Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland Ecosystems
Alex Greenlon, Ella T. Sieradzki, Olivier Zablocki, Benjamin J. Koch, Megan Foley, Jeffrey A. Kimbrel, Bruce A. Hungate, Steven J. Blazewicz, Erin Nuccio, Christine Sun, Aaron Chew, Cynthia-Jeanette Mancilla, Matthew B. Sullivan, Mary K. Firestone, Jennifer Pett‐Ridge, Jillian F. Banfield
Abstract
Soil moisture is a critical factor that strongly shapes the lifestyle of soil organisms by changing access to nutrients, controlling oxygen diffusion, and regulating the potential for mobility. We identified active microorganisms in three grassland soils with similar mineral contexts, yet different historic rainfall inputs, by adding water labeled with a stable isotope and tracking that isotope in DNA of growing microbes. By examining the genomes of active and inactive microorganisms, we identified functions that are enriched in growing organisms, and showed that different functions were selected for in different soils. Wetter soil had higher activity of motile organisms, but activity of pathways for degradation of soil organic carbon compounds, including simple carbon substrates, were comparable for all three soils. We identified many labeled, and thus active bacteriophages (viruses that infect bacteria), implying that the cells they killed contributed to soil organic matter. The activity of these bacteriophages was significantly correlated with activity of their hosts.