Abstract
Introduction:
Large rivers exhibit spatiotemporal heterogeneity, where habitat structure affects spatial and temporal overlap between zooplankton and planktivores. In the central United States, the non-native, planktivorous silver carp (Hypophthalmichthys molitrix) dominates fish communities in complex riverscapes. Understanding how silver carp and native planktivores interact with zooplankton through space and time is essential for anticipating changes to trophic stability and energy pathways and can inform silver carp management. The objectives of this study were to assess spatiotemporal patterns in zooplankton and planktivorous fish densities, including investigating evidence of zooplankton diel vertical migration and whether planktivores display diel patterns in main channel and off channel habitat use.
Methods:
The vertical distributions of three zooplankton taxa and the spatial distributions of silver carp and native planktivores were quantified over a 24-h period in main channel and off channel habitats of three locations in the Illinois River, USA during October 2018.
Results:
Planktivorous fishes > 30 cm total length were dominated by silver carp and were consistently denser in off channel habitats during the day and night. At some sites, densities of cladocerans, copepods, and rotifers differed between the main channel and off channel habitats. Cladoceran, copepod, and rotifer taxa did not exhibit daily changes in vertical distribution. Cladoceran taxa were denser in off channel habitats at night than during the day, while copepod densities were consistently higher near the bottom of the off channel habitat.
Discussion:
Declining densities of off channel cladocerans during the day may have been due to movement from nearshore areas or the sediment, planktivory by diurnally feeding fishes, or drift. Unchanging diel rotifer densities support other research showing that these small-bodied taxa with short life cycles persist in the face of high planktivory. Increases in cladocerans during the night in off channel habitats may have been due to a combination of sediment use, decreased nighttime planktivore foraging rates, drift from upstream sources, water flow, and movement from lateral areas. Zooplankton subsidies from the off channel areas of the riverscape support high densities of invasive silver carp and native planktivores.
Introduction
Large river ecosystems are defined by substantial spatiotemporal heterogeneity (Wohl, 2016), where habitat structure strongly influences species distributions (Wahl et al., 2008; Ginders et al., 2016; Glubzinski et al., 2021). Flow regimes and channel geomorphology generate networks of main channel and off channel environments (e.g., side channels, backwaters) that can differ in depth, velocity, and temperature (Beechie et al., 2011). For lower trophic levels, abundances and spatial distributions can be shaped by physical conditions and biotic interactions (Sobotka et al., 2025), including behavioral responses to predators that can vary over short time periods (Marklund et al., 2001). These dynamics are complex, producing variable patterns of overlap between prey and predators across habitats and timescales (Mehner, 2012). Understanding these dynamic spatial and temporal patterns is essential for characterizing the ecological function of Great Rivers.
Zooplankton are integral to riverine food webs, serving as prey for taxa including larval fishes (Yang et al., 2023) and are a lifelong food source for planktivores (Ning et al., 2010). Although well understood in lakes and oceans, relatively fewer studies have examined the spatially explicit dynamics of zooplankton in large rivers (Chará-Serna and Casper, 2021). This has become particularly important in rivers of the central United States where a highly specialized non-native planktivore, silver carp (Hypophthalmichthys molitrix), has risen to dominance (Chick and Pegg, 2001; Solomon et al., 2016). Silver carp consume a variety of zooplankton and phytoplankton down to very small particle sizes (Garvey, 2012). This has contributed to the decline of larger bodied cladoceran zooplankton while more motile or smaller-bodied taxa, such as rotifers, persist (Sass et al., 2014; Tillotson et al., 2022). Understanding how silver carp and native planktivores overlap with zooplankton in space and time is critical for predicting the stability of food web interactions, projecting changes in planktonic food webs in invaded systems (Pinelalloul, 1995). Although fish movement has been widely studied, fine-scale daily movements in large rivers are often difficult to quantify (Cooke et al., 2022), especially in dynamic large riverscapes which are complex mosaics of flowing and slack water with varying connectivity (Garvey and Whiles, 2023).
Many freshwater invertebrates adjust their spatial distributions to avoid predation. In lakes, a common response is diel vertical migration (DVM), in which zooplankton ascend during the night to feed on phytoplankton and descend during the day to avoid visually feeding predators (Bandara et al., 2021). In rivers, zooplankton may exhibit a complex pattern of vertical and horizontal movement as a function of predation risk. Evidence from the Ohio and St. Lawrence rivers in North America indicates that some zooplankton taxa exhibit diel shifts in vertical distribution consistent with DVM, likely influenced by planktivory (Jack and Thorp, 2002; Jack et al., 2006; Casper and Thorp, 2007). Some river invertebrates also disperse and access new resources by drifting passively at night in the current to avoid visual predators (Flecker, 1992; Kennedy et al., 2014). Silver carp concentrate in phytoplankton-rich habitats (Calkins et al., 2012) where zooplankton tend to also forage. This has the potential to increase spatial overlap between silver carp and zooplankton and could necessitate behavioral strategies by zooplankton to minimize predation risk (e.g., DVM or passive drift at night). Understanding the degree to which the habitat use of silver carp and native planktivores overlaps with zooplankton on a daily basis will help determine whether spatial (e.g., shallow areas) and temporal (e.g., night) refuges exist for plankton prey.
Spatial and temporal variability in water velocity across riverscapes could also affect zooplankton behavior, reproduction, composition, and densities (Picapedra et al., 2022). River main channel habitat may facilitate dispersal of zooplankton due to increased flow (Krepski et al., 2024), but it can be a challenging place for these small organisms to filter phytoplankton and reproduce. In contrast, off channel areas such as lateral side channels and connected backwater lakes may provide areas for algae to accumulate and zooplankton to feed and reproduce, resulting in high planktivore densities in these areas (Sobotka et al., 2025). However, low or seasonally variable flow through off channel areas and locally dense planktivorous fishes may compromise zooplankton communities (Yanygina et al., 2023). Zooplankton may benefit from localized shallow water refuges that exclude large-bodied and densely populated planktivores but allow dispersal through connections to the river main channel (Jack et al., 2006). A combination of variable conditions, including water velocity, depth, and predator and prey densities, are likely responsible for promoting zooplankton composition and density in riverscapes (Chará-Serna and Casper, 2021).
Understanding how diurnal spatial distributions of zooplankton and planktivorous fishes are related is critical for better understanding large river ecology and in managing species invasions, such as through targeting removal efforts to specific locations and times. Our objectives for this study were to (1) examine short-term (24-hr) patterns in spatial distributions of planktivorous fish densities for potential diurnal patterns in habitat use between main channel and off channel habitat, (2) assess short-term patterns in zooplankton densities between main channel and off channel habitats of the Illinois River, and (3) investigate whether zooplankton displayed DVM and determine whether potential DVM varied between main channel and off channel habitats.
Methods
Study sites
The Illinois River is a large, 439-km-long, regulated tributary of the Mississippi River that drains approximately 74,000 km2 of the central United States. It is a diverse riverscape consisting of off channel habitats including backwater sloughs, lakes, oxbow and floodplain lakes, floodplain depressions, and levee-break wetlands, which are remnants of when the river was a reach of the ancient Teays River prior to the Pleistocene epoch. Many of these complex lateral features have been lost due to damming and channelization for navigation, as well as sedimentation from agricultural runoff. Water is managed in the river by being pooled by damming during times of low discharge to maintain the navigation channel, and with dam gates unengaged during times of high discharge. Several dammed pools of the Illinois River have been heavily invaded by silver carp (Coulter et al., 2018).
Diel zooplankton and fish sampling took place at Quiver Island (river km 121.6), Bath Chute (river km 107), and Lilly Lake (river km 83) locations of the LaGrange Reach of the Illinois River (Figure 1A). Sampling occurred within the LaGrange Reach because prior work (Sass et al., 2014) documented high densities of silver carp and other fishes in this reach, and this reach contained representative off channel habitat that is relatively sparse in this modified river system. These specific study areas were chosen within the LaGrange reach because they were within close proximity to one another to limit variation in environmental conditions (e.g., temperature, productivity) among locations. Quiver Island consisted of a broad side channel connected to the main channel separated by Quiver Island (Figure 1B). Bath Chute consisted of a narrow side channel separated from the main channel by a disconnected, shallow lake (Figure 1C). Lilly Lake was a backwater that was not connected upstream but was connected to the main channel via a small ditch downstream (Figure 1D). Sampling at each river location occurred every 4 h during a 24-h period (02:00, 06:00, 10:00, 14:00, 18:00, and 22:00). Sampling occurred at Quiver Island on October 26, 2018, Bath Chute on October 23, 2018, and Lilly Lake on October 22, 2018. Within each river location, main channel habitats were paired with an adjacent, off channel habitat (Figure 1). Off channel habitats were areas of reduced or zero flow relative to the river main channel. Water temperature, water velocity, and zooplankton density were sampled at three replicate sites in each of the main channel and off channel habitats at each site (Figure 1). The fish community was assessed using mobile hydroacoustic sampling that followed transects spanning the most upstream and downstream replicate location within each habitat at a site (see details below). Off channel habitats were similar among sites in that they were relatively shallow compared to adjacent main channel habitats. Off channel habitats also had portions of submerged aquatic vegetation or flooded terrestrial vegetation in shallower areas near shore.
Figure 1

Sites sampled for fishes and zooplankton in the Illinois River in October 2018. The Illinois River flows southward into the Mississippi River (A). MC, main channel habitat; OC, off channel habitat. Numbers represent replicate samples. Scale bar in (B) also applies to (C) and (D).
Fish sampling and density estimates
The fish community was sampled every 4 h in each habitat congruent with zooplankton sampling. Fish were sampled using mobile hydroacoustic surveys from a 9-m research vessel with paired Biosonics 200-kHz horizontally oriented, split-beam transducers (MacNamara et al., 2016, 2018). To cover the entire water column, the transducers were set to two non-overlapping positions with the first position offset to extend parallel to the water's surface and the other set under the surface beam (see MacNamara et al., 2016, 2018). Hydroacoustic sampling followed transects that spanned the most upstream and downstream replicate sampling location within a habitat where physical parameters and zooplankton were sampled (Figure 1). The number of survey transects varied by habitat size, where a single nearshore transect was conducted parallel to the left and right bank at off channel habitats, and a nearshore and a mid-channel transect were conducted at main channel habitats (MacNamara et al., 2016).
Physical sampling of the fish community occurred at the three study sites within three weeks of the hydroacoustic sampling to estimate species-specific densities based on the size distribution and relative abundances in the gears. All fish were collected using pulsed-DC electrofishing and gill nets during daylight hours following protocols outlined in (MacNamara et al., 2016). All fish captured were identified to species and measured to total length (mm).
Hydroacoustic data were processed using Echoview 6.1 (MacNamara et al., 2016). The river bottom was identified during processing and excluded, and a nearfield exclusion zone was established 1.08 m from each transducer. Fish targets were identified using the ‘single target detection' and ‘fish track detection' algorithms in Echoview and were then manually verified. Target strengths were converted to total length using a side-aspect total length to target strength equation (Love, 1971), and only fish with a target strength equating to at least 30 cm total length were included in analyses. This 30 cm cutoff was set as a data quality threshold due to the acoustic noise caused by mobile hydroacoustic sampling in flowing water. Planktivorous fish densities were calculated for each habitat within a site based on physical capture data and consisted of a combination of invasive silver carp and native gizzard shad (Dorosoma cepedianum) and Bigmouth Buffalo (Ictiobus cyprinellus). The number of fish targets from hydroacoustic sampling was first determined across 2 cm length bins and was then multiplied by the proportion of planktivore species from capture sampling for the same 2 cm length bins. The subsequent number of planktivores was summed among length bins and divided by the water volume sampled to estimate planktivore density for each sampling event. See MacNamara et al. (2016) for complete details.
Physical parameters and zooplankton
Surface water temperature and water velocity were quantified at each replicate location and time. Zooplankton were sampled at the surface and at the bottom using a diaphragmatic pump with a weighted hose (Appel et al., 2020). Zooplankton were collected through a 55-μm sieve for crustaceans (30 L of water pumped per sample) and 20-μm sieve for rotifers (10 L of water pumped per sample). Zooplankton samples were stored in a 12% sugar-buffered formalin solution with Rose Bengal dye. Each sample was concentrated and then subsampled. A 5-mL subsample of the concentrated 55-μm zooplankton sample was collected using a Hensen-Stempel pipette and processed under a Leica digital dissecting microscope with a Bogorov counting chamber. Only crustacean zooplankton (e.g., cladocerans and copepods) were enumerated in the 55-μm sample due to the potential for underestimation of rotifers (Chick et al., 2010; Thomas et al., 2017). At least 10% of each concentrated 55-μm zooplankton sample was analyzed with a minimum of 100 individuals identified and enumerated. One-mL subsamples of the concentrated 20-μm zooplankton samples were analyzed using a compound microscope and a gridded Sedgewick-Rafter counting cell, with only rotifers being enumerated. At least 10% of each concentrated 20-μm zooplankton sample was analyzed, with a minimum of 400 rotifers enumerated. Zooplankton were identified to the taxonomic classification of rotifer, copepod (including nauplii) and cladocerans for analysis of density (number/L). These taxonomic classifications were chosen to provide comparable data to prior studies assessing the long-term effects of silver carp on zooplankton in the Illinois River.
Statistical analyses
Water temperature and water velocity were analyzed to determine whether there were any diel changes in environmental conditions. Changes were analyzed using a linear mixed model in program R (Bates et al., 2015), where either water temperature or water velocity was the response variable and sampling sites within habitats were replicate samples. Time and habitat were the fixed explanatory variables and river location was the random effect. If either effect was significant, Tukey's pairwise comparisons with a Holm's p-adjustment were used to evaluate differences between the fixed explanatory variable levels.
Mixed-effect models (Bates et al., 2015) were used to assess changes in density of planktivorous fish between adjacent habitats. Time and habitat type (main channel and off channel) were the fixed explanatory variables, and river location was the random explanatory variable. Likelihood ratio testing was used to assess whether the interaction of time and habitat significantly improved the model. If significant, Tukey's pairwise comparisons were then performed to differentiate between the time and habitat levels. Associations among planktivorous fish densities and the three zooplankton taxa averaged at each site at each time were also explored using Pearson's correlation coefficients.
We next tested for differences in zooplankton densities between habitat types, including diurnal differences. Zooplankton taxa (rotifer, copepod, cladoceran) were analyzed separately within each location (Quiver Island, Bath Chute, Lilly Lake). For these analyses, we calculated the log10-transformed ratio of off channel zooplankton density to main channel zooplankton density. These ratios were calculated between paired replicate samples (e.g., off channel replicate 1 density and main channel replicate 1 density). A positive value of this log ratio would indicate zooplankton density was higher in the off channel habitat. This log ratio was the response variable in a linear model (‘stats' package in R) that had a predictor variable of time (daytime or nighttime). A significant (α = 0.05) time effect would indicate that relative zooplankton densities between habitats changed between day and night. A significant positive intercept from these models would indicate that zooplankton densities were higher in the off channel habitat, a significant negative intercept indicated higher densities in the main channel, and a non-significant intercept indicated similar densities between habitats.
To test for DVM in zooplankton, data were analyzed by density of each taxon (rotifer, copepod, cladoceran) at depths and time sampled at each site. Each taxon was analyzed separately using a generalized linear mixed-effect model in R with the gamma family group. Zooplankton taxon density was the response variable, with time and depth as fixed effects. An interaction term was included in the models. If an explanatory variable was significant in the original model, a pairwise post-hoc test was conducted using a Holm's p-adjustment to decipher differences among levels of the fixed effect.
Results
Environmental conditions differed between main channel and off channel habitats. Water temperature was warmer (approximately 0.3 °C) in off channel habitats than in the main channel (Table 1; F1,96 = 15.0, p < 0.001). Water temperature varied by time (F5,38 = 5.8, p < 0.001). Pairwise comparison revealed that water was cooler at 6:00 (mean temperature across sites: 11 °C) than in the afternoon and night (mean temperature across sites: 12 °C). Water velocity was higher in the main channel and did not vary with time of day (Table 1; F1,95= 64.9, p < 0.001). Among the off channel habitats, Lilly Lake mean flow rates were low (near 0 m/s) compared to the other off channel sites (Table 1).
Table 1
| Site | Habitat | Mean velocity (m/s) | Velocity SD | Mean temperature (°C) | Temperature SD | Depth (m) | Depth SD |
|---|---|---|---|---|---|---|---|
| Quiver Island | Main channel | 1.15 | 0.49 | 10.74 | 0.39 | 3.8 | 1.5 |
| Off channel | 0.77 | 0.24 | 10.93 | 0.33 | 2.0 | 0.8 | |
| Bath Chute | Main channel | 1.33 | 0.12 | 10.93 | 0.41 | 3.6 | 1.0 |
| Off channel | 1.16 | 0.19 | 11.11 | 0.40 | 1.5 | 0.2 | |
| Lilly Lake | Main channel | 1.13 | 0.27 | 11.30 | 0.36 | 4.1 | 1.8 |
| Off channel | 0.08 | 0.06 | 11.91 | 0.98 | 1.7 | 0.3 |
Mean velocity (m/s) and water temperature (°C) in three sites of the LaGrange Reach, Illinois River in October 2018.
SD, one standard deviation.
The majority (95%) of planktivorous fishes identified by independent electrofishing and netting samples at >30 cm total length were silver carp, with the remainder being gizzard shad (2.5%) and bigmouth buffalo (2.5%). Thus, we assumed that most planktivorous fish greater than 30 cm observed with hydroacoustic sampling were silver carp. Planktivorous fish density did not differ by time of day in main channel or off channel habitats (all pairwise comparisons of time, t < 1, p > 0.1). However, planktivorous fish density differed by habitat, with higher densities occurring in off channel habitats than main channel habitats across all time periods (Figure 2; Tukey's pairwise, t = 13.0, p < 0.001).
Figure 2

Mean (± one standard deviation) densities of planktivorous fishes in main channel and off channel habitats of the LaGrange Reach, Illinois River in October 2018 over a 24-h period. Black horizontal bars depict night samples, and asterisks denote significant differences between habitats within a sampling time.
Associations between planktivorous fish and zooplankton differed among taxa. Mean fish densities and mean cladoceran densities were positively correlated among sites (r = 0.53, p = 0.0009). No other significant correlations (all p > 0.05) between fish and zooplankton or between zooplankton taxa occurred (fish vs. copepods, r = −0.25; fish vs. rotifers, r = 0.25; cladocerans vs. copepods, r = 0.03; cladocerans vs. rotifers, r = −0.14; copepods vs. rotifers, r = −0.07).
Zooplankton densities varied among taxa and sites. The grand mean ± one SD density (number/L) of rotifers was 492.4 ± 453.4 in the off channel and 294.5 ± 133.4 in the main channel across all sites and hours. Grand means of copepod densities were 3.8 ± 2.9 in the off channel and 5.3 ± 2.9 in the main channel, while those of cladocerans were 2.3 ± 4.6 and 0.34 ± 0.43 in the off channel and main channel habitats, respectively. The linear models comparing the log10-transformed ratios of these off channel and main channel zooplankton densities through time revealed that they differed by taxon and, for one site, between day and night. Significant, positive model intercept coefficients revealed that rotifer densities were higher in the off channel than the main channel habitats in Quiver Island and Lilly Lake (Figure 3, Table 2). For Bath Chute rotifers, the model intercept did not differ from zero, meaning that densities were similar between habitats (Figure 3, Table 2). Copepod densities displayed varying patterns among locations. Copepod density was higher in the off channel habitat than the main channel at Quiver Island, was higher in the main channel at Bath Chute, and did not differ between habitats in Lilly Lake (Figure 3, Table 2). The analysis also revealed that Bath Chute copepod densities differed between day and night (p = 0.012), with off channel densities converging toward main channel densities at night (Figure 3, Table 2). No other day-night differences in relative zooplankton densities were observed. Cladoceran densities were higher in the off channel habitat than in the main channel at Quiver Island but were similar between habitats in the other two locations (Figure 3, Table 2). Wide variation in density differences was observed between main and off channel sites for cladocerans, as differences among log-ratio values for cladocerans were often at least an order of magnitude greater than those for rotifers and copepods.
Figure 3

Relationships between log10-transformed ratios of off channel to main channel zooplankton densities and time throughout three locations in the LaGrange Reach of the Illinois River during October 2018. Positive log10-ratios (i.e., significant, positive model intercepts; p < 0.05) indicate higher densities in off channel habitats. Note differences in y-axis scale across taxa. See Table 2 for corresponding model output. Open circles represent daytime hours and filled circles represent nighttime.
Table 2
| Taxon | Site | Coefficient | Estimate | Standard error | t-value | p |
|---|---|---|---|---|---|---|
| Rotifer | Quiver Island | Intercept | 0.255 | 0.061 | 4.187 | <0.001 |
| Time | −0.082 | 0.086 | −0.949 | 0.357 | ||
| Bath Chute | Intercept | 0.029 | 0.031 | 0.983 | 0.340 | |
| Time | −0.033 | 0.043 | −0.776 | 0.449 | ||
| Lilly Lake | Intercept | 0.285 | 0.066 | 4.302 | <0.001 | |
| Time | 0.133 | 0.094 | 1.420 | 0.175 | ||
| Copepod | Quiver Island | Intercept | 0.241 | 0.059 | 4.103 | <0.001 |
| Time | −0.149 | 0.831 | −1.796 | 0.091 | ||
| Bath Chute | Intercept | −0.289 | 0.065 | −4.45 | <0.001 | |
| Time | −0.248 | 0.092 | −2.69 | 0.012 | ||
| Lilly Lake | Intercept | −0.132 | 0.116 | −1.14 | 0.271 | |
| Time | 0.053 | 0.164 | 0.321 | 0.752 | ||
| Cladoceran | Quiver Island | Intercept | 0.942 | 0.296 | 3.182 | <0.001 |
| Time | −0.249 | 0.419 | −0.595 | 0.560 | ||
| Bath Chute | Intercept | −0.069 | 0.452 | −0.154 | 0.879 | |
| Time | 1.147 | 0.639 | 1.796 | 0.091 | ||
| Lilly Lake | Intercept | −0.658 | 0.758 | −0.871 | 0.397 | |
| Time | −0.251 | 1.072 | −0.234 | 0.818 |
Results of linear models testing for the effect of time on the log10-tranformed ratio of off channel to main channel zooplankton densities from the Illinois River (N = 18 per site).
In each model, the intercept term determines whether the mean log ratio differed from zero, with a significant positive value indicating higher densities in the off channel habitat (i.e., ratio > 0) and significant negative intercepts indicating higher main channel densities (i.e., ratio < 0). A significant time effect indicated that relative zooplankton densities between habitats differed between day and night hours. See Figure 3 for corresponding relationships between log10-transformed zooplankton density ratios and time. Bolded statistics were significant at p < 0.05.
The mixed-model analysis that quantified zooplankton density every 4 h and between the surface and the bottom of the river revealed patterns between habitats and among taxa. Rotifer densities in main channel and off channel habitats did not show a time or depth effect (Table 3). Main channel cladoceran and copepod densities were also unrelated to time and depth (Table 3). However, off channel copepod density showed a significant effect of depth (F1,100 = 6.4, p = 0.01), with non-significant time and interaction factors (Table 3). Pairwise comparisons of off channel habitats revealed that copepod densities were greater at the bottom (Figure 4, Table 3). Off channel cladoceran density showed a time effect (F5,100=4.2, p = 0.001, Figure 4, Table 3), while neither the depth nor the depth by time interaction were significant (Table 3). Pairwise comparisons showed that off channel cladocerans had a higher density at night than during the day (Figure 4, Table 3).
Table 3
| Taxon | Site | Factor | F | p |
|---|---|---|---|---|
| Cladoceran | Main channel | Time | 0.22 | 0.95 |
| Depth | 2.17 | 0.14 | ||
| Time*Depth | 0.62 | 0.68 | ||
| Off channel | Time | 4.23 | 0.001 | |
| Depth | 0.74 | 0.31 | ||
| Time*Depth | 0.81 | 0.54 | ||
| Copepod | Main channel | Time | 0.62 | 0.26 |
| Depth | 1.29 | 0.71 | ||
| Time*Depth | 0.58 | 0.80 | ||
| Off channel | Time | 2.18 | 0.06 | |
| Depth | 6.35 | 0.01 | ||
| Time*Depth | 0.76 | 0.53 | ||
| Rotifers | Main channel | Time | 1.66 | 0.15 |
| Depth | 1.69 | 0.20 | ||
| Time*Depth | 0.41 | 0.84 | ||
| Off channel | Time | 0.79 | 0.56 | |
| Depth | 0.22 | 0.64 | ||
| Time*Depth | 0.28 | 0.92 |
Generalized linear mixed-effect model results of major zooplankton taxa densities (number/L) across three locations in the LaGrange Reach, Illinois River in October 2018.
Time represents sampling events at 02:00, 06:00, 10:00, 14:00, 18:00, and 22:00. Depth was a categorical variable representing the water surface vs. bottom. Bolded statistics were significant at p < 0.05.
Figure 4

Mean (± one standard deviation) densities of zooplankton in off channel habitats of the LaGrange Reach, Illinois River in October 2018 over a 24-h period. Black horizontal bars depict night samples. Means for time of day not sharing a common letter were different using Holm's comparisons (p < 0.05).
Discussion
Combining diel, mobile hydroacoustic fish surveys with depth-dependent zooplankton sampling in the main channel and lateral off channel areas of the lower Illinois River showed that distributions of planktivorous fishes and their prey were dynamic and related. Unlike studies where average fish densities are inferred from sampling gears that are adjacent to the sites of plankton sampling, hydroacoustic surveys provided unique direct estimates of overlap between the planktivorous fishes and zooplankton in the river. The planktivore guild consisted of gizzard shad and bigmouth buffalo but was dominated by silver carp as expected for this highly invaded river, so this research quantifies the potential for interactions between silver carp and zooplankton and provides a basis for future diet-based investigations of energy pathways. Because silver carp were consistently denser in the off channel areas than the main channel during both day and night, planktivory would have been more intense in these off channel habitats. As we explain below, daily variation in densities of zooplankton and differences among taxa are consistent with the physical and biotic conditions of the main channel and their off channel habitats, and with the distribution of the planktivorous fish.
There were no consistent daily changes in vertical zooplankton distribution in either main channel or off channel habitats, suggesting that zooplankton DVM did not occur. This contrasts with the impounded Ohio River, USA, where copepod distributions shifted from the bottom to the surface at night (Jack et al., 2006). Because the Ohio River is impounded by permanent high-head dams, it is generally much deeper than the Illinois River and has limited off channel habitats, meaning that Ohio River zooplankton may behave more like zooplankton in lentic systems. It is possible that zooplankton in our study could have been performing DVM if they were moving into the bottom sediment, which is a behavior some zooplankton display in other ecosystems (Tavsanoglu et al., 2012; Petrusevich et al., 2020; Yelton et al., 2022). However, it is currently unknown whether, or to what degree, zooplankton move into the sediment in the Illinois River. Zooplankton DVM can also be influenced by temporal factors such as seasonal day length (Hays, 2003), so a lack of DVM observed in our single 24-h study during autumn at each site does not mean that zooplankton DVM does not occur at other times throughout the year. It is also possible that the daily variation in zooplankton was due to a combination of downstream and lateral movement coupled with planktivory (described below). DeBoer et al. (2018) quantified long-term trends in zooplankton densities in the main channel of the Illinois River and observed strong decreases in densities and biomass following the silver carp invasion. High main channel zooplankton densities DeBoer et al. (2018) observed prior to the silver carp invasion were supported by high plankton reproduction in the main channel and were likely supplemented by resting eggs hatching from the substrate, as well as from off channel areas of the river.
In this study, zooplankton taxa differed in their apparent relationship with planktivores, which was likely a function of the planktons' size and perhaps diurnal patterns in planktivore foraging, zooplankton drift, horizontal movement, and vertical movement from the sediment. Cladoceran densities varied spatially in both main and off channel sites, leading to broad log-ratio values in the analysis relative to rotifers and copepods. River environments are typically considered less suitable than those of low-flow habitats for cladocerans (e.g., Vadadi-Fülöp, 2009), with the wide variation in their density that we observed possibly caused by factors such as patchy resources (Houser, 2016), variable reproduction (Cáceres, 1997), and displacement from refuge areas (Jack et al., 2006). Although there was no evidence of cladoceran DVM in our study, the observed pattern of cladoceran densities decreasing during the day and increasing at night in off channel areas was consistent with a combination of planktivory and drift or other alternative movement, such as lateral movement (Jack et al., 2006). In our study, densities of planktivorous fish were positively correlated with densities of cladocerans across all river sites pooled across day and night, suggesting that planktivores may seek areas (i.e., off channel) where cladocerans are present and impact their behavior and abundance. Even though fish densities in off channel habitats were similar between day and night, silver carp feed more during the day, with peak consumption occurring by late morning (Miah et al., 1984), which is when cladoceran densities were lowest in off channel habitats. Silver carp are highly efficient filter feeders and can reduce cladoceran densities to low levels (DeBoer et al., 2018). Lower nighttime consumption rates by silver carp coupled with cladocerans drifting from upstream off channel areas (e.g., Richardson, 1991; Doi et al., 2008) or moving laterally from shallow, nearshore areas (e.g., Thorp et al., 1994; Jack et al., 2006; Casper and Thorp, 2007) may have resulted in the increased cladoceran densities observed at night. However, the exact mechanisms causing these diurnal patterns in cladoceran densities remain unclear. Future work should examine the extent to which zooplankton diel drift and horizontal movement occurs in lotic systems, especially in the presence of high planktivory, as well as the potential for zooplankton to undergo DVM by moving into the sediment during the day.
Patterns in the distribution and density of rotifers and copepods differed somewhat from cladocerans in the Illinois River. Like cladocerans, there was no evidence of DVM in these taxa, but rotifers occurred at relatively higher, but highly variable, mean densities in the main channel and off channel areas. Rotifer densities typically exceeded those of copepods at all sites. Rotifers were more abundant in the off channel than in the main channel at two sites despite high off channel planktivore densities. Fish and rotifer densities were uncorrelated in this study, suggesting that the linkage between them was weak and other factors contributed to rotifer densities among sites. Rotifers have high reproductive rates and consume different prey than crustacean zooplankton (Sommer and Stibor, 2002) which may allow them to persist with variable flow, high predation, and small, diverse food resources occurring in both river mainstems and off channel areas. Rotifers have been found to occur at higher densities despite planktivory by silver carp in the Illinois River (DeBoer et al., 2018; Tillotson et al., 2022) which is consistent with the lack of daily change in density that occurred in this taxonomic group in our study. That said, experiments in ponds with bighead carp (Hypophthalmichthys nobilis), which are closely related to silver carp, revealed that planktivory can suppress small taxa like rotifers (Collins and Wahl, 2018).
Copepods also showed resilience among sites, with their fate possibly depending on the interplay among planktivory, environmental conditions, and spatial refuges. The log-ratio analysis for Bath Chute revealed that copepod densities may have been suppressed by planktivores in the off channel relative to the main channel during the day. At night when planktivory likely decreased (Miah et al., 1984), Bath Chute off channel copepod densities converged toward those in the main channel, suggesting that drift from upstream or lateral areas acted as replenishment (Sobotka et al., 2025). The elevated flow of the Bath Chute off channel area compared to the other two sites supports a drift hypothesis. In apparent contrast, the mixed-effect linear model analyzing copepod densities across all three off channel areas, including Bath Chute, revealed no diel pattern. This contradiction may have occurred because the mixed effect model accounted for depth and did not compare the relative densities between the main channel and off channel areas. Also, the lack of a pattern in the other two sites may have masked the diel response for Bath Chute. The mixed model analysis revealed consistently higher densities of copepods at the off channel's river bottom, suggesting these taxa may benefit from a benthic habit. This makes sense since silver carp typically remain in the upper portion of the water column (MacNamara et al., 2018), possibly creating a benthic refuge from planktivory. Submergence of copepods in the sediment also may have masked or reduced the effects of planktivory (Tavsanoglu et al., 2012). As with rotifers, densities of planktivorous fish and copepods were uncorrelated in this study, meaning that factors other than planktivory were affecting their distributions. Although copepods may be resilient, they can also collapse with planktivores. In a pond experiment, silver carp reduced all zooplankton taxa to near-zero densities (Tristano, 2018), meaning that all taxa, including rotifers and copepods, can be eliminated with intense planktivory and a lack of drift or deep-water refuges.
Flow-dependent drift, sediment use, and perhaps movement from shallow shoreline areas inaccessible to planktivores might have allowed cladocerans and copepods to persist in the river in the face of intense planktivory. In the Ob River of Russia, inundated floodplain areas were critical for subsidizing plankton (Yanygina et al., 2023) and similar processes may occur in the Illinois River. This may be an explanation for why the LaGrange Pool of the Illinois River is able to support arguably the densest population of silver carp in the world (Sass et al., 2010; Garvey et al., 2012). No native planktivores have yet been extirpated by silver carp and perhaps daily pulses of zooplankton from lateral areas draining into the river allows some coexistence between these predators and their prey. However, several studies show that the condition of native planktivores is lower in sympatry with silver carp (Irons et al., 2007; Kowalski, 2023). The relative contributions of diverse and perennial sources of secondary production need to be quantified to assess the maximum carrying capacity of invasive and native planktivores in the river.
Connectivity of the main channel to floodplains has been reduced in the Illinois River and other large rivers worldwide (Tonkin et al., 2018). In the Illinois River, off channel areas have increasingly filled with fine sediments due to greater spring inputs from agricultural runoff and reduced summer consolidation caused by flow regulation (Coulter et al., 2017). Although zooplankton produced in sediment-free, ephemerally flooded shallow areas may benefit invasive fishes, it also will promote diversity of native fishes and enhance resilience. While river ecology frequently focuses on patterns of dispersal and production of macroinvertebrates, river plankton assemblages are poorly explored despite their critical role. The Illinois River has a long history of zooplankton data extending before the invasion by silver carp and is an ideal system for assessing the relative effects of invasive species control. Harvest of silver carp has increased in the past decade as a form of control (Bouska et al., 2020), and Parkos et al. (2023) found that Illinois River zooplankton densities such as Bosmina cladocerans were negatively correlated with silver carp and bighead carp densities. Removals of these invasive fishes should result in positive responses of zooplankton and eventual restoration of natural ecosystem processes (Love et al., 2018; Altenritter et al., 2022).
Foraging may influence silver carp distributions if plankton were concentrated in the off channel areas where these fish were dense. We did not quantify phytoplankton, although these taxa accumulate in the off channel and affect silver carp locations. Calkins et al. (2012) found that telemetered silver carp were associated with elevated phytoplankton concentrations in slack-water areas of the upper Mississippi River. Additionally, silver carp distributions were experimentally shown to be aggregated in areas of high algae in ponds, meaning that they can track these prey (Ghosal et al., 2022). It is currently unclear whether similar silver carp foraging associations occur with zooplankton in rivers, but the positive association between these fish and cladocerans across off channel and main channel sites in this study affirm that these fishes may be seeking them in the river. Alternatively, areas of high algal production may have fostered the herbivorous cladocerans, leading to an apparent relationship with the fish (i.e., fish were actually seeking phytoplankton). In areas with high silver carp, planktivory during the day would suppress densities of all zooplankton, perhaps masking relationships especially in the off channel areas. To understand underlying planktivorous trophic interactions, the production of zooplankton and feeding rates of the fish at each location would need to be quantified. The lack of clear fish-zooplankton associations beyond cladocerans suggest that other factors contributed to the high densities of silver carp in the off channel areas during this study.
Fish energetics may explain the high densities of silver carp in the off channel. In the lower three pools of the Illinois River, Coulter et al. (2017) found that movement by silver carp into off channel habitats was seasonal, with these fish moving into these areas during autumn through spring when the main channel stage height was elevated and water temperature was lower, similar to the conditions during this autumn study in the same system. Although we may have expected daily movement between main and off channel areas in this study as fish tracked prey aggregations, energy conservation may have outweighed lateral movement. Perhaps, silver carp traded off the higher energy cost of maintaining position in the slightly colder, flowing main channel against the lower cost of inhabiting reduced flow in the warmer off channel. In support of this, Schaffer (2023) used bioenergetics modeling of silver carp to determine that the growth potential of the main channel was not conducive to active foraging in the fall even if food intake was higher there. Understanding how food availability and energetic tradeoffs aggregate invasive bigheaded carps allows more efficient management efforts by determining times and locations for mass removals and other control efforts (Bouska et al., 2020). This is supported by annual fall bigheaded carp removals that occur in upper Peoria Pool, Illinois River backwaters removing greater than 340,000 kg of fish per haul (Invasive Carp Regional Coordinating Committee, 2025).
Conclusion
Behavior differed among zooplankton taxa, although it appears that DVM was not occurring in the LaGrange Pool of the Illinois River. Whether this behavior has been eliminated by intense planktivory throughout the water column or still exists but was not detectable with the gears used will require additional sampling, including in areas lateral to the river and in the sediment. The Illinois River historically supported a substantial button industry using planktivorous freshwater mussels (Starrett, 1972), and prior to damming for navigation, the river was dominated by a series of slow-flowing, interconnected off channel lakes and wetlands during much of the year (Lian et al., 2012). The sheer biomass of planktivorous silver carp that appears to have filled the niche of native mussels in addition to that of native planktivorous fishes is testament to the contribution of plankton to primary and secondary production in this complex riverscape. Habitat rehabilitation that serves to improve connectivity among lateral areas and riverine flow conditions may help to restore zooplankton communities but could also benefit silver carp populations.
Statements
Data availability statement
The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.
Ethics statement
The animal study was approved by Southern Illinois University Institutional Animal Care and Use Committee. The study was conducted in accordance with the local legislation and institutional requirements.
Author contributions
GS: Investigation, Writing – review & editing, Writing – original draft, Visualization, Methodology, Supervision, Data curation, Formal analysis. KM: Methodology, Writing – review & editing, Supervision, Conceptualization, Investigation, Formal analysis, Project administration. AH: Conceptualization, Writing – review & editing, Methodology, Supervision, Investigation. AJ: Supervision, Methodology, Investigation, Writing – review & editing, Conceptualization. PK: Supervision, Methodology, Investigation, Conceptualization, Writing – review & editing. JD: Resources, Conceptualization, Project administration, Methodology, Writing – review & editing, Funding acquisition, Supervision, Investigation. JG: Formal analysis, Methodology, Data curation, Supervision, Project administration, Conceptualization, Writing – original draft, Resources, Writing – review & editing, Visualization, Funding acquisition, Investigation. CD: Writing – review & editing, Investigation, Supervision, Conceptualization, Methodology. DC: Conceptualization, Resources, Funding acquisition, Investigation, Writing – original draft, Visualization, Formal analysis, Methodology, Writing – review & editing, Supervision, Project administration.
Funding
The author(s) declared that financial support was received for this work and/or its publication. Funding was provided by the Great Lakes Restoration Initiative via the Illinois Department of Natural Resources (grant number CAWFS-106), the U.S. Fish and Wildlife Service through the Federal Aid in Sport Fish Restoration Program administered by the Illinois Department of Natural Resources (grant number F-101-R), and by the South Dakota Agricultural Experiment Station.
Acknowledgments
All fish collection and handling procedures were approved by the Southern Illinois University Institutional Animal Care and Use Committee (protocol number 18-002). Thanks to the staff and seasonal technicians at the Illinois River Biological Station for assistance in collecting zooplankton samples and providing guidance and expertise in sample processing.
Conflict of interest
The author(s) declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) JG declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.
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Summary
Keywords
diel vertical migration, diurnal, hydroacoustic analysis, invasive carp, river, riverscape, silver carp, spatial distribution
Citation
Schaffer GQ, Maxson KA, Harris ALW, Johnson AL, Kennedy PJ, DeBoer JA, Garvey JE, Davis C and Coulter DP (2026) Spatial and temporal relationships of zooplankton and planktivores in an invaded large river ecosystem. Front. Freshw. Sci. 3:1719766. doi: 10.3389/ffwsc.2025.1719766
Received
06 October 2025
Revised
30 November 2025
Accepted
08 December 2025
Published
15 January 2026
Volume
3 - 2025
Edited by
Phaedra Budy, Utah State University, United States
Reviewed by
Doru Stelian Banaduc, Lucian Blaga University of Sibiu, Romania
Rosemary Hartman, California Department of Water Resources, United States
Timothy Walsworth, Utah State University, United States
Updates
Copyright
© 2026 Schaffer, Maxson, Harris, Johnson, Kennedy, DeBoer, Garvey, Davis and Coulter.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: David P. Coulter, David.Coulter@sdstate.edu
Disclaimer
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