This dataset contains microbial carbon use efficiency (CUE) estimates of sediment microbes from the Logan River, UT, USA, along with stoichiometric parameters and the potential activities of ecoenzymes. The data reflect the CUE of sediment microbes in mesocosms of varying salinities after a 24 hour incubation period. Sediments and stream water were collected on two occasions, 8/26/24 and 9/22/24, from the same location. Mesocosm incubations began on the same day as sediment collection. Salinity treatments (from ambient to +100 us/cm above ambient) were created by adding NaCl to stream water.

In the first experiment, we used an ecoenzyme activity assay and stoichiometric modeling to estimate CUE (Sinsabaugh et al., 2016; Marx et al., 2001; German et al., 2011). Microbial biomass C, N, and P were estimated using chloroform fumigation and extraction methods (Wu et al., 1990; Brookes et al., 1985; Brookes et al., 1982). Total organic C (TOC) and total N extracts were analyzed on a Shimadzu TOC-TN-L and total P extracts were analyzed on an Astoria Pacific Analyzer.

For the second experiment, we used 13C isotope tracing methods to estimate CUE (Geyer et al., 2019). TOC extracts and gas samples were analyzed by the University of Ottawa Ján Veizer Stable Isotope Laboratory. TOC concentrations and isotope ratios were analyzed on a model 1030 wet TIC-TOC analyzer interfaced to a DeltaPlus XP Isotope Ratio Mass Spectrometer via a Conflo 4. CO2 concentrations in the gas samples were analyzed on an SRI GC 8610C, and isotope ratios were analyzed on a Gas Bench peripheral interfaced to an Isotope Ratio Mass Spectrometer Delta XP. We calculated dissolved CO2 concentrations from the headspace samples following the protocols from the Lotic Intersite Nitrogen eXperiment 2 project (Hamilton 2006).

Some parameters are standardized to amount of ash-free dry mass (AFDM) in the sample. We measured the AFDM of the sediments in each mesocosm to standardize the microbial biomass estimates. AFDM was estimated by subtracting the mass of a subsample of sediment after ashing at 450°C for 2 hr from the mass of the sample after drying at 60°C for 48 hr.

The R workflow provided was used primarily to understand the effects of salinity on microbial CUE using beta regressions.

Citations:
Geyer, K. M., Dijkstra, P., Sinsabaugh, R., & Frey, S. D. (2019). Clarifying the interpretation of carbon use efficiency through methods comparison. Soil Biology & Biochemistry, 128, 79–88. https://doi.org/10.1016/j.soilbio.2018.09.036
Wu, J., Joergensen, R. G., Pommerening, B., Chaussod, R., & Brookes, P. C. (1990). Measurement of soil microbial biomass C by fumigation-extraction—an automated procedure. Soil Biology & Biochemistry, 22(8), 1167–1169. https://doi.org/10.1016/0038-0717(90)90046-3
Sinsabagh, R. L., Turner, B. L., Talbot, J. M., Waring, B. G., Powers J. S., Kuske, C. R., et al. (2016). Stoichiometry of microbial carbon use efficiency in soils. Ecological Monographs, 86(2), 172–189. https://doi.org/10.1890/15-2110.1
Brookes, P. C., Landman, A., Pruden, G., & Jenkinson, D. S. (1985). Chloroform fumigation and the release of soil nitrogen: A rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biology & Biochemistry, 17(6), 837–842. https://doi.org/10.1016/0038-0717(85)90144-0
Brookes, P. C., Powlson, D. S., & Jenkinson, D. S. (1982). Measruement of microbial biomass phosphorus in soil. Soil Biology & Biochemistry, 14(4), 319–329. https://doi.org/10.1016/0038-0717(82)90001-3
Hamilton, S. K. (2006). Calculation of dissolved gas concentrations and isotope ratios from measurements made after statis headspace extraction. Lotic Intersite Nitrogen eXperiment (LINX2). Kellogg Biological Station Long-Term Ecological Research.
Marx, M. -C., Wood, M., & Jarvis, S. C. (2001). A microplate fluorimetric assay for the study of enzyme diversity in soils. Soil Biology & Biochemistry, 33(12–13), 1633–1640. https://doi.org/10.1016/S0038-0717(01)00079-7
German, D. P., Weintraub, M. N., Grandy, A. S., Lauber, C. L., Rinkes, Z. L., & Allison, S. D. (2011). Optimization of hydrolytic and oxidative enzyme methods for ecosystem studies. Soil Biology & Biochemistry, 43(7), 1387–1397. https://doi.org/10.1016/j.soilbio.2011.03.017