Understanding Rhizosphere Spatial Heterogeneity in Fabricated Ecosystems using Cultivation-independent and Enrichment Approaches

Understanding plant-microbial interactions in the rhizosphere involves a deeper investigation into the influence of root exudation on spatially defined microbial niches (microbial biogeography). We analyzed the microbial community from two spatially distinct zones of the primary root (the tip vs. the base) in the rhizosphere of Brachypodium distachyon, grown using natural soil, in standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and test tube systems. While the microbial community distributions are similar across the different growth chambers, the EcoFAB displayed higher replicate reproducibility. Analysis of the 16S rRNA of the bacterial communities showed a stronger rhizosphere effect in the root base vs. bulk soil compared to the root tips vs. bulk soil. We observe increase in abundance of Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, Verrucomicrobia and Acidobacteria in the rhizosphere. Metagenomic analysis revealed genes associated with transcriptional regulation, transport of nutrients and catabolic enzymes indicating active metabolism, biofilm formation and root colonization were enriched in root tips when compared to bulk soil.

To probe deeper into the physiology of the abundant microbes, we enriched this rhizobiome on media containing carbon compounds identified in root exudates and transferred them every 3 days or 7 days to capture the community of both fast and slow growing bacteria using high-throughput enrichment techniques. We tested 14 different carbons, and low nutrient commercial media. 16S rRNA amplicon analysis of the enrichments reveals influence of inoculum and carbon source on composition of rhizosphere enriched communities. We have isolated close to 200 strains from these enrichments, many of which match the exact OTUs from rhizosphere including an Acidobacterial isolate (Terriglobus sp.). Acidobacteria are notoriously difficult to isolate. We have further created a consortium with representative strains that will be used for creating a stable, synthetic, reduced complexity, rhizosphere community. This will enable us to gain insights into the complex networks between roots and rhizobiome that are critical for developing plant growth enhancement strategies.