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USGS1995

Water-quality, bed-sediment, and biological data (October 1993 through September 1994) and statistical summaries of data for streams in the Upper Clark Fork basin, Montana

Water, bed sediment, and biota were sampled in streams from Butte to below Missoula as part of a program to characterize aquatic resources in the upper Clark Fork basin of western Montana. Water- quality data were obtained periodically at 16 stations during October 1993 through September 1994 (water year 1994); daily suspended-sediment data were obtained at six of these stations. Bed-sediment and biological data were obtained at 11 stations in August 1994. Sampling stations were located on the Clark Fork and major tributaries. The primary constituents analyzed were trace elements associated with mine tailings from historical mining and smelting activities. Water-quality data include concentrations of major ions, trace elements, and suspended sediment in samples collected periodically during water year 1994. Daily values of streamflow, suspended-sediment concentration, and suspended- sediment discharge are given for six stations. Bed- sediment data include trace-element concentrations in the fine and bulk fractions. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Quality-assurance data are reported for analytical results of water, bed sediment, and biota. Statistical summaries of bed sediment, and biological data are provided for the period of record at each station since 1985.

Open-File Report↗

USGS2015

The first description of oarfish Regalecus glesne ( Regalecus russellii Cuvier 1816) ageing structures

Despite being a large, conspicuous teleost with a worldwide tropical and temperate distribution, the giant oarﬁsh Regalecus spp. remain very rare ﬁsh species in terms of scientiﬁc sampling. Subsequently, very little biological information is known about Regalecus spp. and almost nothing has been concluded in the ﬁeld of age and growth (Roberts, 2012). No studies of otoliths or temporal (annual) markings on any hard structures have been reported, and to our knowledge otoliths have never been recovered from any specimens (Tyson Roberts, personal communication),although a few texts do provide illustrations of Regalecus sp. otoliths (Lin and Chang, 2012; Nolf, 2013). Further inferential diﬃculty comes from the fact that age and growth studies of any Lampridiforme species are rare. Lampris guttatus is perhaps the only Lampridiforme species for which any biological information has been reported(Francis et al., 2004), which stems from the species commercial value. In order to begin understanding any species (for later purposes of management, conservation, etc.), basic biological information is needed. In the present study, we examine not only the ﬁrst Regalecus russellii otolith, but provide suggestions toward future work that should direct data collection that can be used to generate basic biological information for this species.

Journal of Applied Ichthyology↗

USGS2009

2007 Weather and Aeolian Sand-Transport Data from the Colorado River Corridor, Grand Canyon, Arizona

Weather data constitute an integral part of ecosystem monitoring in the Colorado River corridor and are particularly valuable for understanding processes of landscape change that contribute to the stability of archeological sites. Data collected in 2007 are reported from nine weather stations in the Colorado River corridor through Grand Canyon, Ariz. The stations were deployed in February and March 2007 to measure wind speed and direction, rainfall, air temperature, relative humidity, and barometric pressure. Sand traps near each weather station collect windblown sand, from which daily aeolian sand-transport rates are calculated. The data reported here were collected as part of an ongoing study to test and evaluate methods for quantifying processes that affect the physical integrity of archeological sites along the river corridor; as such, these data can be used to identify rainfall events capable of causing gully incision and to predict likely transport pathways for aeolian sand, two landscape processes integral to the preservation of archeological sites. Weather data also have widespread applications to other studies of physical, cultural, and biological resources in Grand Canyon. Aeolian sand-transport data reported here, collected in the year before the March 2008 High-Flow Experiment (HFE) at Glen Canyon Dam, represent baseline data against which the effects of the 2008 HFE on windblown sand will be compared in future reports.

Open-File Report↗

USGS2021

Decision context as an essential component of population viability analysis

Population viability analysis (PVA) is a widely used tool that applies demographic data in simulation frameworks to assess extinction risk for species or populations. It is used in diverse conservation applications, including evaluating management effectiveness, relative risk of threats, and potential changes to protective status (Beissinger & McCullough, 2002 ), and can be a critical tool for making decisions with imperfect knowledge of the system state, often on limited timelines (Meine et al., 2006 ). Chaudhary and Oli ( 2020 ) recently developed a framework to appraise the quality of PVAs based on the presence of essential background, model, and analysis components. They evaluated 160 published PVAs and reported a decline in the quality of PVAs over time (1990−2017). We agree PVA studies should report unambiguous descriptions of their essential components (Table 1 in Chaudhary and Oli) and explicitly state the model's biological and statistical assumptions. The need for increased transparency in PVAs is evident. Morrison et al. ( 2016 ) reported that only 50% of PVAs published in peer-reviewed and gray literature were both reproducible and repeatable. Further, in an examination of 67 studies that used matrix population models (widely used in PVAs), Kendall et al. ( 2019 ) reported that models frequently contained misspecification errors. Given the rapid advancement of simulation techniques, updated guidance for PVA construction is warranted. However, we believe the essential PVA components identified by Chaudhary and Oli contain a critical omission: the decision context in which the PVA was created and its usefulness in that context. Quality and utility are not mutually exclusive; however, some models that do not meet idealized quality standards might still be valuable because they are useful and represent the best available science for a given decision context (hereafter, decision-support models). The definition of quality for decision-support models should be different than models developed for the purpose of learning (hereafter, heuristic models) and should incorporate how useful the model was, despite information gaps. We further argue that assessment questions should be used prospectively to guide modeling projects, rather than for retrospective comparison of model quality.

Conservation Biology↗

USGS1987

Chemical and biological status of lakes and streams in the upper midwest: assessment of acidic deposition effects

Many lakes in three areas in the Upper Midwest - northeastern Minnesota, northern Wisconsin, and the Upper Peninsula of Michigan - have low acid neutralizing capacity (ANC) and may be susceptible to change by acidic deposition. Northcentral Wisconsin and the Upper Peninsula of Michigan together contain about 150-300 acidic lakes (ANC ≤ 0), whereas none have been found in Minnesota. These acidic lakes are precipitation-dominated, Clearwater seepage lakes having small surface area, shallow depth, and low concentrations of dissolved organic carbon. The spatial distribution of these acidic lakes parallels a west to east gradient of increasing sulfate and hydrogen ion deposition. Several of these acidic lakes exhibit chemical characteristics and biological changes consistent with those observed elsewhere in waters reported to be acidified by acidic deposition. However, an hypothesis of recent lake acidification is not supported by analyses of either historical chemical data or diatom remains in lake sediments, and natural sources of acidity and alternative ecological processes have not been conclusively eliminated as causative factors. Streams in this three-state region have high ANC and appear to be insensitive to acidic deposition. The species richness and composition of lacustrine fish communities in the region are partly related to pH and associated chemical factors. Sport fishes considered acid-sensitive and of primary concern with regard to acidification include walleye, smallmouth bass, and black crappie. The fishery in at least one lake, Morgan Lake in Wisconsin (pH 4.6), may have declined because of acidification. Given the general lack of quantitative fishery data for acidic Wisconsin and Michigan lakes, however, more general conclusions concerning impacts or the absence of impacts of acidification on the region's fishery resources are not possible.

Minnesota;Wisconsin;Michigan↗

USGS1997

Acidic deposition, cation mobilization, and biochemical indicators of stress in healthy red spruce

Dendrochemical and biochemical markers link stress in apparently healthy red spruce trees ( Picea rubens ) to acidic deposition. Acidic deposition to spruce forests of the northeastern USA increased sharply during the 1960s. Previous reports related visible damage of trees at high elevations to root and soil processes. In this report, dendrochemical and foliar biochemical markers indicate perturbations in biological processes in healthy red spruce trees across the northeastern USA. Previous research on the dendrochemistry of red spruce stemwood indicated that under uniform environmental conditions, stemwood concentrations of Ca and Mg decreased with increasing radial distance from the pith. For nine forest locations, frequency analysis shows that 28 and 52% of samples of red spruce stemwood formed in the 1960s are enriched in Ca and Mg, respectively, relative to wood formed prior to and after the 1960s. This enrichment in trees throughout the northeastern USA may be interpretable as a signal of increased availability of essential cations in forest soils. Such a temporary increase in the availability of Ca and Mg could be caused by cation mobilization, a consequence of increased acidic deposition. During cation mobilization, essential Ca and Mg as well as potentially harmful Al become more available for interaction with binding sites in the soil and absorbing roots. As conditions which favor cation mobilization continue, Ca and Mg can be leached or displaced from the soil. A measure of the interaction between Ca and Al is the Al/Ca binding ratio (molar charge ratio of exchangeable Al to exchangeable Ca). As the Al/Ca binding ratio in the root zone increased from 0.3 to 1.9, the foliar concentration of the biochemical stress marker putrescine also increased from 45 to 145 nm g −1 . The correlation of the putrescine concentration to the Al/Ca binding ratio (adj. r 2 = 0.68, P < 0.027) suggests that foliar stress may be linked to soil chemistry.

Journal of Environmental Quality↗

USGS1966

Soviet books and publications on geological and chemical oceanography, hydrology, and other subjects acquired during the second international oceanographic congress, Moscow, June 1966: titles and some translated contents and notes

The listed publications represent a selection, by no means complete, of recent Soviet work in geological and chemical oceanography. Some works on hydrogeology and hydrochemistry of the continents, as well as a few publications on other subjects, such as geology, geophysics, and biology, also are included.

Report↗

USGS2005

Regional economic effects of current and proposed management alternatives for Sand Lake National Wildlife Refuge

The National Wildlife Refuge System Improvement Act of 1997 requires all units of the National Wildlife Refuge System to be managed under a Comprehensive Conservation Plan (CCP). The CCP must describe the desired future conditions of a Refuge and provide long range guidance and management direction to achieve Refuge purposes. Sand Lake National Wildlife Refuge (NWR), located 27 miles northeast of Aberdeen, South Dakota, is in the process of developing a range of management goals, objectives, and strategies for the CCP. The CCP for Sand Lake NWR must contain an analysis of expected effects associated with current and proposed Refuge management strategies. Special interest groups and local residents often criticize a change in Refuge management, especially if there is a perceived negative impact to the local economy. Having objective data on income and employment impacts may show that these economic fears are drastically overstated. Quite often, residents do not realize the extent of economic benefits a Refuge provides to a local community; yet at the same time overestimate the impact of negative changes. Spending associated with Refuge recreational activities such as wildlife viewing and hunting can generate considerable tourism activity for the regional economy. Refuge personnel typically spend considerable amounts of money purchasing supplies in the local lumber and hardware stores, repairing equipment and purchasing fuel at the local service stations, as well as reside and spend their salaries in the community. The purpose of this study was to provide the economic analysis needed for the Sand Lake NWR CCP by evaluating the regional economic impacts associated with the Sand Lake NWR Draft CCP management strategies. For Refuge CCP planning, an economic impact analysis describes how current (No Action Alternative) and proposed management activities (alternatives) affect the local economy. This type of analysis provides two critical pieces of information: (1) it illustrates a refuge’s contribution to the local community; and (2) it can help in determining whether local economic effects are or are not a real concern in choosing among management alternatives. Sand Lake NWR is currently managed to improve and maintain habitat for nesting and resting waterfowl and other migratory birds, such as diving and puddle ducks, geese, grebes, herons, egrets, gulls, and terns. There are three alternatives evaluated in the draft CCP. Alternative 1, the No Action alternative, would continue Refuge management at current levels and would not involve extensive restoration of cropland, grassland, and wetland habitat or improvements to roads, interpretive, and administrative facilities. No new funding or staff levels would occur and programs would follow the same direction, emphasis, and intensity as they do at present. Alternative 2 would maximize the biological potential of the refuge for species of grassland-nesting birds. This would be accomplished through intense management of upland habitat for nesting migratory birds, minimal management for resident species, and minimization of public use that may interfere with migratory bird production. The third alternative takes an integrated approach, with management practices that would serve to maximize the biological potential of Sand Lake for migratory birds. This report first provides a description of the local community and economy near the Refuge. An analysis of current and proposed management strategies that could affect the local economy is then presented. The Refuge management activities of economic concern in this analysis are Refuge personnel staffing and Refuge spending within the local community, and spending in the local community by Refuge visitors.

Sand Lake National Wildlife Refuge↗

USGS2023

Characterization of streamflow and nutrient occurrence in the upper White River Basin, Colorado, 1980–2020

In 2016, Colorado Parks and Wildlife identified filamentous algae collected from the main stem White River as Cladophora glomerata , a pervasive nuisance aquatic alga. Excessive levels of filamentous algae can compromise aesthetic quality, limit recreational activities, and have negative effects on aquatic life including strong fluctuations in dissolved oxygen levels and a reduction in overall biodiversity. To increase understanding of the biology of the upper White River Basin in Colorado, identify potential factors promoting or limiting nuisance algal abundance, and outline information to aid in the understanding and protection of water resources, the U.S. Geological Survey (USGS), in cooperation with the White River and Douglas Creek Conservation Districts and the White River Algae Technical Advisory Group, initiated a study to collect and analyze physical, chemical, and biological information for the upper White River Basin. The report describes long-term changes and spatial variations in streamflow and nutrient concentrations and loads in the upper White River Basin and identifies possible nutrient sources in the basin. Long-term streamflow and nutrient data indicate that conditions in the upper White River Basin have become more favorable to benthic algae over varying timescales. Upward trends in total phosphorus concentrations and loads were found at three sites across the basin from 2000 to 2020. Total phosphorus loads increased around 50 percent, ranging from 18 to 48 pounds per year. Annual estimated concentrations of total phosphorus from 2005 to 2020 were above algal-specific nutrient criteria at the North Fork White River at Buford, Colo., indicating that phosphorus concentrations at this site likely promote algal growth. Discrete concentrations of total phosphorus exceeded algal-specific nutrient criteria on the South Fork and main stem White River during the summer season, though less frequently than samples collected from the North Fork White River. Nitrogen to phosphorus molar ratios collected from July to September indicate movement from colimitation (10–22) to nitrogen limited (less than 13) conditions at the North Fork White River at Buford, Colo. and the South Fork White River at Buford, Colo. starting in 2012. The magnitude of trends in phosphorus loads were generally greater than trends in concentrations across all sites, indicating that the largest changes in concentrations occurred during greater streamflow periods. At White River above Coal Creek, near Meeker, Colo., significant downward trends in streamflow were found in August and September for mean streamflow (15 and 14 percent per decade, respectively) and 7-day minimum streamflows (23 and 22 percent per decade, respectively). Significant downward trends in annual 7-day minimum streamflows of 24 percent per decade, or 66 percent over the 40-year period of analysis, were also observed. Though not significant based on 90-percent confidence intervals, downward trends in 1-day maximum and mean streamflows in May and June and corresponding increases in April may indicate a shift toward earlier snowmelt runoff, as observed across western North America and the Colorado River Basin. Alteration of the annual hydrograph can influence factors that influence algae including nutrient input and dilution potential, water temperature, dissolved oxygen, light availability, and physical disturbance. Results from a synoptic-style sampling identified the lower North Fork White River subbasin as a large source of phosphorus to the downstream system. Large increases in phosphorus loads were observed below Marvine Creek. Synoptic samples and samples collected during spring and summer of 2019 and 2020 also show large increases in total nitrogen, orthophosphate, and total phosphorus occurring at the furthest three downstream sites on the White River. To further evaluate sources of nitrogen in the upper White River Basin, the dual isotopic composition of nitrate was compared across four sites. The isotopic compositions of nitrate were all within the expected range of typical soil-derived nitrate, though the same values can also be derived from a mixture of agricultural fertilizer and manure or septic sources.

Colorado↗

USGS2024

Marine heatwaves affect breeding, diet and population size but not body condition of a range-edge little penguin colony

Significant marine heatwaves (MHWs) developed along the Western Australian coast in 1999 and 2011. Despite ecosystem losses and the southwards occurrence of many tropical fish species during and after the extreme MHW in 2011, there have been few studies on the effects of this MHW on seabirds, and no biological impacts related to the 1999 MHW have been reported. Using data from 1986-2019, we investigated the impacts of these events on breeding outcomes, body condition, diet composition, population size and mortality of little penguins on Penguin Island, in the temperate waters off Western Australia. Breeding outcomes were negatively impacted by the MHWs but body condition was not. Diet composition changed after the MHW, with sandy sprat Hyperlophus vittatus , the penguins’ typical major prey component, replaced by scaly mackerel Sardinella lemuru , a tropical fish species. Using an open robust design analysis that accounts for imperfect capture probabilities and staggered annual arrival and departure dates, we found that the population decreased by 80% following the 2011 MHW. Finally, more penguins died from starvation or from novel protozoal parasitic infections in 2011 and 2012 that were potentially introduced with the changed diet. This research highlights that the temporal and spatial influence of MHWs on seabirds depends on several factors. Furthermore, the magnitude and direction of a prey species’ response can be very localised and have significant impacts on avian predators. There are no obvious ways to mediate climate effects, but perhaps measures taken to reduce any synergistic impacts on prey abundance, particularly during MHW events, could be effective.

Penguin Island↗

USGS2015

Characterization of pH dependent Mn(II) oxidation strategies and formation of a bixbyite-like phase by Mesorhizobium australicum T-G1

Despite the ubiquity of Mn oxides in natural environments, there are only a few observations of biological Mn(II) oxidation at pH < 6. The lack of low pH Mn-oxidizing bacteria (MOB) isolates limits our understanding of how pH influences biological Mn(II) oxidation in extreme environments. Here, we report that a novel MOB isolate, Mesorhizobium australicum strain T-G1, isolated from an acidic and metalliferous uranium mining area, can oxidize Mn(II) at both acidic and neutral pH using different enzymatic pathways. X-ray diffraction, Raman spectroscopy, and scanning electron microscopy with energy dispersive X-ray spectroscopy revealed that T-G1 initiated bixbyite-like Mn oxide formation at pH 5.5 which coincided with multi-copper oxidase expression from early exponential phase to late stationary phase. In contrast, reactive oxygen species (ROS), particularly superoxide, appeared to be more important for T-G1 mediated Mn(II) oxidation at neutral pH. ROS was produced in parallel with the occurrence of Mn(II) oxidation at pH 7.2 from early stationary phase. Solid phase Mn oxides did not precipitate, which is consistent with the presence of a high amount of H 2 O 2 and lower activity of catalase in the liquid culture at pH 7.2. Our results show that M. australicum T-G1, an acid tolerant MOB, can initiate Mn(II) oxidation by varying its oxidation mechanisms depending on the pH and may play an important role in low pH manganese biogeochemical cycling.

Frontiers in Microbiology↗

USGS2011

Biological review of 82 species of coral petitioned to be included in the Endangered Species Act

list 83 coral species as threatened or endangered under the U.S. Endangered Species Act. The petition was based on a predicted decline in available habitat for the species, citing anthropogenic climate change and ocean acidification as the lead factors among the various stressors responsible for the potential decline. The NMFS identified 82 of the corals as candidate species, finding that the petition provided substantive information for a potential listing of these species. The NMFS established a Biological Review Team (BRT) to prepare this Status Review Report that examines the status of these 82 candidate coral species and evaluates extinction risk for each of them. This document makes no recommendations for listing, as that is a separate evaluation to be conducted by the NMFS. The BRT considered two major factors in conducting this review. The first factor was the interaction of natural phenomena and anthropogenic stressors that could potentially contribute to coral extinction. After extensive review of available scientific information, the BRT considers ocean warming, disease, and ocean acidification to be the most influential threats in posing extinction risks to the 82 candidate coral species between now and the year 2100. Threats of local origin but having widespread impact, such as sedimentation, nutrient enrichment, and fishing, were considered of medium importance in determining extinction risks. It is acknowledged that many other threats (e.g., physical damage from storms or ship groundings, invasive species or predator outbreaks, collection and trade) also negatively affect corals, often acutely and dramatically, but generally at relatively small local scales. These local threats were considered to be of limited scope and not deemed to contribute appreciably to the risk of species extinction, except in those special cases where species have restricted geographic or habitat ranges or species have already undergone precipitous population declines such that these local threats further contribute to depensatory processes that can magnify extinction risks (e.g., feedback-loops whereby individual survival decreases with smaller population size). The BRT acknowledges that local and global threats operate on different time scales and, though there is high confidence in the general progression of some key global threats, such as ocean warming and ocean acidification, there is much less certainty in the timing and spatial patterns of these threats. There is also substantial uncertainty in the abilities of the 82 candidate coral species to tolerate or adapt to each of the threats examined, as well as uncertainty in the dynamics of multiple simultaneous stresses. The BRT specifically identified increasing human population levels and the intensity of their collective human consumption as the root drivers of almost all global and local threats to coral species. In evaluating future threat impacts, the BRT attempted to project current trends, without assumptions of future policy changes or technological advances that could potentially alter the projections used in this analysis.

NOAA Technical Memorandum↗

USGS1975

The screech owl: Its life history and population ecology in northern Ohio

The screech owl ( Otus asio ) is native to North America and breeds throughout the United States and in portions of Canada and Mexico. It is a small owl, 20 cm (8 in) in length from the tip of the bill to the tip of the tail, with a wing span of 56 cm (22 in); it has yellow eyes and prominent ear tufts (see Frontispiece). Although the species is common throughout much of North America, it has not been studied intensively, particularly over a long period. The published literature is concerned mostly with food habits, color phase, taxonomy, and miscellaneous observations. Breeding biology and population dynamics have received little attention. This report presents the basic life history and population information about screech owls in northern Ohio over a 30-yr period. The owls studied were nesting in boxes (Fig. 1) established for wood ducks ( Aix sponsa ) along rivers, creeks, and marshes in a four-county area (Ottawa, Sandusky, Wood, and Lucas Counties) near Lake Erie (Fig. 2). No special trapping techniques were required as the screech owls readily used these nesting boxes and could be easily captured while in them. More than 3,000 owls were captured and banded; 500 were recaptured after the initial banding, some 10 or 15 times. This process provided a large quanity of basic information for this report.

Ohio↗

USGS2009

A Review and Synthesis of the Scientific Information Related to the Biology and Management of Species of Special Concern at Cape Hatteras National Seashore, North Carolina

The U.S. Geological Survey's Patuxent Wildlife Research Center (PWRC) conducted a study for the National Park Service (NPS) Southeast Region, Atlanta, GA, and Cape Hatteras National Seashore (CAHA) in North Carolina to review, evaluate, and summarize the available scientific information for selected species of concern at CAHA (piping plovers, sea turtles, seabeach amaranth, American oystercatchers, and colonial waterbirds). This work consisted of reviewing the scientific literature and evaluating the results of studies that examined critical life history stages of each species, and focused on the scientific findings reported that are relevant to the management of these species and their habitats at CAHA. The chapters that follow provide the results of that review separately for each species and present scientifically based options for resource management at CAHA. Although no new original research or experimental work was conducted, this synthesis of the existing information was peer reviewed by over 15 experts with familiarity with these species. This report does not establish NPS management protocols but does highlight scientific information on the biology of these species to be considered by NPS managers who make resource management decisions at CAHA. To ensure that the best available information is considered when assessing each species of interest at CAHA, this review included published research as well as practical experience of scientists and wildlife managers who were consulted in 2005. PWRC scientists evaluated the literature, consulted wildlife managers, and produced an initial draft that was sent to experts for scientific review. Revisions based on those comments were incorporated into the document. The final draft of the document was reviewed by NPS personnel to ensure that the description of the recent status and management of these species at CAHA was accurately represented and that the report was consistent with our work agreement. The following section summarizes the biological information relevant to resource management for the species of concern at CAHA.

Open-File Report↗

USGS1977

Reconnaissance examination of the biology, chemistry, and physical characteristics of selected streams in California and Nevada

This report contains hydrological data from several California and Nevada streams. Emphasis is placed upon water-quality data, but stream discharge at the time of making the water-quality measurements also is given. The purpose of the report is to provide personnel of the U.S. Bureau of Land Management with baseline hydrological data from the selected streams and one well. The streams, the stream sites selected for sampling, and the parameters measured, were chosen in consultation with U.S. Bureau of Land Management personnel.

California, Nevada↗

USGS1972

Physical, chemical, and biological aspects of the Duwamish River Estuary, King County, Washington, 1963-67

This report describes the significant results to 1967 of a comprehensive study that began in 1963 to evaluate what changes take place in an estuary as the loads .of raw and partially treated industrial and municipal wastes are replaced by effluent from a secondary treatment plant. The study area is the Duwamish River estuary, about 18.3 river kilometers long. At mean sea level the estuary has a water-surface area of about 1 square mile and a mean width of 440 feet. At the lowest and highest recorded tides, the volume of the estuary is about 205 and 592 million cubic feet, respectively. The estuary is well stratified (salt-wedge type) at fresh-water inflows greater than 1,000 cfs (cubic feet per second), but when inflow rates are less than 1,000 cfs the lower 5.6 kilometers of the estuary grades into the partly mixed type. The crosschannel salinity distribution is uniform for a given location and depth. Salinity migration is controlled by tides and fresh-water inflow. At fresh-water inflow rates greater than 1,000 cfs, water in the upper 8.4 kilometers of the estuary is always fresh regardless of tide. At inflow rates less than 600 cfs and tide heights greater than 10 feet; some salinity has been detected 16.1 kilometers above the mouth of the estuary. Studies using a fluorescent dye show that virtually no downward mixing into the salt wedge occurs; soluble pollutants introduced at the upper end of the estuary stay in the surface layer (5-15 ft thick). On the basis of dye studies when fresh-water inflow is less than 400 cfs, it is estimated that less than 10 percent of a pollutant will remain in the estuary a minimum of 7 days. Longitudinal dispersion coefficients for the surface layer have been determined to be on the order of 100-400 square feet per second. Four water-quality stations automatically monitor DO (dissolved oxygen), water temperature, pH, and specific conductance; at one station solar radiation also is measured. DO concentration in the surface layer decreases almost linearly in a downstream direction. Minimum DO concentration in the surface layer is usually greater than 4 rag/1 (milligrams per liter). The smallest DO values are consistently recorded in the bottom layer at the station 7.7 kilometers above the mouth; monthly means of less than 3 mg/1 of DO have occurred at this point. Manual sampling shows that the DO sag in the bottom layer oscillates between 7.7 and 10.4 kilometers above the mouth of the estuary. Multiple-regression analysis shows that the surface DO content can be estimated from the fresh-water inflow and water temperature. Tidal exchange and fresh-water inflow indirectly control the bottom DO content. Information available from previous studies failed to indicate a progressive decrease in DO content during the period 1949-56, but data from the present study suggest a slight general decrease in the annual minimum DO concentrations in both the upper and lower layers. Average nitrate concentration in fresh water at station 16.2 has increased progressively since 1964, by amounts greater than those which can be attributed to the Renton Treatment Plant, 4.3 kilometers upstream from station 16.2. The BOD (biochemical oxygen demand) in both surface and bottom layers is generally less than 4 rag/1 of oxygen, but values greater than 6 rag/1 have been measured during a period of phytoplankton bloom. Phytoplankton blooms can occur during periods of minimum tidal exchange and fresh-water inflows of less than 300 cfs if solar radiation and water temperature are optimum. Nutrients (nitrogen and phosphorus compounds) do not control the occurrence of a bloom, because sufficient quantities of these nutrients are always present. Nutrients in the treated effluent may increase the biomass of the bloom. Trace-element studies have not defined any role that these elements may play in algal growth. The inflowing fresh water contains principally calcium and bicarbonate and has a dissolved-solids content ra

Water Supply Paper↗

USGS2015

An updated conceptual model of Delta Smelt biology: Our evolving understanding of an estuarine fish

The main purpose of this report is to provide an up-to-date assessment and conceptual model of factors affecting Delta Smelt (Hypomesus transpacificus) throughout its primarily annual life cycle and to demonstrate how this conceptual model can be used for scientific and management purposes. The Delta Smelt is a small estuarine fish that only occurs in the San Francisco Estuary. Once abundant, it is now rare and has been protected under the federal and California Endangered Species Acts since 1993. The Delta Smelt listing was related to a step decline in the early 1980s; however, population abundance decreased even further with the onset of the “pelagic organism decline” (POD) around 2002. A substantial, albeit short-lived, increase in abundance of all life stages in 2011 showed that the Delta Smelt population can still rebound when conditions are favorable for spawning, growth, and survival. In this report, we update previous conceptual models for Delta Smelt to reflect new data and information since the release of the last synthesis report about the POD by the Interagency Ecological Program for the San Francisco Estuary (IEP) in 2010. Specific objectives include: 1. Provide decision makers with a practical tool for evaluating difficult trade-offs associated with management and policy decisions. 2. Provide scientists with a framework from which they can formulate and evaluate hypotheses using qualitative or quantitative models. 3. Provide the general public with a new way of learning about Delta Smelt and their habitat. Our updated conceptual model describes the habitat conditions and ecosystem drivers affecting each Delta Smelt life stage, across seasons and how the seasonal effects contribute to the annual success of the species. The conceptual model consists of two nested and linked levels of increasing specificity. The general life cycle conceptual model for four Delta Smelt life stages (adults, eggs and larvae, juveniles, and subadults) includes stationary ecosystem components and dynamic environmental drivers, habitat attributes, and Delta Smelt responses. The more detailed life stage transition conceptual models for each of the four Delta Smelt life stages describe relationships between environmental drivers, key habitat attributes, and the responses of Delta Smelt to habitat attributes as they transition from one life stage to the next. Our analyses and conceptual model show that good larval recruitment is essential for setting the stage for a strong year class; however, increased growth and survival through subsequent life stages are also needed to achieve and sustain higher population abundance. We used our conceptual model to generate 16 hypotheses about the factors that may have contributed to the 2011 increase in Delta Smelt relative abundance. We then evaluated these hypotheses by comparing habitat conditions and Delta Smelt responses in the wet year 2011 to those in the prior wet year 2006 and in the drier years 2005 and 2010. Larval recruitment was similarly high in both wet years and lower in the drier antecedent years, but juvenile and adult abundance increased only in 2011. In 2005 and 2006, the population was limited by very poor survival from the larval to the juvenile life stage. We found that in 2011, Delta Smelt may have benefitted from a combination of favorable habitat conditions throughout the year, including: 1. Adults and larvae benefitted from prolonged cool spring water temperatures, high 2011 winter and spring outflows which reduced entrainment risk and possibly improved other habitat conditions, and possibly enhanced food availability in late spring. 2. Juveniles benefitted from cool water temperatures in late spring and early summer as well as from improved food availability and low levels of harmful Microcystis. 3. Subadults also benefitted from improved food availability and from favorable habitat conditions in the large, low salinity zone (salinity 1-6) located more toward Suisun Bay,

California↗

USGS1982

Full-time equivalency tracking system

To help meet the goals of the Surface-Mining Control and Reclamation Act of 1977, the U.S. Geological Survey is assessing the physical, chemical, and biological characteristics of surface water within the coal-mining region of southwestern Indiana. This report discussed benthic-invertebrate and periphytic-algal communities in streams draining homogeneous agricultural, forested, active/reclaimed-mine, and unreclaimed mine watersheds, and relates the biological communities to the physical and chemical characteristics of the streams. Alkalinity and pH were lower and the concentrations of dissolved solids, calcium, magnesium, sodium, potassium, sulfate, iron, manganese, aluminum, and zinc were higher in unreclaimed-mine watersheds than in the other land-use watersheds. Numbers and community diversity of benthic invertebrates were less at sites affected by mining than at agricultural or forested sites, owing to (1) synergistic effects of pH, metals, and unsuitable habitat and (2) lack of colonizing drift organisms because of the small drainage area upstream from the mined area. Only a few organisms , such as the caddisflies Cheumatopsyche and Hydrosyche and the chironomids Chironomus and Cricotopus were found in streams draining mine areas. (USGS)

Open-File Report↗