A theoretical and quantitative framework of first principles would benefit estuarine and coastal ecologists in search of predictions to enhance our understanding and management of marine resources. The Metabolic Theory of Ecology describes a possible unifying theory for ecology, including mechanistically derived equations that predict scaling exponents observed in empirical, allometric relationships from individuals to ecosystems. The controversy surrounding this theory should stimulate our exploration of its potential use in the coastal realm, where questions specific to an applied science may suggest new refinements and derivations, contributing to the overall progress of ecology.

Excess nitrogen (N) in freshwater systems, estuaries, and coastal areas has well-documented deleterious effects on ecosystems. Ecological engineering practices (EEPs) may be effective at decreasing nonpoint source N leaching to surface and groundwater. However, few studies have synthesized current knowledge about the functioning principles, performance, and cost of common EEPs used to mitigate N pollution at the watershed scale. Our review describes seven EEPs known to decrease N to help watershed managers select the most effective techniques from among the following approaches: advanced-treatment septic systems, low-impact development (LID) structures, permeable reactive barriers, treatment wetlands, riparian buffers, artificial lakes and reservoirs, and stream restoration. Our results show a broad range of N-removal effectiveness but suggest that all techniques could be optimized for N removal by promoting and sustaining conditions conducive to biological transformations (e.g., denitrification). Generally, N-removal efficiency is particularly affected by hydraulic residence time, organic carbon availability, and establishment of anaerobic conditions. There remains a critical need for systematic empirical studies documenting N-removal efficiency among EEPs and potential environmental and economic tradeoffs associated with the widespread use of these techniques. Under current trajectories of N inputs, land use, and climate change, ecological engineering alone may be insufficient to manage N in many watersheds, suggesting that N-pollution source prevention remains a critical need. Improved understanding of N-removal effectiveness and modeling efforts will be critical in building decision support tools to help guide the selection and application of best EEPs for N management.

Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess ecosystem processes and interactions, simulate future scenarios, and evaluate remedial actions in response to eutrophication, habitat loss, and freshwater diversion. The need to couple hydrodynamic and ecological models to address research and management questions is clear, because dynamic feedbacks between biotic and physical processes are critical interactions within ecosystems. In this review we present historical and modern perspectives on estuarine hydrodynamic and ecological modeling, consider model limitations, and address aspects of model linkage, skill assessment, and complexity. We discuss the balance between spatial and temporal resolution and present examples using different spatiotemporal scales. Finally, we recommend future lines of inquiry, approaches to balance complexity and uncertainty, and model transparency and utility. It is idealistic to think we can pursue a “theory of everything” for estuarine models, but recent advances suggest that models for both scientific investigations and management applications will continue to improve in terms of realism, precision, and accuracy.

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