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Science Spotlight 13.12
October 29, 2013
Contact: Shelley Dawicki
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Map of the study area. Credit: Justin Stevens, NOAA


Click on photo to launch slide show Mike O'Malley sets up acoustics equipment on the Silver Smolt. Photo by Paul Music, NOAA

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Hydroacoustics Provides a Large-Scale, Low-Impact Tool to Monitor Fish and Habitat in Maine's Penobscot Estuary

One day every other week for much of the year, Mike O’Malley places his acoustics gear into an open 19-foot aluminum skiff named the Silver Smolt at Turtle Head Marina in Hampden, near Bangor, and heads downriver to Fort Point on the lower Penobscot River estuary. For the next six hours or so, he monitors fish biomass in the estuary using hydoacoustics.

"The Penobscot River estuary is a complicated, complex system, difficult to monitor, and there is much to know about its function and role in fish production," said O’Malley, a fisheries scientist at the Orono Field Station, which is jointly supported by NOAA’s Northeast Fisheries Science Center and Northeast Regional Office. "Hydroacoustic techniques are a low cost, non-intrusive way to monitor the system on a large scale. Using this approach, we can obtain baseline data for some of the restoration efforts underway to remove dams and restore fish habitat. Changes induced by these efforts may first be detected in the estuary."

The time and location of the acoustic monitoring work is key. Atlantic salmon smolts migrate to the ocean in a small window of time during spring and share the river with many other migratory fish species, including river herring, American shad, rainbow smelt, and Atlantic herring. Juvenile river herring appear in large numbers in July and August; some continue on their outward migration to the Gulf of Maine, while others stay longer in the estuary. Juvenile Atlantic herring also use the estuary extensively in the summer. Other species, like Atlantic tomcod and rainbow smelt, are found in the estuary throughout the year, but particularly in early spring and fall.

After setting up his acoustical equipment aboard the skiff and lowering the transducer, or sound source, into the water, O’Malley and a colleague navigate along a systematic zigzag pattern as they move the skiff with the tides in the river. Humans cannot hear the signals from the split-beam 38 and 120 kiloHertz sound beams. If the beam encounters fish, the sound bounces off it and returns an echo to a monitor on the boat. The echoes can be interpreted to show fish of different sizes, densities, and locations in the estuary, disclosing important information about the Penobscot estuary ecosystem. Fish biomass distributions change with the season as different species use different parts of the estuary.

O’Malley’s survey work begins in March as ice disappears from the upper estuary, and ceases in late November or December when ice returns for the winter. Tides dictate whether the monitoring is conducted upstream or down, but the six-hour survey pattern used between Bangor and Fort Point remains the same.

The locations surveyed encompass the full range of salinity in the estuary – from nearly full salinity to full fresh water. The estuary is a mixing zone of high turbidity, where species seek protection from predators and can normally find sufficient food if they can tolerate the variable estuarine conditions.

Started as a pilot project in 2010, the acoustic surveys have been fully operational since 2012. Trawl catches, salinity and temperature data, and historical information available in the scientific literature are among the sources used to validate―or ground-truth― the acoustic survey results. In early May 2012, a contract fishing vessel worked with a team from the Orono Field station to monitor fish in the river. Data from the trawl catches help to verify data O’Malley obtains from his acoustic equipment as he works in tandem with the vessel.

NOAA Fisheries scientist Justin Stevens works closely with fisherman Josh Conover, who operates the 38-foot contract vessel F/V Odd Ball out of Islesboro, used to conduct the trawl surveys.  “Working with Josh has also helped us connect to the coastal communities and with information about the status of the resources and the estuary," said Stevens.

The Odd Ball tows a trawl net.  A metal box fitted into the cod end protects the fish it encounters and allows most to be released alive."The sampling gear captures pelagic species in the estuary. The surface trawl and live-car cod end allow sampling in the sensitive habitats with endangered species,” Stevens said.

In 2013, the trawl vessel survey work has been spread out during the year, with the surveys conducted once a month instead of just in May when the salmon are running. The result is a holistic, ecosystem approach to monitoring the estuary. The expanded schedule enables O’Malley to monitor how other species use the estuary throughout the year.

"The prolonged use of the estuary by many juvenile species has been an interesting finding," said O’Malley. "Some species seem to prefer certain areas and remain longer in the estuary than we expected."

Using low-impact techniques like hydroacoustics to survey the estuary allows researchers to gain detailed insight into how diadromous species - fish migrating between fresh and salt water such as salmon - transition to the marine environment.

During his survey work, O’Malley also monitors zooplankton in the estuary, which appear as smaller backscatter echoes. Marine mammals and seabirds seen by the researchers are also recorded. Since they prey on fish in the estuary, this information provides another insight into the overall picture of the ecosystem.

"The historical sea-run fish community in the estuary ecosystem, while depleted, is intact," said John Kocik, head of the Orono Field Station. "All the native diadromous species are still present in the Penobscot estuary, and that is good news. Natural reproduction is also occurring in the system; we have evidence of successful spawning of river herring, rainbow smelt, tomcod and American shad, among others."

River herring, while depleted, are the most abundant estuary species detected in the acoustic and trawl surveys during the year, apart from juvenile Atlantic herring which move inshore and dominate in the lower estuary in the summer. Alewife and blueback herring, two diadromous species of river herring, are designated by NOAA Fisheries as species of concern due to their current low abundance.

"As dams along the Penobscot River are removed, upstream access will be improved for many species, especially the historic sea-run fish community," Kocik said. "Hydroacoustics is a valuable tool and will be essential in monitoring the benefits accruing from the reconnection of the lower Penobscot River to the Gulf of Maine."

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