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Ecosystem Status Report for the Northeast Large Marine Ecosystem

10. Stressors and Impacts

dredged vs undredged ocean bottom
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Marine ecosystems are subject to a broad array of anthropogenic and natural stressors. In the following we document trends in pressures affecting systems in the Northeast including contaminants, chemical and oil spill events, eutrophication, hypoxia, nuisance and harmful algal blooms, loss of waterways and riparian systems due to damming of streams and rivers, climate change (specifically sea level rise, ocean acidification and ocean warming), fishing effects on habitat, introduction of exotic species, and underwater noise pollution. We have focused on issues that are directly or indirectly related to anthropogenic stressors. Ultimately, our interest centers on the cumulative impacts of these stressors on the state of the system.

10.1 Contaminants and Water Quality

The Northeastern United States is heavily industrialized and populated, resulting in substantial impacts on sea life, water quality, and natural resources. In this section, we address issues related to pollution and water quality in the region. Specifically, we consider contaminants (heavy metals, pesticides, and bacterial loads), chemical and oil spill events, eutrophication, hypoxia, and nuisance and harmful algal blooms.

10.1.1. Heavy Metals and Pesticides
chart showing heavy metal and total DDT concentrations in blue mussel tissue in the Gulf of Maine Figure 10.1
chart showing ratio of five year mean concentrations for arsenic, cadmium, lead, mercury nickel, and total DDT to the FDA established safety level for that parameter Figure 10.2
chart showing Heavy metal and total DDT (TDDT) concentrations in blue mussel and oyster tissue in the Mid-Atlantic Bight Figure 10.3
chart showing ratio of the five year mean concentrations for arsenic, cadmium, lead, mercury nickel, and total DDT (all forms of DDT) to the FDA established safety level in the Mid-Atlantic Bight Figure 10.4

Heavy metals occur naturally in the environment and concentrations vary with the underlying geology. Human use of metals and their introduction to the environment through urban runoff, industrial effluents and domestic discharge, results in releases into coastal environments. Large populations concentrated in coastal regions, combined with the cumulative effects of shipping traffic and industrial activities along a waterway, can mobilize materials in the marine environment.

Here, we also provide information on tissue concentrations of the pesticide DDT, banned in 1972 in the United States but still present in sediments throughout the region. Pesticide levels were determined from blue mussel samples in the GOM subregion and in oyster and blue mussel inthe MAB subregion.

NOAA Mussel Watch data was analyzed for two subregions within the NES LME; the Gulf of Maine (GOM) and the Mid-Atlantic Bight (MAB). Trace metal concentrations for arsenic (As), cadmium (Cd), copper (Cu),lead (Pb), mercury (Hg), nickel (Ni) , and zinc (Zn) were analysed in blue mussel (Mytilus edulis) tissue in the Gulf of Maine and the northern MAB. Tissue samples were also analyzed for oysters (Crassostrea virginica). Because the uptake kinetics of contaminants differs among these bivalve species, we report results for each individually. For both the GOM and MAB subregions, data analyzed for contaminant trends was obtained from a number of stations and averaged over each ecological production unit (GoM and MAB over a wide geographic range. The Mussel Watch samples were in taken throughout the region during 1986 – 2007; restricted sampling in the MAB also took place in 2012.

Annual mean heavy metal concentrations for blue mussels (Mytilus edulis) in the GOM subregion are characterized by overall downward trends in cadmium, copper, lead, mercury and zinc, an upward trend in arsenic, and a relatively stable pattern for nickel during the study period.

While annual mean lead concentrations have trended downward in the subregion, they are all above the FDA safety level of 1.7 ppm, ranging from 3.03 (2003) to 8.46ppm (1987). Of the 194 individual station samples taken within the subregion 144 (74.2%) are above the safety level with an average of 5.9ppm. Concentrations of total DDT decreased in blue mussel tissue samples throughout the study period. Annual mean concentrations have consistently been below the FDA safety level of 5.0 ppm (Figure 10.1).

Ratios of the five year mean concentration for five metals (As, Cd, Pb, Hg & Ni) and total DDT to the FDA safety level for that parameter during the last five years of the study (2003 – 2007) are shown in Figure 10.2. Polygons extending outside a radius of 1.0 represent an exceedance of the FDA safety level for the parameter. Copper and zinc are not depicted as there is no FDA safety level established for these parameters.

Overall downward trends in cadmium, lead and mercury were observed in blue mussel tissue during the study period in the Mid-Atlantic Bight (Figure 10.3). In contrast, copper, nickel and zinc, increased and arsenic remained relatively steady during 1986 – 2012. Of the analyzed metals, annual mean lead levels exhibit elevated concentrations. While annual mean lead concentrations have trended downward in the subregion, all annual mean values are above the FDA safety level of 1.7ppm, ranging from 2.1 (2000) to 8.21ppm (2004). The annual means for all other parameters are below FDA safety levels during the study period.

An overall downward trend in annual mean concentrations for nickel in oyster tissue in the MAB, while increases were noted for arsenic, cadmium, copper, lead, mercury and zinc concentrations during the study period (Figure 10.3) Of the analyzed metals, annual mean cadmium levels consistently exhibit elevated concentrations above the FDA safety level of 4.0ppm.

The MAB subregion is characterized by an overall downward trend in DDT for blue mussel samples. Annual mean concentrations for the subregion are all below the FDA safety level of 5.0ppm, with the highest concentration (0.17ppm) occurring in 1986. DDT concentrations in oyster tissue also declined in the MAB subregion over the study period. Annual mean concentrations for the subregion are all below the FDA safety level of 5.0ppm, with the highest concentration (0.13ppm) occurring in 1987.

Five year mean concentration for five metals (As, Cd, Pb, Hg & Ni) relative to the FDA safety level during the last five years of the study (2008 – 2012 are provided in Figure 10.4 for Mytilus edulis and Crassostrea virginica. Polygons extending outside a radius of 1.0 excede the FDA safety level for the parameter. Copper and zinc are not shown because there is no FDA safety level established for these metals.

10.1.2. Oil and Chemical Spills
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chemical and oil spill locations
chart showing total annual gallons of chemical and oil spills during 2000-2011 Figure 10.5

The Marine Casualty and Pollution Database provides detailed incident reports for the analysis of coastal spills. This database is being utilized by the NEFSC to understand potential trends associated with spills from marine vessel and coastal facilities. In the following, three spill categories are used including those from coastal facilities, vessels and other sources.

Total discharge (gallons) from facility, vessel and other sources are shown in Figure 10.5 for each of the four subregions located within the NES LME. The plots characterize the total volume of all spills for all contaminants reported by the USCG. Spill volumes range from 1 – 5,000,000 gallons and the magnitude of spills associated with each source type varies considerably, with the largest incidents being associated with either marine vessels or coastal facilities.

A spatial representation of the density of spills within the NES LME during 2001 and 2010 is provided in Figures 10.6 - 10.8. Larger circles represent larger spills.




10.1.3. Eutrophication
map showing eutrophication status for the Northeastern United States Figure 10.9

Eutrophication, the process by which excessive plant and algal growth is caused from the addition of increased nutrients (largely nitrogen and phosphorus) to water bodies resulting in the depletion of dissolved oxygen affects coastal water quality and marine organisms, as well as on coastal industries dependent on estuarine aesthetics and resources. Eutrophication may also cause risks to human health, resulting from consumption of shellfish and finfish contaminated with algal toxins, or direct exposure to waterborne toxins at recreational beaches. Widespread coastal eutrophication is a serious issue affecting the Nation’s beaches (see below) and as coastal populations continue to increase concerns exist that eutrophication and associated symptoms are also increasing as a result of increased anthropogenic nutrient inputs from agriculture, wastewater treatment, urban runoff, and consumption of fossil fuels (Figure 10.9).

The most commonly reported eutrophication-related problems included hypoxia, nuisance and toxic harmful algal blooms (HABs), and losses of submerged aquatic vegetation (Bricker et al. 2007). Additional impacts may include reduced coastal water quality, beach closures, and loses to coastal fisheries due to changes in target species behavior and closures of shellfishing waters.

10.1.4. Hypoxia
map showing hypoxia indicators in the Northeastern United States Figure 10.10

Hypoxic conditions (water with oxygen levels below 2 mg/L) occur naturally but are frequently associated with eutrophication (Whitledge 1985; Bricker et al. 2007; and Diaz et al. 2008).

Hypoxic areas are often termed “dead zones” since few organisms can tolerate areas with little or no oxygen. Hypoxia has been recognized as one of the most important water quality problems worldwide due to the effects it has on both natural systems and economic dependence on coastal resources. In the U.S. hypoxia is evident along all of the Nation’s coasts and in the Great Lakes, with incidences increasing almost thirty-fold since 1960. An estimated 300 U.S. coastal systems experienced documented hypoxia in 2008 (Diaz et al. 2008). As the number of people living and working by the coast continues to grow, the number of hypoxic coastal systems is also anticipated to grow. Bricker et al. identified the mid-Atlantic as the subregion most impacted by eutrophication, with 60% of assessed estuaries highly influenced by human sources of nutrient loading (Figure 10.10).

Under hypoxic conditions, immobile species can succumb to mass mortality; mobile species may experience increased energy expenditures to avoid these areas, reduced foraging grounds, and fish kills when dissolved oxygen concentrations drop rapidly. Habitat loss and community composition changes as a result of hypoxia can also disrupt linkages between algal producers and tertiary predators, alter food web pathways and affect fisheries yields (Diaz et al. 2008). Coastal bays and estuaries undergoing seasonal hypoxia, experience a loss in total benthic secondary production.

10.1.5. Algal Blooms
chart showing Alexandrium cyst counts in the Gulf of Maine Figure 10.11
chart showing red tide associated shellfish closures in the Gulf of Maine expressed as kilometer days of closure Figure 10.12
chart showing standardized anomalies of Phaeocystis density in the Gulf of Maine based on Continuous Plankton Recorder observations Figure 10.13

While high abundances of phytoplankton typically provide increased food for secondary production, some phytoplankton species in sufficiently dense populations can negatively impact human activities and other higher trophic levels. Collectively these occurrences are called Harmful Algal Blooms (HABs) and they vary widely in their causes and consequences. HABs are also known by the colloquial term “red tide” as some harmful species contain the red pigments that can discolor waters at high populations.

In the Gulf of Maine and on Georges Bank, toxic dinoflagellates of the genus Alexandrium blooms annually with direct impacts on secondary production and fisheries. Within the Gulf of Maine, A. fundyense and A. tamarense are morphologically similar varies of the same species (Anderson et al. 1994; Scholin et al. 1995). Both A. fundyense and A. tamarense naturally produce saxitoxins that can cause Paralytic Shellfish Poisoning (PSP).

Alexandrium commonly occurs throughout the Gulf of Maine (Figure 10.11). PSP toxicity has been recorded infrequently in Narragansett Bay, and Alexandrium cells have been observed in Long Island Sound and off the New Jersey coast (Anderson et al. 1982; Cohn et al. 1988). Typically, population densities do not reach harmful concentrations south of Cape Cod, however potentially hazardous cell densities may exist within localized embayments. While typically comprising a small proportion of the overall phytoplankton community across its geographic range, A. fundyense can form nearly monospecific blooms in the Bay of Fundy and eastern Maine with densities reaching 1x105 cells L-1 (Martin et al. 2005). The timing of significant blooms of Alexandrium is dependent on the “endogenous clock” of overwintering benthic cysts (Anderson and Keafer 1987) and the local growth environment. While populations within estuaries and embayments seem to be dominated by the former (Anderson 1997), offshore populations have an inverse relationship with spring diatom blooms and are rarely found in areas of high chlorophyll concentration.

Outbreaks of red tide hold important economic consequences as a result of closures of natural shellfish beds and impacts on mariculture facilities. Kleindinst et al. (2014) provide statistics on the duration of closures and the amount of coastline closed due to red tide in the western and eastern Gulf of Maine. Here we present a combined indicator expressed as the product of the length of the closure period and the length of coastline affected (km days closed). In general, the closures have been more extensive in the western Gulf of Maine and there are clear decadal and multidecadal periodicities (Figure 10.12) with notably lower closure periods during 1992-2002.

Another potentially harmful species is the diatom Psuedo-nitzschia multiseries/pungens, which produces the neurotoxin domoic acid. While little is known about the toxin potency or direct impacts of this species to the NES LME, Pseudo-nitzschia spp. is widespread and common through the Gulf of Maine, and likely the entire shelf.

In the Mid-Atlantic region, nearly homogenous monocultures of Aureococcus anaphogefferens cause “brown tides,” as the abundance of cells can discolor the water and block light penetration. These brown tides are responsible for the collapse of the Long Island Sound bay scallop fishery and significant declines in other shellfish populations as well (Bricelj and Lonsdale 1997).

Phytoplankton species of the genus Phaeocystis cause nuisance algal blooms that can affect fishing activities and water quality (Figure 10.13). Phaeocystis is a polymorphic species, alternating between a colonial stage and a solitary stage. Solitary cells are approximately 3-9 µm in size, while colonies containing up to several thousand cells can be several millimeters in diameter (Colijn 1998; Verity and Medlin 2003) . P. pouchetii, a species sometimes found during the spring in the northern parts of the NES LME, forms organized colonies within a gelatinous matrix surrounded by a distinct colonial skin. The tough and pliable skin protects colonies from viruses and bacteria, while the size of the colony makes it more difficult for larger zooplankton to graze (Hamm 2000). Phaeocystis can outcompete diatoms for nutrients during the spring bloom (Tungaraza et al. 2003) and can grow faster than diatoms in culture experiments (Hegarty and Villareal 1998). These competitive advantages help promote large blooms of Phaeocystis with the potential to impact the organic particle flux, trophic transfer efficiency and the ecological function of the spring bloom (Verity 2000).

10.1.6. Bacteria
chart showing Beach closure metrics for the Gulf of Maine and Mid-Atlantic Bight. Figure 10.14

Beach and shellfish water closures are common occurrences in coastal states. Open shellfish harvesting areas and beaches along the coast are subject to closures based on regulations in place by state health and fisheries management authorities. Closures are often linked to an increased presence of bacteria in coastal waters from stormwater pollution, untreated sewage spills and sewage overflows, harmful algal blooms (see above) and the introduction of animal feces. Elevated bacteria levels may indicate the presence of disease-causing organisms that can cause human illnesses. Shellfish are particularly susceptible to higher bacteria concentration due to their role as filter-feeders (Shimshon and Colwell 2005). Stormwater pollution can be difficult to manage as rainfall events will trigger a closure when threshold amounts are reached for a given area. Rainfall acts as a conduit for pollution to coastal waterbodies, picking up pollutants, bacteria and nutrients as it travels across agricultural lands, through sewers, and along roadways and other surfaces. Rainfall levels required to trigger a closure vary from state to state, as well as within states, and have a variety of factors considered in management decision such as the amount of development and/or impervious surface surrounding receiving waters. Areas under a rainfall closure often cannot be reopened until high bacteria levels have been flushed from coastal systems by tidal cycles, or until shellfish have had enough time to purge themselves of contaminants. The amount of time required for these processes to occur varies seasonally along with water temperature, salinity, tidal height, and other factors affecting shellfish filtering rates. [1]

Beach closures have a direct impact on recreational use of beaches and tourism. Pathogens, bacteria and viruses pose a hazard to swimmers who may come in direct contact with them. Beach closures and advisories are issued by state health departments, and the U.S. Environmental Protection Agency (EPA), through the Beaches Environmental Assessment and Coastal Health Act of 2000, provide grants to monitor coastal beaches for bacteria that indicate the possible presence of disease-causing pathogens and to notify the public when there is a potential risk to public health. Grant recipients report coastal beach monitoring and notification data to the EPA, which maintains a database of that data to support state efforts to reduce the risk of exposure to disease-causing pathogens at recreational beaches. [2]

Figure 10.14 shows trends in beach closures for the MAB and GOM subregions. Data is courtesy of the EPA Beach Advisory and Closing On-line Notification database (BEACON). The figure shows that increasing trends are apparent in both subregions from 2000 – 2009 for: 1) the number of beaches experiencing a closure; 2) the number of beach closures; and 3) the number of beach closure days due to water quality issues. In 2009 there appears to a general peak in all numbers, followed be a reversal or downward trend in the data.

Commercial and recreational shellfishing areas are also impacted by bacterial contamination. Often, shellfish beds are permanently closed when they are located in close proximity to wastewater treatment plant outfalls and marinas, while other areas are closed based on rainfall events or exposure to sewage overflows. The amount of time for a shellfish bed closure varies by state but is generally around 14 days after the rainfall event or spill, in order to allow for adequate flushing of the coastal environment. Waters may be opened sooner if water and shellfish tissue samples show that harvesting conditions are once again safe. Shellfish bed closures may have a direct economic impact on commercial shellfish operations as well as on recreational shellfish harvesting.

1 New Hampshire Department of Health (; North Carolina Department of the Environment and Natural Resources (

2 EPA’s BEACH Report: 2011 Swimming Season, June 2011 (

10.2 Climate Change

Important changes in the physical characteristics of the Northeast Continental Shelf have been observed over the last several decades these include sharp increases in temperature, reduced salinity, and related increased in stratification (see Physical Pressures in Section 3). These changes have been identified as manifestations of climate change in the region. Here we further focus on the impacts of observed patterns of sea level rise, ocean warming, and ocean acidification. (For long term projections of changes in ocean temperature and acidification, see Section 2.2: Climate Projections).

10.2.1. Sea Level Rise
chart showing heavy metal and total DDT concentrations in blue mussel tissue in the Gulf of Maine Figure 10.15

Sea level change occurring in the Northeast Shelf Ecosystem and on global scales reflects increased thermal expansion of the world’s ocean and an increase in ocean water volume resulting from the accelerated melting of glaciers and ice on land and at sea. Sea level has risen by nearly 0.35m in the southern states bordering the Northeast Shelf Ecosystem and on the order of 0.25m in the northern states (Figure 10.15); the data from these gauging stations is set relative to the most recent mean sea level established by NOAA’s Center for Operational Oceanographic Products and Services (CO-OPS). The rate of sea level change is expected to increase in the coming decades. The most recent assessment of world climate by the Intergovernmental Panel on Climate Change (IPCC) provides projections of sea level rise expected to occur by the end of the century. The projections are conditioned on various assumed levels of greenhouse gases called Representative Concentration Pathway (RCP) scenarios. The projected sea level rise by the year 2100 in these projections ranged from 0.26 to 0.98 m depending on the RCP scenario used in the model.

With expectations of rising sea level, coastal communities have to take into account the likelihood of more frequent flooding of coastal structures and land habitats. However, the impact of increasing sea level will not be limited to terrestrial ecosystems. The marine ecosystem of the Northeast Shelf has a dependency on coastal habitats such as marshes that provide both geochemical supports for system cycling and important nursery areas for living marine resources (Day et al. 2008). The emerging threat to coastal habitats revolves around the potential mismatch between the rates of sediment delivery and inundation, which could result in the loss of critical tidal marsh habitats over time (Weston 2014). These changes could impact the communities of fish and invertebrates of the Northeast Shelf and the fisheries these populations support.

10.2.2. Ocean Warming

Center of Biomass of Finfish

Figure showing along-shelf position of the center of biomass for nine fish species over time from the NEFSC autumn bottom trawl survey. Figure 10.16

As water temperatures increase, we expect fish species that prefer cool waters (cold-temperate species) in the ecosystem to respond by shifting their distribution northward to avoid warm waters. We would also expect that their abundances will decrease. However, species that prefer warm water (warm-temperate species) will also shift their distribution northward, but will likely increase in abundance. Using presence/absence data from the NEFSC trawl survey data, we calculated the average along-shelf position of nine fishery species (Figure 10.16). Along-shelf position is used rather than latitude because of the complex shape of the shelf. The four southern species all showed an upshelf (northeastward) progression over time although black sea bass and Atlantic croaker have receded south over the past decade. To put these shifts in distribution in context, the center of mass of black sea bass shifted from Maryland to northern New Jersey and the center of mass of butterfish shifted from New Jersey to Massachusetts. In contrast, Atlantic cod and haddock have shifted downshelf, likely due to the geography of the Gulf of Maine. Without the ability to move further north, they have moved into deeper regions of the Gulf of Maine. Temperature is generally related to these changes in distribution, but there are likely multiple factors involved including temperature, population size, prey distributions, and predator distributions.

Range of Finfish

The center of biomass does not tell the whole story of fish distribution. The area occupied by species also change over time in response to fishing and climate factors (Lucey & Nye 2010). For example, both haddock and Atlantic cod show relatively stable centers of biomass (Figure 10.16) but show very different patterns in their ranges over time. Haddock has contracted and expanded mostly due to several large year classes in 1975, 2003, and 2010 (Movie 10.1, below). In contrast, Atlantic cod have experienced a significant contraction in the area they occupy on Georges Bank and appear to be expanding in nearshore Gulf of Maine (Nye et al. 2009; Movie 10.2, below). Species with shifts in their center of biomass such as red hake show contractions in their southern range and expansion in their northern range as they shift poleward (Nye et al. 2009; Movie 10.3, below).

For a more extensive library of fish distributions please visit

Movie 10.1 Animation of haddock distribution from NEFSC autumn bottom trawl surveys. Warmer colors (i.e. red, yellow) represent areas of higher density while cooler colors (i.e. blue) represent areas of low density.
Movie 10.2 Animation of Atlantic cod distribution from NEFSC spring bottom trawl surveys. Warmer colors (i.e. red, yellow) represent areas of higher density while cooler colors (i.e. blue) represent areas of low density.
Movie 10.3 Animation of red hake distribution from NEFSC autumn bottom trawl surveys. Warmer colors (i.e. red, yellow) represent areas of higher density while cooler colors (i.e. blue) represent areas of low density.
10.2.3. Ocean Acidification
map showing location of dams constructed for power generation, recreational purposes, and other uses Figure 10.17

A recent analysis of carbonate chemistry on the US NES shows that acidification via increases in atmospheric carbon dioxide is occurring in the region near the values expected from previous modeling estimates. Historical data collected as part of the NEFSC’s MARMAP program from 1976-1983 were compared to recent data collected as part of joint NOAA-NASA partnership aboard the ECOMON survey cruises in 2010 and 2011. While there is some variability in magnitude among the different areas throughout the NES, most noticeably in the coastal waters dominated by freshwater inputs, the regional average is a decline in pH of -0.036 over the past ~30 years (Figure 10.17), or about -0.012 per decade. Using the measured pH and total alkalinity measurements to calculate the change in pCO2, the average increase is 50.5ppm over the past ~30 years. Efforts are currently underway to better determine what physical parameters can affect acidification on the NES, as well as how individual species and ecosystems will be affected by the alteration in carbonate chemistry.

10.3. Waterway Obstruction
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hydroelectric dams in NE US
map showing percentage occupancy of historical river habitat for alewife and blueback herring populations in the Northeastern United States Figure 10.21

Construction of dams in the Northeastern United States since colonial times has radically altered both freshwater and estuarine marine ecosystems in the region, affecting migratory pathways of diadromous species, nutrient exchange, and the hydrology of the region. Diadromous species migrate between freshwater and saltwater in relation to reproductive cycles and other life history events. Among the species diadromous specie affected by water way obstruction are Atlantic salmon (Salmo salar), striped bass (Morone saxatilis), alewife (Alosa pseudoharengus), blueback herring (Alosa aestivalis), American shad (Alosa sapidissima), rainbow smelt (Osmerus mordax), Atlantic sturgeon (Acipenser oxyrinchus), shortnose sturgeon (Acipenser brevirostrum), and American eel (Anguilla rostrata). Several of these species are listed as threatened or endangered. Marine food webs and energy flow have been substantially altered as a result of declines in forage fishes with diadromous life histories. Unobstructed rivers, ponds, and lakes act as migratory corridors between freshwater and marine spawning and nursery grounds. Because the history of dam construction and waterway obstruction dates back to the 15th century in this region, pre-dating the development of fisheries and ecological research programs by two centuries, the full impact of these changes in the aquatic ecology of the Northeastern United States is not fully known. We do not have a ‘pristine’ baseline from which to judge alteration of system dynamics.

The widespread distribution of active dams constructed for hydropower, development of impoundments for recreational purposes, and other uses throughout the region based on a compilation by the Nature Conservancy is shown in Figures 10.18-10.20.

A number of factors, including waterway obstruction by dams have altered the amount of available or currently occupied riverine habitats in the region. Dauwalter et  al. (2012) provide estimates of the amount of historical habitat currently occupied by alewife and blueback herring populations in major river systems in the Northeastern United States (Figure 10.21).  These estimates range from less than 20% to 100% for alewife populations.

10.4 Fishing Gear Impacts

As noted in Section 9 (Ecosystem Services), fisheries in the Northeastern United States provide an extremely important benefit to the region in terms of employment, revenues, and as a source of high quality food. However, there are also incidental environmental impacts associated with the provision of this important service. Fishing gear can have adverse effects on geological features and associated benthic faunal assemblages. There are also potential impacts on protected species as a result of incidental by-catch in fishing gear. In the following we document some of the vulnerabilities and impacts on benthic communities and on marine mammal, seabirds, and turtles of fishing activities in the region.

10.4.1. Effects on Benthic Communities
chart showing distribution of major substrate categories on the Northeast US Continental Shelf Figure 10.27
chart showing distribution of natural disturbance categories on the Northeast US Continental Shelf Figure 10.28
chart showing relative risk arrayed by gear type and habitat category for geological features in high energy regimes Figure 10.29
chart showing relative risk arrayed by gear type and habitat category for geological features in low energy regimes Figure 10.30
chart showing relative risk arrayed by gear type and habitat category for biological features in high energy regimes Figure 10.31
chart showing relative risk arrayed by gear type and habitat category for biological features in low energy regimes Figure 10.32
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fishing activity by otter trawls

Fishing gear that comes into contact with the sea bed can affect both geological structures and the benthic communities associated with these structures. With the exception of pelagic fishing gear that does not contact the bottom, all other fishing gear, including otter trawls, dredges, traps, longlines, and gillnets, has the potential to exert adverse impacts on bottom structures and communities. The distribution of fishing activities on the Northeast Continental Shelf is extensive (Figures 10.22-10.26). These impacts differ among gear types, particularly between mobile fishing gear that is actively towed and non-mobile gear which is set in fixed locations and marked by buoys. There are also differential effects depending on levels of natural disturbance associated with bottom currents and other factors and associated traits of benthic communities with respect to susceptibility to anthropogenic disturbance and recovery times.

To assess the vulnerability of benthic habitats and associated benthic organisms, the Omnibus Habitat Plan Development Team of the New England Fishery Management Council undertook and extensive literature of existing information on habitat association of benthic fauna and the effects of disturbance by different fishing gears under high and low natural disturbance levels as measured by bottom shear stress. (NEFMC 2011).

The vulnerability indices were separated into two components: susceptibility and recovery. Different types of structural seabed features (e.g. sponges, biogenic burrows, bedforms, etc.) were assigned to each of five possible combinations of substrate (mud, sand, granule-pebble, cobble or boulder) and two energy categories of natural disturbance (high or low) for a total of 10 combinations. The spatial distribution of the substrate categories and bottom energy levels are provided in Figures 10.27-28. Susceptibility is defined as the percentage of a particular structural habitat feature removed or damaged by a one pass of each of five gear categories, including otter trawl, scallop dredge, hydraulic dredge, pots and longline/gillnets. Recovery is defined as the number of years required for the feature to return to its original state. Susceptibility and recovery scores were assigned individually for each combination of habitat and gear type for both physical habitat and their associated benthic communities.

We have defined an index of relative risk as the product of the NEFMC susceptibility and recovery scores (so that a combination of high susceptibility and long recovery time would represent the highest relative risk category). These risk scores were developed separately for physical and biological attributes of the habitat and for high and low energy scores (Figures 10.29-10.32). In general the highest relative risk was associated with scallop and hydraulic dredges in sand and pebble habitats (the only two habitat types where these gear operate). Biological communities were generally subject to higher relative risk than physical habitats and risk was uniformly higher in low energy habitats (Figures 10.29-10.32). The latter observation reflects the fact that natural disturbance regimes had already shaped the physical structure of the physical habitat and biological communities in high energy environments.

10.4.2. Ship Strikes, Entanglement, Incidental Catch
chart showing number of incidents involving marine mammals through entanglement, entrapment, non-human interactions, unknown  and vessel strikes Figure 10.33
chart showing total number of sea turtle strandings in the Northeastern United States 1986-2013 Figure 10.34

Figure 10.33 charts large whale serious injury and mortality incidents, 1990-2011. Detected incidents represent a sample of true mortalities and serious injuries, actual rates of incidence are unknown. There is some evidence that recently introduced (2008) vessel speed restrictions have reduced the incidence of mortality by ship strike (Conn & Silber 2013; Pace 2011). Historically (1970-2009), entanglement in fishing gear has been the primary cause of death in detected incidents when the cause of death could be established (Van Der Hoop et al 2013).

Although sea turtle stranding data may not be indicative of local abundance, it may give some metric of environmental (i.e. temperature, disease) or human (i.e. boat strikes, fishery gear entanglement) pressures. Figure 10.34 shows the total number of annual sea turtle strandings (both live and dead) from Virginia to Maine based on the Sea Turtle Stranding and Salvage Network’s database. Stranding data from 2008 to 2013 are much less certain and are subject to significantly higher errors than earlier data. The majority of strandings in the U.S. NES LME comprise of loggerhead and Kemp's Ridley turtles followed by leatherbacks and greens. Although the year 2012 was the warmest on record for the U.S. NES LME, loggerhead and Kemp’s Ridley turtle cold stunnings in the north, particularly in Massachusetts waters, were the largest on record. These record-high cold stunnings in 2012 were likely due to the turtles remaining in northern waters longer than normal due to the extremely warm summer and fall but then were cold stunned during the fall-winter transitions on their way south. Therefore, the total stranding numbers in 2012 are likely much higher than reported in Figure 10.34.

10.5. Underwater Noise
chart showing modeled sound levels as a function of vessel traffic for different vessel types for sections of the Northeast U.S shelf. Figure 10.35

Sound is a critically important means of perception and communication for many marine animals. The role of vocalization in the social structure of marine mammals is now widely appreciated.  The more general role of hearing for other groups of species is becoming increasingly evident.  Underwater sound levels generated by different types of human activities, including shipping, sonar, oil and gas exploration, and offshore construction, are increasing and potentially interfering with the exchange of “acoustic” or sound-based information and in some instances directly harming marine life.

Some human activities produce short duration loud sources of noise. Such sources can be directly injurious to hearing or lead indirectly to harm by causing strong adversion reactions in marine animals. Such impacts and source types have been the historical focus of NOAA’s protective actions, working under the Marine Mammal Protection Act and the Endangered Species Act. Through permitting and consultation activity, NOAA works to limit the exposure of these species to sounds above specific threshold levels that can “harass” marine mammals.

Other human activities contribute noise relatively continuously at low frequencies that travel great distances, leading to chronically louder background noise conditions. Rising noise levels can negatively impact ocean animals and ecosystems in complex ways. Higher background noise levels can reduce the ability of animals to communicate with potential mates, other group members, their offspring, or feeding partners. Rising background noise can reduce an ocean animal's ability to hear environmental cues that are vital for survival, including those key to avoiding predators, finding food, and navigation among preferred habitats.Vessels (merchant shipping, ocean-going passenger vessels and mid-sized service, fishing and passenger vessels) are the dominant anthropogenic contributors to chronic low frequency noise levels in most ocean areas.   Marine shipping of course provides an extremely valuable service to society (see Section 9.1 Marine Transportation).  However it also potentially contributes to ecosystem stress related to noise pollution, oil and chemical spills, and ship strikes of marine animals.

NOAA has recognized the importance of augmenting the agency’s management of noise impacts to address chronic sources of background noise and the impacts of such sources on a wide range of marine animals and habitats. The first step taken by the agency was the establishment of the NOAA CetSound Program, which sought to document ambient underwater noise levels in relation to the distribution and abundance of cetaceans (whales, dolphins and porpoises) throughout U.S. managed waters including the Northeast U.S. Continental Shelf Large Marine Ecosystem (see   The program mapped the modeled distribution of underwater noise at different depths and frequencies attributable to large vessels, among other source types.  The modeled sound levels are a function of vessel traffic distributions and densities for different vessel types, each with distinctive sound characteristics.  An illustration of the resulting sound maps is provided in Figure 10.35 for sections of the Northeast U.S shelf at 5 m depth and 50 Hz.

These predicated maps can be ground-truthed with long-term measured sound levels, such as those gathered by NOAA in the Northeast ( They can then be integrated with maps showing the distribution of target species, such as fish, marine invertebrates and cetaceans that are known to produce sounds or be sensitive to sounds. Such maps can highlight places of high abundance, or places of important biological activity such as mating or spawning locations, or habitats that support vulnerable early life stages; this is especially critical when these important biological activities are known to involve the use of sound, such as the spawning sounds made by Atlantic cod or the sound-based detection of preferred settlement habitat by fish larvae or the songs made by breeding large whales. NOAA is using such mapping tools to identify where areas of high use or important use by sound-active species coincide with high chronic noise levels to assist the agency in focusing its science and management efforts ( Studies estimating a 70% loss, on average, of communication opportunities available to feeding and highly endangered North Atlantic right whales in the Northeast’s Stellwagen Bank National Marine Sanctuary ( showcase methods for quantifying chronic noise impacts and provide tools for evaluating accumulated consequences of such non-lethal impacts for wide-ranging populations, as well as integrating noise impacts with other human-contributed stressors.

10.6. Shifts in Fish Distribution

With a changing ocean climate on the Northeast US Continental Shelf, fish populations have responded with time varying shifts in distribution and regional productivity. Habitats characterized by a particular community structure may have lost key species or have new additions to the community, usually species associated with regions located to the south. Many species have shifted north or to higher latitude locations on the Northeast Shelf as a whole (Pinsky et al. 2013). Interestingly, we do see differences on a regional basis in the direction of movement.  In the Gulf of Maine, the movement is in a southwesterly direction rather than the northeasterly movement we observe for the coast as whole  (Kleisner et al., in review).  The magnitude and direction of distributional change as been linked to climate velocity.  However, other factors including fishing can play a role in shifts in distribution.

chart showing average along shelf position for a group of 48 species resident on the Northeast US Continental Shelf. Figure 10.36

Here, we use a rotated axis that roughly parallels the coastline and shelf-break to calculate movements for the coast as a whole. This gives an along coast distance (running from the southwest to northeast. Increased along-coast distance for a species is associated with a displacement in a northeasterly direction. In a composite index of along coast distance for a group of 48 of the more commonly encountered species on the Shelf as a whole, spring distribution of the fish community has shifted from a center around kilometer 850 to a new center well over kilometer 900 during the period 1968 -2014 (Figure 10.36). In the fall the shift has been more dramatic; the assemblage was centered on kilometer 775 at the beginning to the time series and has shifted to a position around kilometer 875.

chart showing average depth of capture for a group of 48 species resident on the Northeast US Continental Shelf. Figure 10.37

Where a majority of species have experienced a shift in the latitude or along coast distribution, there has been more of a balance between the number of specie that have shifted to deeper versus shallower depth distributions. For a species occurring in a habitat that has warmed, thermal refuge may be found in adjusting distribution to deeper depths where water temperatures tend to be cooler. The change in distribution may not be a solution for all species seeking to adjust their thermal regimes since fish habitat can be defined by a wide range of physical and biological parameters. A species may find a desired thermal regime at depth, but bottom substrates in that location may not be acceptable. The depth distribution during spring tended to remain relatively constant over much of the time series with exception of a trend to deeper depths in the last decade or so (Figure 10.37). Where over much of the time series the means depth distribution of these species was around 100m, in recent years the mean depth was greater than 110m. The fall depth distribution has been more variable over time, but the data also suggest a shift to deeper depths at the end of the time series.

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