<p>Breckenridge1, J.K, S.M. Bollens, G. Rollwagen-Bollens, and G.C. Roegner. Plankton assemblage variability in a river-dominated temperate estuary during late spring (high flow) and late summer (low flow) periods. Estuaries and Coasts.</p><p>1 Corresponding author current address: Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, 2020-2207 Main Mall, Vancouver, BC V6T 1Z4, Canada. E-mail: [email protected]</p><p>Online Resource 2 Mesozooplankton cluster description. Average salinity and temperature (Temp) at collection (±1 standard deviation), the number of samples collected during low-flow and high-flow cruises, dominant taxa, and significant indicator taxa with indicator values ≥35</p><p>Mesozooplankton clusters Cluster 1 2a 2b 3a 3b</p><p>Salinity 2.4±1.2 9.3±4.6 17.3±1.4 17.5±5.8 22.4±4.9 Temp 16.1±2.8 17.7±1.6 14.6±0.4 15.4±1.1 13.2±1.8 Low-flow 0 20 10 0 20 High-flow 34 2 0 16 5</p><p>Dominant Eurytemora Pseudodiaptomus Rotifera Rotifera Rotifera taxa affinis forbesi Paracalanus Polychaeta Rotifera parvus</p><p>Indicator Asplanchna Moina sp. Ectinosoma Coryceous anglicus Acartia longiremis taxa spp. Limnoithona spp. Microarthridion Pseudocalanus Oligochaeta tetraspina littoralis spp. Diacyclops Diaphanosoma spp. Microsetella Calanus spp. thomasi Pseudodiaptomus norvegica Centropages Nematoda forbesi Acartia tonsa abdominalis Daphnia spp. Oikopleura dioica Tortanus spp. Leimia vaga Oithona similis Tachidiidae Paracalanus parvus Pseudobradya sp. Online Resource 3 Microplankton cluster description. Average salinity and temperature (Temp) at collection (±1 standard deviation), the number of samples collected during low-flow and high-flow cruises, dominant taxa, and significant indicator taxa with indicator values ≥35</p><p>Microplankton clusters Cluster 1a 1b 2a 2b</p><p>Salinity 2.8±2.4 2.9±1.7 13.3±6.7 4.1±2.9 Temp 16.9±0.8 19.9±0.6 16.8±1.9 20.1±1.2 Low-flow 0 13 5 22 High-flow 35 0 4 0</p><p>Dominant Aulacoseira spp. Mesodinium rubrum Aulacoseira spp. Mesodinium taxa Small centric Aulacoseira spp. Mesodinium rubrum rubrum diatoms Aulacoseira spp.</p><p>Indicator Melosira varians Dictyosphaerium spp. Gyrosigma spp, None taxa Asterionella spp. Dactyliosolen spp. Large centric Chaetoceros diatoms curvisetus Pseudonitzschia “B” Tropidoneis spp. Cerautalina spp, Asterionellopsis glacias Strombidium spp. Dinophysis spp, Ditylum brightwelli Online Resource 4 Mesozooplankton and microplankton NMDS environmental variables with correlations greater than r = 0.5. Percentage of between-sample variation explained is noted beneath each axis. Variables are categorized as spatial (S), temporal (T), water quality (W), or biological (B), Note that many water quality and biological variables vary with space and season. Note that microplankton data were available for only one year, making the temporal variables (julian date and days from spring transition) redundant when correlated to that ordination Mesozooplankton Microplankton Axis 1 Axis 2 Axis Axis 2 Axis 3 1 Variables Category 47% 42% 15% 22% 49% Longitude S 0.56 0.02 -0.57 0.08 0.15 Salinity W -0.92 -0.46 0.58 -0.03 -0.49 Surface Salinity W -0.66 -0.16 0.60 -0.10 -0.17 Salinity stratification W -0.58 -0.52 0.23 0.04 -0.60 Julian Date T 0.07 -0.32 0 -0.11 -0.90 Season (wet/dry) T 0.31 0.84 0 0.08 0.89 Temperature W 0.66 0.11 -0.72 -0.05 0.19 Surface Temperature W -0.07 -0.55 -0.38 -0.10 -0.71 Temperature stratification W -0.57 -0.69 0.19 0 -0.84 River discharge (previous week avg) T 0.30 0.63 0.02 0.11 0.87 Richness B -0.57 -0.02 0.68 -0.08 0.07 Diversity B -0.33 0.34 0.68 -0.07 0.06 Days from spring transition T -0.23 -0.87 ------4 day cumulative wind stress T 0.41 0.72 0.04 0.51 0.67 Online Resource 5 Mesozooplankton 2005-2006 NMDS taxa log(x+1) abundance correlations to NMS ordination axes. Twenty most abundant taxa and taxa with correlation coefficients greater than r = 0.50 are shown in order of ranked average abundance. Commonly recognized taxonomic group and, when known, salinity preference – marine (M), brackish (B), and freshwater (F) - of each taxon are listed. Taxon Group Salinity Axis 1 Axis 2 Rank Rotifera Rotifer -- -0.18 -0.59 1 Eurytemora affinis Copepod B 0.32 0.82 2 Pseudodiaptomus forbesi Copepod B/F 0.14 -0.37 3 Coullana canadensis Copepod B 0.32 0.59 4 Polychaete larvae Annelid -- -0.74 -0.30 5 Paracalanus parvus Copepod M -0.65 0.17 6 Bivalvia Bivalve -- -0.73 -0.21 7 Bosmina longirostris Cladoceran F 0.63 0.60 8 Microsetella norvegica Copepod M -0.54 0.38 9 Pseudobradya sp. Copepod M/B 0.12 0.75 10 Oithona similis Copepod M -0.85 -0.24 11 Tachidiidae Copepod -- -0.14 0.25 12 Oikopleura dioica Appendicularian M -0.75 0.05 13 Cyclopoida Copepod -- 0.42 0.23 14 Acartia tonsa Copepod M/B -0.46 0.27 15 Brachionus spp. Rotifer -- 0.46 0.35 16 Microarthridion littoralis Copepod B -0.03 0.57 17 Daphnia spp. Cladoceran -- 0.52 0.51 18 Pseudocalanus spp Copepod M -0.63 -0.25 19 Nematoda Nematode -- 0.32 0.66 20 Asplanchna spp. Rotifer F 0.48 0.60 21 Oligochaeta Annelid -- 0.49 0.56 23 Diacyclops thomasi Copepod F 0.58 0.57 26 Acartia longiremus Copepod M -0.57 -0.30 31 Centropages abdominalis Copepod M -0.58 -0.13 38 Online Resource 6 Microplankton abundance correlations (r) to NMDS ordination axes. Taxa with correlation coefficients greater than r = 0.50 are shown in order of ranked average abundance. Commonly recognized taxonomic group and, when known, salinity preference – marine (M), brackish (B), and freshwater (F) - of each taxon are listed </p><p>Taxon Group Salinity Axis 1 Axis 2 Axis 3 Rank Aulacoseira spp. Diatom F -0.05 0.15 0.70 1 Small Centric diatoms (unidentified) Diatom -- 0.08 0.12 0.87 2 Fragilaria spp. Diatom F -0.34 0.24 0.57 3 Mesodinium rubrum Ciliate M/B 0.12 0.14 -0.65 4 Small Pennate (unidentified) Diatom -- -0.10 -0.17 0.60 5 Asterionella spp. Diatom F -0.02 0.08 0.84 6 Large Pennate (unidentified) Diatom -- 0.12 -0.39 0.57 7 Synedra spp. Diatom -- 0.03 0.36 0.65 9 Ankistrodesmus spp. Chlorophyte F 0.24 0.68 0.43 10 Skeletonema spp. Diatom M/B 0.58 -0.22 -0.52 11 Melosira varians Diatom M/B -0.02 -0.30 0.69 13 Dictyosphaerium spp. Chlorophyte F -0.11 0.60 0.14 16 Dactyliosolen spp. Diatom M 0.60 -0.22 -0.03 18 Asterionellopsis glacias Diatom M 0.52 0.05 -0.41 20 Large Centric diatoms (unidentified) Diatom -- 0.21 -0.26 0.64 22 Strombidium spp. Ciliate M 0.27 0.29 0.53 24 Ditylum brightwelli Diatom M/B 0.55 -0.34 -0.47 25 Pseudonitzschia 'B' Diatom M/B 0.60 -0.13 -0.09 26 Closteriopsis longissima Chlorophyte F 0.03 0.06 0.56 29 Eucampia zodiacus Diatom M 0.31 -0.30 -0.70 30 Filamentous bacteria Cyanobacteri -- 0.04 0.63 0.50 31 a Asterionellopsis socialis Diatom M 0.52 -0.24 -0.46 33 Scenedesmus spp. Chlorophyte B/F 0.02 0.35 0.53 36 Chaetoceros curvisetus Diatom M 0.54 0.04 -0.04 39 Anabaena spp. Cyanobacteri F 0 0.180 0.51 41 a Cerataulina spp. Diatom M 0.57 -0.30 -0.27 44 Cyclotella spp. Diatom -- -0.01 0.50 0.35 46 Entomoneis spp. Diatom -- 0.45 -0.23 -0.53 68 </p>