Supplementary Table S1. Metadata for the Indicated Delaware Bay Sample

Supplementary Table S1. Metadata for the indicated Delaware Bay sample.

Sample Station / Lat.long / collection_date / depth (m) / Ammo-nium (μM) / bacteria_carb_prod (pM/h) / chlorophyll (μg/L) / light_intensity (10^17 q/cm2/s) / nitrate (μM) / organism_count (cells/ml) / phosphate (μM) / salinity (PSU) / silicate (μM) / temp (°C) / tidal_stage
11 / 39.5166/-75.1503 / 2009-07-06T08:14:34 / 1.0 / 2.96 / 1100.43 / 58.17 / 0.9 / 63.96 / 2.04E+06 / 0.70 / 0.09 / 22.05 / 24 / Flood
12 / 39.5101/-75.1955 / 2009-07-06T09:07:55 / 1.0 / 1.03 / 1158.61 / 84.67 / 1.06 / 66.40 / 1.31E+06 / 0.57 / 0.10 / 11.94 / 24.2 / Ebb
14 / 39.4757/-75.2504 / 2009-07-06T10:17:59 / 1.0 / 0.86 / 774.13 / 49.38 / 1.21 / 73.47 / 1.79E+06 / 0.65 / 0.10 / 3.45 / 24.17 / Ebb
16 / 39.3720/-75.3446 / 2009-07-06T12:18:02 / 1.0 / 0.98 / 407.15 / 8.68 / 1.37 / 86.19 / 8.77E+05 / 1.49 / 1.16 / 12.08 / 24.85 / Ebb
18 / 39.2738/-75.3308 / 2009-07-06T13:43:46 / 1.0 / 2.59 / 197.75 / 4.63 / 1.47 / 77.32 / 1.58E+06 / 1.96 / 6.42 / 18.55 / 25.32 / Ebb
20 / 39.2201/-75.2705 / 2009-07-06T14:39:00 / 1.0 / 1.89 / 283.01 / 8.08 / 1.02 / 61.00 / 3.59E+06 / 1.63 / 10.10 / 26.34 / 25.84 / Flood
22 / 36.1252/-75.1657 / 2009-07-06T15:54:30 / 1.0 / 1.30 / 441.18 / 24.73 / 0.57 / 35.41 / 3.71E+06 / 0.58 / 14.60 / 30.64 / 25.02 / Flood
24 / 39.0507/-75.1095 / 2009-07-06T16:59:34 / 1.0 / 1.10 / 729.08 / 15.73 / 1.17 / 1.90 / 3.97E+06 / 0.13 / 19.53 / 12.01 / 24.94 / Flood
26 / 38.5521/-75.0654 / 2009-07-06T18:19:30 / 1.0 / 1.12 / 214.64 / 3.57 / 0.2 / 0.01 / 1.99E+06 / 0.44 / 26.65 / 9.52 / 23.22 / Flood
Luther Buoy / 38.5107/-75.0637 / 2009-07-07T09:14:42 / 1.0 / 0.92 / 437.53 / 5.43 / 1.2 / BDL / 6.85E+05 / 0.30 / 26.60 / 6.88 / 22.45 / Flood
FB buoy / 38.4608/-74.5498 / 2009-07-07T07:59:37 / 1.0 / 1.14 / 132.83 / 1.82 / 0.83 / 0.33 / 2.08E+06 / 0.14 / 30.50 / 4.24 / 19.53 / Flood

Supplementary Table S2. OTUs in the free-living fraction that had their highest abundance in the indicated salinity range. Only those OTUs with relative 16S rDNA abundances >0.5% were included. Phylogenetic distance was based on pairwise comparisons in MEGA5.05. Classifications were based on the Silva database and were performed in mothur.

Salinity Range / OTU# / Closest Isolate (or BLAST hit if distance >0.2) / Distance / Classification
0-1.2 / 1929 / 103288 AF408966.1 Micrococcineae str. Ellin124 / 0.15 / Actinomycetales
1942 / uncultured actinobacterium gi351693997 / 0.01 / Actinomycetales
1992 / 40713 AF287753.1 Dermabacter sp. oral strain str. B46KS / 0.15 / Actinomycetales
1074 / 103288 AF408966.1 Micrococcineae str. Ellin124 / 0.14 / Actinomycetales
740 / 103288 AF408966.1 Micrococcineae str. Ellin124 / 0.13 / Actinomycetales
1987 / 103288 AF408966.1 Micrococcineae str. Ellin124 / 0.15 / Actinomycetales
1853 / 12356 X79451.1 Sanguibacter inulinus str. ST50 / 0.14 / Actinomycetales
1127 / 40713 AF287753.1 Dermabacter sp. oral strain str. B46KS / 0.15 / Actinomycetales
2314 / 28059 AF233292.1 Tuber borchii symbiont b-Z43 / 0.14 / Bacteroidetes
1897 / 41211 AB079639.1 Kouleothrix aurantiaca str. MYSI / 0.11 / Chloroflexi; Kouleothrix
1898 / 41211 AB079639.1 Kouleothrix aurantiaca str. MYSI / 0.10 / Chloroflexi; Kouleothrix
1888 / uncultured Thermomicrobium sp. gi296172386 / 0.27 / Chloroflexi; Thermomicrobiales
2086 / uncultured Thermomicrobium sp. gi296172386 / 0.01 / Chloroflexi; Thermomicrobiales
1398 / 148264 DQ349098.1 Variovorax limosa str. EMB320 / 0.04 / Comamonadaceae
6 / 237073 AM411934.1 Variovorax sp. str. P-34 / 0.05 / Comamonadaceae
1370 / 150762 DQ413166.1 Variovorax sp. str. EMB 263 / 0.07 / Comamonadaceae
34 / 150762 DQ413166.1 Variovorax sp. str. EMB 263 / 0.05 / Comamonadaceae
2957 / 33534 AJ133166.1 Planktothrix sp. NIVA-CYA 126 str. CYA126 / 0.01 / Cyanobacteria Family XIII GpXIII
2619 / 107995 AJ630446.1 Aphanizomenon issatschenkoi str. 0tu37s7 / 0.01 / Cyanobacteria; Nostocales (Family_1, Gp1)
595 / 107963 AJ630415.1 Anabaena circinalis str. 1tu34s5 / 0.03 / Cyanobacteria; Nostocales (Family_1, Gp1)
1854 / uncultured Bacteroidetes bacterium gi22506766 / 0.00 / Cytophagaceae
2269 / 149498 AM177612.1 Flavobacterium sp. str. WB 3.1-22 / 0.11 / Flavobacteriaceae
1499 / 95477 AY386344.1 marine str. HTCC2188 / 0.04 / Gammaproteobacteria; OMG group
1081 / 1561 AJ229235.1 Opitutus terrae str. PB90-1 / 0.12 / Opitutaceae
712 / uncultured bacterium gi224552773 / 0.08 / Planctomycetaceae
714 / uncultured Crater Lake bacterium CL500-100 gi14149311 / 0.03 / Planctomycetaceae
474 / uncultured bacterium gi190708771 / 0.05 / Planctomycetales
131 / 66822 AF370880.1 Nordella oligomobilis str. N21 / 0.06 / Rhizobiales
153 / 100754 AJ563934.1 Beijerinckia derxii subsp. venezuelae str. DSM 2329 / 0.02 / Rhizobiales
1017 / 5780 D16421.1 Rhodobacter veldkampii str. ATCC35703 / 0.03 / Rhodobacteraceae
1188 / 4442 AF127394.1 Acetobacter sp. SRI1939 / 0.07 / Rhodospirillales; Acetobacteraceae
993 / 358964 AB470450.1 Sediminibacterium sp. str. TEGAF015 / 0.10 / Sphingobacteriales
1102 / 1559 X99392.1 Opitutus sp. str. VeSm13 / 0.13 / Verrucomicrobia
1087 / 1561 AJ229235.1 Opitutus terrae str. PB90-1 / 0.13 / Verrucomicrobia
1105 / 1549 X99390.1 Opitutus sp. str. VeGlc2 / 0.13 / Verrucomicrobia
17 / 1549 X99390.1 Opitutus sp. str. VeGlc2 / 0.15 / Verrucomicrobia
16 / 194127 EF157839.1 Lentimonas marisflavi str. IMCC2112 / 0.14 / Verrucomicrobia
1117 / 1561 AJ229235.1 Opitutus terrae str. PB90-1 / 0.11 / Verrucomicrobia
1078 / 1559 X99392.1 Opitutus sp. str. VeSm13 / 0.13 / Verrucomicrobia
1103 / 1561 AJ229235.1 Opitutus terrae str. PB90-1 / 0.12 / Verrucomicrobia
1098 / 1561 AJ229235.1 Opitutus terrae str. PB90-1 / 0.12 / Verrucomicrobia
8-10 / 142 / 103288 AF408966.1 Micrococcineae str. Ellin124 / 0.13 / Actinomycetales
61 / uncultured bacterium gi190706695 / 0.02 / Planctomycetales
15-27 / 1220 / 5026 U87783.1 Afipia genosp. 12 str. G8997 / 0.07 / Rhizobiales
1926 / 12753 AJ229243.1 Actinobacteria str. VeSm15 / 0.16 / Actinobacterales
2123 / 190052 EF108215.1 Aureimarina marisflavi str. IMCC3054 / 0.05 / Flavobacteriaceae
2154 / 167189 DQ660382.1 Brumimicrobium mesophilum str. YH207 / 0.16 / Flavobacteriaceae
2167 / 192107 EF108212.1 Coccinistipes vermicola str. IMCC1411 / 0.15 / Flavobacteriaceae
2286 / 167189 DQ660382.1 Brumimicrobium mesophilum str. YH207 / 0.14 / Flavobacteriaceae
1923 / 26805 Y14597.1 Candidatus Nostocoida limicola str. Ben67 / 0.17 / Actinobacteria
1962 / 215085 EF467640.1 Cryobacterium psychrophilum str. RuGl 7 / 0.09 / Actinomycetales
743 / 221209 EF468717.1 Marinobacterium marisflavum str. IMCC4074 / 0.12 / Alteromonadaceae
432 / 171956 DQ665838.1 Nisaea denitrificans str. DR41 21 / 0.10 / Rhodospirillaceae
31 / 2164 / 192107 EF108212.1 Coccinistipes vermicola str. IMCC1411 / 0.12 / Flavobacteriaceae
223 / 109582 AJ631302.1 Thalassobacter stenotrophicus str. CECT 5294 5SM22 / 0.02 / Rhodobacteraceae
1735 / 114761 AY951931.1 Bathymodiolus azoricus thioautotrophic gill symbiont / 0.07 / Gammaproteobacteria, sulfur oxidizing symbionts
1012 / 100730 AY682384.1 Parvulomonas gwangyangensis str. GW14-5 / 0.09 / Alphaproteobacteria; Kordiimonadales
1358 / 321327 EU874388.1 Marinimicrobium sp. str. ISL-43 / 0.15 / Alteromonadaceae
395 / 171956 DQ665838.1 Nisaea denitrificans str. DR41 21 / 0.08 / Rhodospirillaceae
2185 / 221580 EF554364.1 Ulvibacter antarcticus str. IMCC3101 / 0.12 / Flavobacteriaceae
1484 / 217507 AM691086.2 EG19 / 0.06 / Gammaproteobacteria
21 / 96014 AY386340.1 marine str. HTCC2120 / 0.05 / Gammaproteobacteria; OMG group
257 / 190052 EF108215.1 Aureimarina marisflavi str. IMCC3054 / 0.16 / Flavobacteriaceae
286 / 310072 EU440958.1 Citreicella thiooxidans str. 2PR57-8 / 0.05 / Rhodobacteraceae
1766 / 98593 AY386332.1 marine str. HTCC2089 / 0.04 / Gammaproteobacteria; OMG group
Free / Whole
Group / OTU / Closest isolate / GenBank# / Distance / Slope / r2 / Slope / r2
Actinobacteria / 1923 / Candidatus Nostocoida limicola str. Ben67 / Y14597 / 0.17 / 0.58 / 0.03 / -0.68 / 0.12
740 / Sanguibacter inulinus str. ST50 / X79451 / 0.15 / 1.76 / 0.20 / 0.85 / 0.68
1074 / Dermabacter sp. oral strain str. B46KS / AF287753 / 0.15 / -0.50 / 0.03
1853 / Sanguibacter inulinus str. ST50 / X79451 / 0.14 / -0.48 / 0.40 / 0.20 / 0.94*
1987 / Sanguibacter inulinus str. ST50 / X79451 / 0.15 / 0.93 / 0.86 / -0.14 / 0.11
1935 / Tetrasphaera australiensis str. 110 ACM 5118 / AF125090 / 0.17 / 1.49 / 0.89 / 0.49 / 0.82
Chloroflexi / 1898 / Kouleothrix aurantiaca str. MYSI / AB079639 / 0.11 / 0.20 / 0.85
Flavobacteriales / 2118 / Gaetbulibacter saemankumensis str. SMK-36 / AY883938 / 0.11 / 0.76 / 0.34 / -0.48 / 0.26
742 / Gaetbulibacter sp. str. NH57N / FJ360684 / 0.16 / 6.64 / 0.22
241 / Ulvibacter antarcticus str. IMCC3101 / EF554364 / 0.07 / 0.85 / 0.93* / 1.01 / 0.94*
243 / Ulvibacter antarcticus str. IMCC3101 / EF554364 / 0.07 / 1.08 / 0.72 / 1.53 / 0.62
Cyanobacteria / 543 / Synechococcus sp. str. LBG2 / AF330249 / 0.01 / 2.22 / 0.82* / 2.84 / 0.32
Bacteria / 669 / Fibrobacter succinogenes str. MC1 / M62693 / 0.24 / 2.20 / 0.02 / 1.22 / 0.58
Rhodobacterales / 104 / Roseovarius aestuarii str. SMK-122 / EU156066 / 0.02 / 1.22 / 0.92* / 1.45 / 0.96*
229 / Paracoccus aminovorans str. JCM 7685 / D32240 / 0.04 / -0.59 / 0.11 / 0.92 / 0.11
226 / Citreicella thiooxidans str. 2PR57-8 / EU440958 / 0.03 / 3.45 / 0.06 / 1.21 / 0.32
270 / Paracoccus alcaliphilus str. ATCC 51199 / AY014177 / 0.06 / 0.98 / 0.62* / 1.17 / 0.86*
223 / Paracoccus aminovorans str. JCM 7685 / D32240 / 0.10 / 0.39 / 1.00* / 0.82 / 0.97*
Rhodospirillales / 102 / Nisaea denitrificans str. DR41 18 / DQ665839 / 0.10 / 1.12 / 0.70* / 1.37 / 0.87*
119 / Nisaea denitrificans str. DR41 18 / DQ665839 / 0.09 / 1.22 / 0.05 / 1.83 / 0.99
298 / Nisaea denitrificans str. DR41 18 / DQ665839 / 0.10 / 2.30 / 0.82* / 1.39 / 0.75*
332 / Nisaea denitrificans str. DR41 18 / DQ665839 / 0.08 / 1.42 / 0.61 / 2.49 / 0.94*
395 / Nisaea denitrificans str. DR41 21 / DQ665838 / 0.08 / 1.20 / 0.56 / 4.13 / 0.74
432 / Nisaea denitrificans str. DR41 21 / DQ665838 / 0.10 / 2.18 / 0.64 / 1.96 / 0.56
Rickettsiales / 124 / Candidatus Pelagibacter ubique str. HTCC1002 / AF510192 / 0.10 / 0.54 / 0.86* / 0.43 / 0.46
125 / Candidatus Pelagibacter ubique str. HTCC1002 / AF510192 / 0.03 / 0.82 / 0.91* / 0.79 / 0.83*
267 / Candidatus Pelagibacter ubique str. HTCC1002 / AF510192 / 0.10 / 0.49 / 0.81* / 0.42 / 0.86*
807 / Candidatus Pelagibacter ubique str. HTCC1002 / AF510192 / 0.11 / 0.72 / 0.86* / 0.34 / 0.91*
Burkholderiales / 34 / Variovorax sp. str. EMB 263 / DQ413166 / 0.05 / 0.24 / 0.03 / 1.28 / 0.99
1370 / Variovorax sp. str. EMB 263 / DQ413166 / 0.07 / 0.89 / 0.28 / 0.94 / 0.74
1693 / Hydrogenophaga flava str. CCUG 1658 / AF078771 / 0.06 / 1.36 / 0.74 / 1.06 / 0.47
Deltaproteobacteria / 132 / Geobacter sp. str. CLFeRB / DQ086800 / 0.21 / 1.86 / 0.39 / 4.02 / 0.00
Gammaproteobacteria / 22 / marine str. HTCC2080 / NZAAVV01000015 / 0.05 / 1.22 / 0.29 / 1.41 / 0.54
21 / marine str. HTCC2120 / AY386340 / 0.05 / 1.36 / 0.97* / 1.52 / 0.96
14 / Halomonas sp. str. Sua-BAC010 / EU870506 / 0.11 / 1.85 / 0.86* / 1.08 / 0.84*
2064 / Chroococcidiopsis sp. str. CC3 / DQ914865 / 0.28 / 0.96 / 0.00 / 0.42 / 0.78*
1456 / marine str. HTCC2246 / AY386337 / 0.11 / -1.47 / 0.04 / 2.66 / 0.69*
1766 / marine str. HTCC2089 / AY386332 / 0.04 / 5.42 / 0.00 / 2.18 / 0.64
1783 / marine str. HTCC2180 / AY386343 / 0.08 / 1.86 / 0.81* / 1.44 / 0.73*
1735 / Bathymodiolus azoricus thioautotrophic gill symbiont / AY951931 / 0.07 / 0.85 / 0.20 / 0.92 / 0.97
18 / Marinomonas sp. str. MED121 / NZAANE01000001 / 0.14 / 1.08 / 0.70* / 0.91 / 0.79*
259 / marine str. HTCC2188 / AY386344 / 0.03 / 2.26 / 0.31 / 2.61 / 0.33
743 / Marinobacterium marisflavum str. IMCC4074 / EF468717 / 0.12 / 1.24 / 0.93* / 1.37 / 0.42
Verrucomicrobia / 16 / Lentimonas marisflavi str. IMCC2112 / EF157839 / 0.14 / 1.19 / 0.15 / 0.78 / 0.96
1103 / Opitutus terrae str. PB90-1 / AJ229235 / 0.12 / 0.90 / 0.93 / 1.65 / 0.98
475 / Alterococcus agarolyticus str. ADT3 CCRC17102 / AF075271 / 0.21 / -1.75 / 0.00 / 2.54 / 0.08

Supplementary Table S3. Relationships of rRNA to rDNA in individual taxa along the Delaware Bay. Forty-six OTUs, defined at the family, order or phylum level were included based on their relative abundance (frequency >0.5) and presence in at least three of the samples. Phylogenetic distance was based on pairwise comparisons in MEGA5.05. Classifications were based on the Silva database and were performed in mothur.

* p value <0.05

Supplementary Table S4. OTUs in the free-living fraction that had their highest 16S rRNA:rDNA ratiosin the indicated salinity range Only those OTUs with relative 16S rRNA or rDNA abundances >0.5% were included. Phylogenetic distance was based on pairwise comparisons in MEGA5.05. Classifications were based on the Silva database and were performed in mothur.

Salinity Range / OTU# / Closest Isolate (or BLAST hit if distance >0.2) / Distance / Classification
0-1.2 / 807 / 61204 AF510192.1 Candidatus Pelagibacter ubique str. HTCC1002 / 0.11 / SAR11
1935 / 103288 AF408966.1 Micrococcineae str. Ellin124 / 0.15 / Actinomycetales
14 / 340723 EU870506.1 Halomonas sp. str. Sua-BAC010 / 0.11 / Gammaproteobacteria; Oceanospirillales; Halomondaceae
543 / 54601 AF330249.1 Synechococcus sp. str. LBG2 / 0.01 / Cyanobacteria Family_II GpIIa
8-10 / 229 / 5761 D32240.1 Paracoccus aminovorans str. JCM 7685 / 0.04 / Rhodobacteraceae
15-27 / 2118 / 190052 EF108215.1 Aureimarina marisflavi str. IMCC3054 / 0.07 / Flavobacteriaceae
475 / uncultured Opitutae bacterium gi307715921 / 0.01 / Verrucomicrobia
259 / 95477 AY386344.1 marine str. HTCC2188 / 0.03 / Gammaproteobacteria; OMG group
18 / 321327 EU874388.1 Marinimicrobium sp. str. ISL-43 / 0.14 / Alteromonadaceae
226 / 310072 EU440958.1 Citreicella thiooxidans str. 2PR57-8 / 0.03 / Rhodobacteraceae
270 / 38102 AY014177.1 Paracoccus alcaliphilus str. ATCC 51199 / 0.06 / Rhodobacteraceae
1693 / 6941 AF078771.1 Hydrogenophaga flava str. CCUG 1658 / 0.06 / Comamonadaceae
102 / 162790 DQ665839.1 Nisaea denitrificans str. DR41 18 / 0.10 / Rhodospirillaceae
1962 / 215085 EF467640.1 Cryobacterium psychrophilum str. RuGl 7 / 0.09 / Actinomycetales
241 / 221580 EF554364.1 Ulvibacter antarcticus str. IMCC3101 / 0.07 / Flavobacteriaceae
243 / 221580 EF554364.1 Ulvibacter antarcticus str. IMCC3101 / 0.07 / Flavobacteriaceae
104 / 255233 EU156066.1 Roseovarius aestuarii str. SMK-122 / 0.02 / Rhodobacteraceae
742 / 362896 FJ360684.1 Gaetbulibacter sp. str. NH57N / 0.15 / Flavobacteriaceae
22 / 185581 NZ AAVV01000015.1 marine str. HTCC2080 / 0.05 / Gammaproteobacteria; OMG group
298 / 162790 DQ665839.1 Nisaea denitrificans str. DR41 18 / 0.10 / Rhodospirillaceae
31 / 125 / 61204 AF510192.1 Candidatus Pelagibacter ubique str. HTCC1002 / 0.03 / SAR11
124 / 61204 AF510192.1 Candidatus Pelagibacter ubique str. HTCC1002 / 0.10 / SAR11
267 / 61204 AF510192.1 Candidatus Pelagibacter ubique str. HTCC1002 / 0.10 / SAR11
2064 / uncultured actinobacterium gi297499100 / 0.00 / Actinomycetales

Supplementary Figure S1. Relationships between 16S rRNA and 16S rDNA frequencies of bacterial OTUs from whole water fractions along the Delaware Bay. The points are paired 16S rRNA and rDNA frequencies for each individual OTU and time point. The right panel (B) is a magnification of the left panel (A).

Supplementary Figure S2. Relative abundance (A) and ratio of 16S rRNA to rDNA (B) of the indicated OTU in relation to salinity along the Delaware Bay. Beta= Betaproteobacteria, Gamma=Gammaproteobacteria.

Supplementary Figure S3. Relative abundance (A and B) and ratio of 16S rRNA to rDNA (C and D) of the indicated OTUs in relation to salinity along the Delaware Bay. OTUs within the Rhodobacteriaceae(A and C); Rhodospirillum(B and D).

Supplementary Figure S4. Relative abundance (A and B) and ratio of 16S rRNA to rDNA (C and D) of the indicated OTU in relation to salinity along the Delaware Bay.OTUs within the Verrucomicrobia (A and C); Actinomycetales (B and D).