DOI: 10.5061/dryad.6bs01
title: Data from: Treating cattle with antibiotics affects greenhouse gas emissions, and microbiota in dung and dung beetles

description: Antibiotics are routinely used to improve livestock health and growth.
 However, this practice may have unintended environmental impacts mediated
 by interactions among the wide range of micro- and macroorganisms found in
 agroecosystems. For example, antibiotics may alter microbial emissions of
 greenhouse gases by affecting livestock gut microbiota. Furthermore,
 antibiotics may affect the microbiota of non-target animals that rely on
 dung, such as dung beetles, and the ecosystem services they provide. To
 examine these interactions, we treated cattle with a commonly used
 broad-spectrum antibiotic and assessed downstream effects on microbiota in
 dung and dung beetles, greenhouse gas fluxes from dung, and beetle size,
 survival and reproduction. We found that antibiotic treatment restructured
 microbiota in dung beetles, which harboured a microbial community distinct
 from those in the dung they were consuming. The antibiotic effect on
 beetle microbiota was not associated with smaller size or lower numbers.
 Unexpectedly, antibiotic treatment raised methane fluxes from dung,
 possibly by altering the interactions between methanogenic archaea and
 bacteria in rumen and dung environments. Our findings that antibiotics
 restructure dung beetle microbiota and modify greenhouse gas emissions
 from dung indicate that antibiotic treatment may have unintended,
 cascading ecological effects that extend beyond the target animal.
description: Greenhouse gas
 fluxesCumulative
 (interpolated) fluxes of CH4, N2O, and CO2 from each dung mesocosm, which
 is associated with cow ID, the presence/absence of beetles, and treatment
 (antibiotic / control). Note that there were missing readings due to
 technical mishaps: two per compound from mesocosm 39 (antibiotic treatment
 + with beetles); one per compound from mesocosm 49 (control treatment + no
 beetles) and one per compound from mesocosm 51 (control + with beetles).
 These missing values were replaced by the appropriate
 treatment-and-day-specific means for each compound.Gas_fluxes.csvNumber of beetle offspringThe total number of dung beetle offspring collected from dung mesocosms over the course of the experiment. Each mesocosm is associated with a cow ID and treatment (antibiotic or control).Beetle_counts.csvPerformance measurements of beetle offspringThe average head capsule size and fresh weight of larval dung beetle offspring collected from each dung mesocosm. Each mesocosm is associated with cow ID and treatment (antibiotic or control). No head size measurement was available for mesocosm #25.Beetle_performance.csvMapping file for sequence dataThe metadata associated with sequenced samples.Mapping_file.txtReplace Demultiplexed sequencesDemultiplexed paired-end 16S rRNA sequence reads (forward and reverse). These sequences are the output of the UPARSE script prep_fastq_for_uparse_paired.py (they have not been merged or quality-filtered). Note that this sequence run was a combination of additional samples/projects not included in the paper (not in the associated mapping file).demultiplexed_seqs.gzOTU tableThe OTU table used in analyses (previous sequence data processing steps described in the Methods). This dataset has not been rarefied or filtered (e.g. to remove mitochondria, chloroplasts, OTUs in negative controls - see Methods). The Greengenes-assigned taxonomy strings associated with each OTU are in the right-most columns.otu_table_raw.txt