Heavy and wet: The consequences of violating assumptions of measuring soil microbial growth efficiency using the 18O water method

Abstract

Soils store more carbon than the biosphere and atmosphere combined, and the efficiency to which soil microorganisms allocate carbon to growth rather than respiration is increasingly considered a proxy for the soil capacity to store carbon. This carbon use efficiency (CUE) is measured via different methods, and more recently, the 18O-H2O method has been embraced as a significant improvement for measuring CUE of soil microbial communities. Based on extrapolating 18O incorporation into DNA to new biomass, this measurement makes various implicit assumptions about the microbial community at hand. Here we conducted a literature review to evaluate how viable these assumptions are and then developed a mathematical model to test how violating them affects estimates of the growth component of CUE in soil. We applied this model to previously collected data from two kinds of soil microbial communities. By changing one parameter at a time, we confirmed our previous observation that CUE was reduced by fungal removal. Our results also show that depending on the microbial community composition, there can be substantial discrepancies between estimated and true microbial growth. Of the numerous implicit assumptions that might be violated, not accounting for the contribution of sources of oxygen other than extracellular water to DNA leads to a consistent underestimation of CUE. We present a framework that allows researchers to evaluate how their experimental conditions may influence their 18O-H2O-based CUE measurements and suggest the parameters that need further constraining to more accurately quantify growth and CUE.

Substrate availability and not thermal acclimation controls microbial temperature sensitivity response to long‐term warming

“…The 18 O enrichment of the DNA was measured using TC/EA‐IRMS (Delta V Advantage, Thermo Fisher) at the UC Davis Stable Isotope Facility. CUE was calculated as per Spohn et al (2016) but using a sample‐specific conversion factor rather than the overall average because large differences in MBC:DNA ratios across community types can bias CUE measurements (Pold, Domeignoz‐Horta & DeAngelis, 2020).…”

Intracellular carbon storage by microorganisms is an overlooked pathway of biomass growth

“…The total measured O content of the sample, the O content of the DNA (31 % by mass), and the 18 O natural abundance of unlabelled control samples were used to calculate the background 18 O from the kit. This background 18 O was deducted to obtain 18 O abundance of the DNA, which was applied in a 2-pool mixing model with 70% of O in new DNA derived from water 39 . This provided the fraction of extracted DNA that had been newly synthesized during the incubation period.…”

Intracellular carbon storage by microorganisms is an overlooked pathway of biomass growth

“…The total measured O content of the sample, the O content of the DNA (31% by mass), and the 18 O natural abundance of unlabelled control samples were used to calculate the background 18 O from the kit. This background 18 O was deducted to obtain 18 O abundance of the DNA, which was applied in a 2-pool mixing model with 70% of O in new DNA derived from water 45 (model detailed in Supplementary B). This provided the fraction of extracted DNA that had been newly synthesized during the incubation period.…”