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Milford Lab: Environmental Research

Aquaculture and environment interactions

Bivalve aquaculture can greatly increase food production, and enhance natural harvests, but methods must be compatible with the environment, habitat, and natural ecology. The goal of our research is to evaluate aquacultural practices by experimentally measuring the biological, chemical, and physical effects of existing aquaculture activities on habitat and ecology. Some activities, such as hydraulic dredging, cause initial disturbance to benthic organisms, but our data indicate that effects are generally short-lived with rapid ecological recovery. Other studies have shown that fixed shellfish aquaculture gear can provide habitat for many organisms and standing stocks of filter feeding bivalves can reduce nutrient loads. Our research goal is to evaluate specific aquacultural practices objectively to help assure that farming practices are sustainable. Marine spatial planning for development of aquaculture will allow for multiple uses of the coastal zone to co-exist and will identify optimal areas for production. Current research activities include conducting cooperative experiments with the shellfish industry to evaluate cultivation practices, and describing physical, chemical, and biological characteristics of shellfish habitat.

Shellfish aquaculture plankton and nutrient interactions

As the demand for aquacultured shellfish increases, so do concerns about possible environmental consequences of shellfish aquaculture expansion. Our group studies the complex interactions of shellfish aquaculture with the surrounding environment. We quantify environmental and shellfish variables, including inputs and outputs of nutrients, plankton and other chemical, physical parameters. Our research also incorporates various time scales from minutes to months. Our findings have highlighted the importance of local nutrient and plankton dynamics, as well as hydrodynamics. The scale of aquaculture setting in a particular site is also crucial in defining interactions. Our findings contribute to siting and scaling decisions made by farmers and by regulatory agencies, including the Northeast Regional Office of NMFS.

For more information, contact Judy Li or Shannon Meseck.

Nutrient bioextraction

A two-year, collaborative study evaluating the potential for aquacultured ribbed mussels to be used to extract nutrients from the Bronx River in New York City yielded important findings about the nutrient and plankton dynamics in that body of water. We discovered that the area studied at the confluence of the East River Tidal Strait and the Bronx River is a high-nutrient, low-chlorophyll (HNLC) system, which has important implications for nutrient management of western Long Island Sound, but also makes the site unsuitable for substantial mussel growth. Based upon these findings, we collected data at two locations in upper Narragansett Bay, RI, with more classic symptoms of eutrophication – high chlorophyll levels and seasonal hypoxia. Data from these sites are being analyzed.

We have also contributed to a modeling effort, led by Suzanne Bricker of NOAA NCCOS, to examine the potential for shellfish aquaculture to remove nitrogen at the scale of whole estuaries (Long Island Sound and Great Bay, NH). We provided local data on environmental conditions and oyster feeding physiology for use in the ecosystem and farm models. Results from this project are expected in early 2015.

In 2015, we will begin a study in collaboration with the town of Greenwich, CT, with a substantial coastline in western Long Island Sound and very active municipal shellfish management. Working with a resource economist at Stony Brook University, we will attempt to quantify local, economic benefits of the ecosystem services realized from existing and potential shellfish aquaculture, including improvements in water quality derived from filtration and assimilation of phytoplankton and associated nutrients in shellfish that then are harvested from the environment.

For more information please contact Julie Rose or Gary Wikfors.

Characterizing salmon habitat

The Atlantic salmon (Salmo salar) once ranged from the Housatonic River, CT north to the St. Croix River on the US/Canadian border.  Overfishing, water quality degradation, and barriers to migration (i.e. dams) have led to range contraction isolated to several small populations native to rivers in the state of Maine.   Despite intensive efforts to recover the Atlantic salmon to its prominence as King of Fish, the altered structure of biological communities, continued poor fish passage at dams, and poor marine survival are just some of the obstacles hindering the recovery of this species.  Current protection and restoration of Atlantic salmon populations native to Maine rivers is meeting with limited success.

Studies from other regions with active timber-based industries and fisheries (e.g., US Pacific northwest) have shown that wood-degradation products, such as ammonia and sulfide, can reach levels that are toxic to fish. Furthermore, the increase in turbidity arising from these activities in the watershed can also have negative effects upon smolt survival.   We propose to characterize the water in one Maine river, the Penobscot, in terms of particle quality and quantity, bacterial loads, and phytoplankton community. We also will sample for harmful algal species, particularly Heterosigma okashiwo which has been shown to be toxic to finfish. H. okashiwo has been implicated in die-offs of various species of adult salmon (both wild and aquacultured) in other locations. We plan on conducting most sampling during the annual smolt runs.

This study is being conducted in cooperation with the Northeast Salmon Team at the Maine Field Station in Orono, Maine, and will provide environmental data which will aid in the understanding and conservation of Atlantic salmon in the northeast.

For more information, contact Shannon Meseck.

Improving phytoplankton quantification methods

Phytoplankton are photosynthetic microscopic algae at the base of marine food webs.  Shellfish feed on phytoplankton directly.  Phytoplankton biomass and productivity are key factors in coastal processes that are important in selecting shellfish aquaculture sites and quantifying interactions between shellfish aquaculture and the environment.  Red fluorescence of chlorophyll a when phytoplankton samples are illuminated with blue light (referred to as ‘in vivo fluorescence) is used widely to estimate phytoplankton biomass, hence food availability for shellfish. Reactions of chlorophyll to light, such as non-photochemical quenching during the day, and circadian rhythms of phytoplankton influence chlorophyll fluorescence yield, compromising the accuracy of chlorophyll measurements from in vivo fluorescence.  Current research is evaluating ways to correct in vivo fluorescence measurements to yield more accurate chlorophyll estimates in environmental and culture-system samples. 

Research is also ongoing developing measurements of phytoplankton/primary productivity with variable fluorescence techniques.  The results will be useful in quantifying carrying capacity of a specific site.  We are also collaborating with EPA and CT Department of Energy and Environmental Protection in aiming at using the information for the water quality management of the Long Island Sound.

For more information, contact Judy Li.

Biogeography of east-coast Vibrio vulnificus populations

Vibrio vulnificus (Vv) is a naturally-occurring bacterial species that inhabits coastal ecosystems, including the entire eastern coast of North America. This bacterium can produce infections and associated illness sometimes leading to death. Human Vv illnesses appear to have a strong geographic component, with much lower incidence of infection in northern regions of the east coast than in the south, despite the presence of this species in northern regions and annual seasonal temperature excursions above the pathogenicity trigger.

Milford staff developed and implemented a plan to determine if there is geographic population structure in Vv on the east coast of the US. Studying cultured isolates already in hand and being supplied by cooperating researchers at several institutions, gene sequences were identified with appropriate variation within the species using the ClonalFrame method and nucleotidic diversity analysis. Milford staff also examined geographical differences inVv virulence between northern and southern strains. Clinical, virulent isolates of Vv were compared to environmental strains of Vv recovered from oysters. These oysters were supplied by growers from South Carolina to Maine during the summer months. Multi Locus Sequence Typing (MLST) and Arbitrarily-Primed Polymerase Chain Reaction (AP-PCR) are molecular techniques being used to study possible genetic differences between virulent and non-virulent Vv. A better understanding of the biogeography of Vv on the east coast of the US will aid both regulatory agencies and shellfish harvesters in quantifying and mitigating the risk of human infection from consuming farmed shellfish.

For more information, contact Steve Pitchford.

Essential Fish Habitat
fish egg

Protecting essential fish habitat is an important element of Federal fisheries management legislation. Shallow-water (< 2 m) microhabitats are important nursery areas and predator refuges for many species of juvenile fish.Habitats we have investigated include eelgrass beds, macroalgal areas, marsh, creeks, and cobble reefs. Sampling methods include beam trawling, beach seining, and trapping. Ecological field experiments have been used to measure habitat-specific growth. We have used single beam sonar for acoustic seabed classification and mapping of habitats in water as shallow as 0.5 meters. Geospatial analysis of fish distributions can also reveal patterns of habitat use.

Coded-wire tags have been used to study habitat fidelity of young-of-year tautog in nearshore habitats. Fish were found to have limited ranges and tag returns allowed us to estimate population size. We determined that in New Haven Harbor there are about 4,000 tautog in an area along 0.5 km of shoreline and within 25 m of shore. Acoustic tags have also been employed that use unique sonic signals that identify individual fish, allowing us to track and map home ranges.

For more information, contact Jose Pereira.
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(File Modified Jun. 17 2016)