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Developing a broader scientific foundation for river restoration: Columbia River food webs

Well-functioning food webs are fundamental for sustaining rivers as ecosystems and maintaining associated aquatic and terrestrial communities. The current emphasis on restoring habitat structure—without explicitly considering food webs—has been less successful than hoped in terms of enhancing the status of targeted species and often overlooks important constraints on ecologically effective restoration. We identify three priority food web-related issues that potentially impede successful river restoration: uncertainty about habitat carrying capacity, proliferation of chemicals and contaminants, and emergence of hybrid food webs containing a mixture of native and invasive species. Additionally, there is the need to place these food web considerations in a broad temporal and spatial framework by understanding the consequences of altered nutrient, organic matter (energy), water, and thermal sources and flows, reconnecting critical habitats and their food webs, and restoring for changing environments. As an illustration, we discuss how the Columbia River Basin, site of one of the largest aquatic/riparian restoration programs in the United States, would benefit from implementing a food web perspective. A food web perspective for the Columbia River would complement ongoing approaches and enhance the ability to meet the vision and legal obligations of the US Endangered Species Act, the Northwest Power Act (Fish and Wildlife Program), and federal treaties with Northwest Indian Tribes while meeting fundamental needs for improved river management.

Proceedings of the National Academy of Sciences of

Differences in Ichthyophonus prevalence and infection severity between upper Yukon River and Tanana River chinook salmon, Oncorhynchus tshawytscha (Walbaum), stocks

Two genetically distinct populations of chinook salmon, Oncorhynchus tshawytscha (Walbaum), were simultaneously sampled at the confluence of the Yukon and Tanana rivers in 2003. Upper Yukon-Canadian fish had significantly higher infection prevalence as well as more severe infections (higher parasite density in heart tissue) than the lower Yukon-Tanana River fish. Both populations had migrated the same distance from the mouth of the Yukon River at the time of sampling but had significantly different distances remaining to swim before reaching their respective spawning grounds. Multiple working hypotheses are proposed to explain the differences between the two stocks: (1) the two genetically distinct populations have different inherent resistance to infection, (2) genetically influenced differences in feeding behaviour resulted in temporal and/or spatial differences in exposure, (3) physiological differences resulting from different degrees of sexual maturity influenced the course of disease, and (4) the most severely infected Tanana River fish either died en route or fatigued and were unable to complete their migration to the Tanana River, thus leaving a population of apparently healthier fish. ?? 2006 Blackwell Publishing Ltd.

Alaska

Relating river discharge and water temperature to the recruitment of age‐0 White Sturgeon (Acipenser transmontanus Richardson, 1836) in the Columbia River using over‐dispersed catch data

The goals were to (i) determine if river discharge and water temperature during various early life history stages were predictors of age‐0 White Sturgeon, Acipenser transmontanus , recruitment, and (ii) provide an example of how over‐dispersed catch data, including data with many zero observations, can be used to better understand the effects of regulated rivers on the productivity of depressed sturgeon populations. An information theoretic approach was used to develop and select negative binomial and zero‐inflated negative binomial models that model the relation of age‐0 White Sturgeon survey data from three contiguous Columbia River reservoirs to river discharge and water temperature during spawning, egg incubation, larval, and post‐larval phases. Age‐0 White Sturgeon were collected with small mesh gill nets in The Dalles and John Day reservoirs from 1997 to 2014 and a bottom trawl in Bonneville Reservoir from 1989 to 2006. Results suggest that seasonal river discharge was positively correlated with age‐0 recruitment; notably that discharge, 16 June–31 July was positively correlated to age‐0 recruitment in all three reservoirs. The best approximating models for two of the three reservoirs also suggest that seasonal water temperature may be a determinant of age‐0 recruitment. Our research demonstrates how over‐dispersed catch data can be used to better understand the effects of environmental conditions on sturgeon populations caused by the construction and operation of dams.

Columbia River

The river as a chemostat: fresh perspectives on dissolved organic matter flowing down the river continuum

A better understanding is needed of how hydrological and biogeochemical processes control dissolved organic carbon (DOC) concentrations and dissolved organic matter (DOM) composition from headwaters downstream to large rivers. We examined a large DOM dataset from the National Water Information System of the US Geological Survey, which represents approximately 100 000 measurements of DOC concentration and DOM composition at many sites along rivers across the United States. Application of quantile regression revealed a tendency towards downstream spatial and temporal homogenization of DOC concentrations and a shift from dominance of aromatic DOM in headwaters to more aliphatic DOM downstream. The DOC concentration–discharge (C-Q) relationships at each site revealed a downstream tendency towards a slope of zero. We propose that despite complexities in river networks that have driven many revisions to the River Continuum Concept, rivers show a tendency towards chemostasis (C-Q slope of zero) because of a downstream shift from a dominance of hydrologic drivers that connect terrestrial DOM sources to streams in the headwaters towards a dominance of instream and near-stream biogeochemical processes that result in preferential losses of aromatic DOM and preferential gains of aliphatic DOM.

Canadian Journal of Fisheries and Aquatic Sciences

Summer habitat use by Columbia River redband trout in the Kootenai River drainage, Montana

The reported decline in the abundance, distribution, and genetic diversity of Columbia River redband trout Oncorhynchus mykiss gairdneri (a rainbow trout subspecies) has prompted fisheries managers to investigate their habitat requirements, identify critical habitat, and develop effective conservation and recovery programs. We analyzed the microhabitat, mesohabitat, and macrohabitat use and distribution of Columbia River redband trout by means of snorkel surveys in two watersheds in the Kootenai River drainage, Montana and Idaho, during the summers of 1997 and 1998. Juvenile (36&ndash;125 mm total length, TL) and adult (>=126 mm TL) fish preferred deep microhabitats (>=0.4 m) with low to moderate velocities (<=0.5 m/s) adjacent to the thalweg. Conversely, age-0 (<=35 mm) fish selected slow water (<=0.1 m/s) and shallow depths (<=0.2 m) located in lateral areas of the channel. Age-0, juvenile, and adult fish strongly selected pool mesohabitats and avoided riffles; juveniles and adults generally used runs in proportion to their availability. At the macrohabitat scale, density of Columbia River redband trout (35 mm) was positively related to the abundance of pools and negatively related to stream gradient. The pool: riffle ratio, gradient, and stream size combined accounted for 80% of the variation in density among 23 stream reaches in five streams. Our results demonstrate that low-gradient, medium-elevation reaches with an abundance of complex pools are critical areas for the production of Columbia River redband trout. These data will be useful in assessing the impacts of land-use practices on the remaining populations and may assist with habitat restoration or enhancement efforts.

Montana

A decade of Indigenous knowledge research in the Yukon River basin: Reflection on “Indigenous observations of change in the lower Yukon River basin, Alaska”

Herman-Mercer reflects on her first article" Indigenous Observations of Change in the Lower Yukon River Basin, Alaska." The observations and knowledge presented in this study have become part of an ever-growing catalog of studies representing, and part of a chorus of Indigenous communities across the Arctic and Subarctic conveying, the impacts of climate change in this region. The broad observations of environmental change reported in Indigenous Observations 2011, including impacts to subsistence and safety, are more dire and apparent than ten years ago when this article was published. Instances of diseased salmon continue to be reported by subsistence fishers, and the salmon runs have declined so severely since Indigenous Observations 2011 was published that there have been several years in which the commercial and or the subsistence salmon fishery was closed on the Yukon River, with impacts to household economies, food security, and culture. The then-new dangers associated with travel on river ice continue to be a concern across the Yukon River where the thinner river ice and inconsistent freeze up and break up have become the norm.

Alaska

Fish assemblage shifts in the Powder River of Wyoming: an unregulated prairie river system previously considered to be relatively pristine.

W y oming &rsquo; s P owder River is considered an example of a pristine prairie river system. While the river hosts a largely native fish assemblage and remains unimpounded over its 1,146-km course to the Y ellowstone River confluence, the hydrologic regime has been altered through w ater dive rsion for agriculture and natural gas extraction and there has been limited study of fish assemblage structure. W e analyzed fish data collected from the mainstem P owder River in W yoming between 1896 and 2008. Shifts in presence/absence and relative abundance of fish species, as well as fish assemblage composition, were assessed among historical and recent samples. The recent P owder Rive r fish assemblage w as characterized by increased relative abundances of sand shiner Notr opis stramineus and plains killifish Fundulus zebrinus , and decreases in sturgeon chub Macrhybopsis gelida . Shifts in fish species relative abundance are linked to their reproductive ecology with species with adhesive eggs generally increasing in relative abundance while those with buoy ant drifting eggs are decreasing. Assemblage shifts could be the result of landscape level changes, such as the loss of extreme high and low flow events and changing land use practices.

Montana, Wyoming

Reconnaissance of the upper Au Sable River a cold-water river in the north-central part of Michigan's southern peninsula

The Au Sable River is one of Michigan’s most popular trout streams and canoe trails. Its riverside campgrounds are enjoyed by thousands of campers each year, and many cabins and homes have been built on its banks. At present, interests of the different recreationists – fishermen, canoers, campers, and riverside property owners – conflict. The conflict results from the face that the recreational potential is limited by the hydrologic characteristics of the river – its streamflow, quality of water, and character of stream channel, bed, and banks. The purpose of this report is to describe these characteristics and to show how they relate to the recreational potential of the stream. From its headwaters near Frederic the Au Sable flows southward to Grayling, then generally eastward to Lake Huron at Oscoda. Recreational use of the river is concentrated in the segment starting at Grayling and extending downstream to Wakeley Bridge, about 15 river miles. This report is concerned mainly with this part of the river.

Michigan

Restored stratigraphic cross sections and coal correlations in the Tongue River member of the Fort Union Formation, Powder River area, Montana

Exposures of the lower two thirds of the Tongue River Member of the Paleocene Fort Union Formation were measured along the Powder River valley in southeastern Montana in the Moorhead and Birney-Broadus coalfields. This report documents the stratigraphic variations, lateral continuity of partly eroded coal beds along the line of section, and shows ten sections for the Tongue River Member in this study area. This report is a companion to the report by Flores and Canavello (1979). The study area represents a linear distance of 35 miles along the Powder River valley and extends from the Wyoming-Montana State line to a point 7 miles southeast of Broadus. Mont. (see index map). Within this area are relatively continuous outcrops of the middle and lower parts of the Tongue River Member.

Montana

Hydrologic data for water years 1933-97 used in the River and Reservoir Operations Model, Truckee River basin, California and Nevada

Title II of Public Law 101-618, the Truckee?Carson?Pyramid Lake Water Rights Settlement Act of 1990, provides direction, authority, and a mechanism for resolving conflicts over water rights in the Truckee and Carson River Basins. The Truckee Carson Program of the U.S. Geological Survey, to support implementation of Public Law 101-618, has developed an operations model to simulate lake/reservoir and river operations for the Truckee River Basin including diversion of Truckee River water to the Truckee Canal for transport to the Carson River Basin. Several types of hydrologic data, formatted in a chronological order with a daily time interval called 'time series,' are described in this report. Time series from water years 1933 to 1997 can be used to run the operations model. Auxiliary hydrologic data not currently used by the model are also described. The time series of hydrologic data consist of flow, lake/reservoir elevation and storage, precipitation, evaporation, evapotranspiration, municipal and industrial (M&I) demand, and streamflow and lake/reservoir level forecast data.

Open-File Report

Distribution, Health, and Development of Larval and Juvenile Lost River and Shortnose Suckers in the Williamson River Delta Restoration Project and Upper Klamath Lake, Oregon: 2008 Annual Data Summary

Federally endangered Lost River sucker Deltistes luxatus and shortnose sucker Chasmistes brevirostris were once abundant throughout their range but populations have declined; they have been extirpated from several lakes, and may no longer reproduce in others. Poor recruitment into the adult spawning populations is one of several reasons cited for the decline and lack of recovery of these species, and may be the consequence of high mortality during juvenile life stages. High larval and juvenile sucker mortality may be exacerbated by an insufficient quantity of suitable rearing habitat. Within Upper Klamath Lake, a lack of marshes also may allow larval suckers to be swept from suitable rearing areas downstream into the seasonally anoxic waters of the Keno Reservoir. The Nature Conservancy (TNC) flooded about 3,600 acres to the north of the Williamson River mouth (Tulana Unit) in October 2007, and about 1,400 acres to the south and east of the Williamson River mouth (Goose Bay Unit) a year later, to retain larval suckers in Upper Klamath Lake, create nursery habitat for suckers, and improve water quality. In collaboration with TNC, the Bureau of Reclamation, and Oregon State University, we began a long-term collaborative research and monitoring program in 2008 to assess the effects of the Williamson River Delta restoration on the early life-history stages of Lost River and shortnose suckers. Our approach includes two equally important aspects. One component is to describe habitat use and colonization processes by larval and juvenile suckers and non-sucker fish species. The second is to evaluate the effects of the restored habitat on the health and condition of juvenile suckers. This report contains a summary of the first year of data collected as a part of this monitoring effort.

Open-File Report

Summary of environmental flow monitoring for the Sustainable Rivers Project on the Middle Fork Willamette and McKenzie Rivers, western Oregon, 2014–15

This report presents the results of an ongoing environmental flow monitoring study by The Nature Conservancy (TNC), U.S. Army Corps of Engineers (USACE), and U.S. Geological Survey in support of the Sustainable Rivers Project (SRP) of TNC and USACE. The overarching goal of this study is to evaluate and characterize relations between streamflow, geomorphic processes, and black cottonwood ( Populus trichocarpa ) recruitment on the Middle Fork Willamette and McKenzie Rivers, western Oregon, that were hypothesized in earlier investigations. The SRP can use this information to plan future monitoring and scientific investigations, and to help mitigate the effects of dam operations on streamflow regimes, geomorphic processes, and biological communities, such as black cottonwood forests, in consultation with regional experts. The four tasks of this study were to: Compare the hydrograph from Water Year (WY) 2015 with hydrographs from WYs 2000–14 and the SRP flow recommendations, Assess short-term and system-wide changes in channel features and vegetation throughout the alluvial valley section of the Middle Fork Willamette River (2005–12), Examine changes in channel features and vegetation over two decades (1994–2014) for two short mapping zones on the Middle Fork Willamette and McKenzie Rivers, and Complete a field investigation of summer stage and the growth of black cottonwood and other vegetation on the Middle Fork Willamette and McKenzie Rivers in summer 2015.

Oregon

Using a food web model to inform the design of river restoration—An example at the Barkley Bear Segment, Methow River, north-central Washington

With the decline of Chinook salmon ( Oncorhynchus tshawytscha ) and steelhead ( O. mykiss ), habitat restoration actions in freshwater tributaries have been implemented to improve conditions for juveniles. Typically, physical (for example, hydrologic and engineering) based models are used to design restoration alternatives with the assumption that biological responses will be improved with changes to the physical habitat. Biological models rarely are used. Here, we describe simulations of a food web model, the Aquatic Trophic Productivity (ATP) model, to aid in the design of a restoration project in the Methow River, north-central Washington. The ATP model mechanistically links environmental conditions of the stream to the dynamics of river food webs, and can be used to simulate how alternative river restoration designs influence the potential for river reaches to sustain fish production. Four restoration design alternatives were identified that encompassed varying levels of side channel and floodplain reconnection and large wood addition. Our model simulations suggest that design alternatives focused on reconnecting side channels and the adjacent floodplain may provide the greatest increase in fish capacity. These results were robust to a range of discharge and thermal regimes that naturally occur in the Methow River. Our results suggest that biological models, such as the ATP model, can be used during the restoration planning phase to increase the effectiveness of restoration actions. Moreover, the use of multiple modeling efforts, both physical and biological, when evaluating restoration design alternatives provides a better understanding of the potential outcome of restoration actions.

Washington

Decadal changes in channel morphology of a freely meandering river—Powder River, Montana, 1975–2016

Few studies exist on the long-term geomorphic effects of floods. However, the U.S. Geological Survey (USGS) was able to begin such a study after a 50-year recurrence interval flood in 1978 because 20 channel cross sections along a 100-kilometer reach of river were established in 1975 and 1977 as part of a study for a proposed dam on Powder River in southeastern Montana. These cross-section measurements (data for each channel cross section are available at the USGS ScienceBase website) have been repeated about 30 times during four decades (1975–2016) and provide a unique dataset for understanding long-term changes in channel morphology caused by an extreme flood and a spectrum of annual floods. Changes in channel morphology of a 100-kilometer reach of Powder River are documented in a series of narratives for each channel cross section that include a time series of photographs as a record of these changes. The primary change during the first decade (1975–85) was the rapid vertical growth of a new inset flood plain within the flood-widened channel. Changes during the second decade (1985–95) were characterized by slower growth of the flood plain, and the effects of ice-jam floods typical of a northward-flowing river. Changes during the third decade (1995–2005) showed little vertical growth of the inset flood plain, which had reached a height that limited overbank deposition. And changes during the final decade (2005–16) covered in this report showed that, because the new inset flood plain had reached a limiting height, the effects of the large annual flood of 2008 (largest flood since 1978) were relatively small compared to smaller floods in previous decades. Throughout these four decades, the riparian vegetation, which interacts with the river, has undergone a gradual but substantial change that may have lasting effects on the channel morphology.

Montana

Sediment mobility and river corridor assessment for a 140-kilometer segment of the main-stem Klamath River below Iron Gate Dam, California

This river corridor assessment documents sediment mobility and river response to flood disturbance along a 140-kilometer segment of the main-stem Klamath River below Iron Gate Dam, California. Field and remote sensing methods were used to assess fundamental indicators of active sediment transport and river response to a combination of natural runoff events and reservoir releases during the study period from 2005 to 2019. Discharge measurements at two gaged sites and bed-material samples at two ungaged sites provided direct and indirect evidence of mobile bed conditions, scour and fill, and surface flushing of fine sediment. Available remote-sensing datasets collected in 2005, 2009, 2010, and 2016 were used to determine sediment storage, flood inundation boundaries, and provide indirect evidence of flood-induced scour. These datasets validate channel-maintenance flows defined by Shea and others (2016). During the study period, flows greater than or equal to 6,030 cubic feet per second mobilized the substrate, caused localized scour, and flushed fine sediment from bar surfaces. Flows greater than or equal to 10,400 cubic feet per second stripped vegetation from bars and floodplains and produced deeper scour. Flood disturbance within the study reach is produced by the combined effect of natural flows and reservoir releases, which resulted in mobile bed conditions during the study period. Periodic scour and substrate disturbance are considered by the U.S. Fish and Wildlife Service to be integral for managing disease-induced mortality of juvenile and adult salmonids. Substrate conditions conducive to parasites that host infectious diseases, particularly Ceratonova shasta, occur periodically. Additional studies are required to determine whether disease prevalence can be mitigated by well-timed reservoir releases. Study results are useful for interpreting linkages among physical and biological processes and for evaluating the effectiveness of flow management targeted to improve river bed conditions for endangered salmonid populations.

California

Drainage divides, Massachusetts; Connecticut River lowlands and Chicopee River basin

Drainage boundaries for selected subbasins of the Connecticut River lowlands and Chicopee River basin in southern Franklin, eastern Hampshire, and western Worcester Counties, Massachusetts , are delineated on 18 topographic quadrangle maps at a scale of 1:24,000. Drainage basins are shown for all U.S. Geological Survey data-collection sites and for mouths of major rivers. Drainage basins are shown for the outlets of lakes or ponds and for streams where the drainage area is greater than 3 square miles. Successive sites along watercourses are indicated where the intervening area is at least 6 square miles on tributary streams or 10 square miles along the Chicopee River, or 20 square miles along the Connecticut River. (USGS)

Open-File Report

Report of the River Master of the Delaware River for the period December 1, 1981, to November 30, 1982

The Amended Decree of the Supreme Court of the United States in 1954 established the position of Delaware River Master to administer provisions of the decree relative to diversions from the Delaware by the City of New York and the State of New Jersey , and releases from reservoirs of the City of New York designed to maintain stipulated rates of flow in the river. Reports to the Court, not less frequently than annually, with copies to the Governors and the Mayor, were stipulated. Water-supply conditions at the beginning of the year were under a status of emergency resulting from drought, which had been declared by the Delaware River Basin Commission. With the filling of the reservoirs, the emergency was lifted April 27. Runoff of Delaware River at Montague, New Jersey, was 19 percent below median during the year as compared to 28 percent below median the previous year. By November, with reservoir storage again declining, reductions in both diversions and releases were imposed. To conserve supplies, reductions were effected on November 13 limiting New York City diversions at 680 mgd and New Jersey to 85 mgd, and the required discharge at Montague was targeted at 1,655 cfs. Water quality of the Delaware River and Estuary was monitored on a continuous basis at six sites for most of the year and on a monthly basis at ten sites to accurately locate the salt front. Highest chloride concentration observed at the Chester, PA, site was 870 mg/l November 4. (USGS)

Open-File Report

Aquatic habitats in relation to river flow in the Apalachicola River floodplain, Florida

This study is part of a larger effort to identify fresh water needs throughout the region and develop a mechanism for basinwide water management. Quantitative estimates of the amount of aquatic habitat in the floodplain in relation to river flow are presented. Plates show streams, lakes, and floodplain forests connected to the main river channel at selected flows; an analysis of long-term flow record in the Apalachicola River; and a review of the literature regarding fishes in floodplains of the Apalachicola River and other rivers of the Eastern United States. Examples show how this report can be used to assess impacts of flow alterations on aquatic habitats and fishes.

Florida