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Mechanisms driving the consumption and transport of tidal marsh nutrients and energy by fishes are of key interest in the San Francisco Estuary, CA, USA. By combining multiple data sources (gill-net catches, gut contents, channel morphology, tides), we modeled spatial and temporal patterns of fish abundance and gut fullness across a tidal marsh elevation gradient. Channel depth, microhabitat, and tide were important predictors of fish abundance and gut fullness. Species, feeding guild, and season were also important to fish abundance but not to gut fullness, suggesting that abundance was more related to physical constraints of shallow water than to prey availability. Multiple feeding guilds overlapped in space and time at interaction hotspots in subtidal channel habitat near the marsh entrance. In contrast, fish use of shallow intertidal marsh channels was more variable and indicated tradeoffs between foraging and predation. Gut content analysis revealed moderate-to-high gut fullness for all feeding guilds and models predicted high gut fullness in subtidal reaches during tidal flooding, after which fish fed intensively throughout the marsh. While mysids, amphipods, and detritus were common prey among feeding guilds, variation in prey consumption was apparent. Overall, complex tidal marsh hydrogeomorphology driving land-water exchange and residence time may diversify and enhance benthic and pelagic food web pathways to fishes and invertebrates. Furthermore, these findings substantiate the notion that dynamic tidal marshes in this system can support robust secondary production, foraging by multiple feeding guilds, and trophic transfer by fishes to the estuarine mosaic.

Tidal wetland restoration is commonly used to recover ecosystem functions and services that were lost when wetlands were diked for reclamation or management. Less research has been conducted on the response of invertebrate and fish assemblages to tidal restoration than on plants and physical attributes. Blacklock Marsh, a wetland in Suisun Marsh, USA, was once managed for waterfowl hunting and cattle grazing until its dike was breached, restoring full tidal action. We sampled water quality, zooplankton, macroinvertebrates, and fishes in Blacklock Marsh, and compared these metrics to adjacent naturalistic waterways and to a managed wetland focused on waterfowl. Our goal was to compare food production and community assemblage on a restoring marsh to other types of nearby waterways. Blacklock Marsh had less chlorophyll-a and dissolved organic carbon than nearby dead-end sloughs and the managed wetland, less zooplankton biomass than the managed wetland, and lower fish diversity—with a fish assemblage dominated by non-native species—compared to all other waterways. The most abundant fish species in the restoring site, Mississippi silverside (Menidia audens), is a non-native fish and known predator of Delta smelt larvae (Hypomesus transpacificus), for which the restoration was targeted. Our research suggests that restoring tidal action to managed wetlands alone may worsen rather than improve conditions for at-risk and native fishes.

Little is known about the ecological importance of low-order tidal marsh channels to fishes in the San Francisco Estuary, California. We conducted a passive mark-recapture study to compare residency, site fidelity, and movement patterns of fishes in a small intertidal channel (0.1 km2) in a large tidal marsh reserve (4.25 km2). We coupled continuous, high-frequency data on movements of fish tagged with Passive Integrated Transponder (PIT) tags and abiotic conditions from a PIT-detector and datasonde, respectively. Novel insights were gained by employing TidalTrend, a software program that characterizes tidal time-series data for ecological interpretation. Overall, we found that fishes exhibited different patterns of intertidal habitat use: the resident species, tule perch (Hysterocarpus traski), consistently spent more time per visit, per day, and per season using the intertidal channel, except during the reproductive window in spring; the transient species, Sacramento splittail (Pogonichthys macrolepidotus) and striped bass (Morone saxatilis), were more opportunistic and exhibited higher individual variation in movement patterns. Generalized additive mixed models indicated that tide height, rate of change in tide height, tidal inequality, time of day, lunar phase, and water temperature better predicted fish detections than other variables, but their effects varied across species. Based on our findings, we posit that time, through tides, allows habitat partitioning among fish species and individuals with different life-history types. Furthermore, functional connectivity between subtidal and intertidal channels in tidal marshes is a feature of the estuarine mosaic that should be integrated into habitat restoration designs in the San Francisco Estuary.

Opportunities to enhance ecosystem functions exist in human‐dominated working landscapes, but understanding of key drivers is often lacking in these novel environments. In Suisun Marsh, California, USA, impounded managed wetlands designed to promote waterfowl incidentally support higher plankton densities—a key resource for imperilled pelagic fishes—than adjacent tidal habitats. Managed wetland operations could produce plankton at critical periods for fish and the aquatic food‐web more broadly, but drivers of plankton production in managed wetlands are poorly understood.We proposed that decaying vegetation resulting from controlled flooding in managed wetlands is important for stimulating plankton blooms, but that the effect varies by plant species and functional type. We conducted a mesocosm experiment to test the effects of different inundated plants on plankton production, including three forb species, three emergent graminoid species and a control treatment without added plant material.Forbs promoted larger phytoplankton blooms and higher zooplankton production—by an order of magnitude—than both emergent graminoids and the control treatment. Emergent graminoids supported larger phytoplankton blooms, but not higher zooplankton production, than the control treatment. Phytoplankton blooms exhibited pulse dynamics in all treatments, with densities increasing initially and crashing by the end of the experiment. Phytoplankton blooms in forb and emergent treatments lasted similar durations, counter to the expectation that emergent graminoids would support diminished production over a relatively prolonged period. Among zooplankton taxa, Daphnia magna and rotifers were strongly associated with all three forbs species while the nonnative cyclopoid copepod Limnothoina tetraspina were associated with cattails (Typha domingensis) and the control. Forbs temporarily depleted dissolved oxygen concentrations during the first week of the experiment, suggesting a tradeoff by which decaying forbs boost plankton production at risk of initial hypoxia.Our results suggest that seasonal drying and flooding operations in managed wetlands are likely to enhance plankton production because dry periods promote forb growth and subsequent flooding introduces labile forb material to the aquatic food web. Results also suggest that seasonal managed‐wetlands act as novel floodplain‐analogues, by which flood pulses drive productivity. Further research is needed to quantify production benefits and tradeoffs to the aquatic ecosystem at the landscape scale and to identify optimal management regimes that will help conserve imperilled species. [ABSTRACT FROM AUTHOR]

The rate of alien species introductions is increasing in aquatic ecosystems, but many invaders appear to co-exist with previous residents, resulting in persistent mixed assemblages of non-coevolved organisms. This study focuses on species’ habitat partitioning of edge habitats in the San Francisco Estuary, a highly altered novel ecosystem that supports mixed assemblages of native and alien fishes and macroinvertebrates. We used minnow traps to address two questions about the demersal assemblage along levees in large tidal sloughs: (1) What is the relative abundance of demersal fish and macroinvertebrate species in shallow water adjacent to levee edges? and (2) Do native and alien species occupy different habitat types? We used our findings to address the broader question: do native and non-native species show habitat segregation, suggesting development of assemblage structure similar to that of co-evolved assemblages? Results indicate that habitat partitioning occurs among some clusters of species, but not all. Native Prickly Sculpin was found most often near riprapped levee edges, while alien Yellowfin Goby occupied adjacent muddy habitat, and the alien Shimofuri Goby showed no preference. Where two non-native species of caridean shrimp co-occurred, Siberian Prawn occupied unvegetated mud, while Oriental Grass Shrimp used primarily riprap. However, when only Siberian Prawn was present, it showed no preference for habitat type. Habitat associations changed slightly in response to seasonal shifts in habitat and spawning requirements. This study demonstrates that non-coevolved assemblages of organisms can develop resource partitioning to assist co-existence in novel habitats.

The overbite clam (Potamocorbula amurensis) is a major invasive species in the San Francisco Estuary, California, and has been implicated in the decline of pelagic productivity and native fish species. Little is known of its impact on Suisun Marsh, a large brackish tidal region of the estuary. We looked at the abundance and spatial distribution of clams in the marsh, including examining the influence of water quality, using long-term (1988–2015) otter trawl surveys. Temporal trends indicated that overbite clam abundance has been increasing, but adult clams were spatially restricted to a single large slough (Suisun). Clams were absent from most interior channels, limiting their overall effect on the marsh aquatic ecosystem. Abiotic variables, particularly salinity, proved important predictors of overbite clam abundance, although the variables examined alone could not explain overbite clam distributions. We propose that connectivity, detritus loads, and/or predation pressure may work in conjunction with abiotic variables to cause poor survival rates for recruits in interior marsh sites, keeping the distribution limited. Overall results are encouraging for restoration projects in brackish tidal marshes that need to deal with overbite clams.

Using stable isotopes of carbon (δ13C) and nitrogen (δ15N) and mixing models, we investigated the trophic levels and carbon sources of invertebrates and fishes of a large tidal marsh in the San Francisco Estuary. Our goal was to better understand an estuarine food web comprised of native and alien species. We found the following: (1) the food web was based largely on carbon from phytoplankton and emergent-aquatic and terrestrial vegetation, but carbon from submerged aquatic vegetation and phytobenthos was also used; (2) alien species increased the complexity of the food web by altering carbon-flow pathways and by occupying trophic positions different from native species; and (3) most consumers were dietary generalists.

Population density might be an important variable in determining the degree of multiple paternity. In a previous study, a high level of multiple paternity was detected in the shiner perch Cymatogaster aggregata, a species with high population density and a high mate encounter rate. The tule perch Hysterocarpus traski is phylogenetically closely related to C. aggregata, but it has relatively lower population density, which may result in distinct patterns of multiple paternity in these 2 species. To test the hypothesis that mate encounter rate may affect the rate of successful mating, we used polymorphic microsatellite markers to identify multiple paternity in the progeny arrays of 12 pregnant females from a natural population of tule perch. Multiple paternity was detected in 11 (92%) of the 12 broods. The number of sires per brood ranged from 1 to 4 (mean 2.5) but with no correlation between sire number and brood size. Although the brood size of tule perch is considerably larger than that of shiner perch (40.7 vs. 12.9, respectively), the average number of sires per brood in tule perch is much lower than that in shiner perch (2.5 vs. 4.6, respectively). These results are consistent with the hypothesis that mate encounter rate is an important factor affecting multiple mating.