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482 records · Page 27Linked to original sources
USGS2002

Hydrologic variability and the application of Index of Biotic Integrity metrics to wetlands: a Great Lakes evaluation

Interest by land-management and regulatory agencies in using biological indicators to detect wetland degradation, coupled with ongoing use of this approach to assess water quality in streams, led to the desire to develop and evaluate an Index of Biotic Integrity (IBI) for wetlands that could be used to categorize the level of degradation. We undertook this challenge with data from coastal wetlands of the Great Lakes, which have been degraded by a variety of human disturbances. We studied six barrier beach wetlands in western Lake Superior, six drowned-river-mouth wetlands along the eastern shore of Lake Michigan, and six open shoreline wetlands in Saginaw Bay of Lake Huron. Plant, fish, and invertebrate communities were sampled in each wetland. The resulting data were assessed in various forms against gradients of human disturbance to identify potential metrics that could be used in IBI development. Our results suggested that the metrics proposed as potential components of an IBI for barrier beach wetlands of Lake Superior held promise. The metrics for Lake Michigan drowned-river-mouth wetlands were inconsistent in identifying gradients of disturbance; those for Lake Huron open embayment wetlands were yet more inconsistent. Despite the potential displayed by the Lake Superior results within the year sampled, we concluded that an IBI for use in Great Lakes wetlands would not be valid unless separate scoring ranges were derived for each of several sequences of water-level histories. Variability in lake levels from year to year can produce variability in data and affect the reproducibility of data collected, primarily due to extreme changes in plant communities and the faunal habitat they provide. Substantially different results could be obtained in the same wetland in different years as a result of the response to lake-level change, with no change in the level of human disturbance. Additional problems included limited numbers of comparable sites, potential lack of undisturbed reference sites, and variable effects of different disturbance types. We also evaluated our conclusions with respect to hydrologic variability and other major natural disturbances affecting wetlands in other regions. We concluded that after segregation of wetland types by geographic, geomorphic, and hydrologic features, a functional IBI may be possible for wetlands with relatively stable hydrology. However, an IBI for wetlands with unpredictable yet recurring influences of climate-induced, long-term high water periods, droughts, or drought-related fires or weather-related catastrophic floods or high winds (hurricanes) would also require differing scales of measurement for years that differ in the length of time since the last major natural disturbance. A site-specific, detailed ecological analysis of biological indicators may indeed be of value in determining the quality or status of wetlands, but we recommend that IBI scores not be used unless the scoring ranges are calibrated for the specific hydrologic history pre-dating any sampling year.

Wetlands↗
USGS2013

Evapotranspiration and water balance of an anthropogenic coastal desert wetland: responses to fire, inflows and salinities

Evapotranspiration (ET) and other water balance components were estimated for Cienega de Santa Clara, an anthropogenic brackish wetland in the delta of the Colorado River in Mexico. The marsh is in the Biosphere Reserve of the Upper Gulf of California and Delta of the Colorado River, and supports a high abundance and diversity of wildlife. Over 95% of its water supply originates as agricultural drain water from the USA, sent for disposal in Mexico. This study was conducted from 2009 to 2011, before, during and after a trial run of the Yuma Desalting Plant in the USA, which will divert water from the wetland and replace it with brine from the desalting operation. The goal was to estimate the main components in the water budget to be used in creating management scenarios for this marsh. We used a remote sensing algorithm to estimate ET from meteorological data and Enhanced Vegetation Index values from the Moderate Resolution Imaging Spectrometer (MODIS) sensors on the Terra satellite. ET estimates from the MODIS method were then compared to results from a mass balance of water and salt inflows and outflows over the study period. By both methods, mean annual ET estimates ranged from 2.6 to 3.0 mm d −1 , or 50 to 60% of reference ET (ET o ). Water entered at a mean salinity of 2.6 g L −1 TDS and mean salinity in the wetland was 3.73 g L −1 TDS over the 33 month study period. Over an annual cycle, 54% of inflows supported ET while the rest exited the marsh as outflows; however, in winter when ET was low, up to 90% of the inflows exited the marsh. An analysis of ET estimates over the years 2000–2011 showed that annual ET was proportional to the volume of inflows, but was also markedly stimulated by fires. Spring fires in 2006 and 2011 burned off accumulated thatch, resulting in vigorous growth of new leaves and a 30% increase in peak summer ET compared to non-fire years. Following fires, peak summer ET estimates were equal to ET o , while in non-fire years peak ET was equal to only one-half to two-thirds of ET o . Over annual cycles, estimated ET was always lower than ET o , because T. domingensis is dormant in winter and shades the water surface, reducing direct evaporation. Thus, ET of a Typha marsh is likely to be less than an open water surface under most conditions.

Ecological Engineering↗
USGS2026

Expansion trends and impacts of Phragmites australis on the Louisiana Gulf Coast

Invasive plant species pose substantial threats to ecosystem integrity by disrupting ecosystem processes, reducing biodiversity, and complicating restoration and management efforts. Non-native lineages of Phragmites australis are invasive in wetlands across parts of North America, causing declines in the diversity of native wetland plants and disrupting biogeochemical cycles. Despite recognition of these effects, important knowledge gaps remain regarding the spatiotemporal dynamics, environmental drivers, and consequences of Phragmites expansion for native communities. Here, we examined long-term data from the Louisiana Coastwide Reference Monitoring System (CRMS), collected from 2006 to 2023 and spanning 390 sites across nine basins, to quantify basin-specific Phragmites cover trajectories and evaluate their associations with co-occurring native plant cover and soil properties. Louisiana supports both long-established noninvasive and (since ~2000) invasive European P. australis lineages, but CRMS cannot distinguish them; thus, our basin-level trajectories reflect species-level cover dynamics that may integrate lineage-specific turnover. Phragmites dynamics varied markedly among basins over the study period: Phragmites cover decreased in the Mississippi River Delta (initially >25%), whereas the Calcasieu-Sabine, Mermentau, Teche-Vermilion, and Terrebonne basins, each starting with <5%, exhibited positive expansion trends. The remaining four basins maintained low and stable Phragmites cover (<5%) over the study period. These distinct basin-level trajectories may reflect basin-to-basin differences in a hydrogeomorphic setting and associated sediment and nutrient inputs. In basins with positive expansion trends, Phragmites cover was associated with decreases in native plant cover. Overall, Phragmites expansion was positively associated with higher soil nutrients, lower pH, and higher salinity, highlighting key environmental factors that could inform targeted management to prevent or mitigate its expansion. Although Phragmites cover remains low in most basins (<10%), expansion in several basins suggests the value of basin-specific early-warning monitoring to maintain native plant cover and associated ecosystem functions. Our two-step framework offers a transferable monitoring template that integrates Phragmites cover trends (expanding/stable/declining), concurrently measured native plant cover, and key soil and pore-water indicators to flag emerging hotspots and prioritize adaptive management in other estuarine and deltaic systems.

Louisiana↗
USGS2024

Physics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary

Executive Summary The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt ( Hypomesus transpacificus ) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid ( Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California. Our approach for this cooperative project is based on the “physics to fish” concept, the idea that high-quality habitat is generated and sustained by the interaction between physical processes and the landscape. These interactions create a template for chemical and biological processes that can change across a variety of spatial and temporal scales. Following this concept, this project (hereafter referred to as “the physics to fish project”) included monitoring and studies of water flows, sediments, water quality, and invertebrate and fish dynamics across a range of spatial and temporal scales and in regions relevant to resource managers tasked with managing water supplies and ecosystem health in the San Francisco Estuary. The intent of this approach was to document the habitat conditions, important processes, and interactions among them that create high-quality habitat for native fishes so that the likely effects of future management actions (for example, habitat restoration) can be objectively assessed at the local (site-specific), regional (within subregions of the estuary), and landscape (across the entire estuary and beyond) scales. Hydrodynamically, the upper estuary (landward of Carquinez Strait) is characterized by a fixed volume of tidally exchanged water (for example, tidal prism) that interacts with the existing channel network and bathymetry to create regions with differing hydrodynamics. Our results indicate that careful study of construction or reoperation of existing infrastructure to perform management actions can help (1) improve the accuracy of hydrodynamic models; (2) further understanding of ecological effects; and (3) enhance abilities to predict ecological outcomes. At the local scale, we developed a new concept called the Lagrangian to Eulerian (LE) ratio that can be used as a tool for understanding the importance of various hydrodynamic processes in specific channels or channel networks and for forecasting transport dynamics. Channels with LE ratios<1 in a channel network or in a dead-end slough are hydrodynamically able to develop an exchange zone between two parcels of water that may have different chemical and physical properties. In a dead-end channel, there is a landward region with long residence time (no-exchange zone) and a seaward region with short residence time (high-exchange zone) that are well mixed with seaward waters. At the transition (exchange zone) between the high and no-exchange regions, a gradient will form in water-quality constituents that differ in concentration between the landward and seaward waters. Turbidity affects fish habitat and has declined through time in the San Francisco Estuary. Average turbidity across the Sacramento–San Joaquin Delta (hereafter referred to as “the Delta”) is dependent on annual hydrology. In dry years, the region around Cache Slough (known regionally as the “Cache Slough Complex”) in the northern Delta is generally more turbid than Suisun Bay and the lower Sacramento River. When the Yolo By-Pass (known regionally as “Yolo Bypass”), a large flood bypass that runs parallel to the Sacramento River in the northern Delta, is not flooding and river flows are lower, sediment is usually transported into the Cache Slough Complex because flood tides dominate ebb tides, resulting in transport of suspended sediment from seaward areas of the upper estuary into the Cache Slough Complex. These hydrodynamic conditions also favor the formation of turbidity maximums (TMs) in the Cache Slough Complex. The TMs are areas of higher suspended-sediment concentration, providing higher-turbidity habitat favored by some fishes, including delta smelt, and they can also concentrate other constituents, including phytoplankton and organic carbon that can be important in food webs. Pelagic primary production by phytoplankton is the basis for Delta food webs supporting pelagic fishes such as delta smelt; however, phytoplankton abundance in the Delta has declined during recent decades. We examined how nutrients, hydrodynamics, and other factors affect phytoplankton blooms. Based on our results, we developed three new concepts of phytoplankton bloom formation in the Delta, each associated with a distinct set of hydrologic conditions. First, productivity cascades highlighted how local processes can contribute to phytoplankton blooms observed at the regional scale. Second, we observed phytoplankton blooms in the upper San Francisco Estuary that were associated with transport out of Yolo By-Pass (transport blooms). Third, we also documented a series of phytoplankton blooms that were in the confluence area at the landward edge of Suisun Bay. The conditions leading to creation of confluence phytoplankton blooms are not yet understood, but the confluence region connects the Cache Slough Complex with Suisun Marsh. Therefore, blooms in this area have the potential to spread to large areas of the Delta. At the landscape scale, the distribution of the invasive clams ( Potamocorbula amurensis and Corbicula fluminea , hereafter referred to as “ Corbicula ”) is driven by salinity. At smaller spatial scales, the distribution of either species is sensitive to multiple factors affecting survival and reproduction, complicating efforts to predict distribution and abundance without considering local-scale conditions across the area of interest. In the Cache Slough Complex, the area landward of the exchange zone in regions with LE ratio<1 were characterized by low abundances of Corbicula probably because recruits from seaward areas are not transported past the exchange zone and because there are no landward tributaries with adult Corbicula to provide an upstream source of recruits. Corbicula biomass was highest near or downstream from the exchange zone consistent with Corbicula grazing on phytoplankton produced in the exchange zone or transported from the no-exchange zone. The severity of Corbicula grazing could be reduced by manipulating the hydrodynamic characteristics of waterways; however, the beneficial and harmful effects on the organisms meant to benefit from increased phytoplankton production, including zooplankton and fish species of concern, should be thoroughly examined before manipulating hydrodynamic characteristics. The distribution of fishes at the landscape scale is generally driven by the position of the salinity field in the estuary. The physics to fish project compared distributions of fishes at Ryer Island, a tidal wetland in Suisun Bay and a region of variable salinity, with fish distributions at the Cache Slough Complex, a freshwater region. At Ryer Island, there was an absence of freshwater invasive species and an abundance of native species, such as Sacramento splittail ( Pogonichthys macrolepidotus ), tule perch ( Hysterocarpus traskii ), and Sacramento pikeminnow ( Ptychocheilus grandis ). The native species were almost exclusively captured in wetland and nearshore shallow-water habitat regardless of water-quality conditions. In the Cache Slough Complex, our regional scale objective was to elucidate how hydrodynamic-physical habitat interactions drive fish-community structure. Our studies showed that dendritic channel systems were better able to support native species, while intertidal habitats supported those species best able to exploit the transient character of the habitat. Habitats upstream from the exchange zone were especially important in supporting high numbers of native fishes relative to within or downstream from the exchange zone. Many of the native species were associated with tidal marsh in the no-exchange zone. More pelagic-oriented, mobile species, such as Striped Bass ( Morone saxatilis ), threadfin shad ( Dorosoma petenense ), and Sacramento pikeminnow, were more affected by water-quality conditions, such as turbidity. The physics to fish concept developed in this project provides a framework for designing individual projects and for considering the cumulative effects of multiple projects in a region, using the LE ratio as a guiding metric. The physics to fish concept may also provide a suitable framework for coordinating management actions. Tidal wetlands can function in several ways in the hydrodynamic framework. Relatively small tidal wetlands with short channel networks and with LE ratios>1 are not able to maintain a landward no-exchange zone or an exchange zone. This likely means that any contributions to pelagic food webs would be limited to resources derived from wetland vegetation, which can include dissolved and particulate organic matter (detritus) and populations of consumers that can increase in abundance based on those resources. The fate of the contributed production from these channels depends on the characteristics of the receiving waters seaward of the tidal wetland. If these channels join a large system such as Suisun Bay, then any contribution is likely to be rapidly dispersed in the larger volume; however, the channel junction might provide a focal point for consumers, such as fishes, to congregate and feed on material leaving the wetland on ebb tides before it is dispersed in the larger volume. Fishes might also access these resources by entering the wetland. The physics to fish project has established a foundation and several new concepts for understanding how habitat restoration can benefit native fish populations at the local and regional levels. Many of the ideas regarding habitat restoration and channel modifications outlined in this report could help guide management actions that could improve conditions for native fishes at little or no water cost beyond water already dedicated to other management actions. A complete list of products originating from this work is provided in appendix 1.

California↗
USGS1998

Long-term effects of a lock and dam and greentree reservoir management on a bottomland hardwood forest

We investigated the long-term effects of a lock and dam and greentree reservoir management on a riparian bottomland hardwood forest in southern Arkansas, USA, by monitoring stress, mortality, and regeneration of bottomland hardwood trees in 53 permanent sampling plots from 1987-1995. The lock and dam and greentree reservoir management have altered the timing, depth, and duration of flooding within the wetland forest. Evaluation of daily river stage data indicates that November overbank flooding (i.e. 0.3 m above normal pool) of 1 week duration occurred only 10 times from 1950 to 1995 and four of these occurrences were the result of artificial flooding of the greentree reservoir. Results of the vegetation study indicate that the five most common dominant and co-dominant species were overcup oak, water hickory, Nuttall oak, willow oak, and sweetgum. Mortality of willow oak exceeded that of all other species except Nuttall oak. Nuttall oak, willow oak, and water hickory had much higher percentages of dead trees concentrated within the dominant and co-dominant crown classes. Probit analysis indicated that differences in stress and mortality were due to a combination of flooding and stand competition. Overcup oak appears to exhibit very little stress regardless of crown class and elevation and, with few exceptions, had a significantly greater probability of occurring within lower stress classes than any other species. Only 22 new stems were recruited into the 5 cm diameter-at-breast height size class between 1990-1995 and of these, three were Nuttall oak, three were water hickory, and one was sweetgum. No recruitment into the 5 cm diameter-at-breast height size class occurred for overcup oak or willow oak. The results of the study suggest that the forest is progressing to a more water-tolerant community dominated by overcup oak. A conservative flooding strategy would minimize tree stress and maintain quality wildlife habitat within the forested wetland.The long-term effects of a lock and dam and greentree reservoir management on a riparian bottomland hardwood forest in southern Arkansas, USA, were investigated by monitoring stress, mortality, and regeneration of bottomland hardwood trees in 53 permanent sampling plots from 1987-1995. Results of the study suggest that the forest is progressing to a more water-tolerant community dominated by overcup oak.

Forest Ecology and Management↗
USGS2019

Efficacy of eDNA as an early detection indicator for Burmese pythons in the ARM Loxahatchee National Wildlife Refuge in the Greater Everglades Ecosystem

Environmental DNA (eDNA) detection of invasive species can be used to delimited occupied ranges and estimate probabilities to inform management decisions. Environmental DNA is shed into the environment through skin cells and bodily fluids and can be detected in water samples collected from lakes, rivers, and swamps. In south Florida, invasive Burmese pythons occupy much of the Greater Everglades in mostly inaccessible habitat and are credited with causing severe declines of native species’ populations. Detection of Burmese pythons by traditional methods, such as trapping and visual searching, have been largely ineffective, making eDNA a superior method for differentiating invaded habitat. We adapted a quantitative PCR eDNA assay for droplet digital PCR, a state-of-the-art method that improves precision and accuracy. From August 2014 to October 2016, locations in and around Arthur R. Marshall Loxahatchee National Wildlife Refuge in southeast Florida were surveyed for Burmese python eDNA. The Refuge is maintained to provide water storage and is considered one of the last remnants of the northern Everglades wetlands. Positive eDNA detections were made at each of the five sampling events, assessing a total of 399 samples, with moderate occurrence (ψ=58-91%) and detection (p=40-70%) probabilities, potentially reduced by high PCR inhibition-levels. The high occurrence rates and geographic distribution of the positive samples within the Refuge suggests a steady release of python eDNA from a resident Burmese python population and reduces support for primarily transport of eDNA through boats or flowing water from the north. The first confirmed sighting of a Burmese python in the Refuge occurred in September 2016, after eDNA testing had indicated the presence of pythons. An established population is not expected this far north, however, the detections likely indicate northern range limit of a consistent population at Loxahatchee on the eastern side of the Florida peninsula. Our study demonstrates the benefit of eDNA for determining more accurate range limits and expansion information for Burmese pythons, as well as laying the foundation for the assessment of control efforts.

Florida↗
USGS2011

Predicting breeding habitat for amphibians: a spatiotemporal analysis across Yellowstone National Park

The ability to predict amphibian breeding across landscapes is important for informing land management decisions and helping biologists better understand and remediate factors contributing to declines in amphibian populations. We built geospatial models of likely breeding habitats for each of four amphibian species that breed in Yellowstone National Park (YNP). We used field data collected in 2000-2002 from 497 sites among 16 basins and predictor variables from geospatial models produced from remotely sensed data (e.g., digital elevation model, complex topographic index, landform data, wetland probabililty, and vegetative cover). Except for 31 sites in one basin that were surveyed in both 2000 and 2002, all sites were surveyed once. We used polytomous regression to build statistical models for each species of amphibian from 1) field survey site data only, 2) field data combined with data from geospatial models, and 3) data from geospatial models only. Based on measures of receiver operating characteristic (ROC) scores, models of the second type best explained likely breeding habitat because they contained the most information (ROC values ranged from 0.70 - 0.88). However, models of the third type could be applied to the entire YNP landscape and produced maps that could be verified with reserve field data. Accuracy rates for models built for single years were highly variable, ranging from 0.30 to 0.78. Accuracy rates for models built with data combined from multiple years were higher and less variable, ranging from 0.60 to 0.80. Combining results from the geospatial multiyear models yielded maps of "core" breeding areas (areas with high probability values for all three years) surrounded by areas that scored high for only one or two years, providing an estimate of variability among years. Such information can highlight landscape options for amphibian conservation. For example, our models identify alternative for areas that could be protected for each species, including 6828-10 764 ha for tiger salamanders; 971-3017 ha for western toads; 4732-16 696 ha for boreal chorus frogs; 4940-19 690 hectares for Columbia spotted frogs.

Yellowstone National Park↗
USGS2022

A forested wetland at a climate-induced tipping-point: 17-year demographic evidence of widespread tree recruitment failure

Regeneration and survival of forested wetlands are affected by environmental variables related to the hydrologic regime. Climate change, specifically alterations to precipitation patterns, may have outsized effects on these forests. In Tennessee, USA, precipitation has increased by 15% since 1960. The goal of our research was to assess the evidence for whether this change in precipitation patterns resulted in shorter growing seasons and recruitment failure in common canopy trees for a forest wetland. In 2001 and 2018, the density of Quercus lyrata (overcup oak), Liquidambar styraciflua (sweetgum), Quercus phellos (willow oak), and Betula nigra (river birch) seedling, sapling and adult density were mapped in an area of 2.3 ha within a seasonally flooded karst depression. Overall, the percentage of the growing season experiencing inundation was 26% greater in the deep than in shallow areas between 2001 and 2018. Saplings and small adults of all four species were restricted to shallow areas, and their abundance has declined substantially. Overcup oak and sweetgum individuals that were recruited into the adult life history stage were repelled from the deep zone. Overcup oak and sweetgum adults experienced lower mortality across the 2.3-ha study area (11% and 26%, respectively) relative to willow oak (56%) and river birch (64%) over the 17-year study. Growing-season inundation showed no relation to mortality in adult sweetgum and willow oak, a positive relation to mortality among adult river birch across size classes and among small adult overcup oak, and an inverse relation to mortality among large adult overcup oak. In shallow regions, overcup oak and sweetgum adults had greater basal area increment relative to the intermediate and deep regions of the pond. Results of hydrologic modeling for the study area, based on rainfall and temperature records covering 1855–2019, show ponding durations after 1970 considerably longer than the historical baseline, across ponding-depth classes. Our results strongly suggest that climate change is a driving factor suppressing tree regeneration since 1970 in this seasonally flooded karst depression.

Tennessee↗
USGS1999

Fishes of Missouri River, chute, and flood plain habitats: Chapter 4 in Initial biotic survey of Lisbon Bottom, Big Muddy National Fish and Wildlife Refuge

The Lisbon Bottom Unit of the Big Muddy National Fish and Wildlife Refuge (Refuge) is approximately 2,200 acres and is the first complete unit of the Refuge. Primary objectives of the Refuge are to create and restore diverse riverine aquatic habitats and reconnect the Missouri River to its flood plain where feasible. Management seeks to accomplish these objectives by encouraging natural processes of erosion, deposition, and succession to the greatest extent possible. One of the most salient aquatic features of the Lisbon Bottom Unit is a newly created 2-mile-long free-flowing chute, or side channel (Fig. 1). This chute began forming as a levee breech scour hole during the Great Flood of 1993. The chute continued to develop during the 1995 flood and finally cut through to a flowing side channel during the 1996 flood. Extensive erosion and bank sluffing continued during 1997 due to sustained high flows that occurred throughout most of the year. The chute has progressively become wider and deeper with a developing meander pattern and channel bars have begun to form. Lisbon Bottom also contains several seasonal and permanent wetlands and is subject to periodic flooding at high Missouri River stages. Eight studies have been completed or are ongoing to evaluate Missouri River fishes associated with various habitat components of Lisbon Bottom and adjacent Missouri River reaches (Table 1). Several are part of much larger investigations to evaluate fish use of flood-created habitat features, basinwide fish assessment, and endangered or candidate species concerns. At the Lisbon Bottom Unit or in the Missouri River adjacent to the unit 54 fish species were collected (Table 2). Eight of these species have either a protected status under State or Federal laws or biologists consider them to potentially qualify for protected status. The status of the following fish is listed in Table 2: pallid sturgeon x shovelnose sturgeon hybrid, paddlefish, northern pike, sturgeon chub, sicklefin chub, ghost shiner, western silvery minnow, plains minnow, and blue sucker. Equally important to note are fish species that were not collected. The flathead chub, currently listed as State endangered and proposed for Federal listing, were not collected in any of the studies. Common fish species, collected in all seven sampling studies, included gizzard shad, common carp, river carpsucker, and freshwater drum. Paddlefish, skipjack herring, silver carp, white sucker, redfin shiner, western silvery minnow, bullhead minnow, and black bullhead were each collected in only one of the seven studies. Pflieger (1971) developed a guild system for the fishes of Missouri based on distribution patterns and centers of abundance. Fish were assigned to one of four primary faunal groups: Ozark, Big River, Lowland, and Prairie. Two secondary groups (Ozark-prairie and Ozark-lowland) were defined for species equally abundant and distributed in two of the primary areas. Two Ozark-prairie species, shorthead redhorse and white sucker, were collected on or near the Lisbon Bottom Unit. Big River species are found primarily in the Missouri and Mississippi Rivers. The environmental factors controlling fish distribution in these rivers appear to be substrate, current velocity, and turbidity. On or near the Lisbon Bottom Unit 18 Big River species were collected (Table 2). Lowland species are intolerant of siltation and high turbidity. They inhabit standing or slow-moving water with sand, fine gravel, and organic debris substrates. Two Lowland species, bullhead minnow and mosquitofish, were collected in connected scours on the Lisbon Bottom Unit. Prairie species have broader ecological tolerances than the Ozark and Lowland species. They are largely absent in high gradient streams and cool, clear waters. Prairie species make up a significant proportion of Missouri and Mississippi River fishes. Seven Prairie species were collected on or near the Lisbon Bottom Unit (Table 2). The last group, Wide-ranging, was defined as the species more widespread than the other faunal groups with broader environmental tolerances. Most Wide-ranging species occur at least occasionally in all sections of the state. Nineteen Wide-ranging species were collected on or near the Lisbon Bottom Unit (Table 2). Kubisiak (1997) found that isolated scours in the Lower Missouri River were dominated by Wide-ranging species. Connected scours also held Wideranging species but they contained Prairie species and were dominated by Big River species. Faunal group diversity and species richness were compared between isolated (Study l) and connected (Studies 4, 5, 7, and 8) scours of the Lisbon Bottom Unit. Species richness was similar with 22 species collected in isolated scours and an average of 24.8 species collected in connected scours. Isolated scour fish catches were dominated by Wide-ranging fish (59%) with 14% Big River fishes and 14% Prairie fishes. Connected scours had a larger percentage of Big River fish (32%) and fewer Wide-ranging (36%) and Prairie (13%) species than the isolated scours. In the combined studies, Wide-ranging fish dominated the connected scours. A similar comparison was made of fish from chute habitats and the Missouri River. Chute habitats include the Lisbon Bottom Chute, the chute between the right bank and island located at river mile 219, and a shallow channel running between a large sandbar complex and the channel border adjacent to Lisbon Bottom. Species richness in the chutes (35 species) was greater than that of the adjacent river (23 species). Big River species (40%) dominated the chute samples, followed by Wide-ranging at 31% Cand Prairie Cut 14%. The river samples contained equal numbers of Wide-ranging species (35%) and Big River species (35%) with 17% Prairie species. Differences in fish guild diversity and species richness may be due to numerous factors including sampling effort and sampling season. River samples were collected only in Study 3 in October; chute samples were collected in July, August, and October. Fish may have been using the chute in July and August to spawn, feed, or escape high river levels. The Lisbon Bottom Chute is a truly unique feature of the Lower Missouri River. It is the first naturally created side channel to develop since the U.S. Army Corps of Engineers tamed the river. The Corps eliminated 89% of the islands in the Missouri River between 1879 and 1954 (Funk and Robinson 1974). The chutes between the islands and the shore were shallower with less current than the main channel. These areas provided diversity to the Missouri River fish habitat, serving as nursery and feeding areas. The Lisbon Bottom Unit of the Big Muddy National Fish and Wildlife Refuge will continue to be studied in an effort to understand the complex role these areas play in river systems.

Missouri↗
USGS2019

Managing effects of drought and other water resource challenges in Alaska and the Pacific Northwest

This is a Cooperator Report. As such, there is no specific abstract. The physical, ecological, and social environments of Alaska and the Pacific Northwest (PNW) region of the United States are extremely diverse. Alaska ranges from the Arctic Ocean and the very cold, dry environments of the North Slope to the cool and very rainy coastal North Pacific region of Southeast Alaska. Most precipitation falls as snow at higher elevations. In Arctic Alaska, average annual temperature is 14.6 F, and average annual precipitation is 11 inches. By contrast, in Southeast Alaska, average annual temperature is 35.8 F, and annual average precipitation is 143 inches. The PNW, defined here as Idaho, Oregon, and Washington, ranges from the Pacific Coast (annual precipitation of 200 inches) to interior semi-arid regions (annual precipitation of 8 inches). Precipitation patterns in the PNW are strongly governed by orographic phenomena, with high, persistent snowpack in the higher mountains (e.g., record annual snowfall of 1,130 in at Mount Baker, Washington in 1999-2000). Ecosystems in the PNW include productive temperate coniferous forests near the Pacific coast and along the (wet) west slope of the Cascade Range, less productive mixed-conifer forest along the (dry) east slope of the Cascades and in interior mountain ranges, and sagebrush-steppe and shrublands at lower elevations in much of the interior and mountain valleys. Large rivers and thousands of smaller tributaries form an extensive network of riparian, wetland, and estuarine systems that provide both critical hydrologic function and biological diversity at broad and fine spatial scales. Although Alaska and the Pacific Northwest differ in important physical, ecological, and social features, the importance of natural resources is evident in both regions. Water is important for wildlife and people. Water provides critical habitat for salmon, which are culturally and economically valuable species. Timber production has declined in recent decades. Recreation has emerged as a major revenue source.

Alaska, Oregon, Washington↗
USGS2014

Spring migration ecology of the mid-continent sandhill crane population with an emphasis on use of the Central Platte River Valley, Nebraska

We conducted a 10-year study (1998–2007) of the Mid-Continent Population (MCP) of sandhill cranes (Grus canadensis) to identify spring-migration corridors, locations of major stopovers, and migration chronology by crane breeding affiliation (western Alaska–Siberia [WA–S], northern Canada–Nunavut [NC–N], west-central Canada–Alaska [WC–A], and east-central Canada–Minnesota [EC–M]). In the Central Platte River Valley (CPRV) of Nebraska, we evaluated factors influencing staging chronology, food habits, fat storage, and habitat use of sandhill cranes. We compared our findings to results from the Platte River Ecology Study conducted during 1978–1980. We determined spring migration corridors used by the breeding affiliations (designated subpopulations for management purposes) by monitoring 169 cranes marked with platform transmitter terminals (PTTs). We also marked and monitored 456 cranes in the CPRV with very high frequency (VHF) transmitters to evaluate length and pattern of stay, habitat use, and movements. An estimated 42% and 58% of cranes staging in the CPRV were greater sandhill cranes (G. c. tabida) and lesser sandhill cranes (G. c. canadensis), and they stayed for an average of 20 and 25 days (2000–2007), respectively. Cranes from the WA–S, NC–N, WC–A, and EC–M affiliations spent an average of 72, 77, 52, and 53 days, respectively, in spring migration of which 28, 23, 24, and 18 days occurred in the CPRV. The majority of the WA–S subpopulation settled in the CPRV apparently because of inadequate habitat to support more birds upstream, although WA–S cranes accounted for >90% of birds staging in the North Platte River Valley. Crane staging duration in the CPRV was negatively correlated with arrival dates; 92% of cranes stayed >7 days. A program of annual mechanical removal of mature stands of woody growth and seedlings that began in the early 1980s primarily in the main channel of the Platte River has allowed distribution of crane roosts to remain relatively stable over the past 2 decades. Most cranes returned to nocturnal roost sites used in previous years. Corn residues dominated the diet of sandhill cranes in the CPRV, as in the 1970s, despite a marked decline in standing crop of corn residues. Only 14% (10 of 74) of PTT-marked migrant cranes stayed at stopovers for ≥5 days before arriving in the CPRV, which limited the contribution of sites south of the CPRV for fat accumulation needed for migration and reproduction. Body masses of cranes (after adjusting for body size [an index of fat]) at arrival in the CPRV varied widely among years (1998–2006), indicating the importance of maintaining productive habitats on the wintering grounds to condition cranes for migration and reproduction. Average rates of fat gain by adult females while in the CPRV remained similar from 1978–1979 to 1998–1999 but declined among males. Distances cranes flew to feeding grounds in the CPRV increased as the percentage of cropland planted to soybeans increased and as density of cranes on nocturnal roosts increased. These results suggest that as habitats of limited or no value to cranes increase on the landscape, more flight time and higher maintenance costs may reduce fat storage. An estimated 40% of diurnal use occurred north of Interstate 80 (I-80) where ≤5% of lands dedicated to crane conservation are located. Seventy-four and 40% of PTT-marked EC–M and WC–A cranes had spring migrations that included staging in eastern South Dakota for an average of 11 and 10 days, respectively. Cranes of the NC–N, WA–S, and WC–A subpopulations staged an average of 25, 17, and 12 days in central and western Saskatchewan/eastern Alberta. Females in these affiliations increased their fat reserves after leaving Nebraska by an estimated 450, 451, and 452 g, respectively, underscoring the key role of these staging areas in preparing the 3 subpopulations for reproduction. After departing Nebraska, MCP cranes roosted primarily in basin wetlands. Most of these wetlands are in private ownership and lack adequate protection, emphasizing the need for effective laws and policies to ensure their long-term protection. The continued success of the current management goal of maintaining the MCP at approximately its current size and providing diverse recreational opportunities over a wide area of midcontinent and western North America is predicated on the ability of MCP cranes to continue to store large fat reserves in the CPRV in advance of breeding. For the CPRV to remain a key fat storage site, active channel maintenance (e.g., clearing of woody vegetation) likely will need to continue, along with establishing minimum stream flows. These actions would help ensure nocturnal roosting habitat remains sufficiently dispersed to provide cranes with daily intake of high-energy food adequate for major fat storage and limit risk of high mortality from storms and disease. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Nebraska↗
USGS2012

A brief history and summary of the effects of river engineering and dams on the Mississippi River system and delta

The U.S. Geological Survey Forecast Mekong project is providing technical assistance and information to aid management decisions and build science capacity of institutions in the Mekong River Basin. A component of this effort is to produce a synthesis of the effects of dams and other engineering structures on large-river hydrology, sediment transport, geomorphology, ecology, water quality, and deltaic systems. The Mississippi River Basin (MRB) of the United States was used as the backdrop and context for this synthesis because it is a continental scale river system with a total annual water discharge proportional to the Mekong River, has been highly engineered over the past two centuries, and the effects of engineering have been widely studied and documented by scientists and engineers. The MRB is controlled and regulated by dams and river-engineering structures. These modifications have resulted in multiple benefits including navigation, flood control, hydropower, bank stabilization, and recreation. Dams and other river-engineering structures in the MRB have afforded the United States substantial socioeconomic benefits; however, these benefits also have transformed the hydrologic, sediment transport, geomorphic, water-quality, and ecologic characteristics of the river and its delta. Large dams on the middle Missouri River have substantially reduced the magnitude of peak floods, increased base discharges, and reduced the overall variability of intraannual discharges. The extensive system of levees and wing dikes throughout the MRB, although providing protection from intermediate magnitude floods, have reduced overall channel capacity and increased flood stage by up to 4 meters for higher magnitude floods. Prior to major river engineering, the estimated average annual sediment yield of the Mississippi River Basin was approximately 400 million metric tons. The construction of large main-channel reservoirs on the Missouri and Arkansas Rivers, sedimentation in dike fields, and protection of channel banks by revetments throughout the basin, have reduced the overall sediment yield of the MRB by more than 60 percent. The primary alterations to channel morphology by dams and other engineering projects have been (1) channel simplification and reduced dynamism; (2) lowering of channel-bed elevation; and (3) disconnection of the river channel from the flood plain, except during extreme flood events. Freshwater discharge from the Mississippi River and its associated sediment and nutrient loads strongly influence the physical and biological components in the northern Gulf of Mexico. Ninety percent of the nitrogen load reaching the Gulf of Mexico is from nonpoint sources with about 60 percent coming from fertilizer and mineralized soil nitrogen. Much of the phosphorus is from animal manure from pasture and rangelands followed by fertilizer applied to corn and soybeans. Increased nutrient enrichment in the northern Gulf of Mexico has resulted in the degradation of water quality as more phytoplankton grow, which increases turbidity and depletes oxygen in the lower depths creating what is known as the "dead zone." In 2002, the dead zone was 22,000 square kilometers (km2), an area similar to the size of the State of Massachusetts. Changes in the flow regime from engineered structures have had direct and indirect effects on the fish communities. The navigation pools in the upper Mississippi River have aged, and these overwintering habitats, which were created when the pools filled, have declined as sedimentation reduces water depth. Reproduction of paddlefish may have been adversely affected by dams, which impede access to suitable spawning habitats. Fishes that inhabit swift-current habitats in the unimpounded lower Mississippi River have not declined as much as in the upper Mississippi River. The decline of the pallid sturgeon may be attributable to channelization of the Missouri River above St. Louis, Missouri. The Missouri River supports a rich fish community and remains relatively intact. Nevertheless, the widespread and long history of human intervention in river discharge has contributed to the declines of about 25 percent of the species. The Mississippi River Delta Plain is built from six delta complexes composed of a massive area of coastal wetlands that support the largest commercial fishery in the conterminous United States. Since the early 20th century, approximately 4,900 km2 of coastal lands have been lost in Louisiana. One of the primary mechanisms of wetland loss on the Plaquemines-Balize complex is believed to be the disconnection of the river distributary network from the delta plain by the massive system of levees on the delta top, which prevent overbank flooding and replenishment of the delta top by sediment and nutrient deliveries. Efforts by Federal and State agencies to conserve and restore the Mississippi River Delta Plain began over three decades ago and have accelerated over the past decade. Regardless of these efforts, however, land losses are expected to continue because the reduced upstream sediment supplies are not sufficient to keep up with the projected depositional space being created by the combined forces of delta plain subsidence and global sea-level rise.

Alabama;Alberta;Arkansas;Colorado;Georgia;Illinois↗
USGS2013

Mobile Bay

Mobile Bay is the largest bay found in Alabama’s coastal area (Handley et al., 2007). It was named an Estuary of National Significance in 1995 under the U.S. Environmental Protection Agency’s (EPA) National Estuary Program (NEP), and its Comprehensive Conservation Management Plan was completed in 2002. Mobile Bay is 1,070 km 2 (413 miles 2 ) in area and 51 km (32 miles) long, making it the sixth largest estuary in the continental United States (Mobile Bay NEP, 2008). Its ecosystem provides habitat for more than 300 species of birds, 310 species of fish, 68 species of reptiles, 57 species of mammals, 40 species of amphibians, and 15 species of shrimp (Mobile Bay NEP, 1997). Mobile Bay lies between the Mississippi and Atlantic Flyways (Mobile Bay NEP, 2003). Commercial and residential development and industrial use is heavy in the Mobile Bay area. Although local growth and industrial markets support the Mobile Bay area economy, the resulting environmental damage to the very ecosystem upon which they depend remains a threat to the environment, economy, and population. The Mobile Bay ecosystem boasts high biological diversity and productivity and supports many freshwater and saltwater species of recreational and commercial importance. The great diversity of Mobile Bay reflects the diversity of Alabama, which is home to the largest number of different plant and animal species of all states east of the Mississippi River (Stein, 2002), and is bolstered by the unique climate and geographic conditions surrounding the bay. Freshwater inflow from the Mobile-Tensaw River Delta, ranging from 60,000 to 3,700,000 gallons per second (Wallace, 1996), mixes with saltwater from the Gulf of Mexico, which enters Mobile Bay via wind and tides (Burgan and Engle, 2006). Because of the unique conditions surrounding Mobile Bay, including shallow waters, a dynamic climate, and artificial hydrologic modifications—such as the construction of the Mobile Bay Causeway in the 1920s, which serves as an unintentional barrier between Delta waters north of the Causeway and saline waters south of the Causeway, the salinity of Mobile Bay is highly variable. Mobile Bay receives an average of 165 cm (65 inches) of rain per year from tropical storms, summer thunderstorms, and winter cold fronts (Stout et al., 1998). The climate and geography that have made Mobile Bay so rich in resources have also contributed to the threats surrounding its ecosystem. The extensive amount of rain in Mobile Bay creates large amounts of runoff, polluting the waters with fertilizers, chemicals, sediment, oil, trash, and sewage (Mobile Bay NEP, 1997). Tourism, ecotourism, recreational and commercial fishing, recreational boating, shipping, and chemical, pulp, and paper production are significant industries in Mobile Bay and the surrounding areas. Despite the approximate \$3 billion and 55,000 jobs these industries bring into the community (Alabama Tourism Department, 2010), the growth, development, and environmental stress they create are major threats to the Mobile Bay ecosystem. Among the nation’s states, Alabama ranks fifth in number of different species (144 endemic species), second in number of extinctions that have already occurred (90 extinct species) and fourth in number of species at risk for extinction (14.8% at risk out of 4,533 total species; Stein, 2002). Twenty-one of these threatened and endangered species are found in Mobile Bay, whose brackish waters provide a nursery area for many species of vertebrates and invertebrates. Some of these species include the Alabama sturgeon, Gulf sturgeon, heavy pigtoe mussel, inflated heel-splitter mussel, West Indian manatee, Alabama beach mouse, Perdido beach mouse, Alabama red-bellied turtle, gopher tortoise, Kemp’s ridley sea turtle, green sea turtle, loggerhead sea turtle, eastern indigo snake, flatwoods salamander, piping plover, red-cockaded woodpecker, and wood stork. Habitat loss underlies the decline of some bird species in Mobile Bay, and large mammals such as the red wolf, Florida panther, and Florida black bear are no longer found in the area. However, some rare species, such as the swallow-tailed kite, sandhill crane, and gopher tortoise can still be found (Duke and Kruczynski, 1992). The value of wetlands in Mobile Bay and the rest of the Gulf of Mexico is still being investigated. Although various monetary valuations of wetlands exist, critics remark that undervaluation of wetlands is inevitable (Mobile Bay NEP, 2008) and that estimates often do not place appropriate value on ecological services (Mitsch and Gosselink, 2000). Additionally, many estimates account only for anthropogenic values. One estimate concludes that one acre of wetlands performs \$3,000 worth of water purification each year (Mobile Bay NEP, 1997). With more than 76,890 hectares (190,000 acres) of wetlands in the Mobile Bay area, that equates to a value exceeding one-half billion dollars every year. Tourism, fishing, boating, production, and shipping are significant industries in the Mobile Bay area. More than 90% of fish landed in recreational and commercial fishing in the bay depend on bay habitat, including wetlands, for life requirements (Mobile Bay NEP, 1997). The Port of Mobile is Alabama’s only ocean-ship port (Mobile Bay NEP, 2008). Baldwin County, on the eastern side of the bay, experienced a population increase of 75% from 1990 to 2007, with an 89% increase in housing units (Mobile Bay NEP, 2008). Development and industry support the Mobile Bay economy, but they depend on the continued health, sustainability, and production of the water and living resources of the Mobile Bay ecosystem. Wetland loss, along with other forms of environmental degradation, remains a threat to the Mobile Bay ecosystem and Mobile Bay’s socioeconomic foundation.

Alabama↗
USGS2012

Simulation of groundwater flow and hydrologic effects of groundwater withdrawals from the Kirkwood-Cohansey aquifer system in the Pinelands of southern New Jersey

The Kirkwood-Cohansey aquifer system is an important source of present and future water supply in southern New Jersey. Because this unconfined aquifer system also supports sensitive wetland and aquatic habitats within the New Jersey Pinelands (Pinelands), water managers and policy makers need up-to-date information, data, and projections that show the effects of potential increases in groundwater withdrawals on these habitats. Finite-difference groundwater flow models (MODFLOW) were constructed for three drainage basins (McDonalds Branch Basin, 14.3 square kilometers (km 2 ); Morses Mill Stream Basin, 21.63 km 2 ; and Albertson Brook Basin, 52.27 km 2 ) to estimate the effects of potential increases in groundwater withdrawals on water levels and the base-flow portion of streamflow, in wetland and aquatic habitats. Three models were constructed for each drainage basin: a transient model consisting of twenty-four 1-month stress periods (October 2004 through September 2006); a transient model to simulate the 5- to 10-day aquifer tests that were performed as part of the study; and a high-resolution, steady-state model used to assess long-term effects of increased groundwater withdrawals on water levels in wetlands and on base flow. All models were constructed with the same eight-layer structure. The smallest horizontal cell dimensions among the three model areas were 150 meters (m) for the 24-month transient models, 10 m for the steady-state models, and 3 m for the transient aquifer-test models. Boundary flows of particular interest to this study and represented separately are those for wetlands, streams, and evapotranspiration. The final variables calibrated from both transient models were then used in steady-state models to assess the long-term effects of increased groundwater withdrawals on water levels in wetlands and on base flow. Results of aquifer tests conducted in the three study areas illustrate the effects of withdrawals on water levels in wetlands and on base flow. Pumping stresses at aquifer-test sites resulted in measurable drawdown in each observation well installed for the tests. The magnitude of drawdown in shallow wetland observation wells at the end of pumping ranged from 5.5 to 16.7 centimeters (cm). The stresses induced by the respective tests reduced the flow of the smallest stream (McDonalds Branch) by 75 percent and slightly reduced flow in a side channel of Morses Mill Stream, but did not measurably affect the flow of Morses Mill Stream or Albertson Brook. Results of aquifer-test simulations were used to refine the estimates of hydraulic properties used in the models and to confirm the ability of the model to replicate observed hydrologic responses to pumping. Steady-state sensitivity simulation results for a variety of single well locations and depths were used to define overall “best-case” (smallest effect on wetland water levels and base flow) and “worst-case” (greatest effect on wetland water levels and base flow) groundwater withdrawal configurations. “Best-case” configurations are those for which the extent of the wetland areas within a 1-kilometer (km) radius of the withdrawal well is minimized, the well is located at least 100 m and as far from wetland boundaries as possible, and the withdrawal is from a deep well (50–90 m deep). “Worst-case” configurations are those for which the extent of wetlands within a 1-km radius of the withdrawal well is maximized, the well is located 100 m or less from a wetland boundary, and the withdrawal is from a relatively shallow well (30–67 m deep). “Best-” and “worst-case” simulations were applied by locating hypothetical wells across the study areas and assigning groundwater withdrawals so that the sum of the withdrawals for the basin is equal to 5, 10, 15, and 30 percent of overall recharge. The results were compared to the results of simulations of no groundwater withdrawals. Results for withdrawals of 5 percent of recharge show that the area of wetland water-level decline that exceeded 15 cm was as much as 1.5 percent of the total wetland area for the “best-case” simulations and as much as 9.7 percent of the total wetland area for the “worst-case” simulations. For the same withdrawals, base-flow reduction was as much as 5.1 percent for the “best-case” simulations and as much as 8.6 percent for the “worst-case” simulations. Results for withdrawals of 30 percent of recharge show that the area of wetland water-level decline that exceeded 15 cm was as much as 70 percent of the total wetland area for the “best-case” simulations and as much as 84 percent of the total wetland area for the “worst-case” simulations. For the same withdrawals, base-flow reduction was as much as 30 percent for the “best-case” simulations and as much as 51 percent for the “worst-case” simulations. Results for withdrawals of 10 and 15 percent of recharge show decreased water levels and base flow that are intermediate between those simulated for 5 and 30 percent of recharge. Several approaches for applying the results of this study to other parts of the Pinelands were explored. An analytical-modeling technique based on the Thiem equation and image-well theory was developed to estimate local drawdown distributions resulting from withdrawals in other areas within the Pinelands. Results of example applications of this technique were compared with those of the numerical simulations used in this study and were shown to be useful. Differences among the three basins in the simulated percentage of basin wetlands affected by drawdown were found to be related to the proximity of wetlands to streams, the proximity of wetlands to pumped wells, and the vertical conductance of the aquifer system. These factors formed the basis for an index of wetland vulnerability to drawdown. An empirically-derived model based on the Gompertz function and the wetland vulnerability index was developed, tested, and shown to be an effective means to evaluate potential drawdown in wetlands at a basin scale throughout the Pinelands. Base-flow reduction can be estimated from generalized results of the numerical models, estimates of evapotranspiration reduction, or available regional groundwater flow models. These approaches could be used to evaluate alternative water-supply strategies and, in conjunction with ecological-modeling results, to determine maximum basin withdrawal rates within the limits of acceptable ecological change.

New Jersey↗