Unearthing the microbial ecology of soil carbon cycling with DNA-SIP

Abstract

We explored the dynamics of microbial contributions to decomposition in soil by coupling DNA Stable Isotope Probing (SIP) and high throughput DNA sequencing. Our experiment evaluated the degradative succession hypothesis, described dynamics of carbon (C) metabolism during organic matter degradation, and characterized bacteria that metabolize labile and structural C in soils. We added a complex amendment representing plant derived organic matter to soil substituting ¹³C-xylose or ¹³C-cellulose for unlabeled equivalents in two experimental treatments which were monitored for 30 days. Xylose and cellulose are abundant components in plant biomass and represent labile and structural C pools, respectively. We characterized 5,940 SSU rRNA gene operational taxonomic units (OTUs) finding evidence for ¹³C-incorporation into DNA from ¹³C-xylose and ¹³C-cellulose in 49 and 63 OTUs, respectively. In the ¹³C-xylose treatment the types of microorganisms that incorporated ¹³C into DNA changed over time dominated by Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These dynamics of ¹³C-labeling suggest labile C traveled through different trophic levels within the soil bacterial community. The microorganisms that metabolized cellulose-C increased in relative abundance over the course of the experiment with the highest number of OTUs exhibiting evidence for ¹³C-assimilation after 14 days. Microbes that metabolized cellulose-C belonged to cosmopolitan soil lineages that remain uncharacterized including Spartobacteria, Chloroflexi, and Planctomycetes. Using an approach that reveals the C assimilation dynamics of specific microbial lineages we describe the ecological properties of functionally defined microbial groups that contribute to decomposition in soil.