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Aquatic Microbial Ecology 77:23 The following supplement accompanies the article Site-specific environmental factors control bacterial and viral diversity in stormwater retention ponds Matthew A. Saxton, Nuha S. Naqvi, Faraz Rahman, Charleton P. Thompson, Randolph M. Chambers, James M. Kaste, Kurt E. Williamson* *Corresponding author: [email protected] Aquatic Microbial Ecology 77: 23–36 (2016) Table S1. Physical, geochemical and biological variables measured from coastal Virginia July 2012. Temp, Temperature; Cond, Conductivity; DO, dissolved oxygen; TDP, total dissolved phosphorus; DOC, dissolved organic carbon; chl a, chlorophyll a concentration; BacAB, bacterial abundance; VirusAB, virus abundance; viral richness via RAPD; bac richness, bacterial richness via tRFLP; BacProd, bacterial production. Bacterial and viral abundance values are the mean of duplicate samples ± standard deviation. Bacterial production values are the mean of triplicate incubations ± standard deviation. Pond Coordinates Drainage Impervious Percent Temp Cond µS DO mg Salinity pH TDP µg NOx µg NH4 µg DOC chl a µg BacAB VirusAB viral Decimal Area Area Impervious °C m-1 L-1 ppt L- L-1 L-1 ppm L-1 ±SD 105cells mL-1 106 VLP mL-1 richness Minutes hectare hectare cover ±SD ±SD JT 37.259870°, 11.75 3.15 26.82 34.9 70.5 11.4 0 7.15 4.34 22.9 0.4 7.95 601.48±15.1 24.3±8.90 32.5±5.73 11 -76.737629° GD 37.271414°, 12.48 4.1 32.69 28 390 3.45 0.2 7 0.48 3.5 4.4 5.75 215.83±19.05 3.73±2.47 5.04±2.35 10 -76.716540° WM 37.274315°, 1.79 0.60 33.41 36.2 82 8.6 0 7.99 0.14 1.1 BDL 5.68 28.43±16.19 7.32±0.59 29.1±2.72 5 -76.757833° NT 37.277627°, 43.51 28.28 64.99 33 132.2 5.7 0.1 7.09 0.95 0.5 0.3 7.09 49.47±5.71 6.59±0.01 9.86±0.54 10 -76.743874° WL 37.347052°, 5.70 4.27 75.03 33.4 18.4 9.2 0 5.41 0.14 1.1 BDL 3.33 61.07±5.41 5.57±0.84 8.00±2.53 14 -76.736233° MT 37.342843°, Data not Data not N/A 35 110.5 10.81 0 7.8 0.95 4.1 0.3 13.71 242.10±0 10.9±0.12 3.70±0.14 14 -76.741803° available available JHS 37.251069°, 14.14 1.96 13.82 37 71.8 6.35 0 7.35 2.62 17 BDL 4.54 716.65±19.83 7.33±1.33 16.5±2.39 11 -76.791905° GS 37.248892°, 6.46 0.69 10.62 35.5 55 11 0 7.66 0.48 2.6 BDL 4.82 118.88±0 3.12±2.07 7.76±7.67 5 -76.787857° PA 37.285761°, 2,79 1.27 45.50 29.8 35.5 4.1 0 6.11 3.48 27 BDL 3.71 73.08±22.50 3.06±0.03 4.37±0.31 9 -76.732202° CD 37.270661°, 5.70 2.14 37.59 29.1 254 6.59 0.1 7.8 1.57 3.2 11 5.57 744.85±317.69 3.35±0.32 14.0±0.60 16 -76.714076° HN 37.358448°, 6.79 1.40 20.59 32 43.5 11.5 0 7.18 0.19 BDL 18.8 4.12 163.54±7.83 5.58±0.59 9.25±0.96 11 -76.767256° SP 37.265934°, 1.44 0.97 67.51 27.7 43.5 3.95 0 7.26 1.76 2.9 BDL 5.67 59.46±11.99 5.68±0.10 5.17±0.15 16 -76.742532° MK 37.254448°, 6.67 5.10 90.00 33.1 17.5 9.36 0 7.32 0.24 BDL BDL 2.72 39.88±0.03 2.95±0.10 3.45±0.18 13 -76.640455° MB 37.256700°, 10.67 7.04 66.00 34 81.8 10.5 0 7.76 0.62 BDL BDL 4.86 200.03±19.83 3.21±0.54 4.00±0.21 14 -76.642349° 1 Pond Coordinates Drainage Impervious Percent Temp Cond µS DO mg Salinity pH TDP µg NOx µg NH4 µg DOC chl a µg BacAB VirusAB viral Decimal Area Area Impervious °C m-1 L-1 ppt L- L-1 L-1 ppm L-1 ±SD 105cells mL-1 106 VLP mL-1 richness Minutes hectare hectare cover ±SD ±SD RR 37.302226°, 62.62 Data not NA 31.7 66.1 10.1 0 7.85 0.76 1.7 0.3 4.12 297.46±39.66 3.92±4.33 3.28±3.75 8 -76.729164° available KW 37.236458°, 4.38 1.72 39.21 30.2 48.5 6.52 0 7.5 0.57 2 0.4 5.87 56.86±0 4.26±0.27 6.96±0.38 10 -76.731598° PJ 37.241049°, 13.74 4.04 29.41 28.8 40.5 11.2 0 7.53 9.49 14.4 BDL 6.32 2060.72±254.04 5.37±0.86 10.1±1.15 11 -76.778123° FF 37.233691°, 5.47 1.28 23.41 33.4 63.8 6.9 0 7.67 0.48 BDL BDL 4.00 67.94±8.38 5.16±0.36 20.4±2.64 11 -76.776248° MP 37.311964°, 8.52 3.49 40.99 28.5 42.7 0.4 0 6.05 0.95 2.2 0.1 7.12 106.68±0.54 6.77±1.20 10.3±0.54 11 -76.786368° LG 37.315057°, 6.79 2.59 38.09 35.6 72.5 9.5 0 8.02 3.58 15.8 BDL 7.03 137.22±3.04 3.75±0.01 16.4±0.97 17 -76.786702° 2 Table S2. Bioenv analysis results showing the set of environmental variables that best describe viral or bacterial community differences. VirusAB; viral abundance, BacAB; bacterial abundance, v-rich; viral richness, Temp; temperature, b-rich; bacterial richness, NOx; NO2 + NO3, Cond; conductivity, drainage area; total drainage area, imperv; impervious drainage area, % imperv, percent impervious drainage area, DO; dissolved oxygen Data Set Variables r VirusAB 0.4548 NOx, VirusAB 0.4467 Bacterial community via tRFLP Cond, BacAB, VirusAB 0.4858 vs environmental variables Cond, NOx, BacAB, VirusAB 0.4749 Cond, NOx, BacAB, VirusAB, v-rich 0.4260 imperv 0.1582 Drainage area, VirusAB 0.2092 Drainage area, % imperv, VirusAB 0.2563 Viral community via RAPD Drainage area, % imperv, VirusAB, b-rich 0.2648 vs environmental variables Drainage area, % imperv, VirusAB, b-rich, imperv 0.2587 Drainage area, % imperv, DO, VirusAB, b-rich, imperv 0.2539 Drainage area, % imper, DO, BacAB, VirusAB, b-rich, imperv 0.2398 pH 0.5728 pH, b-rich 0.7619 pH, NH4, chla 0.7422 % imperv, pH, NH4, chla 0.7126 Bacterial community via 16S Drainage area, DO, pH, NH4, chla 0.7296 sequence vs environmental Drainage area, % imperv, DO, pH NH4, chla 0.7110 variables Drainage area, % imperv, DO, pH, NH4, BacAB, b-rich 0.6924 Drainage area, % imperv, DO, pH, NH4, chla, BacAB, b-rich 0.6617 Drainage area, % imperv, Temp, DO, pH, NH4, chla, BacAB, b-rich 0.6415 Drainage area, % imperv, Temp, DO, pH, NH , chla, BacAB, vrich, 4 0.6360 b-rich Table S3. Sequencing results and alpha diversity measurements for bacterial community as determined via 16S rRNA amplicon sequencing. Alpha diversity measurements are rarefied to lowest read number. PD; phylogenetic diversity. Pond Reads OTUs Chao1 InverseSimpson Faith’sPD GD 9411 353 394.2 21.8 20.0 CD 10904 435 505.8 29.8 24.4 MP 10959 272 304.3 22.1 15.7 GS 14005 451 512.0 65.0 23.5 MT 11041 409 472.5 47.2 22.4 JHS 12880 402 446.6 47.8 20.4 LG 12154 456 507.0 55.3 23.7 JT 10436 353 418.7 14.6 20.0 3 Table S4. Classification of reads affiliated with known virus sequences Group Order Family CD (%) JHS (%) GS (%) JT (%) dsDNA viruses 23.44 64.06 79.37 27.36 Unassigned Adenoviridae 0.01 0.02 0.02 0.00 Ascoviridae 0.03 0.09 0.02 0.20 Baculoviridae 0.00 0.02 0.01 0.00 Caudovirales 20.01 56.52 66.64 22.44 Myoviridae 4.45 7.75 8.86 5.03 Podoviridae 8.85 28.07 37.72 6.87 Siphoviridae 6.27 19.24 18.90 10.02 unclassified 0.45 1.47 1.16 0.53 Herpesvirales Herpesviridae 0.00 0.10 0.01 0.03 Iridoviridae 0.09 0.05 0.12 0.04 Mimiviridae 0.01 0.01 0.00 0.01 Phycodnaviridae 0.15 0.43 0.58 0.41 Polydnaviridae 0.07 0.17 0.01 0.00 Poxviridae 0.01 0.01 0.00 0.01 unclassified dsDNA phages 2.84 6.16 11.29 3.71 unclassified dsDNA viruses 0.11 0.47 0.67 0.42 ssDNA viruses 75.85 34.10 16.65 70.82 Circoviridae 4.23 0.74 0.70 24.34 Geminiviridae 2.87 0.00 0.00 0.00 Microviridae 65.18 30.53 14.92 38.10 Nanoviridae 0.00 0.06 0.37 0.00 unclassified ssDNA viruses 3.55 2.78 0.66 8.39 ssRNA viruses 0.00 0.00 0.00 0.67 Satellites 0.00 0.00 2.73 0.00 unclassified viruses 0.59 1.00 1.24 0.75 unclassified virophages 0.13 0.84 0.03 0.39 Assignments computed via the GAAS tool (Angly et al., 2009), from a BLASTx comparison with NCBI refseq complete viral genomes proteins (E-value < 10-5).
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