Environmental DNA metabarcoding reveals temporal dynamics but functional stability of arthropod communities in cattle dung

Terrestrial invertebrates are highly important for the decomposition of dung from large mammals. Mammal dung has been present in most of Earth’s ecosystems for millions of years, enabling the evolution of a broad diversity of dung-associated invertebrates that process various components of the dung. Today, large herbivore mammals are increasingly introduced to ecosystems with the aim of restoring the ecological functions formerly provided by their extinct counterparts. However, we still know little about the ecosystem functions and nutrient flows in these rewilded ecosystems, including the dynamics of dung decomposition. In fact, the succession of insect communities in dung is an area of limited research attention also outside of a rewilding context. In this study, we use environmental DNA metabarcoding of dung from rewilded Galloway cattle in an experimental setup to investigate invertebrate communities and functional dynamics over a time span of 53 days, starting from the time of depo..., The dataset consists of DNA reads from High Throughput sequencing of samples collected through an natural experiment investigating invertebrate succession in cattle dung. The experiment was conducted in the Mols Laboratory area in Denmark (56°13′36”N, 10°34′33″E), where 60 kg of fresh dung was collected, homogenized, and separated out in 18 pools, which were placed in six experimental plots. Three plots were located in meadows and three were located in pastures. Samples were collected from all 18 dung pools after 1, 4, 11, 25, 39, and 53 days, resulting in 108 samples in total. In addition, three fresh dung samples were collected, and three samples were taken from the homogenized pool before if was divided in the 18 sub-pools, as starting-point controls. DNA was extracted from the samples with the Fast DNA Stool Mini Kit from Qiagen, and amplified by PCR reactions (see PCR reagents and thermal settings, etc. in the associated manuscript) with the BF-1/BR-1 primers (Elbrecht & Leese,..., , # Data from: Environmental DNA metabarcoding reveals temporal dynamics but functional stability of arthropod communities in cattle dung

# Bioinformatic pipeline:

## Setting up the directory structure on a HPC cluster

mkdir root_dir
mkdir root_dir/COI
mkdir root_dir/COI/raw_data
cd root_dir

## Place all downloaded files in the root directory (root\_dir)

## Set up directories for each library

cd COI/raw_data
mkdir Pool_1_1A_2 Pool_2_1B_2 Pool_3_1C_2 Pool_4_1D_2 Pool_5_2A_2 Pool_6_2B_2 Pool_7_2C_2 Pool_7_2C_2_additional Pool_8_2D_2 Pool_9_3A_2 Pool_10_3B_2 Pool_10_3B_2_additional Pool_11_3C_2 Pool_11_3C_2_additional Pool_12_3D_2 Pool_12_3D_2_additional
cd ..

## Putting the files in the right places

mv Pool_1_1A_2* COI/raw_data/Pool_1_1A_2/.
mv Pool_2_1B_2* COI/raw_data/Pool_2_1B_2/.
mv Pool_3_1C_2* COI/raw_data/Pool_3_1C_2/.
mv Pool_4_1D_2* COI/raw_data/Pool_4_1D_2/.
mv Pool_5_2A_2* COI/raw_data/Pool_5_2A_2/.
mv Pool_6_2B_2* COI/raw_data/Pool_6_2B_2/.
mv Pool_7_2C_2* COI/raw_data/P...