Use of a Managed Flow Pulse as Food Web Support for Estuarine Habitat

While freshwater inflow has been a major focus of resource management in estuaries, including the upper San Francisco Estuary, there is a growing interest in using focused flow actions to maximize benefits for specific regions, habitats, and species. As a test of this concept, in summer 2016, we used a managed flow pulse to target an ecologically important region: a freshwater tidal slough complex (Cache Slough Complex–CSC). Our goal was to improve estuarine habitat by increasing net flows through CSC to enhance downstream transport of lower trophic-level resources, an important driver for fishes such as the endangered Delta Smelt Hypomesus transpacificus. We used regional water infrastructure to direct 18.5 million m³ of Sacramento River flow into its adjacent Yolo Bypass floodplain, where the pulse continued through CSC. Simulations using a 3-D hydrodynamic model (UnTRIM) indicated that the managed flow pulse had a large effect on the net flow of water through Yolo Bypass, and between CSC and further downstream. Multiple water quality constituents (specific conductivity, dissolved oxygen, nutrients [NO₃ + NO₂, NH₄, PO₄]) varied across the study region, and showed a strong response to the flow pulse. In addition, the lower Sacramento River had increased phytoplankton biomass and improved food quality indices (estimated from long-chain essential fatty acids) after the flow pulse. The managed flow pulse resulted in increased densities of zooplankton (copepods, cladocerans) demonstrating potential advection from upper floodplain channels into the target CSC and Sacramento River regions. This study was conducted during a single year, which may have had unique characteristics; however, we believe that our study is an instructive example of how a relatively modest change in net flows can generate measurable changes in ecologically relevant metrics, and how an adaptive management action can help inform resource management.

Chinook salmon exhibit long-term rearing and early marine growth in the Fraser River, B.C., a large urban estuary

Estuaries represent a transition zone for salmon migrating from freshwater to marine waters, yet their contribution to juvenile growth is poorly quantified. Here, we use genetic stock identification and otolith analyses to quantify estuarine habitat use by Chinook salmon (<i>Oncorhynchus tshawytscha</i>) – the Pacific salmon species considered most reliant on this habitat – in Canada’s most productive salmon river, the Fraser. Two years of sampling revealed subyearling migrant (“ocean-type”) Chinook from the Harrison River to be the estuary’s dominant salmon population throughout the emigration period. These Chinook salmon were caught predominantly in the estuary’s brackish marshes but shifted to more saline habitats as they grew. Otolith analyses indicated that these Chinook salmon have wide-ranging entry timing (from February to May), and longer estuarine residency (weeks to months, mean 41.8 days) than estimated by prior studies, but similar daily growth rates (mean 0.57 mm +/- 0.13 SD) across entry dates and residency periods, implying sufficient foraging opportunities throughout the emigration period and habitats. Together, these results suggest that estuarine habitat is more important for early marine growth of subyearling migrant Chinook salmon than previously recognized.

Estuarine Habitat Use by White Sturgeon (Acipenser transmontanus)

White Sturgeon (Acipenser transmontanus), a species of concern in the San Francisco Estuary, is in relatively low abundance due to a variety of factors. Patton et al. sought identify the estuarine habitat used by White Sturgeon to aid in the conservation and management of the species locally and across its range. By seasonally sampled sub-adult and adult White Sturgeon in the central estuary using setlines across a habitat gradient representative of three primary structural elements, the authors found that the shallow open-water shoal and deep open-water channel habitats were consistently occupied by White Sturgeon in spring, summer, and fall across highly variable water quality conditions, whereas the shallow wetland channel habitat was essentially unoccupied. In summary, sub-adult and adult White Sturgeon inhabit estuaries in at least spring, summer, and fall and small, shallow wetland channels are relatively unoccupied.

Quantifying the Benefits of Estuarine Habitat Restoration in the Gulf of Mexico: an Introduction to the Theme Section

This collection of papers provides insights into methods and data currently available to quantify the benefits associated with estuarine habitat restoration projects in the northern Gulf of Mexico, USA, with potential applicability to other coastal systems. Extensive habitat restoration is expected to occur in the northern Gulf of Mexico region over the next several decades through funding associated with the 2010 Deepwater Horizon oil spill. Papers in this section examine the development of vegetation, soil properties, invertebrate fauna, and nekton communities in restored coastal marshes and provide a conceptual framework for applying these findings to quantify the benefits associated with compensatory marsh restoration. Extensive meta-analysis of existing data for Gulf of Mexico coastal habitats further confirms that structured habitats such as marsh, submerged aquatic vegetation, and oyster reefs support greater nekton densities than nonvegetated bottom habitat, with oyster reefs supporting different species assemblages than marsh and submerged aquatic vegetation. Other papers demonstrate that while vegetation cover can establish rapidly within the first 5 years of restoration, belowground parameters such as root biomass and soil organic matter remain 44% to 92% lower at restored marshes than reference marshes 15 years after restoration. On average, amphipod and nekton densities are also not fully restored until at least 20 and 13 years following restoration, respectively. Additional papers present methods to estimate the benefits associated with marsh restoration projects, nekton productivity associated with coastal and estuarine habitats, and the benefits associated with the removal of derelict crab traps in Gulf of Mexico estuaries.