/St 11 Diamond v.0.9.30 was used to annotate the ORFs, by conducting a BLASTP search against the NCBI NR database (downloaded on May 29, 2019) at E‐value ≤ 10− 5 (Buchfink et al., 2015). Using 16S rRNA gene amplicon sequencing, we explored the structure and diversity of soil bacterial communities. 3 0 obj Abbreviations are as follows: Act_b (Actinobacteria), Act_m (Actinomadura), Mycobact (Mycobacterium), Solirubro (Solirubrobacterales), MDR (multidrug), Tet (tetracycline), Amg (aminoglycoside), MLS (macrolide‐lincosamide‐streptogramin), Beta (β‐lactam), Bcr (bacitracin), Fos (fosmidomycin), Kas (kasugamycin), Pol (polymyxin), Qns (quinolone), Rif (rifamycin), Tcm (tetracenomycin), Van (vancomycin); Ant_Biocides (Antimicrobial Efflux/Biocides), Verru (Verrucomicrobia). /MediaBox [0 0 595 842] /Annots [82 0 R] /PageLabels 4 0 R 20 0 obj The protein product of nrsC shows no homology to pro-teins encoded by the czc or related operons. /CA 1 Annu Rev Microbiol. High‐quality reads for the 24 selected samples were de novo assembled using the default k‐mer size using Spades v.3.9.0 (Bankevich et al., 2012). Compared with samples from Upper Three Runs, soils from Ash Basins displayed significantly higher abundances of several bacterial orders including Acidobacteriales, Solibacterales (Acidobacteria), Chthoniobacterales (Verrucomicrobia), Solirubrobacterales (Bacteroidetes), Sphingobacteriales (Bacteroidetes), Bacillales among others (Table S2). Proc Natl Acad Sci U S A. /Type /Catalog Fitted variation refers to variance within the linear model created during the DistLM analysis. /BM /Normal 11 0 obj Group differences in soil taxa between Upper Three Runs and Ash Basins. Resulting libraries were verified on a 1.5 % agarose gel, cleaned with SeraPure Speedbeads, quantified using a Qubit 2.0, and pooled for sequencing on a HiSeq 3000 PE150. /CropBox [0 0 595 842] endobj
/MediaBox [0 0 595 842] << Major bacterial hosts of ARGs and MRGs shared between sites were visualized using Circos Table Viewer v0.63‐9 (Krzywinski et al., 2009). To test for the significant variation in taxonomic richness across the four sampling sites, we used the non‐parametric Kruskal–Wallis test with the False Discovery Rate (FDR) correction (Kruskal, 1964; Storey, 2011).
/MediaBox [0 0 595 842] Co‐occurrence patterns revealed significant ARG/MRG subtypes in predominant soil taxa including Acidobacteriaceae, Bradyrhizobium, Mycobacterium, Streptomyces, Verrumicrobium, Actinomadura and Solirubacterales. Table S16. Soils from Ash Basins are contaminated with coal combustion waste containing a range of metals and metalloids such as arsenic (As), chromium (Cr), cadmium (Cd), copper (Cu), iron (Fe), nickel (Ni), selenium (Se) and Zinc (Zn; Tannenbaum and Beasley, 2016). The mean weighted nearest sequenced taxon index (NSTI), which measures the prediction accuracy of PICRUSt, for our soil samples was 0.17 ± 0.02.
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