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Abstract Salt marshes occur globally across climatic and coastal settings, providing key linkages between terrestrial and marine ecosystems. However, salt marsh science lacks a unifying conceptual framework; consequently, historically well‐studied locations have been used as normative benchmarks. To allow for more effective comparisons across the diversity of salt marshes, we developed an integrative salt marsh conceptual framework. We review ecosystem‐relevant drivers from global to local spatial scales, integrate these multi‐scale settings into a framework, and provide guidance on applying the framework using specific variables on 11 global examples. Overall, this framework allows for appropriate comparison of study sites by accounting for global, coastal, inter‐, and intra‐system spatial settings unique to each salt marsh. We anticipate that incorporating this framework into salt marsh science will provide a mechanism to critically evaluate research questions and a foundation for effective quantitative studies that deepen our understanding of salt marsh function across spatial scales.

Abstract Pacific herring (Clupea pallasii) is an ecologically and commercially valuable forage fish in the North Pacific Ocean. However, knowledge gaps exist around the abiotic and biotic drivers behind its variable population dynamics—as well as on the ability of the species to show spatially structured trends that stabilize population portfolios in the face of environmental change. Here we examined how historical hydroclimatic variability in the San Francisco Estuary (California) has driven age‐0 Pacific herring population dynamics over 35 years. First, we used wavelet analyses to examine spatiotemporal variation and synchrony in the environment, focusing on two key variables: salinity and temperature. Next, we fitted multivariate autoregressive state‐space models to environmental and abundance time series to test for spatial structure and to parse out abiotic (salinity and temperature) from biotic influences (spawning and density dependence). Finally, we examined the stabilizing effects of spatially asynchronous population fluctuations (i.e., portfolio effects) across the estuary. Our results showed that temperature, but not salinity, fluctuated synchronously across regions on seasonal and decadal timescales. The top‐ranked model showed strong evidence of regional population structure and regional variation in population responses to the environment. As expected, age‐0 herring were generally associated with cooler, saltier conditions in spring. Density dependence was strong in all regions, suggesting that local factors influencing rearing conditions limited juvenile population growth across the estuary. Additionally, age‐0 abundance fluctuations were on average 15% more stable across the estuary than in individual regions, demonstrating that portfolio effects arising from population asynchrony have helped to stabilize recruitment across the estuary over the past four decades. We contend that ecosystem‐based fishery management strategies to restore eelgrass and tidal marsh rearing habitats could increase the carrying capacity of the estuary, further stabilizing the herring population and reducing the risk of fishery closures.

Salt marshes occur globally across climatic and coastal settings, providing key linkages between terrestrial and marine ecosystems. However, salt marsh science lacks a unifying conceptual framework; consequently, historically well‐studied locations have been used as normative benchmarks. To allow for more effective comparisons across the diversity of salt marshes, we developed an integrative salt marsh conceptual framework. We review ecosystem‐relevant drivers from global to local spatial scales, integrate these multi‐scale settings into a framework, and provide guidance on applying the framework using specific variables on 11 global examples. Overall, this framework allows for appropriate comparison of study sites by accounting for global, coastal, inter‐, and intra‐system spatial settings unique to each salt marsh. We anticipate that incorporating this framework into salt marsh science will provide a mechanism to critically evaluate research questions and a foundation for effective quantitative studies that deepen our understanding of salt marsh function across spatial scales. [ABSTRACT FROM AUTHOR]

Pacific herring (Clupea pallasii) is an ecologically and commercially valuable forage fish in the North Pacific Ocean. However, knowledge gaps exist around the abiotic and biotic drivers behind its variable population dynamics—as well as on the ability of the species to show spatially structured trends that stabilize population portfolios in the face of environmental change. Here we examined how historical hydroclimatic variability in the San Francisco Estuary (California) has driven age‐0 Pacific herring population dynamics over 35 years. First, we used wavelet analyses to examine spatiotemporal variation and synchrony in the environment, focusing on two key variables: salinity and temperature. Next, we fitted multivariate autoregressive state‐space models to environmental and abundance time series to test for spatial structure and to parse out abiotic (salinity and temperature) from biotic influences (spawning and density dependence). Finally, we examined the stabilizing effects of spatially asynchronous population fluctuations (i.e., portfolio effects) across the estuary. Our results showed that temperature, but not salinity, fluctuated synchronously across regions on seasonal and decadal timescales. The top‐ranked model showed strong evidence of regional population structure and regional variation in population responses to the environment. As expected, age‐0 herring were generally associated with cooler, saltier conditions in spring. Density dependence was strong in all regions, suggesting that local factors influencing rearing conditions limited juvenile population growth across the estuary. Additionally, age‐0 abundance fluctuations were on average 15% more stable across the estuary than in individual regions, demonstrating that portfolio effects arising from population asynchrony have helped to stabilize recruitment across the estuary over the past four decades. We contend that ecosystem‐based fishery management strategies to restore eelgrass and tidal marsh rearing habitats could increase the carrying capacity of the estuary, further stabilizing the herring population and reducing the risk of fishery closures. [ABSTRACT FROM AUTHOR]

Investigating the effects of climatic variability on biological diversity, productivity, and stability is key to understanding possible futures for ecosystems under accelerating climate change. A critical question for estuarine ecosystems is, how does climatic variability influence juvenile recruitment of different fish species and life histories that use estuaries as nurseries? Here we examined spatiotemporal abundance trends and environmental responses of 18 fish species that frequently spend the juvenile stage rearing in the San Francisco Estuary, CA, USA. First, we constructed multivariate autoregressive state‐space models using age‐0 fish abundance, freshwater flow (flow), and sea surface temperature data (SST) collected over four decades. Next, we calculated coefficients of variation (CV) to assess portfolio effects (1) within and among species, life histories (anadromous, marine opportunist, or estuarine dependent), and the whole community; and (2) within and among regions of the estuary. We found that species abundances varied over space and time (increasing, decreasing, or dynamically stable); and in 83% of cases, in response to environmental conditions (wet/dry, cool/warm periods). Anadromous species responded strongly to flow in the upper estuary, marine opportunist species responded to flow and/or SST in the lower estuary, and estuarine dependent species had diverse responses across the estuary. Overall, the whole community when considered across the entire estuary had the lowest CV, and life histories and species provided strong biological insurance to the portfolio (2.4‐ to 3.5‐fold increases in stability, respectively). Spatial insurance also increased stability, although to a lesser extent (up to 1.6‐fold increases). Our study advances the notion that fish recruitment stability in estuaries is controlled by biocomplexity—life history diversity and spatiotemporal variation in the environment. However, intensified drought and marine heatwaves may increase the risk of multiple consecutive recruitment failures by synchronizing species dynamics and trajectories via Moran effects, potentially diminishing estuarine nursery function. [ABSTRACT FROM AUTHOR]

Ecosystem management and governance of cross-scale dependent systems require integrating knowledge about ecological connectivity in its multiple forms and scales. Although scientists, managers, and policymakers are increasingly recognizing the importance of connectivity, governmental organizations may not be currently equipped to manage ecosystems with strong cross-boundary dependencies. Managing the different aspects of connectivity requires building social connectivity to increase the flow of information, as well as the capacity to coordinate planning, funding, and actions among both formal and informal governance bodies. We use estuaries in particular the San Francisco Estuary, in California, in the United States, as examples of cross-scale dependent systems affected by many intertwined aspects of connectivity. We describe the different types of estuarine connectivity observed in both natural and human-affected states and discuss the human dimensions of restoring beneficial physical and ecological processes. Finally, we provide recommendations for policy, practice, and research on how to restore functional connectivity to estuaries. [ABSTRACT FROM AUTHOR]

Climate change is altering naturally fluctuating environmental conditions in coastal and estuarine ecosystems across the globe. Departures from long-term averages and ranges of environmental variables are increasingly being observed as directional changes [e.g., rising sea levels, sea surface temperatures (SST)] and less predictable periodic cycles (e.g., Atlantic or Pacific decadal oscillations) and extremes (e.g., coastal flooding, marine heatwaves). Quantifying the short- and long-term impacts of climate change on tidal marsh seascape structure and function for nekton is a critical step toward fisheries conservation and management. The multiple stressor framework provides a promising approach for advancing integrative, cross-disciplinary research on tidal marshes and food web dynamics. It can be used to quantify climate change effects on and interactions between coastal oceans (e.g., SST, ocean currents, waves) and watersheds (e.g., precipitation, river flows), tidal marsh geomorphology (e.g., vegetation structure, elevation capital, sedimentation), and estuarine and coastal nekton (e.g., species distributions, life history adaptations, predator-prey dynamics). However, disentangling the cumulative impacts of multiple interacting stressors on tidal marshes, whether the effects are additive, synergistic, or antagonistic, and the time scales at which they occur, poses a significant research challenge. This perspective highlights the key physical and ecological processes affecting tidal marshes, with an emphasis on the trophic linkages between marsh production and estuarine and coastal nekton, recommended for consideration in future climate change studies. Such studies are urgently needed to understand climate change effects on tidal marshes now and into the future. [ABSTRACT FROM AUTHOR]

Over the last 20 years, innovations have led to the development of exciting new technologies and novel applications of established technologies, collectively increasing the scale, scope, and quality of research possible in tidal marsh systems. Thus, ecological research on marshes is being revolutionized, in the same way as ecological research more generally, by the availability of new tools and analytical techniques. This perspective highlights current and potential applications of novel research technologies for marsh ecology. These are summarized under several themes: (1.) imagery — sophisticated imaging sensors mounted on satellites, drones, and underwater vehicles; (2.) animal tracking — acoustic telemetry, passive integrated transponder (PIT) tags, and satellite tracking, and (3.) biotracers — investigation of energy pathways and food web structure using chemical tracers such as compound-specific stable isotopes, isotope addition experiments, contaminant analysis, and eDNA. While the adoption of these technological advances has greatly enhanced our ability to examine contemporary questions in tidal marsh ecology, these applications also create significant challenges with the accessibility, processing, and synthesis of the large amounts of data generated. Implementation of open science practices has allowed for greater access to data. Newly available machine learning algorithms have been widely applied to resolve the challenge of detecting patterns in massive environmental datasets. The potential integration on digital platforms of multiple, large data streams measuring physical and biological components of tidal marsh ecosystems is an opportunity to advance science support for management responses needed in a rapidly changing coastal landscape. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Coastal salt marshes are distributed widely across the globe and are considered essential habitat for many fish and crustacean species. Yet, the literature on fishery support by salt marshes has largely been based on a few geographically distinct model systems, and as a result, inadequately captures the hierarchical nature of salt marsh pattern, process, and variation across space and time. A better understanding of geographic variation and drivers of commonalities and differences across salt marsh systems is essential to informing future management practices. Here, we address the key drivers of geographic variation in salt marshes: hydroperiod, seascape configuration, geomorphology, climatic region, sediment supply and riverine input, salinity, vegetation composition, and human activities. Future efforts to manage, conserve, and restore these habitats will require consideration of how environmental drivers within marshes affect the overall structure and subsequent function for fisheries species. We propose a future research agenda that provides both the consistent collection and reporting of sources of variation in small-scale studies and collaborative networks running parallel studies across large scales and geographically distinct locations to provide analogous information for data poor locations. These comparisons are needed to identify and prioritize restoration or conservation efforts, identify sources of variation among regions, and best manage fisheries and food resources across the globe. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Estuaries are highly variable environments where fish are subjected to a diverse suite of habitat features (e.g., water quality gradients, physical structure) that filter local assemblages from a broader, regional species pool. Tidal, climatological, and oceanographic phenomena drive water quality gradients and, ultimately, expose individuals to other habitat features (e.g., stationary physical or biological elements, such as bathymetry or vegetation). Relationships between fish abundances, water quality gradients, and other habitat features in the Sacramento-San Joaquin Delta were examined as a case example to learn how habitat features serve as filters to structure local assemblages in large river-dominated estuaries. Fish communities were sampled in four tidal lakes along the estuarine gradient during summer-fall 2010 and 2011 and relationships with habitat features explored using ordination and generalized linear mixed models (GLMMs). Based on ordination results, landscape-level gradients in salinity, turbidity, and elevation were associated with distinct fish assemblages among tidal lakes. Native fishes were associated with increased salinity and turbidity, and decreased elevation. Within tidal lakes, GLMM results demonstrated that submersed aquatic vegetation density was the dominant driver of individual fish species densities. Both native and non-native species were associated with submersed aquatic vegetation, although native and non-native fish populations only minimally overlapped. These results help to provide a framework for predicting fish species assemblages in novel or changing habitats as they indicate that species assemblages are driven by a combination of location within the estuarine gradient and site-specific habitat features. [ABSTRACT FROM AUTHOR]