DOI: 10.5281/zenodo.15882501
title: Stream C to N to P ratios aligned with microbial needs enhance biofilm nitrate uptake and subsequent nitrogen loss

description: General information

This repository belongs to the article "Stream C to N to P ratios aligned with microbial needs enhance biofilm nitrate uptake and subsequent nitrogen loss".

Data files

This repository contains three categories of data files: raw data, R code and result tables.

Raw data files



The Data.csv file contains all data that are used for the article. The parameters were measured in the water column (Depth = W), benthic biofilm (Depth = B), and hyporheic biofilm (Depth = H) on day 7 and day 14 of the experiment. The measured parameters in the water column are dissolved nitrogen (DNb), total nitrogen (TNb), nitrate (NO3-N), nitrite (NO2-N), ammonium (NH4-N), total phosphorus (TP), total organic carbon (TOC) and soluble reactive phosphorus (SRP). In benthic and hyporheic biofilm we measured particulate nitrogen (PN), Particulate organic carbon (POC), Particulate phosphorus (PP) as well as the 15N atom fraction (atom fraction). 

The DataTernary.csv file contains the coordinates for the depletion zones in the ternary diagrams.


R code



The Data_Analysis.Rmd file is the R code document with the entire data analysis. The document reads the files with the raw data Data.csv and the coordinates for the depletion zones DataTernary.csv. All parameters were analyzed with the PERMANOVA for effects of the sampling day and the sup-datasets per sampling day were analyzed for effects of light, C:N:P ratio and their interaction. These results are printed in the output files PERMANOVA_Date.csv and PERMANOVA_Light_CNP.csv. The decreasing signal of 15N in benthic biofilms were analysed with a linear mixed-effect model. The output of this analysis can be found in LMM.csv. A treatment-specific summary of all parameters (mean and standard deviation) are saved as Summary.csv.


Output files



The output file PERMANOVA_Date.csv lists the PERMANOVA results testing an effect of the sampling day for every parameter and sampling depth combination.

The output file PERMANOVA_Light_CNP.csv lists the PERMANOVA results testing an effect of light availability and dissolved reactive C:N:P ratios in the water column for each parameter, sampling depth and day combination.

The output file LMM.csv contains the results of the linear mixed-effect model investigating the decrease of N assimilated during the tracer addition over time.

The output file Summary.csv contains treatment-specific menas and standard deviations of all parameter per sampling depth and day.

There will be an html output document when knitting the code document Data_Analysis.Rmd containing all important information, comments, output tables and figures that can be downloaded as Data_Analysis.html.


R Setup

The R code in this repository was developed with R version 4.4. and uses the following R libraries:



ggplot2

dplyr

lme4

performance

parameters

ggeffects

DHARMa

tidyverse

RColorBrewer

knitr

pairwiseAdonis

multcompView

ggh4x

ggtern

ggpubr

merDeriv


Disclaimers

The authors do not take any responsibility for damage done to the user system by executing the code of this repository.