CO2 artefact can distort estimates of microbial basal respiration rate in closed chambers

This repository contains all necessary raw data as well as the R code used to conduct statistical analysis and create figures of the publication CO2 artefact can distort estimates of microbial basal respiration rate in closed chambers Julia Schroeder1,2 1 Thünen Institute of Climate-Smart Agriculture, Bundesallee 68, 38116 Braunschweig, Germany2 Thünen Institute of Biodiversity, Bundesallee 65, 38116 Braunschweig, Germany DOI: https://doi.org/10.1016/j.geoderma.2026.117766 This methodological study was conducted in order to understand discrepancies observed between microbial respiration rates after 1-hour and 24-hour incubation derived by gas sampling from closed chambers. I systematically identify a methodological ‘abiotic’ artefact as origin of the temporal pattern, while showing that the pattern is neither a biological response to O2 depletion or CO2 toxicity, nor related to a flush in activity. CO2 dissolution is a known pitfall in the assessment of microbial respiration, but it is highly overlooked in the current literature. This study provides recommendations for improving the accuracy of basal respiration assessments, revisits previous recommendations, and highlights specific conditions under which neglecting the described phenomenon can lead to significant errors in the interpretation of basal respiration. The R code was developed under R v4.4.2. The repository includes the following files: Variables_soil_exp.xlsx - Explanation of variables in soil_exp.csv Variables_water_exp.xlsx - Explanation of variables in water_exp.csv Rproj: R_project_Schroeder_CO2_artefact.Rproj - Rproject (load project to work on provided scripts and data) data: site_dat - Provides laboratory soil data for the 10 selected soils from the German Agricultural Soil Inventory. soil_exp.csv - Provides all data collected from the soil incubation experiments (i.e. time-series and pre-incubation experiment). water_exp.csv - Provides all data collected from the pure water-gas system experiment. R scripts: CO2_artefact_soil_experiments.R - Loads soil_exp.csv and site_dat.csv, conducts statistical analyses, and creates figures for the main manuscript and supplemental information, related to the soil incubation experiments. CO2_artefact_water_experiment.R - Loads water_exp.csv, conducts statistical analyses, and creates figures for the main manuscript and supplemental information, related to the pure water-gas system experiment. output: coefficients_linear_regression.csv - Contains the coefficents, the extracted slope normalised per amount of soil incubated (i.e. slope.gsoil), and the calculated CO2 artefact (i.e. intercept-background concentration) as well as potential explanatory variables (WC: water Content, WHC_perc: water holding capacity (%w/w), TOC: total organic carbon (g kg-1), pH: measured in 1:5 w/v soil to bi-distilled water, clay: clay content (%), sand: sand content (%)). Coefficients were derived from a linear regression of measured CO2 concentration over incubation duration (assumin a linear increase).