DOI: 10.5281/zenodo.16367600
title: Contrasting functional responses of benthic and hyporheic stream biofilms to light availability and macronutrient stoichiometry

description: 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.