Inside this issue:Great Works Dam Removal 1

Salmon Smolt Survival 1

American Shad Restoration 2

Water Quality/Insect Monitoring 2

Sea Lamprey Recolonization 3

Geomorphic Process Model 4

Fish Community Assemblages 5

SONAR Monitoring 6

Estuarine Fish Communities 7

PIT Tagging Adult Salmon 8

Acoustic Telemetry 9

Sedgeunkedunk Stream Monitoring 9

Marine-derived Nutrients 10

“You are What You Eat” 10

Shortnose Sturgeon 11

Geomorphic Monitoring 12

Penobscot River Research Newsletter

Acoustically Tagged Atlantic Salmon Smolt Survival in the Penobscot River and Estuary, 2010-2011

Joseph Zydlewski 1,2 Principal InvestigatorDaniel Stitch1, Ph.D. Student

1Department of Wildlife Ecology, University of Maine2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit

Juvenile sea-run fishes require uninterrupted passage through riverine habitats in order to successfully reach the marine environment. During migration, immediate or delayed mortality may result from predation, direct injury from turbines or other dam-related structures. Because impoundments differ in their impact, quantifying passage success at specific sites is an important component of programs that seek to maintain or restore anadromous Atlantic salmon populations. The purpose of this study was to characterize movement rates and survival of seaward migrating Atlantic salmon smolts in the Penobscot River. Tagging of the fish is accomplished by surgically implanting an acoustic tag (about half the size of a triple A battery) and releasing the smolts upstream. The tags are active for several months (until their battery runs

out) and give off a sonic code at a specific frequency (69 kHz). The fish are then tracked on their seaward journey through the river using passive receivers. Since 2005, an array of up to 178 stationary, acoustic receivers have been deployed and maintained in cooperation with NOAA National Marine Fisheries Service. These receivers have omni-directional hydrophones, continuously monitoring at 69 kHz. These receivers were deployed to cover the entire width of the river at each site. When the receivers “hear” a tag, the tag identification, the date and time are recorded. This sequence of detection allows the estimation of survival using a Cormack-Jolly-Seber (CJS) mark-recapture model and the calculation of movement rates through specific river reaches, for example those with and without dams. cont. page 3 ...

January 2013Volume 2, Issue 1

The Great Works Dam removal marks a pivotal time in the Penobscot River Restoration Project. It represents a mile-stone in a long process of engagement, work, and fundraising, and the beginning of a new era of improved fish passage on the Penobscot River. The occasion also marks the end of the initial baseline science that has occurred in the watershed for the last several years. During this period, researchers from academia, the Penobscot Indian Nation, non-profit groups, state and federal agen-cies, and private consultants have been assessing the baseline condition of the Penobscot River watershed ecosystem. They have collected data on fish passage, geomorphology, water quality, wetlands, birds, mammals, and marine nutrients. Although several studies will be ongoing during the next few years, others will be on hold until after the lowermost dam, in Veazie, is also removed.

Following dam removal, many of these studies are planned to resume so that a clear before-after picture can be taken of the effects of dam removal. The hope is that the lessons learned may be applied to river, fish and ecosystem restoration efforts around the country and, possibly, around the world. The following articles are representa-tive of the scientific work that has been conducted in the Penobscot watershed the last few years. Some of the work was con-ducted on behalf of the Penobscot River

Restoration Trust, some of the work was conducted by others. It is presented here as it describes the state of the ecosystem and the collaborative science at this point in time. What the work suggests is that this restoration enterprise has strong potential for success and must be pursued with sustained commitment. Dams impact fish. This is well-known and it has been docu-mented here. Dams delay or prevent mi-grations and they increase mortality. The stark contrast in alewife numbers between Benton Falls (Kennebec River) and Veazie (Penobscot) in 2011 — 3 million fish vs 2 thousand fish — speaks volumes. Open fish passage restores fish runs. Great Works is the pivotal first step towards the Penobscot’s restoration. Congratulations!

~ Charlie Baeder, Monitoring Coordinator, Penobscot River Restoration Trust

Great Works Dam Removal - A Milestone Event on the Penobscot River

1

Several years of

results indicate that

in the Penobscot

River, migrating

salmon move more

quickly through

areas without dams

than those with

dams. Survival is

markedly higher in

river reaches without

dams.

Mixing Technologies to Inform American Shad Restoration

Joseph Zydlewski 1,2 and Michael Bailey 1,3, Co-Principal Investigators Ann Grote1, M.S. Student

1Department of Wildlife Ecology, University of Maine2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit3U.S. Fish and Wildlife Service

The Penobscot River in Maine historically supported a tremendous abundance of migratory fishes including American shad. We have been working to understand the current status of this species and the scope for recovery after the planned removal of two mainstem dams in 2012 and 2013 as part of the Penobscot River Restoration Project. Because the lowermost dam (Veazie Dam) is at the head of tide, spawning habitat for this species is limited, and the very presence of this species was in question. Removal of Veazie Dam and the next up river dam (Great Works Dam) is anticipated to open up significant American shad habitat. We are using population modeling to inform decision-making among potential proposed stocking scenarios. The most significant uncertainty in the recovery strategy has been the status of the current population. Beginning in 2009, Ann Grote began to blend old and new technologies to inform managers of the current state of American shad in the Penobscot River. The goals of this study are to address two main data gaps: characterization of adult shad migratory behavior and characterizing the existing river specific run. The work underway uses Dual-Frequency Identification Sonar (DIDSON). DIDSON works like an ultrasound camera, allowing researchers to “view” fish at night and in turbid water. By deploying a DIDSON camera at the base of Veazie Dam, a continuous video record of fish approaching the base of the dam was recorded. This approach proved effective for making species determinations,

measuring the size of fish, and developing size distributions in a system where sampling methods are limited due to the presence of threatened and endangered species. Analysis of the data indicates that in addition to Atlantic salmon and river herring, large numbers of American shad approach the dam but do not use the fishway. Because Maine Department of Marine Resources monitors the number of Atlantic salmon successfully passing the dam, these data provide a reference for comparing viewed species-specific encounters and ultimately an index of fish abundance at the base of the dam. More conventional approaches have also been use to assess habitat use and behavior. In 2010 and 2011, American shad were captured via boat electrofishing for telemetry work. This effort also provided an opportunity to collect age and spawning data (via scales) as well as length data. Radio telemetry was used in the upper river to characterize residence time and to identify probable spawning areas. Acoustic telemetry efforts exploited an extensive acoustic array cooperatively deployed and maintained by the Maine CRU, the University of Maine and NOAA Fisheries. This array tracked adults leaving the Penobscot River and entering the ocean, presumably after spawning.

Funded through The Nature Conservancy, NOAA-Fisheries, US Geological Survey Maine Cooperative Fish and Wildlife Research Unit and the University of Maine

2

Benthic Macroinvertebrate and Water Quality Monitoring of Great Works and Veazie Dam Project Areas: Pre-dam Removal

Daniel H. Kusnierz1, Principal InvestigatorT. Jason Mitchell1,, Jan Paul1, Angela Reed1 and Rhonda Daigle1

1Penobscot Indian Nation, Water Resources Program

In 2009 and 2010, as part of the Penobscot River Restoration Project (PRRP), the Penobscot Indian Nation Water Resources Program (PIN WRP) conducted studies of water quality and benthic macroinvertebrates at select sites in the lower Penobscot River. The purpose of this monitoring was to gather baseline data in advance of the removal of the Veazie and Great Works Dams, and the construction of the Howland Bypass.

The primary objective of the monitoring is to determine if and how water quality and benthic invertebrate community composition in the Lower Penobscot River changes with barrier removal. Additionally, these data will have useful interpretive value for other lower river research projects.

continued on page 11 ...

Rock-filled basket substrates used for monitoring aquatic insects as water quality indicators.

SALMON SMOLT SURVIVAL ... cont. from page 1

Several years of results indicate that in the Penobscot River, migrating salmon move more quickly through areas without dams than those with dams. Survival is markedly higher in river reaches without dams. Though these results are not unexpected, some dams have more of an adverse effect on migration than others. While the removal of Great Works and Veazie Dams will greatly improve upstream access to spawning habitat for many species

Sea lamprey constructing a nest at Sedgeunkedunk Stream.

including Atlantic salmon, several of the dams that will remain in place greatly impact migrating juveniles. These results underscore the importance of assessing both upstream and downstream migration.

Funded by Penobscot River Restoration Trust, NOAA Fisheries, American Recovery and Reinvestment Act, U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit, and Great Lakes Hydro

The increased return

of sea lamprey

may benefit other

species through

their spawning

activity. Nest

building of these fish

increases stream-

bed complexity

... These changes

persist through

summer and into

fall when Atlantic

salmon spawners

select these habitat

qualities.

3

Dam Removal In The Sedgeunkedunk Stream

Stephen M. Coghlan Jr. 1 and Joseph Zydlewski1,2, Co-Principal InvestigatorsKevin Simon3, Co-InvestigatorRobert S. Hogg1 and Corey Gardner 1,2, M.S. Students

1Department of Wildlife Ecology, University of Maine2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit3The University of Auckland, Auckland, NZ Sedgeunkedunk Stream, a tributary to the Penobscot River, historically supported several anadromous fish species including sea lamprey and Atlantic salmon. However, two small dams constructed in the 1800s reduced or eliminated spawning runs entirely. In 2009, efforts to restore marine-freshwater connectivity in the system culminated with removal of the lowermost dam making 5 km of stream habitat accessible to anadromous fish. Sea lamprey utilized accessible habitat prior to dam removal and were chosen as a focal species to characterize recolonization.

increase in the abundance of spawning sea lamprey, from less than 65 fish to more than 250.

During sea lamprey spawning runs of 2008 through 2011 (pre- and post-dam removal), individuals were marked with passive integrated transponders (PIT tags) and their activity was tracked by walking the stream daily and identifying the fish remotely. Population estimates were derived using a modeling approach (POPAN extension of Program MARK). After dam removal there was a four-fold

The increased return of sea lamprey may benefit other species through their spawning activity. Nest building of these fish increases stream-bed complexity, while reducing fine sediment accumulation and proportion of embedded particles. These changes persist through summer and into fall when Atlantic salmon spawners select these habitat qualities. These changes may also benefit resident drift-feeding stream fishes including juvenile Atlantic salmon. Thus the re-colonization of Sedgeunkedunk Stream by sea lamprey may have lasting effects on stream community dynamics.

Funded by Penobscot River Restoration Trust, NOAA-Fisheries, American Recovery and Reinvestment Act, U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit.

Figure 1. Median bed grain size predicted using a GIS-based model for a reach of the West Branch Pleasant River downstream from the Gulf Hagas canyon.

Developing and Testing a Geomorphic Process Model to Predict Median Bed Grain Size Noah Snyder 1

Andy Nesheim 1, student 1 Boston College, Boston, MA

Over the past several years, a team of graduate and undergraduate geology students working with professor Noah Snyder at Boston College have collected geomorphic data from several rivers in Maine. A previous study (Wilkins & Snyder, published in River Research and Applica-tions, 2011) involved mapping potential Atlantic salmon habitat in the Narraguagus River. Their most recent research focusing on the West Branch of the Pleasant River has a direct link to the ongoing restora-tion efforts on the Penobscot River (the West Branch of the Pleasant River is a tributary of the Piscataquis River, which enters the Penobscot River at Howland). This river is presently inaccessible to most anadromous species, but completion of the Penobscot River Restoration Project should enable increased anadromous spe-cies passage. This research formed the basis for An-drew Nesheim’s recent M.S. thesis, which involved developing and testing a geo-morphic process model to predict median bed grain size. Andrew used standard and LiDAR (light detection and ranging) digital

elevation models to measure channel parameters necessary as model inputs. He found that predicted bed grain size fell within a factor of two of the field-mea-sured median grain size in >70% of the study sites. The model performed best in alluvial single-thread channel segments with gravel-cobble beds in the median grain size range from 16 to 256 mm, which corresponds to ideal spawning and rearing habitat for Atlantic salmon. The model was less successful in depositional segments with relatively fine beds and greater channel variability. Model failures occurred in segments that deviate from the single-thread gravel-bed channel type, and may indicate areas to focus res-toration efforts. These methods are useful for detailed morphologic assessment, and this approach is an easily applied tool for predicting grain size and habitat suitability. Much of this research was just pub-lished in the January 2013 issue of Geological Society of America Bulletin.

Funded by the National Science Foundation.

The model performed

best in alluvial

single-thread channel

segments with gravel-

cobble beds in the

median grain size range

from 16 to 256 mm,

which corresponds to

ideal spawning and

rearing habitat for

Atlantic salmon.

4

Quantifying the Structure of Fish Assemblages in the Penobscot River

Stephen M. Coghlan Jr. 1, Principal InvestigatorJoseph Zydlewski1,2 and Daniel Hayes3, Co-InvestigatorsIan Kiraly1, M.S. Student

1Department of Wildlife Ecology, University of Maine2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit3Michigan State University Department of Fisheries and Wildlife

The Penobscot River once provided spawning and juvenile rearing habitats to migratory fish. The construction of dams blocked migrations of these fish and fragmented habitats, changing the structure of fish assemblages throughout the river. The Penobscot River Restoration Project is anticipated to increase passage of anadromous and resident fishes and improve the connectivity among currently fragmented habitats. The purpose of this study is to quantify and characterize fish assemblages in the lower ~70 kilometers of the Penobscot River, along with major tributaries. This will aid in understanding the influence of fragmentation in a large river system and provide a benchmark from which post-dam removal assessment can measure. Boat electrofishing surveys were conducted during 2010 and 2011, in both the early summer and fall. “Stratified-random” sampling was conducted using 500 meter transects. Three factors had clear effects on fish assemblage composition. In general, fish assemblage structure differed according to longitudinal position along the river. The tidal section

Electrofishing the Penobscot River to survey fish assemblages pre-dam removal. Fish are stunned, held in a holding tank for identification and data collection, then released back to the river. Photos courtesy of Steve Coghlan.

... many diadromous

fishes were restricted

to tidal waters

below Veazie Dam,

although Atlantic

salmon, sea lamprey,

and American eel

were captured or

observed upstream.

Species richness

was relatively high

below Veazie Dam ...

These data indicate

that the restoration

of connectivity

through dam removal

will likely result in

predictable shifts in

fish assemblages.

of the river was distinct in composition: many diadromous fishes were restricted to tidal waters below Veazie Dam, although Atlantic salmon, sea lamprey, and American eel were captured or observed upstream. Species richness was relatively high below Veazie Dam. Lastly, areas above and below dams differed greatly in composition, with dam head ponds favoring more warm water and lentic species. These data indicate that the restoration of connectivity through dam removal will likely result in predictable shifts in fish assemblages.

Funded by Penobscot River Restoration Trust, NOAA Restoration Center and the American Recovery and Reinvestment Act, along with the USGS Maine Cooperative Fish and Wildlife Research Unit, the University of Maine, and Maine Department of Inland Fish and Wildlife, The Nature Conservancy and the Maine Outdoor Heritage Trust

5

SONAR Sampling to Understand Changes in Penobscot River Fish Community Dynamics Resulting from Restoration Efforts

Gayle Zydlewski1, Principal Investigator Joseph Zydlewski2, Co-Investigator Patrick Erbland1, Ph.D. Student 1School of Marine Sciences, University of Maine2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit

SONAR systems are used to monitor fish presence, abundance and movements in rivers, estuaries, and oceans. We have been using this technology to monitor fish passing through a cross section/ transect on the lower Penobscot River, near Bangor/Brewer since 2010. Our goal is to measure and understand changes in fish populations before and after the Penobscot River Restoration Project. We have been developing a standardized approach for long-term SONAR monitoring, and collecting pre-restoration data that will be the baseline for comparison in subsequent years following restoration activities. The SONAR systems are automated to continually record fish passage through a cross section of the river from April to December (under ice-free conditions) each year. In cooperation with the SONAR manufacturer and local community members the systems have been optimized by: adjusting the SONAR to the river form; internet connections to field computers for real-time remote access; and implementing standardized

imaging, sampling and velocity profiling that complement and confirm information from the primary SONAR systems. Data collected by other researchers are also being used to verify/validate fish counts and identifications: boat electrofishing, acoustic and radio tag data of fish moving through the lower river, fish collected in the Veazie fish trap, and mobile side-scan imaging surveys. Four-dimensional GIS software is being used to compile these datasets and provide a more comprehensive picture of fish community dynamics in the lower Penobscot. Future plans include annual deployment of these systems, enabling a long-term assessment of changes in fish presence as it is related to pre- and post-dam removal conditions.

This project is ongoing and funded by Penobscot River Restoration Trust through the NOAA Restoration Center and the American Recovery and Reinvestment Act and Open Rivers Initiative, and the University of Maine.

SONAR systems are

used to monitor fish

presence, abundance

and movements in

rivers, estuaries, and

oceans. We have been

using this technology

to monitor fish

passing through

a cross section/

transect on the lower

Penobscot River, near

Bangor/Brewer since

2010.

6

Echograms of the water column from an area close to the Verona Bridges, 11/08/2011; individual fish distribution (top echogram) and zooplankton aggregations (bottom echogram).

Conducting downward looking mobile hydroacoustic transects using RV Silver Smolt on 07/01/2011. The two split-beam transducers (38 and 120 kHz) are held in place 0.5m below the surface from the port side with an aluminum frame.

The Penobscot Estuarine Fish Community and Ecosystem SurveyMichael O’Malley1

J. Stevens1 Rory Saunders1

Christine Lipsky1

John Kocik 1

1 NOAA Fisheries, Orono, ME In 2010, we began investigating novel fish capture techniques and hydroacous-tics methods to monitor changes in species composition over time and space in the Penobscot estuary. The project began with an exploratory and descriptive phase and is evolving into a study network where long-term monitoring, hypothesis testing, and impact assessments will be possible. Pelagic trawling, fyke netting and beach seining in 2011 revealed multiple size classes of alosines suggesting more exten-sive estuarine use than previously thought. We were excited that initial survey results also found contemporary evidence of natu-ral reproduction of American shad. We conducted mobile transects using downward-looking SIMRAD EK60 split-beam (38 and 120 kHz) to provide acoustic target strength and biomass distribu-tions throughout the estuary. Using Sv dB differencing techniques to distinguish fish and zooplankton, we found that fish and zooplankton biomass (NASC) and

target strength distributions varied across time and space during the survey period (May–June and Nov-Dec 2011). Dam removal upstream may cause changes in estuarine communities, and an expansion of methods will be needed to investigate changes in fish and zooplankton popula-tions over larger spatio-temporal scales. The multifrequency split-beam method can provide fish and zooplankton biomass data over larger scales for relatively small investment over the long term. Knowl-edge gained from this study will improve our ability to: 1) manage estuaries in the future and 2) conduct vital research on the habitats and ecosystem services they provide. The design specifics should be transferable to multiple systems to develop a regional perspective.

Funded by NOAA National Marine Fisheries Service, Northeast Fisheries Science Center

The multifrequency

split-beam method

can provide fish and

zooplankton biomass

data over larger scales

for relatively small

investment over the

long term.

7

Using PIT Telemetry to Track Adult Atlantic Salmon in the Penobscot River

Joseph Zydlewski 1,2 – Principal Investigator Douglas B. Sigourney 2 – Post-Doctoral Associate

1U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit2Department of Wildlife Ecology, University of Maine

The Penobscot River is currently impounded by five main stem dams impeding access to historic spawning grounds. In addition, there are also several dams on the major tributaries to the Penobscot River including the Passadumkeag and the Piscataquis rivers. In cooperation with dam owners, we installed antennas at hydroelectric facilities in the Penobscot River. Antennas (loops of wire a tagged fish must swim through to be “read”) are located near the entrances and exits of fishways. This arrangement allows us to determine if a fish entered a fishway, and, if so, was it successful in passing upstream. Unlike past telemetry studies that tracked the movements of a small number of fish, the use of PIT tag technology allowed large numbers of fish to be tracked. These tags are small (about the size of 2 grains of rice), last indefinitely, and are relatively inexpensive (less than $5.00/tag). Returning adults are captured by the Maine Department of Marine Resources at the lowest-most dam (Veazie Dam) and PIT-tagged before being released. PIT arrays and remote modem connections allow near real-time assessment of passage and management actions. For example, results suggest that live transport resulted in a significant increase in arrival success at the upstream

dams. In addition, live transport resulted in a significant decrease in transit time from Veazie to the upstream dams. There was also no apparent handling effect on passage: there was no difference in success at the upstream dams among adults that were transported and those that were not. In 2012 and 2013, the two lowest-most dams on the Penobscot River are scheduled for removal as part of the Penobscot River Restoration Project. This research will provide pre-removal assessment data to gauge the effects of dam removal. More importantly, this effort is a collaborative enterprise that will continue to inform management through the quantitative assessment of passage in the Penobscot River.

Funded by Penobscot River Restoration Trust, NOAA-Fisheries, American Recovery and Reinvestment Act, U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit

Antennas (loops of

wire a tagged fish

must swim through to

be “read”) are located

near the entrances

and exits of fishways

... to determine if

a fish entered a

fishway, and, if so,

was it successful in

passing upstream

... the use of PIT tag

technology allowed

large numbers of fish

to be tracked.

8

Atlantic salmon at the Veazie fish trap is checked for a PIT tag, measured and weighed before either being transported to the Craig Brook Fish Hatchery or released back into the river.

Acoustic Telemetry: An Established Monitoring Tool for Assessing Pre-dam Removal Conditions for Diadromous Fishes of the Penobscot RiverJames Hawkes1 , Graham Goulette1 ,,Joe Zydlewski3 , Gayle Zydlewski2 , and John Kocik1 , Principal Investigators

1NOAA Fisheries, Orono, ME2School of Marine Sciences, University of Maine 3U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit

Acoustic telemetry is a modern research tool that allows researchers to remotely monitor tagged animals. Passive fixed position receiver networks collect temporal data to provide information on migration behavior, routes, areas of high mortality as well as seasonal activity pat-terns of individual animals. The National Oceanic and Atmospheric Administration, University of Maine and United States Geological Survey have deployed an extensive array of more than 100 telemetry receivers in the Penobscot River, estu-ary and Bay each year since 2005. This array has been used to monitor several diadromous fish species, including Atlantic

salmon and shortnose sturgeon that are protected under the US Endangered Spe-cies Act. Additionally, with the Penobscot River Restoration Project in early planning phases, research on pre-restoration fish ecology was particularly important. As a result, data collected since 2005 have been used for risk assessment of proposed in-stream construction and repair or removal activities which may threaten fish during migration periods or sensitive periods during their life history. Addition-ally, these data provide documentation of habitat use of fish prior to dam removal and other proposed restoration activities. Once dam removal has occurred we will be

able to identify any changes of habitat use, behaviors and migration corridors as spe-cies are reintroduced to areas that have been inaccessible for decades.

Funded by Penobscot River Restoration Trust, NOAA, National Marine Fisheries Service, Northeast Fisheries Science Cen-ter, America’s Recovery and Reinvestment Act, U.S. Fish and Wildlife Service, USGS Maine Cooperative Unit, Great Lakes Hydro

Sedgeunkedunk Stream: One Piece of the Penobscot Puzzle

Stephen M. Coghlan Jr. 1, Joseph Zydlewski1,2 , Kevin Simon3, and Rory Saunders4, Principal Investigators

1Department of Wildlife Ecology, University of Maine2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit3The University of Auckland, Auckland, NZ4NOAA Fisheries, Orono, ME

Sedgeunkedunk Stream is a tributary of the Penobscot River that typifies small streams in Maine impacted by low-head dams. Runs of anadromous fishes in this system declined or disappeared after the building of multiple dams within the watershed. These declines mirror those in the entire Penobscot watershed, which contains over 100 known dams. As part of a collaborative restoration project, fish passage on Sedgeunkedunk Stream has been restored by the removal of two dams between Fields Pond and the confluence with the Penobscot River. The lowermost dam (Mill Dam) was removed in August 2009, and the middle dam (Meadow Dam) was bypassed in August 2008 by a rock-ramp fishway that allows fish passage while maintaining current water levels in Fields Pond and adjacent wetlands. We have been monitoring the distri-

bution and abundance of resident and sea-run fishes in the watershed since 2007. The removal of the lowermost dam resulted in striking changes in fish assem-blage metrics and sea-run species gained access to up river habitat. Sedgeunkedunk Stream can serve as a model of what may result at a much larger scale through the Penobscot River Restoration Project. We view the Penobscot River structurally and functionally as a network of several hundred similarly-sized tributaries. The ef-fects of mainstem dam removal should be readily detectable and quantifiable in these small watersheds.

Funded by NOAA-Fisheries, U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit, Maine Sea Grant, and The University of Maine

9

An acoustic tag surgically inserted into a salmon smolt before release back into the river.

Researchers are recording data on acous-tic telemetry receivers that are used to track Atlantic salmon smolt, hatchery and wild, on their migration to the ocean.

Effects of Marine-derived Nutrients on Juvenile Atlantic Salmon and Their Communities

Cynthia Loftin1,2 and Joseph Zydlewski1,2, Co-Principal Investigators Margaret Guyette1, Ph.D. Student

1Department of Wildlife Ecology, University of Maine2U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit

Prior to dam construction in the Penobscot River watershed, Atlantic salmon and other anadromous species transported marine-derived nutrients to freshwater systems during spawning events in the form of metabolic expenditure and through decomposition of mortalities. These contributions may have strongly influenced productivity in otherwise nutrient limited systems, influencing many components of the stream community. Such input may have bolstered the growth and survival of young Atlantic salmon. To test this hypothesis, we stocked four headwater streams with young-of-the-year Atlantic salmon and manipulated nutrient input with a carcass analog timed to match sea lamprey and Atlantic salmon spawning. We documented nutrient uptake by Atlantic salmon and macroinvertebrates using nitrogen and carbon “stable isotopes”. Interestingly, young-of-the-year Atlantic salmon were larger and had greater fat reserves in treatment reaches

than in controls. Barrier removal in the Penobscot River drainage is anticipated to improve connectivity for Atlantic salmon and other anadromous species within their historic spawning habitat. There is, however, a likely second effect. The resultant marine nutrient pulses may increase Atlantic salmon success in their early life stages through direct and indirect uptake.

Funding through NOAA-Fisheries, US Geological Survey Maine Cooperative Fish and Wildlife Research Unit and the University of Maine

“You are What You Eat”: Using Stable Isotopes to Assess Freshwa-ter and Marine Food Web Change in Response to Dam RemovalKaren Wilson1

Graham Sherwood2

1Dept of Environmental Science, University of Southern Maine2Gulf of Maine Research Institute, Portland, ME

A primary objective of the Penobscot River Restoration Project is to improve anad-romous fish passage between the upper reaches of the river and the nearshore marine environment. Increased connectiv-ity is expected to positively impact resi-dent biota in both marine and freshwater environments in part by providing food web subsidies from the adjacent ecosys-tem. In the freshwater system, spawning anadromous fishes (e.g., river herring) are expected to add marine-derived nutrients to lakes and rivers. In the marine system, it is expected that juvenile anadromous fishes out-migrating from freshwater nurs-ery habitat will be consumed by nearshore marine predators (e.g., cod). In order to quantify linkages between these two systems, we are using stable isotopes to estimate energy flows before (this study) and after (future study) dam removals. Stable isotope studies are based on the

idea that ‘you are what you eat’ because isotope signatures of consumers reflect the isotope values of their prey, which in turn can be used to infer food chain level and habitat associations (in this case marine vs. freshwater). Pre-dam removal data col-lected in 2009-2011 shows strong isotopic distinctions between the freshwater and marine food webs. We found intriguing in-termediate signatures in roving nearshore marine predators such as mackerel who are known to eat out-migrating juvenile river herring. This approach provides reli-able and cost effective indicators of food web change in response to dam removals.

Funded by The Nature Conservancy, and Penobscot River Restoration Trust, through the NOAA Restoration Center and the American Recovery and Reinvestment Act.

Barrier removal

in the Penobscot

River drainage

is anticipated

to improve

connectivity for

Atlantic salmon and

other anadromous

species within their

historic spawning

habitat. There is,

however, a likely

second effect. The

resultant marine

nutrient pulses may

increase Atlantic

salmon success

in their early life

stages through

direct and indirect

uptake.

10

Shortnose Sturgeon of the Penobscot River Gayle Zydlewski1, Principal Investigator Michael Kinnison2, Co-Principal Investigator Joseph Zydlewski3, Co-Investigator Matthew Altenritter, Ph.D. Student Matthew Wegener and Kevin Lachapelle, M.S. Students 1School of Marine Sciences, University of Maine 2School of Biology and Ecology, University of Maine 3U.S. Geological Survey, Maine Cooperative Fish and Wildlife Research Unit

Until recently, the presence of endangered shortnose sturgeon in the Penobscot River was undocumented but presumed based on a single animal caught in Penobscot Bay in 1978. In 2006, their presence was confirmed and research was initiated to document seasonal movement patterns, use of the upper river, and to estimate the size of the population. The primary method used to document movement patterns is acoustic telemetry. Sturgeon are captured using gill nets (under a research permit) and carefully handled to implant a tag that transmits a ping that can be recorded by special devices positioned throughout the river system. To estimate the size of the population, two methods, mark-recapture and acoustic imaging, have been used. Mark-recapture estimates have been made during summer and fall. During winter, shortnose sturgeon form dense aggregations. We can image these aggregations and count the number of fish present. Since only one annual wintering site has been identified in the Penobscot, this gives us a population estimate of the wintering shortnose sturgeon. Estimates to date are consistent between the methods and indicate that nearly 1,000 adult

shortnose sturgeon use the Penobscot River throughout the year. Shortnose sturgeon have not been documented spawning in the Penobscot River, although the presence of reproductive females and suitable spawning habitat in the upper river have been documented. Reproductive females from the Penobscot River have been documented moving to the Kennebec River, potentially indicating a complex reproductive migration pattern. Characterizing the movements, population size, and reproductive patterns of shortnose sturgeon in the Penobscot River provides a baseline for assessing the impact of the Penobscot River Restoration Project and will elucidate the status of sturgeon populations throughout the Gulf of Maine.

This project is funded by the Maine Department of Marine Resources through an Endangered Species Act Section 6 grant from NOAA-Fisheries; Penobscot River Restoration Trust through the NOAA Restoration Center and the American Recovery and Reinvestment Act, and the University of Maine.

Shortnose sturgeon

have not been

documented

spawning in the

Penobscot River

...the presence

of reproductive

females and suitable

spawning habitat in

the upper river has

been documented.

Reproductive

females from

the Penobscot

River have been

documented moving

to the Kennebec

River, potentially

indicating a complex

reproductive

migration pattern.

11

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We monitored aquatic benthic macroinvertebrates from (7) locations associated within the impoundment and tailwater areas of the Great Works and Veazie dams, as well as the tailwater area of the Milford Dam. Following Maine DEP methods, we deployed rock filled baskets as artificial substrates in triplicate sets and allowed them to be colonized by benthos for 28 ± days. The contents of the substrates were removed, sorted, and sent to a taxonomist for identification and enumeration. These data will be used for assessing changes in the aquatic life community structure due to dam removal and for determining whether aquatic life criteria are attained. Attainment status and indices of community structure will be analyzed using the Maine DEP aquatic life statistical model developed for rivers and streams in Maine. To characterize water quality conditions

prior to dam removal we collected water samples and measurements from 10 sites within the Great Works and Veazie dams project areas. Water quality parameters collected included dissolved oxygen, temperature, conductivity, BOD, bacteria, turbidity, secchi transparency, total suspended solids, pH, chlorophyll ā, and total phosphorous. Stations were sampled late-July thru late-October, 2009 and mid-June thru late-October, 2010 at 1-2 week intervals. Additionally we deployed Onset Hobo temperature loggers at 15 locations associated with the Great Works, Veazie, and Howland dam areas and at select free flowing areas. These recorders collected water temperature data continuously at 30 minute intervals. Pending funding we anticipate beginning post-removal monitoring in 2013.

Funding provided by Penobscot River Restoration Trust through NOAA ARRA; BIA PL 638, EPA CWA Section 106.

Pre-Dam Removal Geomorphic Monitoring on the Penobscot River, MaineAlice Kelley1

Daniel Belknap1

Andrew Heller1

Charles Baeder2

Matthias Collins3

1Department of Earth Sciences and Climate Change Institute, University of Maine 2Penobscot River Restoration Trust3NOAA Restoration Center, Gloucester, MA

Dams change the geomorphic and biologic characteristics of watersheds. Frequently, removal is seen as an effec-tive way to restore lost habitats and rebuild ecological communities. The largest of these projects on the North American East coast is currently being under taken in Maine. The Penobscot River Restora-tion Project plans to remove two dams and build a fish by-pass on the Penobscot River, in an effort to restore 11 species of sea-run fish, while maintaining energy production. The removal of the first dam is scheduled for summer of 2012. In anticipation of dam removal, geomor-phic monitoring was undertaken at monu-mented river cross-sections within the dam removal area to provide baseline data on channel bathymetry, sediment size, and bank conditions. Data collection included

repeated, seasonal photographic surveys, bathymetric surveys at each cross section, video-based channel sediment character-ization, bank geomorphology studies, and geophysical characterization of impound-ment sediment thickness. Data collected have been uploaded to Google Earth, a freely available interactive satellite imagery display and mapping program, as a means of displaying information and providing public access to spatially referenced data. Over the two-year monitoring period, few changes were noted in river bathym-etry or bank characteristics. Channel sediment characterization revealed that, within the study area, the Penobscot River channel in both flowing and impounded reaches is dominated by coarse sediment with a predominately sand matrix. This is in striking contrast to fine-grained sediment

The Penobscot River Restoration Trust is the non-profit responsible for carrying out the restoration effort, including purchase of the Veazie, Great Works, and Howland dams in 2010. The Penobscot Trust removed the Great Works Dam in 2012, and will remove the Veazie Dam and decommission and build a bypass around the Howland Dam. Combined with additional fish passage enhancements at four other dams owned by Black Bear Hydro, the project will significantly improve access to nearly 1000 miles of habitat for sea-run fish. Energy enhancements at Black Bear Hydro facilities means energy production will remain at least the same as when the Project began, and likely increase. The Penobscot Trust board includes representatives from the Penobscot Indian Nation, American Rivers, Atlantic Salmon Federation, Maine Audubon, Natural Resources Council of Maine, Trout Unlimited, and The Nature Conservancy, along with three additional directors.

Penobscot River Restoration TrustP.O. Box 5695Augusta, ME 04332207-232-9969 www.penobscotriver.orgwww.facebook.com/PenobscotRiver

The Penobscot River Restoration Trust would like to thank the many researchers, partners and supporters in this comprehensive monitoring effort. In particular, the Trust has worked closely with the National Oceanic and Atmospheric Administration (NOAA) to implement the monitoring program with significant funding through the American Recovery and Reinvestment Act and other NOAA programs. We would also like to acknowledge the involvement of the U.S. Fish & Wildlife Service, Maine Department of Marine Resources, Maine Department of Inland Fisheries and Wildlife, United States Geological Survey, Penobscot Indian Nation, The Nature Conservancy, The University of Maine, University of Southern Maine, Gulf of Maine Research Institute, Diadromous Species Restoration Research Network, Boyle Associates, Black Bear Hydro, LLC, and others that continue to make this work successful.

storage noted in many impoundments, and is interpreted to be an artifact of the region’s complex Late-Pleistocene and Holocene geological history.

Funded by Penobscot River Restoration Trust, through the NOAA Restoration Center and the American Recovery and Reinvestment Act

A publication of the Penobscot River Restoration Trust (c) 2013