16S rRNA gene profiles of the prokaryotic composition of the rhizosphere samples and unplanted soil controls.

Microbiota profiles were dominated by members of the phyla Proteobacteria, Bacteroidetes and Actinobacteria whose enrichment discriminates rhizosphere from soil samples. Depleted phyla in the rhizosphere included Planctomycetes and Nitrospirae with members that intervene in N cycling processes resulting in N losses form the soil. Unlike soil controls, rhizosphere profiles display a significant nitrogen-dependent compositional diversification whose trend is reflected by a biomass gradient observed among the tested plants. Host genotype selective recruitment of bacteria is maximised at zero N, indicating a plant modulation of the microbiota under limited N conditions. The potential microbiota functionality is currently being characterised in a shotgun metagenomics investigation.

Taken together, these results suggest a molecular cross-talk that links members of the rhizosphere microbiota to the host genotype and physiology whose magnitude is amplified under limited nutrient supply.