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At least 991 records · Page 55Linked to original sources

USGS2010

Characteristics of fall chum salmon spawning habitat on a mainstem river in Interior Alaska

Chum salmon (Oncorhynchus keta) are the most abundant species of salmon spawning in the Yukon River drainage system, and they support important personal use, subsistence, and commercial fisheries. Chum salmon returning to the Tanana River in Interior Alaska are a significant contribution to the overall abundance of Yukon River chum salmon and an improved understanding of habitat use is needed to improve conservation of this important resource. We characterized spawning habitat of chum salmon using the mainstem Tanana River as part of a larger study to document spawning distributions and habitat use in this river. Areas of spawning activity were located using radiotelemetry and aerial helicopter surveys. At 11 spawning sites in the mainstem Tanana River, we recorded inter-gravel and surface-water temperatures and vertical hydraulic gradient (an indication of the direction of water flux) in substrate adjacent to salmon redds. At all locations, vertical hydraulic gradient adjacent to redds was positive, indicating that water was upwelling through the gravel. Inter-gravel temperatures adjacent to redds generally were warmer than surface water at most locations and were more stable than surface-water temperature. Inter-gravel water temperature adjacent to redds ranged from 2.6 to 5.8 degrees Celsius, whereas surface-water temperature ranged from greater than 0 to 5.5 degrees Celsius. Some sites were affected more by extremes in air temperature than others. At these sites, inter-gravel water temperature profiles were variable (with ranges similar to those observed in surface water), suggesting that even though upwelling habitats provide a stable thermal incubation environment, eggs and embryos still may be affected by extremes in air temperature. Fine sand and silt covered redds at multiple sites and were evidence of increased river flow during the winter months, which may be a potential source of increased mortality during egg-to-fry development. This study provides documentation of spawning by fall chum salmon and is the first study to continuously measure inter-gravel water temperature at sites in the mainstem Tanana River.

Open-File Report↗

USGS2006

Fate and effects of nitrogen and phosphorus in shallow vegetated aquatic ecosystems

Nitrate concentrations have greatly increased in streams and rivers draining agricultural regions of the Midwestern United States, increasing nitrate transport to the Gulf of Mexico has been implicated in the hypoxic conditions that threaten the productivity of marine fisheries. Increases in nitrate concentrations have been attributed to a combination of factors including agricultural expansion, increased nitrogen application rates, increased tile drainage, and loss of riparian Wetlands, These landscape-level changes have resulted in a decreased natural capacity for nitrogen uptake, removal, and cycling back to the atmosphere. Land managers are increasingly interested in using wetland construction and rehabilitation as a management practice to reduce loss of nitrate from the terrestrial systems. Yet, relatively little is known about the limnological factors involved in nitrate removal by Wetland systems. We conducted a series of studies from 1999-2000 to investigate the functional capacity of shallow, macrophyte-dominated pond wetland systems for uptake, assimilation, and retention of nitrogen (N) and phosphorus (P). We evaluated four factors that were hypothesized to influence nutrient uptake and assimilation: 1) nitrate loading rates; 2) nitrogen to phosphorus (N.P) ratios; 3) frequency of dosing/application; and 4) timing of dose initiation. Nutrient assimilation was rapid; store than 90% of added nutrients were removed from the water column in all treatments. Neither variation in N:P ratios (evaluated range, <13:1 to -114.1), frequency of application (weekly or bi-weekly), nor liming of dose initiation relative to macrophyte development (0%, 15-25%, or 75-90% maximum biomass) had significant effects on nutrient assimilation of wetland community dynamics. Maximum loading of nitrate (60 g N/m 2 2.4 g P/m 2 ) applied as six weekly doses stimulated algal communities, but inhibited macrophyte communities. Predicted shifts from a stable state of macrophyte- to phytoplankton-dominance did not occur due to nutrient additions. Macrophytes, phytoplankton, and the sediment surface were all significant factors in the removal of nitrate from the Water column. Overall, these shallow macrophyte-dominated systems provided an efficient means of removing nutrients from the water column. Construction or rehabilitation of shallow, vegetated wetlands may offer promise as land management practices for nutrient removal in agricultural watersheds.

Report↗

USGS2001

Biology and conservation of the common murre in California, Oregon, Washington, and British Columbia: Vol. 1, Natural history and population trends

Over the past 30 years, the common murre ( Uria aalge californica ) has been recognized as a prominent indicator of marine conservation issues in California, Oregon, Washington, and British Columbia, especially regarding oil pollution, certain fisheries, and human disturbance. To assist the effective management of the common murre and the marine environments in which they live, this summary of available information on the biology and regional status of the common murre has been sponsored by the U.S. Fish and Wildlife Service (Division of Migratory Bird Management). In Volume 1 (Chapter 1), the natural history of the common murre is summarized, drawing heavily on breeding studies from the South Farallon Islands, California, plus a host of detailed breeding studies from the North Atlantic Ocean. Population trends of the common murre are summarized in Volume 1 (Chapter 2), focusing on changes in whole-colony counts determined from aerial photographs between the late 1970s and 1995 in California, Oregon and Washington. Historical data and human impacts to murre colonies since the early nineteenth century are also summarized. Volume 2 will summarize population threats, conservation, and management. Information presented in Volume 1 has been obtained and recorded by a large number of researchers and natural historians over two centuries. From the 1960s to 1995, most work in California, Oregon, and Washington was sponsored by the U.S. Fish and Wildlife Service, Minerals Management Service, and California Department of Fish and Game. Important breeding biology studies were conducted at the South Farallon Islands (Farallon National Wildlife Refuge) by the Point Reyes Bird Observatory, in coordination with the U.S. Fish and Wildlife Service (San Francisco Bay National Wildlife Refuge). Colony surveys in California were conducted mainly by the U.S. Fish and Wildlife Service (San Francisco Bay National Wildlife Refuge), U.S. Geological Survey (Western Ecological Research Center, Dixon Field Station), Humboldt State University, and University of California (Santa Cruz). Colony surveys in Oregon and Washington were conducted mainly by the U.S. Fish and Wildlife Service (Oregon Coast National Wildlife Refuge and Washington Maritime National Wildlife Refuges). In British Columbia, most work from the 1960s to 1995 was sponsored and conducted by the Canadian Wildlife Service and Royal British Columbia Museum.

British Columbia, California, Oregon, Washington↗

USGS2001

Environmental quality and preservation; reefs, corals, and carbonate sands; guides to reef-ecosystem health and environment

Introduction In recent years, the health of the entire coral reef ecosystem that lines the outer shelf off the Florida Keys has declined markedly. In particular, loss of those coral species that are the building blocks of solid reef framework has significant negative implications for economic vitality of the region. What are the reasons for this decline? Is it due to natural change, or are human activities (recreational diving, ship groundings, farmland runoff, nutrient influx, air-borne contaminants, groundwater pollutants) a contributing factor and if so, to what extent? At risk of loss are biologic resources of the reefs, including habitats for endangered species in shoreline mangroves, productive marine and wetland nurseries, and economic fisheries. A healthy reef ecosystem builds a protective offshore barrier to catastrophic wave action and storm surges generated by tropical storms and hurricanes. In turn, a healthy reef protects the homes, marinas, and infrastructure on the Florida Keys that have been designed to capture a lucrative tourism industry. A healthy reef ecosystem also protects inland agricultural and livestock areas of South Florida whose produce and meat feed much of the United States and other parts of the world. In cooperation with the National Oceanic and Atmospheric Administration's (NOAA) National Marine Sanctuary Program, the U.S. Geological Survey (USGS) continues longterm investigations of factors that may affect Florida's reefs. One of the first steps in distinguishing between natural change and the effects of human activities, however, is to determine how coral reefs have responded to past environmental change, before the advent of man. By so doing, accurate scientific information becomes available for Marine Sanctuary management to understand natural change and thus to assess and regulate potential human impact better. The USGS studies described here evaluate the distribution (location) and historic vitality (thickness) of Holocene reefs in South Florida, relative to type of underlying bedrock morphology, and their varied natural response to rising sea level. These studies also assess movement and accumulation of sands, relative to direction of prevailing energy, and origin of the component sand grains. Geophysical data collected with highresolution sound-wave instruments that provide pictures of the sediment and bedrock are used to interpret sediment thickness. Reef thickness is determined by collecting limestone rock cores by drilling. Drill cores through reefs are used to identify the coral species that built them and to determine how reefs reacted to rising sea level. These data are supplemented by using isotope-dating techniques to derive the carbon-14 (C14) age of the corals and mangrove peat in the cores. Mangrove peat forms in very shallow water and at the shoreline but is found today buried beneath offshore reefs.

Open-File Report↗

USGS2015

Marshes to mudflats—Effects of sea-level rise on tidal marshes along a latitudinal gradient in the Pacific Northwest

Summary In the Pacific Northwest, coastal wetlands support a wealth of ecosystem services including habitat provision for wildlife and fisheries and flood protection. The tidal marshes, mudflats, and shallow bays of coastal estuaries link marine, freshwater, and terrestrial habitats, and provide economic and recreational benefits to local communities. Climate change effects such as sea-level rise are altering these habitats, but we know little about how these areas will change over the next 50–100 years. Our study examined the effects of sea-level rise on nine tidal marshes in Washington and Oregon between 2012 and 2015, with the goal of providing scientific data to support future coastal planning and conservation. We compiled physical and biological data, including coastal topography, tidal inundation, vegetation structure, as well as recent and historical sediment accretion rates, to assess and model how sea-level rise may alter these ecosystems in the future. Multiple factors, including initial elevation, marsh productivity, sediment availability, and rates of sea-level rise, affected marsh persistence. Under a low sea-level rise scenario, all marshes remained vegetated with little change in the present configuration of communities of marsh plants or gradually increased proportions of middle-, high-, or transition-elevation zones of marsh vegetation. However, at most sites, mid sea-level rise projections led to loss of habitat of middle and high marshes and a gain of low marshes. Under a high sea-level rise scenario, marshes at most sites eventually converted to intertidal mudflats. Two sites (Grays Harbor and Willapa) seemed to have the most resilience to a high rate of rise in sea-level, persisting as low marsh until at least 2110. Our main model finding is that most tidal marsh study sites are resilient to sea-level rise over the next 50–70 years, but that sea-level rise will eventually outpace marsh accretion and drown most habitats of high and middle marshes by 2110.

California, Oregon, Washington↗

USGS2002

Mexican native trouts: A review of their history and current systematic and conservation status

While biologists have been aware of the existence of native Mexican trouts for over a century, they have received little study. The few early studies that did much more than mention their existence began in the 1930s and continued into the early 1960s, focusing primarily on distributional surveys and taxonomic analyses. Starting in the 1980s the Baja California rainbow trout became the subject of more detailed studies, but very little remains known of mainland trouts of the Sierra Madre Occidental. We review earlier studies and report on our own collections and observations made between 1975 and 2000. We present newly discovered historical evidence that leads us to conclude that a "lost" cutthroat trout, a lineage not previously known from Mexico, was collected more than a century ago from headwaters of the Ri??o Conchos (a major tributary of the Rio Grande (= Ri??o Bravo)), a basin not previously considered to harbor a native trout. We review the last century of regional natural resource management and discuss our own observations of trout habitats. Impacts of logging, road building and overgrazing are widespread and expanding. Many streams suffer from heavy erosion, siltation and contamination, and though long-term hydrologic data are generally not available, there is evidence of decreased discharge in many streams. These problems appear related to region-wide land management practices as well as recent regional drought. Trout culture operations using exotic rainbow trout have rapidly proliferated throughout the region, threatening genetic introgression and/or competition with native forms and predation on them. Knowledge of distribution, abundance, relationships and taxonomy, not to mention ecology and population biology, of native trouts of the Sierra Madre Occidental remains inadequate. Vast areas of most mainland drainages are still unexplored by fish collectors, and even rudimentary information regarding basic biology, ecology and population structure of stocks remains lacking. Concentrated exploration, research and management of this long overlooked and undervalued resource are all urgently needed. The history of natural resources exploitation that placed so many native trouts of the western United States on threatened and endangered species lists is repeating itself in the Sierra Madre Occidental. Without concentrated action and development of region-wide socio-economic solutions for current, largely non-sustainable resource management practices, native Mexican trout gene pools will soon be in grave danger of extinction.

Reviews in Fish Biology and Fisheries↗

USGS1961

Use of 3-trifluormethyl-4-nitrophenol as a selective sea lamprey larvicide

The recent discovery of a group of chemical compounds that are significantly more toxic to sea lampreys than to other aquatic organisms offers promise of an early and effective control of this pest. The sea lamprey has all but destroyed the lake trout populations of Lakes Huron and Michigan. In Lake Superior, production of the lake trout fishery has declined to record low levels. Only a rapid and drastic reduction in sea lamprey predation can save the lake trout population there. Other species of food and game fishes have suffered severe decreases from persistent attack by the lamprey. The sea lamprey spends only a small portion of its life as a parasite in the Great Lakes. The fully grown and sexually mature adults migrate into streams to spawn and thereafter die. The eggs hatch in a week to 10 days and the larvae remain in the stream bottom for 5 years or longer before metamorphosis into the adult form. Following this transformation the young lampreys migrate downstream to the lakes to begin their parasitic existence. The life cycle of the sea lamprey has been described in detail elsewhere (Applegate 1950; Applegate and Moffett 1955). Control of the adult lampreys distributed throughout a body of open water as large as one of the Great Lakes, by known and available techniques, is not feasible. Fortunately, this pest can be attacked effectively at those stages in its life cycle when it is concentrated in restricted areas. Various devices have been developed which prevent spawning by blocking the streams below the spawning grounds. Electrical weirs, that repel or destroy the lampreys, have been used (Applegate, Smith, and Nielsen 1952; Erkkila, Smith, and McLain 1956). A serious shortcoming of this control method is the time required to achieve the desired effect. Even though the adults have been destroyed before spawning, 5 or more generations of larval lampreys are already in the stream-enough to provide an annual supply of parasitic adults for an equal period of time. Almost all the larvae of the sea lamprey live in the spawning streams. Treatment of these streams with selectively toxic chemicals that kill the larvae provides immediate reduction of all generations in the population before they become parasites. Control of the species can thus be achieved without a delay of several years.

Technical Report↗

USGS2022

Geohydrology and water quality of the northern and central parts of the Tug Hill glacial aquifer, Jefferson and Oswego Counties, north-central New York

The northern and central parts of the Tug Hill glacial aquifer consist of a 29-mile-long, crescent-shaped, mixture of glaciofluvial, glaciolacustrine, and recent alluvial deposits of predominantly sand and gravel on the western side of the Tug Hill Plateau in Jefferson and Oswego Counties in north-central New York. Approximately 11,400 people are supplied by groundwater that is withdrawn from municipal and nonmunicipal wells in the northern and central parts of the aquifer. In addition, many farms, several industries, and a large New York State fish hatchery also rely on the water from the aquifer. In the early 2000s, anticipated developmental pressures from potential new industries (including a proposed water-bottling plant in the central part of the Tug Hill glacial aquifer) and expansion of the Fort Drum military base north of Watertown (with the projected increase in population extending into the northern part of the aquifer) prompted the Tug Hill Commission, local municipal officials, and representatives from the New York State Department of Environmental Conservation to initiate a geohydrologic study with the U.S. Geological Survey. The information from this study is intended to help the state, counties, and local communities make sound policy decisions about their use of this large groundwater resource. The northern part of the Tug Hill glacial aquifer is a combination of glaciofluvial outwash and alluvial sand and gravel in the Sandy Creek Valley northeast of Adams, New York, and mostly glaciolacustrine beach and deltaic sand or sand and gravel north and south of the village of Adams. The southern and eastern areas of the central part of the aquifer are composed mostly of glaciofluvial sediments such as kames, kame moraines, and kame terraces, whereas most of the western areas of the central part are composed mostly of glaciolacustrine sediments such as deltaic sand and beach sand and gravel. The northern and central parts of the aquifer are unconfined. Recharge to the northern and central parts of the aquifer is from three main sources: (1) precipitation that falls directly onto the aquifer; (2) unchannelized runoff (overland flow) and groundwater from till and bedrock in the Tug Hill Plateau that seeps into the eastern side of the aquifer; and (3) streams that drain the Tug Hill Plateau and flow across and lose water to the aquifer. Groundwater discharges to springs, seeps, headwaters of streams, and wetlands in the middle area of the central part of the aquifer and along the entire western boundary of the northern and central parts of the aquifer; pumping wells; artificial ditches; and deeply incised streams in the northern and central parts of the aquifer. The groundwater discharge to such streams is critical in supporting the salmonid fishery in the central part of the aquifer. Groundwater levels were measured on July 17, 2014, at 22 wells throughout the northern and central parts of the aquifer. Water-table contours were drawn on the basis of the measured July 2014 water levels, historical water-level data, and surface-water levels where surface water in the channels was expected to be hydraulically connected to the groundwater system. The water table generally slopes from east to west throughout the northern and central parts of the aquifer; this slope also indicates that the direction of groundwater flow is generally from east to west. Water-quality samples were collected from 23 stream sites during base-flow conditions, and groundwater-quality and other types of environmental samples were collected from 20 wells in the northern and central parts of the Tug Hill glacial aquifer. The results of the sampling indicate that surface water and groundwater are generally of good quality. Comparison of the median concentration values of major ions in groundwater samples indicated that hardness in the northern part of the aquifer was about twice as great, and concentrations of calcium and sodium were more than three times as great, as in the central part of the aquifer. As was the case with surface water, the much greater median concentrations in groundwater of calcium, hardness, and alkalinity in the northern part of the aquifer are due to the dissolution of limestone that underlies most of that area and to the high-carbonate content of the clasts in the sand and gravel. There was little to no difference among the median values for bromide, fluoride, silica, and iron in the two parts of the aquifer. Concentrations of most other major ions were slightly greater in the northern part than in the central part of the Tug Hill glacial aquifer, except for magnesium, whose concentration was greater in the central part. Median concentrations of nutrients were generally greatest in surface water and groundwater in the northern part of the aquifer.

New York↗

USGS1975

Changes in the lake trout population of southern Lake Superior in relation to the fishery, the sea lamprey, and stocking, 1950-70

Commercial catch and effort statistics for 1929-70, samples of commercial catches in 1959-62, and records of examinations of all lake trout (Salvelinus namaycush) taken commercially in inshore waters of Michigan and Wisconsin in 1962-70 were the basis for descriptions of changes in the population in 1929-70. Abundance fluctuated cyclically and gradually downward in 1929-49, whereas fishing intensity tended to increase during the same period. In 1950-52, a change from cotton to nylon twine in gillnets raised effective fishing effort to 305% of the 1929-43 average in Michigan waters and to 228% in Wisconsin waters; production held near average. Abundance fell to 18% of average in Michigan in 1953-61 and to 25% of average in Wisconsin in 1956-61; in the same periods, production fell to 11% of average in Michigan and to 19% in Wisconsin. In 1962-70 abundance rose to 160% in Michigan and 246% in Wisconsin while production and fishing intensity were held low (3-14%) by regulation. Changes in abundance of lake trout were attributable to a sequence of developments in successive series of years; intensive fishing in the early 1950's; severe sea lamprey predation in the late 1950's; an 85% reduction in abundance of sea lampreys in mid 1961; and the combination of sea lamprey control, intensive stocking of yearling lake trout, and restrictions on fishing in 1962-70. A decline in average size of lake trout and the near elimination of spawning stocks in 1953-61 curtailed recruitment of native lake trout in the mid 1960's. Stocking of fin-clipped lake trout replaced natural reproduction in the early 1960's. In 1965-70, the lake trout population was composed mainly of hatchery-reared fish. Natural reproduction was reestablished on one major spawning shoal in Wisconsin in 1965, but in 1970 only 10% of the legal (17-inch and longer) and 17% of the undersize lake trout in Wisconsin were native fish. Reduction of sea lamprey abundance resulted in an immediate increase in survival and abundance of lake trout, especially of the larger sizes. As abundance of lake trout progressively increased in 1962-70, survival of the smaller legal-size lake trout increased, probably due to reduction of the predator-prey ratio and an increase in availability of larger lake trout preferred by sea lampreys. Abundance of spawning-size lake trout was limited by high natural mortality in 1965-70. Circumstantial evidence suggested that sea lamprey predation contributed a major part of the high natural mortality.

Technical Report↗

USGS2020

Development and evaluation of an improved TFM formulation for use in feeder stream treatments

The binational Great Lakes Fishery Commission sponsored Sea Lamprey Control Program effectively utilizes a variety of lampricide tools to keep populations of parasitic sea lampreys in the Great Lakes at levels that do not cause undue economic or ecological damage. The most widely used toxicant used in lampricide formulations is 3-trifluoromethyl-4-nitrophenol (TFM). In typical treatments, a liquid TFM formulation is applied to lamprey producing streams continuously for 10–14 hours to produce a moving block of lampricide-treated water that kills larval lamprey before they metamorphose into their parasitic lifestage. In many smaller tributaries of dendritic streams a solid bar formulation of TFM is used to supplement the mainstem treatment block. These supplemental TFM bar applications are coordinated with the arrival of the mainstem lampricide to prevent larval sea lamprey from seeking refuge in untreated waters and surviving the treatment. TFM bars are produced from formulated surfactants and designed to release TFM over an 8–10-hour period, depending on water temperature and velocity. However, some of the surfactants have been discontinued resulting in the reformulation of the TFM bars multiple times. As a result of these reformulations, TFM bar performance has declined. An experimental surfactant-free solid TFM tablet formulation was developed as a potential replacement for TFM bars. Release of TFM from the experimental tablets was evaluated using replicated laboratory dissolution trials conducted at three water temperatures and three water velocities. A continuous-flow laboratory flume was used for the dissolution trials and the decay of the tablets was modeled using logistic decay curves. Time required for the TFM tablet to decay 50 and 99% were compared among the groups using a two-way analysis of variance. Post-hoc Tukey Honest Significant Difference tests indicated that both water temperature and water velocity influenced the decay of the tablet; however, neither water temperature or water velocity appeared to dramatically influence TFM release. Results from this laboratory study indicate that the next stage of evaluating the TFM tablets using field tests is warranted.

Project Completion Report↗

USGS2014

Methow River Studies, Washington: abundance estimates from Beaver Creek and the Chewuch River screw trap, methodology testing in the Whitefish Island side channel, and survival and detection estimates from hatchery fish releases, 2013

Salmon and steelhead populations have been severely depleted in the Columbia River from factors such as the presence of tributary dams, unscreened irrigation diversions, and habitat degradation from logging, mining, grazing, and others (Raymond, 1988). The U.S. Geological Survey (USGS) has been funded by the Bureau of Reclamation (Reclamation) to provide evaluation of on-going Reclamation funded efforts to recover Endangered Species Act (ESA) listed anadromous salmonid populations in the Methow River watershed, a watershed of the Columbia River in the Upper Columbia River Basin, in north-central Washington State (fig. 1). This monitoring and evaluation program was funded to document Reclamation’s effort to partially fulfill the 2008 Federal Columbia River Power System Biological Opinion (BiOp) (National Oceanographic and Atmospheric Administration, Fisheries Division 2003). This Biological Opinion includes Reasonable and Prudent Alternatives (RPA) to protect listed salmon and steelhead across their life cycle. Species of concern in the Methow River include Upper Columbia River (UCR) spring Chinook salmon ( Oncorhynchus tshawytscha ), UCR summer steelhead ( O. mykiss ), and bull trout ( Salvelinus confluentus ), which are all listed as threatened or endangered under the ESA. The work done by the USGS since 2004 has encompassed three phases of work. The first phase started in 2004 and continued through 2012. This first phase involved the evaluation of stream colonization and fish production in Beaver Creek following the modification of several water diversions (2000–2006) that were acting as barriers to upstream fish movement. Products to date from this work include: Ruttenburg (2007), Connolly and others (2008), Martens and Connolly (2008), Connolly (2010), Connolly and others (2010), Martens and Connolly (2010), Benjamin and others (2012), Romine and others (2013a), Weigel and others (2013a, 2013b, 2013c), and Martens and others (2014). The second phase, initiated in 2008, focuses on the evaluation of the M2 reach (rkm 66– 80) of the mainstem Methow River prior to restoration actions planned by Reclamation and Yakama Nation. The M2 study was designed to help understand the inter-relationships between stream habitat and the life history of various fish species to explain potential success or limitations in response to restoration actions. To help document changes derived by restoration, two reference reaches (Upper Methow between rkm 85 and 90, and Chewuch River between rkm 4 and 11) were identified based on relative lack of disturbance, proximity to the restoration reach, and relative unconfined geomorphology. A control reach (Lower Methow between rkm 57 and 64, also referred to as “Silver Reach”) was 2 identified based on its similar disturbance as the reference reach, proximity to the restoration reach, and relatively unconfined geomorphology. Products to date include Barber and others (2011), Bellmore (2011), Tibbits and others (2012), Bellmore and others (2013), Benjamin and others (2013), Romine and others (2013b), Bellmore and other (2014), Martens and others (2014), and Martens and Connolly (2014). The third phase of work has been to help with the development and to provide data for modeling efforts. Most of the planned M2 reach restoration is focused on the creation or improvement of offchannel habitat, especially side channels. The pre-restoration portion of this study has been documented by Martens and Connolly (2014). Side channel restoration actions were initiated in 2012 (Whitefish Island side channel, also referred to as SC3; rkm 76) and are planned to continue over the next several years. The Whitefish Island side channel was modified to maintain hydrological connection with the mainstem throughout the year. In addition, several log structures were installed and pools were deepened to create fish habitat. Prior to restoration, this side channel would lose hydrological connection with the mainstem Methow River, leaving one large pool near the bottom of the side channel and several shallow isolated pools that may or may not go dry. In seasonally connected side channels, juvenile salmonid survival in pools less than 100 cm average depth was lower than in pools greater than 100 cm average depth (Martens and Connolly, 2014). In this report, we document our field work and analysis completed in 2013. During 2013, USGS sampling efforts were focused on resampling of three reaches in Beaver Creek, testing methodology in the Whitefish Island side channel, conducting hatchery survival estimates, and operating a screw trap on the Chewuch River (funded by Yakama Nation; fig. 1). The Beaver Creek sampling effort was a revisit of three index sites sampled continuously from 2004 to 2007 to look at the fish response to barrier removal. Methodology testing in Whitefish Island side channel was done to determine the best method for evaluating fish populations after restoration efforts in side channels (previous sampling methods were determined to be ineffective after pools were deepened). Hatchery survival estimates were completed to monitor fish survival in the Methow and Columbia Rivers, while the screw trap was operated to estimate migrating fish populations in the Chewuch River and track passive integrated transponder (PIT)-tagged fish. In addition, we maintained a network of PIT-tag interrogation systems (PTIS), assisted Reclamation with fish removal events associated with stream restoration (two people for 9 days; 14 percent of summer field season), and conducted a stream metabolism study designed to help parameterize and calibrate the stream productivity model (Bellmore and others, 2014) with model validation.

Washington↗

USGS2021

Climate change vulnerability assessment for the California coastal national monument—Trinidad and Point Arena-Stornetta units

Executive Summary The California Coastal National Monument protects islets, reefs, and rock outcropping habitats in six onshore units, including the Trinidad and Point Arena-Stornetta Units. The California Coastal National Monument provides crucial habitat for resident and migratory species of seabirds, marine mammals, and invertebrates, which includes several federally listed threatened and endangered species. Also, the California Coastal National Monument encompasses important tribal, cultural, and historical sites along the coastline of California. We used three approaches to assess the climate change vulnerability of the Trinidad and Point Arena-Stornetta Units: (1) a qualitative approach using peer-reviewed literature and previous work done in the Climate Change Vulnerability Assessment for the North-central California Coast and Ocean (Hutto and others, 2015), (2) interactive workshops with local stakeholders to identify specific resources, and (3) spatial analysis to estimate sea-level rise vulnerability for the rocky shoreline and key resources within the units. Information from stakeholder workshops held (in 2017) in the cities of Point Arena and Trinidad identified climate change impacts as an important management concern for the resilience, health, and ecosystem services of the California Coastal National Monument units. Impacts that were identified included sea-level rise, changes in precipitation and fog, warming oceans, and loss of species (birds, fisheries, marine mammals). Boat surveys were done for each unit to estimate the number of rocky features and the biota using the rocks. At the Trinidad Unit, 138 rocks were surveyed and 17 different wildlife species were observed, whereas at the Point Arena-Stornetta Unit, 40 rocks were surveyed and 10 different wildlife species were observed. Individual rocky features surveyed within the units were then ranked on sea-level rise exposure and vulnerability scales with 1 being the least vulnerable/exposed and 5 the most. Forty-nine and fifty-eight percent of surveyed rocks had a sea-level rise exposure ranking of 4 or 5 (high) for the Trinidad Unit and Point Arena-Stornetta Units respectively. Forty-eight percent of offshore rocks had a sea-level rise vulnerability score of 3 or greater (high) for the Trinidad Unit, and forty-three percent of rocks had a vulnerability score of 3 or greater for the Point Arena-Stornetta Unit. When examining guild use of vulnerable rocks (vulnerability score greater than 3), at the Trinidad Unit alcid species (here defined as common murres and pigeon guillemots) were observed on only 28 percent of vulnerable rocks, shorebirds on 30 percent, sea lions on 40 percent, gulls on 43 percent, seabirds on 58 percent, and mammals on 75 percent, whereas at the Point Arena-Stornetta Unit alcid species were observed on 0 percent of vulnerable rocks, gulls on 33 percent, seabirds on 57 percent, and mammals on 50 percent. Sea-level rise has the potential to submerge small low-relief offshore rocks and make them uninhabitable for birds and marine mammals but could provide more intertidal and subtidal rocky habitats. We found that nearly half of the offshore rocks at both sites are vulnerable and have the potential to realize this outcome; however, the larger and tall-relief rocks at these sites are less vulnerable to sea-level rise and are expected to continue to provide habitat for avian species.

California↗

USGS1997

Plan of study to determine if the isotopic ratios [delta]15 N and [delta]18 O can reveal the sources of nitrate discharged by the Mississippi River into the Gulf of Mexico

Nitrate and other nutrients discharged from the Mississippi River basin are suspected of causing a zone of depleted dissolved oxygen (hypoxic zone) in the Gulf of Mexico each summer. The hypoxic zone may have an adverse effect on aquatic life and commercial fisheries. Commercial fertilizers are the dominant source of nitrogen input to the Mississippi basin. Other nitrogen sources include animal waste, fixation of atmospheric nitrogen by legumes, precipitation, domestic and industrial effluent, and the soil. The inputs of nitrogen from most of these sources to the Mississippi basin can be estimated and the outputs in surface water can be measured. However, nitrogen from each source is affected differently by physical, chemical, and biological processes that control nitrogen cycling in terrestrial and aquatic systems. Hence, the relative contributions from the various sources of nitrogen to nitrate load in the Mississippi River are unknown because the different sources may not contribute proportionally to their inputs in the basin. It may be possible to determine the relative contributions of the major sources of nitrate in river water using the stable isotopic ratios d15N and d18O of the nitrate ion. A few researchers have used the d15N and/or d18O isotope ratios to determine sources of nitrate in ground water, headwater catchments, and small rivers, but little is known about the isotopic composition of nitrate in larger rivers. The objective of this study is to measure the isotopic composition of nitrate and suspended organic matter in the Mississippi River and its major tributaries, in discharge to the Gulf of Mexico, and in streamflow from smaller watersheds that have distinct sources of nitrogen (row crops, animal wastes, and urban effluents) or are minimally impacted by man (undeveloped). Samples from seven sites on the Mississippi River and its tributaries and from 17 sites in smaller watersheds within the Mississippi River basin will be analyzed for d15N and d18O of dissolved nitrate. Suspended sediment collected from these sites will also be analyzed to determine the d15N, d13C, and d34S of the suspended organic material. Six samples will be collected at each site during the winter, spring, and summer of 1996-97. Results from these samples will be used to identify seasonal and flow-related variability in d15N and d18O ratios from each site and may also help determine the principal sources of the nitrate entering the Gulf of Mexico.

Open-File Report↗

USGS2022

Distribution of niclosamide following granular Bayluscide applications in lotic systems

The granular formulation of Bayluscide [Bayluscide 3.2% Granular Sea Lamprey Larvicide, granular Bayluscide (gB)] is applied in lentic and lotic systems to survey (assessment) and kill (treatment) larval sea lampreys ( Petromyzon marinus ; Linnaeus, 1758) in the Great Lakes basin. Granules are spread on the water surface, settle to the sediment surface, and dissolve. The potential risk of niclosamide exposure (2′,5-dichloro-4′-nitrosalicylanilide), the active ingredient of gB, to non-target organisms located downstream of survey plots, is a concern of partner agencies (state-level natural resource departments, U.S. Fish and Wildlife Service Ecological Services, and Fisheries and Oceans Canada Species at Risk Branch). Spatiotemporal distribution of niclosamide in the water column and sediment was evaluated in and downstream of five larval survey plots in two rivers following the application of gB. Water samples were collected at 0.25, 2, 4, 6, 8, and 24 h from three depths in the water column (10 cm above the sediment, ½ the water column depth, and the water surface) at three locations inside each survey plot, and 1 meter upstream from three sediment sample grids positioned 10, 30, and 100 m downstream. Sediment samples were collected from inside the grids at 0.25, 2, 4, 6, 8, and 24 h, and from inside the survey plots, 8 and 24 h after gB application. Niclosamide was detected in the sediment and water at all sample locations. From 2 to 24 h after application, average water concentrations 1) varied between study sites, 2) decreased from the survey plots to 100 m downstream, 3) varied by depth in the water column, and 4) decreased over time. Average sediment concentrations varied by distance downstream and time post-application, but not by study site or river. Data suggest there would be negligible exposure to non-target organisms downstream of a gB survey plot based on low niclosamide concentrations measured in the water and sediment. The depletion rate of niclosamide was also evaluated in St. Clair River sediment dosed at the field application rate. Niclosamide concentration decreased at a rate of 2.28% per hour over the 24 hours measured, equating to a half-life of 1.27 days. This indicates the length of time an organism in the sediment in a survey plot might be exposed. Underwater cameras were placed along the edge of two St. Clair River survey plots to document gB distribution on the sediment and any potential target and non-target effects. Video was inconclusive in tracking gB through the water column. Larval sea lamprey and non-target mortality were not observed. Additional video footage of one St. Clair River survey plot showed large areas of river bottom without gB.

Michigan↗

USGS1998

Low-flow water-quality characterization of the Gore Creek watershed, upper Colorado River basin, Colorado, August 1996

The Upper Colorado River Basin (UCOL) is one of 59 National Water-Quality Assessment (NAWQA) study units designed to assess the status and trends of the Nation?s water quality (Leahy and others, 1990). The UCOL study unit began operation in 1994, and surface-water-quality data collection at a network of 14 sites began in October 1995 (Apodaca and others, 1996; Spahr and others, 1996). Gore Creek, which flows through Vail, Colorado, originates in pristine alpine headwaters and is designated a gold-medal trout fishery. The creek drains an area of about 102 square miles and is a tributary to the Eagle River. Gore Creek at the mouth near Minturn (site 13 in fig. 1) is one of the 14 sites in the UCOL network. This site was selected to evaluate water quality resulting from urban development and recreational land use. The Gore Creek watershed has undergone rapid land-use changes since the 1960?s as the Vail area shifted from traditional mountain ranchlands to a four-season resort community. Residential, recreational, commercial, and transportation development continues near Gore Creek and its tributaries to support the increasing permanent and tourist population of the area. Interstate 70 runs through the watershed from Vail Pass near site 14, along the eastern side of Black Gore Creek, and along the northern side of the main stem of Gore Creek to the mouth of the watershed (fig. 1). A major local concern is how increasing urbanization/recreation affects the water quality, gold-medal trout fishery, and aesthetic values of Gore Creek. An evaluation of the spatial characteristics of water quality in the watershed upstream from site 13 at the mouth of Gore Creek (fig. 1) can provide local water and land managers with information necessary to establish water policy and make land-use planning decisions to maintain or improve water quality. Historical data collected at the mouth of Gore Creek provide information about water quality resulting from land use, but a synoptic sampling is needed to determine the distribution and sources of water-quality constituents at one point in time. In August 1996, a low-flow synoptic sampling for analyses of water-quality properties and constituents at sites in the Gore Creek watershed was done by the U.S. Geological Survey, in cooperation with the Town of Vail, Eagle River Water and Sanitation District, Upper Eagle River Water Authority, and Northwest Colorado Council of Governments, to evaluate the water quality of Gore Creek. The August low-flow period can be important from water-quality and stream ecology perspectives. There is less water available to dilute any contaminants entering the streams, and stream temperatures are highest during August. Physical habitat for aquatic plants and animals is smaller than during most other times of the year. To address these more extreme water-quality and ecological conditions, the synoptic sampling was conducted during the summer low-flow period. Specific objectives of this sampling included: 1. Establish a current data set representing the spatial characteristics of low-flow water-quality conditions in the Gore Creek watershed, and 2. Develop some understanding of land-use and water-quality relations in the watershed. This fact sheet presents hydrologic background information and an analysis of general water-quality properties and constituents, trace elements, and nutrients collected in water samples during low-flow synoptic sampling of the Gore Creek watershed. The U.S. Geological Survey also is conducting a study of the algae and macroinvertebrate communities and physical habitat of streams in the Gore Creek watershed during low flow. This study is designed to provide information about land-use and stream ecology relations in the watershed.

Colorado↗

USGS2018

Bottom trawl assessment of Lake Ontario prey fishes

Managing Lake Ontario fisheries in an ecosystem-context requires prey fish community and population data. Since 1978, multiple annual bottom trawl surveys have quantified prey fish dynamics to inform management relative to published Fish Community Objectives. In 2017, two whole-lake surveys collected 341 bottom trawls (spring: 204, fall: 137), at depths from 8-225m, and captured 751,350 fish from 29 species. Alewife were 90% of the total fish catch while Deepwater Sculpin, Round Goby, and Rainbow Smelt comprised the majority of the remaining total catch (3.8, 3.1, and 1.1% respectively). The adult Alewife abundance index for US waters increased in 2017 relative to 2016, however the index for Canadian waters declined. Adult Alewife condition, assessed by the predicted weight of a 165 mm fish (6.5 inches), declined in 2017 from record high values observed in spring 2016. Spring 2017 Alewife condition was slightly less than the 10-year average, but the fall value was well below the 10-year average, likely due to increased Age-1 Alewife abundance. The Age-1 Alewife abundance index was the highest observed in 40 years, and 8-times higher than the previous year. The Age-1 index estimates Alewife reproductive success the preceding year. The warm summer and winter of 2016 likely contributed to the large year class. In contrast the relatively cool 2017 spring and cold winter may result in a lower than average 2017 year class. Abundance indices for Rainbow Smelt, Cisco, and Emerald Shiner either declined or remained at low levels in 2017. Pelagic prey fish diversity continues to be low since a single species, Alewife, dominates the catch. Deepwater Sculpin were the most abundant benthic prey fish in 2017 because Round Goby abundance declined sharply from 2016. Slimy Sculpin density continued to decline and the 2017 biomass index for US waters was the lowest ever observed. Prior to Round Goby proliferation, juvenile Slimy Sculpin comprised ~10% of the Slimy Sculpin catch, but since 2004, the percent of juveniles within the total catch is less than 0.5%, suggesting Round Goby are limiting Slimy Sculpin reproduction. Despite Slimy Sculpin declines, benthic prey fish community diversity has increased as Deepwater Sculpin and Round Goby comprise more of the community.

Lake Ontario↗

USGS1989

Physical habitat simulation system reference manual: version II

There are four major components of a stream system that determine the productivity of the fishery (Karr and Dudley 1978). These are: (1) flow regime, (2) physical habitat structure (channel form, substrate distribution, and riparian vegetation), (3) water quality (including temperature), and (4) energy inputs from the watershed (sediments, nutrients, and organic matter). The complex interaction of these components determines the primary production, secondary production, and fish population of the stream reach. The basic components and interactions needed to simulate fish populations as a function of management alternatives are illustrated in Figure I.1. The assessment process utilizes a hierarchical and modular approach combined with computer simulation techniques. The modular components represent the "building blocks" for the simulation. The quality of the physical habitat is a function of flow and, therefore, varies in quality and quantity over the range of the flow regime. The conceptual framework of the Incremental Methodology and guidelines for its application are described in "A Guide to Stream Habitat Analysis Using the Instream Flow Incremental Methodology" (Bovee 1982). Simulation of physical habitat is accomplished using the physical structure of the stream and streamflow. The modification of physical habitat by temperature and water quality is analyzed separately from physical habitat simulation. Temperature in a stream varies with the seasons, local meteorological conditions, stream network configuration, and the flow regime; thus, the temperature influences on habitat must be analysed on a stream system basis. Water quality under natural conditions is strongly influenced by climate and the geological materials, with the result that there is considerable natural variation in water quality. When we add the activities of man, the possible range of water quality possibilities becomes rather large. Consequently, water quality must also be analysed on a stream system basis. Such analysis is outside the scope of this manual, which concentrates on simulation of physical habitat based on depth, velocity, and a channel index. The results form PHABSIM can be used alone or by using a series of habitat time series programs that have been developed to generate monthly or daily habitat time series from the Weighted Usable Area versus streamflow table resulting from the habitat simulation programs and streamflow time series data. Monthly and daily streamflow time series may be obtained from USGS gages near the study site or as the output of river system management models.

Report↗

USGS2021

Habitat suitability index model improvement recommendations

As part of the model improvement effort for the 2023 Coastal Master Plan, the Habitat Suitability Index (HSI) models used during previous master plans were reevaluated to assess how the model relationships could be improved, and to determine what species should be included in the master plan analyses. This process considered the technical reviews, comments, and suggested improvements provided by model developers, advisory groups, and other experts during previous master plans. Reviews were then conducted to determine the availability of data and information that could be used to make model improvements. As a result of this effort, a recommended list of relevant species to model is provided, and HSI model improvements are recommended that are categorized by whether the suitability index (SI) relationship to be improved is statistical-based or literature-based. The species recommended to be included in the 2023 Coastal Master Plan analyses are: eastern oyster, brown shrimp, white shrimp, blue crab, crayfish, gulf menhaden, spotted seatrout, largemouth bass, American alligator, gadwall, mottled duck, brown pelican, seaside sparrow, and bald eagle. These species were selected because they represent a range of taxonomies, life histories, trophic levels, and habitats, and most are commercially- or recreationally-important in coastal Louisiana. Most of these species were also included in the 2017 Coastal Master Plan analyses, and the models used during that effort should be further improved. Seaside sparrow and bald eagle are new for the master plan, and new models should be developed for the analyses. The 2017 fish, shrimp, and blue crab HSI models included a water quality SI that was based on statistical analyses of species catch and environmental data collected by the Louisiana Department of Wildlife and Fisheries. As suggested during the 2017 Coastal Master Plan, the modeling approach used to develop the water quality SI was revisited and alternate modeling approaches were explored. Using literature and an evaluation of the general steps of model development, three components for HSI model improvement were identified, including 1) selecting alternative modeling approach(es); 2) detecting and resolving statistical issues; and 3) improving model fit and evaluation. Multiple options for each component were explored, which resulted in a proposed multi-step phased approach for model improvement. This proposed approach entails improving the generalized linear models used for the 2017 water quality SIs and then, if desired, comparing them to alternative model approaches (e.g., generalized additive models) to explore model performance and select the best approach to use for the 2023 Coastal Master Plan HSI models. All of the existing master plan HSI models include literature-based SIs, which use information from published studies of species-habitat associations to derive suitability relationships. Similar to previous master plans, these literature-based SIs should be updated and improved for the 2023 Coastal Master Plan using recent literature and new ecological knowledge. Preliminary reviews were conducted and recent information was found that could be used to improve the eastern oyster, crayfish, and potentially brown pelican HSI models; but no appropriate recent literature was located for improvement of the American alligator, gadwall, and mottled duck HSI models. However, it is recommended that the literature reviews and information searches be continued. In addition to the statistical-based water quality SI, the 2017 fish, shrimp, and blue crab HSI models also included a structural habitat SI that was based on literature showing high densities of these species in fragmented marsh. The relationship used for this SI, however, did not account for the effects of other estuarine habitats, such as submerged aquatic vegetation and oyster reefs, which are also important to these species. Therefore, a meta-analysis approach is proposed that would estimate the relative importance of these habitats for each species, and the results of this analysis could be used to calculate a new structural habitat SI for the 2023 Coastal Master Plan.

Report↗