GIRF Pulse Experiment

R code for Hastings, Y. D. (2022). Green Infrastructure Microbial Community Response to Simulated Pulse Precipitation Events in the Semi-Arid Western United States (Master's thesis, The University of Utah). This study was supported by a grant from the US National Science Foundation (DEB 2006308).

R code for and Hastings, Y. D., et al. Green Infrastructure Microbial Community Response to Simulated Pulse Precipitation Events in the Semi-Arid Western United States. In review.

Abstract: Nutrient retention in urban stormwater green infrastructure (SGI) of water-limited biomes is not well quantified, especially when stormwater inputs are scarce. We examined the role of plant diversity and physiochemistry as drivers of microbial community physiology and soil N pools and fluxes in bioswales subjected to simulated precipitation and a montane meadow experiencing natural rainfall within a semi-arid region during drought. Precipitation generally elevated soil moisture and pH, stimulated ecoenzyme activity, and increased the concentration of organic matter, proteins, and N pools in both bioswale and meadow soils; but the magnitude of change differed between events. Microbial community growth was static and N assimilation into biomass was limited across precipitation events. Unvegetated SGI plots had greater soil moisture, yet effects of plant diversity treatments on microbial C:N ratios, organic matter content, and N pools were inconsistent. Differences in soil N concentrations in bioswales and the meadow were most directly correlated to changes in organic matter content mediated by ecoenzyme expression and the balance of C, N, and P resources available to microbial communities. Our results add to growing evidence that ecological function of SGI is comparable to neighboring natural vegetated systems, particularly when soil media and water availability are similar.

The file and R code structure is as follows:

Data - Contains all data used for the analysis

Results - Contains all figures, RMANOVA, and Piecewise Structural Equation Modeling results.

renv - R environment used for project

EEA_Vector_Analysis.R - R code used to analyze coenzyme (EEA) responses, including RMANOVA to look for significant differences in EEA response to simulated pulse events and Vector Analysis to determine the nutrient resource acquisition.

Gravimetric_soil_moisture_pH.R - R code used for RMANOVA of gravimetric soil moisture and pH responses to simulated pulse events.

MicrobialBiomass_EEA.Rproj - Downloaded R project

Microbial_biomass.R - R code used for RMANOVA of microbial biomass carbon, nitrogen, and C:N responses to simulated pulse events.

OM_protien_N_pools_fluxes.R - R code used for RMANOVA of organic matter content, proteins, and N pools and fluxes responses to simulated pulse events.

PSEM_final.R - R code used for Pearson Correlation and Piecewise Structural Equation Modeling.

Rclimate.R - R code used to obtain summary statistics of climate data from GIRF and TM climate and soil sensors.

本数据集包含对应Y. D. Hastings（2022）硕士论文《美国西部半干旱地区模拟脉冲降水事件下绿色基础设施微生物群落响应》（犹他大学）的配套R代码。本研究受美国国家科学基金会DEB 2006308号项目资助。
同时包含Y. D. Hastings等人在审论文《美国西部半干旱地区模拟脉冲降水事件下绿色基础设施微生物群落响应》的配套R代码。

摘要：水分受限生物群区内的城市雨水绿色基础设施（Stormwater Green Infrastructure, SGI）的养分滞留能力尚未得到充分量化，在雨水输入稀缺的情况下尤为如此。本研究针对半干旱干旱期内的两类生境开展实验：一是经过模拟降水处理的生物滞留池，二是受自然降雨影响的山地草甸，旨在探究植物多样性与物理化学特征作为驱动因子，如何影响微生物群落生理、土壤氮库与通量。
降水事件普遍提升了两类生境土壤的含水率与pH值，激活了生态酶（Ecoenzyme, EEA）活性，并增加了土壤有机质、蛋白质与氮库浓度；但不同降水事件间的变化幅度存在差异。在所有降水事件中，微生物群落生长均处于停滞状态，且氮向生物量中的同化过程受到限制。无植被覆盖的SGI样地土壤含水率更高，但植物多样性处理对微生物碳氮比、有机质含量与氮库的影响并不一致。生物滞留池与山地草甸的土壤氮浓度差异，最直接地与生态酶表达介导的有机质含量变化，以及微生物群落可利用碳、氮、磷资源的平衡相关。本研究结果进一步佐证了越来越多的研究结论：当土壤介质与水分可获得性相近时，SGI的生态功能可与邻近的自然植被系统相媲美。

本数据集的文件与R代码结构如下：
- 「Data」文件夹：包含本分析所用的全部原始数据
- 「Results」文件夹：包含所有图表、重复测量方差分析（Repeated Measures Analysis of Variance, RMANOVA）及分段结构方程模型（Piecewise Structural Equation Modeling, PSEM）结果
- 「renv」文件夹：本项目所用的R环境
- 「EEA_Vector_Analysis.R」：用于分析辅酶（Coenzyme, EEA）响应的R代码，包含用于探究生态酶对模拟脉冲降水事件响应差异的RMANOVA分析，以及用于确定养分资源获取策略的向量分析
- 「Gravimetric_soil_moisture_pH.R」：用于对重量法土壤含水率与pH响应开展RMANOVA分析的R代码
- 「MicrobialBiomass_EEA.Rproj」：下载获得的R项目文件
- 「Microbial_biomass.R」：用于对微生物生物量碳、氮及碳氮比对模拟脉冲降水事件的响应开展RMANOVA分析的R代码
- 「OM_protien_N_pools_fluxes.R」：用于对有机质含量、蛋白质、氮库及通量对模拟脉冲降水事件的响应开展RMANOVA分析的R代码（注：文件名中「protien」为拼写失误，标准拼写应为「protein」）
- 「PSEM_final.R」：用于开展皮尔逊相关分析与分段结构方程模型的R代码
- 「Rclimate.R」：用于从GIRF与TM气候及土壤传感器获取气候数据统计摘要的R代码