Data and R code for "Do antimicrobial substances impact brown food webs bottom-up? A proof of concept with ciprofloxacin and azoxystrobin"

This repository contains the data and R scripts associated with the manuscript "Do antimicrobial substances impact food webs bottom-up? A proof of concept with ciprofloxacin and azoxystrobin" by Meyer et al. (submitted to Environmental Toxicology & Chemistry). The archive includes: qPCR data: Bacterial and fungal DNA abundances for both azoxystrobin and ciprofloxacin exposures (in .xlsx format). Community composition: Raw and processed macroinvertebrate community data (species and functional feeding groups) from mesocosm experiments. Analytical data: Concentration measurements of antimicrobial substances. Stream and treatment metadata: Channel-level treatment information (stream_info.csv). R scripts (in /code/): Full analysis pipeline, including: 00_setup.R: Package loading and environment setup 01_community.R: Community composition analysis (NMDS, PERMANOVA, SIMPER) 02_qPCR.R: Analysis of microbial abundance (ANOVA, linear modeling) Figures: Output NMDS plots and visualizations (in /figures/). All statistical analyses were conducted in R using vegan, tidyverse, and related packages. An aqua-co-reg_WP1.Rproj file is provided to facilitate project loading in RStudio.