Contrasting functional responses of benthic and hyporheic stream biofilms to light availability and macronutrient stoichiometry

General Information This repository belongs to the article "Contrasting functional responses of benthic and hyporheic stream biofilms to light availability and macronutrient stoichiometry" (https://doi.org/10.1002/lno.70069 ). Data Files There are three categories of data files: raw data, R code and results tables. Raw Data Files The Data.csv table is the collection of all measured variables. The table is structured in flume ID (1-24), sampling depth (B = benthic, H = hyporheic), sampling day (day 7 or day 14), the value, the unit and the parameter that belong to the value. The parameters include some abbreviations: BD is bacterial density, BP is bacterial production, EPS is extracellular polymeric substance as glucose equivalent, Chl a is chlorophyll a, Functional H' is the Shannon diversity index as functional diversity of the substrates in the Biolog Ecoplates, NUSE and PUSE are the share of N and P containing substrates. The Biolog.csv table contains the absorbance data of the Biolog Ecoplates. The table is structured in sampling depth (B = benthic, H = hyporheic), sampling day (day 7 or day 14), light availability (L- = low, L+ = high), C:N:P ratio (CP- = ambient, CP+ = altered), flume ID (1-24), incubation time of Ecoplates (~every 24h for 7 days after the sampling) as well as the absorbance of the 31 substrates. Absorbances are already corrected for background absorbance of the well without substrate. The Treatment.csv table contains the treatment information for every flume. The table is structured in flume ID (1-24), light availability (L- = low, L+ = high), C:N:P ratio (CP- = ambient, CP+ = altered) as well as the treatment in general, what is the combination of light availability and C:N:P ratio. The LoggerMOBICOS.csv table contains the environmental data from the monitoring station located at the experiments site. These data are values for chlorophyll a, conductivity, nitrate, cxygen concentrations and saturation, PAR, turbidity, water temperature and pH value. The LightInput.csv table contains light-data in PAR for 15-min-intervals in September 2020 and 2021. Further descriptions can be found in comparison_light_intensities.qmd. R Code The key code document is the DataAnalysis.Rmd. It contains the entire data analysis of the article. This code document reads the four raw data files (Data.csv, Biolog.csv, Treatment. csv, LoggerMOBICOS.csv) and the functions from Ecoplatesfunctions.R. The output of this code are all figures, including the ones from the supporting information of the article. Furthermore the PERMANOVA output tables (PERMANOVA_date.csv and PERMANOVA_Treatment.csv) will be created to summarize the PERMANOVA results investigating effects of sampling day or light, C:N:P ratios and their interaction on the measured variables. The table LoggerMOBICOS.csv is summarised as mean and standard deviation per parameter over the entire experiments time in the output table EnvironmentalData.csv . We used a method from N. Perujo, A.M. Romaní, J.A. Martín-Fernández, Microbial community-level physiological profiles: Considering whole data set and integrating dynamics of colour development to analyse the Biolog Ecoplates results in canonical variates plots. The data analysis is part of the DataAnalysis.Rmd code and the adapted functions that are needed are stored in the script Ecoplatesfunctions.R. To further explain the selected light intensities for the low and high light treatment, we added the document comparison_light_intensities.qmd to classify the selected light intensities in the context of the experiments site. Therefore the LightInput.csv data from a Master thesis by Frederik Lemke (title: Nitrate assimilation in a stoichiometric and light gradient in a stream under varying land use) were used to get information about the 5th and 95th percentile of the light availabiliy in September at the experiments site. The output of this document is comparison_light_intensities.html. Output Files The output table PERMANOVA_date.csv lists the PERMANOVA results testing an effect of the sampling day for every paramter and sampling depth combination The output table PERMANOVA_Treatment.csv lists the PERMANOVA results testing an effect of light availability, C:N:P ratio and their interaction for every combination of parameter, sampling depth and sampling day The output table EnvironmentalData.csv contains the mean values and standard deviations for chlorophyll a, conductivity, nitrate, oxygen concentration and saturation, PAR, turbidity, water temperature and ph-value in the river Holtemme at the experiments site. There will be an html output document when knitting the code document DataAnalysis.Rmd containing all important information, comments, output tables and figures that can be downloaded as DataAnalysis.html. There will be an html output document when knitting the code document comparison_light_intensities.qmd containing all important information, comments, output tables and figures that can be downloaded as comparison_light_intensities.html. R Setup The R code in this repository was developed with R version 4.4. and uses the following R libraries: dplyr ggplot2 RColorBrewer vegan zCompositions candisc readxl psych magrittr car pairwiseAdonis multcompView ggh4x Disclaimers The authors do not take any responsibility for damage done to the user system by executing the code of this repository.基本信息 本仓库关联于论文《底栖与潜流溪流生物膜对光照可利用性及大量营养元素化学计量比的对比响应》（https://doi.org/10.1002/lno.70069）。 数据文件 本仓库的数据文件分为三类：原始数据、R代码与结果表格。 原始数据文件 Data.csv表格：收录所有实测变量，字段包含水槽ID（1-24）、采样深度（B代表底栖，H代表潜流）、采样天数（第7天或第14天）、数值、单位以及对应参数。参数缩写说明如下：BD为细菌密度（bacterial density, BD），BP为细菌生产力（bacterial production, BP），EPS为以葡萄糖当量计的胞外聚合物（extracellular polymeric substance, EPS），Chl a为叶绿素a（Chlorophyll a, Chl a），Functional H'为Biolog Ecoplates底物功能多样性的香农多样性指数（Shannon diversity index），NUSE与PUSE分别为含氮、含磷底物的占比。 Biolog.csv表格：包含Biolog Ecoplates的吸光度数据，字段涵盖采样深度、采样天数、光照可利用性（L-代表低光照，L+代表高光照）、C:N:P比值（CP-为环境背景值，CP+为改变组）、水槽ID、Ecoplates培养时长（采样后每24小时检测一次，共持续7天）以及31种底物的吸光度。所有吸光度已扣除无底物空白孔的背景吸光度。 Treatment.csv表格：收录每个水槽的处理信息，字段包含水槽ID、光照可利用性、C:N:P比值以及通用处理项（即光照可利用性与C:N:P比值的组合）。 LoggerMOBICOS.csv表格：包含实验站点监测站的环境数据，涉及叶绿素a、电导率、硝酸盐、氧浓度与饱和度、光合有效辐射（Photosynthetically Active Radiation, PAR）、浊度、水温及pH值。 LightInput.csv表格：收录2020年与2021年9月每15分钟间隔的PAR光照数据，更多细节可参见comparison_light_intensities.qmd文档。 R代码 核心代码文档为DataAnalysis.Rmd，包含论文的全部数据分析流程。该代码会读取四个原始数据文件（Data.csv、Biolog.csv、Treatment.csv、LoggerMOBICOS.csv）以及Ecoplatesfunctions.R中的自定义函数，运行后可生成论文所有图表（包括补充材料中的图表）。此外，还将生成置换多元方差分析（Permutational Multivariate Analysis of Variance, PERMANOVA）结果表格（PERMANOVA_date.csv与PERMANOVA_Treatment.csv），用于总结PERMANOVA结果，以探究采样天数、光照可利用性、C:N:P比值及其交互作用对实测变量的影响。LoggerMOBICOS.csv数据将被汇总为实验周期内各参数的均值与标准差，输出至EnvironmentalData.csv表格中。 我们采用了N. Perujo、A.M. Romaní与J.A. Martín-Fernández提出的方法，即《微生物群落水平生理谱：考虑全数据集并整合显色动态以分析Biolog Ecoplates结果的典范变量图法》。该数据分析流程已整合至DataAnalysis.Rmd代码中，所需的适配函数存储于Ecoplatesfunctions.R脚本内。 为进一步阐释所选低、高光照处理的依据，我们补充了comparison_light_intensities.qmd文档，用于在实验站点背景下对所选光照强度进行分类。该文档使用了Frederik Lemke硕士论文（题目为《不同土地利用下溪流中化学计量与光照梯度下的硝酸盐同化作用》）中的LightInput.csv数据，以获取实验站点9月光照可利用性的5%与95%分位数。该文档的输出结果为comparison_light_intensities.html。 输出文件 PERMANOVA_date.csv：列出针对每个参数与采样深度组合检验采样天数效应的PERMANOVA结果。 PERMANOVA_Treatment.csv：列出针对每个参数、采样深度与采样天数组合检验光照可利用性、C:N:P比值及其交互作用效应的PERMANOVA结果。 EnvironmentalData.csv：包含实验站点所在河流Holtemme中叶绿素a、电导率、硝酸盐、氧浓度与饱和度、PAR、浊度、水温及pH值的均值与标准差。 运行DataAnalysis.Rmd代码编织后将生成包含全部关键信息、注释、结果表格与图表的HTML文档，可导出为DataAnalysis.html。 运行comparison_light_intensities.qmd代码编织后将生成包含全部关键信息、注释、结果表格与图表的HTML文档，可导出为comparison_light_intensities.html。 R环境配置 本仓库的R代码基于R 4.4版本开发，使用了以下R扩展包： dplyr、ggplot2、RColorBrewer、vegan、zCompositions、candisc、readxl、psych、magrittr、car、pairwiseAdonis、multcompView、ggh4x 免责声明 作者不对因执行本仓库代码对用户系统造成的任何损害承担责任。