Data from: Short-term microbial dynamics and changes in greenhouse gas emissions in cattle dung treated with ivermectin

[Description of methods used for collection/generation of data] The experiments were conducted at two sites within Doñana National Park (Andalusia, southern Spain) located 10 km apart: the Doñana Biological Reserve, which is traditionally grazed by organic livestock that does not receive veterinary medical products, and Los Sotos, characterised by the long-term presence of livestock treated with ivermectin (“site” factor). At both sites, short-term temporal variation in CO2 and CH4 emissions from dung pats was measured under two conditions: allowing or preventing dung beetle colonisation (“beetle” factor), and using dung pats either with or without ivermectin (“dung treatment” factor). Eight artificial dung pats were placed on the ground to assess CO2 and CH4 emissions at four different time points (“time” factor): immediately after placement (T0), 6 hours (T1), 24 hours (T2), and 48 hours after placement (T3). In total, 256 artificial dung pats were placed (8 dung pats x 4 time levels x 2 beetle levels x 2 dung treatment level x 2 site levels. After estimating CO2 and CH4 emissions using a portable gas analyser, all dung beetles from pats where colonisation was allowed were manually collected and transferred to pots for taxonomic identification, allowing the calculation of species richness, abundance, and biomass (fresh weight). CO2 concentrations were corrected to avoid overestimation by subtracting the contributions of soil respiration (microbiota, edaphic mesofauna, etc.), vegetation respiration, and dung beetle respiration. To estimate microbiota, ten artificial dung pats were arranged in two rows spaced 5 meters apart. One row contained dung pats with ivermectin, and the other without (“dung treatment” factor). Dung samples of 2 cm3 were extracted from non-contiguous portions of the centre of the pats at the same four time points (“time” factor). Of the potential 80 samples (10 dung pats x 2 dung treatment levels x 4 time levels), 14 were damaged. Molecular and bioinformatic analyses were performed to characterize archaea and bacteria present in the dung samples. DNA was extracted and purified, followed by multiplex PCR amplification and Illumina MiSeq sequencing. The V4 variable region of the 16S rRNA gene was amplified, and raw sequences were processed using the UPARSE pipeline. After merging paired reads, approximately 70.5% of the original reads were retained (2,477,067 reads out of 3,512,012). These retained reads were dereplicated (collapsing sequences at 100% identity) and clustered into zero-radius operational taxonomic units (zOTUs), excluding singletons. Over 85.05% of the merged sequence pool (2,912,356 reads) was mapped back to the zOTUs, resulting in 3,427 prokaryotic zOTUs. Taxonomic assignments were carried out using the SILVA_138 database via the SINA reference-based multiple sequence alignment tool. The final curated dataset comprised 3,403 prokaryotic zOTUs. The complete gene sequence dataset has been deposited in the NCBI Sequence Read Archive under BioProject ID PRJNA515520 and is available upon request. Environmental ontology descriptive terms (EnvO terms) were extracted from the closest sequences matches (99% identity) in the GenBank global databases using the SEQenv pipeline.