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					 Microbial Assessment of Thermal Impacts of Dworshak Reservoir Releases

A. Abstract

The primary purpose of this project is to develop a methodology to evaluate the impacts of cold
water releases from Dworshak Reservoir using innovative microbial assessment techniques. The
hypothesis is that incomplete mixing of cold water from the reservoir negatively impacts
steelhead and Chinook rearing habitat in the lower Clearwater. A robust, cost-effective
methodology is needed to evaluate potential impacts caused by management decisions regarding
releases. The project involves collecting and analyzing microbial populations and water
temperature data on the Clearwater River downstream of Dworshak Reservoir during summer
release periods of July, August and September. Similarities and differences in habitat
characteristics are evident at the most fundamental level; the microbial community. The
information would be used in a numerical model to evaluate the effects of reservoir releases as a
function of total mainstem flow and ambient water temperatures on the Clearwater upstream of
its confluence with the North Fork of the Clearwater. The results could be used to formulate
guidelines for releases or demonstrate the need for channel improvement structures to enhance
mixing at the confluence in Orofino. These results could also be used to help understand the
system-wide impacts of altering thermal regimes.

Microbial populations would be sampled from surface and near surface sediments at ten cross-
sections along the lower Clearwater and at one location in the tailrace of Dworshak Reservoir
and one location upstream of the North Fork-Clearwater confluence. At each cross-section, three
samples will be taken representing i) near right-bank, ii) near left-bank, and iii) near mid-
channel. The samples will be taken twice a month during the months of July, August and
September. Four replicate samples will be taken at one cross-section to demonstrate repeatability
and variability of the method. Temperature probes will be operated at these locations during the
same period so that comparisons to temperature regimes can be made.

Researchers from Washington State University (Dr. Jeremy Rentz and Dr. Michael Barber) will
be responsible for conducting the work with the assistance of appropriate graduate level students
and technicians. Samples will be collected in the Clearwater River basin and transported to the
Civil and Environmental Engineering laboratories in Pullman, Washington for analysis.

Finally, cost-effective solutions for uniformly appraising the impacts of habitat and water quality
projects throughout the Columbia River basin are needed to determine which projects are having
the most significant impact. If successful, this microbial assessment methodology could be used
to evaluate the effectiveness of all habitat restoration projects in the basin.

B. Scientific Background

Cold water releases from Dworshak Reservoir are necessary to partially mitigate downstream
summer temperature regimes on the Lower Snake River. However, these releases can
significantly alter the natural temperatures in the lower Clearwater River below the confluence
with the North Fork Clearwater tributary. This problem is controlled by the ratio of unregulated
discharges in the Clearwater versus Dworshak releases and is exasperated by the fact that

complete mixing does not occur immediately at the confluence. Aerial images of the study area
show the tendency of tributary sediment plumes to persist for considerable distances downstream
similar to the evidence indicating complete mixing of the Clearwater and Snake Rivers does not
occur until the water is well into the Lower Granite pool. While cool temperatures are generally
preferable to warm water, excessively cold water can adversely impact rearing habitat by
modifying the food supply and slowing the development of fry and smolt growth rates. This has
been shown to negatively impact the survival rate of migrating juvenile steelhead and Chinook
salmonids in direct opposition to the management goals of the Council’s Fish and Wildlife

Traditional methods of habitat assessment, such as macroinvertebrate investigations and
temperature profiling of the substrate material, are plagued with difficulties related to the
measuring in deep pools, quantifying natural variability across seasonal variations in life-stage of
indicator organisms, and overall cost. What is needed, not only for this watershed but for all
habitat restoration projects, is a rapid, cost-effective, reliable method for evaluating the impact of
management decisions. This innovative method proposes to examine the use of microbial
population distribution and diversity as direct measures of environmental disturbance.

This project could have profound implications to the operation of Dworshak Reservoir and thus
the flows and temperatures in all four lower Snake River dam pools.

C. Rationale and Significance

The Northwest Power and Conservation Council recognizes the negative impact hydrosystem
operation can have on fish populations, specifically with respect to water temperature (page 25
of 2000 Fish & Wildlife Program). Within the Clearwater Sub-basin, the focus of this proposal,
understanding impacts associated with water temperature amelioration using Dworshak
Reservoir waters is a primary goal. Thus, the rationale for our proposed study is the recognition
that understanding thermal impacts of Dworshak Reservoir releases will contribute directly to
goals set by the NPCC and the Clearwater Sub-basin Plan.

Our project is significant because it will lead to specific fish impacts and to the development of
an assessment tool that can be used throughout the Columbia River Basin. Clearwater River
steelhead will benefit from the studies through the development of new Dworshak Reservoir
management plans. These plans will also mitigate high temperatures on the lower Snake River,
which benefits Chinook. Microbial community analysis developed during this project will be
transferable to other reservoirs in the basin that significantly affect water temperature and to
habitat restoration projects that comprise much of the work funded by the BPA. As a rapid, cost-
effective method, microbial community analysis could be easily implemented to evaluate
impacts associated with management decisions.

D. Relationship to other projects

This project is directly related to a number of projects on the Snake and Clearwater Rivers
related to restoration and protection of instream habitat. In particular, it relates to the
considerable efforts being expended on Dworshak Reservoir because of its status as a major
storage reservoir on the system. For example, the Nez Perce Tribe has been working on

examining the impacts of Dworshak Reservoir releases on productivity within the reservoir. The
Idaho Fish and Game, in cooperation with the US Army Corps of Engineers, is examining how
artificial fertilization might improve reservoir fisheries. The US Army Corps of Engineers has
been studying how to minimize reservoir spill because of TDG concerns and multiple agencies
have been involved in evaluating the use of Dworshak in improving downstream water
temperatures on the lower Snake River.

While tied directly to existing concerns, this project is envisioned as an independent effort. No
immediate collaborations are necessary to successfully demonstrate the feasibility of the
proposed methodology. However, over the course of the work, it is hoped that other groups can
be brought in to provide input into the study.

This project has potentially broad impacts throughout the watershed. First, when combined with
other objectives and constraints, it could help define a new management strategy for releases
from Dworshak Reservoir. It would clearly demonstrate the positive or negative impacts of
modified water temperatures in the lower Clearwater. Second, the proposed microbial
fingerprinting methodology could be used to help define the effectiveness of habitat restoration
projects well beyond the current proposed project. If successful, it could become a cost-effective
means of rapidly assessing disturbance impacts such as new logging roads. This would
significantly enhance the monitoring and evaluation efforts required by the Council.

E. Proposal objectives, work elements, methods, and monitoring and evaluation

As previously stated, the overall goal of this project is to investigate the impacts of Dworshak
Reservoir releases on the lower Clearwater River using an innovative microbial fingerprinting
technique. In order to reach this goal, the specific objectives of this proposed study are to:

   1. Determine the extent that Dworshak Reservoir releases in July, August and September
      impact habitat function in the lower Clearwater, and
   2. Evaluate the effectiveness of using microbial populations as a measure of disturbance.

In order to complete these objectives, the following work elements will be completed:

   1. Complete reconnaissance temperature survey profile to identify locations for temperature
      loggers and microbial sampling stations,
   2. Install and monitor temperature arrays,
   3. Collect and analyze microbial populations from surface sediments,
   4. Develop numerical model to evaluate affects of management decisions regarding the
      ratios and absolute flows between Clearwater and Dworshak Reservoir releases,
   5. Statistically analyze combined relationships between water temperature and microbial
      populations, and
   6. Demonstrate management implications on operation of reservoir.

Detailed descriptions of these work elements are provided below. It should be noted that since
the two objectives are related, some of the work elements will be used to satisfy both objectives.
For instance, Objective 1 will include work elements 1, 2, 4, 5, and 6 while Objective 2 will
involve work elements 1, 3, 5 and 6.

Work Element No. 1

The first step of the project will be to complete a reconnaissance temperature survey profile to
identify locations for temperature loggers and microbial sampling stations. Factors such as
channel geometry, islands, and tributary inflow all act to influence the mixing of water in the
lower Clearwater. Visual inspection of the study reach will be required to evaluate the specific
influence of these factors. In addition, temperature profiles (horizontal and vertical) will be
collected using a hydrolab or similar device. Substrate material will also be examined to
determine uniformity of bed material between sites. Based on this information, researchers will
use a global positioning system (GPS) and maps to identify ten (10) cross-sections on the lower
Clearwater having characteristics representative of the river reach. Complete profiles of channel
geometry will be collected at those sites as well as additional sites near tributary inflows. Other
sites may also be surveyed depending on the results of the reconnaissance trip to insure sufficient
input data for the temperature model (see Work Element 4). Two additional sites, one on the
North Fork of the Clearwater immediately downstream of the dam and one upstream of the
confluence will be used as control sites.

Work Element No. 2

Once these sites are identified, temperature probes will be installed near the bottom substrate. At
each cross-section, three probes will be installed to determine near right bank, near left bank and
near mid channel. A total of 30 probes will be used in the mainstem study reach. Additional
probes will be used at the upstream control sites with three probes anticipated for the Clearwater
cross-section upstream of Orofino and up to three probes for the cross-section downstream of the
reservoir depending on the distribution of temperatures in that short reach.

The probes will be installed in late June and operated continuously through the end of
September. The loggers will be programmed to collect temperature data at ½ hour intervals. Data
will be downloaded bi-monthly during July, August and September during the six field trips that
will sample microbial populations (see Work Element 3) in order to insure that data loss due to
malfunctioning equipment will be minimized.

GIS maps of maximum, minimum, and average bi-weekly measured stream temperatures will be
generated for visual comparison. Initially, the assumption that variations between stations are
linear unless directly influenced by tributary inflows such as those from the Potlatch and Lapwei
River basins will be used to present measured data. This assumption will be examined further in
the modeling task. Traditional time-dependent plots of temperature and 7-day min/max averages
will also be produced.

Work Element No. 3

Surficial sediment samples will be collected from locations adjacent to water temperature
monitoring stations at bi-monthly intervals during July, August and September. Microbial

community fingerprints will be determined for each sediment sample using the culture
independent technique terminal-Restriction Fragment Length Polymorphism (Moyer et al.,
1996). The analysis requires extraction of microbial DNA from sediments, which will be used as
a template to amplify a characteristic gene from all bacteria present in the sample. Genes from
different bacterial types will then be separated chromatographically to yield microbial
community fingerprints.

Microbial community fingerprints generated using t-RFLP can be examined several ways (Brito
et al., 2006; Engebretson and Moyer, 2003). First, plots will be visually inspected to observe
differences in microbial community structure. Distribution and relative abundance of microbial
types will be evaluated in this manner. Microbial diversity will also be determined by summing
the different microbial types present within a sediment sample. It is difficult to predict whether
diversity for pristine environments will be higher or lower than polluted environments, but
differences will be observed (Nocker et al., 2007).

Work Element No. 4

A two-dimensional depth averaged numerical model of the lower Clearwater River will be
developed based on information on channel geometry collected during the reconnaissance study,
aerial photographs, and maps. FLOW2D will be used as the base model. The model will be
calibrated to the temperature data collected and information regarding releases and stream flow
from the USACE and the USGS. A portion of the measured data will be used to run the model in
verification mode. Once calibration and validation are complete, potential operating scenarios for
reservoir releases will be evaluated. The spatial distribution of temperature as a function of the
ratio between mainstem flows upstream of the confluence and reservoir releases will be
thoroughly investigated. Management options, including channel modifications to increase
mixing will be examined.

Work Element No. 5

The results from Work Element 3 will yield spatial and temporal variations in microbial
communities at 30 locations in the lower Clearwater River. This task will statistically analyze the
combined relationships between sediment microbial populations and water temperature using
analysis of variance (ANOVA) methods. Microbial community parameters to be considered
include distribution and relative abundance of microbial types and overall community diversity.
The hypothesis is that a cause/effect relationship can be identified and used to predict the impact
of management decisions.

Work Element No. 6

Using indexes of microbial populations and the temperature results, we will examine the
implications of release patterns on the Clearwater River. Comparison of the projected changes
will be used with known information regarding the growth rates of steelhead as a function of
temperature to demonstrate the potential impact of release schedules compared to reservoir
inflow and upstream discharges in the Clearwater. The goal will be to end up with the same
reservoir pool elevation on October 1. Ultimately, this will be one more parameter to factor into
the operation of the reservoir. It is not the purpose of this work to suggest it is the only parameter

that should be considered. The downstream impacts below the Snake-Clearwater confluence will
not be adequately addressed in this study. Nor does the investigation attempt to analyze the
impact on Kokanee in the reservoir.

Critical Assumptions

An underlying critical assumption of the proposed project is that microbial communities are
directly influenced by water temperatures and that population differences can be uniquely
identified with sufficient certainty to permit definitive cause-effect relationships. While we
know the first part of this is true, temperature do impact microbial development, variability in a
natural environment has not been studied adequately enough to guarantee the latter.

Monitoring and Evaluations

Interpretation of results will be subject to rigorous statistical analyses. These analyses will be
verified by consulting with the Statistics Department at Washington State University, a service
routinely provided by the department. In situ measurements of temperature during field trips will
be compared to recorded values to insure that probes are operating correctly. Four microbial
community fingerprints will be determined for three sampling locations to ascertain the inherent
variability of sample results.

A final report will be submitted documenting the procedures, data, results and conclusions of this
work. We plan on presenting the findings to the US Army Corp of Engineers office in Walla
Walla, Washington at which time representatives from NOAA fisheries will also be invited. In
addition, we anticipate presenting the results at a minimum of one regional and one national
conference and submitting a peer-reviewed journal paper to help disseminate the findings.

F. Facilities and equipment

Washington State University is a major research institution in the region. As a result, it is fully
equipped with routine field equipment, motor pool vehicles, and laboratory facilities. In addition,
the Department of Civil and Environmental Engineering has modern computer facilities that will
be used to process and analyze data and run the numerical model. Dr. Rentz occupies a new
microbiology laboratory (~900 sq ft) outfitted to complete the project, and he also has access
10,000 sq ft of laboratory space controlled by the Environmental Research Center (ERC).

Project funds will be used to purchase temperature probes, a thermal cycler and miscellaneous
supplies related to installation of the probes. In addition, disposable laboratory supplies related to
collection and processing of microbial samples will be needed. The WSU DNA core will be used
for t-RFLP analysis.

G. Literature Cited

Brito,E.M., Guyoneaud,R., Goni-Urriza,M., Ranchou-Peyruse,A., Verbaere,A., Crapez,M.A. et
al. (2006) Characterization of hydrocarbonoclastic bacterial communities from mangrove
sediments in Guanabara Bay, Brazil. Res. Microbiol. 157: 752-762.

Engebretson,J.J. and Moyer,C.L. (2003) Fidelity of select restriction endonucleases in
determining microbial diversity by terminal-restriction fragment length polymorphism. Appl.
Environ. Microbiol. 69: 4823-4829.

Moyer,C.L., Tiedje,J.M., Dobbs,F.C., and Karl,D.M. (1996) A computer-simulated restriction
fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of
selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl.
Environ. Microbiol. 62: 2501-2507.

Nocker,A., Lepo,J.E., Martin,L.L., and Snyder,R.A. (2007) Response of Estuarine Biofilm
Microbial Community Development to Changes in Dissolved Oxygen and Nutrient
Concentrations. Microb Ecol.

H. Key Personnel

The project will be conducted by Dr. Jeremy Rentz and Dr. Michael Barber. Each researcher will
contribute 348 hours to the project over the 18 month period. This is equivalent to approximately
two person-months per investigator. Dr. Rentz will be responsible for designing the experimental
work related to the microbial sampling and analysis. As indicated in the attached resume,
Jeremy’s graduate and post-doctoral research in environmental microbiology provided him with
the skills necessary to conduct this portion of the work. Dr. Rentz will also be responsible for
project management and supervision of the graduate student. Dr. Barber will be responsible for
field work related to temperature monitoring and numerical model development. Michael has
more than 15 years experience in field data collection and modeling. He will also be involved in
the combined analysis of temperature/microbial population data.

One full-time Graduate Students will be funded by this project. Responsibilities shared by the
students include collecting field samples and completing microbial community analysis.

      Ph. D., Civil and Environmental Engineering
       The University of Iowa, Iowa City, IA, 2004
              Degradative repression and co-metabolism, plant-microbe interactions
              affecting polycyclic aromatic hydrocarbon phytoremediation.
              Jerald L. Schnoor, Thesis advisor
      B. S., Chemical Engineering
       The University of Iowa, Iowa City, IA, 1999
      Assistant Professor
       Washington State University, Pullman, WA, 2006 – Present
           50% Teaching & 50% Research appointment
      Post Doctoral Fellow
       Northwestern University, Evanston, IL, 2005 – 2006
      Post Doctoral Research Scientist
       American Type Culture Collection, Manassas, VA, 2004 – 2005
I conduct general environmental microbiology research that evaluates both natural and
engineered systems. Natural systems are investigated using molecular methods to determine the
function and structure of microbial communities. Engineered systems focus on biological
degradation of polycyclic aromatic hydrocarbons (PAH) and biological removal of phosphorus
and heavy metals from water supplies.
Rentz, J. A., Alvarez, P. J. J., & Schnoor, J. L. 2007. Benzo[a]pyrene degradation by
Sphingomonas yanoikuyae JAR02. Environmental Pollution (In Press).
Rentz, J. A., Alvarez, P. J. J., & Schnoor, J. L. 2005. Benzo[a]pyrene co-metabolism in the
presence of plant root extracts and exudates: Implications for phytoremediation. Environmental
Pollution 136, 477-484.
Kamath, R., Rentz J. A., Schnoor, J. L., & Alvarez, P. J. J. 2004. Phytoremediation of
hydrocarbon-contaminated soils: principles and applications. In Petroleum Biotechnology:
Developments and Perspectives Studies in Surface Science and Catalysis. R. Vazquez-Duhalt
and R. Quintero-Ramirez (eds.). Elsevier Science, Oxford, UK. pp. 447-478.
Rentz, J. A., Alvarez, P. J. J., & Schnoor, J. L. 2004. Repression of Pseudomonas putida
phenanthrene-degrading activity by plant root extracts and exudates. Environmental
Microbiology. 6, 574-583.
Rentz, J. A., Chapman, B., Alvarez, P. J. J., & Schnoor, J. L. 2003. Stimulation of hybrid
poplar growth in petroleum-contaminated soils through oxygen and soil nutrient amendments.
International Journal of Phytoremediation. 5, 57-72.

                            MICHAEL ERNEST BARBER
                        State of Washington Water Research Center
                     Department of Civil and Environmental Engineering
                                Washington State University
                             Pullman, Washington 99164-3002
                      Phone: (509) 335-6633 C Email:
      Institution                                 Degree         Year
      University of Texas at Austin               Ph.D.          1991
      Purdue University                           MSCE           1983
      University of New Hampshire                 BSCE           1981

Employment History
     From 12/01 to Present, Director - State of Washington Water Research Center &
     From 8/99 to Present, Associate Professor, Washington State University, Pullman, WA.
     From 8/94 to 8/99, Assistant Professor, Washington State University, Pullman, WA.
     From 8/91 to 8/94, Assistant Professor, Tulane University, New Orleans, LA.
     From 9/88 to 8/91, Research Assistant, University of Texas, Austin, TX.
     From 6/83 to 7/88, Project Engineer, KKBNA Inc., Wheat Ridge, CO.
     From 9/81 to 12/82, Teaching Assistant, Purdue University, West Lafayette, IN.
     Summers 80/81, Civil Engineer, US Army Corps CRREL, Hanover, NH.

       Registered Professional Engineer in State of Colorado
       Associate Member of American Society of Civil Engineers
       Member of American Water Pollution Control Federation
       Member of American Water Resources Association
       Member of American Geophysical Union

Selected Publications
    1. G.N. Teasdale and M.E. Barber, “Aerial Assessment of Ephemeral Gully Erosion from
       Agricultural Regions in the Pacific Northwest” accepted ASCE Journal of Irrigation and
       Drainage Engineering, Winter 2005.
    2. G. Fu, M.E. Barber and S. Chen, “The Impacts of Climate Change on Regional
       Hydrological Regimes in the Spokane River Watershed,” accepted ASCE Journal of
       Hydrologic Engineering - HE/2005/022945, Fall 2005.
    3. Guang-Te Wang, S. Chen, M.E. Barber, and D.R.Yonge, (2004). “Modeling Flow and
       Pollutant Removal of a Wet Detention Pond Treating Stormwater Runoff,” Journal of
       Environmental Engineering, American Society of Civil Engineers, Vol.130, No. 11, pp
    4. M.E. Barber, S.G. King, D.R. Yonge, and W.E. Hathhorn, (2003). “The Ecology Ditch:
       A BMP for Stormwater Mitigation,” Journal of Hydrologic Engineering, American
       Society of Civil Engineers, Vol 8, No. 3, pp 111-122.
    5. E. Rowland, R.H. Hotchkiss, and M.E. Barber, (2003). “Predicting Fish Passage Design
       Flows at Ungaged Streams in Eastern Washington,” Journal of Hydrology, Vol. 273, pp


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