Disentangling Stationary and Dynamic Estuarine Fish Habitat to Inform Conservation: Species-Specific Responses to Physical Habitat and Water Quality in San Francisco Estuary

American Fisheries Society (AFS) | October 12th, 2021

Estuaries represent critical aquatic habitat that connects surface water distributed between Earth’s landmasses and oceans. They are dynamic transitional ecosystems, wh

Estuaries represent critical aquatic habitat that connects surface water distributed between Earth’s landmasses and oceans. They are dynamic transitional ecosystems, which provide important habitat for fishes and other aquatic organisms. Effective conservation of species inhabiting estuaries requires knowledge of the habitat features that drive their abundance and distribution. We sought to elucidate how stationary (i.e., wetlands, shoals, and channels) and dynamic (i.e., salinity, temperature, turbidity, and chlorophyll concentration) habitat features interact to drive distributions of individual fish species. The Pacific coast of the conterminous United States has over 400 estuaries of various types. The largest (historical surface area) is San Francisco Estuary, California. We conducted extensive field observations of fishes in the central San Francisco Estuary among stationary habitat types (i.e., wetland, shoal, and channel) over a 19-month period encompassing substantial variability in dynamic water quality conditions. Most of the species observed, especially native species of special management interest, were associated with tidal wetland habitat. Few species exhibited associations with water quality conditions driven by seasonal (temperature) or a combination of broad- and fine-scale ecosystem processes (salinity and turbidity). Our study provides (1) an empirical demonstration of how researchers can deal with the complex and dynamic expressions of habitat in estuarine systems to address urgent natural resource problems and (2) a clear demonstration of the urgent need for habitat restoration and its likely outcome in systems such as San Francisco Estuary. Restoration of suitable tidal wetland habitat on the West Coast of the United States is likely to be an effective conservation tool to support estuarine fishes given that over 90% of historical tidal wetland habitat in San Francisco Estuary and 85% of vegetated wetland habitat along the Pacific coast of the United States has been lost due to human modification.

Dissolved Oxygen in South San Francisco Bay: Variability, Important Processes, and Implications for Understanding Fish Habitat

San Francisco Estuary Institute (SFEI) | October 30th, 2018

Dissolved oxygen (DO) is a key water quality parameter that is related to nutrient enrichment in estuaries around the world. In 2017-2018, the San Francisco Estuary Inst

Dissolved oxygen (DO) is a key water quality parameter that is related to nutrient enrichment in estuaries around the world. In 2017-2018, the San Francisco Estuary Institute (SFEI) launched a study to investigate the potential effects of low-DO on habitat quality in Lower South Bay (LSB) to inform decisions about nutrient regulation. The goal of the study was to understand where and when regions of LSB provide adequate DO to support resident fish species. The study approach involved convening a team of experts to advise on methods, analyzing high frequency DO measurements from seven mooring stations in LSB, and partnering with researchers from UC Davis to interpret several years of monthly fish abundance data in LSB relative to DO and other factors.

Downscaling global ocean climate models improves estimates of exposure regimes in coastal environments

Nature Portfolio (Springer Nature) | August 26th, 2020

Climate change is expected to warm, deoxygenate, and acidify ocean waters. Global climate models (GCMs) predict future conditions at large spatial scales, and these pred

Climate change is expected to warm, deoxygenate, and acidify ocean waters. Global climate models (GCMs) predict future conditions at large spatial scales, and these predictions are then often used to parameterize laboratory experiments designed to assess biological and ecological responses to future change. However, nearshore ecosystems are affected by a range of physical processes such as tides, local winds, and surface and internal waves, causing local variability in conditions that often exceeds global climate models. Predictions of future climatic conditions at local scales, the most relevant to ecological responses, are largely lacking. To fill this critical gap, we developed a 2D implementation of the Regional Ocean Modeling System (ROMS) to downscale global climate predictions across all Representative Concentration Pathway (RCP) scenarios to smaller spatial scales, in this case the scale of a temperate reef in the northeastern Pacific. To assess the potential biological impacts of local climate variability, we then used the results from different climate scenarios to estimate how climate change may affect the survival, growth, and fertilization of a representative marine benthic invertebrate, the red abalone Haliotis rufescens, to a highly varying multi-stressor environment. We found that high frequency variability in temperature, dissolved oxygen (DO), and pH increases as pCO2 increases in the atmosphere. Extreme temperature and pH conditions are generally not expected until RCP 4.5 or greater, while frequent exposure to low DO is already occurring. In the nearshore environment simulation, strong RCP scenarios can affect red abalone growth as well as reduce fertilization during extreme conditions when compared to global scale simulations.

Draft finding of no significant impact, 2-Gates Fish Protection Demonstration Project.

U.S. Bureau of Reclamation (USBR) | November 13th, 2009

The proposed Demonstration Project is a 5-year experiment to validate a new delta smelt behavioral model and study the effects of modifying flows in the Sacramento-San Jo

The proposed Demonstration Project is a 5-year experiment to validate a new delta smelt behavioral model and study the effects of modifying flows in the Sacramento-San Joaquin Delta (Delta) to protect delta smelt and other sensitive aquatic species from entrainment in Central Valley Project (CVP) and State Water Project (SWP) export pumps. Research suggests that the pre-spawning migration of adult delta smelt is tied to sediment/suspended particles in the water (turbidity). Temporary gates would be placed across Old River and Connection Slough in the central Delta and operated from December to March to keep turbid water away from the CVP and SWP export pumps, thus keeping adult delta smelt away from the pumps, and in March and June to prevent larvae and juvenile delta smelt from being entrained by the export pumps.

DRAFT Staff Report/Substitute Environmental Document in Support of Potential Updates to the Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary for the Sacramento River and its Tributaries, Delta Eastside Tributaries, and Delta

California State Water Resources Control Board (SWRCB) | September 28th, 2023

DRERIP Ecosystem Conceptual Model: Chinook Salmon & Steelhead

California Department of Fish and Wildlife (CDFW) | September 4th, 2012

This report constitutes the conceptual model for Chinook and steelhead for the Delta Regional Ecosystem Restoration Implementation Plan (DRERIP). The report describes

This report constitutes the conceptual model for Chinook and steelhead for the Delta Regional Ecosystem Restoration Implementation Plan (DRERIP). The report describes conceptual models, not numerical models, but several important considerations apply to both kinds, especially when they are used for management of living natural resources. First, the proper purpose of models is to help people think, not to think for them. Ignoring this can be disastrous, as exemplified by the current economic crisis. The world of credit default swaps was built on highly sophisticated models that persuaded many intelligent people that the associated risk was negligible, but they failed to recognize that a market based on houses that people could not pay for from their earnings is unsustainable. In short, the most important output of a good conceptual or numerical model is clear thinking. To help people think, the model must be focused on selected features of the world that are thought to be important for the purpose at hand: in this case, management of the Delta. A model that tries to include everything will be too complex to be useful for this purpose. Second, to be useful for management of natural living resources, numerical models must be unrealistic, because our knowledge of such resources is incomplete, and is based on data that includes measurement errors. According to Ludwig‘s paradox, "Effective management models cannot be realistic" (Ludwig 1994:516), because two kinds of uncertainty must be balanced (Figure I-1; see Ch. 14 in Williams (2006) for elaboration of this point). In our view, something similar applies to conceptual models of natural systems: to be useful, they must be simple. A schematic of the wiring in some electronic device is a conceptual model that may be useful as well as complex, but trying to develop a similar schematic of an ecosystem or part of an ecosystem is not useful, because our knowledge of such a system is much less complete than our knowledge of engineered devices, and we have only estimates of the relevant parameters. Finally, reality is too complex to capture with a single model. Eric Lander, a noted geneticist who co-chairs President Obama‘s Council of Advisors on Science and Technology, recently remarked that "You can never capture something like an economy, a genome or an ecosystem with one model or one taxonomy – it all depends on the questions you want to ask." (NY Times, 11/11/08). Models are tools that we use to try to think, and multi-purpose tools generally do nothing well. Therefore, although the complete life cycle of Chinook and steelhead is described here, the parts or aspects of the cycle that we think may be affected by management of the Delta are emphasized, and we try to keep it as simple as possible. More detail on most of the topics described here can be found in Quinn (2005), or in Williams (2006), from which this document draws very heavily.

DRERIP Ecosystem Conceptual Model: Delta smelt

California Department of Fish and Wildlife (CDFW) | October 22nd, 2010

This Conceptual Model is part of a suite of conceptual models which collectively articulate the current scientific understanding of important aspects of the Sacramento-Sa

This Conceptual Model is part of a suite of conceptual models which collectively articulate the current scientific understanding of important aspects of the Sacramento-San Joaquin River Delta ecosystem. The conceptual models are designed to aid in the identification and evaluation of ecosystem restoration actions in the Delta. These models are designed to structure scientific information such that it can be used to inform sound public policy. The Delta Conceptual Models include both ecosystem element models (including process, habitat, and stressor models) and species life history models. The models were prepared by teams of experts using common guidance documents developed to promote consistency in the format and terminology of the models http://www.delta.dfg.ca.gov/erpdeltaplan/science_process.asp . The Delta Conceptual Models are qualitative models which describe current understanding of how the system works. They are designed and intended to be used by experts to identify and evaluate potential restoration actions. They are not quantitative, numeric computer models that can be “run” to determine the effects of actions. Rather they are designed to facilitate informed discussions regarding expected outcomes resulting from restoration actions and the scientific basis for those expectations. The structure of many of the Delta Conceptual Models can serve as the basis for future development of quantitative models.

DRERIP Ecosystem Conceptual Model: Fish Habitat Linkages

California Department of Fish and Wildlife (CDFW) | January 19th, 2008

The Delta Regional Ecosystem Restoration Implementation Plan (DRERIP) is one of four regional plans intended to guide the implementation of the CALFED Ecosystem Restorati

The Delta Regional Ecosystem Restoration Implementation Plan (DRERIP) is one of four regional plans intended to guide the implementation of the CALFED Ecosystem Restoration Program (ERP) element. The DRERIP will refine the planning foundation for the Delta, develop and refine specific restoration actions and provide project implementation guidance, program tracking, performance evaluation and adaptive management feedback specific to the Delta. The DRERIP Fish Habitat Linkage Model (FHL model) provides a roadmap for how the various conceptual models designed for the DRERIP process intertwine to define fish habitat and ultimately produce fish. The model identifies the key linkages between hydrology and numerous other components of fish habitat. The FHL model shows that hydrodynamics and water operations exert influences on fish recruitment by directly influencing transport fates, the water quality components of habitat, and some biotic interactions. The water quality components of habitat interact with structural components of habitat; their interaction affects the strength of biotic interactions (Peterson 2003). Because the FHL model is a generalized model serving as a template or road map, the relative importance of drivers and linkages, and their direction of impact (positive or negative), are not shown in the model diagram because they will depend on which species, contingent (sensu Secor 1999), or life stage is being evaluated. Additional general descriptions of the state of knowledge about these linkages are provided in the text boxes for each model component.

DRERIP Ecosystem Conceptual Model: Floodplain

California Department of Fish and Wildlife (CDFW) | January 22nd, 2008

Elements common to all models (Figure 1). Gray shapes (“plaques” in Word parlance) are other DRERIP models. Brown polygons are modifying factors. Pink rectangles are

Elements common to all models (Figure 1). Gray shapes (“plaques” in Word parlance) are other DRERIP models. Brown polygons are modifying factors. Pink rectangles are primary outputs of direct interest to Delta restoration planners (e.g., splittail). Blue rectangles are hydrological characteristics or variables, primarily pertaining to the primary river that is the source of inundation to the floodplain of interest but some rectangles represent “secondary hydrology” such as water deriving from direction precipitation on the floodplain, and groundwater and tributary inputs. Blue-green rectangles represent inundated habitat characteristics – properties of the floodplain during periods of inundation. Model 1 (Creating the Template) captures the linkages and processes that create the habitat mosaic—the physical template of a given floodplain, such as topography and vegetative communities (Figure 2). Note that habitat mosaic is more than vegetative communities as it also includes topographic features like side channels, oxbows, and wetlands. This is a very basic model, so we didn’t attempt to use the information-coded arrows to indicate importance, predictability, etc. This model describes how floodplain topography and vegetation, important features treated as more or less static in the other models, are created and maintained. This model encompasses time scales ranging from a single flood event (e.g., bank erosion) to decades or centuries (successional processes in a floodplain forest). Delta restoration planners can use model 1 to understand management options for creating and maintaining habitat mosaics on a given floodplain. Model 2 (Inundating the template) depicts how a given floodplain, with topography and vegetation created within Model 1, is inundated by river flows and other sources of water to create specific conditions within the inundated floodplain that are important to the species or processes described in model set 3 (Figure 3). The hydrology first encounters river-floodplain topography (e.g., the relative elevations of floodplain to river stage) to determine if the floodplain becomes inundated; the other linkages only occur if flow magnitude is capable of exceeding the inundation threshold. Inundation is a function of flow magnitude in the river, along with contributions from other hydrological sources (e.g., local tributaries, high water table), and the relative elevation and connectivity of the river-floodplain topography. If inundation occurs, the floodwaters interact with the topography and vegetation created in Model 1. As inundation occurs across this mosaic it results in a variety of inundated habitat characteristics—conditions that directly affect biota and processes during the period of inundation. These inundated habitat characteristics are the primary inputs for Model Set 3. This model is primarily focused at the temporal scale of a single flood season. Delta restoration planners can use model 2 to evaluate how management actions can influence the inundation of floodplain habitat mosaics and characteristics of the inundated habitat. Model Set 3 (Management outputs) illustrates how the inundated habitat characteristics, developed in Model 2, interact with a few other key elements to influence the production of biota of direct interest to delta restoration planners, including algae, zooplankton, splittail, and juvenile Chinook salmon (Figures 4 - 7). Model Set 3 encompasses a temporal scale of a single flood season. Model Set 3 can be used to evaluate how specific characteristics of the inundated floodplain affect specific outputs of management interest. Figure 4 provides a basic overview of the inputs and outputs and relationships between the models in Model Set 3. Figure 5 focuses on the production of algae (phytoplankton and epibenthic algae) and zooplankton, structured as a food web. Figures 6 and 7 show how the inundated habitat characteristics and base of the food web (algae and zooplankton) affect the production of splittail and Chinook salmon, respectively. Primary management outputs from floodplain models: 1. Primary productivity, in terms of phytoplankton, the most nutritious organic matter for the downstream delta (Muller-Solger et al. 2002) and secondary productivity (zooplankton and macroinvertebrates). Because several important species in the delta are food-limited, as indicated by low first-year survival, floodplain restoration has been promoted as a means of increasing productivity to these species and ecosystems (Jassby and Cloern 2000). 2. Juvenile Chinook 3. Splittail 4. Habitat mosaic and riparian structure for a variety of species. The first three management outputs are Model 3 outputs. For these a user can work backwards through the models to understand how management options can increase the productivity of a specific desired output. For example, if the desired output is biologically available Carbon for downstream ecosystems (algae), then Figure 5 (Model 3) indicates that residence time and intra-annual frequency are important characteristics; for these characteristics of inundation to occur, Figure 3 (Model 2) indicates that the frequency of inundation can be influenced either through hydrologic or topographic manipulations, and the narrative for Model 1 provides background information on the processes that create and maintain floodplain topography. The management output ‘riparian structure’ is a Model 1 output.

DRERIP Ecosystem Conceptual Model: Green sturgeon

California Department of Fish and Wildlife (CDFW) | December 27th, 2008

The purpose of this report is to develop a conceptual life history model of North American green sturgeon (Acipenser medirostris) and the factors that affect reproduction

The purpose of this report is to develop a conceptual life history model of North American green sturgeon (Acipenser medirostris) and the factors that affect reproduction, growth, and survival in the Sacramento and San Joaquin rivers and San Francisco Bay-Delta. This model can be used to organize, visualize, and evaluate how the complex life history of green sturgeon relates to the spatial and temporal variability of riverine and estuarine ecosystems and potential consequences of ecosystem restoration and water management alternatives. This model is compatible with the suite of environmental and species models developed by the Department of Fish and Game Ecosystem Restoration Program (ERP) to assess and prioritize proposed restoration actions for the Delta. The model has a geographic emphasis on the Sacramento River and Bay-Delta regions, though the entire distribution of green sturgeon must be considered when population level responses are of concern, due to the unique, highly-migratory life history of this species. The conceptual life history model incorporates information from numerous sources about green sturgeon, often relying upon life history information from populations outside the Southern Distinct Population Segment (DPS) and occasionally considering information from the sympatric white sturgeon (A. transmontanus). While surrogate information from other North American sturgeon could have been used in the model, the distinctive anadromous and ecological characteristics of green sturgeon limited the utility of these species’ information. Due to the limits of quantitative information about green sturgeon, this model is presented in a qualitative narrative with numerical information provided, when available. While it will not provide quantitative limits on species take relative to maintaining a stable population size, it could be further developed into a population forecasting model since it divides the life history into life history stages, transition probabilities, and factors whose affects on reproduction and survival could be quantified. Life history stage transitions are visualized in a series of life stage submodels highlighting the processes and relationships among ecological factors influencing the transition between stages (Figures 1 and 2). A complex set of conditions and processes are necessary to determine whether an individual fish completes the transition from one life stage to the next. Our knowledge of green sturgeon life history remains limited as to the relative importance of biotic and abiotic factors critical for maintaining self-sustaining populations of green sturgeon. Thus, the importance, predictability, and understanding of each of these linkages are identified in the model. Lastly, a similar characterization of independent stressors is undertaken to describe potential factors affecting survival during each life history stage in a known geographic region. This model is dynamic and not intended to be a final version. As new information becomes available, the model should be refined so managers and biologists have the most current information available.