Plants release up to 20 % of their photosynthetically fixed carbon from roots into the rhizosphere. Most of the released carbon is assimilated and metabolized by complex communities of microorganisms in the rhizosphere. Characterization of rhizosphere communities sheds light on a critical link in the carbon cycling of terrestrial ecosystems. In return for the plant-derived carbon, rhizosphere communities help plants extract nitrogen and phosphorus from soil, withstand environmental stresses, and defend against soil-borne pathogens. Mechanistic understanding of the mutually beneficial relationship between plants and rhizosphere communities may facilitate the development of plant growth-promoting rhizobacteria to improve the sustainability and productivity of agriculture. To investigate organism-resolved molecular details of nutrient metabolism in rhizosphere communities, we grew maize, wheat, and Arabidopsis for 30 days under a normal atmosphere and then we initiated continuous 13C labeling of the plants under a 13CO2-enriched atmosphere for 3 and 8 days. We collected 2 replicate initial soil and 12 rhizosphere soil samples (2 per plant species per labeling duration) for metagenomic sequencing and metaproteomic measurements. We also conducted a soil microcosm experiment to validate the existence of the functional activity carried out by the most abundant protein identified in the initial soil and rhizosphere soil samples.
Results/Conclusions
We recovered 42 draft metagenome-assembled genomes (MAGs). Phylogenomic analysis showed few of these MAGs are closely related to 523 known root-associated reference genomes. We observed plant host preference for these MAGs. For example, all six MAGs in the order Sphingomonadales had higher abundance in the rhizosphere of Arabidopsis compared to that of maize. We identified 26 13C-labeled microbial proteins, revealing carbon transfer from plants to rhizosphere communities. We recovered four MAGs encoding some of these 13C-labeled proteins, three of which had substantially increased abundance in the rhizosphere relative to the initial soils. Metaproteomics identified sugar, amino acids, and phosphate transporters for obtaining C, N, and P, respectively, and arylsulfatase for obtaining S in a MAG in the genus Pseudomonas. The most abundant protein across the rhizosphere communities is a methanol dehydrogenase XoxF, suggesting methanol oxidation is a major activity. To validate the existence of this activity, we added 13C-labeled methanol into the initial soil in microcosms. We identified three 13C-labeled XoxF across triplicate microcosms, indicating the presence of methanol stimulated biosynthesis of new XoxF and organisms harboring these XoxF incorporated carbon from methanol into protein.
In summary, this study revealed organism-resolved molecular details of nutrient metabolism in plant-selected rhizosphere communities.