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

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.

Digestion in defaunated and refaunated sheep fed soybean oil hydrolysate or crushed toasted soybeans

Defaunated then refaunated sheep were given diets containing soyabean oil hydrolysate (SOH: 70 g/day) or an equivalent amount of lipids administered as crushed toasted soyabeans (TSB). Defaunation increased molar percentage of propionate in the rumen, while butyrate decreased. SOH caused a similar effect in both the defaunated and refaunated rumen, while the effect on acetate proportions was variable. Protozoal counts were lower after feeding SOH. Crushed toasted soyabeans had a minor effect on rumen fermentation pattern. Rumen digestibility of organic matter was decreased by both defaunation and SOH feeding, with a concomitant shift in digestion to the lower intestinal tract. Total tract digestibility was not affected. Both treatments increased nonammonia N flows at the duodenum, but this was only significant with defaunation. Total tract digestion of N remained almost constant. Defaunation resulted in more microbial protein reaching the duodenum. Except for the TSB diet, total lipid leaving the rumen equalled intake. Total tract digestibility of total lipid was much higher with SOH and TSB than with controls. Defaunation almost doubled microbial growth efficiency and this value tended to increase by SOH feeding. The decrease of protozoal count or even elimination of protozoa after lipid feeding could not entirely explain the change in rumen metabolism, as additional changes in defaunated sheep were shown.