Deforestation for agriculture increases microbial carbon use efficiency in subarctic soils

This repository contains all necessary raw data as well as the R code used to conduct statistical analysis and create figures of the publication Deforestation for agriculture increases microbial carbon use efficiency in subarctic soils Julia Schroeder1, Tino Peplau1, Frank Pennekamp2, Edward Gregorich3, Christoph C. Tebbe4, Christopher Poeplau1 1 Thünen Institute of Climate-Smart Agriculture, Bundesallee 68, 38116 Braunschweig, Germany 2 Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland 3 Research and Development Centre, Central Experimental Farm, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada 4 Thünen Institute of Biodiversity, Bundesallee 65, 38116 Braunschweig, Germany DOI: https://doi.org/10.1007/s00374-022-01669-2 This study investigated how and through which pathways deforestation and conversion to agricultural land (i.e. grassland, cropland) alters the microbial carbon use efficiency (CUE) in subarctic soils to allow the development of mitigation strategies to alleviate C losses. We assessed CUE using 18O-labelled water in a paired-plot approach on soils collected from 19 farms across the subarctic region of Yukon, Canada, comprising 14 pairs of forest-to-grassland conversion and 15 pairs of forest-to-cropland conversion. Microbial CUE significantly increased following conversion to grassland and cropland. Land-use conversion resulted in a lower estimated abundance of fungi, while the archaeal abundance increased, as assessed by qPCR. Interestingly, structural equation modelling revealed that increases in CUE were mediated by a rise in soil pH and a decrease in soil C:N ratio rather than by shifts in microbial community composition, i.e. the ratio of fungi, bacteria and archaea. Our findings indicate a direct control of abiotic factors on microbial CUE via improved nutrient availability and facilitated conditions for microbial growth. The R code was developed under R v3.6.3 and adapted to work under version R v.4.1.2. The repository includes the following files: general_soil_parameters_per_site.csv - general soil data assessed on pooled reference forest plot (n=19) general_soil_parameters_per_plot.csv - general soil data assessed on pooled replicated field samples (n=48) sample_data.csv - data measured for each laboratory sample (n=147) Land-use change effects on 18O-CUE.Rproj - Rproject (load project to work on provided scripts and data) load_data_script.R - loads required data Multivariate_normality_script.R - tests for multivariate normaility in dataset PCA_script.R - calculates PC1 and 2 of clay mineralogy data to reduce dimensions map_Yukon_script.R - create Figure 1 plot_density_script.R - create Figure 2 linear_mixed-effects_models_script.R - calculates response ratios plot_boxplots_script.R - plot boxplots per land use including compact letter display indicating significant differences, create Figure 3 + 4 correlogram_script.R - correlation analysis to identify drivers of CUE, create Figure 6 plot_correlations_script.R - plot drivers of CUE, create Figure 5 + 7 SEM_script.R - development of structural equation model, create Figure 8本仓库包含论文《农业开垦提升亚北极土壤微生物碳利用效率》的全部必要原始数据，以及用于开展统计分析、绘制论文插图的R代码。 《农业开垦提升亚北极土壤微生物碳利用效率》 Julia Schroeder¹, Tino Peplau¹, Frank Pennekamp², Edward Gregorich³, Christoph C. Tebbe⁴, Christopher Poeplau¹ ¹ 屠能农业智能研究所，德国不伦瑞克市联邦大道68号，38116 ² 苏黎世大学生态与环境演化系，瑞士苏黎世市温特图尔大道190号，8057 ³ 加拿大农业与农业食品部中央实验农场研发中心，加拿大安大略省渥太华市卡林大道960号，K1A 0C6 ⁴ 屠能生物多样性研究所，德国不伦瑞克市联邦大道65号，38116 DOI: https://doi.org/10.1007/s00374-022-01669-2 本研究旨在明确农业开垦（即转为草地、农田）如何以及通过何种途径改变亚北极土壤的微生物碳利用效率（microbial carbon use efficiency, CUE），从而为缓解碳损失制定减缓策略。研究采用配对样地法，通过18O标记水测定微生物碳利用效率，采样覆盖加拿大育空地区亚北极带的19个农场，包含14对林转草地样地与15对林转农田样地。结果显示，转为草地与农田后，微生物碳利用效率显著提升。通过定量PCR（quantitative polymerase chain reaction, qPCR）检测发现，土地利用转变后真菌的预估丰度降低，而古菌丰度上升。有趣的是，结构方程模型（structural equation modelling, SEM）结果表明，微生物碳利用效率的提升由土壤pH升高与土壤碳氮比降低所介导，而非微生物群落组成（即真菌、细菌与古菌的比例）变化。本研究结果表明，非生物因素可通过提升养分有效性与优化微生物生长条件，直接调控微生物碳利用效率。 本R代码基于R v3.6.3开发，并适配R v4.1.2版本运行。本仓库包含以下文件： general_soil_parameters_per_site.csv：各点位基础土壤参数数据集，包含19个混合参考林地表样的实测基础土壤数据（n=19） general_soil_parameters_per_plot.csv：各样地基础土壤参数数据集，包含48个混合重复田间采样的实测基础土壤数据（n=48） sample_data.csv：样本实测数据集，包含147个实验室样本的各项检测数据（n=147） Land-use change effects on 18O-CUE.Rproj：《土地利用变化对18O标记碳利用效率的影响》R项目文件，加载该项目即可运行配套脚本与数据 load_data_script.R：数据加载脚本，用于加载所需实验数据 Multivariate_normality_script.R：多元正态性检验脚本，用于对数据集开展多元正态性检验 PCA_script.R：主成分分析脚本，用于计算黏土矿物学数据的PC1与PC2以实现维度降维 map_Yukon_script.R：育空地区采样地图绘制脚本，用于生成图1 plot_density_script.R：密度图绘制脚本，用于生成图2 linear_mixed-effects_models_script.R：线性混合效应模型脚本，用于计算响应比 plot_boxplots_script.R：箱线图绘制脚本，用于绘制不同土地利用类型的箱线图，附带表示显著性差异的紧凑字母标注，生成图3与图4 correlogram_script.R：相关图分析脚本，用于开展相关性分析以识别碳利用效率的驱动因子，生成图6 plot_correlations_script.R：相关性可视化脚本，用于可视化碳利用效率的驱动因子，生成图5与图7 SEM_script.R：结构方程模型脚本，用于构建结构方程模型，生成图8