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Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil

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Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil https://t.co/Jd94ZE1smd #microbiomebot
Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil https://t.co/P8mlfxUPuh
272 days ago
Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil https://t.co/i9FdEZiLvD
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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).

DOI: 10.7287/peerj.preprints.3484v1/supp-1

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).

DOI: 10.7287/peerj.preprints.3484v1/supp-2

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.

DOI: 10.7287/peerj.preprints.3484v1/supp-3

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.

DOI: 10.7287/peerj.preprints.3484v1/supp-4

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.

DOI: 10.7287/peerj.preprints.3484v1/supp-5

Supplemental Tables: Supplemental tables accompanying the manuscript

Supplemental tables accompanying the manuscript.

DOI: 10.7287/peerj.preprints.3484v1/supp-6

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Taylor K Dunivin conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Ashley Shade conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Metagenomes are fully available through the DOE's IMG/GOLD study ID Gs0114513 and are accessible via the link: https://gold.jgi.doe.gov/studies?id=Gs0114513

Data Deposition

The following information was supplied regarding data availability:

We have provided all of our analysis code on our GitHub repository: https://github.com/ShadeLab/PAPER_Dunivin_Antibiotics_2017

Funding

Metagenome sequencing was supported by the Joint Genome Institute Community Science Project #1834. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. TKD was supported by the Department of Microbiology and Molecular Genetics Ronald and Sharon Rogowski Fellowship for Food Safety and Toxicology Graduate Fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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