Geology Reports⌕ Search

SEARCH · Geology Reports

Results for “Aquatic Biology”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42Linked to original sources

Some effects of pollutants in terrestrial ecosystems

Summary: Pollutants tend to simplify plant and animal communities by causing a progressive loss of species. At the extreme, this leads to erosion and loss of soil fertility. Weedy, broadly adapted species increase. Among animals, carnivorous species and groups are often the first to suffer. This is partly because of their exposure at the top of the food chain, and partly, it appears, because of physiological differences. Species differences in susceptibility are abundant and are often critical. One result is that when one pest is controlled another is likely to flare up. Resistance appears commonly in insects and is known in other fast-breeding forms, including fishes, frogs, and rodents. Resistant individuals can carry toxicant loads that make them dangerous food for other animals. Some groups, including mollusks and annelids, are naturally resistant to many organohalogens and tend to accumulate them. Animals such as birds may carry lipophilic pollutants in large amounts with apparent safety until forced to draw upon their fat. They may then suffer delayed mortality, and no doubt suffer reproductive or behavioral effects at sublethal levels. Lipophilic pollutants in the brain rise when body lipids decrease and fall when body lipids increase. Mutagenesis can be caused by some common pollutants and the mutagenic properties of most chemicals are far too little known. Fortunately, common pesticides are not likely to be strong mutagens. Mutagenicity may be affecting certain long-lived and slow-breeding species in the wild, but most species have enough population turnover to swamp an occasional mutagenic event. Behavioral changes can be caused by relatively low levels of contaminants, but it is often hard to demonstrate them without using high dosages. Reproduction may or may not be affected adversely by low exposures. At certain exposures that are below the toxic levels of a chemical, a biostimulatory effect is to be expected. Food chain accumulations definitely do occur when persistent chemicals enter organisms that eliminate them poorly. However, loss of chemicals in the food chain must be more common than accumulation. The great concentration from water to aquatic organism is chiefly a physical phenomenon, not a food chain effect, but it affords high starting levels for these chains. Terrestrial food chains often start at a high level with heavily contaminated, struggling prey. Litter feeders are another important base. Vegetation may be contaminated enough to be dangerous to animals that eat it. Dermal and respiratory routes of intoxication occur in the wild, but the oral route is far more important at most times and places. The organisms that govern soil fertility and texture are affected more by cultivation than by pesticides. Above ground, growing knowledge of resistance, species differences, and biological controls is leading to integrated control, in which use of chemicals is limited and specific. We do not know what is happening to most nontarget invertebrates. Amphibians and reptiles may be killed by applications of insecticides, but are not highly sensitive and can carry large residues. Effects of these residues on reproduction are little known. Heavy kills of birds by pesticides still occur in the field. Fish-eating and bird-eating birds also undergo shell thinning and related reproductive troubles in many areas, sometimes to the point of population decline and local or regional extermination. DDE most often correlates with shell thinning in the wild and in experiments. No other known chemical approaches DDE in causing severe and lasting shell thinning. Herbivorous birds seem to be largely immune to this effect. It is uncertain how much dieldrin and PCBs contribute to embryotoxicity in carnivorous birds. Mammals may be killed by the more toxic pesticides, but some of the commonest small rodents are so resistant, and lose their residues so rapidly, that they are of little

Book chapter↗

Gaining decision-maker confidence through community consensus: Developing environmental DNA standards for data display on the USGS Nonindigenous Aquatic Species database

To advance national efforts for the detection and biosurveillance of aquatic invasive species (AIS), we employed a community consensus process to enable the incorporation of environmental DNA (eDNA) detection data into the U.S. Geological Survey’s (USGS) Nonindigenous Aquatic Species (NAS) database (https://nas.er.usgs.gov/eDNA/). Our goal was to identify minimum standards and best practices for the verification of eDNA data by working closely with AIS eDNA community practitioners and natural resource managers across government, private and academic sectors. To better inform management decisions, verified AIS eDNA data will be displayed on a separate mapping layer alongside visual sighting data with the inclusion of additional information on the eDNA methods employed to collect and produce the data. To allow for eDNA data display, we produced consensus derived online documents including a submission application and data submission template and are developing a guidance document for detailing the eDNA data submission process. We also developed a communication plan including a mechanism for reporting detections to appropriate managers for consideration prior to display. The products of these efforts are an application and data submission process that will be used in the new environmental DNA data layer on the Nonindigenous Aquatic Species (NAS) database. Herein, we detail how we engaged the eDNA community for consensus of our standards, share lessons learned from the process, and describe the benefits of such an approach at instilling confidence among the research and decision-maker community.

Management of Biological Invasions↗

Characterization of habitat and biological communities at fixed sites in the Great Salt Lake basins, Utah, Idaho, and Wyoming, water years 1999-2001

Habitat and biological communities were sampled at 10 sites in the Great Salt Lake Basins as part of the U.S. Geological Survey National Water-Quality Assessment program to assess the occurrence and distribution of biological organisms in relation to environmental conditions. Sites were distributed among the Bear River, Weber River, and Utah Lake/Jordan River basins and were selected to represent stream conditions in different land-use settings that are prominent within the basins, including agriculture, rangeland, urban, and forested. High-gradient streams had more diverse habitat conditions with larger substrates and more dynamic flow characteristics and were typically lower in discharge than low-gradient streams, which had a higher degree of siltation and lacked variability in geomorphic channel characteristics, which may account for differences in habitat. Habitat scores were higher at high-gradient sites with high percentages of forested land use within their basins. Sources and causes of stream habitat impairment included effects from channel modifications, siltation, and riparian land use. Effects of hydrologic modifications were evident at many sites. Algal sites where colder temperatures, less nutrient enrichment, and forest and rangeland uses dominated the basins contained communities that were more sensitive to organic pollution, siltation, dissolved oxygen, and salinity than sites that were warmer, had higher degrees of nutrient enrichment, and were affected by agriculture and urban land uses. Sites that had high inputs of solar radiation and generally were associated with agricultural land use supported the greatest number of algal species. Invertebrate samples collected from sites where riffles were the richest-targeted habitat differed in species composition and pollution tolerance from those collected at sites that did not have riffle habitat (nonriffle sites), where samples were collected in depositional areas, woody snags, or macrophyte beds. Invertebrate taxa richness, pollution tolerance, and trophic interactions at riffle and nonriffle sites responded differently to environmental variables. Fish communities were assessed in relation to the designated beneficial use for aquatic life for each site. Fish-community sites in basins where agriculture and urbanization were prevalent consistently had poorer conditions than sites with forest and rangeland uses. Warm temperatures appear to be limiting most native fish species, and more introduced, warm-water fish species were present at sites with warmer temperatures. Ranges of environmental conditions where native species were present or absent were identified. The farthest-upstream site in each of the three basins had better ecological condition overall, as indicated by the integrity of habitat and the presence of more sensitive algae, invertebrate, and fish species than were observed at sites downstream. The farthest-downstream site in each of the three basins showed the poorest ecological condition, with more tolerant organisms present, degraded habitat and water-quality conditions, and a high degree of effects from agriculture, grazing, and urbanization. Of the mid-basin sites, the site most affected by urbanization had more degraded biological condition than the agricultural indicator site of similar basin size.

Idaho, Utah, Wyoming↗

An ecological response model for the Cache la Poudre River through Fort Collins

The Poudre River Ecological Response Model (ERM) is a collaborative effort initiated by the City of Fort Collins and a team of nine river scientists to provide the City with a tool to improve its understanding of the past, present, and likely future conditions of the Cache la Poudre River ecosystem. The overall ecosystem condition is described through the measurement of key ecological indicators such as shape and character of the stream channel and banks, streamside plant communities and floodplain wetlands, aquatic vegetation and insects, and fishes, both coolwater trout and warmwater native species. The 13- mile-long study area of the Poudre River flows through Fort Collins, Colorado, and is located in an ecological transition zone between the upstream, cold-water, steep-gradient system in the Front Range of the Southern Rocky Mountains and the downstream, warm-water, low-gradient reach in the Colorado high plains. The City wanted to better understand the ecological response of the Poudre River ecosystem to potential changes in stream flow and other physical parameters through the conceptual framework of a multivariable integrated model. This goal was met through the use of a probabilistic model based on Bayesian concepts. This construct allowed the integration of a wide range of data and expert opinion (as informed by local data) to predict potential changes to ecosystem conditions under various flow scenarios. Nine flow scenarios representing past, present, and possible future hydrology were developed as the primary model input. Both reach-scale drivers such as stream channel conditions and pollutant loads, as well as ecological conditions, including species composition, interactions, and habitat requirements influenced model-predicted ecosystem outcomes. Model output consisted of probability distributions for eight ecological indicators collectively representing the physical setting, aquatic life, and riparian habitats of the river ecosystem. We are confident in model predictions related to probable trends, relative magnitude of changes and potential ecosystem responses to changing flow conditions, though data availability and the process of converting diverse data types into a common unit (probabilities) limit precision of individual results. Key findings suggest that: The present ecological function of the Poudre River is altered as a result of more than 150 years of human influences that include highly managed flows, urbanization, gravel mining, channelization and urban and industrial encroachment in the floodplain, underscoring the vulnerable and complex character of the Poudre River; A continuation of today’s flow management will lead to ongoing changes in ecosystem condition, and additional water depletions will compromise ecological conditions; High flows play an essential role in maintaining and improving the aquatic and riparian condition of the river; Adequate flows in base-flow periods are critical to desirable water quality, and thriving fish and insect populations; Improvement of native aquatic life is possible if issues related to channel modifications, siltation, invasive species, and base and high flow conditions are managed properly; The present confined river channel and modified flows has reduced the potential for a keystone and iconic species, plains cottonwood, to be self-sustaining in the study area; The streamside corridor retains the potential to support a functioning riparian forest that provides important ecological services if periodic floodplain inundation occurs. Environmental flows that combine stable and adequate flows in base-flow periods with occasional rejuvenating high flows that meet target levels defined in this study are likely improve all biological indicators across the system. ERM test scenarios that include both stable base flows and rejuvenating high flows indicate that substantial improvements in the river ecosystem can be achieved with improved management of flow volumes similar to those observed in the river during the last half century of intensive water development. These results underscore the possibility of improving the river ecosystem through active management while still maintaining the Poudre’s diverse economic benefits and role as a working river. The ERM was designed to represent the multi-dimensional ecological character of the contemporary urban Poudre River. It provides a scientific foundation that can serve as a decision support tool and foster a more informed community discussion about the future of the river as it provides a better understanding of the likely response of the Poudre River ecosystem to environmental flow management and other stewardship activities. In particular, model results can assist managers in developing specific management actions to achieve desirable goals for key indicators of river health.

Colorado↗

Recent range expansion and documentation of a reproductive population of northern snakehead Channa argus (Cantor, 1842) in the Saint Francis River Drainage, Missouri

Northern snakehead Channa argus (Cantor, 1842) is an aquatic invasive fish species in the United States with first documented occurrence in the wild in the 2000s. Management efforts to control their populations in the eastern United States are ongoing. In the Mississippi River basin, limited resources have been allocated to control its distribution, after initial detection and rapid response in Arkansas were unsuccessful. Northern snakehead distribution in the Mississippi River basin was limited to Arkansas and Mississippi until 2019 when a single northern snakehead was detected on the southern border of Missouri in the Saint Francis River drainage, the furthest northern detection. Described here are additional northern snakehead detections following public reports and subsequent monitoring in the Mingo basin of the Saint Francis River drainage, a historical braided channel and floodplain habitat of the Mississippi River with intermittently flooded bottomland hardwood forests and wetlands, and other consistent aquatic habitats. These increasing captures document the recent range expansion of northern snakehead. Most of the 11,300 ha Mingo basin consists of Mingo National Wildlife Refuge and Duck Creek Conservation Area; these areas are protected aquatic ecosystems possessing sensitive species and serve as a potential example of prioritized areas for northern snakehead control efforts. Additionally, we highlight the significance of these detections in the Mingo basin which is connected via the Castor River water-control structure to the Upper Mississippi River and may facilitate further range expansion.

Missouri↗

Smaller body size under warming is not due to gill-oxygen limitation in a coldwater salmonid

Declining body size in fishes and other aquatic ectotherms associated with anthropogenic climate warming has significant implications for future fisheries yields, stock assessments and aquatic ecosystem stability. One proposed mechanism seeking to explain such body-size reductions, known as the gill oxygen limitation (GOL) hypothesis, has recently been used to model future impacts of climate warming on fisheries but has not been robustly empirically tested. We used brook trout ( Salvelinus fontinalis ), a fast-growing, cold-water salmonid species of broad economic, conservation and ecological value, to examine the GOL hypothesis in a long-term experiment quantifying effects of temperature on growth, resting metabolic rate (RMR), maximum metabolic rate (MMR) and gill surface area (GSA). Despite significantly reduced growth and body size at an elevated temperature, allometric slopes of GSA were not significantly different than 1.0 and were above those for RMR and MMR at both temperature treatments (15°C and 20°C), contrary to GOL expectations. We also found that the effect of temperature on RMR was time-dependent, contradicting the prediction that heightened temperatures increase metabolic rates and reinforcing the importance of longer-term exposures (e.g. >6 months) to fully understand the influence of acclimation on temperature–metabolic rate relationships. Our results indicate that although oxygen limitation may be important in some aspects of temperature–body size relationships and constraints on metabolic supply may contribute to reduced growth in some cases, it is unlikely that GOL is a universal mechanism explaining temperature–body size relationships in aquatic ectotherms. We suggest future research focus on alternative mechanisms underlying temperature–body size relationships, and that projections of climate change impacts on fisheries yields using models based on GOL assumptions be interpreted with caution.

Journal of Experimental Biology↗

Archive of bathymetry data collected in South Florida from 1995 to 2015

Description Land development and alterations of the ecosystem in south Florida over the past 100 years have decreased freshwater and increased nutrient flows into many of Florida's estuaries, bays, and coastal regions. As a result, there has been a decrease in the water quality in many of these critical habitats, often prompting seagrass die-offs and reduced fish and aquatic life populations. Restoration of water quality in many of these habitats will depend partly upon using numerical-circulation and sediment-transport models to establish water-quality targets and to assess progress toward reaching restoration targets. Application of these models is often complicated because of complex sea floor topography and tidal flow regimes. Consequently, accurate and modern sea-floor or bathymetry maps are critical for numerical modeling research. Modern bathymetry data sets will also permit a comparison to historical data in order to help assess sea-floor changes within these critical habitats. New and detailed data sets also support marine biology studies to help understand migratory and feeding habitats of marine life. This data series is a compilation of 13 mapping projects conducted in south Florida between 1995 and 2015 and archives more than 45 million bathymetric soundings. Data were collected primarily with a single beam sound navigation and ranging (sonar) system called SANDS developed by the U.S. Geological Survey (USGS) in 1993. Bathymetry data for the Estero Bay project were supplemented with the National Aeronautics and Space Administration's (NASA) Experimental Advanced Airborne Research Lidar (EAARL) system. Data from eight rivers in southwest Florida were collected with an interferometric swath bathymetry system. The projects represented in this data series were funded by the USGS Coastal and Marine Geology Program (CMGP), the USGS South Florida Ecosystem Restoration Project- formally named Placed Based Studies, and other non-Federal agencies. The purpose of the data collection for all these projects was to support one or more of the following scientific aspects: numerical model applications, sea floor change analysis, or marine habitat investigations. This report serves as an archive of processed bathymetry sounding data, digital bathymetric contours, digital bathymetric maps, sea floor surface grids, and formal Federal Geographic Data Committee (FGDC) metadata. Refer to the Abbreviations page for explanations of acronyms and abbreviations used in this report. Since 2006, the USGS St. Petersburg Coastal and Marine Science Center (SPCMSC) assigns a unique identifier or Field Activity Number (FAN) for each field data collection. Projects described in this report conducted prior to 2006 do not have a FAN. Data from the 13 projects presented in this report provided critical hydrographic information to support multiple science projects in south Florida. The projects and the types of sounding data collected are: Florida Bay (1995-1999) - single-beam Lake Okeechobee (2001) - single-beam Tampa Bay (2001-2004) - single-beam Caloosahatchee River (2002)- single-beam Estero Bay to Matlacha Pass and offshore to Wiggins Pass (2003) - single-beam and airborne lidar North and Northwest Forks of the Loxahatchee and Lower St. Lucie Rivers (2003) - single-beam South Charlotte Harbor and offshore Sanibel Island (2003-2004) - single-beam Shark River and Trout Creek (2004) - single-beam and interferometric swath Southwest Florida Rivers (2004) - interferometric swath Offshore from Wiggins Pass to Cape Romano (2005) - single-beam Ten Thousand Islands (2009) - single-beam Lemon Bay (2011) - single-beam Southwest Florida Rivers (2015) - interferometric swath

Florida↗

Thresholds of lake and reservoir connectivity in river networks control nitrogen removal

Lakes, reservoirs, and other ponded waters are ubiquitous features of the aquatic landscape, yet their cumulative role in nitrogen removal in large river basins is often unclear. Here we use predictive modeling, together with comprehensive river water quality, land use, and hydrography datasets, to examine and explain the influences of more than 18,000 ponded waters on nitrogen removal through river networks of the Northeastern United States. Thresholds in pond density where ponded waters become important features to regional nitrogen removal are identified and shown to vary according to a ponded waters’ relative size, network position, and degree of connectivity to the river network, which suggests worldwide importance of these new metrics. Consideration of the interacting physical and biological factors, along with thresholds in connectivity, reveal where, why, and how much ponded waters function differently than streams in removing nitrogen, what regional water quality outcomes may result, and in what capacity management strategies could most effectively achieve desired nitrogen loading reduction.

Connecticut, Delaware, District of Columbia, Maine↗

Forestry practices and aquatic biodiversity: Fish

In the Pacific Northwest, fish communities are found in a diverse array of aquatic habitats ranging from the large coastal rivers of the temperate rainforests, to the fragmented and sometimes ephemeral streams of the xeric interior basins, and high-elevation streams and lakes in the mountainous areas (Rieman et al. 2003). Only high-elevation lakes and streams isolated above barriers to fish passage remained historically devoid of fish because they were never invaded following Pleistocene glaciation (Smith 1981). Despite this widespread distribution and once great population abundances, taxonomic diversity of fishes in these forested systems is naturally lower than in aquatic habitats in the eastern U.S. (Reeves, Bisson, and Dambacher 1998). Interactions among factors that influence species richness in aquatic systems (e.g., basin size, long-term stability of habitat, and barriers to colonization; Smith 1981) continue to influence the occurrence and persistence of fishes in these systems today. Consequently, the larger low-elevation rivers and estuaries support the greatest variety of fish species. In the high-elevation tributary streams, fish communities are less complex because these aquatic systems were less climatically and geologically stable, and fish populations were smaller and more prone to local extirpation. Furthermore, barriers to fish passage inhibited dispersal and colonization (Smith 1981). Streams in forested landscapes generally support salmon and trout, Oncorhynchus spp., whitefish Prosopium spp., sculpins Cottus spp., suckers Catostomus spp., and minnows (Cyprinidae), but in some of the colder streams, chars (e.g., Salvelinus confluentus and Salvelinus malma ) and lampreys (Petromyzontidae)may also occur (Rieman et al. 2003). Although biodiversity defined in terms of fish species richness is low in the Pacific Northwest, intraspecific variability is high, and polytypic fish species are common in the diverse aquatic habitats of the region. For example, the salmonids in the coastal rivers and streams, and the larger interconnected streams, rivers, and lakes of the interior exhibit a variety of ecotypes and migratory life histories (Healey 1986; Trotter 1989; Larson and McIntire 1993; Northcote 1997). This life-history variation appears to be associated with adaptation to spatial and temporal variation in environment (e.g., Schaffer and Elson 1975; Carl and Healey 1984; Beacham and Murray 1987), and there is some evidence of the genetic heritability of life-history traits (Carl and Healey 1984; Gharrett and Smoker 1993; Hankin, Nicholas, and Downey 1993). Persistence of any level of biological organization (e.g., life-history type, population, metapopulation, subspecies, species, community) is related to the interaction of environmental and biological components, and intraspecific diversity is a means of spreading risk ( sensu den Boer 1968) of extirpation in dynamic environments (Gresswell 1999). Unfortunately, despite the broad distribution and extensive intraspecific diversity, persistence of native fishes is uncertain in the Pacific Northwest. Many populations of anadromous salmonids, once synonymous with vigorous biological communities throughout the region, are threatened with extinction (Nehlsen, Williams, and Lichatowich 1991; Frissell 1993; Thurow, Lee, and Rieman 1997). Furthermore, over half of the native taxa in the Columbia River Basin are either listed under the Endangered Species Act, are being considered for listing, or are deemed sensitive by the management agencies (Lee et al. 1997; Thurow, Lee, and Rieman 1997). Potamodromous species like bull trout Salvelinus confluentus are estimated to occur as strong populations in less than 5% of their potential range (Rieman, Lee, and Thurow 1997). Although not currently listed under the endangered species list, the coastal cutthroat trout Oncorhynchus clarki is managed as a sensitive species in Oregon and California (Hall, Bisson, and Gresswell 1997). Native non-game fishes have rarely been monitored, but populations of species such as large-scale suckers ( Catostomus macrocheilus ), squawfish ( Ptychocheilus umpquae ), and Pacific lamprey ( Lampetra tridentata ) also are declining in some drainages (Oregon Department of Fish and Wildlife, unpublished data).

Pacific Northwest↗

Baseline assessment of physical characteristics, aquatic biota, and selected water-quality properties at the reach and mesohabitat scale for reaches of Big Cypress, Black Cypress, and Little Cypress Bayous, Big Cypress Basin, northeastern Texas, 2010–11

In 2010 and 2011, the U.S. Geological Survey (USGS), in cooperation with the Northeast Texas Municipal Water District and the Texas Commission on Environmental Quality, did a baseline assessment of physical characteristics and aquatic biota (fish and mussels) collected at the mesohabitat scale for reaches of Big Cypress, Black Cypress, and Little Cypress Bayous in the Big Cypress Basin in northeastern Texas, and measured selected water-quality properties in isolated pools in Black Cypress and Little Cypress. All of the data were collected in the context of prescribed environmental flows. The information acquired during the course of the study will support the long-term monitoring of biota in relation to environmental flow prescriptions for Big Cypress Bayou, Black Cypress Bayou, and Little Cypress Bayou. Data collection and analysis were done at mesohabitat- and reach-specific scales, where a mesohabitat is defined as a discrete area within a stream that exhibits unique depth, velocity, slope, substrate, and cover. Biological and physical characteristic data were collected from two sites on Big Cypress Bayou, and one site on both Black Cypress Bayou and Little Cypress Bayou. The upstream reach of Big Cypress Bayou (USGS station 07346015 Big Cypress Bayou at confluence of French Creek, Jefferson, Texas) is hereinafter referred to as the Big Cypress 02 site. The downstream site on Big Cypress Bayou (USGS station 07346017 Big Cypress Bayou near U.S. Highway 59 near Jefferson, Tex.) is hereinafter referred to as the Big Cypress 01 site and was sampled exclusively for mussels. The sites on Black Cypress Bayou (USGS station 07346044 Black Cypress Bayou near U.S. Highway 59 near Jefferson, Tex.) and Little Cypress Bayou (USGS station 07346071 Little Cypress Bayou near U.S. Highway 59 near Jefferson, Tex.) are hereinafter referred to as the Black Cypress and Little Cypress sites, respectively. A small range of streamflows was targeted for data collection, including a period of low flow during July and August 2010 and a period of very low flow during July 2011. This scenario accounts for variability in the abundance and distribution of fish and mussels and in the physical characteristics of mesohabitats present during different flow conditions. Mussels were not collected from the Little Cypress site. However, a quantitative survey of freshwater mussels was conducted at Big Cypress 01. Of the three reaches where physical habitat data were measured in 2010, Big Cypress 02 was both the widest and deepest, with a mean width of 62.2 feet (ft) and a mean depth of 5.5 ft in main-channel mesohabitats. Little Cypress was the second widest and deepest, with a mean width of 49.9 ft and a mean depth of 4.5 ft in main-channel mesohabitats. Black Cypress was by far the narrowest of the three reaches, with a mean width of 29.1 ft and a mean depth of 3.3 ft in main-channel mesohabitats but it had the highest mean velocity of 0.42 feet per second (ft/s). Appreciably more fish were collected from Big Cypress 02 (596) in summer 2010 compared to Black Cypress (273) or Little Cypress (359), but the total number of fish species collected among the three reaches was similar. Longear sunfish was the most abundant fish species collected from all three sites. The total number of fish species was largest in slow run mesohabitats at Big Cypress 02, fast runs at Black Cypress, and slow runs at Little Cypress. The catch-per-unit-effort of native minnows was largest in fast runs at Big Cypress 02. More species of native minnows, including the ironcolor and emerald shiner, were collected from Little Cypress relative to all other mesohabitats at all sites. Fifteen species and 182 individuals of freshwater mussels were collected, with 69.8 percent of the individual mussels collected from Big Cypress 02, 23.6 percent collected from Big Cypress 01, and 6.6 percent collected from Black Cypress. Big Cypress 01was the most species rich site with 13 species, and washboards were the most abundant species overall. Mussels were not collected from Little Cypress because there was no flow in this stream during the targeted sampling period in 2011. On July 30, 2010, when the estimated streamflow at the site (based on daily mean discharge measured at the upstream gage in conjunction with powerplant withdrawals) was 45 cubic feet per second (ft 3 /s), Big Cypress 02 had a mean width of 62.2 ft and a mean depth of 5.5 ft in main-channel mesohabitats. On July 27, 2011, when instantaneous streamflow at the site was 10 ft 3 /s, the mean width and mean depth in main-channel mesohabitats decreased to 49.6 ft and 3.1 ft, respectively. Mean velocity in 2010 (0.31 ft/s) was approximately twice as high as 2011 (0.17 ft/s) in main-channel mesohabitats. About 14 percent more fish were collected from Big Cypress 02 in 2010 relative to 2011, and about 18 percent fewer fish species were identified in 2011 at this site compared to 2010. Longear sunfish, which was the most abundant fish species collected in 2010, was second to western mosquitofish in 2011. In the absence of flow during fall 2011, the reach at Black Cypress was reduced to four isolated pools, and the reach at Little Cypress was reduced to three isolated pools. Dissolved oxygen, temperature, pH, and specific conductance data were collected from the pools because it was hypothesized that these conditions would be the most limiting with respect to aquatic life. Dissolved oxygen concentrations ranged from 0.58 milligrams per liter (mg/L) to 4.79 mg/L at Black Cypress and from 0.24 mg/L to 5.33 mg/L at Little Cypress; both sites exhibited a stratified pattern in dissolved oxygen concentrations along transect lines, but the pattern was less pronounced at Black Cypress.

Texas↗

Refuge identification as a climate adaptation strategy to promote fish persistence during drought

Climate change is leading to global increases in extreme events, such as drought, that threaten the persistence of freshwater biodiversity. Identification and management of drought refuges, areas that promote resistance and resilience to drought, will be critical for preserving and recovering aquatic biodiversity in the face of climate change and increasing human water use. Although several reviews have addressed the effects of droughts and highlighted the role of refuges, a need remains on how to identify functional refuges that can be used in a drought management framework to support fish assemblages. We synthesize literature on drought refuges and propose a framework to identify and manage functional refuges that incorporate species physiological tolerances, behaviours and life-history strategies. Stream pools, perennial reaches and off-channel habitat were identified as important drought refuges for fish. The ability of refuges to improve species resistance and resilience to drought requires careful consideration of the biology of the target species and targeted management to promote persistence, quality and connectivity of refuges. Case studies illustrate that management of drought refuges can be challenging because of competing demands for water, incomplete knowledge of ecological requirements for target species and the increasing occurrence of multi-year droughts. Climate adaptation is increasingly important, and drought refuges can increase fish resistance and resilience to climate-related drought across the riverscape.

Fish and Fisheries↗

Changes in backwater plant communities from 1975 to 1995 in Navigation Pool 8, Upper Mississippi River

Water elevation in the Upper Mississippi River (UMR) is highly regulated by an extensive system of locks and dams. Completion of this system in the 1930s created productive, biologically diverse backwater habitats. The status of plant communities in these backwater areas may now be threatened by several factors, including sediment accumulation, recreational use, and navigation traffic. Aerial photography, taken in 1975 and from 1991 to 1995, was used to describe vegetation changes occurring in four UMR backwater areas of Navigation Pool 8. The objectives were to determine (1) if changes occurring in these areas are consistent with hydrarch succession, (2) if the diversity of their plant communities has declined since 1975, and (3) how a large flood event that occurred in 1993 affected the composition and diversity of plant communities in these areas. Three general cover classes were recognized, representing an aquatic to terrestrial gradient. Coverages of specific vegetation types were estimated and evaluated using two indices of community diversity (vegetation richness and the Shannon diversity index). Though some vegetation changes were consistent with expected successional patterns (e.g. increased terrestrialization), other changes were not (e.g. loss of marsh vegetation). Diversity indices and coverages of most aquatic macrophytes declined from 1975 to 1991/1992 but then increased following the 1993 flood. The results suggest that disturbance–diversity concepts, including the flood pulse model, are applicable to the vegetation dynamics of these systems.

Mississippi River, Navigation Pool 8↗

NASA's surface biology and geology designated observable: A perspective on surface imaging algorithms

The 2017–2027 National Academies' Decadal Survey, Thriving on Our Changing Planet , recommended Surface Biology and Geology (SBG) as a “Designated Targeted Observable” (DO). The SBG DO is based on the need for capabilities to acquire global, high spatial resolution, visible to shortwave infrared (VSWIR; 380–2500 nm; ~30 m pixel resolution) hyperspectral (imaging spectroscopy) and multispectral midwave and thermal infrared (MWIR: 3–5 μm; TIR: 8–12 μm; ~60 m pixel resolution) measurements with sub-monthly temporal revisits over terrestrial, freshwater, and coastal marine habitats. To address the various mission design needs, an SBG Algorithms Working Group of multidisciplinary researchers has been formed to review and evaluate the algorithms applicable to the SBG DO across a wide range of Earth science disciplines, including terrestrial and aquatic ecology, atmospheric science, geology, and hydrology. Here, we summarize current state-of-the-practice VSWIR and TIR algorithms that use airborne or orbital spectral imaging observations to address the SBG DO priorities identified by the Decadal Survey: (i) terrestrial vegetation physiology, functional traits, and health; (ii) inland and coastal aquatic ecosystems physiology, functional traits, and health; (iii) snow and ice accumulation, melting, and albedo; (iv) active surface composition (eruptions, landslides, evolving landscapes, hazard risks); (v) effects of changing land use on surface energy, water, momentum, and carbon fluxes; and (vi) managing agriculture, natural habitats, water use/quality, and urban development. We review existing algorithms in the following categories: snow/ice, aquatic environments, geology, and terrestrial vegetation, and summarize the community-state-of-practice in each category. This effort synthesizes the findings of more than 130 scientists.

Remote Sensing of Environment↗

Transcriptome signatures of wastewater effluent exposure in larval zebrafish vary with seasonal mixture composition in an effluent-dominated stream

Wastewater treatment plant (WWTP) effluent-dominated streams provide critical habitat for aquatic and terrestrial organisms but also continually expose them to complex mixtures of pharmaceuticals that can potentially impair growth, behavior, and reproduction. Currently, few biomarkers are available that relate to pharmaceutical-specific mechanisms of action. In the experiment reported in this paper, zebrafish ( Danio rerio ) embryos at two developmental stages were exposed to water samples from three sampling sites (0.1 km upstream of the outfall, at the effluent outfall, and 0.1 km below the outfall) during base-flow conditions from two months (January and May) of a temperate-region effluent-dominated stream containing a complex mixture of pharmaceuticals and other contaminants of emerging concern. RNA-sequencing identified potential biological impacts and biomarkers of WWTP effluent exposure that extend past traditional markers of endocrine disruption. Transcriptomics revealed changes to a wide range of biological functions and pathways including cardiac, neurological, visual, metabolic, and signaling pathways. These transcriptomic changes varied by developmental stage and displayed sensitivity to variable chemical composition and concentration of effluent, thus indicating a need for stage-specific biomarkers. Some transcripts are known to be associated with genes related to pharmaceuticals that were present in the collected samples. Although traditional biomarkers of endocrine disruption were not enriched in either month, a high estrogenicity signal was detected upstream in May and implicates the presence of unidentified chemical inputs not captured by the targeted chemical analysis. This work reveals associations between bioeffects of exposure, stage of development, and the composition of chemical mixtures in effluent-dominated surface water. The work underscores the importance of measuring effects beyond the endocrine system when assessing the impact of bioactive chemicals in WWTP effluent and identifies a need for non-targeted chemical analysis when bioeffects are not explained by the targeted analysis.

Iowa↗

Export of pelagic fish larvae from a large Great Lakes connecting channel

The St. Clair-Detroit River System is located in the heart of the North American Laurentian Great Lakes, connecting lakes Huron and Erie, contributing over 90% of the inflow to Lake Erie, and providing spawning habitat for many fishes including walleye (Sander vitreus), yellow perch (Perca flavescens), and lake whitefish (Coregonus clupeaformis). Dredging and channelization have greatly altered the Detroit River thereby reducing available spawning habitat and redirecting a majority of river discharge through deep canal-like channels to offshore areas of western Lake Erie at high velocities. Fish reproduction has been measured in the Detroit River using larval surveys for over 10 years. However, quantitative estimates of contributions from spawning in the system to Lake Erie fish populations have not been determined. We use long-term biological sampling and physical habitat surveys to characterize larval drift patterns and a Bayesian approach to quantify larval export from the Detroit River. Larval export from the Detroit River into Lake Erie varied by species, across years (2006–2015), and spatially among the multiple navigational channels in the lower Detroit River. Total annual export of walleye larvae ranged from 12 million in 2013 to 114 million in 2014, yellow perch larvae ranged from 319 million in 2014 to 690 million in 2013, and lake whitefish larvae ranged from 29 million in 2010 to 84 million in 2011. Given the widespread spawning, large numbers of larvae produced, and continued system-wide water quality and aquatic habitat improvements, the Detroit River provides valuable habitat and added resilience to Lake Erie fisheries despite suffering from severe anthropogenic disturbances.

Michigan, Ontario↗

Characteristics of water, sediment, and benthic communities of the Wolf River, Menominee Indian Reservation, Wisconsin, water years 1986-98

Analyses and interpretation of water quality, sediment, and biological data from water years 1986 through 1998 indicated that land use and other human activities have had only minimal effects on water quality in the Wolf River upstream from and within the Menominee Indian Reservation in northeastern Wisconsin. Relatively high concentrations of calcium and magnesium (natural hardness), iron, manganese, and aluminum were measured in Wolf River water samples during water years 1986-98 from the three sampled sites and attributed to presence of highly mineralized geologic materials in the basin. Average calcium and magnesium concentrations varied from 22-26 milligrams per liter (mg/L) and 11-13 mg/L, respectively. Average iron concentrations ranged from 290-380 micrograms per liter ( μ g/L); average manganese concentrations ranged from 53-56 mg/L. Average aluminum concentrations ranged from 63-67 μ g/L. Mercury was present in water samples but concentrations were not at levels of concern. Levels of Kjeldahl nitrogen, ammonia, nitrite plus nitrate, total phosphorus, and orthophosphorus in water samples were often low or below detection limits (0.01- 0.10 mg/L). Trace amounts of atrazine (maximum concentration of 0.031 μ g/L), deethylatrazine (maximum 0.032 μ g/L), and alachlor (maximum of 0.002 μ g/L) were detected. Low concentrations of most trace elements were found in streambed sediment. Tissues of fish and aquatic invertebrates collected once each year from 1995 through 1998 at the Langlade and Keshena sites, near the northern and southern boundaries of the Reservation, respectively, were low in concentrations of most trace elements. Arsenic and silver in fish livers from both sites were less than or equal to 2 μ g/g arsenic and less than 1 μ g/g silver for dry weight analysis, and concentrations of antimony, beryllium, cadmium, cobalt, lead, nickel, and uranium were all below detection limits (less than 1 μ g/g dry weight). Concentrations of most other trace elements in fish were low, with the exceptions of chromium, copper, mercury, and selenium; however, these concentrations are not at levels of concern. Concentrations of all trace elements analyzed in whole caddisfly larvae also were low compared to those reported in the literature. During 1998, a total of 48 species of macroinvertebrates were identified at each of two sampled sites, with similar numbers of genera represented at both: 41 at Keshena and 44 at Langlade. The percentage EPT (Ephemeroptera, Plecoptera, and Trichoptera) was 52 at Keshena and 77 at Langlade; these relatively large percentages suggest very good to excellent water quality at these sites. A total of 52 algal taxa were identified at the Wolf River near Langlade. Diatoms made up 96 percent of the algal biomass. A total of 58 algal taxa were identified at Keshena, including 48 diatom taxa (83 percent). Although diatoms accounted for just 22 percent of the algal relative abundance, in cells per square centimeter, diatoms contributed 91 percent of the total algal biomass. The overall biological integrity of the Keshena and Langlade sites, based on diversity, siltation, and pollution indexes for diatoms is excellent.

Wisconsin↗

Fisheries research and monitoring activities of the Lake Erie Biological Station, 2025

Lake Erie has the most populated watershed of all the Great Lakes and has undergone dramatic anthropogenic changes. Since the 1800s, overexploitation of fish populations, habitat destruction, non-native species proliferation, industrial contamination, and changes in nutrient loading have impacted the fish community including declines in or extirpation of many native species (Regier et al. 1969, Hartman 1973; Leach & Nepszy 1976; Ludsin et al. 2001). Implementation of the Clean Water Act and Great Lakes Water Quality Agreement in the 1970s improved habitat conditions (Reutter 2019), which contributed to several strong percid year-classes (Vandergoot et al. 2019). These strong year-classes also benefited from more restrictive management practices that reduced harvest, ultimately rehabilitating Lake Erie percid stocks (Kayle et al. 2015, STC 2020). Historically, Lake Erie supported a cool water fish community dominated by percids and salmonids. Recently updated FCOs set forth a vision that “Lake Erie will consist of diverse fish communities that support ongoing societal benefits, including thriving commercial and recreational fisheries, improved fish habitat and desirable ecosystem performance, and reduced adverse impacts from invasive fish” (Francis et al. 2020). Today, mixed fisheries resulting from seasonally changing cool and warm water habitats have developed in Lake Erie, and the new FCOs reflect a desire to manage both predator and prey fish communities within them. Although Lake Erie management agencies have traditionally focused on numerical indices of a few economically important species, aquatic ecosystem models are typically evaluated in terms of entire fish community biomass. As a result, our understanding of fish community structure and ecosystem dynamics from biomass-based models has been limited to short-term investigations and proxy measurements (e.g., length-weight conversion; FTG 2020). Therefore, many Lake Erie fish community databases are now incorporating biomass-based measurements. In response, USGS revised the Lake Erie trawl program to provide biomass-based measurements for all encountered species (Table 1). The survey design change occurred in 2012, coincident with commissioning of a new research vessel and a change in bottom trawl gear. These modifications already altered the existing time series; therefore, the survey design was also expanded to include greater spatial coverage and increased sample size generating a new time series. The purpose of this report is to develop a comprehensive understanding of the long-term changes and fish community dynamics including population dynamics of key fishes of interest to management agencies, such as native percids and their prey. Here, we summarize survey results for the most recent series of West Basin trawl data from 2013 through 2025. Note that a detailed description of the sampling process along with traditional numericallybased catch data (e.g., fish/ha) for individual species can be downloaded online (DuFour et al. 2026) or obtained for earlier years (https://doi.org/10.5066/F75M63X0; U.S. Geological Survey, Great Lakes Science Center 2019).

western Lake Erie↗

Temporal gamma-diversity meets spatial alpha-diversity in dynamically varying ecosystems

Community measures collected at a single instance or over a short temporal period rarely provide a complete accounting of biological diversity. The gap between such “snapshot” measures of diversity and actual diversity can be especially large in systems that undergo great temporal variation in environmental conditions. To adequately quantify diversity in these temporally varying ecosystems, individual measures of diversity collected throughout the range of environmental variation, i.e., temporal alpha-diversity measures, must be combined to obtain temporal gamma-diversity. Such a time-integrated gamma-diversity measure will be a much closer approximation of a site’s true alpha-diversity and provide a measure better comparable to spatial alpha-diversity measures of sites with lower temporal variation for which a single or a few “snapshot” measures may suffice. We used aquatic-macroinvertebrate community-composition data collected over a 24-year period from a complex of 16 prairie-pothole wetlands to explore the rate that taxa accumulate over time at sites with differing degrees of temporal variation. Our results show that the rate of taxa accumulation over time, i.e., the slope of the species–time relationship, is steeper for wetlands with ponds that frequently dry compared to those with more-permanent ponds. Additionally, we found that a logarithmic function better fit species accumulation data for seasonally ponded wetlands whereas a power function better fit accumulations for permanently and semi-permanently ponded wetlands. Thus, interpretations of ecological diversity measures, and conservation decisions that rely on these interpretations, can be biased if temporal variations in community composition are not adequately represented.

North Dakota↗