Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil
- Published
- Accepted
- Subject Areas
- Bioinformatics, Ecology, Microbiology, Soil Science, Environmental Impacts
- Keywords
- thermophile, gene-targeted assembly, metagenome, rplB, coal fire
- Copyright
- © 2017 Dunivin et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil. PeerJ Preprints 5:e3484v1 https://doi.org/10.7287/peerj.preprints.3484v1
Abstract
Soils are reservoirs of antibiotic resistance genes, but dynamics of antibiotic resistance genes in the environment are largely unknown. Long-term disturbances offer extended opportunities to examine microbiome responses at scales relevant for both ecological and evolutionary processes, and therefore can be insightful for studying the dynamics of antibiotic resistance genes in the environment. We examined antibiotic resistance genes in soils overlying the underground coal seam fire in Centralia, PA, which has been burning since 1962. As the fire progresses, previously hot soils can recover to ambient temperatures, which creates a gradient of contemporary and historical fire impact. We examined metagenomes from fire-affected, recovered, and reference surface soils to examine gene-resolved dynamics of antibiotic resistance using a gene-targeted assembler. We targeted 35 distinct types of clinically-relevant antibiotic resistance genes and two horizontal gene transfer-related genes (intI and repA). We detected 17 antibiotic resistance genes in Centralia, including AAC6-Ia, adeB, bla_A, bla_B, bla_C, cmlA, dfra12, intI, sul2, tetA, tetW, tetX, tolC, vanA, vanH, vanX, and vanZ. The diversity and abundance of several antibiotic resistance genes (bla_A, bla_B, dfra12, tolC) decreased with soil temperature, and changes in ARGs could largely be explained by associated changes in community structure. We also observed sequence-specific dynamics along the temperature gradient and observed compositional shifts in bla_A, dfra12, and intI. These results suggest that increased temperatures can reduce soil antibiotic resistance genes but that this is largely due to a concomitant reduction in community-level diversity.
Author Comment
This is a preprint submission to PeerJ Preprints.
Supplemental Information
Figure S1: Sampling strategy along the Centralia temperature gradient
Twelve surface soils were collected along two fire fronts. Sampling sites are classified based on historical fire activity (Elick 2011) and observations of fire activity at the time of sampling: fire affected (red), recovered (yellow), and recovered (green, reference). Red bullseye indicates fire origin, and fire fronts one and two are indicated with arrows (F1 and F2, respectively).
Figure S2: Comparison of community structure assessed using two different methods
Community structure determined by rplB (A) is similar to previously described community structure determined by 16S rRNA gene sequencing reported in Lee and Sorensen et al. 2017(B). Samples are classified by their fire history: fire affected (n = 6), recovered (n = 5), and reference (n = 1).
Figure S3: Pair-wise Spearman’s correlations of normalized ARG abundances in Centralia
Spearman’s rho is indicated in each cell and by color, where negative correlations are red and positive correlations are blue. False discovery rate adjusted significance is noted by asterisks.
Figure S4: Relationship between normalized abundance of ARGs and soil temperature
Point shape indicates soil fire classification. Coverage-adjusted abundance for each gene was normalized to total abundance of single copy gene rplB. Normalized abundance is plotted against soil temperature. Note the differences in y-axes. Shape indicates soil classification based on fire history.
Figure S5: Beta diversity of Centralia microbial communities with rplB and ARGs
Principal coordinate analysis (PCoA) based on weighted Bray-Curtis distances of community structure (A) and ARG structure (B). Colors represent soil temperature, and shape indicates soil classification based on fire history.
Supplemental Tables: Supplemental tables accompanying the manuscript
Supplemental tables accompanying the manuscript.