Title: Documentation of food-web linkages in the mainstem Columbia River – towards
understanding the role of invasive species and establishing a baseline trophic state
A. Abstract and statement of innovation
Understanding the sources of production supporting salmonids, native and nonnative predators, white sturgeon, and other resident fish species could provide crucial
information to guide management of rivers. Recovery efforts for Pacific salmon have
focused on altering dam operations, improving bypass structures, and predator removal
programs to increase survival of migrating juvenile salmonids. However, very little is
known of how these mitigation efforts have affected the ecosystem function of the
mainstem Columbia River. Further introductions of non-native and, in some instances,
invasive animal and plant species have altered the trophic-level dynamics of the
mainstem Columbia River. The use of naturally occurring stable isotopes to estimate the
structure of the reservoir’s food web can be accomplished with minimal sampling and
can provide a cost effective way to assess the current structure of the mainstem Columbia
River above Bonneville Dam. Our objectives in this research are to 1) provide
information to mangers that will facilitate the management of fisheries and 2) develop a
unique approach to understanding how non-native species are affecting ecosystem
processes and relationships in the mainstem Columbia River. In particular, how the
proliferation of Eurasian watermilfoil has affected ecosystem processes. To achieve
these objectives we propose to conduct a pilot study to develop methods and a sampling
strategy to collect samples, determine isotopic signatures of representative trophic levels
in Bonneville Reservoir, use multi-source mixing models to quantify food web sources
and pathways.
B. Technical and/or Scientific Background
The mainstem Columbia River is an important migration corridor for endangered
and threatened salmonids and also supports important fisheries for native resident fish
such as white sturgeon Acipenser transmontanus. Recovery efforts for Pacific salmon
have focused on altering dam operations, improving bypass structures, and predator
removal programs to increase survival of seaward migrating juvenile salmonids.
However, very little is known of how these mitigation efforts have affected the ecosystem
function of the mainstem Columbia River. Further introductions of non-native and, in
some instances, invasive animal and plant species have altered the trophic-level dynamics
of the mainstem Columbia River. For instance, the invasive aquatic plant, Eurasian
watermilfoil Myriophyllum spicatum L., now occupies significant portions of the littoral
habitats in some mainstem reservoirs (USGS unpublished data). The current distribution
of Eurasian watermilfoil has to affect the nature of primary and secondary production in
these habitats and how these contribute to the trophic structure of the ecosystem. The
Asian clam Corbicula fluminea and American shad Alosa sapidissima have also become
abundant in the mainstem Columbia River. The Asian clam has been shown to constitute
a major portion of the diet of white sturgeon (Muir et al. 1988). The abundance of
American shad is likely to affect the structure of the zooplankton community.
Understanding how energy is processed through food web linkages in the Columbia
River will facilitate an understanding of the potential cascading effects of mitigation
actions. Establishing a baseline condition will provide a means to assess the effects of
mitigation or restoration actions or attempts to control or manage invasive animals or
plants on the trophic level dynamics of the Columbia River ecosystem. For instance, if
control efforts for Eurasian watermilfoil were conducted, what trophic levels would be
most affected? Given that the Columbia River is a regulated river system, are there any
potential positive effects of Eurasian watermilfoil? These types of questions will be
difficult to answer without knowledge of how energy is processed through the trophic
levels.
The use of naturally occurring stable isotopes to estimate the structure of the
reservoir’s food web can provide a cost effective way to assess the current structure of
the mainstem Columbia River above Bonneville Dam. Stable isotopes provide two kinds
of information for very minimal field sampling, (1) the source of an isotopic signature
and (2) the change of the isotopic signature due to fractionation by physical and chemical
reactions as the isotopes are consumed and metabolized in a food web (Peterson and Fry
1987). Measurements of naturally occurring stable isotope ratios of carbon (δ13C) and
nitrogen (δ15N) allow us to understand the carbon flow and trophic structure over larger
scales than those typically possible by experimental or observational approaches (Schell
et al. 1989, Hobson 1999). Stable isotope signatures of organic materials change from
food to consumer in a highly predictable manner because of selective uptake and
metabolic fractionation of isotopes. Carbon isotope signature values increase typically by
only 0.0 to 1.0‰ during trophic transfer (Peterson and Fry 1987), thus they can be
preserved through several trophic levels and are often used as a dietary tracer (Perry et al.
2003, Bilby et al. 1998). The nitrogen isotopic signatures for consumers typically
increase by 3-5‰ relative to its prey and values may increase by 10 to 15‰ in many food
webs, due to successive trophic transfers (Peterson and Fry 1987). Thus, nitrogen
isotopes are typically used to indicate trophic position (Vander Zanden and Rasmussen
1996, Vander Zanden et al. 1997). There is no change with sulfur at increasing trophic
levels, making this a good indicator as to which plant or bacterial food sources are most
important to the consumers. Furthermore, stable isotopes are temporally integrative,
allowing the possibility of estimating seasonal diet composition (Fry and Sherr 1984).
The use of stable isotopes can allow for the identification of food web pathways that
support salmon as well as those that are affected by invasive species (e.g. shad, zebra
mussels, etc).
Several stable isotope studies on large river systems and reservoirs (Kendall et al.
2001; Lewis et al. 2001; Saito et al. 2001; Fry 2002; Johnson et al. 2002) have
demonstrated that fish communities integrate much of the isotopic variability present at
lower trophic levels. Some studies have evaluated stable isotopes in the Columbia River
mainstem with a focus on evaluating suspended particulate matter that includes biota at
lower trophic levels (bacteria, phytoplankton, & zooplankton) (Prahl et al. 1998, Sullivan
et al. 2001). Further, studies are ongoing in the lower Columbia River and estuary
(Bottom et al. 2003; BPA proposal 2000301000; see:
http://www.cbfwa.org/FWProgram/ResultProposal.cfm?PPID=CE2003000030001) that
have also proposed to use stable isotopes to assess the food web structure in the lower
Columbia River. Similar to the assertions of Bottom et al. (2003) regarding our
knowledge of food web pathways in the estuary, we suggest that there are major gaps in
our understanding of how ecosystem processes have been altered.
Spatial and temporal scales of connections between food webs and habitats are
poorly understood in the mainstem Columbia River above Bonneville Dam. This
information is important to understanding processes controlling the dynamics of local
populations, communities, and ecosystems across habitats and landscapes (Polis et al.
1997, Laurance et al. 2001). Trophic connections between habitats or ecosystems may
strongly influence production and structure of reservoir and stream food webs. Food
webs in adjacent habitats (tributaries, reservoirs, and anthropogenic sources) and
ecosystems may be strongly linked by fluxes of nutrients, detritus, or organisms (e.g.
invasive species) (Finlay et al. 2002, Polis et al. 1997). By using the natural variation in
δ13C and δ15N we can determine carbon sources and infer trophic positions in the
reservoir ecosystem. Carbon can vary spatially and seasonally and by tracking the
naturally occurring isotope variation we can also infer spatial scale of carbon flow to food
webs that support mobile predators. In reservoirs, δ13C can be used to differentiate
between major sources of available energy, such as, littoral production from attached
algae and detritus, and pelagic production from phytoplankton, because the δ13C of the
base of the littoral food web tends to be enriched in 13C (less negative than δ13C) relative
to the base of the pelagic food web (France 1995). In lotic ecosystems, factors such as
geomorphology and discharge (dam operations) may strongly influence carbon sources to
consumers, through effects on transport of organic matter, algal production, and
consumer movement. Lotic ecosystems demonstrate the spatial complexity of trophic
dynamics (Finlay et al. 2002). Stable isotope techniques can provide a continuous
measure of trophic position that integrates the assimilation of energy or mass flow
through all the different trophic pathways leading to an organism. Stable isotopes have
the potential to simultaneously capture complex interactions, including trophic omnivory,
and to track energy or mass flow through ecological communities (Peterson and Fry
1987).
Understanding the sources of production supporting salmonids, native and nonnative predators, white sturgeon, and other resident fish species could provide crucial
information to guide management of rivers. Our objectives in this research are to 1)
provide information to managers that will facilitate the management of fisheries and 2)
develop a unique approach to understanding how non-native species are affecting
ecosystem processes and relationships in the mainstem Columbia River. In particular,
how the proliferation of Eurasian watermilfoil has affected ecosystem processes. To
achieve these objectives we propose to establish a habitat based probabilistic sampling
design to collect samples, determine isotopic signatures of representative trophic levels in
Bonneville Reservoir, and use multi-source mixing models to quantify food web sources
and pathways.
C. Rationale and Significance to the Council’s Fish and Wildlife Program
Specifically, the research proposed here is in support of research needs identified
in the Northwest Power and Conservation Council (NPCC) Research plan. As stated
previously in section B, we feel that an understanding of how energy is processed
through the trophic levels of the Columbia River ecosystem will facilitate a better
understanding of the effects of mitigation and restoration actions on non-target species.
Establishing a baseline condition will also provide a means to assess the effects of
attempts to control or manage invasive animals or plants on the trophic level dynamics of
the Columbia River ecosystem. For instance, if control efforts for Eurasian watermilfoil
were conducted, what trophic levels would be most affected? Given that the Columbia
River is a regulated river system, are there any potential positive effects of Eurasian
watermilfoil? These types of questions will be difficult to answer without knowledge of
how energy is processed through the trophic levels.
We feel that this research will develop methods that if fully implemented, would
address the following critical management uncertainty listed in the NPCC Research Plan
with respect to invasive species management (see p. 32):
1. To what extent do invasive and nonnative species affect native fish and wildlife
species in the Columbia River Basin?
and is consistent with the following regional research recommendations (see p. 97;
Appendix H.):
9.2
Identify the interactions between native and invasive species, including:
 Predators, prey, food chain organisms, pathogens, and those that alter habitat
structure;
 How competitors respond to altered systems and to restoration and recovery
actions; and,
 How food supplies have been altered and how they can be restored.
9.3
Determine the ecological and economic consequences of invasions on native fish
fauna and aquatic organisms e.g. competition, predation, and cascading trophic effects on
native species, nutrient cycling, effect of management activities.
 Determine the impact of nonnative aquatic and terrestrial species that are
invasive on salmonid recovery.
 Determine the impacts of nonnative species invasions i.e., rainbow and
eastern brook trout, on abundance, distribution, life history and genetic
diversity on bull trout, redband trout, and west slope cutthroat trout
populations.
9.4
Determine the trophic impacts of nonnative species.
 Determine whether the economic and ecological effects of invasive
species have greater impacts at some trophic levels or in specific guilds
than others.
 Determine the current extent of the colonization of reservoirs by nonnative estuarine and mountain stream species and their role in reservoir
food webs and headwater storage projects.
9.5 Determine the ecological impacts of “naturalized” non-indigenous species.
9.6 Determine whether regionally accepted non-indigenous species, such as warmwater fish, can be managed to minimize ecological effects.
We propose this research as a pilot monitoring activity. Our intent is to structure
the sampling design so that it can be redone in a repeatable fashion and would allow long
term monitoring types of comparisons. We also propose that the sampling approach
should be applicable to other mainstem reaches. As such, the research will inform
regional monitoring activities such as the Pacific Aquatic Monitoring Partnership
(PNAMP).
D. Relationships to other projects
As implied in Section’s B and C, we feel that the information that we would
collect would inform a variety of projects currently being conducted in the Fish and
Wildlife Program. Specifically, we feel that the information would be beneficial to
projects that are charged with management and research activities for white sturgeon.
We would also need to coordinate and utilize the fish sampling efforts from these projects
to avoid duplication of effort and reduce the costs of this proposal. In general, we feel
the information provided in this project would provide an insightful context to most
management activities and research being conducted in this river reach.
We will coordinate intensively with ODFW to obtain tissue and stomach samples
for target fish species and other fish species opportunistically through the White Sturgeon
Mitigation and Restoration in the Columbia and Snake Rivers Upstream from Bonneville
Dam (BPA project 198605000) and the Northern Pikeminnow Management Program
(Tom Rien personal communication). Additional samples will be obtained from the
USGS white sturgeon young-of-the year index trawling that is conducted annually (BPA
project 198605000).
We are participating in the PNAMP (see project # 20040200, title "PNAMP
Funding") technical workgroups regarding Estuaries and Large Rivers. This research
will be coordinated with PNAMP to ensure consistency with regional monitoring
activities and efforts to establish a universal sampling design for monitoring in the Pacific
Northwest.
E. Proposal objectives, work elements, and methods and monitoring and evaluation
Major gaps in our understanding of how energy is processed through food webs in
reservoirs on the mainstem Columbia River exist despite the importance of these habitats
to popular native sport fisheries (e.g., white sturgeon) and other native resident fish
species. Certain introduced animals and plants have become established and are now
abundant (e.g., Asian clam, Eurasian watermilfoil, smallmouth bass, etc.). However, how
these and other introduced species have affected the trophic level dynamics of these river
reaches is poorly understood. Further, as part of mitigation efforts for Pacific salmon,
reservoir operations are manipulated to increase the survival of juvenile salmon. Dam
operations may strongly influence carbon sources to consumers, through effects on
transport of organic matter, algal production, and consumer movement. Our primary
biological objectives are to 1) provide information to mangers that will facilitate the
management of fisheries and 2) develop a unique approach to understanding how nonnative species are affecting ecosystem processes and relationships in the mainstem
Columbia River. In particular, how the proliferation of Eurasian watermilfoil has
affected ecosystem processes.
Bottom et al. (2001) recommended the use of natural stable isotope analyses or
other methods to investigate potential food web disruptions due to habitat loss and
degradation. In this research we suggest that a similar approach is warranted to
understand the effects of mitigation actions for Pacific salmon and the effects of invasive
species on ecosystem processes and the fish community of the mainstem Columbia River
above Bonneville Dam. As per previous recommendations by the ISRP, we specifically
propose to address the following hypothesis:
Ho: Despite the fact that Eurasian watermilfoil is now abundant in shallow water habitats
and likely constitutes a large proportion of the plant biomass in Bonneville Reservoir, the
production of this aquatic plant does not contribute significantly to the food web.
Management implication: Programs to limit the distribution of this invasive plant
will increase the energetic inputs to Bonneville Reservoir by increasing
periphyton production that will be more palatable to secondary consumers. (Note:
the alternative hypothesis here is that milfoil does contribute significant resources
to the food web and thus the management implication would be that the removal
would alter a significant energetic pathway).
We will address hypotheses 1 by determining the link between consumers and diet using
the techniques outlined in Work element 2.
Work element 1. Determine isotopic signatures of representative trophic levels in
Bonneville Reservoir.
The spatial and temporal scales of connections between food webs are poorly
understood in the mainstem Columbia River above Bonneville Dam. Food webs in
adjacent habitats (tributaries, reservoirs, and anthropogenic sources) and ecosystems may
be strongly linked by fluxes of nutrients, detritus, or organisms (e.g. invasive species)
(Finlay et al. 2002, Polis et al. 1997). In reservoirs, δ13C can be used to differentiate
between major sources of available energy, such as, littoral production from attached
algae and detritus, and pelagic production from phytoplankton, because the δ13C of the
base of the littoral food web tends to be enriched in 13C (less negative than δ13C) relative
to the base of the pelagic food web (France 1995). We will collect samples from
representative habitat types that correspond to a hierarchical habitat classification system
being developed by the USGS. The classification will be based on the hydrogeomorphic
characteristics of reservoirs with further delineations based on channel morphology
(bathymetry), shoreline type (rip-rap etc.), and other landscape and land-use
characteristics (island, tributary mouths, marinas, etc.). Locations to be sampled will be
randomly selected for the representative habitat classes from cells overlain as a grid on
the reservoir in a GIS as per probabilistic sampling methods typically employed by
EMAP. To account for temporal variability in some trophic levels, samples will be
collected at different times of the year. Site selection and sampling procedures will be
coordinated with regional monitoring groups such as PNAMP.
Task 1.1 Riverine particulate organic matter (POM)
During two periods (late spring and late fall, during periods of increased terrestrial
POM input) we will obtain samples of riverine POM, separated into a phytoplankton and
non-phytoplankton component for isotopic analysis. Additionally, we will obtain
samples from major tributaries to Bonneville Reservoir during the two periods and during
winter, high discharge events.
Task 1.2 Periphyton
Periphyton will be sampled by various methods. For sampling coarse/hard substrate,
a stiff brush will be used to remove periphyton from a known area. A gravel sampler
made of PVC may also be used depending on substrate composition. For finer substrate,
the inverted petri dish method outlined in the NAWQA protocol will be utilized.
Epiphytic algae will be sampled in conjunction with aquatic macrophytes described
below.
Task 1.3 Aquatic macrophytes
Macrophyte samples will be collected using a stovepipe sampler. Specific collection
locations will be determined using a point-intercept (grid) or line-intercept (transect)
method described by Madsen (1999). Macrophytes will be rinsed with water, brushed or
agitated for sampling attached algae.
Task 1.4 Zooplankton and benthos
Riverine zooplankton will be collected by plankton net sampling at locations that
correspond to a habitat classification system that is being developed for Bonneville
Reservoir by the USGS. Vertically integrated zooplankton samples will be taken with 2
Wisconsin-style plankton nets attached side-by-side to a metal frame. One net will have
a mesh size of 64 μm to capture cladocerans and postnaupliar copepods, and the other net
will have a mesh size of 35 μm to capture rotifers and nauplii. The nets will be towed
from near the bottom to the surface, obliquely in flowing waters, and vertically in low
flow and slack water areas. Zooplankton taxa may be composited into a single sample
for isotope analysis. Benthic organisms will be collected using a ponar dredge,
disturbance methods, or benthic cores. To collect invertebrate taxa on aquatic
macrophytes we will use a stovepipe sampler. Crayfish spp. will be collected using traps.
Taxa will be sampled and classified according to the following functional (trophic)
groups:
1) pelagic zooplankton,
2) benthic infauna, separated into representative suspension feeders and detritivores;
certain amphipod taxa, bivalves, crayfish spp., etc.
3) epibenthic organisms, e.g., mysids
4) aquatic insects, e.g., chironomid larvae and pupae
5) fallout insects, separated into those of aquatic and terrestrial origin e.g., adult
dipterans
Task 1.5 Fish
We will coordinate intensively with ODFW to obtain tissue and stomach samples
for target fish species and other fish species opportunistically through the White Sturgeon
Mitigation and Restoration in the Columbia and Snake Rivers Upstream from Bonneville
Dam (BPA project 198605000) and the Northern Pikeminnow Management Program
(Tom Rien personal communication). Additional samples will be obtained from the
USGS white sturgeon young-of-the year index trawling that is conducted annually (BPA
project 198605000). Specifically we will obtain at least five tissue samples from multiple
year classes of white sturgeon Acipenser transmontanus, Common carp Cyprinius carpio,
Northern pikeminnow Ptychocheilus oregonensis , smallmouth bass Micropterus
dolomieu, and American shad Alosa sapidissima. Other common species of fish will also
be collected and processed. Dorsal muscle samples from fish larger than 67 mm total
length will be collected. For smaller fish (less than 67 mm), whole fish will be collected
to assure a large enough sample (Saito et al. 2001). Stomach samples will also be taken,
preserved and processed in the laboratory to corroborate what fish are eating. Since
ODFW are already processing stomach samples as part of the Northern Pikeminnow
Management Program, we will coordinate with them to ensure that are methodologies are
consistent and that we minimize duplication of effort so that we are as cost effective as
possible.
Task 1.6 Sample processing for isotopes
All samples will be dried for at least 48 h in a 60º C oven and then ground to a
homogenous powder using a mortar and pestle. To economize on mass spectrometer
costs, individual fish samples can be pooled into composite samples according to length
classes that approximate age classes and reservoir locations. Composite samples should
contain an equal mass of each individual sample (Saito et al 2001). In order to
characterize the mean stable isotope and the associated variation about the mean for each
taxonomic grouping across time periods and locations, a minimum of five samples will
be processed (Lancaster and Waldron 2001). A 1-2 mg sample will be individually
processed for δ13C, δ15N, and δ34S signatures in a mass spectrometer. The quantity
measured in stable isotope analysis, δ, is the relative difference between isotope ratios of
the sample and a standard:
δ = Rsample - Rstandard/ Rstandard • 103
where δ (‰) is the per mil difference, Rsample is the isotopic ratio of the sample, and
Rstandard is the isotopic ratio of the standard. The standards will we employ are Vienna
Pee Dee Belmnite for 13C/12C and atmospheric N2 for 15N/14N (Lajtha and Michener
1994). Isotopic δ34S signatures will be analyzed using similar methods. Stable isotope
samples will be sent to the Colorado Plateau Stable Isotope Laboratory based at Northern
Arizona University in Flagstaff, AZ for analysis. The laboratory processes isotope
samples for a diverse array of research organizations (see: http://www4.nau.edu/cpsil/).
Work element 2. Establish food web linkages.
Task 2.1 Estimate autotrophic sources for consumers.
Simple mixing models are limited by the number of sources and tracers used,
therefore they do not adequately describe complex food webs having multiple
contributing sources and pathways (Lubetkin and Simenstad 2004). We propose to use a
similar approach as that of Lubetkin and Simenstad (2004) that use companion models
SOURCE and STEP that overcome these limitations and can model complex food webs
in aquatic ecosystems. The SOURCE model estimates the assortment of autotrophic
sources for consumers using the equations:
s1 s2 s3 ··· sn 1
(a)
s1t1 s2t2 s3t3 ··· sntn L Ct
(b)
s1u1 s2u2 s3u3 ··· snun L Cu
(c)
s1v1 s2v2 s3v3 ··· snvn L Cv
(d)
where t,u, and v are tracers; represent average trophic level shifts; Ct, Cu, Cv,
represent overall consumer tracer levels, which reflect it’s diet at trophic level L;
and 0 si 1.
An exact solution for the above equations cannot be calculated, therefore, sets of linear
equations for subsets of sources are solved iteratively to model the mixture of multiple
sources.
Task 2.2 Determine direct links between consumers and their diets
The STEP model is used to determine links between consumers and their diets.
This model estimates the isotopic signature for each consumer as a composite of its diet
modified by one metabolic fractionation, and is represented by the equations below:
f1 f2 f3 ··· fm 1
(e)
f1t1 f2t2 f3t3 ··· fmtm Ct  

f1u1 f2u2 f3u3 ··· fmum Cu 

(f)

(g)
f1v1 f2v2 f3v3 ··· fmvm Cv  

(h)
where f are fractions that m potential foods contribute to a consumers diet. The STEP
model estimates direct diets of each consumer and calculates the trophic level position
using the equation:
f1L1 f2L2 f3L3 ··· fmLm 1 L
(i)
where, fi is the fraction each food source contributes to the diet of the consumer, and Li is
the trophic level for each food source, and L is the trophic level of interest. For a more
complete and thorough description of the model and how mathematical solutions are
determined, see Lubetkin and Simenstad (2004).
Task 2.3 Validate food web model
Model validation will be done in a similar manner to Lubetkin and Simenstad
(2004) where simulations will be run on data assumed to be perfect (no variability) and
data assumed to be more representative of multiple samples (introduced variability). By
performing these simulations we can evaluate how the model performs under ideal
conditions, focusing on the mathematical validity of the model and how natural
variability in the data would affect the model’s performances.
Work element 3. Report results in technical reports, peer reviewed publications, and
presentations.
All work will be summarized and presented in a final technical report, peer
reviewed publications, and presentations to professional and public interest groups.
F. Facilities and Equipment
The U.S. Geological Survey (USGS) is the primary research arm of the
Department of the Interior, which manages nearly one-fifth of all land in the United
States. The Department of the Interior co-chairs the National Invasive Species Council,
and the USGS plays a significant role in implementing the National Invasive Species
Management Plan, called for in the Presidential Executive Order 13112 on Invasive
Species. To meet the goals of the Plan, the USGS Invasive Species Program provides
management-oriented research and delivers information needed to prevent, detect,
control, and eradicate invasive species, and to restore impaired ecosystems. The
Columbia River Research Laboratory has been conducting research in the Columbia
River Basin for over 25 years. The laboratory has state of the art computing resources
and GIS capabilities, and approximately 30 research vessels deployed throughout the
basin. In addition to the facilities, equipment, and staff specifically at the Columbia
River Research Laboratory, we will seek and utilize the expertise that exists in other
centers, disciplines, and programs in the USGS.
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Salmon in the Columbia River Estuary and Their Implications for Managing River
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of energy sources to growth of juvenile chinook salmon (oncorhynchus tshawytscha) in
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H. Key personnel
Timothy D. Counihan
U.S. Geological Survey
Biological Resources Division
Columbia River Research Laboratory
5501-A Cook Underwood Road
Cook, Washington 98605
Education:
M. S., Wildlife Science, New Mexico State University, 1991
B. S., Biology, Montana State University, 1989
Work Experience
1993-Present Research Fishery Biologist, U.S. Geological Survey, Biological Resources
Division, Columbia River Research Laboratory, Cook, WA.
Current responsibilities: Current projects include research examining the distribution and
abundance of Eurasian watermilfoil in relation to the hydraulic characteristics of
Bonneville Reservoir, Columbia River with emphasis on the effects of hydrosystem
operation on the distribution of this invasive aquatic plant and modeling the potential
spread of New Zealand mudsnail in Bonneville Reservoir. Other research includes
modeling the survival of endangered and threatened juvenile salmonids as they pass
through the lower Columbia River dams and working on a multi-agency team to
formulate a habitat classification system and habitat and ecological monitoring program
for the lower Columbia River.
Expertise: Primary areas of expertise include the design and analysis of fish and ichthyoplankton
surveys, survival assessment using mark-recapture models, white sturgeon ecology, larval fish
ecology, and biometrics.
Publications and Reports
Counihan, T. D. J.M. Hardiman and J.R. Hatten. In preparation. Modelling the
influence of channel morphology and reservoir operations on the distribution of
Eurasian watermilfoil in an impoundment of the Columbia River.
Simenstad, C.A., J.L. Burke, I. R. Waite, T.D. Counihan, and J.R. Hatten. In
preparation. Lower Columbia River and Estuary Ecosystem Classification:
Phase I. Prepared for Lower Columbia River Estuary Partnership
Counihan, T. D., A. I. Miller, and M. J. Parsley. 1999. Indexing the relative abundance
of age-0 white sturgeon in an impoundment of the lower Columbia River from
highly skewed trawling data. North American Journal of Fisheries Management.
Counihan, T. D., and C. N. Frost. 1999. Influence of externally attached transmitters on
the swimming performance of juvenile white sturgeon. Transactions of the
American Fisheries Society.
Counihan, T. D., A. I. Miller, M. G. Mesa, and M. J. Parsely. 1998. The effects of
dissolved gas supersaturation on white sturgeon larvae. Transactions of the
American Fisheries Society 127:316-322.
Jill M. Hardiman
U.S. Geological Survey
Biological Resources Division
Columbia River Research Laboratory
5501-A Cook Underwood Road
Cook, Washington 98605
Education
Colorado State University, M.S. Fishery and Wildlife Biology, 2003
University of Puget Sound, B.S. in Biology, 1992
Work Experience
Fishery Biologist - USGS/Columbia River Research Laboratory, Cook, WA -3/04 to present
 Prepare professional presentations, annual reports, research proposals, and manuscripts
 Evaluate juvenile salmonid passage and survival at three hydroelectric facilities on the
Lower Columbia River
 Investigate hydrodynamic modeling and community dynamics with regard to invasive
species in Bonneville Dam reservoir
Fishery Biologist IV - Johnson Controls Inc. contract for USGS/Columbia River Research
Laboratory - 8/03-3/04
 Prepare professional presentations, annual reports, research proposals, and manuscripts
 Use SAS to analyze and summarize age frequency data from 14 years of white sturgeon
trawl surveys
 Prepare Geographic Information Systems (GIS) maps for study design, sampling
protocols, presentations, spatial analysis, and reports for Eurasian Watermilfoil surveys
Graduate Teaching Assistant/Research Assistant - Colorado State University, Department of
Fishery and Wildlife Biology, Fort Collins, CO 8/00-5/03
 Conduct limnology surveys for stratified zooplankton tows, temperature, dissolved
oxygen and light profiles, conductivity, and Secchi depth measurements
 Track zooplankton seasonal densities to determine effects on age-0 kokanee distribution
and use in bioenergetics models to determine stomach capacity, feeding rates, and time to
satiation
 Conduct sampling of age-0 kokanee with hydroacoustics, gill nets, seines and trawls in
rivers and reservoirs
 Collect benthic, zooplankton, and fish samples for stable isotope analysis
Selected Publications
Counihan, T. D., J. M. Hardiman, C. E. Walker, A. L. Puls, and G. S. Holmberg. 2005. Survival
estimates of migrant juvenile salmonids in the Columbia River through Bonneville Dam
using radio-telemetry, 2005. Prepared by the U. S. Geological Survey, Cook, WA for the
U. S. Army Corps of Engineers, Portland, OR.
Hardiman, J. M., B. M. Johnson, and P. J. Martinez. 2004. Do predators influence distribution of
age-0 kokanee in a Colorado reservoir? Transactions of the American Fisheries Society
133:1366-1378.
Johnson, B. M. and J. M. Hardiman. 2003. Kokanee in Blue Mesa Reservoir: Causes for their
decline and strategies for recovery, Final Report. Fisheries Ecology Laboratory,
Department of Fishery and Wildlife Biology, Colorado State University. Prepared for:
National Park Service, Gunnison, CO, November 3, 2003.
Christopher E. Walker
U.S. Geological Survey
Biological Resources Division
Columbia River Research Laboratory
5501-A Cook Underwood Road
Cook, Washington 98605
Education
Portland State University, M.S. Environmental Sciences/Biology
Portland State University, B.S. Environmental Science/Biology
Work Experience
United States Geological Survey, BRD, Cook, WA, 5/01-present, Biologist
Duties: report and proposal writing, publication writing and review, prepare graphs and charts for
reports and presentations, collection and analysis of other biological data, experimental set-up and
study design, database management and use of GIS, statistical analysis, analyze samples for
chlorophyll a, ID and enumerate phytoplankton, coordinate project with contractors and other
agencies
Portland State University, Portland, OR, 8/99-4/01, Research Assistant
Duties: collecting water samples, macroinvertebrates, and algae, mini-piezometer
installation (small wells), took water and biological samples, measured stream habitat
parameters (i.e. discharge, morphometry, riparian conditons, instream substrate),
analyzed samples for nutrients (ortho-phosphate, NO3+NO2, NH4+, TP, TN),
chlorophyll a, ash-free dry mass, identify aquatic macroinvertebrates and algae, statistical
analysis using multivariate and univariate approaches for relating biotic communities to
environmental variables, report writing, publication writing and review, methods
development, prepared graphs and charts for reports and presentations, experimental setup, data base management, spatial analyses using GIS
Department of Environmental Quality, State of Oregon, 6/00-9/00 Field Tech.
Duties: conduct water quality, habitat, macroinvertebrate, and fish, included backpack
electroshocking, use of other instruments such as GPS, conductivity meter, pH meter, performing
DO titrations and Fish measurements/Ids (salmonids) and Macroinvertebrate IDs, stream
measurements such as discharge, measurements of riparian conditions, and instream substrate
Selected Publications
Walker, C.E., Schrock, R.M., Reilly, T.J., and A.L. Baehr. 2005. A direct immunoassay for
detecting diatoms in groundwater as an indicator of the direct influence of surface water.
Journal of Applied Phycology 17(1):81-90.
Walker, C.E., and Y. Pan. 2005. Changes in Diatom Assemblages Along an Urban-to-Rural
Gradient. Hydrobiologia. (in press)
Sonoda, K. Yeakley, J.A. Walker, C.E. 2001. Near-stream landuse effects on streamwater
nutrient distribution in an urbanizing watershed. Journal of the American Water
Resources Association 37(6):1517-1532.
Counihan, T.D., Holmberg, G.S., Walker, C.E., and J.M. Hardiman. 2003. Survival Estimates of
migrant Juvenile Salmonids in the Columbia River through John Day Dam using RadioTelemetry, 2003. Prepared by U. S. Geological Survey, Cook, Washington for the U.S.
Army Corps of Engineers, Portland, Oregon, contract W66QKZ31005684.
Amy L. Puls
U.S. Geological Survey
Biological Resources Division
Columbia River Research Laboratory
5501-A Cook Underwood Road
Cook, Washington 98605
Education
M.S., Marine Biology, Oregon Institute of Marine Biology, University of Oregon, 2002
B.S., Biology, University of Oregon, 1997
Work Experience
Fisheries Biologist - USGS, Columbia River Research Laboratory, Cook, WA, 4/04-present
Investigated survival and egress of juvenile salmonids during hydroelectric dam passage on the
Columbia River using radio telemetry.
 Design and plan experiments examining the behavior and survival of radio-tagged
juvenile salmonids at hydroelectric projects
 Use SAS to manage, manipulate, and analyze large datasets of fish distribution data
 Compose and prepare research proposals, technical presentations, reports and
manuscripts
 Formulate and implement quality assurance/quality control procedures for data
processing
Graduate Research; Zooplankton Ecology - Oregon Institute of Marine Biology, Charleston, OR,
1/98 - 3/02
Investigated spatio-temporal variation of abundance for ~20 zooplankton species in relation to
physical forcings and larval behavior in the Coos Bay estuary, Oregon. Gained insights into
zooplankton transport mechanisms and exchange of zooplankton between the estuary and the
ocean.
 Developed hypotheses, designed study, and wrote grant proposals
 Collected biological data from boats using neuston nets and standard plankton nets;
collected physical data using CTD, DO meter, velocity meter, and GPS
 2000+ hours spent identifying and enumerating zooplankton
Research Assistant - Oregon Institute of Marine Biology, Charleston, OR, 1/98 - 12/00
Investigated physical and biological processes influencing the larval transport and recruitment of
Dungeness crabs and other marine invertebrates as part of the Pacific Northwest Coastal
Ecosystems Regional Study (PNCERS), a multi-institute, interdisciplinary study.
 Collected and preserved 3-5 light trap samples daily
 Constructed and maintained light traps
 Used dissecting scope to identify and enumerate larvae from samples
Select Publications
Puls, A.L. 2002. Transport of zooplankton in South Slough, Oregon. Master's thesis. 96p.
University of Oregon,Eugene.
Puls, A.L. 2001. Arthropoda: Decapoda. Pages 89-161 in A.L. Shanks, editor. An Identification
Guide to the Larval Marine Invertebrates of the Pacific Northwest. Oregon State
University Press, Corvallis.
Meeuwig, M.H., AL Puls, J.M. Bayer. Provisionally accepted. Survival and tag retention of
Pacific lamprey larvae and macrophthalmia marked with coded wire tags. North
American Journal of Fisheries Management.
Puls, A.L., G.C. Roegner, A.L. Shanks. In prep. Fluxes of invertebrate larvae through South
Slough, Oregon.