Linking soil bacterial biodiversity and soil carbon stability

Abstract

Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this 'priming' effect. A single-substrate pulse suppressed native soil C loss and reduced bacterial diversity, whereas repeated substrate pulses stimulated native soil C loss and increased diversity. Increased diversity after repeated C amendments contrasts with resource competition theory, and may be explained by increased predation as evidenced by a decrease in bacterial 16S rRNA gene copies. Our results suggest that biodiversity and composition of the soil microbial community change in concert with its functioning, with consequences for native soil C stability.

Quantitative Microbial Ecology through Stable Isotope Probing

“…In past priming studies employing 13 C-SIP, some components of the microbial community were found to utilize as growth substrates the 13 C-labeled compounds added to initiate priming, though inferences about the organisms responsible for priming-i.e., degrading native soil organic matter-were weak, because no independent marker could validate their activity (62)(63)(64). Combining isotope tracers (using both 13 C and 18 O) can help by distinguishing microorganisms that respond to the original substrate pulse from those that respond indirectly by degrading soil organic matter (11), an approach useful for testing hypotheses about which groups of microorganisms contribute to priming. qSIP advances this one step further, by enabling quantitative comparisons of microorganisms' utilization of the added substrate and of soil organic matter for growth.…”

“…Based on the qPCR data, we produced a conventional SIP density curve by graphing the proportion of total 16S rRNA gene copies as a function of density, an approach often used to visualize the effect of isotope incorporation on the distribution of densities across the bacterial assemblage, delineating heavy and light regions for sequencing (9)(10)(11). We also calculated the average DNA density for each tube as a weighted average of the density of each fraction in which 16S rRNA gene copies were detected, weighted by the proportional abundance of total 16S rRNA gene copies measured in that fraction for each tube.…”

“…The nucleic acids in density regions defined as "heavy" or "light" are then sequenced. Organisms disproportionately represented in the heavy region are interpreted as having utilized the labeled substrate for growth (8)(9)(10)(11).…”

Direct and indirect effects of climate change on soil microbial and soil microbial‐plant interactions: What lies ahead?

“…By using meta-genomics, -transcriptomics, -proteomics, and -metabolomics, scientists are able to define changes in microbial communities that will result in a better understanding of which microbes are present in an ecosystem and what their potential functions are (e.g., Castro et al 2012, Muller et al 2013). Further, with technologies such as stable isotope probing, it is possible to target the active microbial community involved in a myriad of functions (e.g., Mau et al 2015).…”

Soil microorganisms can overcome respiration inhibition by coupling intra- and extracellular metabolism: 13C metabolic tracing reveals the mechanisms

“…Sufficient amounts of glucose in soil solution can activate microbial metabolism and induce growth (Blagodatskaya and Kuzyakov, 2013;Mau et al, 2015), hence accelerating SOM decomposition. In sterile soil, approximately 98% of glucose remains K 2 SO 4 -extractable within 24 h (Bremer and van Kessel, 1990).…”