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USGS2015

The natural sediment regime in rivers: broadening the foundation for ecosystem management

Water and sediment inputs are fundamental drivers of river ecosystems, but river management tends to emphasize flow regime at the expense of sediment regime. In an effort to frame a more inclusive paradigm for river management, we discuss sediment inputs, transport, and storage within river systems; interactions among water, sediment, and valley context; and the need to broaden the natural flow regime concept. Explicitly incorporating sediment is challenging, because sediment is supplied, transported, and stored by nonlinear and episodic processes operating at different temporal and spatial scales than water and because sediment regimes have been highly altered by humans. Nevertheless, managing for a desired balance between sediment supply and transport capacity is not only tractable, given current geomorphic process knowledge, but also essential because of the importance of sediment regimes to aquatic and riparian ecosystems, the physical template of which depends on sediment-driven river structure and function.

BioScience↗

USGS2016

Bed texture mapping in large rivers using recreational-grade sidescan sonar

The size-distribution and spatial organization of bed sediment, or bed ‘texture’, is a fundamental attribute of natural channels and is one important component of the physical habitat of aquatic ecosystems. ‘Recreational-grade’ sidescan sonar systems now offer the possibility of imaging, and subsequently quantifying bed texture at high resolution with minimal cost, or logistical effort. We are investigating the possibility of using sidescan sonar sensors on commercially available ‘fishfinders’ for within-channel bed-sediment characterization of mixed sand-gravel riverbeds in a debris-fan dominated canyon river. We analyzed repeat substrate mapping of data collected before and after the November 2014 High Flow Experiment on the Colorado River in lower Marble Canyon, Arizona. The mapping analysis resulted in sufficient spatial coverage (e.g. reach) and resolutions (e.g. centrimetric) to inform studies of the effects of changing bed substrates on salmonid spawning on large rivers. From this preliminary study, we argue that the approach could become a tractable and cost-effective tool for aquatic scientists to rapidly obtain bed texture maps without specialized knowledge of hydroacoustics. Bed texture maps can be used as a physical input for models relating ecosystem responses to hydrologic management.

Conference Paper↗

USGS2021

How does climate change affect emergent properties of aquatic ecosystems?

Emergent properties of ecosystems are community attributes, such as structure and function, that arise from connections and interactions (e.g., predator–prey, competition) among populations, species, or assemblages that, when viewed together, provide a holistic representation that is more than the sum of its individual parts. Climate change is altering emergent properties of aquatic ecosystems through component responses, a combination of shifts in species range, phenology, distribution, and productivity, which lead to novel ecosystems that have no historical analog. The reshuffling, restructuring, and rewiring of aquatic ecosystems due to climate impacts are of high concern for natural resource management and conservation as these changes can lead to species extinctions and reductions in ecosystem services. Overall, we found that substantial progress has been made to advance our understanding of how climate change is affecting emergent properties of aquatic ecosystems. However, responses are incredibly complex, and high uncertainty remains for how systems will reorganize and function over the coming decades. This cross‐system perspective summarizes the state of knowledge of climate‐driven emergent properties in aquatic habitats with case studies that highlight mechanisms of change, observed or anticipated outcomes, as well as insights into confounding non‐climate effects, research tools, and management approaches to advance the field.

Fisheries↗

USGS2024

Connecting conservation practices to local stream health in the Chesapeake Bay watershed

The Chesapeake Bay Partnership is implementing conservation practices (CPs) throughout the Chesapeake Bay watershed to reduce nutrient and sediment delivery to the Bay. This study intends to provide an integrated and detailed understanding of how local streams respond to these CP-driven management efforts. Key issue: To what extent do CPs positively affect the health of local streams in the nontidal watershed (cobenefits)? Critical unknown: How do CPs change water quality and the stressors that affect stream aquatic life? Which CPs improve stream health more effectively? Critical knowledge to be delivered to stakeholders includes— the effects of CPs on local water-quality conditions, the degree to which these same CPs also provide local stream-ecosystem benefits, and a deeper understanding of local stream-ecosystems, including stressors and CPs, to guide the selection of management efforts that enhance both water quality and overall stream-ecosystem health.

Chesapeake Bay watershed↗

USGS2019

Fishing for conservation of freshwater tropical fish in the Anthropocene

1. Biodiversity and fisheries are two important assets of freshwater ecosystems that are currently at risk from external threats. Establishing an equitable resolution to these threats is a major challenge of the Anthropocene. 2. This is particularly pertinent in developing nations where hotspots for biodiversity converge with rapid, and often environmentally degrading, economic development, and high dependency on aquatic biota and fisheries by local communities. 3. Here, we present global case studies that demonstrate how building upon a shared need for healthy environments and ecological integrity can meet both biodiversity conservation and fishery objectives. 4. These case studies provide evidence that addressing biodiversity conservation needs is possible through partnerships (especially with fishers), shared knowledge, and innovation in fisheries management. 5. In the pursuit of sustainable use of fresh water in development, both conservation and fisheries agendas are better served if efforts focused on synergising fishing activities with local ecosystem functioning and yield long-term livelihood and food security perspectives. 6. A partnership between conservationists (e.g., practitioners, environmental NGOs) and fisheries communities provides a unified voice advocating for biodiversity and social interests in freshwater governance decisions, which has more socio-economic and political capital than when voices are independent or in competition.

Aquatic Conservation: Marine and Freshwater Ecosys↗

USGS2004

Importance of salmon to wildlife: Implications for integrated management

Salmon ( Oncorhynchuss pp.) are an important resource for terrestrial wildlife. However, the salmon requirements of wildlife populations and the role wildlife play in nutrient transport across ecosystems are largely ignored in salmon and habitat management. Any activity that reduces the availability of or access to salmon by wildlife may adversely affect wildlife populations and, potentially, ecosystem-level processes. Thus, when the conservation of specific wildlife populations or healthy ecosystems is the management objective, allocation of salmon to wildlife should be considered. We provide an example of how such allocations could be calculated for a hypothetical bear population. Ultimately, salmon allocation for wildlife calls for integrated management of natural resources across agencies, across species, and across ecosystems. We summarize the current state of knowledge relative to the interaction between Pacific salmon and the terrestrial ecosystem , with special emphasis on the import of salmon to terrestrial wildlife and the import of wildlife to terrestrial and aquatic ecosystems

Ursus↗

USGS1997

Streamwater chemistry and nutrient budgets for forested watersheds in New England: Variability and management implications

Chemistry of precipitation and streamwater and resulting input-output budgets for nutrient ions were determined concurrently for three years on three upland, forested watersheds located within an 80 km radius in central New England. Chemistry of precipitation and inputs of nutrients via wet deposition were similar among the three watersheds and were generally typical of central New England. In contrast, chemistry and nutrient outputs in streamwater varied dramatically between watersheds, with chemistries ranging from acidic to alkaline. Comparisons with data reported for 159 other upland, forested watersheds in central New England show that our study watersheds span the regional range likely to be encountered in stream chemistry. The regional variability stems in part from past natural disturbances such as wildfire, and variations in source of soil parent material. An approach is presented for predicting the important influence of glacial till on stream chemistry, including acid-base relationships, aluminum content, and nutrient outputs. Knowledge of streamwater chemistry and controlling factors can serve as an index of how terrestrial and aquatic ecosystems will respond to forest management activities and atmospheric deposition.

Forest Ecology and Management↗

USGS2015

Fire effects on aquatic ecosystems: An assessment of the current state of the science

Fire is a prevalent feature of many landscapes and has numerous and complex effects on geological, hydrological, ecological, and economic systems. In some regions, the frequency and intensity of wildfire have increased in recent years and are projected to escalate with predicted climatic and landuse changes. In addition, prescribed burns continue to be used in many parts of the world to clear vegetation for development projects, encourage desired vegetation, and reduce fuel loads. Given the prevalence of fire on the landscape, authors of papers in this special series examine the complexities of fire as a disturbance shaping freshwater ecosystems and highlight the state of the science. These papers cover key aspects of fire effects that range from vegetation loss and recovery in watersheds to effects on hydrology and water quality with consequences for communities (from algae to fish), food webs, and ecosystem processes (e.g., organic matter subsidies, nutrient cycling) across a range of scales. The results presented in this special series of articles expand our knowledge of fire effects in different biomes, water bodies, and geographic regions, encompassing aquatic population, community, and ecosystem responses. In this overview, we summarize each paper and emphasize its contributions to knowledge on fire ecology and freshwater ecosystems. This overview concludes with a list of 7 research foci that are needed to further our knowledge of fire effects on aquatic ecosystems, including research on: 1) additional biomes and geographic regions; 2) additional habitats, including wetlands and lacustrine ecosystems; 3) different fire severities, sizes, and spatial configurations; and 4) additional response variables (e.g., ecosystem processes) 5) over long (>5 y) time scales 6) with more rigorous study designs and data analyses, and 7) consideration of the effects of fire management practices and policies on aquatic ecosystems.

Freshwater Science↗

USGS2022

Chapter 1: General conceptual model for climate change in the Upper San Francisco Estuary

This report is a collaboration by many state and federal agencies working in the Upper San Francisco Estuary to analyze the potential impacts of climate change to different ecosystems found here. Management stategies for ecological values in the face of climate change require reliable and focused information. In this technical report, our focus is on the Upper San Francisco Estuary (SFE), which contains the Sacramento-San Joaquin Delta and Suisun Bay. This area is home to three interconnected ecosystems: open water, floodplain, and tidal marsh. For this geographical area, we have decades of in-depth monitoring information and scientific investigations that have been successfully used to address a number of management needs. In 2019, the Interagency Ecological Program established a diverse work team to improve our ability to anticipate and respond to climate change impacts. The charge to the group was to: • synthesize science relevant to climate change, • determine important knowledge gaps, and • identify ecosystem metrics for climate change. We focus our analyses on the likely impacts of climate change on interconnected aquatic habitats. We illustrate how changes in habitats are likely to affect diverse species. In this report we describe ecological trends attributable to climate change and likely future impacts. We address four principal questions: 1. How have the habitats and biotic communities changed due to climatic trends and events? 2. How are estuarine habitats, flora, and fauna likely to change as climate change trends continue? 3. What are key metrics to document ecosystem change as a result of climate change? 4. How should our monitoring change to improve information value? Our work builds on the similar work of the San Francisco Baylands Goals Project (Goals Project 2015), which addressed climate change impacts to wetlands downstream of the confluence of the Sacramento and San Joaquin Rivers. We aim to contribute to an integrated baseline understanding of climate change impacts for the entire San Francisco Estuary.

California↗

USGS2013

Great Lakes rivermouth ecosystems: scientific synthesis and management implications

At the interface of the Great Lakes and their tributary rivers lies the rivermouths, a class of aquatic ecosystem where lake and lotic processes mix and distinct features emerge. Many rivermouths are the focal point of both human interaction with the Great Lakes and human impacts to the lakes; many cities, ports, and beaches are located in rivermouth ecosystems, and these human pressures often degrade key ecological functions that rivermouths provide. Despite their ecological uniqueness and apparent economic importance, there has been relatively little research on these ecosystems as a class relative to studies on upstream rivers or the open-lake waters. Here we present a synthesis of current knowledge about ecosystem structure and function in Great Lakes rivermouths based on studies in both Laurentian rivermouths, coastal wetlands, and marine estuarine systems. A conceptual model is presented that establishes a common semantic framework for discussing the characteristic spatial features of rivermouths. This model then is used to conceptually link ecosystem structure and function to ecological services provided by rivermouths. This synthesis helps identify the critical gaps in understanding rivermouth ecology. Specifically, additional information is needed on how rivermouths collectively influence the Great Lakes ecosystem, how human alterations influence rivermouth functions, and how ecosystem services provided by rivermouths can be managed to benefit the surrounding socioeconomic networks.

Great Lakes↗

USGS2023

Gains and gaps in knowledge surrounding freshwater mollusk ecosystem services

Ecosystems provide essential services to people including food, water, climate regulation, and aesthetic experiences. Biodiversity can enhance and stabilize ecosystem function and the resulting services natural systems provide. Freshwater mollusks are a diverse group that provide a variety of ecosystem services through their feeding habits (e.g., filter feeding, grazing), top-down and bottom-up effects on food webs, provisioning of habitat, use as a food resource by people, and cultural importance. Research focused on quantifying the direct and indirect ways mollusks influence ecosystem services may help inform policy makers and the public about the value of mollusk communities to society. The Freshwater Mollusk Conservation Society highlighted the need to evaluate mollusk ecosystem services in their 2016 National Strategy for the Conservation of Native Freshwater Mollusks, and, while significant progress has been made, considerable work remains across the research, management, and outreach communities. We briefly review the global status of native freshwater mollusks, assess the current state of knowledge regarding their ecosystem services, and highlight recent advances and knowledge gaps to guide further research and conservation actions. Our intention is to provide ecologists, conservationists, economists, and social scientists with information to improve science-based consideration of the social, ecological, and economic value of mollusk communities to healthy aquatic systems.

Freshwater Mollusk Biology and Conservation↗

USGS2017

Behavioral response of giant gartersnakes (Thamnophis gigas) to the relative availability of aquatic habitat on the landscape

Most extant giant gartersnake ( Thamnophis gigas ) populations persist in an agro-ecosystem dominated by rice, which serves as a surrogate to the expansive marshes lost to flood control projects and development of the Great Central Valley of California. Knowledge of how giant gartersnakes use the rice agricultural landscape, including how they respond to fallowing, idling, or crop rotations, would greatly benefit conservation of giant gartersnakes by informing more snake-friendly land and water management practices. We studied adult giant gartersnakes at 11 sites in the rice-growing regions of the Sacramento Valley during an extended drought in California to evaluate their response to differences in water availability at the site and individual levels. Although our study indicated that giant gartersnakes make little use of rice fields themselves, and avoid cultivated rice relative to its availability on the landscape, rice is a crucial component of the modern landscape for giant gartersnakes. Giant gartersnakes are strongly associated with the canals that supply water to and drain water from rice fields; these canals provide much more stable habitat than rice fields because they maintain water longer and support marsh-like conditions for most of the giant gartersnake active season. Nonetheless, our results suggest that maintaining canals without neighboring rice fields would be detrimental to giant gartersnake populations, with decreases in giant gartersnake survival rates associated with less rice production in the surrounding landscape. Increased productivity of prey populations, dispersion of potential predators across a larger landscape, and a more secure water supply are just some of the mechanisms by which rice fields might benefit giant gartersnakes in adjacent canals. Results indicate that identifying how rice benefits giant gartersnakes in canals and the extent to which the rice agro-ecosystem could provide these benefits when rice is fallowed would inform the use of water for other purposes without harm to giant gartersnakes. Our study also suggests that without such understanding, maintaining rice and associated canals in the Sacramento Valley is critical for the sustainability of giant gartersnake populations.

California↗

USGS2021

Disentangling stationary and dynamic estuarine fish habitat to inform conservation: Species-specific responses to physical habitat and water quality in San Francisco Estuary

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.

California↗

USGS2024

Intrinsic and extrinsic regulation of water clarity in a large, floodplain-river ecosystem

Ecosystem processes in rivers are thought to be controlled more by extrinsic than intrinsic factors, that is, the result of processes that occur upstream or within their watersheds. However, large floodplain rivers have a diverse assemblage of aquatic areas spanning gradients of connectivity with the main channel and internal controls may at times regulate long-term dynamics. When and where internal controls are important has not been widely explored in rivers. The Upper Mississippi River System (UMRS) provides a unique opportunity to assess regulation of ecosystem processes in a large floodplain river as water clarity has increased in several reaches over the last two decades. To better understand when and where intrinsic variables (for example , aquatic vegetation and common carp) and extrinsic variables (for example , upstream main channel total suspended solids (TSS) concentration and discharge) regulate water clarity, we describe 24-year trends of TSS in six study reaches of the UMRS. We evaluated the degree to which trends were shared across aquatic areas within each study reach and identified potential drivers of long-term TSS dynamics. Results varied across and within UMRS reaches, but common carp abundance was the strongest predictor in nearly all study reaches. Several models indicated associations with both intrinsic and extrinsic factors, and the marginal model r 2 values (0.26–0.61) suggest that additional environmental factors may have influenced water clarity. Knowledge of the degree to which intrinsic and extrinsic processes regulate water clarity is important for understanding and managing large, floodplain rivers worldwide.

Ecosystems↗

USGS2010

Detailed seafloor habitat mapping to enhance marine-resource management

Pictures of the seafloor capture important information about the sediments, exposed geologic features, submerged aquatic vegetation, and animals found in a given habitat. With the emergence of marine protected areas (MPAs) as a favored tactic for preserving coral reef resources, knowledge of essential habitat components is paramount to designing effective management strategies. Surprisingly, detailed information on seafloor habitat components is not available in many areas that are being considered for MPA designation or that are already designated as MPAs. A task of the U.S. Geological Survey Coral Reef Ecosystem STudies (USGS CREST) project is addressing this issue.

Fact Sheet↗

USGS2020

Changing nitrogen inputs to the northern San Francisco Estuary: Potential ecosystem responses and opportunities for investigation

Anthropogenic activities have resulted in elevated ambient nitrogen (N) and phosphorus (P) concentrations in many regions of the Sacramento-San Joaquin Delta and Suisun Bay (northern San Francisco Estuary, (nSFE). The Sacramento Regional wastewater treatment plant (SRWTP WWTP) currently acts as the largest N point source to the system, discharging 13,000-15,000 kg/d of ammonium-N (NH4) near the nSFE’s northeastern boundary. By end of 2021, SRWTP will complete major upgrades that will reduce its effluent dissolved inorganic nitrogen (DIN) loads by >65% and release the remaining DIN as predominantly nitrate (NO3). This major change in nitrogen inputs provides a unique opportunity to study ecosystem-scale responses to an altered nutrient regime. While, in general, the nSFE has not experienced some classic symptoms of nutrient over-enrichment typical in other estuaries—e.g., large phytoplankton blooms and hypoxia—other concerning nutrient- related impacts have been hypothesized, including: occurrence of harmful algal blooms (HABs) and the production of cyanotoxins; excessive growth of invasive aquatic vegetation; and declines in the abundance and nutritional quality of phytoplankton. These impacts have repercussions for the system’s food web, habitat quality, and the way we manage for transportation, recreation, water conveyance, and drinking water quality. This report develops and applies a framework for i) identifying and examining ecosystem response scenarios to the forthcoming decreased N loads; and ii) identifying opportunities, and constraints or considerations, for investigating those responses, including key data needs or knowledge gaps. Through applying this framework, we identify a set of plausible response scenarios, and evaluate the feasibility of studying or observing those responses along with key study considerations and data and knowledge gaps.

California↗

USGS2018

Executive summary. In Second State of the Carbon Cycle Report (SOCCR2): A Sustained Assessment Report

Central to life on Earth, carbon is essential to the molecular makeup of all living things and plays a key role in regulating global climate. To understand carbon’s role in these processes, researchers measure and evaluate carbon stocks and fluxes. A stock is the quantity of carbon contained in a pool or reservoir in the Earth system (e.g., carbon in forest trees), and a flux is the direction and rate of carbon’s transfer between pools (e.g., the movement of carbon from the atmosphere into forest trees during photosynthesis). This document, the Second State of the Carbon Cycle Report (SOCCR2), examines the patterns of carbon stocks and fluxes—collectively called the “carbon cycle.” Emphasis is given to these patterns in specific sectors (e.g., agriculture and energy) and ecosystems (e.g., forests and coastal waters) and to the response of the carbon cycle to human activity. The purpose of SOCCR2 is to assess the current state of the North American carbon cycle and to present recent advances in understanding the factors that influence it. Concentrating on North America—Canada, the United States, and Mexico—the report describes carbon cycling for air, land, inland waters (streams, rivers, lakes, and reservoirs), and coastal waters (see Figure ES.1, p. 23). The questions framing the publication A U.S. Carbon Cycle Science Plan (Michalak et al., 2011) inspired development of three slightly modified questions that guide SOCCR2’s content and focus on North America in a global context: How have natural processes and human actions affected the global carbon cycle on land, in the atmosphere, in the ocean and other aquatic systems, and at ecosystem interfaces (e.g., coastal, wetland, and urban-rural)? How have socioeconomic trends affected atmospheric levels of the primary carbon-containing gases, carbon dioxide (CO2) and methane (CH4)? How have species, ecosystems, natural resources, and human systems been impacted by increasing greenhouse gas (GHG) concentrations, associated changes in climate, and carbon management decisions and practices? SOCCR2 synthesizes the most recent understanding of carbon cycling in North America, assessing new carbon cycle findings and information, the state of knowledge regarding core methods used to study the carbon cycle, and future research needed to best inform carbon management and policy options. Focusing on scientific developments in the decade since the First State of the Carbon Cycle Report (SOCCR1; CCSP 2007), SOCCR2 summarizes the past, current, and projected state of carbon sources, sinks, and natural processes, as well as contributions by human activities. In addition to CO2 and CH4, the report sometimes discusses nitrous oxide (N2O), a GHG associated with activities and processes that affect fluxes of carbon gases.1 SOCCR2 also describes improvements in analysis tools; developments in decision support; and new insights into ecosystem carbon cycling, human causes of changes in the carbon cycle, and social science perspectives on carbon. Since publication of SOCCR1, coordinated research from agencies in the three North American countries has enabled innovative observational, analytical, and modeling capabilities to further advance understanding of the North American carbon cycle (see Appendix D: Carbon Measurement Approaches and Accounting Frameworks, p. 834). Some of the report’s main conclusions, based on the Key Findings of each chapter, are highlighted in Box ES.1, Main Findings of SOCCR2, p. 24.

Report↗

USGS2021

Preface to book: Wetland carbon and environmental management

The idea for this book, including its organization and contents, has its origin in the latest environmental and climate policy requirements in the United States, as well as science advances. In 2007, the U.S. Congress passed the Energy Independence and Security Act (EISA), from which Section 712 required U.S. Federal agencies to provide a better understanding of carbon and greenhouse gas fluxes across the United States. As a result, largescale and coordinated efforts were launched to assess carbon storage, carbon fluxes, and greenhouse gas fluxes including CO2, CH4, and N2O from all major terrestrial and freshwater aquatic ecosystems, including forest, grassland/shrub, agricultural lands, wetlands, and rivers, streams, lakes, and impoundments. The EISA assessment produced major results (Selmants et al., 2017; Zhu, 2011; Zhu & McGuire, 2016; Zhu & Reed, 2012, 2014), but recognized that wetlands remained a significant source of uncertainty, especially for those wetlands that were being actively managed. The more recent Second State of the Carbon Cycle Report by the U.S. Global Change Research Program (USGCRP), which devoted two separate chapters to inland and coastal wetlands, respectively, noted that large knowledge gaps still remain, ranging from inadequate analysis of restored and managed wetlands, and consequences of management decisions, to future wetland responses to climate change (USGCRP, 2018). In recent literature, wetland management is suggested as a potential natural solution to mitigate climate change (Fargione et al., 2018, Kroeger et al., 2017) and help offset direct losses of wetlands from sea level rise, subsidence, and coastal erosion (Wang et al., 2017). The recognition that a synthesis of wetland carbon management was urgently needed was the genesis of Wetland Carbon and Environmental Management; discerning the relationships between wetland management and carbon flux (loss or gain) is an international goal.

Geophysical Monograph Series↗