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The ecological condition of estuaries in the Gulf of Mexico

The Gulf of Mexico is a vast natural resource encompassing the coastal areas of western Florida, Alabama, Mississippi, Louisiana, and Texas, as well as a portion of Mexico. Many estuaries flow into the Gulf of Mexico and serve as nursery grounds for fish, habitat for a wide variety of wildlife, shipping routes, and a source of recreation. Estuarine-dependent species constitute more than 95 percent of the commercial fishery harvests from the Gulf of Mexico, and many important recreational fishery species depend on estuaries during some part of their life cycle. Gulf estuaries are diverse and productive ecosystems that provide a variety of valuable resources, including fish and shellfish, recreation, transportation, and water supply. Assessing the overall condition of Gulf of Mexico estuaries required incorporating data from other federal, state, and local monitoring programs to augment the information on ecological indicators collected by the U.S. Environmental Protection Agency’s (USEPA) Environmental Monitoring and Assessment Program (EMAP). The resulting document would provide a synthesis of the available knowledge about the condition of Gulf of Mexico estuaries. This document is intended for use by scientists and other citizens concerned with the ecological condition of estuaries, as well as by managers and lawmakers interested in the sustained use of estuaries for commercial and recreational purposes. It also addresses public concerns about the aesthetic quality of coastal areas vital to tourism and recreation. By producing this report on the ecological condition of estuaries in the Gulf of Mexico, we have taken one step in assessing the health of this environmental resource. We have produced an environmental “report card” to be used as a guide in the evaluation of management decisions and research directions. This report is organized in three parts: (1) an introduction that gives background information on the Gulf of Mexico, estuarine ecology, and the factors that impact estuaries in the gulf, (2) the main section on priority ecological indicators used to measure the condition of estuaries in the gulf and (3) an ecological report card that summarizes the data on ecological indicators and provides a rating of the condition of estuaries in each gulf state and for gulf estuaries overall. Many of the ratings were based on the percent area of estuaries in each state exhibiting degraded or adverse levels of an indicator. Eutrophication, a condition of high nutrients often resulting in low oxygen levels and other adverse effects, is an important water quality concern for estuaries along the gulf coast. The National Oceanic and Atmospheric Administration (NOAA) has compared the Gulf of Mexico to other coastal regions like the middle Atlantic and has ranked the Gulf of Mexico as having the highest number of point sources of nutrients and the highest percentage of land use devoted to agriculture. We evaluated monitoring data for nitrogen, chlorophyll, and dissolved oxygen as indicators of eutrophication. Although most of the estuaries exhibited high nitrogen or chlorophyll or low dissolved oxygen concentrations at least once during a survey, many times these conditions were observed in small rivers or bayous rather than in the entire estuary. Often, the percent area affected was low. The gulf estuaries had moderate conditions overall for nutrients and dissolved oxygen. Definite nutrient problems were observed in >25% of the estuarine area in Louisiana and Texas and definite dissolved oxygen problems were observed in Alabama. Contaminants in estuarine sediments provide evidence of the accumulation of chemicals from anthropogenic sources. We compared the concentrations of sediment contaminants to established guideline values to determine the proportion of estuarine area that could have potential adverse effects on living organisms. Although detectable levels of contaminants were measured in almost every estuary in the Gulf of Mexico, <25% of the estuarine area in all states had contaminant concentrations that exceeded these guidelines. Wetlands are integral parts of estuarine systems. Declining acreage means habitat loss that may be the result of commercial and residential development, hydrologic alterations, or dredge and fill operations. The Gulf of Mexico region contains more than 50% of the coastal wetland acreage in the U.S. and yet it also has the highest rate of coastal wetland loss. Nine of the top ten estuarine drainage areas ranked by total wetland area are in the Gulf of Mexico region. The most current estimates of total wetland loss over the past 200 years range from 41% to 54% for the gulf states. Although coastal wetlands continue to be altered or destroyed, some estimates indicate that the rate of loss has slowed. All gulf states were rated as having severe problems with wetland loss. The condition of benthic (bottom-dwelling) invertebrates, fish and shellfish, birds, and threatened and endangered species was used to evaluate the health of estuarine fauna. Degraded benthic communities inhabited <25% of the estuarine area in all gulf states except for Texas. Commercial fish and shellfish landings may be used as an indicator of population stability while fish biomarkers are used to measure the health of individuals in the population. Commercial landings of the top four fisheries (shrimp, menhaden, blue crab, and oyster) are stable in the gulf states while fish biomarkers indicate fair to poor fish health in Alabama and Texas and good fish health elsewhere. Coastal and marine bird populations appear to be in good condition throughout the gulf. Four threatened or endangered species inhabit coastal areas in the Gulf of Mexico: brown pelican, Gulf sturgeon, manatee, and Kemp’s ridley sea turtle. In general, populations of these species are in good to fair condition in the gulf states. Public health indicators include shellfish bed closures and chemicals found in edible fish tissue. Harvest of shellfish (primarily oyster in the Gulf of Mexico) is restricted or prohibited when concentrations of bacteria or other pathogens reach levels that could impair human health. The gulf states contain the most acreage of shellfish-growing waters in the U.S. but also have the most acreage restricted for harvest. All gulf states except Mississippi have >25% of their shellfish-growing waters restricted for harvest, mostly due to pollution from wastewater treatment plants or other upstream sources. Advisories may be issued that limit consumption when the concentrations of chemicals in fish tissue exceed levels known to be harmful to humans. Although seafood consumption advisories have been issued in all gulf states, the percent of the fish population with high concentrations of contaminants is relatively low in the gulf overall.

Alabama, Florida, Louisiana, Mississippi, Texas↗

Surface water-quality and water-quantity data from selected urban runoff-monitoring sites at the Rocky Mountain Arsenal, Commerce City, Colorado, water years 1988-2004

The U.S. Geological Survey has monitored the quality and quantity of streamflow at the Rocky Mountain Arsenal (RMA) northeast of Denver, Colorado, since the early 1990s in cooperation with the U.S. Army. This report, prepared in cooperation with the U.S. Fish and Wildlife Service, documents existing surface-water-quality conditions on the RMA. All RMA water-quality data for the Irondale Gulch and First Creek Basins adjacent to and on the RMA were reviewed. Where applicable, water-quality data were compared to State standards established by the Colorado Department of Public Health and Environment. At both the Havana Interceptor below 56th Avenue gaging station and the Uvalda Interceptor below 56th Avenue gaging station, all of the dissolved-oxygen concentrations met the State standard requiring at least 5.0 milligrams per liter (mg/L) of dissolved oxygen for the protection of aquatic life. In contrast, the dissolved-oxygen concentrations at the Peoria Interceptor below 56th Avenue gage commonly were less than 5.0 mg/L. Excluding one suspect concentration of 1.6 mg/L, the dissolved-oxygen concentrations for the First Creek Basin ranged from 4.2 to 12.6 mg/L. Excluding the one suspect value, three dissolved-oxygen concentrations failed to meet the State standard of 5.0 mg/L at the First Creek below Buckley Road site. At the Peoria Interceptor below 56th Avenue site, all pH values were within the range specified by the State standard (6.50-8.99). Results of seven sampling events at the Havana Interceptor below 56th Avenue gaging station indicated a pH greater than or equal to 9 (pH values of 9 or greater exceed the upper limit of the standard). No sampling events indicated a pH less than 6.50. Results from one sampling event at the Uvalda Interceptor below 56th Avenue indicated pH values outside the range specified by the State standard. The concentrations obtained for chloride, magnesium, and sodium generally were below 200 mg/L at all three Irondale Gulch monitoring stations for the entire period of record, but there were a few sampling events at each of these sites where much higher concentrations for these analytes were obtained. The median concentrations for calcium, magnesium, and sodium generally were higher at the First Creek below Buckley Road site than in the three Irondale Gulch sites, while the 90th percentile and maximum concentrations for magnesium and sodium generally were higher at the three Irondale Gulch sites than at the First Creek below Buckley Road site. The urban runoff flowing onto the RMA had low concentrations and few, if any, detections for most organic contaminants. Part of the reason for low detections of organic contaminants may be in how the samples are collected. The existing surface-water sampling program was not designed specifically to target storm runoff and therefore does not characterize water quality for all hydrologic regimes, most notably storm runoff. As a result, the existing data may not adequately represent potential contaminant transport onto the RMA. In addition, during stormwater-runoff events, the sites examined for this report frequently are subject to sharp increases in discharge, and just as quickly the discharge rapidly recedes. These types of transient flow events make water-quality sampling difficult, and none of the sites have a safe place to sample the higher flows that occur in any given year. As a result, most of the surface-water-quality samples were collected after the flow had decreased substantially from the peak flow, which may have transported much of the chemical contaminant load through the system. Thus, little is known about the water quality during the critical initial stormwater-runoff period when contaminants are most likely to be mobilized and transported through the stormwater conveyances past the locations where gaging stations are located.

Colorado↗

Mississippi’s resiliency and changing environmental conditions

Mississippi is experiencing shifts in environmental conditions, many of which are expected to intensify in the coming decades, and will have important implications for ecosystems, species, and natural resource management across the state. Historical climate analyses and downscaled projections summarized for the state’s Environmental Protection Agency (EPA) level III Ecoregions show that Mississippi will likely face increases in extremely hot days, more intense heatwaves, greater evapotranspiration, and reductions in cold-season extremes. Temperature trends indicate that while Mississippi has warmed relatively little over the last century, recent years have been among the warmest on record. Projections suggest substantial increases in the number of days with maximum temperatures at or above 95°F across all Ecoregions, particularly under higher warming scenarios. Correspondingly, the number of freezing nights is expected to decline, with statewide decreases of 7–21 days depending on the global warming level and timeframe. These combined patterns are likely to reshape habitat conditions, influence species’ thermal stress, and alter ecological processes such as soil moisture retention and stream temperature regimes. Mississippi’s hydrological systems are also expected to be significantly affected. Extreme rainfall events, particularly the most intense 1% of precipitation days, are projected to increase across the state, raising risks of flooding, erosion, and altered stream flow. Coastal Mississippi faces additional stress from sea‑level rise, which is already contributing to more frequent high‑tide flooding; projections show continued increases in inundation risk throughout the century. These flooding patterns, combined with stronger hurricane rainfall rates and the potential for landfalling storms to stall, pose ongoing threats to coastal ecosystems and communities. The state is also vulnerable to extreme weather hazards such as tornadoes. Recent research shows a geographic shift in tornado activity toward the Southeast, with Mississippi experiencing some of the nation’s greatest increases in favorable tornado days and nighttime tornado frequency—hazards that have direct implications for wildlife, habitat stability, and human safety. Drought conditions may intensify as well: higher temperatures and increased evapotranspiration during dry spells could worsen water stress regardless of uncertainty in average annual precipitation. These changing environmental conditions have important consequences for Mississippi’s Species of Greatest Conservation Need (SGCN). Vulnerability assessments and ecological niche models indicate that several fish, mussel, crayfish, plant, amphibian, bird, and mammal species may face heightened stress due to warming temperatures, shifting hydrology, habitat loss, and increases in extreme events. For example, many cold‑water and moisture‑dependent species in the state’s rivers and wetlands are already near their thermal limits, and further warming could reduce suitable habitat. Birds breeding in bottomland hardwood forests, such as the Prothonotary Warbler, are increasingly susceptible to nest loss from flooding. Similarly, species like the Louisiana Black Bear may encounter higher risks from habitat inundation and shifting food availability. The “A Closer Look” section underscores the vulnerability of the Mississippi Alluvial Plain—one of the state’s most ecologically rich yet heavily altered Ecoregions. Its bottomland hardwood forests, wetlands, and floodplain habitats support diverse wildlife but are increasingly threatened by rising temperatures, hydrological changes, development pressures, and compounded disturbances. These habitats provide critical ecosystem services such as water filtration, flood attenuation, and biodiversity support, making their conservation particularly urgent under future conditions. Collectively, these findings indicate that Mississippi’s ongoing and projected environmental changes present both challenges and opportunities for natural resource management. Incorporating adaptation strategies into the State Wildlife Action Plan will be essential for sustaining habitats, mitigating risks, and supporting the long‑term resilience of Mississippi’s wildlife and ecosystems.

Mississippi↗

Proceedings of the 2024 Asia-Pacific Wildlife Health Workshop—Collaborating against shared threats

Emerging diseases of wildlife origin are increasingly transboundary (they spread rapidly across geographic regions and across continents). In recent years, examples include the rapid spread of African swine fever across Europe and Asia with negative effects on food security, and the near global spread of highly pathogenic avian influenza which has devastated wildlife populations, caused economic harm, and which threatens public health; consequently, international partnerships and networks are essential to facilitate the sharing of information for improved situational awareness and better preparedness and response. In this regard, the U.S. Geological Survey and the Korea National Institute for Wildlife Disease Control and Prevention have had a long-standing partnership to foster scientific collaboration. A key part of the activities has been annual scientific workshops, which commenced in 2016. The 2024 workshop in Hilo, Hawaii, was the most recent in these series of workshops and included participants from across Asia and the Pacific region, including Thailand, Vietnam, China, Republic of Korea, Japan, Australia, Cook Islands, Fiji, and the United States. The goals of the workshop were: to continue to build the wildlife health community of practice in the Asia-Pacific region and expand the participants to agencies and institutions from other countries in the region; and exchange scientific knowledge among the participants to share best practices, create scientific networks, and build capacity in wildlife health science for the Asia-Pacific region. The themes discussed at the workshop included wildlife health risk management, avian Influenza, African swine fever, climate change and emerging diseases, and international cooperation. This report contains the author-submitted abstracts which provide a summary of the presentations and discussions during the workshop. The aim is to share this information to continue to foster international scientific exchange to protect wildlife health, livestock, and public health from the negative impacts of infectious and noninfectious diseases.

Open-File Report↗

Black Hills hydrology study

The Black Hills area of western South Dakota is a valuable resource center. The area has attracted numerous residents and industries because of the availability of mineral, timber, agricultural, recreational, and water resources. The water resources of the area have been stressed locally by increasing population, periodic drought, and development of other resources. In response to residents' concerns about these stresses on the water resources, the Black Hills Hydrology Study was initiated in 1990 as a cooperative effort among the U.S. Geological Survey, the South Dakota Department of Environment and Natural Resources, and the West Dakota Water Development District. West Dakota represents the various local and county cooperators. This report describes the purpose, scope, approach, and status of the study and presents highlights from the first project data report produced for the study.

Open-File Report↗

Guam's water resources

How do climate and humans impact freshwater resources, and how can we plan for change?

Cooperator Report↗

Freshwater availability in Guam with projected changes in climate

Guam receives 85 to 116 inches of rain a year, two-thirds of which has historically fallen during the wet season. On average, three tropical storms and one typhoon pass within 80 nautical miles of Guam each year, generally during the rainy season. Both drought and flooding can impact freshwater supply and the associated infrastructure. Department of Defense (DoD) installations and non-military populations on Guam share freshwater resources, which will be impacted by changes in demographics, freshwater demand, and climate. This DoD Strategic Environmental Research and Development Program (SERDP) funded study evaluated potential climate impacts on freshwater supplies in Guam, and identified methods of increasing the water distribution system’s resilience.

Cooperator Report↗

Final project memorandum: Southeast Climate Adaptation Science Center Project

Low-lying public lands along the northern Gulf of Mexico coast are vulnerable to sea-level rise. Coastal planners and resource managers in the region have requested customized information that can be used to concisely communicate local sea-level rise scenarios and identify potential impacts to the missions of management agencies. In this project, researchers worked with the Northern Gulf of Mexico Sentinel Site Cooperative to develop information sheets outlining potential sea-level rise scenarios for the region through 2100 including their potential impact on the missions of federally-managed lands. Researchers drew from existing information on regional and global sea-level rise scenarios to develop customized information sheets for 54 federally-managed lands in the region (e.g., National Wildlife Refuges, National Park Service lands, National Estuarine Research Reserves) (Chivoiu et al. 2020). This project was developed in response to a request for customized sea-level rise scenario products from partners at the Northern Gulf of Mexico Sentinel Site Cooperative and the U.S. Fish and Wildlife Service’s Gulf Restoration Program. The results of this project support the conservation stewardship missions of the U.S. Fish and Wildlife Service and National Park Service by providing science to inform management of their lands along the Gulf of Mexico.

Alabama, Florida, Louisiana, Mississippi, Texas↗

Final project memorandum: Identifying conservation objectives for the Gulf Coast habitats of the black skimmer and gull-billed tern

Many shorebirds and nearshore waterbirds are of conservation concern across the Gulf of Mexico due to stressors such as human disturbance, predation, and habitat loss and degradation. Conservation and protection of these birds is important for the functioning of healthy ecosystems and for maintaining biodiversity in North America. Consequently, resource managers along the Gulf need decision-aiding tools that can help to answer important conservation questions for different species (e.g., how much area should be targeted by management actions to meet a species’ needs). To address this need, project researchers developed statistical models that could help identify habitat conservation objectives and actions for bird species taking into account different Gulf coast conservation scenarios that might occur in response to sea-level rise. The project focused specifically on the Black Skimmer ( Rynchops niger ) and Gull-billed Tern ( Gelochelidon nilotica ), two species designated as U.S. Fish and Wildlife Service Species of Conservation Concern and Gulf Coast Joint Venture Priority Species. These two birds are also representative of a variety of other beach and barrier-island nesting birds whose nesting habitats are threatened by sea-level rise (e.g., Least Tern, Snowy and Wilson’s Plover). The statistical models linked each bird’s abundance to habitat characteristics that could be influenced by different management actions. This information could be used to identify conservation objectives under different conservation scenarios.

Gulf of Mexico↗

Standardized guide to the examination and necropsy of the horseshoe crab using Limulus polyphemus as Limulidae prototype

The Atlantic, or American, horseshoe crab (L imulus polyphemus ) has existed largely unchanged for over 100 million years. Millions of individuals are commonly observed ashore in spring and summer months during spawning events along the entire North American coastline expanding from the East to the Gulf coasts of the United States and Mexico. Other species can be found in the Indian and Pacific Ocean. The massive deposit of eggs in nearshore sand provides a critical source of food for endangered migrating birds, especially the Red Knot ( Calidruis canutus rufa ) in the Delaware Bay. Horseshoe crabs are also an important component of the sea turtle diet. In addition to the ecological importance, horseshoe crabs are used commercially for bait in eel and conch fisheries and for biomedical purposes in the production of Limulus Amebocyte Lysate (LAL) to detect bacterial toxins in injectable drugs and implantable devices. Commercial demands have led to population declines in some regions. Fisheries are regulated by state and the current International Union for Conservation of Nature (IUCN) listing for L. polyphemus is vulnerable. A small number of individuals are housed in public aquaria for educational purposes. With growing interest in animal welfare, the health and stability of populations, and potential stressors that can contribute to decline , it is important to have clear and detailed descriptions of horseshoe crab anatomy and necropsy techniques. The purpose of this guide is to illustrate the normal anatomy and the step-by-step technique for dissection of horseshoe crabs. The contents are largely excerpts of the master’s thesis of artist, Katie (Bergdale) Roorda, which was based on photographs from C. Meteyer documenting the sequence and procedure used for necropsy dissection.

Cooperator Report↗

Mapping climate change resistant vernal pools in the northeastern U.S.

Vernal pools are seasonal wetlands that provide important breeding habitat for a variety of amphibian species. As future climate projections indicate warmer growing seasons and earlier seasonal increases in evapotranspiration, some managers of vernal pools have expressed concern that pools may dry earlier in the season, potentially interfering with completion of amphibian life cycles. In this context, a subset of pools might function as hydrologic refugia by providing wetland habitat later into the year under relatively dry conditions, thus supporting species persistence even as summer conditions become warmer and droughts more frequent. This study used approximately 3,000 field observations of inundation from 450 pools in the northeastern United States—located from West Virginia to Maine—to train machine-learning models for predicting the likelihood of pool inundation. Inputs to these models included pool size, day of the year, climate conditions, short-term weather patterns, and attributes of the landscapes in which pools were embedded. Predictions of pool wetness were generated on a daily time step from late April through late July using three short-term weather scenarios (dry, wet, and average) under historical climate conditions and four sets of downscaled climate projections (2050s and 2080s under Representative Concentration Pathways 4.5 and 8.5). The modeling and inundation prediction process was replicated using four inundation thresholds on wetted area and depth. Model outputs can enable users to examine the inundation thresholds, time points, weather scenarios, and future climate projections most relevant to their management needs. Together with long-term monitoring of individual pools at the site scale, this regional-scale study can support amphibian conservation by helping to identify subsets of pools that may be most likely to function as hydrologic refugia from changing climate conditions.

Connecticut, Delaware, Maine, Maryland, Massachuse↗

Improving predictions of water supply in the Rio Grande under changing climate conditions

This product is a case study summarizing the original work authored by David Gutzler, Shaleene Chavarria, and Nels Bjarke. The content will be part of a collection of Case Studies shared via the Collaborative Conservation and Adaptation Strategy Toolbox (CCAST). The research featured in this case study is an analysis of historical observations and climate models developed by the US Bureau of Reclamation. The work aims to identify changes to streamflow predictability, assess future predictability, and inform the development of more reliable water supply outlooks essential for planning purposes in the Upper Rio Grande Basin.

Colorado, New Mexico↗

Research to inform Caltrans best management practices for reptile and amphibian road crossings

In October of 2014, the U.S. Geological Survey (USGS) began a 5-year project to conduct research to inform Best Management Practices (BMPs) for amphibian and reptile crossing and barrier systems in California. To inform future conservation and transportation planning, this project involved identification of species at highest risk of negative road impacts, creation of geodatabase and spatial mapping tools that crosswalk with California Essential Habitat Connectivity Planning, and field research to address information gaps in the efficacy of reptile and amphibian passage and barrier systems. Per the agreement with California Department of Transportation (Caltrans; agreement 65A0553), this project was part of a broader collaborative effort between the Western Transportation Institute (WTI) of Montana State University and USGS Western Ecological Research Center (WERC). As part of this broader project, WTI conducted a worldwide literature review and gap analysis and produced the BMP manual for herpetofauna in California. WTI and USGS were contracted separately although we worked closely together throughout this broader effort and each brought particular expertise to the project. WTI has expertise in highways, the attributes of the highway environment, and has broad international experience with road ecology and herpetofauna connectivity systems worldwide. USGS WERC has expertise with California amphibian and reptile species and their ecology, study design and implementation, as well as expertise in landscape connectivity and road ecology.

California↗

A review of remote sensing and grasslands literature

Studies between 1971 and 1980 dealing with remote sensing of rangelands/grasslands in the multispectral band are summarized and evaluated. Vegetation and soil reflectance properties are described. In the majority of the studies, the effect of the reflectance of green rangelands vegetation on the reflectance from the total scene is the primary concern. Developments in technique are summarized and recommendations for further research are presented.

Cooperator Report↗