Article Figures & Data
- FIG 1
Schematic showing the sampling points at the DWTP (black circle) and in the three sectors of the DWDS (blue circles, sector 1; yellow circles, sector 2; orange circles, sector 3) included in this study and the layout of the pipe network connecting them. Dashed lines are scaled to the pipe lengths, and bold lines are scaled to the pipe surface area between any two sampling points. Scale bars for pipe length and surface area are shown at the bottom of the figure. Sampling points in sector 1 are located along a linear flow path, while sectors 2 and 3 have two and three branches, respectively.
- FIG 2
(A) Class-level relative abundances based on all sequences detected at all sampling locations within each month. Five classes of Proteobacteria are shown separately, while the remaining 19 phyla are shown as a single group (i.e., other bacteria). (B) The changes in relative abundance of one alphaproteobacterial OTU (blue) are compared to those of three betaproteobacterial OTUs (red) for each of the sampling months. Error bars for each data point represent standard deviations in relative abundance across all monitoring locations within each month.
- FIG 3
Temporal change in richness (i.e., observed OTUs) averaged across sampling locations within each month (A) correlates with water temperature (black squares), conductivity (black circles), and the surface water/ground water ratio (smooth black line) (B). Error bars indicate standard deviations in respective metrics/measurements across sampling locations within each month.
- FIG 4
(A) Bray-Curtis distances (black squares) and weighted UniFrac distances (black circles) of the DWDS sampling locations (x axis) from the reservoir at the DWTP averaged over the duration of the study. (B) Correlations between Bray-Curtis distances (black squares) and weighted UniFrac distances (black circles) of bacterial communities sampled at any two locations in sector 1 and the pipe surface area connecting them. Error bars for both plots show variability over the 15-month sampling campaign in the respective beta diversity metric.
- FIG 5
(A) Principal-coordinate biplot showing the temporal variability of the bacterial community structure constructed using the Bray-Curtis distance metric. Data points are colored by month, and the legend is provided above the plot. Environmental and process parameters, with significant Pearson’s correlation (P < 0.000001) with either of the two principal axes, are shown here. Beta diversity distance between samples as a function of time difference (months) between them using membership-based (Jaccard [black circles]; unweighted UniFrac [black squares]) (B) and structure-based (Bray-Curtis [open diamonds]; weighted UniFrac [open triangles]) (C) metrics. Error bars in panels B and C indicate variability in beta diversity distance for sample comparisons for each time difference.
- FIG 6
(Left) Network visualization of associations between OTUs with a detection frequency greater than 30%. Each node depicts an individual OTU, with the size of the node corresponding to its log (1 + X)-normalized relative abundance and the color depicting its detection frequency (white, 30%; dark blue, 100%). The edges indicate associations between OTUs; the thickness of an edge is scaled to the association strength (MIC range = 0.4 to 1), and color indicates positive (green) or negative (red) associations. Square, diamond, and triangle OTU nodes belong to clusters 1, 2, and 3, respectively, while the group of isolated taxa consists of circular OTU nodes. (Right) Relative abundances of the clusters discovered through association analyses for each sampling month. Blue hatched, cluster 1; red hatched, cluster 2; solid green, cluster 3; solid white, isolated taxa.
- FIG 7
(A) The Hanski-Gyllenberg model (Table 1) resulted in the best fit (red line) to the frequency-abundance data from the Ann Arbor DW system. The OTU abundances were estimated by averaging the relative abundances of each taxon across all sampling locations within each sampling time point (i.e., month); frequency represents the proportion of samples in which the OTU was detected within each sampling time point. (B) The fitted value of α for each month (red circles) was within bounds of the permuted random α values (box plot: black, first quartile; gray, third quartile; whiskers, minimum and maximum values) obtained from 1,000 permutations and the overall α value for the entire data set (red line). February 2011 was the exception, with a lower-than-expected α value.
- TABLE 1
Interspecific occupancy-abundance modeling with the maximum-likelihood-based determination of the best-fit modela
Model Model form Maximum likelihood Mean absolute deviance Reference Poisson −109082.22 0.1716 30 Nachman −10659.83 0.0359 33 Hanski-Gyllenberg −10622.13 0.0347 34 Power −109022.28 0.1716 32 Negative binomial −109021.05 0.1716 31 ↵a For the model-fitting exercise, β was fixed as 1. Thus, the model fitting involved only iterative variation in α values, followed by estimation of maximum likelihood and mean absolute deviance.
Supplemental Material
Table S1
Phylum-level classification of sequences detected at all sampling locations within each month shown as relative abundance (%). The phylum Proteobacteria is divided into its respective classes. Table S1, DOCX file, 0.1 MB.
Copyright © 2014 Pinto et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Figure S1
Shannon evenness (A) and nonparametric Shannon diversity (B) values averaged across all sampling locations within each month did not show significant correlations to measured water quality parameters. Download Figure S1, PDF file, 0.3 MB.
Copyright © 2014 Pinto et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Table S2
Water quality data for all sampling locations and time points. Table S2, DOCX file, 0.2 MB.
Copyright © 2014 Pinto et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Figure S2
Contribution of site-specific (red) and non-site-specific (blue) OTUs to the relative abundance (top panel) and membership (bottom panel) at each sampling location for the entire sampling period. Download Figure S2, PDF file, 0.2 MB.
Copyright © 2014 Pinto et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Table S3
(A) Summary of PERMANOVA results indicating the explanatory power of temporal and seasonal factors with respect to bacterial community structure. The top table compares the month and location, while the bottom table compares the season and sector for all four beta diversity metrics. (B) Global ANOSIM summaries and respective significance values for comparing samples grouped by month, location, season, and sector. Table S3, DOCX file, 0.1 MB.
Copyright © 2014 Pinto et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Figure S3
Effect of OTU filtering based on detection frequency (top panel) and relative abundance threshold (bottom panel) on Mantel’s r. The lower the Mantel r, the lower the correlation between the full data set with all OTUs and the data set with a subset of OTUs based on the detection frequency or relative abundance threshold. Download Figure S3, PDF file, 0.2 MB.
Copyright © 2014 Pinto et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Table S4
MIC statistics used to construct the network visualization (A) and taxonomy (B) of OTUs selected for this purpose. Table S4, DOCX file, 0.2 MB.
Copyright © 2014 Pinto et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Figure S4
MIC associations between the three connected clusters are shown here. Isolated OTUs have been removed. Green edges indicate positive MIC associations (A), while red edges indicate negative MIC associations (B). These network visualizations are clearly demonstrated within cluster positive associations and across cluster negative associations for cluster 1 (far right) and cluster 2 (far left). Download Figure S4, PDF file, 2.2 MB.
Copyright © 2014 Pinto et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Table S5
Pipe characteristics for the three sectors of the Ann Arbor DWDS included in this study (Fig. 1). NA, not applicable. Table S5, DOCX file, 0.1 MB.
Copyright © 2014 Pinto et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Additional Files
Supplementary Data
Supplementary Data
Files in this Data Supplement:
- Figure sf01, PDF - Figure sf01, PDF
- Figure sf02, PDF - Figure sf02, PDF
- Figure sf03, PDF - Figure sf03, PDF
- Figure sf04, PDF - Figure sf04, PDF
- Table st1, DOCX - Table st1, DOCX
- Table st2, DOCX - Table st2, DOCX
- Table st3, DOCX - Table st3, DOCX
- Table st4, DOCX - Table st4, DOCX
- Table st5, DOCX - Table st5, DOCX
