14 Sep 2022

Is Mean Discharge Meaningless for Environmental Flow Management?

PURPOSE: River ecosystems are highly dependent on and responsive to hydrologic variability over multiple time scales (e.g., hours, months, years). Fluctuating river flows present a key challenge to river managers, who must weigh competing demands for freshwater. Environmental flow recommendations and regulations seek to provide management targets balancing socio-economic outcomes with maintenance of ecological integrity. Often, flow management targets are based on average river conditions over temporal windows such as days, months, or years. Here, three case studies of hydrologic variability are presented at each time scale, which demonstrate the potential pitfalls of mean-based environmental flow criteria. Each case study shows that the intent of the environmental flow target is not met when hydrologic variability is considered. While mean discharge is inadequate as a single-minded flow management target, the consequences of mean flow prescriptions can be avoided in environmental flow recommendations. Based on these case studies, a temporal hierarchy of environmental flow thresholds is proposed (e.g., an instantaneous flow target coupled with daily and monthly averages), which would improve the efficacy of these regulations.

14 Sep 2022

Ecological Model Development: Evaluation of System Quality

PURPOSE: Ecological models are used throughout the US Army Corps of Engineers (USACE) to inform decisions related to ecosystem restoration, water operations, environmental impact assessment, environmental mitigation, and other topics. Ecological models are typically developed in phases of conceptualization, quantification, evaluation, application, and communication. Evaluation is a process for assessing the technical quality, reliability, and ecological basis of a model and includes techniques such as calibration, verification, validation, and review. In this technical note (TN), we describe an approach for evaluating system quality, which generally includes the computational integrity, numerical accuracy, and programming of a model or modeling system. Methods are presented for avoiding computational errors during development, detecting errors through model testing, and updating models based on review and use. A formal structure is proposed for model test plans and subsequently demonstrated for a hypothetical habitat suitability model. Overall, this TN provides ecological modeling practitioners with a rapid guide for evaluating system quality.

13 Sep 2022

waterquality for ArcGIS Pro Toolbox: User’s Guide

Abstract: Monitoring water quality of small inland lakes and reservoirs is a critical component of the US Army Corps of Engineers (USACE) water quality management plans. However, limited resources for traditional field-based monitoring of numerous lakes and reservoirs covering vast geographic areas often leads to reactional responses to harmful algal bloom (HAB) outbreaks. Satellite remote sensing methodologies using HAB indicators is a good low-cost option to traditional methods and has been proven to maximize and complement current field-based approaches while providing a synoptic view of water quality (Beck et al. 2016; Beck et al. 2017; Beck et al. 2019; Johansen et al. 2019; Mishra et al. 2019; Stumpf and Tomlinson 2007; Wang et al. 2020; Xu et al. 2019; Reif 2011). To assist USACE water quality management, we developed an Environmental Systems Research Institute (ESRI) ArcGIS Pro desktop software toolbox (waterquality for ArcGIS Pro) founded on the design and research established in the waterquality R software package (Johansen et al. 2019; Johansen 2020). The toolbox enables the detection, monitoring, and quantification of HAB indicators (chlorophyll-a, phycocyanin, and turbidity) using Sentinel-2 satellite imagery. Four tools are available: (1) automating the download of Sentinel-2 Level-2A imagery, (2) creating stacked image with options for cloud and non-water features masks, (3) applying water quality algorithms to generate relative estimations of one to three water quality parameters (chlorophyll-a, phycocyanin, and turbidity), and (4) creating linear regression graphs and statistics comparing in situ data (from field-based water sampling) to relative estimation data. This document serves as a user’s guide for the waterquality for ArcGIS Pro toolbox and includes instructions on toolbox installation and descriptions of each tool’s inputs, outputs, and troubleshooting guidance.

12 Sep 2022

Properties and Detectability of Rogue Synthetic Biology (SynBio) Products in Complex Matrices

Abstract: Synthetic biology (SynBio) aims to rationally engineer or modify traits of an organism or integrate the behaviors of multiple organisms into a singular functional organism through advanced genetic engineering techniques. One objective of this research was to determine the environmental persistence of engineered DNA in the environment. To accomplish this goal, the environmental persistence of legacy engineered DNA building blocks were targeted that laid the foundation for SynBio product development and application giving rise to “post-use products.” These building blocks include genetic constructs such as cloning and expression vectors, promoter/terminator elements, selectable markers, reporter genes, and multi-cloning sites. Shotgun sequencing of total DNA from water samples of pristine sites was performed and resultant sequence data mined for frequency of legacy recombinant DNA signatures. Another objective was to understand the fate of a standardized contemporary synthetic genetic construct (SC) in the context of various chassis systems/genetic configurations representing different degrees of “genetic bioavailability” to the environmental landscape. These studies were carried out using microcosms representing different environmental matrices (soils, waters, wastewater treatment plant (WWTP) liquor) and employed a novel genetic reporter system based on volatile organic compounds (VOC) detection to assess proliferation and persistence of the SC in the matrix over time.

12 Sep 2022

Application of Clean Dredged Material to Facilitate Contaminated Sediment Source Control

Abstract: Navigation channels, turning basins, and other US Army Corps of Engineers (USACE)–managed navigation infrastructure often serve as repositories for contaminated sediment from off-site sources. As much as 10% of the material that USACE dredges on an annual basis is contaminated such that it requires additional and more costly management (for example, rehandling and placement in managed confined disposal facilities). Presence of contaminated sediments constrain potential management options resulting in additional costs and opportunity loss from the inability to beneficially use the material. One potential solution is applying clean dredged material to stabilize and isolate contaminated sediment sources, preventing further transport and introduction to USACE-managed infrastructure. This document summarizes a comprehensive literature review of laboratory and field case studies relevant to using clean dredged material to isolate or stabilize contaminated sediments, focusing on the physical, chemical, and biological parameters critical to establishing its feasibility and long-term effectiveness. Potentially effective engineering control measures were also reviewed where erosion and site hydrodynamics are facilitating the transport of contaminated sediments to USACE-maintained navigation infrastructure. This literature review documents and summarizes those factors considered in establishing feasibility and long-term effectiveness of the approach as well as the applicable engineering tools employed and constraints encountered.

29 Aug 2022

Remote Sensing Capabilities to Support EWN® Projects: An R&D Approach to Improve Project Efficiencies and Quantify Performance

PURPOSE: Engineering With Nature (EWN®) is a US Army Corps of Engineers (USACE) Initiative and Program that promotes more sustainable practices for delivering economic, environmental, and social benefits through collaborative processes. As the number and variety of EWN® projects continue to grow and evolve, there is an increasing opportunity to improve how to quantify their benefits and communicate them to the public. Recent advancements in remote sensing technologies are significant for EWN® because they can provide project-relevant detail across a large areal extent, in which traditional survey methods may be complex due to site access limitations. These technologies encompass a suite of spatial and temporal data collection and processing techniques used to characterize Earth's surface properties and conditions that would otherwise be difficult to assess. This document aims to describe the general underpinnings and utility of remote sensing technologies and applications for use: (1) in specific phases of the EWN® project life cycle; (2) with specific EWN® project types; and (3) in the quantification and assessment of project implementation, performance, and benefits.

29 Aug 2022

Financing Natural Infrastructure: South Bay Salt Pond Restoration Project, California

PURPOSE: This technical note is part of a series collaboratively produced by the US Army Corps of Engineers (USACE)–Institute for Water Resources (IWR) and the US Army Engineer Research and Development Center (ERDC). It describes the funding and financing process for the South Bay Salt Pond Restoration Project in San Francisco Bay, California and, like the other technical notes in this series, documents successful examples of funding natural infrastructure projects. The research effort is a collaboration between the Engineering With Nature® (EWN®) and Systems Approach to Geomorphic Engineering (SAGE) programs of USACE. A key need for greater application of natural infrastructure approaches is information about obtaining funds to scope, design, construct, monitor, and adaptively manage these projects. As natural infrastructure techniques vary widely by location, purpose, and scale, there is no standard process for securing funds. The goal of this series is to share lessons learned about a variety of funding and financing methods to increase the implementation of natural infrastructure projects.

18 Aug 2022

Geospatial Suitability Indices (GSI) Toolbox: User’s Guide

Abstract: Habitat suitability models have been widely adopted in ecosystem management and restoration to assess environmental impacts and benefits according to the quantity and quality of a given habitat. Many spatially distributed ecological processes require application of suitability models within a geographic information system (GIS). This technical report presents a geospatial toolbox for assessing habitat suitability. The geospatial suitability indices (GSI) toolbox was developed in ArcGIS Pro 2.7 using the Python 3.7 programming language and is available for use on the local desktop in the Windows 10 environment. Two main tools comprise the GSI toolbox. First, the suitability index (SIC) calculator tool uses thematic or continuous geospatial raster layers to calculate parameter suitability indices using user-specified habitat relationships. Second, the overall suitability index calculator (OSIC) combines multiple parameter suitability indices into one overarching index using one or more options, including arithmetic mean, weighted arithmetic mean, geometric mean, and minimum limiting factor. The result is a raster layer representing habitat suitability values from 0.0–1.0, where zero (0) is unsuitable habitat and one (1) is ideal suitability. This report documents the model purpose and development and provides a user’s guide for the GSI toolbox.

17 Aug 2022

Ecological Model Development: Toolkit for interActive Modeling (TAM)

Overview: Ecological models provide crucial tools for informing many aspects of ecosystem restoration and management, ranging from increasing understanding of complex ecological functions to prioritizing restoration sites and quantifying benefits for project reporting. The diversity of ecosystem types and restoration objectives often precludes the use of existing models; as such, model development is commonly required to inform restoration decision-making. Index-based habitat models are a common approach for assessing ecosystem condition. These models relate habitat quality to species’ distributions. Habitat suitability (quality) typically ranges on a scale from 0 to 1. Habitat models have been developed to assess habitat suitability for specific taxa, communities, or ecosystem functions. Restoration-project timelines often require that these models be developed rapidly and in conjunction with many external stakeholders or partners. Here, the Toolkit for interActive Modeling (TAM) is proposed as a platform for rapidly developing index-based models, particularly for US Army Corps of Engineers’ (USACE) ecosystem-restoration or mitigation planning processes. The TAM is a consistent quantitative framework that allows for development of a generic platform for index-based model development

17 Aug 2022

Evaluation of Methods for Monitoring Herbaceous Vegetation

Abstract: This special report seeks to advance the field of ecological restoration by reviewing selected reports on the processes, procedures, and protocols associated with monitoring of ecological restoration projects. Specifically, this report identifies selected published herbaceous vegetation monitoring protocols at the national, regional, and local levels and then evaluates the recommended sampling design and methods from these identified protocols. Finally, the report analyzes the sampling designs and methods in the context of monitoring restored herbaceous vegetation at US Army Corps of Engineers (USACE) ecosystem restoration sites. By providing this information and the accompanying analyses in one document, this special report aids the current effort to standardize data-collection methods in monitoring ecosystem restoration projects.