Identification of the rhizosphere microbes that actively consume plant-derived carbon

Abstract

Rhizosphere microbial communities play essential roles in plant growth and health, with plant-derived carbon serving as the primary resource fueling the growth and activity of these root-associated communities. However, not all rhizosphere microbes are likely equivalent in their ability to metabolize root-derived carbon inputs, and far fewer studies have sought to identify the rhizosphere taxa, and the traits of those taxa that actively consume plant photosynthates. Here, we labeled wheat plants (Triticum aestivum L.) with 13C–CO2, combining stable isotope probing, quantitative PCR, marker gene sequencing, and shotgun metagenomic sequencing to identify rhizosphere microbes that metabolized plant-derived carbon and their genomic attributes. Those rhizosphere taxa that incorporated the plant-derived 13C were not necessarily the most abundant taxa in the rhizosphere. Rhizosphere microbes clearly differed in their capacity to consume plant-derived carbon, with the bacterial photosynthate consumers having distinct metabolic and genomic profiles with higher estimated potential growth rates and more genes associated with carbon metabolism, resource uptake, and potential for plant growth promotion. Together, this work highlights the important roles and the differential contributions of rhizosphere microbes to belowground carbon dynamics, building a more nuanced understanding of the complexity of plant-microbe interactions in the rhizosphere.