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Annual Program Direction for FY 2005

[**Introduction**](#intro)

[**Section I -- Integrated Science Directions for FY 2005**](#SectionI)

[Understanding Large River Systems](#Understanding)

[Forecasting Landscape Change](#forecasting)

[Restoration and Recovery of Impaired Habitats](#restoration)

[Water for Human and Ecological Use](#Waterfor)

[Monitoring and Remote Sensing](#Monitoring)

[Status and Trends](#Status)

[Carbon Studies](#Carbon)

[Priority Ecosystems Science](#Priority)

[Science on the DOI Landscape](#Science)

[Central Region Integrated Science Partnerships](#Central)

[Western Region Flexibility Funds](#Western)

[Ecological Systems Mapping Initiative](#Ecological)

[**Section II -- Discipline Directions for FY 2005**](#SectionII)

[Biology](#Biology)

[Contaminant Biology Program](#contaminant-biology-program)

[Fisheries: Aquatic and Endangered Resources
Program](#the-fisheries-aquatic-and-endangered-resources-faer-program-mission-supports-the-conservation-restoration-and-adaptive-management-of-our-nations-valued-fisheries-and-aquatic-resources-by-providing-scientific-research-expertise-to-doi-other-federal-state-tribal-and-non-governmental-natural-resource-managers.-research-studies-focus-on-health-and-diseases-diversity-natural-history-species-interactions-and-habitat-requirements-of-fishes-and-other-aquatic-organisms.-at-risk-species-and-those-that-are-imperiled-or-endangered-receive-special-research-interest.-faer-program-scientists-have-developed-a-5-year-strategic-plan-that-elucidates-the-future-faer-science-challenges-and-research-efforts.-the-fy05-annual-program-guidance-reflects-changes-in-program-direction-as-identified-in-the-5-year-strategic-plan.)

[Invasive Species Program](#Invasives)

[Status and Trends of Biological Resources Program](#statustrends)

[Terrestrial, Freshwater, and Marine Ecosystems Program](#Terrestrial)

[Wildlife: Terrestrial & Endangered Resources Program](#Wildlife)

[Biological Informatics Program](#Biological)

[Cooperative Research Units Program](#Cooperative)

[Geographic Information Office](#GeographicInfor)

[Enterprise Information Program](#Enterprise)

[Water](#Water)

[Ground-Water Resources Program](#Groundwater)

[Hydrologic Networks and Analysis Program](#Hydrologic)

[National Streamflow Information Program](#National)

[Water Resources Research Act
Program](#water-resources-research-act-program)

[Toxic Substances Hydrology Program](#Toxic)

[Cooperative Water Program](#CoopWater)

[Hydrologic Research and Development](#hrd)

[National Water Quality Assessment](#NAQWA)

[Geography](#geography)

[Cooperative Topographic Mapping Program](#CTM)

[Land Remote Sensing Program](#LRS)

[Geographic Analysis and Monitoring Program](#GAM)

[Geology](#Geology)

[Earthquake Hazards Program](#Earthquake)

[Global Seismographic Network](#Global)

[Geomagnetism Program](#Geomag)

[Volcano Hazards Program](#Volcano)

[Earth Surface Dynamics Program](#earth-surface-dynamics-program)

[National Cooperative Geologic Mapping Program](#NCGMP)

[Landslide Hazards Program](#Landslide)

[Coastal and Marine Geology Program](#Coastal)

[Mineral Resources Program](#Mineral)

[Energy Resources Program](#Energy)

[Administrative Services and Policy](#science-support)

[Science Support](#Sciencesupport)

[Facilities](#facilities)

**Annual Program Direction for FY05**

**Introduction**

[]{#intro .anchor}The Annual Program Direction is a collaborative effort
between the Bureau Program Coordinators and Regional managers and
scientists. It contains details on opportunities to address new science
thrusts; major changes in direction of, or emphases of, program goals
and related increases or decreases in funding; opportunities supported
by multiple programs; and identification of new capabilities,
facilities, and expertise available to support project work in the
coming year. In his Annual Guidance, the Director has reminded us again
that appropriations and reimbursable funding will be tight for the next
few years, due to world events and changing priorities within the
Administration. He has encouraged us to be strategic about where
possibilities for growth may exist or where we can add value to ongoing
work:

> "...This year, I urge you to look for ways to partner *internally*,
> within the USGS......Look for ways to coordinate related scientific
> efforts, to coalesce projects for greater impact, and to integrate
> scientific expertise to address complex scientific problems. Consider
> using people short on funding in other programs or disciplines,
> instead of temporary hires and contract people, to meet short-term
> program staffing needs."

####### *Chip Groat*

The full Director's Annual Guidance, released on April 1, 2004, can be
accessed at
<http://internal.usgs.gov/director/planning/2005/dirguid05final.doc>.

Below you will find two sections. Section I describes new directions in
integrated science, i.e., new projects, project re-direction or
expansions of projects that utilize expertise from several disciplines
and are typically funded by several programs, and sources of data and
expertise. Most are organized under integrated science themes. The
themes were identified at the REx-PC Meeting in November, 2002, in
Reston, VA, and remained a priority in the 2003 meeting. Also, most of
the Issue Papers that discuss the integrated science themes have been
updated and can be accessed at:
<http://internal.usgs.gov/director/planning/drafts/> for background in
planning new work or modifying continuing projects.

Section II describes new directions and opportunities from within
Disciplines. For more information about any of these new opportunities
from both sections, it is important that you contact the individual
identified before proceeding with project plans.

There are few new funding opportunities in this document. However, we
have taken an important step in establishing a scientific basis for our
integrated science and are embarking on a slow process to re-direct both
people and funding in new directions.

[]{#SectionI .anchor}**Section I: Integrated Science Directions for
FY05**

# [Understanding Large River Systems]{.underline}

[]{#Understanding .anchor}*Please see updated Large River Systems Issue
Paper for background:
<http://internal.usgs.gov/director/planning/drafts/large_rivers.doc>*

The health and productivity of large rivers, growth of regional
economies, and viability of urban and rural communities are linked to
the Nation's watersheds. Large river watersheds promote commerce,
provide water supplies and electric power generation, improve water
quality, transport sediment, affect land-use, accommodate floods,
compensate for drought, carry away toxic contaminants, and promote the
health of aquatic and riparian biological communities. Understanding
regulated rivers means understanding regulation procedures and
processes, especially collaborative decision-making and conflict
resolution. The ability of regulated rivers to maintain seasonal flow
cycles, transport sediment, assimilate nutrients and contaminants and to
function as self-regulatory systems has been highly altered. Properly
managed rivers are necessary for the Nation's well-being, and regulating
rivers such that they maintain the maximum benefits and protections
requires understanding physical and biological system variability,
sources of stress on aquatic and riparian environments, and
socio-economic impacts on human communities.

Independent, multidisciplinary integrative science, uniquely available
from the USGS, is critical to help stakeholders make informed choices
and decisions about best use, management effects, and conservation of
river systems. Understanding stakeholder processes means investigating
the social and institutional processes for citizen involvement. The
goals for integrative research on rivers in FY04 were to: (1) facilitate
the development of an intra- and inter-agency framework for integration,
coordination, and implementation of integrated science to support
management activities on large river systems, (2) develop a better
understanding of the ecology large rivers, (3) monitor physical,
chemical, and biological resource change, (4) support the planning,
implementation, and evaluation of management actions, (5) support
natural resource management through geospatial technologies, and (6)
support decision-making through sound data management and information
sharing.

There is a need in USGS for inter-disciplinary science efforts that
focus talents and resources on critical river system management issues
requiring scientific support. Multi-disciplinary programmatic interest
to develop new or expanded collaborative studies on selected large river
systems for FY05 includes:

**Mississippi River**

On the *Lower Mississippi River*, reduction in sediment distribution to
the Louisiana Coastal Plain is the single most important reason for the
loss of over1500 sq miles of coastal wetlands. Currently there is no
integrated science project focusing on the Mississippi River, however,
there are several ongoing projects that have interest acquiring broader
expertise and developing new partnerships. The Coastal and Marine
Geology Program, with primary river interest in the Lower Mississippi
River will continue to support research and program staff in efforts to
coordinate with the Army Corps, LADNR, and the broad agency and academic
community; and looks to better coordinate ongoing efforts with other
USGS programs, including existing coastal monitoring, studies of
contaminants at the river/ocean interface, subsidence studies. Contacts:
**Dawn Lavoie and Bob Stewart.** A Hydrologic Research and Development
Program/Biologic Resources Discipline collaborative effort is being
planned to evaluate the role that wetland systems (both bottomland
hardwoods and coastal wetlands) of the Lower Mississippi play in carbon
and nutrient sequestration and transformation. Quantitative studies are
needed in order to understand the potential of these wetlands to reduce
the discharge of nutrients into coastal waters and the impacts of high
levels of nutrient loadings on wetlands and their hydrogeomorphic and
ecological function. This work is to be carried out within existing
funding. Contacts: **Matt Larsen and Bob Stewart.**

On the *Upper Mississippi River*, support is anticipated for increased
internal and external cooperation to address priority management needs
of DOI partners with decision support tools for large river systems to
allow optimal use of existing data from USGS and other agencies, to
increase analyses of existing data sets to enhance work on the role of
habitat mosaics in determining distribution and abundance of biota
within the Upper Mississippi River; and to develop a new risk analysis
for invasive aquatics within the Mississippi River system, with emphasis
on Asian carp. Contact: **Leslie Holland-Bartels.** The Office of Water
Quality is interested in exploring collaborative opportunities to extend
data collection activities or expand on use of the NASQAN data. One
critical issue is movement of nutrients within the Mississippi River
Basin and delivery to the Gulf of Mexico. Funds are limited but the
database is rich, and sampling activities can provide a logistical base
for collaborative science. Contact: **Tim Miller**. The National
Streamflow Information Program, with additional funding support would
increase the number of new stream gages for high priority large river
(all discussed under this theme) sites needing streamflow information.
Additionally, the National Streamflow Information Program plans to
assess the regional characteristics of streamflow information, with the
intent to show trends (e.g. for climate variability); and to provide
techniques for estimating streamflow characteristics at ungaged
locations. Contact: **Mike Norris**.

The Enterprise Information Program would like to provide in-kind support
for the development of information strategies that will help achieve the
Large River theme's objectives and also increase the "integratability"
of data and information within and across themes. Contact: **Tom
Gunther.**

**Mississippi River FY05 Update (Eastern Region)**

Changes in sediment deposition, flood severity and frequency, water
tables, and water clarity due to impoundments have resulted in serious
declines in the aquatic and floodplain vegetation that many species
depend on for parts or all of their life cycle. Construction of locks
and dams has created barriers to fish passage and has restricted the
movements of species to a fraction of their former ranges. However, as
biologically important as large rivers are, they are critical to the
public for their roles in commerce, recreation, water supply, effluent
discharge, hydroelectric generation, and flood control. As a society we
struggle to balance our need for healthy ecosystems with our needs for a
growing economy and ample places for quality recreation.

*Lower Mississippi River-* The Lower Mississippi River Conservation
Committee (LMRCC), an organization of the 6 states bordering the lower
Mississippi River (MO, AR, LA, KY, TN, & MS) sponsored a meeting to
discuss generating a report on the water quality of the Lower
Mississippi River. In attendance were Ron Nasser, a U.S. Fish and
Wildlife Service employee, current Executive Director of LMRCC; Richard
Ingram (MDEQ) the facilitator of the meeting; Bob Delaney (USGS-BRD)
with the Lafayette Science Center but has his office in Vicksburg; Dave
Soballe, formally of BRD La Crosse Science Center but now with the USACE
in Vicksburg; Henry Folmar, lab director for MDEQ; Phil Bass and Richard
Coupe, USGS. The USGS, in cooperation with the LADNR and the Governor's
Office, sponsored and organized a workshop to outline the state of
knowledge with respect to regional subsidence and to identify priority
research and information needs to provide a comprehensive model of
subsidence as it impacts planned restoration efforts.

*Upper Mississippi River-* The Upper Mississippi River supports a \$145
billion annual economy, drains some of the most fertile farm land in the
country, and is home to a myriad of biological resources including some
of our Nation's most imperiled fauna. Cooperative work between USGS BRD
and WRD focuses on identifying large-scale hydraulic and biologic
factors related to abundance of imperiled native mussels. USGS
scientists with Federal and state partners held a workshop in May 2004
to continue development of regional science priorities for
interdisciplinary research on nutrients and water quality within the
basin. Several research and monitoring efforts by USGS and others on the
Mississippi River (BEST, Long Term Resource Monitoring Program
\[LTRMP\], Metropolitan Council Environmental Services River Monitoring,
NASQWAN, and NAWQA) and its tributaries provide a body of data and
decision support tools to federal and state managers. The LTRMP is
operated by a partnership among USGS Upper Midwest Environmental
Sciences Center, Army Corps of Engineers, other Federal agencies, and
field stations operated by state conservation agencies (MN, WI, IA, IL,
MO). The LTRMP collects monitoring data annually and is now engaged in
analyses and modeling of over 10 years of monitoring data to develop
baseline dynamics of water quality, biotic, and habitat parameters and
to determine relations among habitat and biota. Thus far, limited
resources have been applied toward partnerships on the river focused on
modeling and research studies of processes supporting biological
production. The USGS Biological Resources Discipline is in the process
of developing new partnerships with Mapping Division and other Federal
and state agencies to determine the role of habitat distribution, flow
dynamics, and invasive species on biotic production and communities.

**Mississippi River FY05 Update (Central Region)**

An FY05 Coastal Louisiana Initiative was developed that would bring
together what has been primarily single-discipline pieces regarding the
Louisiana vanishing wetlands along the coast. Principles on the initial
development team are Jimmy Johnston (BRD-Lafayette), Charlie Demas
(WRD-LA District), and Dawn Lavoie (CMGP). FY04 work will continue into
FY05. There is another piece on carbon sequestration in the floodplain
hardwoods led by Steve Faulkner (BRD-Lafayette). FY05 has CRISP funds
for Gulf of Mexico coastal ecosystems for an integrated database and
information management system. The lead is Jimmy Johnston
(BRD-Lafayette). This is a joint project with Eastern Region.

## Colorado River

Integrated science is needed for the Colorado River Basin to meet
competing water quality and availability issues in this fastest growing
region in the Nation. The USGS stands out as the pre-eminent
multi-disciplinary research institution for the Colorado River,
challenged to meet partner needs for scientific information relating to
water delivery and power generation, navigation, recreation, salinity,
and species preservation, and other issues that are relevant across the
extent of the Basin. In FY05, opportunities should build on USGS
successes providing science information for the Adaptive Management
Program, a logical base for expansion of integrated science pertaining
to riverine systems of the lower Colorado; ongoing collaborative efforts
to build on USGS-Bureau of Reclamation database-centered decision
support system linkages, and potential USBR support for research on
invasive species eradication related water conservation; to enhance USGS
science in response to DOI land management bureau needs, inter-regional
linkages to ongoing efforts should be developed for all disciplines on
Upper Colorado River to assess multiple issues affecting land managers,
including toxic element geochemistry and invasive species. Along the
US-Mexico Border for Southern CA, newly completed imagery
(1:40,000-scale CIR photography; Digital Orthoimagery in preparation,
and planned acquisition of LIDAR for modeling applications over the
Colorado Delta area, when completed) provides important new data and a
base for an integrative science effort in the Colorado River Delta.
Contacts: **Denny Fenn, John Klein, Dick Grauch, and Mark Shasby.**

-   **Colorado River FY05 Update (Western Region)**

The portion of the Colorado River below Glen Canyon Dam traverses
approximately 300 miles of riverine and riparian habitat in Glen Canyon
National Recreation Area and Grand Canyon National Park. A portion of
this corridor is bounded by three Native American reservations
(Havasupai, Hualapai, and Navajo) and holds cultural significance to the
Hopi, Zuni, and Southern Paiute tribes. The Glen Canyon Adaptive
Management Program is a result of the 1996 Record of Decision regarding
the downstream impacts of the operation of Glen Canyon Dam on the Marble
and Grand Canyon portions of the Colorado River Ecosystem. The USGS
Southwest Biological Science Center has primary responsibility for
providing scientific and technical information to support decision
making in this adaptive management program through the Grand Canyon
Monitoring and Research Center, one of four field stations in the SBSC.
GCMRC operates science programs through internal staff, collaborations
with the USGS WRD, and outside cooperators and contractors including
state and federal agencies, universities, and consulting firms. Research
and monitoring activities include fisheries, aquatic ecology, sediment
resources, hydrology, geomorphology, remote sensing, cultural resources
and water quality. Field activities extend over 500 miles of the
Colorado River from the headwaters of Lake Powell to the headwaters of
Lake Mead. Principle collaborators in DOI are the Bureau of
Reclamation-Upper Colorado River Region, the National Park Service, US
Fish and Wildlife Service, and the Bureau of Indian Affairs. Contact:
**Denny Fenn**

-   **Colorado River FY05 Update (Central Region)**

A USGS team has been working with BLM on three sites, primarily Gunnison
Gorge NCA. Continued funding is anticipated. Most of the funds come from
the Minerals Program, and the rest has been FY03 CRISP Funds matched by
BLM. This project grew in FY04 and moved from CRISP to Science for DOI
Landscapes. Principles are Dick Grauch (GD-Minerals), Paul von Guerard
and John Elliott (WRD-CO District), John Kosovich (NMD-RMMC), and Geneva
Chong (BRD-FORT). The USBR would be a valuable additional partner
because of their Lower Colorado salinity and selenium concerns.

## Missouri River

Missouri River investigations across the Disciplines that can be focused
into an integrated effort include: Geography's ongoing study of
geographic changes since the Lewis and Clark expedition of 1804 -- 1806
on habitat restoration and Biology's pallid sturgeon studies, working
with stakeholders across the basin to develop interdisciplinary efforts
on the relation among river morphology, flow, and habitat needs for both
carp and sturgeon, the ecological factors contributing to successful
spawning and survival, and on understanding the role of invasive Asian
carp. Additionally, the Earth Surface Dynamics Program has ongoing
long-term interest in new activities along the Missouri River.

Contacts: **Mike Mac, Doug Muchoney, Martha Garcia, and Mark Shasby.**

-   **Missouri River FY05 Update (CR)**

A new team exists that is funded by FY03 and FY04 CRISP funds. New
funding by Earth Surface Dynamics would be welcome to bring GD in as a
more robust player. Current principles are **Robb Jacobson** (BRD-CERC),
**Dale Blevins** (WRD-Independence), **Milan Pavich** (GD-Reston), and
**Jeff Spooner** (NMD-MCMC).

**Columbia River**

Integrated science and scientific leadership are needed in the Columbia
River Basin to provide the research and monitoring necessary to restore
and sustain native fish and aquatic resources, and for multi-use water
management. For example, the decline of Pacific salmon and steelhead in
the Columbia River continues to be a significant natural resource issue.
The declines are related to large-scale changes in Basin landscapes, the
structure and function of aquatic ecosystems, and reduced biological
productivity in native populations. These environmental changes and
population effects are the direct biological outcomes and consequences
of a poorly understood mosaic of natural influences and human
interventions. Because many aquatic organisms, including salmonids, have
complex life cycles and specific habitat and ecological requirements,
their conservation requires knowledge about the spatial and temporal
interactions between biotic and abiotic environments. The Columbia River
is a highly engineered and regulated system of major power-producing
reservoirs and smaller dams, diversions, and other alterations to its
natural state. Ecosystem changes and effects associated with hydropower
generation are further complicated, and potentially magnified, by
additional sources of habitat degradation (e.g., agriculture and
invasive species) and population mortality (e.g., fishing). To date,
USGS science in the Basin has been largely mission-oriented and
responsive to tribal, state and other federal agency needs. As a result,
the bureau's science tends to be uncoordinated and broadly distributed
(e.g., fish movements and migrations, contaminants, and water quality
monitoring) although fledgling multidisciplinary efforts are underway
(Coastal and Marine Geology, WRD, BRD to describe the community dynamics
of the Bonneville Pool, e.g., physical habitat characterization,
hydraulic modeling, and biological observations). Other planning would
address water quality in the Handford Reach and inclusion of invasive
species data in the National Map. In FY 2005, new and existing funds
will allow study of instream flow requirements, linkages between aquatic
and terrestrial ecosystems, and biological productivity in mainstem and
tributary study areas. Continued emphasis will be for the acquisition of
physical and biological information regarding the habitats and
populations of key DOI trust resources in the Columbia River Basin.
Contacts: **Lyman Thorsteinson, Cindy Barton, Vicky Lucas, and Guy
Cochrane.**

-   **Columbia River FY05 Update (Western Region)**

Investigators from BRD (WFRC), GD (Menlo Park and Woods Hole), and WRD
(Oregon District) worked collaboratively, in research and technical
assistance, to obtain or portray data and information about lower
estuarine and Bonneville Pool aquatic resources and ecosystems. A pilot
investigation on the sediment history using estuarine cores, was
completed (BRD, GD, and others). Side-scan sonar surveys were used to
characterize the bathymetry of the Bonneville Pool (GD) and to provide
physical baseline data for habitat characterization (BRD) and boundary
conditions for flow and sediment transport models (GD and WRD). BRD\'s
primary objectives focused on aquatic invasive plants, habitat
utilization by fish and other aquatic species, and trophic interactions
of riverine biota. Dr. Bill Sexton (WR REX for Water) was identified as
the coordinator for the newly formed Columbia Plateau focus area in
early FY 05.

**Cooperative Water Program** - Data collection and projects in the
Cooperative Water Program provide long-term data on flow and quality in
large rivers, and help to define flood and low-flow frequency relations.
Some Coop projects address the integration of biologic and hydrologic
monitoring and modeling. Many State and local cooperators have
responsibilities for managing the quality and quantity of large rivers,
as well as their tributary streams. As such, new Coop projects
addressing main stem and tributary issues will contribute to our
understanding of large river conditions and processes. New Coop projects
will focus on improved watershed characterization and flow-system
simulation to support the management of aquifers and streams that serve
as important regional sources of water supply and as important aquatic
ecosystems. Because aquifers and streams often are highly
interdependent, improved tools will be developed and applied for
simulating interactions between ground water and surface water as well
as accounting quantitatively for effects of withdrawals and climate
variations. Contacts: **Glenn Patterson and WRD District Chiefs in area
of interest.**

The **Hydrologic Networks & Analysis Program** (HN&A) elements of
Climate Change Hydrology and National Stream Quality Accounting Network
(NASQAN) provide data and interpretive results that are directly related
the theme of Large Rivers. Contact: **Matt Larsen**.

**[Forecasting Landscape Change]{.underline}**

[]{#forecasting .anchor}*Please see updated Forecasting Landscape Change
Issue Paper for background:*

[*http://internal.usgs.gov/director/planning/drafts/landscape_change_integrated_science_paper_2004.doc*](http://internal.usgs.gov/director/planning/drafts/landscape_change_integrated_science_paper_2004.doc)

**Land Cover Trends** Land use and land cover change is one of the most
pervasive and consequential of all environmental changes because of the
chain of events in which land use change modifies land cover
characteristics, which subsequently affects a broad range of
socio-economic, biologic, and hydrologic systems. Understanding the
impacts and feedbacks of land use and land cover change on environmental
systems requires that we understand the rates and patterns of past,
present, and projected future land use change. The USGS Geographic
Analysis and Monitoring Land Cover Trends research project is focusing
on understanding the rates, causes, and consequences of contemporary and
future United States land use and land cover change. The research
addresses the following questions: (1) what are the land use and land
cover characteristics, including biophysical properties and spatial
configuration of contemporary change (e.g., 1973-2000)? (2) Based on
current rates, characteristics, and drivers of change operating in each
study area, what are the likely land cover patterns and biophysical
properties for 2020? (3) What are the impacts and feedbacks between land
cover change on regional carbon dynamics, land surface hydrology, and
regional weather and climate variability? This research includes the
development of models for forecasting regional land use and land cover
change given specific economic, political, social, and environmental
scenarios. Contact: **Doug Muchoney**

An improved understanding of climate change across the scales of
watershed to continent is an essential component of models that forecast
landscape change. The Hydrologic Networks & Analysis Program elements of
Climate Change Hydrology, DOI Cost-Share, Water Quality in National
Parks, and the Hydrologic Benchmark Network generate data and
interpretive results that are directly related to the theme of
Forecasting Landscape Change. Contact: **Matt Larsen**

**[Restoration and Recovery of Impaired Habitats]{.underline}**

[]{#restoration .anchor}*Please see updated Restoration and Recovery of
Impaired Habitats for background:*

<http://internal.usgs.gov/director/planning/drafts/restoration_and_recovery_of_impaired_habitats.doc>

Our quality of life depends on healthy and sustainable environments. The
societal value of these environments is demonstrated through society's
commitment to spending billions of dollars annually to restore some of
these ecosystems By incorporating science into the design,
implementation, and monitoring of restoration projects, the USGS can
provide information that will be used to increase understanding of
issues critical to restoration success. Many programs are already
involved in restoration because of the multidisciplinary science needs
of restoration efforts. A wide range of physical, chemical and
biological expertise is required to characterize the structure and
function of an impaired ecosystem and its potential for recovery.
Studies that integrate and contribute to a better understanding of the
physical, chemical, and biological processes of these ecosystems and
their watersheds are needed to evaluate development and management
alternatives.

# Chesapeake Bay 

> The ecosystem of the Chesapeake Bay, the Nation\'s largest estuary,
> has been in decline due to poor water quality, loss of habitat, and
> over harvesting. These conditions have adversely affected DOI trust
> resources including interjurisdictional fisheries, migratory water
> birds, and their associated habitats. The Chesapeake Bay Program
> (CBP), which includes the states in the Bay watershed and the Federal
> Government (including three DOI Bureaus), developed Chesapeake 2000,
> which is a 10-year plan for restoration of the Bay and its watershed.
> To support the expanded technical needs of Chesapeake 2000, the USGS
> began in 2001 to carry out a 5-year science plan that coordinates
> studies, carried out through multiple USGS Programs and science teams,
> to provide unbiased scientific information to understand, protect, and
> restore the Chesapeake Bay and its watershed. The studies provide
> information on the ecosystem linkages between land-use, generation of
> sediment and nutrients, and the impact on water quality, habitats, and
> living resources in the Bay. Studies being conducted between 2001 to
> 2005/6 have helped the CBP formulate restoration strategies to attempt
> to meet the goals of Chesapeake 2000.
>
> With the restoration strategies now being implemented, the CBP is in
> need of science to understand ecosystem response to population growth,
> management actions, and natural variability. The information is needed
> to help assess and adapt management strategies in 2007 in an attempt
> to meet restoration goals in 2010. Additionally, DOI is requesting
> expanded science to meet the needs of USFWS Chesapeake Bay Ecosystem
> Plan and the new needs associated with the NPS study to include parts
> of the Bay and its watershed in the NPS system.
>
> To meet the expanded needs of DOI and the ongoing needs of the CBP,
> USGS Chesapeake Bay Studies in FY05 will be completing planned
> projects, integrating information for synthesis products, and revising
> its science plan to reflect projects to be conducted in 2006-2010. The
> CBP and DOI have requested the USGS addresses several topics
> including: (1) rates and forecasting of land-cover change, (2) the
> sources and transport of sediment, nutrients, and contaminants to the
> Bay, (3) determine the impact of these stresses on vital habitats in
> the Bay (water quality to support fisheries, submerged aquatic
> vegetation, tidal wetlands, and stream corridors) and (4) enhance
> decision-support systems for delivering information. In FY05, the USGS
> Chesapeake Bay studies will work with multiple USGS programs to
> identify potential projects that can be conducted in FY06-2010 to
> understand these issues to help DOI and CBP formulate, and evaluate
> the effectiveness of, strategies to restore the function and integrity
> of these vital habitats. **(Contacts: Scott Phillips, Dave Russ, and
> Martha Garcia)**

1.  **Puget Sound**. Concern for the health of the Puget Sound
    near-shore ecosystem has risen with the Endangered Species Act (ESA)
    listing of several species of salmon. Declining fisheries and
    threatened aquatic populations have been tied to the loss of
    critical ecosystem functions, the result of a degraded coastal
    habitat. Federal, state, and local government scientists and
    resource managers have begun working together as part of the Puget
    Sound Near shore Ecosystem Restoration (PSNER) Project to address
    the effects of urbanization on fragile coastal environments. PSNER
    goals are to develop recovery programs and ecosystem restoration
    plans that sustain life on the Sound and continue the region's
    economic prosperity. The USGS partner role will be to provide
    scientific expertise, technology development, and information
    transfer to guide coastal restoration and project decisions in
    support of adaptive management strategies that conserve and protect
    the region's unique coastal resources.

> The Western Fisheries Research Center studies aquatic invasive species
> and the life history and disease effect on the Pacific salmon and
> other fish populations. These groups (Coastal and Marine Geology
> Program and Western Fisheries) will continue to plan and participate
> in integrated research in Puget Sound with emphasis on coastal
> transport and ecosystem processes, salmon restoration science,
> landscape ecology, and geologic hazard evaluations. The Coastal and
> Marine Geology Program intends to provide \$160,000 in OE. Additional
> funding may be available depending on the ability/interest of the
> Coastal & Marine teams to meet existing objectives while redirecting
> staff and resources to support this new effort. Contacts: **Frank
> Shipley and John Haines.**

2.  **Coastal Louisiana.** Coastal subsidence, sea level rise, and fault
    activation related to fluid energy production are major concerns in
    the Gulf Coast Basin. These physical processes, along with storms
    and erosion, negatively impact coastal communities. Federal and
    state agencies in Louisiana are collaborating to develop strategies
    that will effectively mitigate the effects of coastal change hazards
    and restore disappearing wetlands and submerged habitats.
    Interdisciplinary efforts currently exist among the following
    Programs: Energy Resources (ERP), Coastal and Marine Geology (CMGP),
    Status and Trends of Biological Resources (Monitor and assess
    environmental status and trends) and Terrestrial, Freshwater and
    Marine Ecosystems (TFME). ERP and CMGP support research to
    understand fault dynamics, subsidence, and attendant changes in land
    characteristics related to withdrawal of petroleum resources. CMGP
    supports efforts to assess: natural subsidence on regional scales;
    the vulnerability of coastal resources to subsidence, sea level
    rise, and coastal storms; and regional sand resources for hazard
    mitigation and restoration planning. TFME and S&T programs, working
    with other federal and state agencies, are supporting research and
    monitoring to determine rates of coastal wetlands loss, sea-level
    rise and sediment deposition; and the vegetation biomass needed to
    maintain the marsh and provide excess material for marsh rebuilding.
    Coastal and Marine Geology and TFME interests include monitoring,
    mapping, and forecasting landscape change for restoration. The
    President\'s budget shows an increase in the Louisiana Coastal Area
    restoration effort to increase coordination and planning efforts by
    the U.S. Army Corps of Engineers with USGS and other agencies for
    large-scale restoration. This increase in funds will further
    interagency efforts on methods development to decrease the rate of
    marsh degradation and on efforts to determine the rate of landscape
    change. Contacts: **Colleen Charles, Martha Garcia and Dawn
    Lavoie.**

# Tampa Bay Integrated Science Study

> Many of the Nation's estuaries have been environmentally stressed
> since the turn of the century and will continue to be impacted in the
> future. Estuarine research is an essential component of USGS
> scientific investigation and Tampa Bay, one of the Gulf of Mexico's
> largest estuaries, exemplifies the threats that our estuaries have
> faced, including alteration by planned anthropogenic modifications.
> State agencies and universities currently participating in Tampa Bay
> monitoring and research efforts have identified a critical need for
> USGS expertise to provide an integrated science approach for gathering
> information necessary for establishing links between geological,
> biological, and chemical processes in the Bay. This project partners
> all four USGS disciplines with other State and Federal agencies and
> universities to implement a multidisciplinary, integrated science
> strategy developed during FY2001 to evaluate environmental health of
> Tampa Bay. The strategy focuses on a synthesis of existing data,
> synoptic characterization of the geologic framework, hydrologic,
> geochemical, and biological measurements of contamination,
> productivity, ecological indicators, and carbon cycling within Tampa
> Bay and associated wetlands. Specific high priority issues among the
> stakeholders include: 1) documentation of urbanization, historical
> land use change, bathymetry, benthic habitat; 2) Tampa Bay aquatic
> health; 3) sea grasses as indicators of estuarine health; and 4) water
> and sediment quality and quantity as indicators of estuarine health.
>
> Investigations initiated during FY2001 will continue and will be
> expanded to include additional high priority geographic locations
> within Tampa Bay, new tasks addressing critical scientific issues
> identified by the Tampa Bay Estuary Program and other partners, and
> development of predictive models. The primary objective of the Tampa
> Bay Study is to evaluate and develop an integrated science strategy
> that can be applied to other Gulf of Mexico Estuaries. Information and
> data from the Tampa Bay study will contribute directly to the USGS
> Gulf of Mexico Estuaries Integrated Science Data Support and Query
> System and web site. Contacts: **Lisa Robbins, John Haines, and David
> Russ.**

Water Discipline programs collect and analyze large quantities of water
quality data that are useful for work on habitat restoration and
characterization. Data and interpretive results generated through the
**Hydrologic Networks & Analysis (HN&A) Program** elements, Water
Quality in the National Parks, DOI Cost-Share, National Atmospheric
Deposition Program, and Hydrologic Benchmark Network provide data and
interpretive results that are directly related the theme of Restoration
of Impaired Habitats. Contact: **Matt Larsen.**

[]{#Waterfor .anchor}**[Water for Human and Ecological
Use]{.underline}**

*Please see the Water for Human and Ecological Use Issue Paper for
background:*

[*http://internal.usgs.gov/director/planning/drafts/water_availability.doc*](http://internal.usgs.gov/director/planning/drafts/water_availability.doc)

A question being faced by many communities and water resource managers
that rely on aquifers for water supply is how can they, in a cost
effective manner, assess the availability of water for their future
needs.

**Atlantic Coastal Plain**

The Atlantic Coastal Plain (ACP), extending from northern Florida to
Long Island, New York is one of the largest unified coastal environments
in the Nation. In FY 2004 planning began to develop a new project that
focuses and integrates current USGS activities, and USGS-wide
capabilities to address the issue of water availability for human and
ecological needs along the Atlantic Coastal Plain (both on- and
off-shore). Specific issues include salt-water intrusion, rate of
ground-water level declines, ground-water movements across political
boundaries, and other changes in the hydrologic regime, sediment erosion
and deposition, contamination, and habitat loss and remediation. This is
one of the highest priority issues in the Eastern Region of the US for
conducting research on a critical issue that encompasses support from
the Ground Water Program, Coastal and Marine Geology Program, National
Cooperative Geologic Mapping Program, Water Coop Program, and Hydrologic
Research and Development Program. In FY 2004, the project is developing
a science plan that includes both regional-scale components and areas of
focused research.

Several new investigations in the Atlantic Coastal Plain in FY 2005 will
include: (1) Comparison of methods of assessing water availability in
fractured-rock aquifers at the water- or community-scale, (2)
Understanding salt-water intrusion of the coastal plain aquifer system
of Eastern Shore of Virginia where the population is rapidly expanding.
A 3-D salt-water intrusion model will be constructed in this area that
will serve as a benchmark case to illustrate the current potential of
using 3-D models at other coastal sites. (3) Work will start in the
Chesapeake bolide impact crater to drill a deep well to understand how
deep the salt-water is and what the effect of pumping is on the
salt-fresh water boundary. Geophysical interpretations will lead to a
deeper hole being drilled at a later time (with GD). Contacts: **Matt
Larsen and Kevin Dennehy**, Hydrologic Research & Development and
Ground-Water Resources Programs.

Also in FY 2005, activities will include the implementation of the
Science Plan and the development of partnerships, public relations
documents, and a web-based database of existing information. To the
greatest extent possible, future work should integrate on-going
activities along the Mid-Atlantic Coastal Plain.

Contacts: **Dave Russ, Bruce Campbell, John Haines, Kevin Dennehy, Peter
Lyttle, and Ward Staubitz.**

The current FY 2005 budget for the Ground-Water Resources program
proposes \$800K for a water availability initiative. If this work were
funded, it would comprise three components (Contact: Bill Alley). The
first component will provide information on existing conditions and
historical trends in ground-water storage and depletion in the
Southwestern U.S. Initial efforts will identify wells that can be used
to develop indices of ground-water-level changes for specific geographic
regions and aquifers. The second component will focus on methods for
characterization of the spatial distribution of saline-water resources
and their chemical characteristics to support the potential for
desalination of brackish ground water. A case study will be conducted in
part of New Mexico. The third component will focus on methods to link
models that describe flow and transport with critical information on the
health of biological systems. A case study will be undertaken in
Washington State.

The Ground-Water Resources Program began three new 3-year regional
aquifer studies in mid-FY04 that will undertake quantitative assessments
in three major aquifer systems: the North Carolina-South Carolina
coastal plain, including a focus area for geologic mapping by the
Geologic Division, the Denver ground-water basin in Colorado, and the
Central Valley of California. Contacts: **Tom Reilly or Kevin Dennehy**.

#### Karstic Ground Water Systems. In recent years the Great Valley in the northern Shenandoah Valley has experienced rapid growth from new residents who commute to the metropolitan Washington, D.C. area. This growth has the potential to profoundly influence the region's land, water, and biological resources. Regional and local resource managers have real concerns over this karstic region's ability to sustain future growth. An integrated research approach is addressing resource-management concerns centering on the availability, sustainability, and vulnerability of the region's water resources and their ability to provide a reliable long-term water supply to maintain the population growth and water resources to maintain the environment. In addition, the Leetown Science Center is supporting work in the ecology of karst systems in the panhandle of West Virginia. Contacts: Hugh Bevans, Ward Staubitz, Peter Lyttle, and Jim McNeal.

**Assessment of Fractured-Rock Aquifers** is needed to increase
knowledge of the flow, storage, and chemical interaction of ground water
in fractured-bedrock aquifers. Our understanding of these complex
systems will improve by integrating geologic mapping and related
geologic data with hydrologic investigations to gauge the effects of
bedrock lithology and structure on ground-water flow and chemistry. The
National Cooperative Geologic Mapping Program's Bedrock Regional-Aquifer
Systematics Study Project is completing a study in FY 2005 and will be
developing a plan for follow-on work beginning in FY 2006 in the New
England and Appalachian regions in conjunction with proposed
regional-aquifer analyses supported by the Ground-Water Resources
Program Contacts: **Peter Lyttle, Dave Russ, and Rich Harrison.**

**Other Activities**

In many parts of the country, increasing competition for water requires
resources planners, managers, and elected officials to consider the
varied demands of domestic suppliers, agriculture, industry, as well as
environmental and recreational interests. New projects will focus on
ground-water/surface-water interactions, estimates of recharge,
evapo-transpiration, inter-basin transfers, and other components of the
water cycle, as well as suitable water quality for intended uses. These
projects will afford opportunities for interactions with the Geology
discipline in establishing the hydrogeologic framework; with the Biology
discipline in determining the effects of changing ground-water and
surface-water supplies on aquatic habitat; and with the Geographic
discipline in obtaining land-characterization/land-cover data.

Contact: **Glenn Patterson**

Changes in climate over short and long time scales have profound effects
on water budgets. Anthropogenic effects on the chemical character of
rainfall alter lacustrine and soil pH and nutrient status. The
Hydrologic Networks & Analysis (HN&A) Program elements of Climate Change
Hydrology, DOI Cost-Share, and National Atmospheric Deposition Program
collect and publish data and interpretive results that are useful to
scientists studying issues related to Water for Ecological and Human
Use. Contact: **Matt Larsen.**

######## [Monitoring and Remote Sensing]{.underline}

[]{#Monitoring .anchor}

About half of the Cooperative Water Program consists of water-resources
data collection, involving ground water and surface water, mostly
through *in-situ* sensors and manual measurements and sampling. Some of
the monitoring and research involves remote sensing, such as LIDAR
surveys for flood-inundation mapping, and INSAR surveys for subsidence
due to aquifer compaction. Contact: **Glenn Patterson.**

The USGS conducts a variety of monitoring activities at local to global
scales; continuously, periodically, or a-periodically; and in-situ or
remotely. Data are acquired from systems such as Earth observing
satellites, seismic networks and stream flow gauges. Phenomena monitored
are many and varied including water quantity and quality, earthquakes,
volcanic activity and landslides, wildlife health and habitat, land
surface structure, land cover, fire fuels, invasive species, and the
geomagnetic field of the earth. These data, collected and archived in
ways to ensure high quality and long-term consistency, are essential for
USGS and external user applications. The Monitoring/Remote Sensing
Action Plan as well as Regional and Program reviews of that document
suggested a number of steps for improving USGS monitoring. These can be
grouped into two broad categories:

**Monitoring partnerships --** Partnerships among programs within USGS
and with external partners to improve and enhance monitoring. Monitoring
partnerships can be achieved both through a geographic focus, and
through shared programmatic interests in particular types of monitoring
data, technologies, methodologies, or strategies. In both cases, care
should be exercised to ensure that monitoring data are effectively
integrated and archived in national databases. The following examples
are planned for FY-2005:

-   The Land Remote Sensing, Volcano, Earthquake and Ground Water
    Programs are working together and with external partners to develop
    prototype operational Synthetic Aperture Radar Interferometry
    (InSAR) monitoring systems. Each of these programs is contributing
    staff time and OE through existing projects, and all are
    collaborating with external partners in NASA, NSF, and NOAA to
    develop community data policies and community advocacy in support of
    wider access to and use of SAR imagery. Contingent upon
    congressional appropriations for the FY-2005 USGS InSAR initiative,
    VHP will provide up to \$1,100,000 for acquisition of new satellite
    imagery from existing Canadian and European satellites, acquisition
    of digital elevation models for high-priority volcanoes lacking
    these data, support of essential ground-based monitoring needed to
    evaluate and validate the significance of deformation detected by
    InSAR, and research to enhance the use of InSAR as a monitoring tool
    and to develop better models for interpreting crustal deformation.
    Representatives from the program partners will continue to work
    together and with partners from NASA, NSF, and NOAA on joint
    planning for a consolidated approach to advance the use of InSAR for
    mission objectives and in support of NSF's EarthScope initiative in
    FY-2005. Contacts: **Jim Quick, Roz Helz, and Jay Feuquay.**

-   The Famine Early Warning System, which was developed as an
    international application funded by Geographic Analysis and
    Monitoring and Land Remote Sensing Programs, will cooperate with the
    National Stream Information Program (NSIP), to determine its
    usefulness in conjunction with the WRD-supported network of 7,000+
    streamflow stations in the United States. Contact **Jim Verdin**.

-   The Land Remote Sensing Program continues a partnership with NASA
    and 15 international space agencies to observe the earth via the
    Landsat system. The system consists of the Landsat 5 and Landsat 7
    spacecraft and a network of coordinated but, independently operated
    ground receiving stations. Contact **Jay Feuquay**.

-   The implementation of President's Commercial Remote Sensing Space
    Policy is being accomplished by an interagency working group lead by
    the Commercial Remote Sensing project within the Land Remote Sensing
    Program. This activity will result in an understanding of
    government-wide requirements for high-resolution satellite image
    data and a mechanism to make purchases of the required data more
    efficient. Contact: **Greg Snyder**.

-   The Multi-Resolution Land Characteristics (MRLC) Consortium, is a
    partnership of 10 federal organizations (EPA, NOAA, USFS, USGS, BLM,
    NRCS, NPS, NRCS, NASA, and USFWS) that have pooled their land cover
    mapping requirements and resources to produce the National Land
    Cover Database (NLCD) 1992 and NLCD 2001. In FY 2004, the Consortium
    began testing methods to compare NLCD 1992 and NLCD 2001 with the
    intention of producing a change product that could be used for a
    variety of applications. Contact: **Nick Van Driel**.

**Evaluation, planning and reporting --** This category includes
bureau-wide activities such as evaluating and reporting on the status
and needs of our monitoring programs and the development of strategies
to improve and enhance monitoring and related data and database issues.
In general, programs with extensive monitoring activities are taking the
lead, with development and coordination of multi-year monitoring plans
(e.g., Advanced National Seismic System, National Water Information
System, NSIP, Landsat Data Continuity Mission, InSAR, Geographic
Analysis and Monitoring, National Volcano Monitoring System, and
others), as well as collaborating in the development of the FY-2006 USGS
Earth Observing and Monitoring (EOM) Initiative. Contact: **Jay
Feuquay.**

-   The Northern Rocky Mountain Science Center is participating with the
    National Park Service in the Greater Yellowstone Inventory and
    Monitoring Network. Contact: **Richard Jachowski.**

-   The Enterprise Information Program will assist bureau programs with
    information-related issues regarding security, data handling,
    collaborative networks, standards, integration, analysis,
    visualization, and customer feedback. Contact: **Tom Gunther.**

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-   The Volcano Hazards Program is developing a plan for a National
    Volcano Monitoring System to provide multi-parametric, comprehensive
    monitoring of all potentially hazardous volcanic centers in the
    United States. Contact: **Marianne Guffanti.**

[]{#Status .anchor}**[Status and Trends]{.underline}**

The streamflow and other water-resources data collected by the
Cooperative Water Program become part of the USGS long-term hydrologic
database and are available through the National Water Information
System. The streamflow data help to define long-term changes in
streamflow, such as the trend toward earlier snowmelt in northern and
mountain areas. Contact: **Glenn Patterson**.

The Geographic Analysis and Monitoring Program will publish a Status and
Trends Synthesis report in FY 2006, providing a national assessment and
synthesis of regional investigations on the rates, trends, causes, and
consequences of land surface change. Specific project tasks planned for
FY05 include data synthesis and publication of Status and Trends Topical
Reports. Contact: **Doug Muchoney**.

# [Carbon Studies]{.underline}

[]{#Carbon .anchor}

The Department of the Interior (DOI) manages nearly 25 percent of the
Nation's lands. Recent studies by the USGS (Open File Report 03-304)
indicate that 22% of the nation's soil organic carbon (SOC) is on DOI
lands. Of this, over half is on lands managed by the Bureau of Land
Management. Much of this carbon is stored in wetlands and other areas
affected by seasonal melting/freezing of ice and permafrost. Currently,
these areas are regarded as net carbon sinks, but the impact of climate
change and variability and land management practices could change many
of these areas from carbon sinks to carbon sources.

These estimates of carbon on DOI lands are based on existing (often
incomplete) databases and need to be refined to provide an accurate
estimate of carbon sources and sinks on DOI lands. Currently, there is
no focused research on factors that might reduce or enhance the capacity
of land to sequester carbon in current and future climate scenarios and
no mechanism for incorporating information from carbon cycle research in
land management decisions.

## Carbon stocks and carbon cycling on DOI Lands

If funding becomes available through the initiative process, Earth
Surface Dynamics (ESD) program will consider new proposals and requests
for enhanced funding for existing projects. Proposed work should build
on current efforts and expand the scientific base by providing
monitoring, research, and assessment/data coverage to meet increased
land use planning and monitoring requirements.

Proposals should address one or more of the following focus areas:

-   Characterizing and assessing carbon exchange mechanisms;

-   Establishing landscape controls over carbon exchange mechanisms;

-   Evaluating carbon resources and forecasting their status in future
    climate scenarios;

-   Improving estimates of soil carbon inventories to facilitate carbon
    sink/source estimates;

-   Assessing the effectiveness of resource management and restoration
    practices on carbon sequestration and trace-gas emissions;

-   Identifying ecological and resource tradeoffs that might accompany
    carbon sequestration strategies on managed lands;

-   Integrating ongoing applied research on the CO~2~ storage capacity
    of geologic formations with the detailed geology of Federal Lands

Amount of funding potentially available: \$1,500,000

Contacts: **Nick Lancaster, Martha Garcia**.

Data collected in the **Cooperative Water Program** help to determine
carbon storage and fluxes in rivers and other water bodies, and help to
characterize the carbon involved in hydrologic processes. Contact:
**Glenn Patterson.**

**Hydrologic Networks and Analysis (HN&A) Program** elements of Climate
Change Hydrology, DOI Cost-Share, National Stream Quality Accounting
Network, and the Hydrologic Benchmark Network collects and publishes
data and interpretive results that focus on precipitation inputs and
streamflow outputs, applicable to Carbon Research. Contact: **Matt
Larsen.**

[]{#Priority .anchor}**[Priority Ecosystems Science]{.underline}**

Through Priority Ecosystems Science (PES), formerly Place Based Studies,
the USGS provides integrated science support for adaptive management of
priority ecosystems. Activities include collaboration and integration of
expertise from, Earth Surface Dynamics, Geographic Analysis and
Monitoring, Toxic Substances Hydrology, Hydrologic Networks and
Analysis, and Biological Research and Monitoring to achieve a
system-scale understanding of the natural and anthropogenic factors
affecting ecosystems and to better understand the interactive nature of
resources and the environment. Additionally, PES studies expand the
scientific base by providing temporal and spatial monitoring, research,
and assessment/data coverage to meet land use planning and monitoring
requirements. PES activities are currently concentrated in the following
study units: Chesapeake Bay, Greater Everglades, Mojave Desert, Platte
River, San Francisco Bay, and Yellowstone.

PES does not foresee any increases to funding in FY05 and does not
anticipate any new starts. Funding levels for ongoing activities in FY05
may be decreased due to increased Bureau costs. The PES National
Coordination Council will evaluate future funding scenarios and provide
recommendations to the PES Study Unit coordinators.

**Chesapeake Bay.** The ecosystem of the Chesapeake Bay, the Nation\'s
largest estuary, has been in decline due to poor water quality, loss of
habitat, and over harvesting. USGS efforts provide information on the
critical linkages between land-use, generation of sediment and
nutrients, and the impact on water quality, habitats, and living
resources in the Bay to help formulate and evaluate strategies to
restore the function and integrity of the Bay. Contacts: **Scott
Phillips, Dave Russ, and Martha Garcia**

Greater Everglades

The Greater Everglades ecosystem is a unique network of diverse habitats
that encompasses a large part of southern Florida. Much of the area has
been dramatically changed due to major urbanization and agriculture.
Water is the principal driving force within this system and supplying
sufficient water to support these diverse habitats is a continuing
challenge for water and resource managers and the focus of USGS
research. Contacts: **Ronnie Best, Tom Armstrong, and Martha Garcia**

Platte River

The central Platte River Valley in Nebraska is the staging area for
migratory water birds of the Central Flyway. Changes in water and land
use have transformed the river system and impacted the habitat. Ongoing
USGS efforts are in support of an MOU between the DOI and the States of
Colorado, Wyoming, and Nebraska to develop a basin-wide management plan
for habitat recovery. Contacts: **Randy Olsen, Martha Garcia**

Mojave Desert

The Mojave Desert Ecosystem lies over southern Nevada, western Arizona,
southwestern Utah, and southern California. USGS research provides an
understanding of the physical and biological processes that influence
vulnerability of the desert ecosystem to disturbance and recovery.
Providing practical guidance for land managers aimed at restoring
damaged ecosystems and minimizing future disturbances. Contacts: Jayne
Belnap, Martha Garcia, Allison Shipp

San Francisco Bay

More than 8 million people reside or work around San Francisco Bay.
Human encroachment endangers the natural habitat and the quality of
water. USGS efforts in the bay support the construction of an
interdisciplinary model of the Bay system to address questions on
habitat, sediment, toxic contaminants, and water flow.

Contacts: **Jan Thompson, Martha Garcia, and Allison Shipp**

**Yellowstone**

Efforts aimed at studying the effects of human activities on wildlife
ended in FY04. For further information on Yellowstone activities
Contacts: **Martha Garcia or Dick Jachowski**

[]{#Science .anchor}

**[Science on the DOI Landscape]{.underline}**

Science on the DOI Landscape (estimated funding: FY 2003, \$0; FY 2004,
\$1.5 million; FY 2005, \$2.7 million) (modified from the Greenbook)

With new funding from Congress in FY 2004, the Science on the DOI
Landscape initiative began to respond to the burgeoning requirements of
DOI bureaus for the type of scientific research that USGS has to offer.
Through increased communication and collaboration with those bureaus at
the regional level, USGS is addressing some of the relating bureaus'
priority needs to their land and resource management responsibilities.

Funds were leveraged via jointly developed work plans that lay out the
objectives, science needs, resource management benefits, outcomes and
specific deliverables, and deadlines. Products such as decision support
tools, models, systematic analyses, and technical assistance will be
tailored to provide essential information to DOI bureaus, ensuring that
they have the information and tools to make credible land and resource
decisions. This synergy between science and resources also allows all
bureaus to meet their strategic and annual performance metrics.

In FY 2004, USGS received \$1,500,000. Consequently, each region with
concurrence from the partner DOI bureaus built on existing projects for
DOI bureaus and leveraging internal programmatic funds and/or
reimbursable funds to continue priority work for bureaus.

The additional \$1,225,000 requested in FY 2005 will build on FY 2004
work and allow initiation of selected priority activities. Developed in
concert with DOI bureaus, project criteria will be based on critical DOI
needs assessed at the time of appropriation, on multi-bureau partnership
opportunities, on results that can be applied across multiple
landscapes, and on meeting urgent bureau needs with tactical science.

# Eastern Region

There are two DOI Landscape initiatives in the Eastern Region, mercury
in the environment and coral reef health. The mercury dollars are
supplementing funding for the following programs, Atmospheric Deposition
Study; Compiling, Modeling, and Web-Serving USFWS Fish-Mercury Data;
Baseline Assessment of Mercury across the Freshwater -- Marine
Interface; and a Mercury Science Workshop. The coral reef health dollars
are funding a project to look at freshwater input to Biscayne Bay
National Park. The funding will be used to develop a long-term proposal
and some fieldwork this year.

*Coral Reefs* - The deteriorating health, biodiversity, and productivity
of reef ecosystems, including corals, fishes, and adjacent seagrass and
mangrove communities are major issues for DOI resource managers.
Attempts to maintain, conserve, and restore the living marine resources
of coastal parks and refuges have been limited, in part, by a lack of
understanding of natural versus anthropogenic changes, including the
uncertain impacts of many potentially confounding stressors. USGS
geologists, biologists, and hydrologists have teamed with NPS managers
to evaluate the causes of such environmental declines, specifically for
Florida's Biscayne Bay National Park. Eastern Region, FY04 DOI Landscape
funds are being used to supplement and enhance research activities in
Biscayne Bay by promoting strategic planning and the integration of
ongoing multidisciplinary research. In FY05, these efforts are expected
to further consolidate available information gleaned from monitoring
data, diver surveys of disease occurrence, remote sensing and habitat
mapping. New sampling methods and locations may be required. USGS
scientists will assess and model ground water/surface water circulation
and any associated flux of contaminants and pathogens into the Bay.
Ultimately, the goal is to determine cause and affect relationships
between the declining health of the biota and variable water quality.
Contacts: **Tom Armstrong, Sonya Jones, and Chris Langevin**.

# Central Region

The Central Region staff will leverage funds for three projects: Mancos
Shale landscapes with BLM; coalbed methane with BLM, BIA, Tribes and
others; and rapid response with BLM, NPS, FWS, and USBR.

Mancos Shale Landscapes - USGS is providing technical assistance at the
request of BLM to develop and implement a land-use plan for the Gunnison
Gorge National Conservation Area (NCA). Integrated research includes
soil sampling and characterization, isotope chemistry,
mineralogy/petrology, interpretation of remote-sensing data, landscape
classification, simulated rainfall studies, characterization of physical
and chemical erosion, characterization of landforms, plant inventories
(including threatened and endangered plants), and investigation of the
relationships among soil, soil chemistry, and plant populations.
Information and interpretations will be used to help formulate land use
plans, and long-term research will produce tools and science solutions
that can be applied to other Mancos Shale landscapes and other

BLM lands.

Coalbed Methane - Coalbed methane (CBM) is playing an increasingly
significant role in meeting the energy needs of the United States. One
of the most active CBM areas in the country is in the Powder River Basin
(PRB) of Montana and Wyoming. The rapid pace of development in the PRB
is taxing regulatory and land management agencies in both States and
raising concerns about the environmental impact of CBM development. At
the same time energy companies are frustrated by the amount of time
needed to obtain the required permits to drill for and produce gas. In
the PRB, land impacted by development includes land managed by BLM,
tribal lands, and State-owned and privately owned land. CBM is produced
by pumping large volumes of water from subsurface coal beds. USGS will
enhance hydrologic monitoring and studies in cooperation with BLM, the
Bureau of Indian Affairs, the Northern Cheyenne and Crow Tribes, and the
Montana and Wyoming Departments of Environmental Quality to track the
impact of disposal of CBM-produced waters on water quality in streams in
the development area.

Missouri River -- The Central Region has begun discussion with BLM on a
possible new start with BLM on the Missouri Breaks National Monument,
starting with a small pilot project addressing their most urgent Land
Use Plan science needs. Other agencies (USBR, BIA, NPS, and FWS) may
have science needs in the area as well.

Rapid Response to Land Management Agencies -- In FY04, USGS is
conducting a demonstration project to respond rapidly to science needs
of DOI land management bureaus. The tasks under the project include
information sharing, technical assistance, and synthesis of existing
data and information. Targeted states are Colorado, Wyoming, and
Montana, and targeted bureaus are the National Park Service, the U.S.
Fish and Wildlife Service, and the Bureau of Land Management. Decades of
specialized research, assessments, and monitoring will be shared.
Technical assistance includes consultation based on data assessment and
use. Complex synthesis of existing data and information will result in
the design of tools tailored to the needs of land managers. In FY05, the
Bureau of Reclamation will be added and the area of consideration
increased. Contact: **Randy Olsen**.

# Western Region

In consultation with DOI Bureaus, the Western Region determined to
concentrate activities on a single landscape area to 1) build on
existing work with our DOI partners and 2) leverage funds so that the
new funding will make an incremental difference.

> **[Arid Southwest]{.underline}**
>
> Two sites, the Mojave Desert and the Lower Colorado River, met all of
> the selection criteria and had support from regional and State
> directors for the BLM, FWS, USBR, and NPS. FY 2004 funds were used to
> augment Mojave work. If the FY 2005 request is fully funded, WR will
> initiate a project that is currently targeted for Lower Colorado
> River. The Mojave Desert ecosystem covers 125,000 square kilometers in
> southern Nevada, western Arizona, southwestern Utah, and southeastern
> California. Most of this ecosystem is under the jurisdiction of
> Federal land management agencies, including four national parks, a
> matrix of BLM land, and six military training bases. The objectives of
> this project are to determine the living and non-living
> characteristics of high-quality habitat for selected rare, threatened,
> or endangered species in the Mojave Desert; identify and quantify
> long-term change that would directly or indirectly impact high-quality
> habitat in this ecosystem; determine monitoring protocols for short-
> and long-term evaluation of ecosystem change, particularly in
> high-quality habitat; and use geospatial models to extrapolate changes
> identified on monitoring plots to ecosystem scales. For DOI bureaus to
> effectively manage endangered species such as the desert tortoise and
> certain plant species, managers must have effective tools to quantify
> and model the characteristics of high-quality habitat. The objectives
> for the Lower Colorado will be determined through consultation with
> the other DOI bureaus and the proposal process for FY2005. Contact:
> **Allison Shipp**.

# [Alaska]{.underline} 

> Funds for Science on the DOI Landscape in Alaska will support the
> North Slope Science Initiative (NSSI) and high-priority resource needs
> of the BLM and the USFWS in Alaska through the establishment of an
> integrated science plan for issues associated with energy development
> on the North Slope. The long-term objective is to develop the capacity
> to provide integrated and scientifically based landscape forecast
> modeling tools to project the implications of alternative management
> scenarios on the biotic and physical components of Arctic Coastal
> Plain and Foothills. The USGS in FY 2004, working closely with BLM and
> USFWS, initiated a research project that builds toward this
> forecasting capacity.
>
> This project, implemented through a peer-review process, will serve as
> a prototype to assist BLM and USFWS in understanding the potential
> outcomes of policy and management decisions through use of predictive
> landscape modeling at decade scales as key for managing for long- term
> ecosystem health and sustainability. Contact: **Mark Shasby**.

[Other USGS Programs also fund DOI-related projects, for
example:]{.underline}

The Hydrologic Networks & Analysis (HN&A) Program elements of Water
Quality in the National Parks, DOI Cost-Share, and the Hydrologic
Benchmark Network collect and publish data and interpretive results that
are applicable to studies conducted under Science on the DOI Landscape.
Contact: **Matt Larsen**.

The Enterprise Information Program intends to work with both the Mancos
Shale Landscapes and Mercury Contamination integrated science projects
to provide in-kind support (technical expertise and access to hardware
and software infrastructure) in the development of information-related
tools and capabilities for scientists, partners and customers. These
tools and capabilities, in combination with those developed with other
projects, will form the initial elements of a bureau integrated
information environment. Contact: **Tom Gunther**.

[]{#Central .anchor}**[Central Region Integrated Science Partnerships
(CRISP)]{.underline}**

The Central Region is assuming continuation of regional partnership
funding at the level of \$500,000 each. FY05 will be the final year of
funding for Carbon Storage in the Prairie Potholes, Lower Missouri
River, and NativeView sites. Other continued funding will be the FY04
new starts: South Platte Aggregate Study, Perchlorate in Water, Gulf
Coast Data Base and Information Management System, and Canyons of the
Ancients Fire Study. New starts will be selected from other ideas that
were solicited from our Cost Centers in FY04. Contact: **Randy Olsen.**

[]{#Western .anchor}**[Western Region Flexibility Funds
(WRFF)]{.underline}**

The Western Region will continue to fund and foster new integrated
science efforts in the Region using the \$500,000 in Western Region
Flexibility Funds. Funds will be used to support the work developed by
the Region in collaboration with other DOI agencies, state, federal, and
local stakeholders. These efforts address multi-disciplinary problems
associated with the Lower Colorado River Basin, the Great Basin in
Nevada and adjoining states, the Upper Columbia River Plateau, and
linkages between upland watershed and coastal reef issues in Hawaii.

In addition, the Western Region will provide smaller amounts of WRFF to
support integrated science workshops and efforts to build collaborative
interdisciplinary science efforts in the Region. Contact: **Allison
Shipp**.

[]{#Ecological .anchor}**[Ecological Systems Mapping
Initiative]{.underline}**

Ecological Systems Mapping is an FY05 USGS Initiative led by the
Geographic Analysis and Monitoring and the Biology Discipline\'s
Ecosystem Programs. It will begin in FY05 with a comprehensive
assessment of current ecological systems mapping activities across the
nation. This assessment will provide the framework for the development
of strategic Science and Business Models/Plans to implement mapping, to
establish priorities for new mapping information needed, and to guide
the selection of pilot locations. Contingent on funding for FY06 and
FY07, pilot activities at two scales, national and regional, may be
initiated. A national pilot is needed to demonstrate and test the
ability to synthesize and use ecological data, in conjunction with
remote sensing, physical and thematic map data, to map across multiple
scales: ecoregions, ecosystems, species assemblages, and species. This
will build on a largely untapped strength of USGS to manage a rich
national and global spatial database, and our ability to analyze these
data to support ecological mapping at scales ranging from local to
national. Contacts: **Doug Muchoney and Bill Walker.**

[]{#SectionII .anchor}**Section II: Discipline Directions for FY05**

**Biology Discipline**

[]{#Biology .anchor}

**BIOLOGICAL RESEARCH AND MONITORING PROGRAMS**

The six programs of the Biological Resources and Monitoring subactivity
are identified under the Resource Protection theme within the DOI One
Plan Goal to "Improve Health of Watersheds, Landscapes." The DOI One
Plan provides the framework for currently ongoing efforts to establish
and develop five year strategic plans for each of the six programs.
Although the five year plans are not yet finalized, at a minimum, each
program has completed an initial scoping of focus issues and program
goals. The following annual program guidance reflects to a large extent
the goals, themes, and program objectives likely to be codified in final
five year strategic program plans. As such, the scientific emphases in
the following annual program guidance relate directly to both bureau and
department-wide strategic goals.

######## [Contaminant Biology Program]{.underline} 

The Annual Program Guidance for 2005 is based on the results of the
Contaminant Biology Program Review. The report from the Review can be
found at <http://biology.usgs.gov/contam/about.htm> In FY 2004; the
Program is developing its 5-year plan. The Plan will be organized around
eight focal areas, which are based on an analysis of the Review
recommendations, partner needs, and current scope of the Program. These
focal areas are nested within the three Program goals as follows:

> Goal 1. Toxicology and Chemistry:
>
> Chemistry and toxicology of emerging chemicals and new generation
> pesticides
>
> Endocrine Disruption
>
> Toxicity testing/ criteria development
>
> Monitoring and biomarkers sampling devices, molecular biology
>
> Goal 2. Contaminated Habitats:
>
> Assessment and restoration of contaminated habitats
>
> Mercury
>
> Metals and mine waste
>
> Goal 3. Integration of Ecological Stressors:
>
> Effects of multiple stressors on species, communities and ecosystems

The Contaminant Biology Program is identified under Resource Protection
within the DOI One Plan Goal to "Improve Health of Watersheds,
Landscapes". Most of the projects will fall within the work activity,
"L4 Conduct Assessments..." or "L5 Conduct Research ..." though some
tasks will be more closely related to "L3 Provide technical
assistance...", or "P1 Manage and distribute data..."

[Goal 1. Toxicology and Chemistry]{.underline}: Determine the causes,
fate, exposure and effects (including sublethal effects) of
environmental contaminants. Develop and standardize biomarkers,
molecular biology methods and other analytical and toxicological
methods.

Increase: New work should emphasize:

-   Identification, fate and effects of emerging chemicals (e.g.,
    pharmaceuticals, new pesticides, personal care products, brominated
    diphenylethers). (PWRC, CERC, FRESC, FISC and others)

-   Work on endocrine disruption should strive to include a
    population-level or reproductive fitness component that can be tied
    to population-level effects to extend biomarker research. Emphasis
    should be placed on laboratory to field efforts(CERC, PWRC, FISC)

-   Differential sensitivity across species and prediction of the
    comparative sensitivity of untested species, especially imperiled
    species or groups such as amphibians and freshwater mussels, and
    those whose populations have declined. This information should build
    toward a stronger understanding of the physiological/genetic or
    environmental basis of toxic response. Work should help determine
    the adequacy of surrogates for assessment and criteria. (PWRC, CERC,
    FISC, WERC, UMESC)

-   A synthesis of existing information to develop a prioritized list of
    compounds for study using multiple lines of evidence is needed.

-   For many years, the Contaminant Biology Program has supported
    development of assessment methods involve swallows. An assessment of
    our accumulated experience with this technique is needed to better
    focus future scientific studies that use swallows to assess
    contaminated sites. Researchers using this technique should work
    together to develop a white paper in FY 2004 to inform the Program
    5- year plan, The white paper should review what has been learned
    about this technique and what unknowns should be studied in order to
    improve its effectiveness, interpretability, reliability,
    application and ease of use. The white paper should also explore
    alternatives, including improved modeling capabilities and describe
    the questions that the technique can and cannot address. (PWRC,
    CERC, UMESC)

-   Development of molecular biology methods for determining contaminant
    exposure, and tying molecular-level effects to effects at higher
    levels of biological organization. (FISC, CERC, PWRC, LSC)

> Maintain to completion: Scientists should continue to determine the
> causes, fate, exposure and effects (including sub-lethal effects) of
> environmental contaminants. Continuing research should develop and
> standardize biomarkers and other analytical and toxicological methods,
> and support development of criteria for water quality, wildlife, and
> sediments to protect species of National interest (all centers).
>
> Decrease: Existing tasks should be completed, but no new swallow work
> should be started unless it is responsive to the conclusions of the
> white paper. (PWRC, UMESC, CERC, et al)
>
> Capabilities: Enhance molecular biology facilities, staff and
> supporting capabilities for work on contaminant-driven questions.
> (LSC, FISC, CERC, PWRC)

Goal 2. [Contaminated Habitats]{.underline}: Develop the scientific
basis for assessment, restoration and monitoring of habitats that are
contaminated by mining, agriculture, urban wastewater, industry, and
chemical control agents. Develop the toxicological basis to remediate
and prevent contamination by providing information on the safety of
chemical concentrations, biological controls, non-target effects of
chemical controls for invasive species, fire, and other hazards.

Increase:

-   Science and assessment to support goal-setting, monitoring and
    restoration of damaged or degraded ecosystems for Departmental
    Natural Resource Damage Assessment and Restoration (NRDAR)
    activities. (CERC, PWRC, FRESC, WERC and other centers)

-   Convene a workshop on restoration of contaminated sites to develop
    the conceptual framework for building this area of science and to
    improve cross-ecosystem understanding of restoration lessons
    learned. (CERC)

-   New work on mercury should include components related to molecular
    biology techniques, reproduction, metabolism, endocrine function and
    environmental aspects of mercury fate and bioaccumulation. (CERC,
    PWRC, FISC, LSC)

-   Support an Eastern Region workshop to present and synthesize
    technical information on mercury and foster discussion with DOI
    agencies. (FISC, PWRC, LSC, and other centers)

-   Expand energy research to include effects of energy exploration,
    development, transportation, production and use on federal lands,
    toxicity and decontamination of wastewater from coal bed methane,
    drilling mud and other byproducts. (CERC, ABSC, PWRC)

Maintain to completion:

-   Research on assessment and monitoring of habitats contaminated by
    mining, energy development, agriculture, urban wastewater, industry,
    and chemical controls. (WERC, FRESC, CERC, PWRC, FISC et al.)

-   Toxicological research on the safety of chemical concentrations,
    biological controls, non-target effects of chemical controls for
    invasive species, fire, and other hazards. (CERC)

-   Studies on bioaccumulation, fate and effects of contaminants related
    to recreational activities (e.g., lead shot, exhaust fumes and grey
    water from recreational vehicles), excessive nutrients and
    sediments, agriculture, and industry. Develop options related to
    mine waste and acid mine drainage. (all contaminants centers)

-   Maintain studies of the effect and transformation of mercury on
    avian maturation and reproduction. Continue studies on
    species-specific differences in mercury toxicity. (PWRC, FRESC,
    CERC)

[Goal 3. Integration of Ecological Stressors]{.underline}: Improve the
scientific basis for evaluating the effect of multiple stressors,
multiple levels of biological organization and multiple temporal and
spatial scales.

Increase:

-   Establish demonstration sites to link ecological models, biomarker
    responses and toxicological tests in collaboration with other
    disciplines, NAWQA and BEST. (FORT, CERC, WFRC and other Centers)

-   Determine the effects of exposure to multiple contaminants, and
    multiple stressors. Determine the cause of dieoffs. (All
    contaminants centers)

-   Expand databases that gather existing information on contaminant
    exposure and effects. (PWRC, CERC)

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-   Continue efforts to determine the interacting stresses to
    Departmentally important species or groups of species, such as sea
    ducks, mussels and salmon (WFRC, CERC, PWRC, FISC, LSC, WERC)

# Decrease

-   The President's budget has a decrease for Mark Twain. Please take
    this into consideration in planning for 2005. (CERC, Missouri
    District and other centers)

Contact: **Sarah Gerould.**

## *[Fisheries: Aquatic and Endangered Resources Program]{.underline}*

## ***The Fisheries: Aquatic and Endangered Resources (FAER) Program mission supports the conservation, restoration and adaptive management of our Nations valued fisheries and aquatic resources by providing scientific research expertise to DOI, other federal, state Tribal, and non-governmental natural resource managers. Research studies focus on health and diseases, diversity, natural history, species interactions and habitat requirements of fishes and other aquatic organisms. At risk species and those that are imperiled or endangered receive special research interest. FAER Program scientists have developed a 5-year strategic plan that elucidates the future FAER science challenges and research efforts. The FY05 Annual Program Guidance reflects changes in program direction as identified in the 5-year strategic plan.*** 

New Resources: An increase of \$1M for Upper Klamath Basin Studies will
expand biological assessments of fisheries and aquatic resources in
response to needs identified at a recent Klamath Basin workshop.
Research needs were identified by DOI (USGS, FWS, USBR and BLM), other
Federal agencies (USFS, NRCS), state and Tribal natural resources
agencies, and the Klamath Basin water user groups. An additional \$400K
of research scientist expertise is being redirected within Biological
Resources to expand the scope of ongoing integrated biological and
hydrologic research and monitoring in the Basin where endangered fish
species and agriculture share limited water supplies of poor quality. An
increase of 500K for the Great Lakes basin will enhance research of the
Deepwater Science Program to develop the knowledge and technical basis
for assessing, protecting, and rehabilitating the valuable fishery
resources and aquatic habitats in the Great Lakes. The USGS program is
critical to State, Federal, and Tribal management of fisheries resources
throughout the lakes.

# **[Goal 1. Aquatic Animal Health:]{.underline} Determine the biotic and abiotic factors that affect the health and sustainability of fish, aquatic organisms and aquatic habitats.**

Start new research to:

-   Develop new and improved molecular genetic methods, biomarkers and
    genomic studies to detect pathogens, vectors, and to understand
    disease resistance.

-   Develop new disease treatments, vaccines, and disease risk
    management technologies.

-   Determine the long-term effects of environmental stressors at the
    organism, population, community and ecosystem levels in aquatic
    systems.

Continue research to:

-   Identify the effects of natural and altered habitats on the health
    of freshwater fishes, mussels, corals, invertebrates and their
    habitats.

-   Collaborate with FWS, USDA and the States in new fish drugs and
    chemical research to determine effects on fish and aquatic habitats.

### **New capabilities needed: Updated molecular biological staff and facilities. Disease models of interactions of environmental factors, aquatic organisms, and pathogens.**

[Goal 2. Aquatic Species at Risk:]{.underline} Determine the biotic and
abiotic factors that affect the sustainability and survival of
individuals and populations of fishes and other aquatic species.

Start new research to:

-   Develop new microbial, genetic and molecular techniques to identify
    emerging diseases and invasive species, and for the protection of
    imperiled native species.

-   Development of conservation genetics methods including biomarkers
    and data banks for rare and endangered aquatic species.

-   Develop population viability, risk and limiting factor analyses, and
    mechanistic models to assess the impacts of invasives on native
    aquatic organisms and aquatic habitats.

Continue research to:

-   Determine biological, life history, and habitat conditions that
    limit populations of at risk, imperiled, threatened and endangered
    species.

-   Determine biological, life history, and habitat conditions that
    favor invasive species.

### **New capabilities needed: Updated molecular biological staff and facilities. Models of interactions of aquatic organisms and environmental factors that displace native species and favor invasive, introduced and exotic species.** 

### **[Goal 3. Aquatic Species Diversity]{.underline}: Describe the genetic, spatial and temporal relationships among species to understand aquatic community structure and function.**

Start new research to:

-   Develop new molecular genetic, systematic, and genomic techniques
    with appropriate bioinformatic database systems for landscape-scaled
    assessments of aquatic community diversity and function.

-   Develop population viability analyses, risk assessment, limiting
    factor determinations and mechanistic modeling based on aquatic
    community structure.

Continue research to:

-   Describe the genetics, life history, habitat requirements and
    distribution of native, introduced, and invasive fishes and other
    aquatic organisms.

### **New capabilities needed: Genomic and metagenomic analysis, bioinformatic databases and bioinformatic systems to accommodate life history, community and landscape-scaled analyses of species and community diversity.** 

[Goal 4. Aquatic Species and Habitat Interactions:]{.underline} To
understand functional relationships among aquatic species and their
habitats to provide scientific guidance for their conservation and
management.

Start new research to:

-   Evaluate habitat limitations that inhibit successful survival,
    reproduction and sustainability of fish and other aquatic organisms.

-   Investigate the energy dynamics of aquatic ecosystems and the
    effects on aquatic communities.

-   Quantify habitat integrity and connectivity and to measure habitat
    disturbance.

Continue research to:

-   Determine the effect of habitat processes at various scales on
    fisheries and aquatic system productivity.

-   Understand the biology and community dynamics of fishes and other
    aquatic organisms at different trophic levels.

-   Identify limiting factors that affect fish populations and other
    aquatic organisms.

###### **New capabilities needed: Biometricians and modelers for mechanistic models of habitat disturbance effects on populations and species assemblages. Landscape-scaled bioenergetic and nutrient cycle models.**

###### **[Goal 5. Restoration of Species and Habitats:]{.underline}** Provide scientific research capabilities in support of the conservation and restoration of aquatic species in altered aquatic systems.

Start new research to:

-   Identify and quantify changes to aquatic habitats focusing on
    land-use effects on water quality and quantity that affect the
    health of fish and other aquatic organisms.

-   Develop conceptual models of aquatic habitats that identify
    indicator species, species assemblages, stressors, effects, and
    pathways.

-   Identify and quantify baseline conditions as a reference for early
    warning indicators of declining ecosystem health to help establish
    restoration goals.

Continue research to:

-   Determine how trophic dynamics, fish behavior, and population
    structure changes in altered habitats such as impounded rivers.

-   Determine the effect of changes in water quality, quantity, and
    hydraulics on aquatic organisms and communities to aid development
    of mitigation, conservation, and restoration of aquatic habitats at
    in-stream and landscape scales.

[Goal 6. Research Technical Assistance:]{.underline} Provide scientific
support as research technical assistance and information transfer to DOI
bureaus, other federal and state agencies, Tribes and non-governmental
natural resource managers.

Start new research to:

-   Increased timely interdisciplinary and collaborative research in
    response to scientific information needs identified by stakeholders.

-   Quick response to emerging science needs with a special emphasis on
    imperiled species and habitats affecting fish, other aquatic
    organisms.

Continue research to:

-   Ensure timely, responsive, cost effective, and scientifically
    credible products and information.

-   Use the multi-disciplinary expertise and experience of USGS to
    provide sustained scientific support.

-   Anticipate research and development needs to anticipate emerging
    issues.

Contact: **Jim Preacher**

####### **[Invasive Species Program]{.underline}** 

[]{#Invasives .anchor}In FY 2005, the USGS will again strive to support
priority interagency initiatives developed cooperatively with the
National Invasive Species Council (NISC), including continuing projects
initiated through the \$2.025 M FY04 program increase. New thrusts,
through proposed increases in the President's FY05 budget, will focus on
developing innovative control methods for invaders of inland waters and
expanded research on brown tree snake. The National Institute of
Invasive Species Science (NIISS), through its newly established
Coordinating Committee and core staff, will facilitate cooperation among
BRD centers, USGS programs, and research partners in developing accurate
surveys, multi-scale smart monitoring, modeling and forecasting of
invasions, and in facilitating technical assistance to DOI resource
managers and cooperative state and regional pilot projects.

[Goal 1: Prevention:]{.underline} Conduct research and develop methods
and technologies to prevent the introduction of invasive species

# **Expand and increase coordination of ballast water research, including improved methods for identifying and monitoring ballast water-related organisms in coastal ecosystems and assessing ballast water treatment technologies in cooperation with Federal and state partners, and the ANS Task Force (NISC-FY05-Initiative 5). (WFRC, CARS, LSC)**

# Increase research on potentially destructive invaders not yet established in Hawaii, such as fire ants. **(PIERC)**

[Goal 2: Early Detection and Rapid Response:]{.underline} Identify and
report new invasions and assess risks to natural areas and waters.

-   Through NIISS, continue developing a national network for early
    detection (ED), monitoring and rapid assessment of new invasive
    species and outbreaks of established invasive species in U.S.
    ecosystems in cooperation with the NBII and the NISC task teams,
    technical assistance for ED pilot projects for plant invasions in
    the mid-south and New England, invasions on DOI lands (with NPS,
    FWS, and BLM) and to facilitate pest and host plant surveys to
    support early detection and rapid response to the highly invasive
    cactus moth in the Florida panhandle (NISC-FY05-Initiative 9).
    (FORT, Hdq.)

-   Through NIISS, continue expanding detection, reporting, and
    near-real-time mapping of tamarisk in western North America
    (NISC-FY05-Initiative 2). (FORT, SBSC)

[Goal 3: Monitoring:]{.underline} Assess changes in populations and
distributions of established invaders

-   Continue cooperation with the Smithsonian Environmental Research
    Center, NOAA and the ANS Task Force to design survey and monitoring
    of particular taxonomic groups in vulnerable coastal aquatic
    habitats, including the harmonization of databases for reporting and
    disseminating species occurrences (NISC-FY05-Initiative 8). (CARS)

-   Continue diversifying efforts to integrate multi-scale monitoring,
    field survey and remote sensing methods in mapping existing and
    potential distributions of invasive plants in western rangelands and
    riparian areas; and invasive insects, including emerald ash borer in
    the Great Lakes region. Expand cooperation with NPS, FWS, and BLM to
    develop protocols for mapping invasions in public lands and inland
    waters. (NISC-FY05-Initiative 3). (FORT, NMD)

[Goal 4: Effects:]{.underline} Determine effects of invasive species and
susceptibility of habitats to invasion

-   Continue integrated research on the factors influencing spread and
    impacts of invasive species, including international cooperation to
    develop information on particular species in their native and
    invaded ranges. Priority areas include: western US (relationship
    between invasive plants and wildfires), southeastern forests and the
    Gulf Coastal plain, native prairies, continental montane ecosystems,
    the Mississippi/Missouri River System, the Great Lakes and
    Hawaii/Pacific Territories. (CERC, FRESC, FORT, GLSC, NPWRC, NWRC,
    PIERC, SBSC, UMESC, WERC)

-   Continue development and testing of models to predict species
    invasiveness, vulnerable habitats, probable pathways, and the likely
    rates and risks and impacts of invasions in different habitats. The
    models will be used in development of science-based risk assessments
    for species of priority concern to resource managers and other
    stakeholders in cooperation with NISC. (CARS, FORT, UMESC, NWRC)

# **Continue to provide technical assistance to DOI managers in utilizing USGS information and risk assessment tools in making decisions on management priorities and strategies. (facilitated through NIISS)** 

# **Continue to develop a risk assessment and decision support system for predicting aquatic invasions and their impacts, with emphasis on the Upper/Mid Mississippi Basin. (CARS, CERC, UMESC)**

-   Continue development of methods and capabilities for rapid
    assessment and forecasting of plant and insect invasions, with
    emphasis on the mid-South region. (FORT, NWRC)

[Goal 5: Control and Management:]{.underline} Provide approaches to
contain, reduce, and eliminate populations of invasive species and
restore habitats and native species

-   Centers should continue to increase emphasis on developing
    innovative and integrated methods for achieving environmentally and
    economically sustainable control of widespread invasive species at
    ecosystem and landscape levels. Applications of genetics and
    molecular technologies for controlling invasions should receive
    particular attention in centers having relevant capabilities. (CARS,
    CERC, FORT, FRESC, GLSC, LSC, NWRC, PWRC, SBSC, UMESC, WERC, WFRC)

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-   Through additional funding in FY04, in cooperation with appropriate
    WRD programs, continue developing methods for control of tamarisk in
    the southwest riparian ecosystems (NISC-FY05- Initiative 2) (FORT,
    SBSC)

-   Continue research to support control of nutria in the Chesapeake Bay
    region and Louisiana (NISC FY04 initiative). (LSC, NWRC, PWRC)

-   Continue experimental research to develop integrated control methods
    for widespread invasive plants that minimize post-control reinvasion
    and facilitate restoration of native grasslands, including efforts
    to develop an effective strategy for controlling leafy spurge
    (NISC-FY05- Initiative 4). (NPWRC)

-   Enhance research on the nature and timing of post-fire management
    interventions to control cheat grass to favor native plant and
    animal species in the Great Basin. (FRESC)

Increases:

-   Brown Tree Snake (300K) \-- FORT will build upon existing efforts
    supported with base funds to provide technical assistance and
    increase research to support effective interagency responses to
    prevent the spread and control the brown tree snake in U.S. Pacific
    Islands. (NISC-FY05- Initiative 1)

-   Innovative Control Technologies (700K) -- CARS, CERC, LSC and UMESC
    should coordinate development of integrated methods for monitoring,
    assessing, predicting, and controlling the rapid spread of several
    species of Asian carp (and other aquatic invaders) in the
    Mississippi Basin and the southeast, and preventing their
    introduction into the Great Lakes. Genetic and molecular approaches
    should be fully considered, and the initiative coordinated with
    other USGS programs in such areas as remote sensing applications,
    information systems and public reporting. (NISC FY05- Initiative 10)

[Goal 6: Information Management:]{.underline} Provide and coordinate the
collection, synthesis, and accessibility of invasive species information

Ongoing Program Activities:

-   Continue expansion of center-based national and regional invasive
    species information systems (i.e., National Non-indigenous Aquatic
    Species Database, Southwest Exotics Mapping Project, Hawaii Invasive
    Species Database) and their appropriate integration into the NBII as
    components of the Invasive Species Information Node. (CARS, FORT,
    SBSC, PIERC)

Contact**: Bill Gregg**

**[Status & Trends of Biological Resources (S&T) Program]{.underline}**

[]{#statustrends .anchor}Mission: To measure, predict, assess, and
report the status and trends of the Nation\'s biological resources to
facilitate research, enable resource management and stewardship, and
promote public understanding and appreciation of our living resources.

New Resources: In FY 05 the President's budget proposes an increase of
\$500K to support Great Lakes deep water fish monitoring and research
for stock assessments of biodiversity & community dynamics of deepwater
fisheries, enhancement of partnerships with State, Tribal, & Federal
entities, and vessel operations and equipment.

Directions for FY 05:

Aside from the above referenced increase, no new funding exists in the
Status and Trends of Biological Resources Program in FY05. However,
opportunity exists to better enable the Program to address the mission
and goals within existing funds and by leveraging reimbursable funding
sources such as Bonneville Power supporting work on the Columbia River,
and the U.S. Army Corps of Engineers supporting the Long Term Resource
Monitoring Program on the Upper Mississippi River.

[Goal 1:]{.underline} Provide a framework that facilitates the
integration of information from a variety of sources at multiple spatial
and temporal scales to describe and track the abundance, distribution,
productivity, and health of the Nation\'s plants, animals, and
ecosystems.

> Increase emphasis to:

-   Enhance communication among partners and seek to develop coordinated
    monitoring networks within Regions and among Center partners for
    ongoing biological inventory and monitoring (I&M) activities.

-   Develop comprehensive monitoring strategies for the Great Lakes
    System; Colorado River; Great Basin; sagebrush/sage-grouse habitats;
    desert and urban ecosystems.

-   Respond to, and leverage as opportunities arise, the need to develop
    monitoring frameworks re: North American Bird Conservation
    Initiative (NABCI), the National Fire Plan, National Invasive
    Species Management Plan, FWS Comprehensive Conservation Plans and
    the *Promise* report for Refuges, BLM Resource Management Planning,
    States through their Wildlife Conservation Planning.

-   Where opportunities exist, focus beyond single species to monitor
    guilds, habitat suites, biomes, systems.

[Goal 2:]{.underline} Develop and evaluate inventory and monitoring
methods, protocols, experimental designs, analytic tools, models, and
technologies to measure biological status and trends.

> Increase emphasis to:

-   Provide web access to peer reviewed protocols.

-   Develop methodologies and models to measure public knowledge,
    attitudes, and perceptions re: federal land and resource management
    issues and practices; environmental issues.

-   Develop methodologies/measures to better utilize and coordinate the
    complementary amphibian monitoring approaches of NAAMP and ARMI.

-   Develop measures of detectability within the context of existing
    monitoring efforts e.g., Breeding Bird Survey (BBS), point counts,
    ARMI, Great Lakes fish stock assessments.

-   Develop measures of comparability among lake fish stock
    assessments/techniques.

-   Develop and apply new tools and techniques to inventory and monitor
    biological resources utilizing a variety of approaches i.e.,
    molecular and genetic, isotopic, sound, satellites.

-   Develop methodologies to respond to NPS monitoring needs at multiple
    scales Park, region, ecosystem.

-   Develop BEST sampling strategies for large rivers in the Northeast
    including a possible joint demonstration project with NAWQA.

-   Develop tools and techniques to more effectively identify and
    evaluate the status of plant and animal species at risk and provide
    scientific guidance for their conservation and management.

-   Develop methodologies to measure and assess the impact and value of
    scientific studies to enhance our understanding of natural resources
    and processes and inform resource management and policy practices.

-   Develop and implement a schedule for the periodic review of
    long-term monitoring efforts.

-   Explore opportunities/approaches to acquire additional information
    on habitats within the context of existing monitoring efforts.

-   Partner with resource management bureaus to provide monitoring
    strategies to permit the evaluation of resource response to various
    management actions in an adaptive management context.

[Goal 3:]{.underline} Collect, archive, and share critical, high-quality
monitoring data in cooperation with our partners to enable a
determination of the status and trends of biological resources.

> Increase emphasis to:

-   Develop and implement, in concert with FWS a strategy to expand
    1-800 band reporting capabilities into Mexico.

-   Expand the Contaminant Exposure and Effects-Terrestrial Vertebrates
    database (CEE-TV) to incorporate contaminant exposure and effects
    information for terrestrial vertebrates (birds, mammals, amphibians
    and reptiles) residing in selected large river basins of the US.

-   Pilot an effort to utilize National Land Cover Data (NLCD) in
    combination with BBS data to assess the potential of these for the
    evaluation relation of land use change and bird population change.

-   Develop and implement, in concert with FWS, a strategy to catalog
    and report status and trends of visitorship at the Nation\'s
    wildlife refuges.

-   Ensure the availability, via web, of all S&T data and information
    products and where feasible ensure access using the infrastructure
    of the NBII.

At the Upper Midwest Environmental Sciences Center, the National Land
Cover Dataset 1992 was combined with Breeding Bird Survey data and made
available in a query-enabled ArcIMS Web site:
([http://www.umesc.er.usgs.gov/terrestrial/migratory_birds/bird_conservation_web_tools.html]{.underline}).
This site allows visitors to the website to download land cover and
associated bird count data at a variety of spatial scales. Continued
support will allow this site to include National Land Cover Data 2000,
the spatial implementation of analytical tools developed at Patuxent
Wildlife Research Center, and, possibly, the incorporation of other data
(e.g., Christmas Bird Count).

[Goal 4:]{.underline} Produce and provide analyses and reports that
synthesize information on the status and trends of our Nations\' flora,
fauna, and ecosystems and are responsive to the needs of the scientific
community, land and resource managers, policy makers, and the public.

> Increase emphasis to:

-   Document and assess the "lessons learned" through some of our
    longer-term efforts to monitor "systems" i.e., the Long Term
    Resource Monitoring Program on the Upper Mississippi for the purpose
    of identifying potential "indicators" of system condition and
    integrity and identifying those methods, practices, and experiences
    transferable to other efforts.

-   Work with other bureaus to provide training re: designing,
    conducting, and analyzing inventory, monitoring, and baseline
    surveys.

-   Provide on-line reporting of S&T (taxa; ecosystem; region)
    activities.

Contact: **Paul Dresler**

#### [Terrestrial, Freshwater, and Marine Ecosystems Program]{.underline}

[]{#Terrestrial .anchor}

Terrestrial, Freshwater and Marine Ecosystems Program (TFME) research
focuses on understanding the factors controlling the structure,
function, and condition of terrestrial, freshwater, and marine
ecosystems. Investigations identify, explain, and predict the ecological
consequences of short-term and long-term environmental changes,
including how human activities modify ecosystem components and processes
and how modified ecosystems can be restored and managed. Research
includes causal relationships underlying interactions between natural
biotic and abiotic communities and their environments.

The TFME Program is in the process of developing a 5-Year Strategic
Science Plan which will identify the priorities/needs for ecosystem
science research for the next 5 years. The planning effort is
emphasizing multi-disciplinary integrated research to achieve objectives
of the 5 Year Plan. The Science Plan is emphasizing integrated research
in the following areas: wetlands research, global change research, coral
ecosystem research and fire research, as well as landscape ecosystem
research.

New Resources: In FY05 the President's budget proposes increases of
\$500K for Northern Prairie Carbon Crediting work and \$350K for Science
on the DOI Landscape to support USGS performance in meeting the DOI
Resource Protection outcome goal of improve health of watersheds. This
increase will be used to do studies on the impacts of coal-bed methane
extraction on wetlands and aquatic resources and on the effects of
land-based sources of pollution on coral reefs in Hawaii.

Decreased Resources: The President's Budget calls for a reduction in
Fire Science funding of \$2.76 M. Regions and Science Centers should
plan to accommodate this reduction primarily within their fire science
and fire science related activities. (Note -- in prior years the
Congress has restored the reductions in the Fire Science funding however
there is no assurance funding will be restored for FY2005). Further work
on Lake Tahoe Decision Support System, which supports Lake Tahoe Land
use planning, will not be funded (-\$494K).

[Goal 1:]{.underline} To quantify and understand factors influencing
patterns of temporal and spatial variability in key ecosystem
components.

> Increased Emphasis to:

-   Focus on understanding coastal ecosystems -- coastal wetland loss
    and accretion and biodiversity in the Gulf of Mexico and impacts due
    to sea level rise.

-   Increase understanding of linkage between wetlands, rivers, lakes,
    and surrounding landscapes, determining causal mechanisms underlying
    ecosystem responses to global change.

-   Develop multi-disciplinary landscape level studies (ridge to reef)
    to address land-based sources of pollution, type of sediments and
    pollutants delivered to reef systems and the effects they have on
    the reef ecosystem including disease. These studies will be done in
    cooperation with States and other Federal agencies in support of the
    Local Action Strategies developed to address priorities of the U. S.
    Coral Reef Task Force.

-   Increase Global Change Research that directly supports the new
    strategic plan for climate change science program in: alpine
    ecosystems, coastal and wetland ecosystems, carbon cycle/carbon
    sequestration and arid lands.

> [Goal 2]{.underline}: To model factors controlling ecosystem patterns
> at various scales and develop decision support systems which integrate
> this information with management options.
>
> Increased Emphasis to:

-   Develop predictive models of land change based on restoration
    techniques, ecological function models for vegetation (coastal and
    terrestrial), monitoring of real-time hydrological and
    meteorological data.

-   Develop models and DSS tools to manage water quality and key
    biological populations in lakes (including Great Lakes), adjacent
    wetlands, and coastal wetlands.

-   Increase understanding of the key factors controlling riverine
    ecosystem patterns and processes and develop predictive models to
    better manage regulated river systems and riparian areas to slow the
    decline of key species (Mississippi R., Colorado R., and Missouri
    R.).

-   Develop adaptive management tools to predict implications of
    management policies on ecosystem structure and function.

> [Goal 3]{.underline}: To develop indexes of ecosystem sensitivity to
> change and vulnerability to potential stressors, and tools to predict
> ecosystem responses to environmental change.
>
> Increase emphasis to:

-   Increase knowledge of restoration strategies for prairie wetlands
    and riparian wetlands in the Mississippi Valley to increase the
    storage of atmospheric carbon in these wetlands.

-   Increase the understanding and effects of climate global change on
    coastal wetlands and migratory birds; sensitive species and island
    ecosystems; response of desert vegetation to increased temperature;
    and the effects of climate on carbon and nitrogen biogeochemistry in
    national parks; increased temperature and sea level rise on coral
    ecosystems in national parks and refuges.

-   Increase understanding on the relationship between vegetation and
    surface and subsurface hydrology, wetland and lake linkages and
    geologic processes.

-   Increase research for DOI lands on effects of land-based pollution
    on coral reefs in Hawaii and on impacts of coal-bed methane on
    wetland and aquatic resources.

> [Goal 4]{.underline}: To devise a restoration and adaptive management
> frame-work for impaired ecosystems.

Increase emphasis to:

-   Develop methodologies to assess post-fire impacts on natural
    resources, watersheds and municipal water sources.

-   Increase the scientific basis for wetlands restoration within the
    landscape with emphasis on the Everglades, San Francisco Bay, and
    coastal Louisiana, and riverine wetlands.

-   Develop ecological assessment tools to determine sustainable
    structure and function of terrestrial system linkages for recovery
    strategies for riparian systems, and develop multi-species
    approaches to restoration.

-   Focus on restoration research to support the Puget Sound coastal
    ecosystem of ecosystems.

-   Develop early warning indicators of declining ecosystem health;
    understand aquatic-restoration initiative with cross-cuts to include
    invasives, fisheries biology, and the associated wetland dynamics in
    coastal ecosystems.

Contact: **Stan Coloff**

##### [Wildlife: Terrestrial & Endangered Resources Program]{.underline} 

[]{#Wildlife .anchor}

The Wildlife: Terrestrial & Endangered Resources Program supports
research on terrestrial endangered species, migratory birds, amphibians,
mammals, and their habitats. Results directly support the management
programs of Federal and State wildlife agencies and non-governmental
conservation organizations. Specific reductions from 2004 funding levels
include: Diamondback terrapins research (-\$200K), Grizzly bear
population research using DNA (-\$1M), and Manatee population studies
(-\$500K).

Goal 1: To provide specific management models for declining migratory
bird populations:

-   Increase: Efforts to link landscape habitat change to responses in
    migratory bird populations, including neo-tropical migrants.

-   Decrease: None.

-   Capabilities needed: 1) Ability to model the population level
    impacts of avian disease. 2) Ability to use stable radioisotope
    analyses to elucidate geographic/habitat associations with critical
    life stages of migrants.

-   Opportunities: The Joint Venture partnerships established under the
    North American Waterfowl Management Plan seek participation by
    qualified scientists to help guide regional bird conservation
    activities. Opportunities exist to refine management models and
    engage partners in research efforts.

Goal 2: To develop restoration strategies for federal lands & critical
environments:

-   Increase: 1) Research to identify and counter long term threats to
    wildlife habitats on federal lands. When threats are unavoidable,
    seek measures that minimize/mitigate their effects on native
    species. 2) Partner with resource management bureaus to couple
    science experiments with management activities in an adaptive
    resource management context. Conduct these efforts to support sage
    grouse conservation.

-   Decrease: None

-   Capabilities needed: Ability to model the effects of catastrophic
    events (fire, flood, storms) and long term change (climate, invasive
    species) on wildlife and its habitats. When conditions permit,
    enhance staffing with expertise in habitat modeling, decision
    support tool, and adaptive resource management.

-   Opportunities: (Wildlife biologists should note that the \$1M FY2005
    request for Invasive Species may offer opportunities to address
    human-wildlife conflict issues)

Goal 3: To develop tools such as predictive models, decision support,
and expert systems for science-based management of wildlife and plant
populations and their habitats:

-   Increase: 1) Develop approaches that synthesize information on
    critical demographic parameters across species, life stages, and
    life strategies in order to better predict species/population
    vulnerability before declines occur. 2) Enhance research to assess
    the impacts of disease at the population level. Begin research that
    links environmental conditions and ecological factors in determining
    disease outbreaks and distribution. 3) Enhance capabilities to
    synthesize existing information and provide predictive tools to
    directly support resource management needs. 4) Evaluate the effects
    of energy development practices on critical life stages, important
    habitats, and disease dynamics.

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-   Decrease: None.

-   Capabilities needed: Spatially explicit risk assessment and
    management approaches to prevent, control, and eradicate disease
    agents. Ability to determine and quantify transmission pathways
    across species, including humans, with a focus on prevention.

-   Opportunities: Where opportunities arise, enhance staffing with
    biometric, statistical, population and habitat modeling, decision
    tool, and expert system expertise.

Goal 4: To evaluate the status of plant and animal species at risk and
provide scientific guidance for their conservation and management:

-   Increase: 1) Enhance efforts to assess the vulnerability of rare and
    imperiled species to adverse impacts from changes in land use and
    where possible, provide the information needed to mitigate these
    impacts and recover populations. 2) Apply the use of new
    technologies such as analyzing genetic materials in taxonomic,
    systematics, and conservation genetics research to enhance the
    determination of population viability and extinction rates.

-   Decrease: Reduce research on: Diamondback terrapin nesting behavior
    and habitat in the Chesapeake Bay (-\$200K), Grizzly bear
    populations in the Northern Continental Divide Ecosystem using DNA
    analysis (-\$1M), and Manatee population estimation methods in
    Florida (\$500K).

-   Capabilities needed: Consider opportunities for partnerships to
    increase expertise in botany, invertebrate zoology (Arthropod,
    Mollusc, Crustacean), herpetology, and bat biology.

-   Opportunities: As opportunities arise, support research projects for
    the geographic areas with the biggest information gaps and with
    greatest conservation urgency (not in any order): Southeastern
    rivers; Southern Appalachian lands; Hawaii; Great Basin; California;
    and Midwest grasslands.

Goal 5: To manage a national amphibian research and monitoring program:

-   Increase: Efforts to integrate population monitoring sponsored by
    the Amphibian Research and Monitoring Initiative (ARMI) with that
    being performed by others, thereby achieving a greater understanding
    of population trends on a landscape scale.

-   Decrease: None.

-   Capabilities: Spatially explicit models that park, refuge, and other
    managers can use to evaluate habitat management alternatives are
    needed to guide future amphibian conservation activities.

-   Opportunities: Under the provisions of the State Wildlife Grants
    program, many State wildlife agencies are developing amphibian
    monitoring programs in 2004-2005. There is an unprecedented
    opportunity for USGS scientists to engage in the planning process
    and help the States to design programs that complement USGS
    amphibian monitoring efforts.

Contact: **Greg Smith**

##### BIOLOGICAL INFORMATION MANAGEMENT AND DELIVERY

## *[Biological Informatics Program]{.underline}*

[]{#Biological .anchor}

The Biological Informatics Program is the one program funded by the
budget sub-activity Biological Information Management and Delivery
(BIMD). The Biological Informatics Program is identified under the
Serving Communities theme within the DOI One Plan Goal to "Advance
Knowledge through Scientific Leadership and Inform Decisions through the
Application of Science." The Program seeks to gather the biological
information generated by USGS and others, organize and integrate it in
useful ways, and promote its use through the development of tools and
standards to apply good science to societal challenges. A five-year plan
is currently being developed for the Biological Informatics Program;
however, the goals toward which the Program has been working remain
valid and provide direction for this annual program guidance. This
guidance assumes a slightly decreased budget for FY2005 from FY 2004.

Goal 1: Increase the availability and utility of biological resources
data and information.

Identify biological data and information resources at regional, center,
and field station level requiring informatics applications to preserve,
manage, increase utility of, and/or improve access to these resources
through incorporation in the National Biological Information
Infrastructure (NBII). Emphasize the management of those scientific
information resources most relevant to Bureau priorities.

Identify and establish or reinforce collaborations with providers of
content applicable to the priority themes and integrated science
initiatives of the Bureau. Emphasize, in existing partnerships, the
development, integration, sharing and use of information particularly
pertinent to those priorities.

In collaboration with FWS, modify and expand Gap Analysis tools and
processes to address issues in the National Wildlife Refuge System

In collaboration with NPS, incorporate Big Bend National Park
information requirements into NBII; continue collaboration to address
vegetation mapping in new parks. In collaboration with BLM, adapt the
vegetation-mapping program for BLM lands.

In collaboration with the Smithsonian Institution and other museums and
herbaria, develop the U.S. node of the Global Biodiversity Information
Facility, providing access to digital information on specimens contained
in natural history collections.

Within the NBII, proceed with building previously established NBII
nodes. Continue the initiation of the newly established Northeast
Information Node and the Mid-Atlantic Information Node, and expand the
capabilities of the Southern Appalachian Information Node, to address
biological resource issues critical to those respective regions.

Goal 2: Develop and apply standards, protocols, and techniques that
enhance the information discovery and retrieval capabilities.

Continue supporting and organizing interagency technical working groups
related to portal development, XML (eXtended Markup Language) adoption
with the federal government, and other emerging standards and
technologies.

Continue efforts to:

-   Develop and apply information standards and tools to enable better
    data discovery, management, mining, and delivery

-   Implement and adopt National Biological Information Infrastructure
    (NBII)/FGDC biological data standards

-   Develop customized controlled vocabulary subsets for priority
    Programs (e.g., invasive species, global change)

-   Develop the necessary open standards-based tools to support these
    standards.

Goals 3: Develop technologies and tools for the integration, analysis,
visualization, and application of biological information to natural
resources stewardship.

Increase efforts in the research, development and application of data
visualization tools. Develop integrated predictive models and decision
support systems that can be applied to priority programs or issues of
the Bureau and its customers and partners.

In collaboration with DOD, develop and apply information technologies
for the management of biological resources on military lands.

Goal 4: Apply innovative technologies and best practices to improve the
development, description, and dissemination of biological information.

Advance the application of geospatial technologies to support
understanding of land cover, species distribution and conservation
status. Increase availability of geospatial data through the NBII,
ensuring that national NBII Geospatial standards are applied to the
development and dissemination of geospatial data and information.
Support Open GIS geospatial standards in the development of biological
web mapping applications.

In collaboration with NASA, develop advanced information models, tools
and technologies to support natural resource science and
decision-making.

Goal 5: Conduct an information science research program to support the
advancement of biological informatics capabilities.

In collaboration with NSF, NASA, and other agencies continue funding a
joint grant initiative related to biodiversity and ecosystems.

Contact: **Barbara Bauldock**

[]{#Cooperative .anchor}**[Cooperative Research Units
Program]{.underline}**

-   Sustain a national network of state/university/federal partnerships
    pursuant to the Cooperative Research Units Act, with a legislated
    mission of research, education, and technical assistance on issues
    related to fish, wildlife, ecology, and natural resources.

-   Sustain a quality-driven, results-oriented, network of expertise for
    research, teaching, and technical assistance that is responsive to
    the resource information needs of state resource agencies and host
    universities participating in the Cooperative Research Units
    program.

-   Maintain science capabilities that are responsive to resource
    management information needs of agencies in the Department of the
    Interior, and provide Department agencies with access to these
    capabilities.

-   Enhance and support science programs in USGS by providing
    coordination and access to research capabilities at 40 host
    universities.

-   Maintain science capabilities that are responsive to resource
    management information needs of non-DOI federal agencies, state
    governments, non-government organizations, and other program
    partners, and provide partners with access to these capabilities.

Contact: **Ken Williams or Jim Fleming**.

[]{#GeographicInfor .anchor}**Geographic Information Office**

## [Enterprise Information Program]{.underline}

[]{#Enterprise .anchor}

The Enterprise Information Program (EIP) is developing an initial 5-year
program plan.

For FY 2005 and beyond, the Program will continue to emphasize two major
objectives:

-   Provide the overall policy, management, and operation of
    bureau-level systems and activities in information technology (IT),
    information security, information services, information resources
    management, and capital asset planning.

-   Provide in-kind support (primarily in the form of technical
    expertise and assistance) for collaborative activities with USGS
    science programs and integrated science themes to assist them in
    meeting their information-related objectives.

Key program priorities for FY 2005 include the following that, with one
exception noted below, will be conducted within existing base resources.

-   **Collaborate on Selected Science Information Integration
    Projects:** The Program will provide in-kind support (technical
    expertise and assistance, access to specialized hardware and
    software infrastructure, etc.) to collaborate on selected USGS
    science information integration projects. The goals are to assist in
    meeting specific information-related objectives of each project,
    while also documenting successful approaches and techniques that can
    be transferred to meet similar requirements across the Bureau. For
    FY 2005, emphasis in this area will be on collaborating on
    integrated science projects that address: the Mancos Shale, Urban
    Earth, and Mercury Contaminants, and on assisting in development of
    information management strategies for science programs and field
    science centers.

-   **Continue to Enhance USGS IT Security:** Enhancement of IT security
    infrastructure and operations continues to be the highest IT
    priority for the Department. The USGS is engaged in completing a
    significant enhancement of its underlying IT security operations
    infrastructure (including extensive network perimeter controls,
    separation of public and private systems and content, and enhanced
    vulnerability scanning and intrusion detection), and in providing
    program oversight necessary to maintain this secure infrastructure
    on a continuing basis. For FY 2005, the USGS is requesting an
    increase of \$1.8 million in the President's Budget to support these
    enhanced efforts. In addition, DOI has directed USGS to ensure that
    all information technology systems receive full IT security
    certification and accreditation (C&A) by the end of FY 2005. For the
    USGS, this includes major/critical application information systems
    (i.e., for science and for business/administration) and general
    support systems (i.e., infrastructure systems). The Enterprise
    Information Program is overseeing the bureau-wide C&A effort and
    providing technical expertise and funding to support completion of
    C&A for bureau-level systems by the end of FY 2005.

-   **Implement Active Directory:** Implementation of the Microsoft
    Windows Active Directory as the DOI-wide IT directory service is one
    of the key DOI-wide IT mandates. Use of a single directory service
    across the organization provides a centralized and standardized
    system to manage distributed network resources and services,
    administer user accounts, and provide more interoperability between
    offices. Benefits for USGS will include enhanced IT security,
    efficiencies and potential costs savings in management of our
    computing resources (desktops, laptops, and servers), and providing
    a fundamental building block of an integrated information
    environment that will make it easier for USGS scientists across the
    Bureau to collaborate and to share data, information and
    applications. USGS has been directed by DOI to ensure that all USGS
    offices have completed implementation of Active Directory by the end
    of FY 2005. The Enterprise Information Program is overseeing this
    bureau-wide effort.

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-   **Enhance USGS Public Web Sites:** The USGS maintains approximately
    300 public Web sites providing our science information to a wide
    variety of customers. The Enterprise Web project team works with
    interested science programs and offices to provide technical
    assistance and access to tools and services that can help ensure
    their public Web sites are secure, reliable, easy-to-maintain and
    update, and that they are carefully organized, designed, and
    equipped to allow customers to find, get, and use the data and
    information they need. Some of the important services provided
    through Enterprise Web include: a comprehensive USGS-wide thesaurus
    of technical and scientific terms and a thesaurus-based alphabetical
    index that supports more efficient indexing and searching of all
    USGS web sites; usability testing and automated customer feedback
    tools, tools to ensure web pages are fully compliant with Section
    508 accessibility requirements; and an on-line USGS "Publications
    Warehouse" that provides an integrated mechanism to search more than
    60,000 bibliographic citations for USGS reports and thematic maps
    and, in many cases, to link directly to the full on-line content of
    a given publication. In addition, the NatWeb component of Enterprise
    Web provides a highly secure, reliable, consolidated, and
    failure-resistant web server infrastructure that ensures that
    critical USGS public web sites will remain available during
    emergency situations. Migrating existing USGS science web sites into
    this secure infrastructure is helping USGS reduce the number of
    vulnerable public Web servers, reduce security related workload for
    content owners (i.e., science programs) and reduce traffic on
    internal networks.

Contact: **Tom Gunther**.

[]{#Water .anchor}**Water Discipline**

[]{#Groundwater .anchor}**[Ground water Resources Program]{.underline}**

The Ground-Water Resources Program and others have been supporting
development of a coupled surface-water/ground-water model. It is
anticipated that two to three field basins across the country will be
selected for model testing beginning in FY05. Contact: **Paul Barlow**.

## [Hydrologic Networks and Analysis Program]{.underline}

[]{#Hydrologic .anchor}

The FY 2005 budget request for the Hydrologic Networks and Analysis
(HNA) Program is \$29,492,000, which is a decrease of \$360,000 from
FY04. The HNA Program is a collection of activities designed to meet the
eight goals listed below. (See
<http://water.usgs.gov/usgs/prgmplans/hna_prgmplan.html> for additional
information).

# Monitor and assess important chemical constituents in precipitation and study the effects of atmospheric deposition on aquatic and terrestrial ecosystems. 

# Provide hydrologic data in support of interstate compacts, international treaties, border issues, and Congressional requests.

# Provide technical assistance and interpretive science to DOI bureaus.

# Characterize variations in hydrologic systems in response to atmospheric circulation and past climate changes, and improve climate and hydrologic models.

# Provide long-term data on streamflow and water quality in areas with little human impact.

# Provide basic water quality information at fixed sites in the Nation's largest rivers.

# Provide a secure repository for water data, improve the reliability of real-time water data delivered over the Internet, and increase the availability of water data holdings.

# Develop and test a decision support system for daily management of four western river basins, including basin-specific watershed and related hydrologic and biological models.

Contact: **Matt Larsen**.

Various projects within the HNA program that offer opportunities for
collaboration with scientists potentially funded through FY05 Annual
Program Direction Themes include:

1.  Climate Change Hydrology---Focuses on hydrologic causes and effects
    related to climate change, and paleohydrologic records. Contact:
    Bill Kirby.

2.  Water Quality in the National Parks---Projects selected by the
    National Park Service to help meet needs for water-quality data in
    the Parks. Contact: Mike Focazio.

3.  DOI Cost-Share---USGS helps to meet the science needs of other
    Interior bureaus. This program was expanded in FY04. Contact: Matt
    Larsen.

4.  A component of HNA funded from reimbursable (DOD) sources is the
    Department of Defense Environmental Contamination Program, headed by
    Bill Alley. Emitt Witt, in Rolla, MO, now serves as the Geography
    liaison for this program.

5.  NASQAN: Monitoring of the Yukon River began in FY 2001, and is
    planned to continue through FY 2005. The objective of the Yukon
    River effort is the establishment of baseline water-quality
    conditions for comparison with anticipated conditions 2 to 3 decades
    in the future. These observations will be important for
    understanding the release of carbon due to the expected partial
    melting of permafrost in the Yukon basin. Contact: Steve Sorenson

6.  Hydrologic Benchmark Network (HBN): Starting in FY 2004, annual
    interpretive products on HBN monitoring results are being produced,
    along with more intensive assessments at 5-year intervals; these
    annual products will include the release of some products in
    FY 2005. Contact: Mark Nilles

7.  NADP: The National Acid Deposition program supports 88 sites in an
    interagency program. NADP studies include: (1) detect trends in
    mercury deposition since the mid-1990s at over 50 NADP mercury
    deposition monitoring sites; (2) improve the understanding of
    long-term forest soil changes caused by acid rain by re-analyzing
    soil cores that were collected as early as 1893.

[]{#National .anchor}**[National Streamflow Information
Program]{.underline}**

In FY2005, the National Streamflow Information Program (NSIP) will not
start any new activities. Level funding since FY2001 and effects of
internal USGS restructuring will result in up to 50 existing streamgages
being discontinued. In addition, funding for understanding hydrologic
extremes (floods and droughts), funding for development and maintenance
of a reliable data delivery system, funding for regional and national
assessments of streamflow characteristics, and funding for research to
develop more reliable, less costly, and safer methods to measure
streamflow and to understand flow in rivers will all be held near FY2004
levels. The major emphasis in FY2005 will be to maintain as many
existing streamgages as possible given the funding level and increasing
costs. It is anticipated that each Water Resources District will receive
approximately the same level of funding as in FY2004. Contact: **Mike
Norris**.

## [Water Resources Research Act Program]{.underline}

The National Competitive Research Grant program authorized by the Water
Resources Research Act focuses on "water problems and issues of a
regional or interstate nature beyond those of concern only to a single
State and which relate to specific program priorities identified jointly
by the \[USGS\] and the institutes." The program will work with the
institutes and USGS discipline offices to develop specific priorities
for FY05. Probable FY05 priorities include research in the following
areas:

-   Methods of water availability assessment

-   Effectiveness of Best Management Practices in sustaining urban raw
    water supply qualify

-   Characteristics of watershed planning and management organizations
    that have a demonstrated capability to protect water supply quality.

    Work plans are solicited from investigators of all disciplines at
    universities across the nation. Work plans involving collaboration
    with USGS scientists are encouraged and are given preference in the
    selection process, though Federal employees cannot receive funds
    under these grants. Funding target -- within current funding (\$1
    million). Contact: **John Schefter.** More information is provided
    at <http://water.usgs.gov/wrri/>

## [Toxic Substances Hydrology Program]{.underline}

[]{#Toxic .anchor}

The Toxic Substances Hydrology (TOXICS) Program conducts water-quality
research on problems related to subsurface point-source contamination
and watershed- and regional-scale contamination. It provides unbiased
scientific information and tools that explain the occurrence, behavior,
and effects of toxic substances in the Nation\'s hydrologic environments
and support sound decision-making by resource managers, regulators,
industry, and the public. More information is available on the Internet:
[http://toxics.usgs.gov](http://toxics.usgs.gov/). Contact: **Herb
Buxton.**

Program funding in recent years for ongoing Program activities has
decreased. Therefore, Activities for FY05 are expected to focus on
maintaining focus on the highest priorities within existing resources.
Opportunities for work with the TOXICS Program in FY05 will occur in
selected project activities which are focusing on prioritizing ongoing
activities and maintaining the highest priority research within a
shrinking budget framework. Priority areas for such opportunities are
described as follows.

-   Subsurface Point-Source Contamination -- In FY05, a process will be
    initiated to develop research priorities and a revised strategy for
    investigations of contamination from subsurface point-source
    contamination. This is one of two primary Program goals and
    constitutes approximately 40 percent of program resources. This
    process will include a national meeting of active TOXICS Program
    researchers, other USGS researchers, University partners, and a wide
    range of stakeholders.

-   Contaminant plume characterization and remediation in fractured rock
    aquifers -- Cleanup of contaminant plumes in fractured rock aquifers
    lacks the fundamental knowledge of the geologic, geochemical and
    microbiological process affecting contaminant transport. An
    interdisciplinary team is being formed to conduct research at a
    contaminated site at the Naval Air Warfare Center in Trenton, New
    Jersey. Opportunities will exist in FY05 for detailed study of the
    geologic processes that affect the formation of fracture networks
    and the chemical and microbial processes that affect contaminant
    transformation and fate in fractured rock aquifers. Contacts:
    **Allen Shapiro and Pierre Lacombe.**

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-   Contamination related to mined lands -- After successful completion
    of the USGS Abandoned Mine Lands (AML) Initiative and development of
    a watershed based approach for remediation of AML contamination,
    opportunities exist to extend multi-disciplinary research to
    additional hydrogeologic and mining settings. A new research plan
    currently is being prepared for FY05. Contacts**: Briant Kimball and
    Chris Fuller.**

-   Pesticides and emerging environmental contaminants -- Emerging
    water-quality issues are identified and addressed through
    development of new laboratory methods and collection of baseline
    environmental information related to potential human and ecological
    health effects. A research agenda, which focuses on priorities for
    development of new laboratory methods to analyze pesticides and
    their byproducts along with field studies in common pesticide use
    settings, is being developed for FY05. Contacts**: Dana Kolpin and
    Kathy Kuivila.**

## [Cooperative Water Program]{.underline}

[]{#CoopWater .anchor}

About half of the total Cooperative Water (Coop) Program funding
supports hydrologic data collection and half supports interpretive
projects. Of this latter half, about 20 to 30 percent of the projects
end each year and others begin based on discussions developed between
district offices and cooperators on a continuing basis. Other USGS
disciplines and programs are welcome to participate in these discussions
by contacting the Regional Program Officers (Northeast: Eric Evenson;
Southeast: Sonya Jones; Central: Linda Britton; Western: Keith Prince,
or by contacting the individual District Chiefs. Priority issues for the
Cooperative Water Program include:

-   Hydrologic Hazards

-   Water Quality

-   Hydrologic Data Networks

-   Water Availability And Use

-   Wetlands, Lakes, Reservoirs, and Estuaries

-   Water Resources Issues In The Coastal Zone

-   Environmental Effects On Human Health

Details on these priority issues are available at
<http://water.usgs.gov/coop/priorities.html>.

In FY 2004 the Coop program received \$64 million in Federal funding,
which was matched with \$137 million in funding from non-Federal
cooperators (State, local, and tribal governments), for a total program
budget of \$214 million. The President's proposed budget for FY 2005
proposes a net decrease of about 1.4 percent for the Federal side of the
Coop program. Scientific priorities for the program are set at the
Headquarters level, in consultation with regions, field offices, and the
Bureau. Funding decisions are made primarily at the regional and
district level.

**[Hydrologic Research and Development]{.underline}**

[]{#hrd .anchor}(within existing funds)

\(a\) New efforts in extending the use of ground-water models include:
(1) model analysis of fracture flow and transport in hydrothermal and
volcanic systems (with GD scientists); (2) investigation of
flux-limiting algorithms for improving the accuracy of solution of the
transport equations; (3) adding features and processes into
solute-transport models such as a new particle tracking method and
random-walk solver into MODFLOW

\(b\) Enhancement of methods to characterize aquifer properties will
include: (1) experiments to provide estimates of hydraulic properties in
less-ideal (less-homogeneous) environments; (2) methods for determining
hydraulic properties that are related to areas of coal-bed methane, and
(3) evaluation methods to determine recharge rates in agricultural areas
(with NAWQA Program).

\(c\) The development of a multi-dimensional surface water modeling
system has been on going for a few years. A new code will be developed
for a 2-D depth-averaged surface flow code that contains a steady state
and an unsteady solver.

\(d\) In watershed modeling, a new approach to watershed modeling in
selected western U.S. basins will involve configuring multiple
hydrologic models within the Modular Modeling System using various
existing techniques for simulating components of the hydrologic budget.
The procedures develop will serve as a basis for improvement in the
efficiency of hydrologic simulations, provide estimates of the
reliability of hydrologic forecasts, and provide information for
regionalizing parameter sets for various model configuration across the
U.S.

\(e\) New work related to had-rock mining is being considered in the
area of eco-hydrologic feedback between aquatic and emergent vegetation,
effects of channel transport characteristics, and accompanying changes
in rates of transport and reaction of metal contaminants (with the
Toxics Program)

\(f\) New biogeochemical studies are intended to: (1) understand how
nitrogen is cycled in atmospheric and hydrologic cycles, new isotopic
methods will be developed that will improve the quantification of
atmospheric components in terrestrial nitrate; (2) investigate nitrogen
cycling in acid mine drainage areas by focusing on characterizing the
diversity of the microbial community in general and nitrogen cycling
populations specifically in a pristine, naturally acidic, and an
impacted streams (3) examine the trace element and isotope distributions
in corals and evaluate the relationships between chemical and isotopic
concentrations and weather/climate change characteristics; and (4)
expand our understanding of arsenic, mercury, selenium, and tungsten
cycling in surface and ground waters. The new discovery of tungsten in
water near Fallon, NV will be investigated by use of geochemical
modeling to form hypotheses about its transport and possible link to a
leukemia cluster.

\(g\) New and enhanced water chemistry investigations include: (1) field
sampling for aquatic humic substances from diverse environments to
investigate the role of hydrologic conditions and land use practices on
the reactivity of dissolved organic carbon in aquatic systems. A major
objective is to identify useful surrogates to estimate the potential for
disinfection by-product formation for water supply; (2) a study of the
fate of pharmaceutical and endocrine disrupting compounds during
treatment by on-site wastewater disposal systems and their impact of
ground water and surface water (with the Colorado School of Mines); (3)
a study of the fate and distribution of free and conjugated steroidal
hormones in surface waters; and (4) examination of the isotopic
characteristics of natural and anthropogenic perchlorate, a contaminant
of recent interest in water.

\(h\) Investigations will focus on how processes of natural and imposed
landscape disturbances interact with the processes of climate,
hydrology, and sediment transport. Flow and transport modeling will be
conducted in the 50-mile reach of the Rio Puerco to include in a
channel-flow model realistic roughness, streambed infiltration, and
flood attenuation without using arbitrarily estimated parameters.
Contact: **Pierre Glynn**.

## [National Water Quality Assessment]{.underline}

[]{#NAQWA .anchor}

In FY 2005, the National Water-Quality Assessment (NAWQA) Program will
begin 14 new studies in 14 geographic study areas (study units). Most of
the new topical studies will begin in FY 2005 or FY 2006 with a planning
year and are intended to operate for at least 4 more years. Studies to
be undertaken within the five topics are designed to improve
understanding of the human and natural influences on water-quality
conditions. New topical studies are focusing on:

1\. **Agricultural Chemicals: Sources, Transport, and Fate** ---the
question addressed is: how do environmental processes and agricultural
practices interact to affect the transport and fate of agricultural
chemicals in the hydrologic system of nationally important agricultural
settings, and what are the effects on water quality and implications for
management of water resources? New studies will be started in the
Mississippi Embayment and in the Eastern Iowa Basins. Contact: **Paul
Capel.**

2\. **Ecological Effects of Nutrient Enrichment**---the question
addressed is: how do biological communities and processes respond to
varying levels of nutrient enrichment among agricultural streams from
contrasting environmental settings? New studies will be started in the
Ozark Plateau, Upper Mississippi River Basin, and Upper Snake River
Basin. Contact: **Mark Munn.**

3\. **Mercury Bioaccumulation in Aquatic Ecosystems** ---the primary
question is: what environmental and biological factors govern the
methylation of mercury (Hg) and its resulting bioaccumulation in aquatic
biota and stream ecosystems? New studies include the Lake Erie-Lake St.
Clair Drainages, Hudson River Basin/Long Island and ew Jersey Coastal
Plain, and Santee Basin and Coastal Drainages. Contact**: Mark
Brigham.**

4\. **Transport of Anthropogenic and Natural Contaminants to
Public-Supply and Domestic Wells** ---the question addressed is: what
are the primary contaminant sources and aquifer processes that control
transport and transformation of anthropogenic and natural contaminants
in representative water-supply aquifers? New studies will be started in
the South Central Texas Basins, in the Rio Grande River Basin, in the
Long Island and New Jersey Coastal Plain, and in the Lower Illinois
River Basin. Contact**: Sandra Eberts.**

5\. **Effects of Urbanization on Stream Ecosystems** ---the questions of
interest are: how do the hydrologic, geomorphic, chemical, and
biological characteristics of stream ecosystems respond to urbanizing
land-use change, and how do responses vary across environmental
settings? New studies include the Sacramento River Basin and Puget Sound
Drainages. Contact: **Cathy Tate.**

In addition to topical studies, the NAWQA Program operates a network of
stream and ground-water trend sites within 42 study units. Trend
detection in streams and ground water is determined by characterization
of water quality over time (1990s-current year) from samples of
nutrients, pesticides, and selected major ions at sites representing
major land-use and water-use settings of the Nation. In streams, trends
in aquatic biota are characterized by sampling assemblages of fish,
aquatic invertebrates, algae, and habitat. At present, the NAWQA online
data warehouse includes more than 8 million records, which enable water
resource managers, scientists, and the public to find data about the
quality of water at more than 4,000 stream sites and 6,500 wells. Data
on fish communities are available for nearly 1,000 stream sites in 51
major river basins collected in the first Cycle of NAWQA (1991-2001).
Data for aquatic invertebrates, algae, and stream habitat are coming on
line within the next several months. More information is available at
the URL <http://water.usgs.gov/nawqa>. Contact: **Donna Myers.**

**Geography Discipline**

[]{#geography .anchor}

**Mapping, Remote Sensing, and Geographic Investigations Programs**

The three programs of the Mapping, Remote Sensing, and Geographic
Investigations subactivity are identified under the DOI Strategic goal
of "Serving Communities". The DOI Strategic Plan provides the framework
for the Geography five year strategic plans for each of the three
programs. All three Geography Discipline programs collectively comprise
Geography's implementation of *The National Map* as described in the
five-year plans, which are complete and in the implementation stage. The
Cooperative Topographic Mapping Program will undergo a Program Review
during FY04, and the five-year will be updated as a result. Land Remote
Sensing and Geographic Analysis and Monitoring will undergo program
reviews in the subsequent FY's, which will trigger updates of those
five-year plans. The following annual program guidance reflects
Geography's commitment to carrying out the vision of *The National Map*,
which is central to the Bureau's science and mapping missions.

## [Cooperative Topographic Mapping Program]{.underline}

[]{#CTM .anchor}

1.  Complete high-resolution (1/3 meter, true color) imagery for
    remaining Urban Areas and begin refresh cycle for outdated urban
    imagery.

2.  Develop partnerships and make available current content of *The
    National Map* (the 8 geospatial data layers) for Urban Areas for
    which high resolution imagery are available, providing access to
    partner data and additional critical infrastructure data as
    appropriate. Continue to develop those statewide partnerships that
    can be achieved for moderate investment on our part.

3.  Respond to DOI bureau-designated needs for imagery, elevation, and
    hydrography data.

4.  Improve national datasets of The National Map by incorporating
    high-resolution, current content. Pilot data hydrography and
    geographic names data steward program with other Federal and state
    organizations.

5.  Continue participation in Geospatial One-Stop to improve
    interoperability with *The National Map* and implement information
    content standards developed under the Geospatial One-Stop processes.

6.  Complete transition away from traditional printing and warehouse
    functions to map-on-demand and other digital map distribution
    processes.

7.  Implement a National Synthesis activity to provide expert
    implementation advice to geography and partner organizations and
    provide on-call support for short-term, rapid response situations.

8.  Pursue governance and other projects to prepare for Phase II
    implementation of *The National Map.*

Contact: **Mark Naftzger**.

[]{#LRS .anchor}**[Land Remote Sensing Program]{.underline}**

In FY05, the program will:

-   Operate the Landsat satellite missions.

-   Coordinate and oversee implementation of the national Commercial
    Remote Sensing Space Policy.

-   Populate, preserve and provide access to data archives of
    scientifically relevant remotely sensed observations of the land and
    near-land masses of the Earth.

-   Compile and evaluate requirements of the DOI and civil user
    community for access to remote sensing data and related support
    services, and seek to satisfy those requirements.

-   Investigate, calibrate and characterize existing sensors and
    associated data collected to support science and operational
    requirements.

## Develop methods and contracts to ensure USGS scientists have access to commercially acquired remotely sensed data.

-   Investigate technological advancements in remote sensing missions,
    instruments, processing techniques, products and product
    dissemination methods.

-   Establish agreements, partnerships and strategic plans for
    cooperative activities with Federal, commercial and international
    institutions for access, distribution, and application of remote
    sensing data and technology.

-   Expand the application of remotely sensed data within the Bureau and
    the Department of the Interior.

Contact: **Jay Feuquay**

## [Geographic Analysis and Monitoring Program]{.underline}

[]{#GAM .anchor}

The Geographical Analysis and Monitoring Program (GAM) seeks to mamimize
scientific impact by focusing its activities in five areas that are
designed to support core GAM research*, The National Map* (TNM)
requirements and the Director's Guidance.

**1. Status and Trends** **Reporting** - The goal is to publish a Status
and Trends Synthesis report in FY 2006, providing a national assessment
and synthesis of regional investigations on the rates, trends, causes,
and consequences of land surface change. Specific project tasks planned
for FY05 include:

-   Synthesis of disparate datasets

-   Strategic planning and coordination

-   Maximize science impacts

-   Efficient and cost-effective information access and delivery.

-   Conduct cost-benefit analyses of using land cover data

**2. Landscape Change** - Comprehensive, integrative, encompassing and
accurate land cover data are required to produce the Status, and Trends
reports, as well as serving as critical elements in much of GAM funded
research. Land cover data are also critical components in many analyses
of overall environmental health, including the Heinz Center's *The State
of the Nation's Ecosystems* and EPA's *Report on the Environment*, as
well as being one of eight map themes comprising *The National Map*.
Specific project tasks planned for FY05 include:

-   Production of high-resolution land cover datasets

-   Development of 1km land cover data products

-   Development of a comprehensive accuracy assessment program

-   Research on integrating 1km, 30m (TM) and high resolution data, with
    a focus on long-term monitoring of land cover change

-   Develop methodologies for creating and sustaining a national land
    cover monitoring program

-   Organize and host a Land Cover Summit that seeks to insure
    institutional commitments to land cover mapping

-   Organize and host a users meeting to facilitate the use of GAM land
    cover information

-   Organize and host an International Mapping and Monitoring Workshop

-   Production of the NLCD 2001 dataset

-   Research on developing a NLCD 1992 -- 2001 land cover change product

-   Develop and test a phenology monitoring program operating at various
    spatial and temporal scales

-   Estimate the types, rates, and temporal variability of land cover
    change for a set of ecoregions

-   Prepare a national synthesis document of land cover change

-   Conduct research identifying the key drivers and consequences of
    land cover change in the eastern US

-   Identify relevant indicators of land-surface change such as
    agricultural practices, forested lands, wetlands loss, and urban
    development

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-   Develop, and validate models for forecasting landscape change

**3. Ecosystems Dynamics** - This activity uses ecosystems as a
contextual and integrating factor to synthesize GAM research from a
number of existing activities that are directed toward meeting national
program needs and regional priorities. Specific projects tasks planned
for FY05 include:

-   Continuation of Comprehensive Urban Ecosystem Studies (CUES). The
    GAM CUES sites are:

-   Charleston, South Carolina

Washington, D.C.

St. Louis, Missouri

Denver, Colorado

Tampa Bay, Florida

Tahoe/Reno, Nevada

Sacramento, California

-   Comprehensive assessment of current ecological systems mapping
    activities across the nation

-   **Ecological Systems Mapping** is an FY05 USGS Initiative led by the
    Geographic Analysis and Monitoring and the Biology Discipline\'s
    Ecosystem Programs. It will begin in FY05 with a comprehensive
    assessment of current ecological systems mapping activities across
    the nation. This assessment will provide the framework for the
    development of strategic Science and Business Models/Plans to
    implement mapping, to establish priorities for new mapping
    information needed, and to guide the selection of pilot locations.
    Contingent on funding for FY06 and FY07, pilot activities at two
    scales, national and regional, may be initiated. A national pilot is
    needed to demonstrate and test the ability to synthesize and use
    ecological data, in conjunction with remote sensing, physical and
    thematic map data, to map across multiple scales: ecoregions,
    ecosystems, species assemblages, and species. This will build on a
    largely untapped strength of USGS to manage a rich national and
    global spatial database, and our ability to analyze these data to
    support ecological mapping at scales ranging from local to national.

-   Initiate pilot mapping activities at two scales, national and
    regional

-   Continuation of fire science research, including reducing fire
    hazards in the urban-wildland interface and improved understanding
    of wildfire behavior and post-fire rehabilitation.

##### 4. Science Data and Analytical Tools for The National Map - A major theme will be the compilation, development, analysis and synthesis of a broad set of primary and derived biogeophysical land surface parameters, as well as climate and socio-economic data. This project includes data harvesting, packaging, analysis and delivery. Specific project tasks planned for FY05 include:

##### Landscape-species interaction and global change model applications

##### Develop and maintain a plot database of biogeohysical variables to support land surface parameterization and land calibration and validation

**5. Synthesis and Applications** -- this activity seeks to combine
various components of

USGS research and synthesize them into useful products for
decision-makers and the public. Specific project tasks planned for FY05
include:

-   Influences of landscape structure on the spread of diseases

-   Invasive species modeling

-   Amphibian research and monitoring

-   Transportation studies

-   Global change studies

-   Integrated analyses of land cover impacts on water quantity and
    quality

-   Linkages of human and environmental health

-   Topographic research

-   Environmental hazards

Contact: **Doug Muchoney**

[]{#Geology .anchor}**Geology Discipline**

**[Earthquake Hazards Program]{.underline}**

[]{#Earthquake .anchor}

The president\'s budget request for fiscal year (FY) 2005 provides the
Earthquake Hazards Program (EHP) with \$46.54 million, a 2% reduction
from the program\'s FY 2004 appropriation of \$47.40 million. When fixed
cost increases (uncovered uncontrollable costs and increased network
operation costs) are taken into consideration, the program faces a \$2
million shortfall in real terms below the FY 2004 level, which is
already below that needed to conduct a viable program. Just considering
the increase in uncontrollables, the program\'s percentage of operating
expenses relative to total appropriation is projected to drop from 8.8%
in FY 2004 to 4.5% in FY 2005.

Roughly a quarter of the program\'s budget goes to the External Grants
Program, which funds regional monitoring networks, hazards assessments,
and research by universities, state geological surveys, and
private-sector consultants. In order to maintain the proportional share
of external grants in the overall EHP effort, no more than a \$0.5
million reduction will be sought in this area. Such a reduction is made
with the understanding that any future increases will also be shared
proportionally with external grants.

The Advanced National Seismic System (ANSS) is a flagship effort of the
EHP and should represent a major area of growth. The FY 2005 request
level of \$4.4 million maintains a congressionally directed increase of
\$0.5 million provided in FY 2004. In order to ensure the ability of
ANSS to deliver reliable data and information products, the program
proposes to partially address the shortfall by absorbing \$0.5 million
in product development and related costs into ANSS that are currently
borne by the program as a whole. The remaining funds will be used to
maintain instruments previously installed to expand the networks as
outlined in the ANSS Capital Asset Plan and to further system
integration as recommended by the ANSS National Steering and National
Implementation committees.

The remaining \$1.0 million shortfall in minimum operating expenses will
be absorbed by projects led out of the Earthquake Hazards Team in
Western Region and the Geologic Hazards Team in Central Region. The Team
Chief Scientists have indicated that they can expect to obtain a maximum
of \$0.5 million from increased reimbursable activities on behalf of
other federal agencies as well as other sources. Given staffing
limitations, further offsets would compromise the ability of the teams
to meet internal program goals. The remainder of the shortfall that
cannot be offset by reimbursables will have to be absorbed by the Teams
through other means.

Guidance to Project Chiefs: In planning for FY2005, EHP will establish
budgetary targets for the regional and topical areas that define its
management structure, rather than targets for each individual project.
The Program Office receives guidance from a group of Regional and
Topical Coordinators, who have responsibility for overseeing, at a high
level, the suite of research, both internal and external, performed in
the region or topic, and for making funding recommendations to the
Program Office. The regions and topics, and associated coordinators,
are:

-   Northern California (Mary Lou Zoback)

-   Southern California (Lucile Jones)

-   Pacific Northwest (Craig Weaver)

-   Central & Eastern U.S. (Eugene Schweig)

-   Inter-mountain West (Mark Petersen)

-   Earthquake Physics and Occurrence Research (Michael Blanpied)

-   Earthquake Effects Research (Art Frankel)

-   Seismic Monitoring (Harley Benz)

-   Geodetic Monitoring (John Langbein)

-   Strong Motion and Structural Monitoring (William Savage)

Project chiefs are advised to work directly with the appropriate
coordinators and team chiefs to define work plans and budgets that
contribute effectively to EHP\'s interests in those areas. An
agreed-upon plan should be crafted before work plans are committed to
BASIS+. A given project may have tasks aligned with two or more regions
and topics, and a given research task may require discussion with more
than one Coordinator. (For example, research on site response in
Southern California should be discussed with both the Southern
California and the Earthquake Effects Research Coordinators.)

Through this process, the suite of BASIS+ proposals will define a
credible, balanced, and vetted research program that meets the
anticipated budget. This process should allow projects to better
anticipate what work will be funded in FY2005, and allow the Program
Office to dispense money to teams as early as practicable in the fall.

Contacts: **Dave Applegate, Mike Blanpied, Bill Leith, and John Unger**

[]{#Global .anchor}**[Global Seismographic Network]{.underline}**

The request for the Global Seismographic Network program is \$3.37
million, a 2% reduction from the FY 2004 appropriation. No new
activities are anticipated, and continuing activities will have to
absorb the shortfall. Continued emphasis should be given to meeting the
data availability targets from network stations.

Contacts: **Dave Applegate and Bill Leith**

[]{#Geomag .anchor}**[Geomagnetism Program]{.underline}**

The request for the Geomagnetism program is \$2.00 million, a 2.5%
reduction from the FY 2004 appropriation. No new activities are
anticipated, and continuing activities will have to absorb the
shortfall. Emphasis should be given to improving the fidelity of the
observatory data and improving real-time magnetic field monitoring and
modeling capabilities.

Contacts: **Dave Applegate and Bill Leith**

## [Volcano Hazards Program]{.underline}

[]{#Volcano .anchor}

The Volcano Hazards Program supports long-term volcano monitoring,
volcanic hazard assessment, and research into volcanic processes. This
work is conducted at five volcano observatories, and nationally, with
the support of allied projects in the geologic, hydrologic and
geographic disciplines, as well as external cooperators, in all three
USGS regions. The program will continue to build cooperative projects to
improve our understanding of volcanic hazards, and to expand USGS
monitoring networks at active volcanoes in the US, where we currently
monitor 48 of the more than 70 potentially hazardous volcanic centers.
Subject to the availability of funds in FY05, the program will continue
expansion of volcano monitoring in the Aleutian Arc, to be coordinated
through the Alaska Volcano Observatory (AVO) project, and will work on
linking the observatories and allied labs through the development of a
National Volcanic Monitoring System. Contingent upon congressional
appropriations for the FY-2005 USGS InSAR initiative, VHP will provide
up to \$1,100,000 for acquisition of new satellite imagery from existing
Canadian and European satellites, acquisition of digital elevation
models for high-priority volcanoes lacking these data, support of
essential ground-based monitoring needed to evaluate and validate the
significance of deformation detected by InSAR, and research to enhance
the use of InSAR as a monitoring tool and to develop better models for
interpreting crustal deformation.

Contacts: **Jim Quick** (Program Coordinator), **Roz Helz** (Associate
Program Coordinator), **Jeff Wynn** (Volcanoes Team Chief), **Keith
Prince** (WRD/WR), **Tom Murray** (AVO), **Elliot Endo** (CVO), **Don
Swanson** (HVO), **Dave Hill** (LVO), **Jake Lowenstern** (YVO), **Manny
Nathenson** (Menlo Park).

## [Earth Surface Dynamics Program]{.underline}

In FY05, all major projects in the Earth Surface Dynamics Program (ESDP)
will be continuing. The Program will seek to align program priorities
and project activities more closely with the U.S. Climate Change Science
Program (CCSP) goals as documented in the Strategic Plan for the U.S.
Climate Change Science Program. As a result, the mix of project tasks to
be undertaken in FY05 will evolve to reflect revised program priorities.
These will include an increased emphasis on studies that: (1) determine
the range of climate variability on time scales ranging from
inter-annual to millennial; (2) identify and characterize conditions
during intervals of rapid change; (3) assess the response of ecosystems
and landscapes to climate change and variability; and (4) develop
regional to global scale paleo-environmental reconstructions for key
periods of the Late Tertiary and Quaternary.

Abrupt Climate Change in the Eastern United States: Patterns, Causes,
and Impacts

In view of recent interest in this topic, a project will be developed to
examine the paleoclimatic record from marine, estuarine, and lacustrine
sediments in order to reconstruct temperature and precipitation
variability during periods of rapid climatic change.  The Project will
focus on the last deglaciation and the Holocene interglacial period, and
will include a study of Younger Dryas cooling, the early Holocene, the
Medieval Warm Period, the Little Ice Age, and changes during the past
two centuries. FY05 is viewed as a formative year of project design with
a funding level of approximately \$30,000.

Contacts: **Nick Lancaster, Tom Cronin, Dave Russ, Rich Harrison**.

[]{#NCGMP .anchor}**[National Cooperative Geologic Mapping
Program]{.underline}**

The National Cooperative Geologic Mapping Program (NCGMP) plans to
complete a new 5-year plan by the end of FY04, and invites any Project
Chief throughout the bureau to offer suggestions on cooperative research
ideas in the coming months.

Two projects funded primarily by NCGMP will end in FY04

-   Central Death Valley Region Project

-   Great Lakes Surficial Geologic Mapping Project

Additionally, five projects funded primarily by NCGMP will end in FY05:

-   Bedrock Regional Aquifer Systematics Study Project (BRASS)

-   Southern California Areal Mapping Project (SCAMP)

-   Surficial Geologic Mapping in the Southwest Project

-   Geologic Mapping in Support of Land, Resources and Hazards Issues in
    Alaska Project

-   Geologic Mapping and Basalt-Volcanic Framework Studies, Eastern
    Snake River Plain, Idaho

This is a rather large turn over for NCGMP, which will require careful
planning with the scientists on these projects. It also presents a
unique opportunity to plan our scientific future and fine-tune important
aspects of our new 5-year plan. To facilitate this planning, NCGMP is
asking for project reviews of GLASS, BRASS, and the Surficial Geologic
Mapping in the Southwest Projects during FY05. NCGMP will work closely
with Regional Geologists in all three regions to structure these
reviews.

**New Project Start in FY05**: NCGMP is requesting a work plan for a new
project in Southern California beginning in FY05. This project should
build upon the excellent geologic mapping begun by the Southern
California Areal Mapping Project, and should explore the relations
between landforms on basement highlands and fill sequences of adjoining
basins in a variety of tectonic settings. While this project will start
off with modest funding in FY05, it is expected to grow in FY06, and
thus increase opportunities for cooperative work. Contacts: **Jon Matti,
Chris Menges, Robert Powell, and Peter Lyttle.**

FY05 also provides opportunity to further develop inter-program plans
(NCGMP, CMGP, GWRP) for work in the Atlantic Coastal Plain of North
Carolina and Virginia that is compatible with long term Eastern Region
Science plans. For NCGMP this planning involves both the Carolina
Coastal Margin Project and the Chesapeake Bay Impact Crater Project.

Contact: **Peter Lyttle, Randy Orndorff, Laurel Bybell**

[]{#Landslide .anchor}**[Landslide Hazards Program]{.underline}**

The Landslide Hazards Program (LHP) is engaged in implementing a
national landslide hazards mitigation strategy as presented in USGS
Circular 1244 (<http://pubs.usgs.gov/circ/c1244/>). This strategy
includes developing new partnerships among government at all levels,
academia, and the private sector and expanding landslide research,
mapping assessment, real-time monitoring, forecasting, information
management and dissemination, mitigation tools, and emergency
preparedness and response. Such a strategy calls for expertise
associated with other related hazards such as floods, earthquakes, and
volcanic activity, and utilizes incentives for the adoption of loss
reduction measures nationwide. The National Academy of Sciences was
engaged to assess the effectiveness of this strategy and has just
published a report *Partnerships for Reducing Landslide Risk*
(<http://www.nap.edu/books/0309091403/html/>) which commends the USGS
for its strategy. LHP will finalize its new 5-year plan by the end of
FY04, and welcomes input from any USGS Project Chief who envisions
opportunities for cooperative work.

Two significant changes are being made in FY05 by LHP that implement
aspects of the strategy and offer opportunities for cross program
cooperation. However, a projected level budget, increased salary load,
and increased bureau expenses in FY05 will severely impact our operating
expense budget. This re-emphasizes the importance of leveraging funds
within USGS and with outside partners in order to achieve these
objectives.

Opportunity 1---Western Oregon and other areas: LHP has been engaged for
a number of years in landslide studies in the greater Seattle area, and
has worked closely with the Earthquake Hazards Program, the National
Cooperative Geologic Mapping Program, and local emergency response
managers. The major part of this effort is ending in FY04. LHP would
like to apply many of the lessons learned, particularly in rainfall
induced landslides, in Seattle to another area in the Pacific Northwest
and will begin a new project in western Oregon. The Pacific Northwest
Urban Corridor Geologic Mapping Project (funded primarily by NCGMP) made
a similar migration from Washington to Oregon in FY03. LHP sees
excellent opportunities for LHP, NCGMP and the Oregon Department of
Geology and Mineral Resources (DOGAMI) to cooperate in this new effort.
The new project would also benefit from the close ties already
established between DOGAMI and the Oregon Department of Transportation.
Contacts: **Rex Baum, Peter Lyttle, and Paula Gori.**

Opportunity 2---Fire-related landslides in southern California and other
areas: LHP requests a project plan for a new project studying
fire-related landslide hazards in southern California in FY05. This work
will build on the excellent start begun in FY04 in response to the
disastrous fires in southern California. This project will focus on
developing tools and methods for characterizing post-fire debris-flow
hazards specific to the southern California setting, and will require
expertise in the fields of post-fire erosion and runoff processes,
debris-flow hazards analysis, terrain analysis, and the establishment of
rainfall intensity-duration thresholds as the basis of warning systems.
Contacts: **Sue Cannon, Peter Lyttle, and Paula Gori**.

[]{#Coastal .anchor}**[Coastal and Marine Geology Program]{.underline}**

The Coastal and Marine Geology Program (CMGP) expects to have
substantially less funds available as Operational Expenses (OE) for
science projects in FY2005. Based on projections of increased salary and
other costs and anticipated appropriations we estimate that OE for
science projects, relative to FY2004, will be reduced by approximately
9%. Projections are subject to change; however this required OE
reduction exceeds projections of funds made available through completion
of ongoing projects. In light of the uncertainty associated in funding
projections project chiefs are requested to carefully prioritize tasks,
as an aid to program management.

We do not anticipate funding any new projects in FY2005, beyond modest
projects that effectively leverage committed program funds with
reimbursable activities that may arise. Any obligations associated with
such efforts should represent an offset of continuing program
obligations. As always we will address such opportunities as they are
brought to our attention by regional and team leadership.

There is the potential that relocation of Western Coastal and Marine
Team marine facilities (MarFac) may impact program resources and
projects. We expect regional and team leadership to keep us apprised as
and where MarFac relocation impacts support for CMGP-supported projects
or requires program resources. We expect that the development of
strategies to provide support for marine operations on the west coast
will reflect a broader assessment across all the marine and GD teams of
how operational support can be effectively provided to best meet
long-term program and team needs.

As indicated in program response to FY2004 workplans, future workplans
will be provided for external review. FY2005 workplans should be
consistent with program guidance provided in response to FY2004
workplans. Contact: **John Haines**.

[Guidance for Continuing Projects:]{.underline} Any enhancements to
continuing projects should reflect a redistribution of program resources
to more effectively meet multi-project and programmatic objectives
within overall budgetary limitations. Proposed changes in funding must
be, unless otherwise indicated, revenue neutral across the program. For
guidance Contacts: **John Haines, Dawn Lavoie**, and the appropriate
team chief scientist: **Sam Johnson, Lisa Robbins, or Bill Schwab**.
Specific areas where regional and programmatic interests may support
alterations of project structure or funding include:

a)  Effective coordination towards program goals that cross project
    boundaries. For example, projects addressing **benthic habitats**
    may suggest modifications that effectively address regional project
    goals (for example, Puget Sound), that build upon ongoing regional
    and programmatic efforts (for example, New England regional studies
    or programmatic efforts related to sea-floor processes and process
    model development), or that demonstrate effective coordination and
    cost-sharing with stakeholders in NOAA, the National Park Service,
    and other DOI and/or State agencies.

b)  Continuing studies related to **Coastal Watershed Restoration**
    should reflect the completion of several tasks with future work
    supporting DOI priorities in the Grand Canyon and linking with
    integrated regional efforts in the Puget Sound area.

c)  The CMGP supports a number of projects pursuing the development and
    application of sediment transport and coastal evolution models
    (including **Community Sediment Transport Modeling, Coastal
    Evolution Modeling, North Carolina Erosion, South Carolina Erosion,
    Tampa Bay Ecosystem, and Pacific Northwest Regional Studies).** In
    FY2005 the PI's for the respective projects should develop
    coordinated strategies for a) prioritizing experimental work, b)
    maximizing the impact/results of past and ongoing regional studies
    to meet both regional study and broad modeling objectives, c)
    technical support for model evaluation, development, and provision,
    and d) delivery of data, tools, and model evaluations. This effort
    should result in a collaborative effort to provide a coherent
    description (through the web) of CMGP supported modeling efforts.
    Coordinated plans should be developed with the perspective of
    research staff pursuing model development and application within
    regional studies and in support of national program goals.

d)  The program will solicit a workplan to provide a coherent strategy
    for program supported efforts related to **Coastal Groundwater
    Resources.** Research staff from the Coastal and Marine teams should
    define a focus, strategy, and objectives for groundwater studies.
    This would include assessment of those areas where program resources
    can most effectively support cost-shared multi-disciplinary
    investigations, meet regional priorities, and leverage existing
    program investments. The program expects to provide an additional
    \$40,000 relative to FY2004 funding levels for this effort.

e)  Program supported **Data Management** project should include an
    assessment of accomplishments and establish priorities for future
    efforts that target priorities developed collaboratively with team
    management and science staff.

f)  Program-supported science planning efforts with respect to **Coastal
    Hazards**, **Gas Hydrates,** and **Coral Reef Systems** should be
    reflected in FY2005 workplans. Workplans should be consistent with
    those developing science plans. In particular,

    a.  **Coastal Hazards (Earthquakes, Tsunami, Landslides):** Within
        level funding, workplans should provide support for continued
        acquisition and translation of industry seismic data and begin
        to define science priorities for translation and application of
        data resources towards science objectives.

    b.  **Coastal Hazards (Erosion, Storms, Sea-level Rise):** Workplans
        should clearly establish priorities that reflect balanced
        allocations amongst regional, national, and fundamental research
        efforts towards achievement of interim and long-term program
        goals. Given current funding restrictions goals must be
        prioritized to reflect multi-year phased development of
        milestone products.

    c.  **Gas Hydrates:** Workplans should reflect a consistent
        rationale for the support and application of hydrate laboratory
        capabilities across the discipline.

    d.  **Coral Reef Systems:** FY2004 is the final year of the initial
        phase of this effort. Funding levels will, as overall program
        resources permit, remain near FY2004 levels depending on the
        specifics of the workplans provided. The CMGP expects project
        workplans to include well-developed integrated components that
        may require CMGP support for efforts developed outside the
        geologic discipline. Workplan activities, whether multi- or
        single discipline, must establish coherent and complete science
        plans, promise significant science products, and address
        critical issues that address management needs and reflect a
        knowledge of Local Action Strategy and Coral Reef Task Force
        goals. Mapping efforts should support DOI partners and/or be
        integral to the success of research efforts and reflect a
        developing standardization of tools and products.

The CMGP expects that program support for the following studies will be
completed in FY2004:

**FOQUS-LA**

**Pacific Northwest Regional Studies**

**Biogeochemistry of Ecosystems in Biscayne Bay**

**Chesapeake Bay Impact Crater**

**Regional Geologic Assessment of the U.S. Marine Realm**

**Joint Fact Finding/MIT Detail**

**Massachusetts Bay Experiment**

Continuing efforts currently supported within **Pacific Northwest
Regional Studies** should be incorporated in the **Coastal Evolution
Modeling** project and reflect the priorities established for that
project and the broader planning effort for Coastal Change Hazards. The
**Massachusetts Bay Experiment** will be replaced by a new project,
**Coastal Geologic Processes and Long-term Environmental Change in the
Northeast U.S.** funded primarily through reimbursable support. Efforts
required to complete any remaining obligations associated with the above
studies should be developed in consultation with **John Haines** and/or
**Dawn Lavoie** and the appropriate Team Chief Scientist or Regional
Executive.

The CMGP expects program support for the following studies will be
reduced consistent with approved workplans. Targeted funding reductions
provided refer to net OE. For all projects uncontrollable salary changes
are expected to be reflected in workplan budgets:

**Southern California Coastal and Marine Geology Regional
Investigations:** OE requests will be reduced to reflect completion of
field efforts and most analyses. Substantial support requirements will
remain associated with product completion. Modest support may be
provided to support new efforts that reflect regional and program
priorities, that are cost-effective, and that are sustainable given the
long-term funding prospects for the program. Target reduction relative
to FY2004 funding is \$125,000. Contacts: **John Haines**, **Dawn
Lavoie**, and **Sam Johnson**.

**Sediment Transport Pathways through Monterey Canyon:** Some funds will
be provided for analysis and to complete commitments to partners. Target
reduction relative to FY2004 funding is \$50,000. Contacts: **John
Haines**, **Dawn Lavoie**, and **Sam Johnson**.

**South Carolina Erosion Study:** Project should, consistent with
meeting obligations of work previously funded, require significantly
reduced OE. Target reduction relative to FY2004 funding is \$200,000.
Contacts: **John Haines**, **Dawn Lavoie, and Bill Schwab**.

**Atlantic Estuaries:** Supported work in FY2005 should be focused on
completing current project obligations -- presumably at a reduced
funding level. Target reduction relative to FY2004 funding is \$40,000.
Contacts: **John Haines**, **Dawn Lavoie**, and **Lisa Robbins**.

**An Investigation of Quaternary History of Modern Tropical Epeiric
Seas:** Support is expected to be reduced consistent with status and
requirements of pending external funding process. Contacts: **John
Haines**, **Dawn Lavoie**, **Lisa Robbins**.

**Evaluating Basin/Shelf Effects in the Delivery of Sediment-Hosted
Contaminants:** Project is expected to require only modest funds for
completion. Target reduction relative to FY204 is \$50,000. Contacts:
**John Haines**, **Dawn Lavoie** and **Lisa Robbins**.

**Sea and Lake Floor Mapping:** Program anticipates reduced funding
reflective of FY2004 completion of several tasks. Remaining obligations
may be combined with continuing Atlantic Habitats efforts as a single
coordinated project with a target reduction relative to FY2004 of
\$30,000. Contacts: **John Haines**, **Dawn Lavoie**, and **Bill
Schwab**.

The Program will assess, in cooperation with regional leadership, the
long-term prospects for continued work in Kachemak Bay**.** The level of
funding will be contingent on that assessment and overall program
priorities. Contacts:**John Haines**, **Dawn Lavoie**, and **Sam
Johnson**.

The Program will continue to fund the **Tampa Bay Ecosystem Study**
consistent with appropriated levels. Contacts: **John Haines**, **Dawn
Lavoie**, and **Lisa Robbins**.

Modest redirections for remaining continuing studies have been the
subject of discussions between the program, teams, and research staff.
Consistent with overall funding targets directions to projects include:

**Tsunami Risk Assessment:** As existing workplan goals are met focus
may shift to tsunami potential within Southern California. Target
funding is level with FY2004. Contacts: **John Haines**, **Dawn
Lavoie**, **Sam Johnson**.

**Coastal and Marine Slope Stability and Landslides:** Workplan,
consistent with Hazards planning efforts, may reflect a shifting of
resources to support Alaska fjord landslide investigations. Target
funding is level with FY2004. Contacts:,**John Haines**, **Dawn
Lavoie**, and **Sam Johnson**.

**National Knowledge Bank:** Workplan should be consistent with results
of pending review. We anticipate review will define a programmatic focus
(for example, coastal change hazards) for continued implementation.
Project efforts should be coordinated with ongoing **Data Management**
project. Target funding is level with FY2004. Contacts: **John Haines**,
**Dawn Lavoie**, and **Bill Schwab**.

**Marine Aggregate Resources and Processes:** Workplan should be
consistent with results of pending review. We anticipate review will
define a project focus on provision of model products for Louisiana
suitable for future synthesis of existing data resources from completed
regional studies. Target funding is level with FY2004. Contacts: **John
Haines**, **Dawn Lavoie**, and **Bill Schwab**.

Modest funding decreases are required by the overall program financial
projections for the following projects:

**North Carolina Coastal Erosion:** Target funding level is reduced by
\$60,000 from FY2004 levels.

**National Assessment of Shoreline Change Hazards:** Target funding
level is reduced by \$60,000 from FY2004 levels.

Unless otherwise indicated all projects should anticipate level funding
or modest decreases consistent with overall program financial picture
and interests.

[]{#Mineral .anchor}**[Mineral Resources Program]{.underline}**

The USGS Mineral Resources Program (MRP) is the sole Federal provider of
scientific information for objective resource assessments and unbiased
research results on mineral potential, production, consumption, and
environmental effects. This information is used to characterize the life
cycles of mineral commodities from deposit formation and discovery to
mineral recycling and disposal. The MRP continues to increase the
availability and usefulness of its data resources by designing and
implementing methods for integrating and delivering spatially referenced
digital data via the Internet using standard World Wide Web technology
and software. Analyses based on these data are critical to the
formulation of economic and environmental policy and also provide land
managers with decision options when there are conflicting demands for
resources.

The Administration's budget for FY05 recommends substantial decreases to
MRP. Acknowledging this proposal, MRP is pursuing a two-pronged approach
to planning for FY05. Full funding levels have been determined for all
new and continuing projects, and are reported here for new projects and
in Geology's Annual Science Plan for continuing projects. However,
project chiefs are requested to carefully prioritize tasks, as an aid to
program management in the event that significant cuts are enacted.

**Tracers of Surficial Processes**

MRP anticipates funding new work on environmental geochemistry issues in
humid environments. This work should address primarily (but not
necessarily entirely) issues arising from minerals-related contamination
in eastern states.

Funding target: If the proposed cuts to MRP are restored, this project
will be funded by MRP at about \$550,000 in FY05. Out-year funding
should be about level with FY05.

Contacts: **Kate Johnson, Sharon Swanson** or **Art Schultz.**

**Earth materials and human health**

Building on the success of the sunsetting Mineral Dusts project, MRP
anticipates funding new work on the relation between earth materials and
human health. The project should investigate how the geological,
mineralogical, geochemical, and toxicological properties of a broad
variety of mineral particulates (and their source materials) may play a
role in human health. The previous project had considerable emphasis on
asbestos; the new project should expand its activities to other earth
materials, including metal-bearing mine wastes, mill tailings, and
smelter emissions. Secondary priorities, depending on available funding,
are for studies of dusts from dry lake beds, soils, volcanic ash, and
coal and coal fly ash.

Funding target: If the proposed cuts to MRP are restored, this project
will be funded by MRP at about \$430,000 in FY05. Out-year funding
should be about level with FY05.

Contacts: **Kate Johnson, Sharon Swanson, Vic Labson or Jim Coleman.**

**Research Chemistry**

MRP has been a world leader in development of analytical methods for
trace constituents of earth materials for decades. In FY 2005 we
anticipate funding a new project whose goals will be to continue this
leadership role, with particular attention to development of new,
state-of-the-art geoanalytical tools that can be applied to topical
studies in geology, climate history, mineralogy, ecology, and biology.
Methods to be developed will include ultra-trace analyses of both solid
and liquid samples, highly precise isotope determinations using the
newly acquired MC-ICP-MS, and isotope dilution mass spectrometric
methods for determinations of trace elements using high resolution
ICP-MS. Other project activities will include continued development of
new standard reference materials, including micro-beam standard
reference materials for use in calibration of laser-ablation ICP-MS
methods.

Funding target: If the proposed cuts to MRP are restored, this project
will be funded by MRP at about \$716,000 in FY05. Out-year funding
should be about level with FY05.

Contacts: **Kate Johnson, Sharon Swanson, or Vic Labson.**

**Research and development for geophysical methods and equipment**

MRP anticipates funding new work supporting the development of new and
existing geophysical techniques for addressing critical geological
problems. Research conducted under this project will include development
of needed geophysical methods and software, development of new
geophysical instrumentation, and applications of geophysical techniques
to frontier areas of geology. Highest priorities will be on development
of methods that address current challenges in mineral resources program
projects.

Funding target: If the proposed cuts to MRP are restored, this project
will be funded by MRP at about \$900,000 in FY05. Out-year funding
should be about level with FY05.

Contacts: **Kate Johnson, Sharon Swanson, or Vic Labson.**

**Application of secular trends and continent-scale geophysics to
mineral resource assessment**

MRP anticipates funding a two year project demonstrating the
applicability of data on global secular trends and continent-scale
geophysics to regional- to continent-scale mineral resource assessments.
Project outcomes should include specific applications of these
data-types to current mineral resource assessment activities funded by
MRP.

Funding target: If the proposed cuts to MRP are restored, this project
will be funded by MRP at about \$450,000 in FY05. Out-year funding
should be about level with FY05.

Contacts: **Kate Johnson, Sharon Swanson, or Bruce Gamble.**

**Advanced Resource Assessment Methods**

MRP anticipates funding new work aimed at improving methods of assessing
potential for mineral resources. Project outcomes should be
identification of major sources of uncertainty and risk in mineral
resources and approaches to incorporating these factors in
decision-making processes in order to reduce controllable risk;
continued maintenance and updating of mineral deposit models, and
updating and documentation of MARK3. Project work should include
sensitivity analysis of sources of uncertainty and risk in resource
assessment; identification of risk reduction methods for covered areas,
as well as for assessments and exploration; and characterization of
risks of adverse effects of mining.

Funding target: If the proposed cuts to MRP are restored, this project
will be funded by MRP at about \$450,000 in FY05. Out-year funding
should be about level with FY05.

Contacts: **Kate Johnson, Sharon Swanson, or Peter Vikre.**

[]{#Energy .anchor}**[Energy Resources Program]{.underline}**

Geothermal Resource Assessment of the Great Basin:

The Energy Resources Program solicits a work plan for a three-year
geothermal resource study of the Great Basin region of the western
United States. The new study should involve collaboration with the
Department of Energy, the Bureau of Land Management, universities, and
State agencies to investigate the nature and extent of geothermal
systems in the Great Basin and to produce an updated assessment of
available geothermal resources. This new study will require an improved
understanding of the thermal, chemical, hydrologic, and mechanical
processes that lead to the formation of geothermal systems. The final
products will include an assessment of the geothermal potential of the
Great Basin Region and should include both discovered and undiscovered
geothermal systems and an allocation of those resources to Federal
lands. Additionally, the assessment will incorporate the compilation of
online geospatial databases of regional and system-specific geological,
geophysical, geochemical and hydrological information relevant to
geothermal resources. Proposed work in FY05 should include the
definition of specific scientific objectives, the development of a new
assessment methodology, and the collection of geothermal data required
for the assessment.

Funding target: \$500,000 gross.

**Contact: Brenda Pierce** (This work will go forward only if funds
proposed in the President's FY05 budget are appropriated.)

**Gulf Coast Energy Resources**:

The Energy Resources Program solicits a work plan for a five-year
project studying and assessing the energy resources and
geologic/stratigraphic framework of the Gulf Coastal Plain of the United
States. This project should focus on understanding the geologic
framework of oil, gas, and coal in order to determine the commodities'
origin, geology, and technically recoverable resources in the Gulf
Coast. The ultimate goal of this project will be to assess these
resources and provide to a variety of customers, cooperators, and
partners information on the various energy resources in the Gulf Coast.
Collective planning efforts in the current Gulf Coast project are
addressing the priorities that will determine the assessment schedule.
The Gulf Coast is a region with a great deal of oil and gas development,
a lot of information, and competing needs. Priority planning efforts
need to determine the USGS niche in order to significantly contribute to
the oil, gas, and coal assessment effort in this region, while
maintaining a unique Federal role. Assessments must be aligned with the
current ERP oil and gas assessment methodologies and the new coal
methodology now being developed. Assessment products will be used by BLM
and others, especially in the Energy Policy and Conservation Act of 2000
studies.

Funding target: \$1,500,000 (gross).

**Contact: Brenda Pierce, Peter Warwick, and Jennie Ridgely.**

# Administrative Policy and Services

# [Science Support]{.underline}

[]{#Sciencesupport .anchor}

USGS is widely recognized as a leader and standard setter for excellence
in our scientific endeavors and in FY 2005 there is a proposed increase
of \$2.7 million for financial management improvement that will enable
the USGS to continue the improvements we began in FY 2004. Our goal is
to have business excellence to match our scientific excellence.

In order to better support the project managers and cost centers, we are
continuing several Financial Management Improvement projects that we
started in FY 2004:

> Providing financial management core competencies training

Integrating performance, budget, and accounting processes

Implementing Interior Department Electronic Acquisition System (IDEAS)

In FY 2005, USGS will continue implementing financial management
training to improve the core competencies of the bureau's fiscal
community. The fiscal community includes accountants, financial
managers, fiscal analysts, budget analysts, and science center
administrative officers in the field. Predicated upon the core
competencies developed by the Chief Financial Officers Council and the
Joint Financial Management Improvement Program, the USGS will offer a
series of financial management courses offered by the Department of the
Treasury, as well as private management-training vendors to ensure that
employees with financial management duties and responsibilities possess
the competencies needed to effectively perform those duties. USGS cannot
hope to fulfill the Administration's financial management initiatives,
without well-trained employees who possess up-to-date required
competencies.

Department of the Interior has mandated that all procurements will be
on-line by FY 2007. On-line procurement can only be accomplished through
the use of IDEAS, the single system used to manage the procurement
process and collect vital data. USGS has implemented IDEAS at the high
volume sites that include Headquarters, the centralized Regional
acquisition offices, and 6 other sites. In order to accomplish the goals
established, USGS must implement IDEAS at all sites with procurement
authority exceeding the micro purchase threshold (\$2,500). During FY04
we consolidated our field procurement resources to reduce the number
sites where IDEAS will be implemented. For FY05 we expect to implement
in approximately 18 additional sites. Contact: **Pat Dunham.**

# [Facilities]{.underline}

USGS is dependent upon appropriate facilities to effectively carry out
its science mission. In recent years, space and facilities costs have
escalated. While the total USGS budget has remained relatively flat from
FY 2000 to FY 2004, facilities costs have increased almost 30% from
\$100 million to nearly \$130 million. Per capita costs to house
employees, contractors, and volunteers increased from nearly \$8
thousand per person in FY 2001 to nearly \$10,000 per person in FY 2004.
This means that increasingly we are diverting funds to facilities that
could otherwise be spent on other aspects of our science programs.

In November 2003, the USGS issued a Strategic Facilities Management Plan
that, among other things, lays out a number of principles and guidelines
to control and reduce space costs. These include limiting major space
changes, planning facility changes based on relevant program and
business factors, and seeking opportunities for cost centers to
consolidate with other USGS facilities or to co-locate with
Universities, other DOI bureaus, or other government agencies when it
further our science objectives and provides real cost savings. For
further information, the plan is available at:
<http://internal.usgs.gov/ops/oms/index.html>.

USGS had previously established an Investment Review Board to review the
bureau's portfolio of information technology projects. In FY 2005, the
IRB will review proposed construction projects over \$2 million as well
as new or renewed leases or GSA occupancy agreements with life cycle
costs greater than \$5 million. Cost center managers will be required to
present the business case for these acquisitions, including a discussion
of co-location or consolidation opportunities. *Survey Manual* Chapter
421.1 -- Facility Plans and Investments provides additional information
on this review process. It is in clearance and will be posted on the
USGS intranet when signed. Contact: **Keith Anderson**.