Article Figures & Data
Figures
- FIG 1
Geographical distributions of NYC WWTPs. This New York City map indicates the drainage areas for the 14 WWTPs across the five NYC boroughs from which samples were obtained for this study. The map was plotted with the Maptools package in R using GIS data obtained from Open Sewer Atlas NYC (http://openseweratlas.tumblr.com/data).
- FIG 2
Alpha diversity in 102 sequenced sewage samples. Rarefaction was based on (A) phylogenetic diversity. (B) Observed number of OTUs. The x axes represent the numbers of sequences used in the rarefaction analysis. (C) Box-and-whisker plots depicting the species-level richness and diversity of OTUs based on the Shannon diversity index in the sewage samples. Within the boxes, the central line represents the median values, and the upper and lower boundaries indicate the 75th and 25th percentiles, respectively. The whiskers show the maximum and minimum values. Top panels show results based on location (NYC borough); bottom panels show results based on sampling season. Statistical significance was tested by one-way analysis of variance using the Kruskal-Wallis test, followed by multiple comparisons using Dunn’s test (****, P < 0.0001).
- FIG 3
Beta diversity in sewage samples. PCoA results represent unweighted (A and C) and weighted (B and D) UniFrac distances by NYC major drainage area (lower panels) and sampling season (upper panels). Statistical significance was tested by the Adonis test using the Vegan package in R. Each of the data sets indicated distinctions between the tested groups at P < 0.001.
- FIG 4
Relative taxonomic abundances of the assignments in 102 sewage samples. Samples are grouped by family according to NYC borough and sampling season. Taxonomy was assigned to the identified OTUs based on Greengenes database v13.8. Only families represented by >3% abundance are listed.
- FIG 5
Differentially abundant OTUs identified in 102 sewage samples. LEfSe analyses were performed based on NYC borough (A) and sampling time point (B). Significantly abundant OTUs were determined based on an alpha value of <0.05 and a logarithmic LDA score (effect size) of >4.0.
- FIG 6
16S rRNA gene copies in NYC sewage samples. (A) Abundances normalized against the volume of sample used. (B) Biomass concentrations of the sewage samples determined by the ratio of the 16S rRNA copies to the total DNA extracted (ng) for each sample. Each box represents a scatter of the mean values of the 17 replicated sewage samples collected at that particular time point. Error bars indicate the standard deviations at each time point. Statistical significance was determined by using a one-factor Friedman’s test, followed by Dunn’s multiple-comparison test (**, P < 0.01; ***, P < 0.001; ****, P < 0.0001).
- FIG 7
Antibiotic resistance gene representation in proportion to the 16S rRNA gene copies in the NYC sewage samples. Collections were made during February, May, and August 2015. (A) A Circos diagram represents the percent breakdown of the presence of the measured ARG concentrations in each month and vice versa indicated by the connecting ribbons. (B) Ratios were calculated by normalization of antibiotic resistance gene abundance against the 16S rRNA gene abundance for each sample at each time point. Each box represents a scatter of the mean values of the ratios for the 17 replicated sewage samples collected at that time point. The bars indicate the standard deviations at each time point. Statistical significance was determined using a one-factor Friedman’s test, followed by Dunn’s multiple-comparison test (**, P < 0.01; ***, P < 0.001; ****, P < 0.0001).
Tables
- TABLE 1
Summary of the results obtained after quantitative monitoring of the 16S rRNA gene and seven ARGs in the sewage samples obtained from 14 NYC WWTPs over three sampling time pointsa
Gene
testedFebruary May August Mean gene
copies/ml
of sewageMean %
resistance gene/
16S gene copiesMean gene
copies/ml
of sewageMean %
resistance gene/
16S gene copiesMean gene
copies/ml
of sewageMean %
resistance gene/
16S gene copies16S 2.68E+08 NA 7.1E+08 NA 8.13E+07 NA mecA 3.65E+03 0.002 9.1E+02 0.0001 2.51E+01 0.00003 blaTEM-1 2.00E+05 0.31 7.47E+06 1.17 2.57E+05 0.3248 ermB 5.95E+05 0.13 2.27E+06 0.27 1.02E+05 0.13 tetO 3.72E+06 3.19 1.06E+07 1.53 2.35E+06 3.148 tetC 8.44E+05 0.3 3.04E+07 4.2 3.36E+06 4.15 vanA 4.05E+05 0.21 1.22E+07 1.83 1.70E+06 1.81 sul1 7.37E+05 0.44 1.2E+07 1.77 1.44E+06 1.72 ↵a NA, not applicable. Boldfacing indicates data for the 16S gene.
FIG S1
Beta diversity in the 102 sewage samples presented using the open-reference OTU picking algorithm. PCoAs show unweighted (A and C) and weighted (B and D) UniFrac distances based on sequencing run (upper panels) and sampling month (lower panel). Statistical significance was tested with the Adonis test using the vegan package in R. Download FIG S1, TIF file, 1.0 MB.
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This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
TABLE S1
Details of the sample IDs and sampling and sequencing information for the sewage samples included in this study. Download Table S1, XLSX file, 0.01 MB.
Copyright © 2019 Joseph et al.
This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
FIG S2
Beta diversity in the technical replicates of the sewage samples. PCoAs representing unweighted (A and C) and weighted (B and D) UniFrac distances in the May replicate samples using the open-reference OTU picking algorithm (upper panels) and after exclusion of the OTUs differing between the replicate groups (lower panels). Statistical significance was examined with the Adonis test using the vegan package in R. Download FIG S2, TIF file, 1.0 MB.
Copyright © 2019 Joseph et al.
This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
FIG S3
Beta diversity in the 102 sewage samples using a closed-reference OTU picking algorithm. PCoA plots showing unweighted (A and C) and weighted (B and D) UniFrac distances, respectively, based on sequencing runs (upper panels) and sampling month (lower panels). Statistical significance was tested with the Adonis test using the vegan package in R. Download FIG S3, TIF file, 0.9 MB.
Copyright © 2019 Joseph et al.
This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
FIG S4
Abundance of seven ARGs detected in the NYC sewage samples. Collections were made during February, May, and August 2015. Each box represents the scatter of the mean abundance values of the 17 replicated sewage samples collected at that particular time point. The error bars indicate the standard deviations at each time point. Statistical significance was determined using a one-factor Freidman’s test, followed by Dunn’s multiple-comparison test (**, P < 0.01; ***, P < 0.001; ****, P < 0.0001). Download FIG S4, TIF file, 1.1 MB.
Copyright © 2019 Joseph et al.
This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
TABLE S2
Details of the antibiotic resistance genes and primers used in the qPCR studies of the sewage samples. Download Table S2, XLSX file, 0.01 MB.
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This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
TABLE S3
Complete list of the 73 bacterial families identified from 384 OTUs and their relative abundances based on their sampling locations and season. Download Table S3, XLSX file, 0.03 MB.
Copyright © 2019 Joseph et al.
This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
TABLE S4
Results of linear regression analysis to compare the abundances of the 16S rRNA genes in the population to the abundances of the seven AR genes for the three sampling time points. Analysis was conducted using GraphPad Prism 7 on the log-transformed values of the qPCR data. Download Table S4, XLSX file, 0.01 MB.
Copyright © 2019 Joseph et al.
This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.
