Priority Ecosystems Science Initiative

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U. S. Geological Survey's Priority Ecosystems Science Program

Program Priorities

November 30, 1999

We shall not cease from exploration
And the end of all our exploring
Will be to arrive at where we started
And to know the place for the first time.

    T. S. Elliot

Program Priorities - Synopsis

"The complex nature of natural ecosystems, and the increasingly complex nature of human stresses and demands on ecosystems, means that simple and narrowly focussed approaches are not sufficient to penetrate modern environmental problems."

Enhancing Integrated Science, Workshop Report,
Ecological Society of America and Geological Society of America

The U.S. Geological Survey (USGS) is the principal center for scientific investigations within the U.S. Department of the Interior (DOI). Although it does not manage or regulate public lands or activities, the USGS, through its various programs, provides data and analyses that are responsive to the needs of Federal, State and local agencies, and other resource management and policymaking partners and clients (stakeholders). One of these programs is the Place-Based Studies Program (PBS), formerly the Ecosystem Program or Integrated Natural Resource Science Program, which was established by the USGS in fiscal year (FY) 1995.

Map showing distribution of PBS study areas within Bailey's Ecoregions Figure 1. PBS is actively involved in many of the county's major ecoregion divisions (sensu Bailey, et al (1993)). Most major domains and divisions are represented, although there are no study areas in the Polar domain, the Dry Savanna/Steppe, the temperate rainforest of the Pacific coast, the boreal forest or the Sub-tropical Semi-Desert Steppe (figure 1).2

The Program is concentrated in selected study areas. Activities in San Francisco Bay and south Florida began in 1995. Chesapeake Bay was added in FY 1996, and Platte River, Greater Yellowstone, and Mojave Desert in FY 1998. The existing USGS work in Salton Sea will be incorporated into the program in FY 2000. Programs in each study area are expected to last approximately five years, but additional follow-up studies or monitoring may extend the timeframe. Additional ecosystem study areas are added as funding levels permit.

The fundamental scientific goals of the program are to elucidate the interactions between ecosystem stresses and responses. Improved societal understanding of the structure and function of ecosystems is needed to improve our stewardship of the nation's environment and natural resources. The objective of the Program is to provide relevant, high-quality, impartial scientific information to enable resource-management agencies that require an improved scientific information base to make informed planning decisions and to help resolve and prevent resource-management conflicts. The information is designed to have a direct, significant, and immediate impact on management and policy decisions. The Program draws upon a diverse pool of scientific expertise primarily resident in the USGS. Integrated, inter-disciplinary teams link information on physical, chemical, and biological responses to environmental and resource management involving water, minerals, land, fish and wildlife. Such information has transfer value for similar situations in other geographic locations.
Ecosystem management is a collaborative approach to natural and cultural resource management that integrates scientific knowledge of ecological relationships with resource stewardship pratices for the goal of sustainable ecological, cultural, and socioeconomic systems.

(National Park Service)

This approach enables the USGS to solve longstanding problems in new, more comprehensive ways and to explain more fully the interactive nature of resources and the environment.

The PBS establishes priorities by soliciting stakeholder input. Input at the regional level helps to ensure that the form and content of the information provided in each ecosystem are relevant and timely to our partners. Input is gathered through formal and informal interactions with local and regional coordination groups, sponsorship of workshops and meetings with Federal, State and local agencies to discuss program components, study design and results. At the National level, representatives of relevant Federal agencies within the DOI Science Board and the Ecosystem Advisory Committee provide guidance to the Program.

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Societal Rationale

The costs of restoration can be large, both for physical environmental alterations, and for forgone use of land and water resources. These economic realities demand effective environmental solutions and efficient resource use. Scientific information helps to ensure
"The administration's initiatives to implement ecosystem management governmentwide face several significant barriers. For example, although ecosystem management will require reliance on ecological and socioeconomic data, the available data, collected independently by various agencies for various purposes, are often noncomparable and insufficient, and scientific understanding of ecosystem is far from complete... Furthermore, there is still much uncertainty about how ecosystems function--uncertainty that contributes to strong differences in the interpretation of scientific evidence."1

(GAO report on Ecosystem management)

that future plans have realistic expectations for restoration, structures under construction are optimally managed, and managers have the tools to predict outcomes of possible restoration actions. The essence of many, if not most, ecosystem issues is competition for and conflict over the use of resources such as water, minerals, and land, when their use causes degradation and (or) threatens other uses. Improved scientific understanding of ecological processes and systems can help managers circumvent potential problems by predicting environmental and resource changes that result from environmental stresses.

Resolution of resource management issues often requires information from diverse scientific disciplines that are at the heart of USGS capabilities and responsibilities. Under PBS, the teams that are formed to integrate the scientific disciplines bring a diversity of scientific skills to solve the complex, multifaceted environmental problems that are characteristic of major environmental debates. These teams face similar challenges across the country - defining historical ecosystem changes, designing monitoring programs for restoration and management, developing decision support systems (and science that supports those systems) that can be used to predict the effects of management actions. Scientifically derived relationships are needed to relate different types of ecosystem data.

Regional environmental resource issues in many ecosystems are at critical decision- making junctures. In south Florida, a restoration costing $11 billion to $15 billion will be based in part on scientific predictions of the probable effects of restoration actions. In San Francisco Bay, multimillion-dollar modifications of wetlands and the water management system require multidisciplinary scientific information. In Chesapeake Bay, implementation of changes in land use practices requires information on the effects of those practices on nutrient and sediment loading into Chesapeake Bay. The primary audience for the technical information is intended to be managers and their scientific support staff, but the public is also becoming increasingly able to use the data resources that are available over the Internet. The time may come when private landowners will approach the management of their own land with a degree of sophistication that rivals experienced agency managers.

Goals and Objectives

The goal of the Program is to enable resource managers to use sound science as a basis for informed planning decisions and resolution and prevention of resource-management problems. The objectives of the Program are to:

  • Provide high-quality, impartial, and timely scientific information that can be accepted and used by all sides of resource-management and environmental issues;
  • Be responsive to the needs of Federal, State, and local agencies and other ecosystem stakeholders by providing timely, relevant information from the broad diversity of disciplines within the USGS; and
  • Develop multi- and inter-disciplinary and interdivisional approaches to ecosystem science.

The Scientific Foundation

Scientists seeking to define predictive relationships within ecosystems face a high degree of uncertainty and troubling lack of information. The National Academy of Sciences has described the limitations of the current state of science related to restoration.

"Even where general trends, such as wildlife population declines or changing stream quality, are clear, scientists are often unable to determine the impact of a specific action on those trends with any precision (or even whether the trends are a consequence of previous human actions or are natural). Problems of cumulative effects, lack of site-specific ecological knowledge, and the natural variability of ecological systems conspire to add substantial uncertainty to almost all uses of scientific knowledge in environmental decision-making. As a consequence, we must place as much emphasis today on techniques and policies for coping with uncertainty as we do on efforts to reduce that uncertainty."3

The Committee on Global Change Research identified "Scientific Questions"4, answers to which are critically needed to move forward the state-of–the-art. These issues are the foundation for scientific activities within Place-Based Studies.

  • What are the interactions of changing land use, climate, nutrient and toxic inputs, and hydrology on ecosystems and their ability to produce goods and services?
  • What are the required data sets, theory and models needed to understand the regional coupling of physical and chemical climate, land use, and ecosystems?
  • How do changes to terrestrial and hydrological systems alter coastal marine [and freshwater] systems?
  • Are there critical (keystone) species governing large-scale ecosystem function, and can we identify what species could become keystone under changing environmental conditions?

The Interdisciplinary Framework - The PBS niche is to provide integrated,
Paleoecological information from Biscayne Bay has shown that seagrasses, once thought to be keystone species, have only flourished in the last hundred years. Prior to that, Biscayne Bay was not saline enough to support them. Based on these new data, managers must decide if they want to manage the system to return to fresher water and less seagrass, or manage for more saline conditions that are more similar to what residents are used to.
interdisciplinary information on the ecological framework that underlies environmental responses. Taken as a whole, the interdisciplinary framework allows the Program to approach complex problems in comprehensive ways. Individually, each discipline provides parts of the lens through which the environment can be seen and understood. This understanding will improve management of "places" within the Place-Based Studies Program, and in similar environments and problems throughout the country.

  • Geologic and paleontological information set the climatologic, morphologic and geochemical bounds for the ecosystem. Historical climatic variability drives fluctuations in the water regime, which affects such things as plant tolerances, nutrient dynamics, and geochemical processes. Climate and geology control geomorphic processes, which shape topography and landforms. Geologic signatures can be found in the geochemistry of streams and terminal lakes, in soil type, sediment particle characteristics and in the plants and animals that depend on them.
  • Water distribution controls habitat for biota, and the geomorphology of river systems. Water use drives economic prosperity and powers the natural productivity of ecosystems. It is a critical resource for humans and the heart of many resource management conflicts.
  • Biological response is the critical endpoint for measuring success or failure of ecosystem restoration actions. It is closely tied to human well being, the economy and to our quality of life. Many endangered species, the trust responsibilities for the Department of the Interior, are central pillars of the resolve to restore and manage ecosystems.
  • Scientific integration of spatial data help scientists and managers understand the connections between diverse factors driving change. When integration is successful, the whole is greater than the sum of its parts. By working with related information from several disciplines, scientists can improve the state-of-the-science in interpreting environmental processes, and thus their service to those who manage our natural resources.

Cross-disciplinary Programmatic Elements –Certain Programmatic elements are shared across all of the "places" within PBS, because many of the problems encountered in managing environmental resources are similar across the country. In each of the "places", USGS information helps to set goals for management and restoration, helps to determine criteria and measure management success, improves understanding of ecosystem processes and status, and improves the modeling capability to predict the outcome of management strategies. The Program provides information in forms that are of maximum utility to resource and environmental managers, landowners and the general public. Setting Goals - Information on historic environmental conditions and natural variation is the first step to developing attainable and relevant goals for the future. Understanding how the region functioned before disturbance provides a framework for understanding what has been sustainable in the past under natural climatic variability. It is often difficult to distinguish between natural climatic variability and the effects of human activities. Ecosystem history can also provide clues as to the pitfalls of proceeding along certain paths in the future. Documentation of landscape change also helps scientists determine
Data from hydrographic and topographic surveys from the 1850s to the 1990s, in combination with data on historical trends in sediment metal contamination in San Francisco Bay, have helped predict contaminant levels that might occur in dredged or newly exposed sediments.
why the environment responds to change the way it does, because causal factors are sometimes buried in sediments, soils (e.g., contaminants) or the biological community (e.g., remnant populations).

Success Criteria - Selection of success criteria for restoration should be closely tied to goal setting. Commonly these are easily measured metrics that relate closely to societal goals, e.g., a healthy fishery, adequate water, etc. Success criteria are part of the monitoring strategy for achieving success for the restoration.

Ecosystem Processes and modeling - Effective predictive tools, either conceptual or mathematical, combine information on environmental conditions with understanding of the underlying processes that control the response of natural or stressed systems. Though modeling has made much progress in the last 20 years, predictive capability in multi-stressor systems, such as implications of interactions between dissolved organic carbon, contaminants and microbial communities for contaminant exposure; community level effects of contaminants and sediments; the roles of geology, geochemistry and land use change in shaping animal and plant communities; and natural and anthropogenic factors that alter resistance and resilience of different types of landscapes, lags behind the needs of society.

Scientific Issues - The Program seeks to improve the understanding of structure and function of ecosystems by examining the causes and interactions between ecosystem stresses and responses. These stressors can be the direct result of human activities such as competition for and utilization of water, land, energy, harvested species or other major resources, or an incidental result of other human activities, such as transportation, waste assimilation, and dumping of ballast water. Some problems, like climate change, are global in nature and are not amenable to local solutions, unless those solutions involve shifting goals to accommodate changing conditions. Others problems may be locally caused and remediated yet are present throughout the region or nation. For instance, the problems caused by water withdrawal in the Platte River are similar in many locations throughout the semiarid West.

These ultimate causes of environmental problems - climate change, competition for resources, waste assimilation, and incidental activities - are factors in a manageable list of stressors that focus the science on what is needed for restoration. Each of these causes can lead to disruptions of community dynamics, species imbalances, and ultimately threaten and endanger species viability. All are issues in PBS Study Areas. These issues are a part of the programmatic purview, as agents of ecosystem change. Each location has issues that are of major importance and others that are relevant but not major foci of the program (Table 1).

Table showing issues that are of major importance in each PBS Study Area
Table 1. Issues: Agents of Ecosystem Change
  • Climate change and variability - Important in setting goals for restoration, and for distinguishing between human and climatic impacts
  • Land use change drives habitat loss, fragmentation and degradation, causing disruption of surficial deposits, loss of soil and sediment stabilizing mechanisms, erosion, resuspension, and sedimentary imbalances. This topic covers many kinds of problems, including off-road vehicle use, road building, fire suppression, and urbanization.
  • Competition for and utilization of resources - Water, land, energy, and harvested species is at the heart of many restoration efforts. Hydrologic alteration includes channelization, water withdrawal, levee construction, in- stream flow changes, aquifer storage, floods and droughts. It leads to changes in sediment transport and channel morphology and is frequently caused by resource competition or land use change. Climate change can exacerbate or moderate the effects of hydrologic alteration.
  • Assimilation of wastes - Inputs of contaminants, nutrients and sewage cause altered biogeochemical cycling, ecological imbalances, disease and toxic effects. Waste assimilation is one of the many services that humans expect from the environment, and excesses in chemical and nutrient contamination resulting from non-point source and end of pipe releases are a primary cause of environmental degradation.
  • Incidental activities such as transportation, and dumping of ballast water sometimes introduce or exacerbate invasions of nonnative species and spread disease.

Ecosystem Services --Natural ecosystems benefit human societies in many ways. Ecosystems produce a diversity of goods, such as seafood, fodder, and timber, which represent an important part of the economy. In addition, natural ecosystems perform fundamental life-support services, such as purifying air and water, detoxifying and decomposing wastes, regulating climate, regenerating soil fertility, and producing and maintaining biodiversity. These functions are worth trillions of dollars annually to the agricultural, pharmaceutical, and industrial sectors. However, since most are not traded in economic markets they do not have prices that could signal changes in their supply. Economic development that destroys habitats and impairs services can create costs in the long term to humanity that may greatly exceed the short-term economic benefits attributed to such development. Today, growing impacts of human activities imperil the delivery of ecosystem services. Ecosystem services operate on such a grand scale and in such intricate and little-explored ways that most could not be replaced by technology. Scientific information will help society to understand how to balance sustaining ecosystem services and pursuing the worthy short-term goals of economic development.

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Using sound science as a basis for informed planning decisions and resolution and prevention of resource-management problems requires that the scientific scope of the Place-Based Studies Program include all of these issues. In each place, a different combination of issues is important. All of the issues are represented in the program. The opportunity for providing science for restoration is present in areas where restoration has become an important focus of management. The selection of sites for the program is driven by the presence of restoration activities and the priority given to those activities at the Departmental level. Currently, activities are based in South Florida, San Francisco Bay, Chesapeake Bay, Greater Yellowstone, Mojave Desert, Platte River, and Salton Sea (to be brought into the program as part of the budget restructure of FY 2000). If the USGS budget is augmented as requested in the President's FY 2000 budget, activities in the Great Lakes will begin. Many of the issues under investigation are also problems in other regions of the country, and the scientific acumen gained or approach successfully used in one study area is applicable to similar locations to those within the Program.

Program Direction and Evolution

Program Staging - In each study area, scientific activities follow a similar path. The primary components of ecosystem studies are problem definition, database development, measurement of important ecosystem attributes (such as flows, populations, elevation and stratigraphy) ecosystem history, process studies, modeling, and monitoring. Appendix A provides details on the planned activities in each study area.

  • The impetus to restore an area (and thus selection as a study area) usually follows formal or informal monitoring that indicates that the area needs management attention. A monitoring program that is directed towards specific restoration success criteria should be implemented in the early phases of the restoration action, or before restoration begins, so that change can be detected. Monitoring of restoration success is phased in and modified as information on ecosystem processes becomes better known, and the scientific opinion coalesces around reliable and informative metrics.

  • Database and web- related activities are most intense in the early years of these programs because the accumulation of available information forms a springboard for further study of processes.

  • Measurement of ecosystem attributes is needed at the beginning to ensure that models are based on accurate data. Depending on the quantity, quality, and types of information available, modeling may be delayed.

  • Process studies provide the fundamental understanding of the linkage between ecosystem components and are the basis for modeling. As monitoring results become available, further studies are needed to understand how processes have changed.

  • Models formalize the predictive capability in useable tools. As more is learned about the processes governing ecosystem interactions, as the system itself changes in response to management, models must be refined to incorporate new understanding.

  • Ecosystem history provides a scale against which to measure the relative impacts of human alteration, sea level rise and climate change.

Program Priorities for Each Study Area –

(See Appendix A for timelines and Appendix B for GPRA documentation)


[South Florida website]

Issues - In the last 100 years, requirements for water supply and flood protection for urban areas and agriculture have resulted in construction of an extensive canal system and prompt drainage of water into the Atlantic Ocean rather than seasonal seepage through the Everglades and into Florida Bay. Water diversions and excessive nutrients and mercury within the Everglades have decimated bird populations and driven the Florida panther to the brink of extinction. In Florida Bay, declines in seagrasses result in decreasing water clarity and declining fish populations. The South Florida Ecosystem Restoration Task Force is drawing up plans for restoring the Everglades and Florida Bay. Like many areas, national and regional monitoring programs and local stakeholders provided most of the original indications that the Everglades and Florida Bay were in trouble.

The USGS Place-Based Studies Program in South Florida The program encompasses data, ecological and hydrologic processes and models, information integration and synthesis, and tools to make scientific information available to Federal and State agencies and the public. Ecosystem and hydrologic models are used to evaluate the effects on species and habitats of restoration actions. Predictive capability of these models draws upon process studies and data from many disciplinary and interdisciplinary areas. Much of the research on hydrologic, cartographic and geologic, biological / ecological issues relevant to DOI's research role in South Florida ecosystem restoration reflects a strong collaborative program between the USGS and the NPS through DOI's Critical Ecosystems Studies Initiative (CESI).

Program Elements

USGS provides extensive scientific information to inform the restoration.

  1. Comprehensive regional scale monitoring information is important to track restoration trends. Studies related to development of success criteria will be augmented in coordination with the Corps of Engineers, the National Park Service and the South Florida Water Management District. Hydrologic monitoring of the southern and southwest coasts of the Everglades will continue to supply data for model development. USGS provides information on sustainability of restoration targets, success criteria, and the methods for determining whether success has been achieved.
  2. The database and Internet access system, known as SOFIA (South Florida Information Access), will continue to distribute USGS information electronically and expand by providing the same capabilities for data from Fish and Wildlife Service and National Park Service. Database efforts will continue to incorporate existing and new datasets, and continue the information framework for South Florida.
  3. USGS builds ecological and hydrologic models that include USGS information on hydrology, biology, geology, and other land characteristics. At the present time, funding is augmented through the Critical Ecosystem Studies Initiative of the National Park Service. Data and an extensive understanding of the processes that govern the interactions between biological, physical and chemical components are used in predictive models. Hydrologic and ecological models, under construction by USGS and others, use USGS hydrologic, ecological, geophysical, geologic, cartographic, bathymetric, biological and paleontological information to establish salinity yardsticks to measure restoration success, to predict where water will flow under different scenarios, and to assess its potential impact on the biota. These predictive models will help the USACE redesign the flow through the Everglades to restore Everglades bird populations and natural ecological dynamics in Florida Bay, while ensuring that the urban and agricultural areas have sufficient water to maintain their economy.
    • ATLSS is a system of interlocking models that use hydrologic information and land characteristics to predict responses of critical species to hydrologic modifications. Ecological and landscape models will be developed for additional species and ecosystem zones. Scientific studies related to responses to ecosystem stressors such as environmental contaminants will be begun and the information incorporated into models in following years (FY 2000-2005).
    • The Southern Inland Coastal System (SICS) model will be expanded to include Everglades National Park. It incorporates USGS process-level information on vegetative resistance to flow, wind effects, and evapotranspiration, and USGS data on elevation, and flows. The SICS model will ultimately include the mangrove fringe, Biscayne Bay, Everglades National Park, and the urban corridor. Efforts will be reduced when the studies in the enlarged area are completed (FY 2002 timeframe).
    • Coarse-scale (400 m), high-accuracy elevation data collection for Shark River Slough, Big Cypress, western mangroves and west of the Park Road will be continued into FY 2000 and complete by FY 2001. Collection of fine-scale elevation-data using advanced techniques will provide information on high priority areas, such as the newly acquired preserve lands.
  4. Aquifer Storage and Recovery (ASR) activities are expected to increase in response to needs for "Getting the Water Right". Groundwater studies related to ASR will start in FY 2000 and continue for 3-5 years. The Program expects to redirect significant resources to this activity in the future, but it is anticipated that an additional million dollars in FY 2000, possibly with budgetary support from the U. S. Army Corps of Engineers, will be needed to start up this activity.
  5. Estuarine and Bay Studies in Biscayne Bay and Florida Bay have sought to understand the linkage between the hydrologic, ecological and historic changes. These studies will be integrated in FY 2000 and continue for a few more years.
  6. Geochemistry studies will continue to provide process-level information on the impacts of hydrologic and nutrient changes. Much of the work to date provided the fundamental science regarding regional processes. Geochemical work in the future will assess the potential effects (e.g., enhanced methylation rate of mercury) of restoration in actions in particular geographic areas. For example, it will help managers decide how to manage planned stormwater treatment and nutrient removal areas in the north so that they don't exacerbate the problem of mercury in the foodchain. Funding may be augmented through the Critical Ecosystem Studies Initiative of the National Park Service. The Environmental Protection Agency partially funded this work in FY 1998 and 1999.
  7. Much of the ecosystem history work in the Everglades, Florida Bay. Biscayne Bay will be completed in the next few years, although work in the Bays may continue into FY 2002.
In the first few years, the program in South Florida focussed on research and data collection. The programmatic emphasis on synthesis (integration of science and enhancement of the electronic availability) will be largely complete by the end of FY 2001. The synthesis will integrate the accumulated scientific knowledge and understanding from USGS studies, help to chart the future scientific direction of the USGS program, and contribute to interagency synthesis activities.

After FY 2001, several programmatic changes will take place in response to needs for science to support the evolving restoration. As the NPS Critical Ecosystem Studies Initiative funds diminish there will be a gradual shift toward biological studies, especially studies related to contaminants. Studies that enhance our understanding of the linkages between biological and physical parameters will be emphasized.

Integration with other USGS Programs

Activities in the South Florida are also supported by Hydrologic Research and Development, the National Cooperative Geologic Mapping Program, the Federal-State Cooperative Water Program, the National Water Quality Assessment Program, the National Mapping Program- Geographic Research and Applications, Ground-Water Resources, Toxic Substances Hydrology, Water Data Collection and Management, and the Biological Research and Monitoring Program.

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[San Francisco Bay website]

Issues - Historical destruction of wetland habitats, diversion of freshwater for irrigation and drinking water supplies, introduction of exotic species, and contamination from urban, agricultural and industrial sources have all contributed to declines in populations of fish and wildlife in San Francisco Bay estuary.


Initiated in FY 1995, the Program has supported research studies on flow dynamics, distribution and biological effects of contaminants, and sedimentary and population-level effects related to wetland restoration. Funding from the Program has allowed for the development of new tools and procedures to make existing and new information more widely available via the Internet. The FY 1999 restructuring of the San Francisco Bay- Delta study into two new integrated program elements will continue into FY 2003, with a possible decline in funding in the final year. The two projects address some of the key components of the mission of the CALFED (the major ecosystem management stakeholder group for the San Francisco Bay/Delta issues): to restore ecosystem health and improve water management for beneficial uses of the Bay-Delta system".

  • Studies of the hydrological, ecological attributes and functioning, and use by resident plant, invertebrate, fish, and waterbird communities of a key non-tidal wetland habitat (salt evaporation ponds) prior to an important decision regarding their possible conversion/restoration to tidal wetland habitat. Augmentation of the bathymetric components of this project would be a useful addition if funds were available.
  • Studies of the interactions between water flow, salinity, bathymetry, sediment and pollutant (pesticides and metals) transport, and effects on populations of resident species. The understanding gained in this component will be tested in San Pablo Bay in the future (2002 timeframe) in conjunction with an ongoing study of contaminant exposure and effect on waterfowl in San Pablo Bay, if funds are available.

Integration with other USGS Programs

Activities in the South Florida are also supported by the Hydrologic Research and Development, the National Mapping Program- Geographic Research and Applications, Water Data Collection and Management, Toxic Substances Hydrology, the Biological Research and Monitoring Program, the National Water Quality Assessment Program, the Federal-State Cooperative Water Program, The Coastal and Marine Program, the National Cooperative Geologic Mapping Program, The National Park Service, the U.S. Army Corps of Engineers, the South Florida Water Management District, Florida Department of Environmental Protection and other cooperating agencies.


[Chesapeake Bay website]

Issues - In Chesapeake Bay, the Nation's largest estuary, excessive nutrients have caused periods of hypoxia (insufficient dissolved oxygen to support living resources). The high levels of nutrients, and associated sediment loads and algal blooms also decrease water clarity, which is largely responsible for the decline in submerged aquatic vegetation (SAV).


The objectives of the U. S. Geological Survey (USGS) Chesapeake Bay Ecosystem program are:

  • Determine the response of water-quality and selected living resources of the Bay watershed and estuary to changes in nutrient inputs and climatic variability;
  • Better define and evaluate the natural and anthropogenic controls on water quality and living resource response; and
  • Provide resource managers with the management implications of the above scientific findings so they may evaluate the effectiveness of different nutrient-reduction strategies.
A critical aspect of the program is the analysis of history of Bay ecology. The Chesapeake region has seen 300 years of human activity - clearing land for agriculture, changing agricultural practices, reforestation, and urbanization, for which we have good documentation. As State and Federal managers try to put in place best management practices, one of the best ways of determining the potential effects of the land use actions is to examine the sedimentary record in this area. Many of the efforts in Chesapeake Bay will be coming to a close in FY 2001. Priorities in Chesapeake Bay are expected to shift to put a greater emphasis on contaminants and sediments. The program may be given the option of refocusing efforts into new areas in FY 2001.

Integration with other USGS Programs

Activities in the Chesapeake Bay are supported by the Hydrologic Research and Development, the National Cooperative Geologic Mapping Program, the Federal-State Cooperative Water Program, the National Mapping Program- Geographic Research and Applications, the National Water Quality Assessment Program, Water Data Collection and Management, Ground-Water Resources, and the Biological Research and Monitoring Program.


Studies in Greater Yellowstone, Mojave Desert, and Platte River were at pilot stages in FY 1999. Augmented funding has been requested for FY 2000. The programs were designed to last approximately five years at the $1.5-2.0 million level, with efforts spread out over a longer time frame at lower funding levels. Current pilot funding levels are in the $500-$700K range for these studies.


[Mojave Desert website]

Issues - Encompassing six military bases, four national park units, and considerable Bureau of Land Management (BLM) and other Federal lands, the Mojave Desert is home to a rapidly growing population of well over a million people. The desert also is home to active and abandoned mines, off-road recreation areas, and waste disposal sites. Crossed by a web of utility corridors and aqueducts that sustain southern California cities and provide local road access, the most remote area of the desert lies within three miles of a road. Estimating the effects of continued population growth and increased resource use in the region is difficult given the limited knowledge of biological diversity, mineral wealth, and surface- and ground-water hydrology. The desert is dynamically linked to global climate that modulates seasonal and annual weather patterns, which influence floods, droughts, wildfires, and water availability. Human activities, such as grazing animals, off-highway vehicle use, construction, mining, urban expansion, waste disposal, recreational uses, and water withdrawal, and natural processes influenced by man, such as fire and invasive species, have increased the vulnerability of the desert environment to soil erosion and ultimately habitat degradation.


The Mojave Desert Ecosystem Science Program is an interdisciplinary study of vulnerability and recoverability of land to natural and human-induced disturbances characterized by soil compaction, wind or water erosion, or disruption of water flow. The ultimate goal is to provide a deeper understanding of arid-land ecosystems that helps land managers devise policies that allow human use of the desert while also protecting its vulnerable resources. It aims to accomplish this goal by studying selected sites in detail and extrapolating the attributes of those areas to the whole of the Mojave. The program provides direct assistance to land-management agencies in using these data and interpretations in geographic information systems (GIS). At the base level of funding, a model of vulnerability of lands in the Mojave Desert to wind erosion will be completed by the end of FY2004. This model will be demonstrated within the framework of a prototype decision support system that allows desert managers to forecast capability the anticipated consequences of alternative land use decisions by the end of FY 2005. The first soil compaction model will be refined to forecast plant coverage rates and speciation of recovering sites. These products will be measured on the basis of how well they meet the requirements for usage in land use decision making by desert managers and their staffs. Augmented funding in FY 2000, would allow the program to include formulation of a monitoring plan for the Mojave, incorporate a greater range of habitat types, include vertebrate response to roads, and move the date of completion from FY 2005 to FY 2004. Additional augmentation in FY 2001 would be used to ad invasive plants and vertebrate responses to urbanization and move up the completion date to FY 2003. Studies of the Mojave will have applicability to restoration activities in other arid-land ecosystems

Task Description

During FY98, the first year of study, investigations were begun at three sites with varying histories. During FY99 investigations were extended to the Nevada Test Site and to a transect through Joshua Trees National Park and 29 Palms Marine Corps Base. These studies will continue and be extended to include approximately 12-15 sites over the life of the program. If the program expands, remote sensing will be investigated for its potential to extend local landscape characterization to larger areas or to obtain specific variables (like soil particle size). Existing studies on ecosystem dynamics, fire history and ecology, invasive species, climatic variability, soil-moisture budgets, human population impacts, and similar topics affecting disturbance and recovery of desert lands will be examined, synthesized, and published as a series of review papers. Specific studies will be undertaken to examine biological and physical processes acting at the surface, including identifying thresholds of change controlled by these processes. The insights gained from these studies will form the scientific framework necessary to develop vulnerability and recoverability models for desert ecosystems. Multi-scale integration of data and methods for displaying vulnerability and recoverability indices and estimating error ranges will be critical components of the effort. The objective is to provide information to a decision support system that uses scientific findings from the program to help land managers look at ecosystem health yesterday, today, and tomorrow.

Throughout the life of the program, data, interpretations, and models will be made available to desert land managers and other clients in an expeditious fashion. Important program findings will be interpreted and made available to the general public through both print and web publications to enhance popular understanding and appreciation of desert ecosystems and USGS science. Scientists will publish their results in the peer reviewed scientific literature and present their findings at appropriate conferences.

The Mojave project captures the spirit of the DMG and NPR by taking on the challenge of using the integrated scientific capabilities of the USGS to determine which desert lands are most vulnerable to disturbance, what the effects of that disturbance is likely to be on the biota, and what recovery rates are anticipated. The project works directly with the DMG Science and Data Management Team, which provides oversight of the project.

Integration with other USGS Programs

Hydrologic Research and Development, National Cooperative Geologic Mapping Program, Earth Surface Dynamics, National Mapping Program - Geographic Research and Applications, and the Biological Research and Monitoring Program support activities in the Mojave.


[Greater Yellowstone website]

Issues - The greater Yellowstone ecosystem contains natural phenomena that are unique on our continent: migrating herds of wildlife, indigenous predators, and geothermal features associated with one of the largest dormant volcanic areas in North America. Human and wildlife activities in the Greater Yellowstone are often structured around its unique geologic features: the ancient volcano caldera and the associated geothermal features. An ever-increasing number of people live and recreate in this landscape. Humans have fragmented the landscape by physically altering the habitat and changing vegetative characteristics. Roadbuilding, hunting, trapping, and the diverse management strategies of different agencies compound the impacts of fragmentation. Long-range planning for wildlife and human activities in the greater Yellowstone depends on understanding the influence of human activities on wildlife, and the cascading interactions among wildlife and their physical and biological habitat.

The Greater Yellowstone Initiative (GYI) is designed to:

  • Improve understanding of the uses of habitat by wildlife and humans,
  • Develop information resources that are consistent across management units,
  • Improve knowledge about ecological resources and regional biophysical processes
  • Improve knowledge of ecological effects of population growth and economic development
  • Apply scientific knowledge and advanced information systems to decision making

Augmentation of the GYI effort is needed in several areas. The development of the decision support system would be greatly enhanced with additional effort in the areas of database development, model construction, socioeconomics and fieldwork to supply information for wildlife habitat use. Models for additional species would allow better interpretation of the interaction among species and prediction of the effects of habitat modification on a more diverse group of species. Socioeconomic factors are an important driver of land use change and information on these factors will provide the foundation for predictive models.

Integration with other USGS Programs

Activities in the Yellowstone are supported by the National Cooperative Geologic Mapping Program, Geographic Research and Applications, the National Water Quality Assessment Program and the Biological Research and Monitoring Program. The Minerals Program has an ongoing study of mineralization processes in Yellowstone Lake.


[Platte River website]

Issues - The Platte River is an internationally significant staging area for migratory water birds of the Central Flyway and critical habitat for the whooping crane. The landscape has been transformed by major reservoirs and water diversion projects, which have changed the river channel and adjacent wet meadows. These changes were brought on by irrigation and power development that is critically important to sustain the economic base of the area.

The objectives of the USGS study are to:

  • Increase access to information on Platte River ecology, historical spatial information, and hydrology; and
  • Assess the impact of restoration activities by describing the interactions between fluvial geomorphology and biological system health, through studies involving relations between wet meadows, migratory bird habitat and health, vegetation, sediment transport, river hydraulics, and restoration actions.

The Platte River Program has been kept at the pilot level (many people making introductory efforts) because of lack of funds for several years. Additional field efforts are needed to improve sediment model reliability, to relate species habitat requirements to physical habitat attributes, and to improve understanding of the effects of restoration actions. These efforts will require an additional $1M to move beyond the pilot stage.

Integration with other USGS Programs

Activities in the Platte River are supported by the Hydrologic Research and Development, the Energy Resources Program, Geographic Research and Applications, and the Biological Research and Monitoring Program.

SALTON SEA (Begun in FY 1999)

Issues - The Salton Basin is a highly productive ecosystem with tremendous importance to the migration, wintering, and breeding for many water birds in the Pacific Flyway birds. The decline of wetlands on western flyway during this century makes the Salton Sea much more crucial for many birds. Since the Sea's accidental formation early in this century, salinity and nutrient levels have increased dramatically because, as a terminal lake, incoming irrigation drainwater evaporates under the intense heat of the desert. Although it continues to be important for wildlife, wildlife diseases appear to be increasing, and the economic and recreational benefits from hunting, fishing and tourism have declined. The focus of the effort is currently largely biological, with a primary emphasis on fish and wildlife diseases.

Additional efforts are needed to supply information on the physical and geochemical framework that biota depend on. Ultimately, this ecosystem should be brought to the $2M level. The first step towards that goal is the development and integration of geochemical components with existing biological components. ($400K)

Integration with other USGS Programs

The Biological Research and Monitoring Program support activities in the Salton Sea.

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Opportunities for Interprogram Cooperative Efforts

The Program is currently at $15 Million with inputs from other programs within the USGS. However, PBS relies heavily on the resources and skills of single discipline programs in formulating interdisciplinary teams. Each discipline provides critical information that is used in managing an ecosystem. Geologic and paleontological information set the climatologic, morphologic and geochemical bounds for the ecosystem. Historical climatic variability drives fluctuations in the water regime, which affects such things as plant tolerances, nutrient dynamics, and geochemical processes. Geology and geomorphic processes control topography and landform, another essential element of climate. Geologic signatures can be found in the geochemistry of streams and terminal lakes, in soil type, sediment particle size and in the plants and animals that depend on them. Water distribution controls habitat for biota, and the geomorphology of river systems. It drives economic prosperity and powers the natural productivity of ecosystems. Biological responses are the critical endpoint for measuring success or failure of ecosystem restoration actions. They are critical to human wellbeing, economy and to our quality of life. Many endangered species, the trust responsibilities for the Department of the Interior, are central pillars of the resolve to restore and manage ecosystems. The diversity of disciplines demonstrates that the whole is greater than the sum of its parts, and that by working with related information from several disciplines, scientists can improve their interpretation of their own data.

Personnel Needs

The program requires scientific expertise in database management, construction of web pages, fish and wildlife ecology with expertise in each biome (marine, estuarine, riverine, lacustrine, terrestrial, montaine, grassland, wetland, desert, upland, tropical, eastern deciduous, etc) taxonomy, paleoecology (expertise in pollen, geochemical dating, stable isotope chemistry, invertebrates), cartography, remote sensing, geochemistry, ecology, sedimentary geology, structural geology, environmental toxicology, fate and transport of organic and inorganic chemicals, glacial geology, hydrology, water quality, water and sediment chemistry, and other disciplines within the USGS.

1Government Accounting Office.1994. Ecosystem Management, Additional Actions needed to adequately test a promising approach. B256275 GAO/RCED-94-111. 87pp.
2Bailey, Robert G.; Avers, Peter E.; King, Thomas; McNab, W. Henry, eds. 1994. Ecoregions and subregions of the United States (map).Washington, DC; U.S. Geological Survey. Scale 1:7,500,000; colored. Accompanied by a supplementary table of map unit descriptions compiled and edited by McNab, W. Henry, and Bailey, Robert G. Prepared for the U.S. Department of Agriculture, Forest Service.
3Reid, Walter V. 1996. Status of ecological knowledge related to policy decision-making needs in the area of biodiversity and ecosystems in the United States. Pages 327-344 in: linking Science and Technology to Society's Environmental Goals. National Academy of Sciences Press 554 pp.
4Global Environmental Change, Research Pathways for the next decade. 1998. National Research Council. National Academy Press

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