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Susitna-Watana Hydroelectric Project Document
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Title:
River productivity study, Study plan Section 9.8 : Final study plan
SuWa 200
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Alaska Energy Authority
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Final study plan
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Series (ARLIS-assigned report number):
Susitna-Watana Hydroelectric Project document number 200
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[Anchorage : Alaska Energy Authority, 2013]
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July 2013
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Study plan Section 9.8
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32 p.
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All reports in the Susitna-Watana Hydroelectric Project Document series include an ARLIS-
produced cover page and an ARLIS-assigned number for uniformity and citability. All reports
are posted online at http://www.arlis.org/resources/susitna-watana/
Susitna-Watana Hydroelectric Project
(FERC No. 14241)
River Productivity Study
Study Plan Section 9.8
Final Study Plan
Alaska Energy Authority
July 2013
FINAL STUDY PLAN RIVER PRODUCTIVITY STUDY 9.8
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 9.8-1 July 2013
9. FISH AND AQUATIC RESOURCES
9.8. River Productivity Study
On December 14, 2012, Alaska Energy Authority (AEA) filed with the Federal Energy
Regulatory Commission (FERC or Commission) its Revised Study Plan (RSP), which included
58 individual study plans (AEA 2012). Included within the RSP was the River Productivity
Study, Section 9.8. RSP Section 9.8 focuses on collecting baseline data to assist in evaluating the
effects of Project-induced changes in flow and the interrelated environmental factors upon the
benthic macroinvertebrate and algal communities in the Middle and Upper Susitna River.
On February 1, 2013, FERC staff issued its study determination (February 1 SPD) for 44 of the
58 studies, approving 31 studies as filed and 13 with modifications. FERC requested additional
information before issuing a SPD on the remaining studies. The Susitna River Productivity Study
Implementation Plan (RP IP) was presented and discussed during a Technical Work Group
(TWG) meeting on February 14, 2013. With consideration of the comment and suggestions
received from licensing participants, a RP IP was filed with FERC on March 1, 2013. On April
1, 2013 FERC issued its study determination (April 1 SPD) for the remaining 14 studies ;
approving 1 study as filed and 13 with modifications. RSP Section 9.6 was one of the 13
approved with modifications. In its April 1 SPD, FERC recommended the following:
Modified Sampling Locations
- We recommend that AEA remove the proposed Upper River mainstem study stations (RP-
248 and RP-233).
Macrohabitat Replicates
- We recommend that AEA sample in all unique macrohabitat types present at each proposed
study station for river productivity sampling in the Middle River and Lower River segments.
This would result in 16 sites in the Middle River and five sites in the Lower River. AEA
should collect samples in each macrohabitat type as feasible using sampling methods and
devices proposed in its RSP and final RP IP, with the modifications we recommend below in
Turbidity and Vegetation Influence, Benthic Sampling Methods, Water Column and Surface
Sampling, Organic Matter Sample Processing, Benthic Macroinvertebrate Sampling on
Snags, Emergence Sampling, and Trophic Modeling.
Turbidity and Vegetation Influence
- We recommend that AEA conduct macroinvertebrate drift sampling upstream and
immediately downstream of tributary mouths to collect information needed to assess the
relative contribution of tributaries and the mainstem Susitna River to fish food resources.
Benthic Sampling Methods
- We recommend AEA collect BMI and algae samples in macrohabitats with fine substrate
and low velocities using a bottom dredge or grab sampler. AEA should select the most
appropriate sampler according to the bottom substrate, water velocity, and other conditions
(see Klemm et al. 1990), but should endeavor to use the same sampler in all macrohabitats of
this type to ensure consistency among samples. Additionally, AEA should sample benthic
algae on cobble substrates at multiple depths up to 3 feet (e.g., depth categories of 0–1 foot,
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1–2 feet, and 2–3 feet) at each macrohabitat site (main channel, tributary confluences, side
channels, and sloughs), to the extent feasible given the limits of field safety.
Water Column and Surface Sampling
- We recommend that AEA sample invertebrates in the water column and the water surface of
still water areas in one side slough, one upland slough, and one tributary mouth (if present)
at each study station in the Middle River and Lower River using a modified plankton tow or
similar sampler. Five replicates should be collected along a single transect at each site.
Organic Matter Sample Processing
- We recommend that AEA obtain AFDM measures of biomass from samples of benthic and
transported organic matter, using generally accepted scientific methods (section 5.9(b)(6)).
Benthic Macroinvertebrate Sampling on Snags
- We recommend that AEA sample BMI on measured and representative portions of LWD in
situ by dislodging organisms by hand and collecting them in a net as they enter the water
column at each sample site.
- For consistency, we also recommend that AEA use of the term “large woody debris”
(LWD) as defined here: “LWD must be at least 0.1 meter (4 inches) in diameter, and at least
1.0 meter (39 inches) of the LWD must be below the water’s surface at bankfull flow” and
apply it consistently when referring to “wood” and “snags” in its RSP and future study
reports.
Emergence Sampling
- We recommend that AEA sample aquatic insect emergence in ice free areas, if available,
beginning in April, then remove the traps during ice breakup and redeploy them following
ice breakup in late May or early June.
Trophic Modeling
- For fish sampled for use in the growth and trophic modeling studies, we recommend that
AEA measure, weigh, and mark the first 50 fish of each target species and age class captured
within each sampled macrohabitat by PIT-tagging to identify the capture station and date.
We recommend that AEA collect fish for the trophic modeling studies at all available
macrohabitat types (up to five per study station) in each Middle River and Lower River study
station. Growth data collected from fish marked and recaptured in the same macrohabitat
site should be used (if possible) to validate AEA’s proposed growth rate potential model. We
also recommend that AEA incorporate flow velocity into its foraging models and account for
associated capture efficiencies when establishing consumption rate.
Stable Isotope Analysis
- We recommend that AEA consult with NMFS and FWS when identifying the appropriate
two focus areas for stable isotope sampling, where within the focus areas each type of stable
isotope samples would be collected, and the number of adult salmon tissue samples to be
collected.
Talkeetna River Reference Study Station
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- We recommend that AEA consult with the TWG when selecting the Talkeetna River
reference study station.
In accordance with the April 1 SPD, AEA has adopted the FERC requested modifications in the
FDA IP and this Final Study Plan. The Susitna River Productivity Implementation Plan has
similarly been updated with FERC staff recommendations from the April 1, 2013 Study Plan
Determination and provides further detail.
9.8.1. General Description of the Proposed Study
The production of freshwater fishes in a given habitat is constrained both by the suitability of the
abiotic environment and by the availability of food resources (Wipfli and Baxter 2010). Algae
are an important base component in the lotic food web, being responsible for the majority of
photosynthesis in a river or stream and serving as an important food source to many benthic
macroinvertebrates. In turn, benthic macroinvertebrates are an essential component in the
processes of an aquatic ecosystem, due to their position as consumers at the intermediate trophic
level of lotic food webs (Hynes 1970; Wallace and Webster 1996; Hershey and Lamberti 2001).
Macroinvertebrates are involved in the recycling of nutrients and the decomposition of terrestrial
organic materials in the aquatic environment, serving as a conduit for the energy flow from
organic matter resources to vertebrate populations, namely fish (Hershey and Lamberti 2001;
Hauer and Resh 1996; Reice and Wohlenberg 1993; Klemm et al. 1990). In turn, nutrients and
energy provided by spawning salmon have the potential to increase freshwater and terrestrial
ecosystem productivity (Wipfli et al. 1998; Cederholm et al. 1999; Chaloner and Wipfli 2002;
Bilby et al. 2003; Hicks et al. 2005), and may subsidize otherwise nutrient-poor ecosystems
(Cederholm et al. 1999).
The significant functional roles that macroinvertebrates and algae play in food webs and energy
flow in the freshwater ecosystem make these communities important elements in the study of a
stream’s ecology. The operations of the proposed Project would likely affect one or more of the
factors that can affect the abundance and distribution of benthic algae and benthic
macroinvertebrate populations, which could ultimately affect fish growth and productivity in the
system. The degree of impact on the benthic communities and fish resulting from hydropower
operations will necessarily vary depending on the magnitude, frequency, duration, and timing of
flows, as well as potential Project-related changes in geomorphology, ice processes, temperature,
and turbidity. By investigating the current populations of algae, benthic macroinvertebrates, and
fish in the Susitna River and the trophic relationships between them, this study will generat e
information about the current health and status of these populations throughout the varied
habitats in the Susitna River, and provide a better understanding on the availability and
utilization of food resources in the system. In addition, by applying wh at is known about the
effects of river regulation and hydropower operation on these populations in riverine ecosystems,
AEA can begin to assess the potential impacts of Project operations on river productivity in the
Susitna River, as well as provide information to inform development of any necessary protection,
mitigation, and enhancement (PM&E) measures.
Study Goals and Objectives
The overarching goal of this study is to collect baseline data to assist in evaluating the effects of
Project-induced changes in flow and the interrelated environmental factors (temperature,
substrate, water quality) upon the benthic macroinvertebrate and algal communities in the
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Middle and Lower Susitna River. Individual objectives that will accomplish this are listed
below.
1. Synthesize existing literature on the impacts of hydropower development and operations
(including temperature and turbidity) on benthic macroinvertebrate and algal
communities.
2. Characterize the pre-Project benthic macroinvertebrate and algal communities with
regard to species composition and abundance in the Middle and Lower Susitna River.
3. Estimate drift of benthic macroinvertebrates in selected habitats within the Middle and
Lower Susitna River to assess food availability to juvenile and resident fishes.
4. Conduct a feasibility study in 2013 to evaluate the suitability of using reference sites on
the Talkeetna River to monitor long-term Project-related change in benthic productivity.
5. Conduct a trophic analysis to describe the food web relationships within the current
riverine community within the Middle and Lower Susitna River.
6. Develop habitat suitability criteria for Susitna benthic macroinvertebrate and algal
habitats to predict potential change in these habitats downstream of the proposed dam
site.
7. Characterize the invertebrate compositions in the diets of representative fish species in
relationship to their source (benthic or drift component).
8. Characterize organic matter resources (e.g., available for macroinvertebrate consumers)
including coarse particulate organic matter, fine particulate organic matter, and
suspended organic matter in the Middle and Lower Susitna River.
9. Estimate benthic macroinvertebrate colonization rates in the Middle Susitna Segment
under pre-Project baseline conditions to assist in evaluating future post-Project changes
to productivity in the Middle Susitna River.
9.8.2. Existing Information and Need for Additional Information
A number of evaluations of the benthic macroinvertebrate community were conducted on the
Susitna River in the 1970s and in the 1980s for the original Alaska Power Authority (APA)
Susitna Hydroelectric Project (Friese 1975; Riis 1975, 1977; ADF&G 1983; Hansen and
Richards 1985; Van Nieuwenhuyse 1985; Trihey and Associates 1986). ADF&G studies in the
1970s included sampling of macroinvertebrates using artificial substrates (rock baskets)
deployed for a set period of time to allow for colonization. Friese (1975) and Riis (1975) set a
total of eight rock baskets in Waterfall Creek, Indian River, and the mainstem Middle Susitna
River for 30 days during summer (July – September). Riis (1977) also deployed rock baskets in
the Susitna River near the mouth of Gold Creek for a colonization period of 75 days; however,
only two of seven baskets were retrieved. Results were limited to low numbers of invertebrates
per basket, identified to taxonomic family.
Studies conducted in the 1980s for the original APA Susitna Hydroelectric Project focused on
benthic macroinvertebrate communities in the sloughs, side channels, and tributaries of the
Middle Segment of the Susitna River from river mile (RM) 125 to RM 142 during the period
from May through October. Efforts included direct benthic sampling with a Hess bottom
sampler and drift sampling. Alaska Department of Fish and Game (ADF&G) efforts in 1982 and
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1984 also involved collection of juvenile salmon in these side channels and sloughs, and an
analysis was conducted to compare gut contents with the drift and benthic sampling results
(ADF&G 1983; Hansen and Richards 1985). In addition, Hansen and Richards (1985) collected
water velocity, depth, and substrate-type data to develop habitat suitability criteria (HSC), which
were used to estimate weighted usable areas for different invertebrate community guilds, based
on their behavioral type (swimmers, burrowers, clingers) in slough and side channel habitats.
Efforts in 1985 (Trihey and Associates 1986) expanded to include sampling at nine sites in the
Middle Susitna River Segment: three side channels, two sloughs, two tributaries, and two
mainstem sites.
Algal communities were periodically sampled and analyzed for chlorophyll-a at Susitna Station
from 1978 to 1980. In the 1980s, algae samples were collected as part of the APA Susitna
Hydroelectric Project water quality studies, with sampling conducted at Denali, Cantwell (Vee
Canyon), Gold Creek, Sunshine, and Susitna Station on the Susitna River, as well as on the
Chulitna and Talkeetna rivers (Harza-Ebasco 1985 as cited in AEA 2011). Analysis showed low
productivity (less than 1.25 mg/m3 chlorophyll-a) and indicated algal abundance was most likely
limited by high concentrations of turbidity (AEA 2011).
Baseline field data for benthic primary and secondary production was also collected in 1985, as
part of the Primary Production Monitoring Effort (Van Nieuwenhuyse 1985). Chlorophyll -a
(chl-a), and macroinvertebrates were collected from early April to late October 1985 from a
variety of off-channel and mainstem habitat sites. Early April sampling took place in an open -
water lead in Slough 8A, and revealed high macroinvertebrate densities (average 17,600
individuals/m2) comprised almost entirely of chironomid larvae, and chlorophyll-a densities
averaging 34.4 mg/m2. Sampling in early May in Slough 8A revealed macroinvertebrate
densities averaging 2,950 individuals/m2, again almost entirely chironomids, and chl-a densities
averaging 37mg/m2. Results from five mainstem habitat sites showed similar macroinvertebrate
numbers, with densities ranging from 393 to 8,820 individuals/m2 in May 1985, but with
considerably more diversity; chironomids accounted for an average of 53 percent of the density,
and only 8 percent of the macroinvertebrate biomass. Algae samples beyond May 1985 had not
been analyzed; therefore, no data were available for summer or fall. No sampling results were
given for summer macroinvertebrate sampling (June and July). August and September 1985
sampling showed low average densities at mainstem sites (44 – 164 individuals/m2), with large
increases occurring in October 1985 (1,729 – 7,109 individuals/m2). Average densities in Slough
8A in August 1985 remained similar to spring levels, at 2,851 individuals/m2, with a surge in
September 1985 (13,964 individuals/m2); again, chironomids represented over 80 percent of the
numbers. No further information or reports were available concerning the Primary Production
Monitoring Effort task.
Benthic macroinvertebrate information from the 1980s is focused on a limited number of
mainstem, side channel, and slough habitats located within a 17-mile reach of the Middle Susitna
River. Additional information is needed on mainstem benthic communities, as well as those in
side channel and slough habitats, within both the Middle and Lower Susitna River segments.
Benthic algae information needs to be collected in conjunction with the macroinvertebrates to
define their relationship in the river’s trophic system. To assess the impact of future hydropower
operations on the benthic communities within the Susitna River, additional information must be
collected through an increased sampling effort, including more sampling sites along the river in
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relation to the distance both downstream from the proposed dam site and upstream from the
proposed Project reservoir area.
9.8.3. Study Area
The River Productivity Study will entail field sampling throughout the Middle Segment and
Lower Segment of the Susitna River (Table 9.8-1; Figures 9.8-1 through 9.8-2). The Middle
Susitna River Segment encompasses the 86-mile section of river between the proposed Watana
Dam site and the Chulitna River confluence, located at RM 98 (Figure 9.8-1). The Lower
Susitna River Segment is defined as the approximately 98-mile section of river between the
Chulitna and Talkeetna rivers confluence and Cook Inlet (Figure 9.8-2). Sampling activities
within these segments will investigate the benthic communities that may be affected by the
Project and its regulated flows. Sampling will be conducted at various distances from the
proposed dam site to document longitudinal variability, and estimate the effects that the proposed
Project will have on benthos in the river system downstream.
AEA will reevaluate how far downstream Project operational significant effects extend based in
part upon the results of the Open-water Flow Routing Model (see Section 8.5.4.3), which is
scheduled to be completed in Q1 2013. Thus, an initial assessment of the downstream extent of
Project effects will be developed in Q2 2013 with input of the TWG. This assessment will
include a review of information developed during the 1980s studies and study efforts initiated in
2012, such as sediment transport (Section 6.5), habitat mapping (Sections 6.5 and 9.9),
operations modeling (Section 8.5.4.2.2), and the Mainstem Open-water Flow Routing Model
(Section 8.5.4.3). The assessment will guide the need to extend studies into the Lower River
Segment and if needed, will identify which geomorphic reaches will be subject to detailed
instream flow analysis in 2013. Results of the 2013 studies would then be used to determine the
extent to which the study should be modified to include sampling in the Lower River Segment in
2014.
9.8.4. Study Methods
This study will employ a variety of field methods to build upon the existing information related
to the benthic macroinvertebrate and algal communities in the Middle and Lower Susitna River.
The following sections provide brief descriptions of study site selection, sampling timing, the
approach, and methods that will be used to accomplish each objective of this study.
River Productivity Implementation Plan
This study includes a description of the sampling scheme. However, specific details regardin g
site locations, timing, sampling devices, processing, and analyses will be dependent upon the
results of 2012 data collection efforts.
The final sampling scheme will be included in the River Productivity Implementation Plan,
which will be filed with FERC prior to March 15, 2013.
The Implementation Plan development will include: (1) a summary of relevant
macroinvertebrate and algal studies in the Susitna River, (2) an overview of the life -histories of
the target fish species in the Susitna River that are selected for the trophic analysis (Section
9.8.4.5.1), (3) a review of the preliminary results of habitat characterization and mapping efforts
(Section 9.9) and “Focus Areas” (Section 8.5.4.2.1.2), (4) a description of site selection
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protocols, (5) a description of sampling protocols, (6) a description of sample processing
protocols, (7) a discussion of data analysis methods, (8) development field data collection forms,
and (9) development of database templates that comply with 2012 AEA QA/QC procedures.
The implementation plan will include the level of detail sufficient to instruct field crews in data
collection efforts. In addition, the plan will include protocols and a guide to the decision -making
process in the form of a chart or decision tree that will be used in the field, specific sampling
locations, details about the choice and use of sampling techniques and apparatuses, and a list of
field equipment needed. The implementation plan will also help ensure that field collection
efforts occur in a consistent and repeatable fashion across field crews and river segments.
Proposed sampling methods by objective are presented below. The Susitna River River
Productivity Implementation Plan has similarly been updated with FERC staff recommendations
from the April 1, 2013 Study Plan Determination and provides further detail.
9.8.4.1. Synthesize existing information on the impacts of hydropower development
and operations (including temperature and turbidity) on benthic
macroinvertebrate and algal communities
Several reviews have been written on the effects that modified flows have on the benthic
communities residing below dams (Ward 1976; Ward and Stanford 1979; Armitage 1984; Petts
1984; Cushman 1985; Saltveit et al. 1987; Brittain and Saltveit 1989). A majority of these
reviews indicate that temperature and flow regimes are often the most important factors affecting
benthic macroinvertebrates below dams. The type of dam and its mode of operation will have a
large influence over the type and magnitude of effects on the receiving stream below. General
information on the effects of hydropower on riverine habitats, especially glacially-fed river
systems, as well as Project-specific information, will be reviewed and synthesized in a written
report. Specifically, AEA will prepare a written report that provides a literature review
summarizing relevant literature on macroinvertebrate and algal community information in
Alaska, including 1980s Susitna River data; review and summarize literature on general
influences of changes in flow, temperature, substrates, nutrients, organic matter, turbidity, light
penetration, and riparian habitat on benthic communities; and review and summarize the
potential effects of dams and hydropower operations, including flushing flows and load-
following, on benthic communities and their habitats. To the extent consistent with copyright
laws, electronic copies of all cited publications will be provided through the ARLIS library.
9.8.4.2. Characterize the pre-Project benthic macroinvertebrate and algal
communities with regard to species composition and abundance in the
Middle and Lower Susitna River
9.8.4.2.1. Benthic macroinvertebrate sampling
Macroinvertebrate sampling will be stratified by reach and mainstem habitat type defined in the
Project-specific habitat classification scheme (mainstem, tributary confluences, side channels,
and sloughs). To accomplish this objective, sampling will occur at five stations, each with three
to five sites (one site for each unique macrohabitat type present in a station), for a total of 21
sites. In the Middle Segment, two stations will be located between the dam site and the upper
end of Devils Canyon, and two stations will be located below Devils Canyon, within the
Geomorphic Reaches MR-6 and MR-8 (Table 9.8-1; Figure 9.8-1). All stations established
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within the Middle Segment will be located at Focus Areas established by the Instream Flow
Study (Section 8.5.4.2.1.2), in an attempt to correlate macroinvertebrate data with additional
environmental data (flow, substrates, temperature, water quality, riparian habitat, etc.) for
statistical analyses, and HSC/HSI development. In the Lower Segment, sampling will occur at
one station within the Geomorphic Reach LR-1 (Table 9.8-1; Figure 9.8-2). Specific station and
site locations will be determined during the first quarter of 2013, and detailed in the River
Productivity Implementation Plan.
Three sampling periods will occur from April through October in both study years (2013 –2014)
to capture seasonal variation in community structure and productivity. Seasonal periods are
tentatively scheduled for April through early June for Spring, late June through August for
Summer, and September through October for Autumn. Specific details on timing will be
provided in the River Productivity Implementation Plan. Timing of life history events for coho,
Chinook salmon, and rainbow trout (target species for Objective 5, Section 9.8.4.5.1) will be
consulted when scheduling sampling efforts.
Sampling will be conducted in riffle/run mesohabitats within mainstem and off-channel
macrohabitat types (i.e., tributary confluences, side channels, and sloughs). Higher flows may
inundate new shoreline substrates, which poses the risk of sampling in areas that are not fully
colonized. The shoreline bathymetry for each site will be evaluated such that changes in water
level due to increasing or decreasing flows must remain constant enough that the substrates
accessible for sampling will be continually inundated for a period of at least one month, to
facilitate colonization of those substrates.
Benthic macroinvertebrate sampling will be conducted using a stream-type sampler (Hess,
Surber, Slack) commonly used for other Alaskan benthic macroinvertebrate studies to allow for
comparable results; state and federal protocols (Hansen and Richards 1985; Barbour et al. 1999;
Klemm et al. 1990; Klemm et al. 2000; Carter and Resh 2001; Moulton et al. 2002; Peck et al.
2006), as well as methods used in the Susitna River studies in the 1980s, will be considered
when designing the sampling approach, which will be detailed in the River Productivity
Implementation Plan. Replicate samples (n=5) will be collected to allow for statistical testing of
results for short- and long-term monitoring. Measurements of depth, mean water column
velocity, mean boundary layer velocity (near bed), and substrate composition will be taken
concurrently with benthic macroinvertebrate sampling at the sample location for use in HSC /HSI
development in the instream flow studies. Water temperatures will be monitored hourly at sites
with submerged temperature loggers deployed at all sampling sites throughout the ice-free
season. Fine-scale (1 meter vertical and horizontal resolution) measurements of flow will be
recorded within a 5-m radius of selected sampling sites. Temperature and flow monitoring will
be coordinated with the Baseline Water Quality Study (Section 5.5) and the Instream Flow Study
(Section 8.5), and supplemental temperature loggers will be deployed if necessary to cover all
River Productivity Study sites.
Some macrohabitats may lack adequate riffle/run mesohabitat (e.g., side sloughs and upland
sloughs), instead featuring deeper pools, fine substrates, and low velocity. Use of a Hess
sampler in this type of slow-water habitat is not appropriate; therefore, a grab sampler (e.g
Ekman, Ponar) will be instead be used to sample macroinvertebrates in macrohabitats with fine
sediment and low velocities. Similar to Hess sample collections, replicate samples (n=5) will be
collected to allow for statistical testing of results for short- and long-term monitoring.
Measurements of depth, mean water column velocity, mean boundary layer velocity (near bed),
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and substrate composition will be taken concurrently with benthic macroinvertebrate sampling at
the sample location
In addition, floating emergence traps will be deployed at each site to determine both the timing
and the amount of adult insect emergence from the Susitna River (Cushman 1983). Adult
aquatic insect emergence mass is a product of aquatic insect production from the stream, and is
therefore a good surrogate for actual production (minus predation), and will be especially useful
for relative comparisons between river sections and years (personal communication, M. Wipfli,
University of Alaska-Fairbanks). Emergence traps will be checked and reset every month.
Trapped adults will be identified, enumerated, and weighed. Exact trap design will be
determined according to methods compatible with those used for other studies in comparable
streams/basins in Alaska, and will be detailed, along with sampling and processing methodology,
in the River Productivity Implementation Plan.
Due to the prevalence of large woody debris (LWD) in the Susitna River, LWD, if present at a
sampling site, also will be sampled as a substrate strata for benthic macroinvertebrates, as
requested by the U.S. Fish and Wildlife Service (USFWS) (USFWS River Productivity Study
Request; May 31, 2012). Sampling methods for LWD will be semi-quantitative, based upon
protocols established by the USGS (Moulton et al. 2002). Suitable LWD will have been
submerged for an extended period of time so as to be clearly colonized. Immobile LWD present
will be sampled in situ by dislodging organisms by hand and collecting them in a D-net
positioned immediately downstream as they enter the water column. Smaller, removable LWD
to be sampled will be removed from the water by using a saw and placed over a plastic bin or in
a bucket, and all benthic macroinvertebrates will be removed by handpicking, brushing, and
rinsing. The removed LWD sections will be allowed to dry for a period of time so that missed
organisms will crawl out of the crevices and can then be collected. Removed sections sampled
will be measured for length and average diameter to determine surface area sampled. Each
section will originate from a separate piece of LWD, and therefore count as a separate, replicate
sample. Sampling and processing methodology will be detailed in the River Productivity
Implementation Plan.
In order to address the effects of changing flow patterns on benthic macroinvertebrates, algae
(Section 9.8.4.2.2), and benthic organic matter (BOM) (Section 9.8.4.8), baseline data will be
collected to assess the benthic community responses to storm events within side slough habitats.
Additional sampling will be conducted both before and after storm events that meet or exceed a
1.5-year flood event at two side slough sites, located in two separate Focus Areas in the Middle
River Segment between Portage Creek and Talkeetna (Section 8.5.4.2.1.2). Replicate samples
(n=5) will be collected at both the upstream and downstream ends of each slough, and will
include benthic macroinvertebrates, algae, and BOM. Sampling will be conducted for two storm
events per year. Specific details on locations and targeted flows will be based on information
from the Instream Flow (Section 8.5) and Geomorphology (Section 6.5) studies available in early
2013, and will be provided in the River Productivity Implementation Plan.
Benthic macroinvertebrate replicate samples collected will be stored in individual containers and
immediately preserved in the field with 95 percent ethanol (non-denatured). Samples will be
processed in a laboratory using methods compatible with those used for other studies in
comparable streams/basins in Alaska. State and federal protocols (Barbour et al. 1999; Major
and Barbour 2001; Moulton et al. 2002) will be considered when making decisions about the
sample processing protocols, including sub-sampling protocols and the taxonomic resolution of
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specimen identifications. Sampling and processing methodology will be detailed in the River
Productivity Implementation Plan.
Results generated from the collections will include several descriptive metrics commonly used in
aquatic ecological studies, such as density (individuals per unit of area), taxa richness (both mean
and total), EPT taxa (i.e., Ephemeroptera, Plecoptera, Trichoptera) richness, diversity (H’),
evenness (J’), percent dominant taxa, the relative abundance of major taxonomic groups, and the
relative abundance of the functional feeding groups. In conjunction with the bioenergetics
modeling (Section 9.8.4.5.1), biomass estimates will be taken for primary invertebrate taxa
collected for benthic and emergence sampling. The fresh blotted wet mass of invertebrate taxa in
samples will be recorded, the samples will be oven dried at 60 ˚C until reaching constant mass,
and the dry mass will be recorded. For a select sub-sample of the collection, energy density (J /
g wet weight) will be estimated from the percent dry mass (dry mass / wet mass) of each sample
(Ciancio et al. 2007; James et al. 2012). Energy density will be determined separately for the
aquatic and terrestrial (adult) life-stages of each primary invertebrate taxon. For two selected
stations, benthic macroinvertebrates and organic matter in samples will then be utilized for stable
isotope analysis (Objective 5, Section 9.8.4.5.2).
Data collected during this study will be compared to the results of 1980s studies (ADF&G 1983;
Hansen and Richards 1985; Van Nieuwenhuyse 1985; Trihey and Associates 1986) to evaluate
any differences between the historic and current community structure. In addition, any invasive
benthic macroinvertebrates identified in the sample collections will be identified and their
collection locations will be recorded using the Geographic Information System (GIS) (NAD 83).
9.8.4.2.2. Benthic algae sampling
Benthic algae sampling will be collected concurrently with benthic macroinvertebrate sampling
at all five stations (21sites total) to allow for correlation between the two collections (Table 9.8-
1), plus the additional baseline sampling effort addressing the effects of changing flow patterns
on benthic communities in sloughs, as discussed in Section 9.8.4.2.1. Benthic algae sampling
will be conducted using methods compatible with other Alaska benthic algal studies, to allow for
comparison of results. Algal sampling methods will be based on the EPA’s field operations
procedures for periphyton single or targeted habitat sampling when designing the sampling
approach (Eaton et al. 1998; Barbour et al. 1999; Peck et al. 2006). Measurements of depth,
mean water column velocity, mean boundary layer velocity, turbidity, and substrate composition
will be taken concurrently with algae sampling at the sample location for use in HSC
development in the instream flow studies. Light availability will be measured at each sample
location with an underwater light sensor, to measure the photosynthetically active radiation
(PAR) available to the algal community. Turbidity measurements will also be taken at the site to
determine water clarity. Benthic algae samples will be processed in a laboratory, using methods
compatible with those used for other studies in comparable streams/basins in Alaska, considering
state and federal protocols (Eaton et al. 1998; Barbour et al. 1999; Moulton et al. 2002; Peck et
al. 2006) to determine sample processing protocols, including sub-sampling protocols. Algal
sampling and processing methods will be detailed in the River Productivity Implementation Plan.
Results generated from the collections would include both dry weight and chlorophyll-a, and
several descriptive metrics to describe the algal community; full details will be provided in the
River Productivity Implementation Plan. For two selected stations, portions of algal material
will then be utilized for stable isotope analysis (Objective 5, Section 9.8.4.5.2). In addition, any
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invasive algae taxa identified in the sample collections will be identified and their locations will
be recorded using GIS (NAD 83).
9.8.4.3. Estimate drift of invertebrates in selected habitats within the Middle and
Lower Susitna River to assess food availability to juvenile and resident fishes
Invertebrate drift sampling will be conducted concurrently with benthic macroinvertebrate
sampling at all sites within the five established sampling stations to allow for comparisons
between the drift component and the benthic macroinvertebrate community, as well as revealing
the availability of terrestrial invertebrates to fish predation. Sampling will be conducted in
riffle/run habitats within the mainstem sites, and their associated off-channel habitat sites (Table
9.8-1). For tributary mouth macrohabitats, drift sampling will be conducted upstream and
immediately downstream of the tributary mouth to collect information about the relative
contribution of tributaries and the mainstem Susitna River to fish food resources.
Invertebrate drift sampling will be conducted using a drift net similar to those used for other drift
studies in Alaska to allow for comparison of results; state and federal protocols will be
considered (Keup 1988; Klemm et al. 2000). Drift sampling will be conducted during pre-dawn
hours, as a measure of drift that is available to feeding fish (Waters 1972; Brittain and Eikeland
1988; Keup 1988). Sampling methods will involve collecting duplicate samples to allow for
statistical testing of results for short- and long-term monitoring (Klemm et al 1990; Klemm et al.
2000). Water velocity will be recorded with an in-net flow meter. Invertebrate drift samples will
be processed in a laboratory, using methods compatible with other studies conducted in
comparable streams/basins in Alaska. State and federal protocols (Barbour et al. 1999; Major
and Barbour 2001; Moulton et al. 2002) will be considered when making decisions about the
sample processing protocols, including sub-sampling protocols, taxonomic resolution of
specimen identifications, and length measurements for individual specimens. Samples at two
selected stations will be tested for the stable isotope analysis task (Section 9.8.4.5.2). The two
Focus Areas, specific sample site locations, and number of adult salmon tissue samples to be
collected will be determined with input from with the TWG. Organic matter (OM) content will
be retained and analyzed by size (coarse and fine particulate OM) as discussed in Section 9.8.4.8.
Results generated from these collections will include drift density, drift rate, and drift
composition. In conjunction with the bioenergetics modeling (Section 9.8.4.5.1), biomass
estimates will be taken for primary invertebrate taxa collected for drift sampling. The fresh
blotted wet mass of invertebrate taxa in samples will be recorded, the samples will be oven-dried
at 60˚C until reaching constant mass, and the dry mass will be recorded. For a select sub-sample
of the collection, energy density (J / g wet weight) will be estimated from the percent dry mass
(dry mass / wet mass) of each sample (Ciancio et al. 2007; James et al. 2012). Energy density
will be determined separately for the aquatic and terrestrial life stages of each primary
invertebrate taxon. For two selected stations, portions of terrestrial invertebrate composition and
organic matter in samples will then be utilized for stable isotope analysis (Objective 5, Section
9.8.4.5.2).
Some off-channel macrohabitats may lack adequate velocities (e.g., side sloughs and upland
sloughs), for the use of a drift net for sampling. Therefore, a modified plankton net (250 µm
mesh) will be instead be used in these still water areas to sample macroinvertebrates t he water
column. Replicate samples (n=5) will be collected along a single transect at the site location.
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Sampling and processing methods will be detailed in the River Productivity Implementation
Plan.
Data collected as part of this study will be compared to data from the benthic macroinvertebrate
collections (Section 9.8.4.2.1) and the fish dietary analysis (Section 9.8.4.7). In addition, drift
results will be compared to the results of 1980s drift studies (ADF&G 1983; Hansen and
Richards 1985; Trihey and Associates 1986) to evaluate any differences between the historic and
current drift components of the macroinvertebrate communities.
9.8.4.4. Conduct a feasibility study in 2013 to evaluate the suitability of using
reference sites on the Talkeetna River to monitor long-term Project-related
change in benthic productivity
Sampling sites will be established in the Talkeetna River in areas that are physically similar to
those sampled in the Middle Susitna River Segment, to ensure comparability. Sampling will be
conducted in riffle habitats within the mainstem, side channels, and sloughs. One station will be
established, with a mainstem site and two off-channel habitat sites associated with the mainstem
site. Final site selection will occur with input from the TWG. Benthic and drift sampling will
occur during approximately the same periods as sampling in the Middle Susitna River Segment
(Objectives 2 and 3, Sections 9.8.4.2 and 9.8.4.3), with seasonal samplin g during 2013. Benthic
macroinvertebrate, benthic algal, and drift sampling methods and processing protocols will be
identical to those used in sampling the Middle Susitna River Segment (Objective 2, Section
9.8.4.2). In the first quarter of 2014, sampling results from Talkeetna sites will be compared to
results from similar sites in the Middle Susitna River Segment to determine whether the
Talkeetna River would serve as a suitable reference site. Statistical analyses will test for
similarities and significant differences between Talkeetna sites and Middle Susitna Segment sites
by comparing community compositions and a collection of calculated metrics. Methods will be
detailed in the River Productivity Implementation Plan, and may include ANOVA, MANOVA,
cluster analysis using Non-Metric Multi-Dimensional Scaling (NMDS) ordinatation with the
Bray-Curtis Dissimilarity Coefficient, and/or other multivariate ordination techniques (Principal
Components Analysis, Canonical Correspondence Analysis). Results indicating close
similarities, or no significant differences, between sites on the two rivers would indicate
suitability as a reference. If suitable, sites on the Talkeetna River can be used in a long-term
monitoring program with Susitna River sites to help differentiate potential long-term changes
that are Project-related versus those occurring for other reasons outside Project influence. Such a
monitoring program would ideally collect multiple years of both pre-Project and post-Project
data.
9.8.4.5. Conduct a trophic analysis, using trophic modeling and stable isotope
analysis, to describe the food web relationships in the current riverine
community within the Middle Susitna River
9.8.4.5.1. Develop a trophic model to estimate how environmental factors and food
availability affect the growth rate potential of focal fish species under current and
future conditions
To complement the fish habitat suitability analysis (Section 9.8.4.6), which focuses on physical
habitat features, trophic models will be developed to incorporate the density and quality of prey
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into an estimate of habitat quality. Growth rate potential models integrate knowledge of the
foraging capabilities and bioenergetic physiology of a consumer with field data on its physical
environment and prey base to quantify the values of different habitats (Brandt et al. 1992; Nislow
et al. 2000; Jensen et al. 2006; Farley and Trudel 2009). The currency of these models, growth
rate potential (GRP), is the expected growth rate of a consumer occupying a given habitat. Fo r
salmon, juvenile growth is strongly correlated with early marine survival and overall stock
dynamics (Pearcy 1992; Beamish and Mahnken 2001; Moss et al. 2005; Duffy and Beauchamp
2011), making GRP a particularly valuable metric of freshwater habitat quality.
One drawback of typical GRP models is that modeled fish are often assumed to occupy a single
uniform habitat (e.g., Brandt and Kirsch 1993). However, real fish may be able to exceed the
growth rate predicted by these models by moving among nearby habitats to feed, rest, and digest.
For example, by regularly moving between habitats of differing temperatures, some sculpin can
increase their growth rates by as much as three-fold, relative to a strategy of using a single
habitat (Wurtsbaugh and Neverman 1988; Neverman and Wurtsbaugh 1994). The growth of
juvenile coho and Chinook salmon is relatively insensitive to the range of temperatures typically
found in Alaskan streams, suggesting that small temperature differences among habitats may not
substantially affect growth (Beauchamp 2009). However, thermal heterogeneity has a strong
influence on the growth of juvenile coho salmon in the Bristol Bay region, due to the short
growing season and the potential for faster-growing individuals to consume energy-rich salmon
eggs (Armstrong et al. 2010). Further, resident fishes such as rainbow trout can exploit thermal
variation patterns by moving from colder to warmer streams to prolong their access to salmon
eggs and carcasses during the summer (Ruff et al. 2011). Thus, the local movement patterns of
both juvenile salmon and non-anadromous resident fishes among habitat types within the Susitna
River study area could potentially have important consequences for their growth rates.
Growth rate potential models will be developed to quantify the effects of environmental
conditions and food availability on fish growth at each sampling location, while allowing for
local movement among habitats. Due to the relatively data -intensive nature of GRP models, this
analysis will focus on two species: coho salmon and rainbow trout. Coho salmon will be
included due to their high ecological and economic value in the Susitna Basin and Cook Inlet.
Rainbow trout will be included as a representative resident species and a potentially important
competitor and predator of juvenile salmon. Importantly, detailed foraging parameters are
available for both species (e.g., Dunbrack and Dill 1984; Berg and Northcote 1985; Piccolo et al.
2007; Piccolo et al. 2008a, 2008b), enabling the development of well-supported foraging models.
The necessary bioenergetics model parameters are also available for both species (Stewart and
Ibarra 1991; Rand et al. 1993).
Species-specific GRP models for coho salmon and rainbow trout will couple a foraging model
(Fausch 1984; Hughes and Grand 2000; Hayes et al. 2007) with a Wisconsin bioenergetics
model (Kitchell et al. 1977; Hanson et al. 1997). The foraging models will take inputs of flow,
turbidity, and prey density and predict a consumption rate. Flow velocity and velocity-dependent
capture probabilities will be incorporated into the GRP models for juvenile coho salmon and
juvenile rainbow trout. The bioenergetics models will take inputs of consumption, body size,
water temperature, diet composition, and the energy density of prey and predict a growth rate.
Each GRP model will allow for the potential of local movement among habitats within a
sampling location to enhance growth rates. Optimal simulated movement patterns will be
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estimated and compared with the observed movements documented by the radio telemetry and
PIT tagging components of the Fish Distribution and Abundance Study (Section 9.6).
Preliminary growth models for each species will be developed using data from the 2013 field
season as well as from prior Susitna Basin studies. Initial model predictions of the growth
potential of particular sites will be tested by comparison with the observed growth and
distribution of fish captured in those sites. A sensitivity analysis will be conducted to id entify
the most important parameters for further refinement (Beaudreau and Essington 2009). Field
sampling during 2014 will focus on improving estimates for these parameters.
In addition, a separate trophic analysis will determine how water temperature, food availability,
and food quality influence the growth performance of juvenile Chinook salmon in different
habitats. Mechanistic drift foraging models for Chinook salmon are not yet available to allow
the estimation of growth rate potential under changin g conditions. However, field data and
bioenergetics analysis will allow useful comparisons of growth rates, consumption rates, and
growth efficiency (the growth achieved per gram of food consumed) among different habitats
under current conditions. To make these comparisons, a Wisconsin bioenergetics model
parameterized for Chinook salmon (Stewart and Ibarra 1991; Madenjian et al. 2004) will take
field inputs of body size, growth rate, water temperature, diet composition, and the energy
density of prey. The model will estimate the consumption rate and growth efficiency. These
metrics will be compared among habitats to determine whether growth is currently limited
primarily by water temperature, food consumption, or food quality in the study area, and whether
these limiting factors differ among habitats (McCarthy et al. 2009).
9.8.4.5.2. Conduct stable isotope analysis of food web components to help determine energy
sources and pathways in the riverine communities
Stable isotope analysis is a method which examines the naturally-occurring stable isotopes of
elements (typically carbon and nitrogen) stored in organic materials. The analysis is frequently
used to answer questions related to trophic structure and energy pathways within freshwater
ecosystems and the interfaces with marine and terrestrial ecosystems (Chaloner et al. 2002;
Finlay and Kendall 2007). Carbon isotope ratios (δ13C) are indicators of an organism’s diet
because consumers tend to reflect the carbon isotope values of the food they consume, whereas
nitrogen isotopes (δ15N) indicate an organism’s trophic level because the heavier nitrogen
isotope accumulates in the consumer with each successive trophic transfer (approximately 3– 4
parts per thousand, according to DeNiro and Epstein 1981) (Chaloner et al. 2002). If food
resources move in a predictable manner through the food chains, these stable isotopes can be
used to trace the sources of productivity within aquatic food webs and the trophic position of
consumers, which can be essential information for understanding the food web dynamics or for
detecting responses to environmental and human-driven change (Chaloner et al. 2002; Finlay and
Kendall 2007).
Several recent studies have used stable isotopes to investigate the contribution of marine -derived
nutrients (MDN) from spawning salmon to freshwater ecosystems, and have estimated that
salmon can contribute 17–30 percent (Bilby et al. 1996) to > 50 percent (Kline et al. 1990) of the
nitrogen, and 23–40 percent (Bilby et al. 1996) of the carbon present in freshwater organisms.
Adult salmon incorporate rich marine nutrients during their time in the ocean and are thereby
enriched with the heavier isotopes of nitrogen and carbon, which they retain after entering fresh
water to spawn, as they do not feed in fresh waters, and therefore remain isotopically distinct
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from terrestrially-derived organic material (Kline et al. 1990). Stable isotope analysis can be
used to trace MDN through freshwater ecosystems, and ultimately can be used to quantify the
contribution of marine-derived nitrogen or carbon to freshwater food webs (Kline et al. 1990;
Hicks et al. 2005).
To better understand the trophic relationships in the Middle Susitna River, a stable isotope
analysis will be conducted at two selected stations in the Middle River Segment. Selection of
these two stations will be made in the initial sampling efforts in the second quarter, based on how
representative the site is in respect to the reach, and its suitability to provide ample materials for
testing. Tissue samples from multiple study components (benthic macroinvertebrates, benthic
algae, benthic organic matter, terrestrial invertebrates and organic matter in drift samples, salmon
carcasses, and fin clip samples from the fish diet analysis collections) at the sites within these
two stations will be collected for stable isotope analysis. The two Focus Areas (stations),
specific sample site locations, and number of adult salmon tissue samples to be collected will be
determined with input from the TWG. Results will be used in conjunction with the bioenergetics
model (Section 9.8.4.5.1) to further explain the energy source pathways and trophic relationships
in the Susitna River food web.
9.8.4.6. Generate habitat suitability criteria for Susitna benthic macroinvertebrate and
algal habitats to predict potential change in these habitats downstream of the
proposed dam site
Habitat Suitability Index (HSI) models provide a quantitative relationship between numerous
environmental variables and habitat suitability. An HSI model describes how well each habitat
variable individually and collectively meets the habitat requirements of the target species and life
stage under the structure of Habitat Evaluation Procedures (USFWS 1980). Alternatively,
Habitat Suitability Criteria (HSC) curves are designed for use in the Instream Flow Incremental
Methodology to quantify changes in habitat under various flow regimes (Bovee et al. 1998).
HSC describes the instream suitability of habitat variables related only to stream hydraulics and
channel structure. Both models and habitat index curves are hypotheses of species–habitat
relationships and are intended to provide indicators of habitat change, not to directly quantify or
predict the abundance of target organisms. For the Susitna-Watana Hydroelectric Project aquatic
habitat studies, HSC (i.e., depth, velocity, and substrate/cover) and HSI (i.e., turbidity, duration
of inundation, and dewatering) models will be integrated to analyze the effects of alternate
operational scenarios.
Literature-based draft HSC/HSI curves will be developed for benthic macroinvertebrate and
algae communities. Potential sources of information include the Internet, university libraries,
peer-reviewed periodicals, and government and industry technical reports. Special emphasis will
be given to the existing 1980s study (Hansen and Richards 1985) for applicable information and
methodology. Because benthic macroinvertebrate (BMI) and periphyton communities are
comprised of numerous taxa, the HSC/HSI curves will be developed for commonly used benthic
metrics (e.g., biomass, chlorophyll-a [algae], density, diversity, or dominant taxa) selected to
summarize and describe the communities. The selection of individual species of interest will
consider the dietary preferences of the target fish species selected for the trophic analysis
(Objective 5, Section 9.8.4.5.1). The review will also examine macroinvertebrate life histories,
behavior, and functional feeding groups to assist in grouping taxa into guilds as possible metrics.
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Habitat suitability information will address BMI and algal responses to changes in depth,
velocity, substrate, turbidity, and frequency of inundation and dewatering.
Next, a histogram (i.e., bar chart) will be developed for each of the habitat parameters (e.g.,
depth, velocity, substrate, frequency of dewatering) using site-specific field observations (from
Objectives 2, Section 9.8.4.2, and Objective 9, Section 9.8.4.9). The histogram developed using
field observations from 2013 will then be compared to the literature-based HSI curve to validate
applicability of the literature-based HSI curve for aquatic habitat modeling. This stage will be
conducted by the third quarter of 2014.
As a final step TWG will confirm HSC/HSI curves for each benthic metric. Using a roundtable
discussion format, the TWG will review literature-based benthic community information and
site-specific data to develop a final set of HSC/HSI curves. These curves will be used in the
Instream Flow Study (Section 8.5) to define the relationship between habitat quantity and quality
for each of the selected benthic metrics under various operational scenarios. Analysis and
modeling efforts will be coordinated with the Instream Flow Study Team.
9.8.4.7. Characterize the invertebrate compositions in the diets of representative fish
species in relationship to their source (benthic or drift component)
In order to investigate and understand the trophic relationships within a river system and how
they ultimately relate to fish, it is critical to examine not only the food source (Objective 2,
Section 9.8.4.2) and its availability to fish via drift (Objective 3, Section 9.8.4.3), but also the
consumption by fish predators. Because both benthic macroinvertebrates and terrestrial
invertebrates are a primary food source for fish and other organisms (Wipfli 1997; Hershey and
Lamberti 2001; Allan et al. 2003), any significant disturbance to the benthic community and the
shoreline riparian vegetation has the possibility of affecting their predators. Therefore, it is
important to investigate the trophic relationship between fish and these food sources by
conducting a fish gut analysis and comparing results to drift and benthic macroinvertebrate data.
In support of the bioenergetics modeling (Objective 5, Section 9.8.4.5.1), fish species targeted
for dietary analysis will include juvenile coho salmon, juvenile Chinook salmon, and juvenile
and adult rainbow trout, as identified in consultation with the TWG. Fish collection sites will
correspond to all sites within the five sampling stations identified for the study (Table 9.8-1),
benthic macroinvertebrate collection sites (both benthic and drift sampling, to allow for
comparison with the benthic macroinvertebrate community (Section 9.8.4.2.1) and drift
compositions (Section 9.8.4).
A total of eight fish per species/age class per sampling site collection will be sampled for fish
stomach contents, using non-lethal methods (Meehan and Miller 1978; Hyslop 1980; Bowen
1996; Kamler and Pope 2001). All fish will have fork length and weight recorded with the
stomach sample. In addition, scales will be collected from the preferred area of the fish, below
and posterior to the dorsal fin, for age and growth analysis (DeVries and Frie 1996). At two
selected sampling stations in the Middle Segment, fin clips will be obtained from five fish at
each site for use in the stable isotope analysis (Section 9.8.4.5.2). The fish collection methods
and scheduled sampling efforts will be coordinated with the appropriate fish study team (Fish
Distribution and Abundance in the Middle and Lower Susitna River Study, Section 9.6; Fish
Distribution and Abundance in the Upper Susitna River Study, Section 9.5). Methods for
collecting fish specimens are included in Sections 9.5.4, and 9.6.4.
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Fish gut content samples will be processed in a laboratory using methods compatible with studies
conducted in other comparable streams/basins in Alaska. State and federal protocols (Hyslop
1980; Bowen 1996; Barbour et al. 1999; Major and Barbour 2001; Moulton et al. 2002) will be
considered in determining the sample processing protocols, the taxonomic resolution of
specimen identifications, and data analysis approach. Data collected during this study will be
compared to the results of 1980s fish diet studies (ADF&G 1983; Hansen and Richards 1985) to
evaluate any differences between the historic and current fish diets. Additional details on
sampling and processing methodology and analysis will be described in the River Productivity
Implementation Plan.
9.8.4.8. Characterize organic matter resources (e.g., available for macroinvertebrate
consumers) including coarse particulate organic matter, fine particulate
organic matter, and suspended organic matter in the Middle and Lower
Susitna River
Organic matter materials serve as an important food resource to benthic macroinvertebrates,
serving as a conduit for the energy flow from organic matter resources to vertebrate populations,
such as fish (Hershey and Lamberti 2001; Hauer and Resh 1996; Reice and Wohlenberg 1993;
Klemm et al. 1990). Given the dominant characteristics of the Susitna River system (large, cold,
and turbid during the growing season), secondary productivity is not likely to be driven by
primary production or from the algal community within the system, but rather by allocthanous
inputs of organic material from the terrestrial environment. Benthic organic material is one of
the most important “interrelated environmental factors” influencing the macroinvertebrate
community, and damming the river will have significant consequences for the transport of
organic matter from the upper watershed. Therefore, to address the importance of organic matter
to productivity in this type of system, quantifying benthic organic matter as part of this study is
essential.
This organic matter exists as both fine particulate organic matter (FPOM) and coarse particulate
organic matter (CPOM). FPOM includes particles ranging from 0.45 to 1000 µm in size, and
can occur in the water column as seston, or deposited in lotic habitats as fine benthic organic
matter (FBOM) (Wallace and Grubaugh 1996). CPOM is defined as any organic particle larger
than 1 mm in size (Cummins 1974). In order to quantify the amounts of organic matter available
in the Susitna River for river productivity, CPOM and FPOM (specifically FBOM) will be
collected concurrently with all benthic macroinvertebrate sampling, including the baseline
sampling effort addressing the effects of changing flow patterns on benthic communities in
sloughs (Objective 2, Section 9.8.4.2.1). Organic debris collected within each sample will be
retained after processing for organisms. In order to streamline the collection efforts, a net mesh
size of 250 µm for sampling devices will retain FPOM in the 250–1,000 µm size range for
analysis, as well as CPOM particles. Suspended FPOM (seston) will be collected from material
in invertebrate drift samples, utilizing the 250-µm mesh size for drift nets, as well (Objective 3,
Section 9.8.4.3). Organic matter retained after organism sorting and processing will be separated
from inorganic material, rinsed through sieves to separate particles into size classes, and
processed for ash free dry mass (AFDM). Results will be calculated as AFDM amounts of
CPOM and FPOM per unit area (g/m2 and g/m3, respectively). For the two selected stations,
portions of the material will be utilized for stable isotope analysis (Objective 5, Section
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9.8.4.5.2). Additional details on sampling and processing methodology and analysis will be
described in the River Productivity Implementation Plan.
9.8.4.9. Estimate benthic macroinvertebrate colonization rates in the Middle Susitna
River Segment t under pre-Project baseline conditions to assist in evaluating
future post-Project changes to productivity in the Middle Susitna River.
Colonization is a process in which organisms move into and become established in new areas or
habitats (Smock 1996). In disturbed habitats, this process is more accurately called
recolonization. Numerous studies have shown that macroinvertebrates can rapidly colonize new
or disturbed substrates (Shaw and Minshall 1980; Ciborowski and Clifford 1984; Williams and
Hynes 1977; Townsend and Hildrew 1976; Miyake et al. 2003). The rate of recolonization is
dependent on several factors, including time of the year, substratum particle size, the structure of
the macroinvertebrate assemblages available to colonize at the time, and the distance of the
colonist assemblages from the new or disturbed area (Robinson et al. 1990; Smock 1996;
Mackay 1992).
Two additional factors, predicted as major post-Project effects, that may affect colonization rates
are changes in turbidity and temperature. In order to assess the influences of turbidity and
temperature on the benthic community colonization rates, a field study will be conducted for
both study years (2013 and 2014) to estimate potential benthic macroinvertebrate colonization
rates for four different habitat types that reflect these conditions in the Susitna River. Due to the
difficulty of isolating each of these conditions under natural conditions, colonization will be
examined under turbid/warm, clear/warm, turbid/cold, clear/cold conditions. Sampling locations
and scheduling will be determined after a review of 2012 study results, from both AEA studies,
as well as from data collected outside of AEA, and site reconnaissance to assess candidate sites.
Sets of three preconditioned artificial substrates will be deployed incrementally for set periods of
colonization time (e.g., 8, 6, 4, 2, and 1 week[s]) and then pulled simultaneously at the
conclusion of the colonization period. Artificial substrates will be deployed at two depths at
fixed sites along the channel bed. Benthic macroinvertebrate processing protocols will be
identical to those used in Objective 2 (Section 9.8.4.2.1). Specific details on site locations, the
choice of artificial substrates, and timing of colonization tests will be provided in the River
Productivity Implementation Plan.
Colonization information will be compared with colonization results from similar river systems
and with post-Project colonization results. In addition, results will be utilized in HSC/HSI
development (Objective 6, Section 9.8.4.6), and in the varial zone modeling task in the Instream
Flow Study (Section 8.5.4.6.1.6) to assist in determining the potential Project effect of short-term
flow fluctuations, most commonly the result of hydroelectric power generation, on benthic
macroinvertebrates.
9.8.5. Consistency with Generally Accepted Scientific Practices
The methods described above have been developed in consultation with agency and Technical
Workgroup (TWG) participants. All data collection and processing efforts will follow state
(ADF&G) or federal (EPA, USGS) guidelines referenced throughout the study methods
discussion (Agradi 2006; Barbour et al. 1999; Bovee et al. 1998; Eaton et al. 1998; Keup 1988;
Klemm et al. 1990, 2000; Major and Barbour 2001; Moulton et al. 2002; Peck et al. 2006;
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USFWS 1980). In addition, any laboratory analysis will be conducted by a state - or federally-
certified facility.
9.8.6. Schedule
The preliminary schedule for the river productivity study elements is presented in Table 9.8-2.
During 2013, the literature review summarizing the impacts of hydropower development and
operations on benthic macroinvertebrate and algal communities will be prepared and presented to
the TWG. Research, field sampling, and sample processing and analysis will begin in the latter
half of the first quarter of 2013, following FERC’s approval of the study plan. Field sampling at
the Susitna River sites and the Talkeetna River test reference sites for benthic
macroinvertebrates, algae, organic matter, drift, fish diet analysis, and stable isotopes will be
conducted for three seasonal sampling periods from April through October in both study years
(20132014). These seasonal periods are tentatively scheduled for April through early June for
Spring, late June through August for Summer, and September through October for Autumn
(Table 9.8-2), due to annual variability in the timing of seasons. Specific details on timing will
be provided in the River Productivity Implementation Plan. Two additional sampling events for
benthic macroinvertebrates, algae, and organic matter to capture responses to storm events will
occur during April through October. Exact timing is subject to storm event occurrences. Sample
processing of organisms and materials collected in the 2013 field efforts will require extensive
laboratory efforts, and will continue throughout the remainder of 2013 and into the first quarter
of 2014. Trophic analysis efforts will also begin in the latter half of the first quarter of 2013 and
continue throughout 2013 and 2014. The Initial Study Report summarizing these 2013 activities
will be issued within one year of FERC’s Study Plan Determination (i.e., February 1, 2013).
Results from the 2013 effort will be utilized in the effort to generate habitat suitability criteria,
which begin early in the first quarter of 2014. Second-year field sampling efforts, adhering to
the same tentative scheduling as in 2013, will resume in the latter half of the first quarter of
2014, with sample processing, data analysis, trophic analysis research continuing through the
fourth quarter. The Updated Study Report will be produced within two years of FERC’s Study
Plan Determination.
9.8.7. Relationship with Other Studies
The flow of information into and out of the River Productivity Study is anticipated to occur over
the two year study period through an iterative process. The River Productivity Study is
interrelated to several AEA studies (Figure 9.8-3). The Instream Flow Study (Section 8.5),
Characterization and Mapping of Aquatic Habitat Study (Section 9.9), and the Geomorphology
studies (Sections 6.5 and 6.6) will provide useful information, expected by Q1 2013, to assist in
the site selection process. The Baseline Water Quality Study (Section 5.5) will provide useful
input information for analysis of river productivity for use in the trophic analysis (Section
9.8.4.5). The Upper (Section 9.5) and Middle and Lower River (Section 9.6) Fish Distribution
and Abundance studies will provide information on target fish species for the trophic analysis,
including life history event timing to assist in sampling scheduling and seasonal locations in Q1
2013 and Q1 2014, as well as throughout the 2013 and 2014 field seasons. The Fish Distribution
and Abundance studies will also coordinate with the collection of samples for gut content
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analysis (Section 9.8.4.7) and stable isotope analysis (Section 9.8.4.5.2) throughout the field
seasons. Output information from the multiple objectives of the River Productivity Study will
provide additional input information to the trophic analysis, Objective 5, Section 9.8.4.5, of the
River Productivity Study as well as any water quality field measurements (e.g., temperature,
turbidity, and PAR data) collected to the Baseline Water Quality Study (Section 5.5) and site-
specific field observations from Objective 2 and Objective 9 for use in the Instream Flow
Study’s IFIM and varial zone models (Section 8.5.4.6). Information flowing out from the River
Productivity Study will be communicated with other Fish Progam Study Lead. Additional
formal data sharing also will occur among study after completion of QA/QC procedures and with
delivery of the Initial Study Report (Q1 2014) and Updated Study Report (Q1 2015).
9.8.8. Level of Effort and Cost
The initial cost estimate for completion of the nine study objectives described above is
$1,200,000. Efforts such as the literature review, trophic analysis (bioenergetics model and
stable isotope analysis), and HSC criteria development will be office-based studies. Collection
of benthic macroinvertebrates, algae, and organic matter, drift samples, and the analysis of fish
diets will require three extensive field efforts per year for the two study years. Adult emergence
sampling will require monthly to bi-weekly site visits from April through October to collect
samples and reset the traps. The colonization study will require frequent site visits each month
to deploy additional sets of samplers over the course of the study. A majority of the work effort
will take place in the laboratory to sub-sample, sort, and identify the macroinvertebrate and algae
samples, as well as to conduct the stable isotope analyses on the numerous sample components.
After sample processing, the remainder of the study effort will be office-based, consisting of data
entry, analysis, and synthesis and report writing.
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9.8.10. Tables
Table 9.8-1. Preliminary macroinvertebrate and algae sampling sites, stratified by reach and habitats. Refer to Figures
9.8-1 – 9.8-2 for locations of the preliminary sampling reaches and stations.
Sampling Reach Reach Description Number of
Mainstem Sites
Number of
Associated
Off-channel Sites1
Middle Segment
MR-1 Immediately below dam site 1 2
MR-2 Upstream of Devils Canyon 1 3
MR-6 Downstream of Devils Canyon 1 3
MR-8 Upstream of the Three Rivers Confluence 1 4
Lower Segment
LR-1 Downstream of the Three Rivers Confluence 1 4
Susitna River Totals 5 16
Notes: 1 Side-channels, sloughs, tributary confluences associated with a mainstem sampling site.
Table 9.8-2. Preliminary schedule for River Productivity Study.
Activity 2013 2014 2015
1Q 2Q 3Q 4Q 1Q 2Q 3Q 4Q 1Q
Literature Review on Hydropower Impacts
Sampling benthic macroinvertebrate
communities, algal communities, and
organic matter.
Invertebrate drift sampling
Sampling Talkeetna for Reference Site
Feasibility Study
Trophic analysis with bioenergetics and
stable isotope analysis
Generate habitat suitability criteria
Conduct a fish gut analysis
Establish baseline colonization rates
Data Analysis and Reporting
Initial Study Report ∆
Updated Study Report
Legend:
Planned Activity
Tentatively scheduled sampling event
∆ Initial Study Report
▲ Updated Study Report
FINAL STUDY PLAN RIVER PRODUCTIVITY STUDY 9.8
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9.8.11. Figures
Figure 9.8-1. Middle Susitna River Segment, with the Instream Flow Focus Areas under consideration for the four sampling locations proposed for the River
Productivity Study.
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Figure 9.8-2. Lower Susitna River Segment, with one proposed River Productivity sampling station /Instream Flow study sites selected for the River Productivity Study.
FINAL STUDY PLAN RIVER PRODUCTIVITY STUDY 9.8
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Figure 9.8-3. Study interdependencies for River Productivity Study.