3 research outputs found
Effect of Manure Application on Abundance of Antibiotic Resistance Genes and Their Attenuation Rates in Soil: Field-Scale Mass Balance Approach
The development of models for understanding
antibiotic resistance
gene (ARG) persistence and transport is a critical next step toward
informing mitigation strategies to prevent the spread of antibiotic
resistance in the environment. A field study was performed that used
a mass balance approach to gain insight into the transport and dissipation
of ARGs following land application of manure. Soil from a small drainage
plot including a manure application site, an unmanured control site,
and an adjacent stream and buffer zone were sampled for ARGs and metals
before and after application of dairy manure slurry and a dry stack
mixture of equine, bovine, and ovine manure. Results of mass balance
suggest growth of bacterial hosts containing ARGs and/or horizontal
gene transfer immediately following slurry application with respect
to <i>ermF</i>, <i>sul1</i>, and <i>sul2</i> and following a lag (13 days) for dry-stack-amended soils. Generally
no effects on <i>tet</i>(G), <i>tet</i>(O), or <i>tet</i>(W) soil concentrations were observed despite the presence
of these genes in applied manure. Dissipation rates were fastest for <i>ermF</i> in slurry-treated soils (logarithmic decay coefficient
of −3.5) and for <i>sul1</i> and <i>sul2</i> in dry-stack-amended soils (logarithmic decay coefficients of −0.54
and −0.48, respectively), and evidence for surface and subsurface
transport was not observed. Results provide a mass balance approach
for tracking ARG fate and insights to inform modeling and limiting
the transport of manure-borne ARGs to neighboring surface water
Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element
The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in D. ananassae. To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae. Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5′ ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains