Abstract
We explored the dynamics of microbial contributions to decomposition in soil by coupling DNA Stable Isotope Probing (SIP) and high through-put 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.
Significance Soil microorganisms drive C flux through the terrestrial biosphere, and models that predict terrestrial C flux can benefit by accounting for microbial ecophysiology in soils. However, characterizing the ecophysiology of microbes that mediate C decomposition in soil has proven difficult due to their overwhelming diversity. We characterized microbial C metabolism in soil and show that different types of C have distinct decomposition dynamics governed by different microbial lineages. For example, we found that uncharacterized microbial taxa, which are cosmopolitan in soils, assimilated cellulose-C into DNA. These microbes may drive cellulose decomposition on a global scale. We identify microbial lineages engaging in labile and structural C decomposition and explore their ecological properties.
Footnotes
Abbreviations: C, Carbon; OTU, Operational Taxonomic Unit; SOM, Soil Organic Matter; BD, Buoyand Density; SIP, Stable Isotope Probing