Essential Fish Habitat for Nearshore Sentinel Species of Fishes and Crabs in Heavily Urbanized New York Harbor
Kenneth W. Able1,* and Thomas M. Grothues1
1Rutgers University Marine Field Station, 800 c/o 132 Great Bay Boulevard, Tuckerton, NJ 08087. *Corresponding author - able@marine.rutgers.edu.
Urban Naturalist, No. 16 (2018)
Abstract
Our objective was to evaluate nearshore fish and crab habitat use and quality in New York Harbor, a heavily urbanized area. We determined Essential Fish Habitat at several levels (abundance, reproduction, growth, survival, and habitat fidelity) for specific sentinel species of estuarine fishes (Fundulus heteroclitus [Mummichog], Fundulus majalis [Striped Killifish], Menidia menidia [Atlantic Silverside]) and Callinectes sapidus (Blue Crab). “Heavily altered” and “altered” shorelines at different sites typically had a steep slope and fabricated break on the upland side with very little or no vegetation; other “naturalized” shallow shorelines had gradually sloping mudflats or beaches with some intertidal and supratidal vegetation. Resident species (Mummichog, Striped Killifish) completed their life cycle along these shallow beaches and marsh shorelines, as evidenced by collections that included all size classes from newly hatched larvae to gravid adults. Mark–recapture efforts involving Mummichog demonstrated minimal dispersal, suggesting that all habitat needs were met in these limited shallow areas. The non-resident, but frequent users of these shorelines either migrated in to reproduce, grow, and survive (e.g., Atlantic Silverside) or grew from settlement from the plankton and survived to juveniles (e.g., Blue Crab). Given these findings, even small and potentially fractured restoration projects that seek to restore shallow, naturalized habitat with marsh features should be encouraged in this and other heavily urbanized estuaries.
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K.W. Able and T.M. Grothues
22001188 URBAN NATURALIST No. 16N:1o–. 2156
Essential Fish Habitat for Nearshore Sentinel Species of
Fishes and Crabs in Heavily Urbanized New York Harbor
Kenneth W. Able1,* and Thomas M. Grothues1
Abstract - Our objective was to evaluate nearshore fish and crab habitat use and quality
in New York Harbor, a heavily urbanized area. We determined Essential Fish Habitat at
several levels (abundance, reproduction, growth, survival, and habitat fidelity) for specific
sentinel species of estuarine fishes (Fundulus heteroclitus [Mummichog], Fundulus majalis
[Striped Killifish], Menidia menidia [Atlantic Silverside]) and Callinectes sapidus (Blue
Crab). “Heavily altered” and “altered” shorelines at different sites typically had a steep
slope and fabricated break on the upland side with very little or no vegetation; other “naturalized”
shallow shorelines had gradually sloping mudflats or beaches with some intertidal
and supratidal vegetation. Resident species (Mummichog, Striped Killifish) completed their
life cycle along these shallow beaches and marsh shorelines, as evidenced by collections
that included all size classes from newly hatched larvae to gravid adults. Mark–recapture
efforts involving Mummichog demonstrated minimal dispersal, suggesting that all habitat
needs were met in these limited shallow areas. The non-resident, but frequent users of these
shorelines either migrated in to reproduce, grow, and survive (e.g., Atlantic Silverside) or
grew from settlement from the plankton and survived to juveniles (e.g., Blue Crab). Given
these findings, even small and potentially fractured restoration projects that seek to restore
shallow, naturalized habitat with marsh features should be encouraged in this and other
heavily urbanized estuaries.
Introduction
Estuaries, and the fishes and crabs that live there, have been subjected to numerous
anthropogenic impacts (Rochette et al. 2010, Seitz et al. 2014, Whitfield and
Elliott 2002). Shallow areas (Blaber et al. 2000, Islam and Tanaka 2004) of estuaries,
in particular (Ruiz et al. 1993, Rypel et al. 2007, Vincent 2011), are habitats that
function as Essential Fish Habitat (defined as those waters and substrate necessary
for spawning, breeding, feeding, or growth to maturity [Baird 1999, Schmitten
1999]) for many species of economically and ecologically important fishes and
their prey (Able and Fahay 2010, Levin and Stunz 2005). Essential Fish Habitat is
typically applied to managed species, but has been applied to non-managed species
as well (Able 1999, Able and Hagan 2003, Able et al. 2008) including some sentinel
species (Weinstein et al. 2009). Its application has several levels of increasing
complexity including presence/absence (Level 1), abundance/density (Level 2),
reproduction, growth, and survival (Level 3), and production (Level 4) (Able 1999,
Weinstein et al. 2009). Thus, evaluation of Essential Fish Habitat across an array of
1Rutgers University Marine Field Station, 800 c/o 132 Great Bay Boulevard, Tuckerton, NJ
08087. *Corresponding author - able@marine.rutgers.edu.
Manuscript Editor: John Waldman
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highly altered to naturalized shorelines will provide a baseline for managing shallow
shorelines in urbanized estuaries.
Prior sampling efforts in the New York Harbor area (Festa 1975, Friedman
and Hamilton 1980) and elsewhere in the region, suggest that 2 year-round residents
(Fundulus heteroclitus (L.) [Mummichog] and Fundulus majalis (Walbaum)
[Striped Killifish]), and a seasonal resident (Menidia menidia (L.) [Atlantic Silverside])
fish, as well as Callinectes sapidus M.J. Rathbun (Blue Crab), are among the
most abundant and thus useful sentinel species (Able and Fahay 2010, Finley et
al. 2009, Teather et al. 2012). Mummichog is among the most numerous fish along
shallow, temperate estuarine systems of the US east coast. (Able and Fahay 2010).
Further, the value of these natural habitats is evident because this resident species
spawns, undergoes embryonic and larval development, feeds, and grows there. In
addition, the secondary production due to Mummichog in natural estuarine habitats
is among the highest measured for any fish species (Hagan et al. 2007, Meredith
and Lotrich 1979, Teo and Able 2003a). Most of this production results from the
high abundance and growth of the young-of-the-year; thus, they are of particular
importance. All life-history stages are also critical to trophic pathways because they
are important predators and prey (Able and Fahay 2010, Able et al. 2007, Griffin
and Valiela 2001, Nemerson and Able 2003).
Striped Killifish is a common inhabitant of high salinity, sandy intertidal areas
in natural, temperate estuaries from New Hampshire to Florida (Able and Fahay
2010). Adults of this species (Able and Fahay 1998) spawn on sandy intertidal areas
and deposit eggs as deep as 7.6–10.2 cm within the sediment (Newman 1909,
Sumner et al. 1913) on spring tides (Able and Fahay 1998). Larvae occur in intertidal
sand-bottomed pools (Able and Fahay 1998). Individuals of this species are
important as both predator and prey along sandy beaches (Able a nd Fahay 2010).
Another sentinel species, Atlantic Silverside, is among the most abundant forage
fish species in US temperate estuaries during the spring through fall, after which
individuals move offshore for the winter (Able and Fahay 2010, Griffin and Valiela
2001). The importance of this species as a food source for piscivores such as Morone
saxatilis (Walbaum) (Striped Bass), Cynoscion regalis Bloch and Schneider
(Weakfish), Pomatomus saltatrix (L.) (Bluefish), and other fishes is well documented
(Able and Fahay 2010). Spawning of Atlantic Silverside occurs between April
and July in the Mid-Atlantic (Middaugh et al. 1981) in the intertidal zone, where
fish lay demersal, adhesive eggs at high tide (Middaugh 1981). The eggs are laid
~1.2–2.4 m above mean low water to reduce exposure to aquatic predators (Middaugh
et al. 1981, Tewksbury and Conover 1987). Filamentous algae are the preferred
attachment substrate even in the presence of many other substrates (Conover
and Kynard 1984) such as rip-rap and bulkheads (Balouskus and Targett 2012).
Blue Crab is both abundant and widely distributed in the Hudson River estuary
and New York Harbor (Wilson and Able 1992). The recently hatched larvae are
carried away from estuaries onto the continental shelf (Epifanio and Garvine 2001)
where they continue to develop until they recruit back to the estuary as megalopae
and then settle to the bottom as small juveniles. The juveniles typically occupy a
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2018 No. 16
number of habitats along the estuarine salinity gradient where they feed and grow
through several molt stages until they attain adulthood and mate (Rakocinski and
McCall 2005 and literature cited therein).
Materials and Methods
Habitat characterization
We selected our study sites in Upper New York Harbor based on the availability
of accessible shorelines between Liberty State Park Marsh Cove and the Arthur
Kill (Table 1, Fig. 1). This portion of Upper New York Harbor has been heavily
altered over time by human activities (Fig. 2). The degree of alteration varied between
sites as a function of their differing history of commercial or recreational
use, maintenance or neglect, intentional restoration efforts, and exposure resulting
from differences in shape and bathymetry. All, however, were in close proximity to
each other in southeast-facing embayments. We examined these sites by land and
boat during several reconnaissance trips in 2013 to determine final site selection
and begin site characterization and sampling for the 8 sites examined in detail. We
classified these locations as heavily altered (i.e., steeply sloping shoreline of construction
rubble or boulders with no marsh, marsh pools, culverts/creek, or beach),
altered (i.e., shallower, sloping shoreline of varying amounts of rubble with small
amounts of marsh, no marsh pools, and varying amounts of culverts/creeks), and
naturalized (i.e., shared some characteristics of natural marsh such as fringing
marsh, marsh pools, creeks, and beaches) (Table 1).
We determined the details of each site using a variety of approaches. Shoreline
slope data was measured along transects using a Leica Viva CS15 unit on 15 December
2014. The length of transects varied between sites because of site-specific
variation in shoreline width. The number of transects increased with the diversity
and span of shoreline types at each site. Two transects were taken at Coast Guard
Embayment–North, Coast Guard Embayment–South, SIMS Recycling Embayment,
and Liberty State Park Marsh Cove; 4 transects were completed at Bayonne
Golf Club, Alexan CityView, and Army Corps of Engineers Embayment; and 3
transects were established at Embayment North of Global Marine. We recorded
elevation whenever a change in slope was present along transects perpendicular to
the beach. The number of such measurements varied from 13 total points at SIMS
Recycling Embayment to 81 total at Alexan CityView. We calculated the slope for
each transect along with the within-site mean slope and standard deviation.
We collected sediment samples at each site on 23 and 24 October 2014, at locations
where the sediment was exposed, to further characterize each site. We did not
include SIMS Recycling Embayment, the heavily altered site, in sediment sampling
because of the steeply sloping large boulders with little interstitial sediments. Number
and location of each sample varied somewhat among these sites. We used a 6.3-
cm diameter core to collect samples, each 4 cm deep. For each sample, we dried 100
grams of each core in an oven at 53 °C, recorded the mass again, and then sorted each
sample using a sediment shaker to determine the composition and sorting following
Folk (1954). We used sieve sizes of 2 mm to 0.0625 mm and weighed sorted grainUrban
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Table 1. Characteristics of sampling sites in Upper New York Harbor in New Jersey during 2013 and 2014. + indicates presence, 0 indicates absence. See
Figure 1 for locations. The degree of alteration (1 = heavily altered, 2 = altered, 3 = naturalized) are described in more detail in Materials and Methods.
Embayment Habitats
Shoreline type
width at Marsh Culvert/ Degree of
Embayment location/site head (m) pools creek Beach alteration Intertidal Supratidal
Liberty State Park Marsh 80 + + + 3 Narrow rip-rap and fringing Iva frutescens, Baccharis halimifolia
Cove Spartina alterniflora
Army Corps of Engineers 360 + + + 3 Broad with S. alterniflora, Phragmites, I. frutescens, B. halimifolia,
Embayment I. frutescens and pools in marsh peat P. australis
SIMS Recycling 49 0 0 0 1 Very narrow, steep with rubble Rubble boulders, no vegetation
Embayment boulders, no vegetation
Embayment North of 118 + + + 3 Broad, sandy beach with some S. Bulkhead
Global Marine alterniflora, pool, some rip-rap
Coast Guard Embayment 400 0 + + 2 Broad, sandy beach with some S. P. australis, I. frutescens, B.
(North) alterniflora halimifolia
Coast Guard Embayment 400 0 0 + 2 Steep beach with rubble, small P. australis, I. frutescens, B.
(South) patches of S. alterniflora halimifolia
Alexan CityView 240 0 + + 3 Broad, beach with rip-rap and Bulkhead
S. alterniflora, I. frutescens
Bayonne Golf Club 240 0 0 + 3 Rubble with S. alterniflora Golf course
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Figure 1. Study sites (closed circles) in New Jersey along the Upper New York Harbor. See
Table 1 for description of shoreline characteristics.
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Figure 2. Diagrammatic representation of two major habitat types over time (1900–1989)
in Upper New York Harbor shorelines (after Squires 1992). “Marshland” indicate areas of
emergent aquatic vegetation. “Madeland” indicate areas where marshlands and shallow
shorelines were filled with spoil disposal, railroad construction, industrial development,
and other sources as the result of human activity .
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size fractions to determine the percentage of sediment grain size components following
Wentworth (1922). Analysis of sorting was performed in the script SANDY_C
v.1.75 (Ruiz-Martinez et al. 2016) running in the MATLAB environment.
We sampled above-ground salt marsh vegetation, where it occurred, in September
at the peak of the growing season. At each sample position at each site, we
clipped all vegetation within 2 replicate 0.25-m quadrats, counted the live and dead
plant stems, measured the length of live stems, and dried all stems to a constant
weight (at 60 °C) prior to recording their mass.
We used a handheld YSI Professional Plus (Yellow Springs Instruments, Yellow
Springs OH) to collect water quality data (temperature, salinity, dissolved oxygen,
pH) on 12 occasions from a total of 16 sampling dates between 28 August 2013
and 14 July 2015. Salinity values were calculated from conductivity at temperature
and are unitless following UNESCO (1981).
Fish and crab distribution by habitat
Reconnaissance sampling began in fall 2013. We conducted regular seine
sampling to characterize the target fishes and crabs at each site from spring 2014
to summer 2015 (Table 2). Sampling events at each site were influenced by local
topography. Additionally, we conducted irregular sampling with dip nets where
shallow marsh pools and depressions occurred at Liberty State Park Marsh Cove,
Army Corps of Engineers Embayment, and the Embayment North of Global
Marine. SIMS Recycling Embayment site was not sampled by seine because this
heavily altered site consists of a steeply sloping shoreline of large boulders.
Mummichog tag and recapture
We used tag–recapture to determine residency and the possibility of dispersal
among and within sites for Mummichog, whose populations at the study sites are
intermediate forms between a northern and southern subspecies (Able and Felley
1986, Bell et al. 2014, Mugue and Weis 1995). Tag–recapture addressed the extent
of ranging among sites (space covered to meet demands of life including foraging,
refuge, and reproduction, all metrics of habitat quality).
The tagged (Alexan CityView = 36–101 mm, Army Corps of Engineers Embayment
= 36–100 mm) and recaptured fish at both of the study sites were representative
in size for large juveniles and adults of Mummichog. At Alexan CityView, we
tagged 396 Mummichog on 17 September 2013 and an additional 76 on 1 July of the
following year, after first checking for any that had been tagged previously. At the
Army Corps of Engineers Embayment, we tagged 319 Mummichog in September
2013 and another 401 on 2 June 2014, again first checking for and removing previously
tagged individuals.
We used coded wire tags (1.1 mm long x 0.28 mm diameter; Northwest Marine
Technology, Inc., Shaw Island, WA) to mark individuals >36 mm TL from both
gears. We tagged fish on the left side of the dorsal musculature with a handheld coded
wire tag injector (Northwest Marine Technology, Inc.) or an MKIV tag injector
(Northwest Marine Technology Inc.). Subsequently, tagged fish were then checked
for tag retention using a magnetic detector specific to the purpose (Wand Detector,
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Northwest Marine Technology Inc.), hereafter simply referred to as the “wand”
(Teo and Able 2003). After all the fish were tagged and measured (total length),
we released them in the same location in which they were caught. During the first
tagging session, coded wire tags were erroneously batch marked. Thus, they could
be identified to date but not individual. The error was discovered and rectified with
Table 2. Overall rank based on total abundance by site and month of sentinel fish species and Blue
Crabs in Upper New York Harbor seine sampling pooled across all dates during June, July, September,
and October 2014 and July 2015. Dashes indicate no seine sample s occurred.
Atlantic Striped Blue
Site Year Month Silverside Mummichog Killifish Crab
Liberty State Park Marsh Cove 2014 Jun - 5 - 3
Jul 805 210 128 32
Sep 1798 1 1 17
Oct 28 21 18 6
2015 Jul 1142 5671 2445 -
Army Corps of Engineers 2014 Jun - 95 6 9
Embayment Jul 1403 329 187 86
Sep 268 - 28 8
Oct 121 154 119 11
2015 Jul 806 1 2 -
SIMS Recycling Embayment - - - -
Embayment North of Global 2014 Jun - 36 - 24
Marine Jul 40 236 287 26
Sep 310 612 103 8
Oct 24 188 132 86
2015 Jul 406 116 358 -
Coast Guard Embayment (North) 2014 Jun 2 - 94 6
Jul 1170 28 97 68
Sep 225 - 30 1
Oct 559 15 106 8
2015 Jul 1465 100 69 -
Coast Guard Embayment (South) 2014 Jun - - - 27
Jul 54 15 3 34
Sep 31 169 - 17
Oct 7 124 - 66
2015 Jul 216 315 - -
Alexan CityView 2014 Jun - 1 - 44
Jul 4285 1972 916 105
Sep 448 348 65 52
Oct 51 291 122 11
2015 Jul 2119 817 453 -
Bayonne Golf Club 2014 Oct 916 5 23 -
2015 Jul 36 3 6 -
Overall number 18,735 11,878 5798 755
Overall rank 1 2 3 6
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individually marked tags for subsequent events. Calculation of recaptures did not
include fish that were too small to have been previously tagged.
Tagging and recapture with seines (15.2 m, 4.8-mm mesh) and wire mesh traps
(41 cm long by 22 cm diameter, 6-mm mesh) were focused at 2 different sites
(Alexan CityView, Army Corps of Engineers Embayment) near Bayonne, between
the Arthur Kill and Jersey City, NJ, but we attempted recaptures at all 8 regularly
sampled sites (Table 1, Fig. 1). Recapture sampling took place at Army Corps of
Engineers Embayment and Alexan CityView on 24 October 2013, 2 June 2014, 1
July 2014, 22 July 2014, 2 September 2014, 23 October 2014, and 13 July 2015. We
kept the fish from both seine and traps separated by location. Buckets of fish were
batch sampled with the wand and divided into aliquots if any tags were detected;
we then repeated the procedure with further aliquot reduction until all tagged fish
were isolated. We measured and recorded all of the tagged fish as well as a random
subset of 20 untagged fish. After all the samples were processed, all the untagged
fish were released in their capture location.
Reproduction, growth, and survival
Evidence for successful reproduction at each study site was based on the occurrence
of young-of-the-year (YOY) of the 3 sentinel fish species (Mummichog ≤ 40
mm TL, Striped Killifish ≤ 50 mm TL, Atlantic Silverside ≤ 70 mm TL; Able and
Fahay 2010) in seine, trap, and dip-net samples, all with meshes small enough to
capture YOY. This interpretation is based on composite length-frequencies across
all sites. Evidence for successful post-settlement recruitment of Blue Crab was
based on their occurrence in seine samples.
We based estimates of growth and size attained at the end of the year for fishes
and Blue Crabs on analysis in modal length frequencies (after Able and Fahay
2010) from seine collection at each site. Survival, on a sampling site specific basis,
was implied based on continued occurrence and growth of young-of-the-year fishes
and Blue Crabs during the spring through fall, and on the recapture of marked fish.
Results
Habitat characterization
The study sites in Upper New York Harbor were all impacted by human activity.
We characterized them as heavily altered (SIMS Recycling Embayment), altered
(Coast Guard Embayment [North and South]), and naturalized (Bayonne Golf
Club, Alexan CityView, Embayment North of Global Marine, Army Corps of Engineers
Embayment, and Liberty State Park Marsh Cove) (Table 1). These indices are
somewhat arbitrary because the shoreline varied even within the same site. Thus,
we quantitatively describe each site individually in this section. The heavily altered
shoreline of New York Harbor, such as at SIMS Recycling Embayment (mean
among-transect slope b = 0.57 ± 0.028), was steeply sloped. Other steep shorelines
were most evident at Coast Guard Embayment–South (b = 0.16 ± 0.018), Bayonne
Golf Club (b = 0.12 ± 0.057), Alexan CityView (b = 0.08 ± 0.026), Embayment
North of Global Marine (b = 0.06 ± 0.028), and Coast Guard Embayment–North
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(b = 0.05 ± 0.019). The least sloping shoreline in New York Harbor was at Liberty
State Park Marsh Cove, which had much less slope (b = 0.02 ± 0.003) and a flat,
fringing marsh.
Some of the sites had construction rubble or boulders exposed along the shoreline
and were impossible to core. Where sediment samples could be taken, they
were dominated by medium sand and were “very well sorted” with some differences
in skew and kurtosis (Fig. 3). In particular, the coarser sediments were poorly
represented at Bayone Golf Club, but better represented at Coast Guard Embayment–
North than at other sites. At SIMS Recycling Embayment, gravel and sand
could be seen between the boulders, but could not be sampled.
The dominant intertidal vegetation at all sites, except the SIMS Recycling
Embayment, which had no intertidal vegetation, was Spartina alterniflora Loisel
(Smooth Cordgrass; 67.1–100% of quadrats sampled; Table 1). At sites where
this intertidal species did occur, the growth was robust, with 22–144 live stems,
biomass of 132–604 g, and stem height of 7–118 cm per 0.25 m2 quadrat. Other,
species that were less abundant included Spartina patens (Aiton) Muhl (Saltmeadow
Cordgrass), Phragmites australis (Cav.) Trin. Ex Steud. (Common Reed), and
Salicornia spp. (saltworts). Supratidal vegetation included Baccharis halimifolia
L. (Eastern Baccharis), Iva frutescens L. (Jesuit’s Bark), and Schoenoplectus pungens
(Vahl) Palla (Common Threesquare).
The range of salinity, dissolved oxygen, and pH were relatively similar across
all sites. During regular sampling, salinity varied from 16 to 25 with a mean ±
standard deviation of 20.5 ± 2.9. Daytime dissolved oxygen rarely fell below stress
Figure 3. Sediment grain size distribution among sample sites in New Jersey along the
Upper New York Harbor at CGN (Coast Guard Embayment–North), CGS (Coast Guard
Embayment–South), LSP (Liberty State Park Marsh Cove), ACE (Army Corps of Engineers
Embayment), GTE (Embayment North of Global Marine), ALE (Alexan CityView), and
BGC (Bayonne Golf Club).
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levels and was often near or well above saturation, generally 4.45–16.0 mg/L and
averaging 8.2 ± 2.6 mg/L across all sites for all times, but with a single standout
minimum value of 3.2 mg/L at SIMS Recycling Embayment on 22 July 2014. pH
was variable across most sites with a mean of 7.8 ± 0.35, but varied from 7.0 to
8.8. The highest and lowest values occurred at Liberty State Park Marsh Cove.
Temperatures were far more variable across sites due to the seasonal insolation
cycle, with a mean of 22.0 ± 4.6 °C, a minimum of 11.8 °C in October 2013, and a
maximum of 28.7 °C in July 2014.
Fish and crab distribution and abundance
Atlantic Silverside, Mummichog, and Striped Killifish had similar overall ranking
in abundance in composite samples, representing over 36,000 individuals,
across all New York Harbor seine sampling sites (Table 2). The overall abundance
of Atlantic Silverside was greatest, followed by Mummichog with a similar order of
magnitude. Striped Killifish was one order of magnitude lower in abundance. Blue
Crab abundance was another order of magnitude less.
The species-specific abundance, when expressed as catch per unit effort (CPUE),
varied between and within alteration types based on seine collections during
Figure 4. Abundance of sentinel species collected with a seine and pooled across all sampling
dates at LSP (Liberty State Park Marsh Cove), ACE (Army Corps of Engineers Embayment),
GTE (Embayment North of Global Marine), CGN (Coast Guard Embayment–North),
CGS (Coast Guard Embayment–South), ALE (Alexan CityView), and BGC (Bayonne Golf
Club) during 2013–2015. The SIMS Recycling Embayment (a heavily altered site) was not
included because seine samples were not possible. Several outlier points were left off of the
figures to make overall spatial patterns more easily visible (Fundulus heteroclitus: 717/tow
at ACE and 2576 and 3095/tow at LSP; Fundulus majalis: 765 /tow at ALE, 1040 and 1099/
tow at LSP; Menidia menidia: 1911/tow at ACE).
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2013–2015 (Fig. 4). Mummichog was most abundant at some of the naturalized
sites (Alexan CityView, Embayment North of Global Marine, Liberty State Park
Marsh Cove) and 1 altered site (Coast Guard Embayment–South), whereas some
of the lowest values for that species occurred at 2 naturalized sites (Army Corps of
Engineers Embayment, Bayonne Golf Club). Striped Killifish were most abundant
at a naturalized site (Embayment North of Global Marine) and an altered site (Coast
Guard Embayment–North), but both types of sites had low values as well. Atlantic
Silverside were most abundant at naturalized sites (Liberty State Park Marsh Cove,
Alexan CityView) and an altered site (Coast Guard Embayment–North), but again
both types of sites also had low values. Blue Crab were most abundant at naturalized
sites (Embayment North of Global Marine, Alexan CityView) and at altered
sites (Coast Guard Embayment–North and Coast Guard Embayment–So uth).
Reproduction
Many aspects of the early life history of the sentinel species were consistent
across sites based on composite length-frequencies for each of the 4 species (Figs.
5, 6, 7, 8). Maturing adults (~40 – 80 mm TL) of Mummichog were evident in September
and October 2013, June and July 2014, and July 2015 (Fig. 5). Their larvae
and small juveniles (less than 20 mm) were detected in dip-net collections from shallow
marsh pools or depressions in July 2014 where they occurred at naturalized sites
(Alexan CityView, Embayment North of Global Marine, Army Corps of Engineers
Embayment, and Liberty State Park Marsh Cove) and an altered site (Coast Guard
Embayment–North). The larger (at ~10–40 mm TL) YOY were also evident in
seine collections in July 2014 and 2015, as well as age 1+ individuals (at >60–100
mm TL) in July 2014 and 2015. By September and October 2014, the length frequencies
were dominated by YOY at sizes of ~20–60 mm TL and ~30-70 mm TL,
respectively. The size of YOY individuals in October 2014 was similar to that from
October 2013.
Adult-sized Striped Killifish (most >40–100 mm TL) were collected in fall of
2013 and in all collections during 2014, as well as July 2015 (80–120 mm TL)
(Fig. 6). Based on the occurrence of YOY (10–60 mm TL) in July 2014 and 2015,
it appears this species was reproducing at many of the embayments during 2013–
2014 (Fig. 6). The lack of representative collections in other months at several sites
(Coast Guard Embayment–South, Embayment North of Global Marine, Liberty
State Park Marsh Cove) may be the result of reduced vulnerability to the sampling
gear due to burial in the substrate. The YOY were evident in July 2014 and 2015
(at ~15–45 mm TL) as well as a few adults at ~75–100 mm TL. By September and
October 2014, the length-frequencies were dominated by YOY and presumed 1+
age adults over the combined size range of 45–100 mm TL. The size of individuals
in September and October of 2014 overlap in size with those from the same months
in 2013 from Alexan CityView and Army Corps of Engineers Embayment.
Maturing adult Atlantic Silverside (~50–100 mm TL) were abundant in fall
2013, but few were found in June 2014 (Fig. 7). YOY were caught in July 2014
and 2015 (at ~30–60 mm TL) with perhaps some age 1+ individuals (>60 mm TL)
also present at most sites. By September and October of 2013 and 2014, the lengthUrban
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2018 No. 16
frequencies were dominated by presumed YOY at 40–100 mm TL. These sizes are
similar to those from September and October in 2013.
For Blue Crab, the recruitment of small YOY (less than 15 mm) occurred in September
of 2013 and June, September, and October of 2014 (Fig. 8). These smaller
Figure 5. Composite monthly length frequencies of Fundulus heteroclitus (Mummichog)
from seine and dip-net samples across all study sites during 2013–2015. Note differences
in y-axis scales.
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individuals were evident at most naturalized sites but not at the altered sites (Bayonne
Golf Club [infrequently sampled] and Coast Guard Embayment–North) and
the heavily altered site (SIMS Recycling Embayment).
Figure 6. Composite monthly length frequencies of Fundulus majalis (Striped Killifish)
from seine and dip-net samples across all study sites during 2013–2015. Note differences
in y-axis scales.
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Growth and survival
Estimates of growth, based on modal length-frequency progression, suggested
that it was similar across most sites and across years for each species as indicated by
the shared sizes in the above treatment (Figs. 5, 6, 7, 8). In addition, survival of all
Figure 7. Composite monthly length frequencies of Menidia menidia (Atlantic Silverside)
from seine samples across all study sites during 2013–2015. Note differences in y-axis scales.
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3 of the target fish species at most sites was supported by the continued occurrence
of increasingly larger individuals from July, when the YOY first become apparent,
Figure 8. Composite monthly length frequencies of Callinectes sapidus (Blue Crab) from
seine samples across all study sites during 2013–2015. Note dif ferences in y-axis scales.
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2018 No. 16
into the fall when sampling was discontinued (Figs. 5, 6, 7, 8). Survival of Blue
Crabs during 2014 was evident from the progression of sizes from June through
July at most sites with the exception of the Bayonne Golf Club and SIMS Recycling
Embayment (both infrequently sampled).
Movements/residency
There was no evidence of Mummichog movement from the 2 naturalized tagging
sites to other sampled locations. No tagged fish, either batch-marked or
individually marked were re-captured at any of the other re-sampled study sites,
although 4 of these are between the 2 tagging sites. Therefore, we assume there was
no dispersal beyond an individual embayment. In addition, recaptures within a tagging
site demonstrated site fidelity over time. Recaptures at Alexan CityView were
highest soon after tagging (4%) and lower later (0.3%), with no returns occurring
in the final sampling in fall 2014 and summer 2015.
At Army Corps of Engineers Embayment, recaptures were again highest (17.5%)
after initial tagging and later varied from 0.3% to 10%, with no recapturing in late
fall 2014 and summer 2015.
Discussion
The separate components of an Essential Fish Habitat evaluation examined in
this study—i.e., distribution and abundance, reproduction, growth, and survival—
implied that these structural and functional components were satisfied across all of
the selected sentinel species and across most of the shallow portions at the head of
these embayments. The clear exception was the heavily altered SIMS Recycling
Embayment site with its steeply sloping shorelines composed of large boulders and
the lack of shallow water. Of the indices measured, abundance was the most variable,
both between and within types of sites. This finding may be due, in part, to
the large within-site variation across many of the sites. A separate analysis, based
on the same sampling approaches at the same sites, but for the distribution and
abundance of the total fish and crab fauna, indicated that the shallow portion of the
embayments supported a fauna with many components intact (T.M. Grothues and
K.W. Able, unpubl. data). The patterns of reproduction for all 3 of the fish species
are consistent with other studies in New Jersey estuaries (Able 1990, Able and Fahay
2010). Growth, another important indicator, is an important measure of habitat
quality (Able 1990, Houde 1989). For example, continued growth throughout the
important summer season, when most growth occurs for Middle Atlantic Bight fishes,
including these sentinel species (Able and Fahay 1998), implies that continued
survival has occurred and makes survival during the overwinter period more likely
(Hales and Able 2001, Sogard 1997). Growth rates, based on size attained at the end
of the year, were similar in all study sites in New York Harbor in which the sentinel
species occurred. In most instances, sentinel fish growth during the summer and fall
allowed the target species to attain size for reproduction. As a result, fishes in the
general study area attained an adult size at these sites, an important criterion for the
shallow sites to be considered as nursery locations (Beck et al . 2003).
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The fidelity of Mummichog to the 2 tagging sites confirmed that these embayments
allow for populations to reproduce, grow, and survive. The small-scale site
fidelity observed in this study is typical for other populations of this species, but is the
first for such a highly urbanized estuary. In many prior studies in natural and restored
marsh creeks, there is almost complete fidelity to a single creek watershed (Able et al.
2006, 2012; Fritz et al. 1975; Hagan et al. 2007; Teo and Able 2003a, b). While Mummichog
occur in natural marshes primarily in creeks, as pointed out, they also occur
in pools (Able et al. 2005, Hunter et al. 2009, Smith and Able 1994), basins (Able and
Fahay 1998, Able et al. 2010), and occasionally along unvegetated shorelines (Able
et al. 1996, 2002; Ruiz et al. 1993). This flexibility in habitat use is consistent with the
observations for shallow waters in the heavily urbanized study site.
Since tagged fish were only recaptured at tagging sites, it can be concluded that
the embayments, which are separated generally by deep bulk-headed habitat, are
closed regarding population dynamics (i.e., vary independently in population size,
habitat use, growth, and reproduction). This finding does not suggest that they are
genetically isolated, since it takes very little exchange to spread genes. Rather, it
provides some confidence that metrics associated with a sample site are in fact
representative of that site and, in this case, supports that the sites from urbanized
Upper New York Harbor are capable of sustaining populations of these fish.
Essential fish habitat
This examination supports the concept that the limited shallow-water habitats in
most of the studied embayments in Upper New York Harbor provide Essential Fish
Habitat for many of the sentinel species that are the focus of this study (Table 3).
For Mummichog, many embayments, both naturalized and altered, provided critical
biological and ecological attributes necessary for growth and development. Most
studied embayments had juveniles and adults of sentinel fishes and juvenile Blue
Crabs present. Overall abundance varied between sites with many showing high
levels. The exceptions were a heavily altered site at SIMS Recycling Embayment
(which lacked shallow shorelines and associated habitats), Bayonne Golf Club
(which had limited habitat at the specific site we sampled), and Liberty State Park
Marsh Cove (which was difficult to sample at high tide where the fringing marsh
was flooded, making Mummichogs unavailable). There was a high degree of residency
for this species at the 2 naturalized sites (Army Corps of Engineers Embayment,
Alexan CityView) where tag/recapture experiments took place. Evidence of
reproduction occurred at all sites, except the heavily altered site at SIMS Recycling
Embayment. Evidence for YOY growth and survival occurred at all sites, except
at SIMS Recycling Embayment where this species did not occur or was rare. As a
result of these characteristics, functional attributes of Essential Fish Habitat for this
species were similar across most sites.
For Striped Killifish, the occurrence of life-history stages were generally consistent
with most sites having juveniles and adults, though with some exceptions at
those classified as heavily altered and altered. These patterns were similar for abundance,
with the occurrence of both juveniles and adults consistent with high overall
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Table 3. Response of shallow-water sentinel fish species to Essential Fish Habitat structural and functional components for multiple sites in New York
Harbor during 2013–2015. - indicates no assessment, ? indicates insufficient sampling to assess clearly, J = juveniles, A = adults. ++ = high, + = low, and
0 = absent or, in the case of survival, not measured. M = Mummichog, SK = Striped Killifish, AS = Atlantic Silverside, and BC = Blue Crab.
Structural attributes Functional attributes
Life-history
composition (J, A) Abundance Residency Reproduction Growth Survival
Site M SK AS BC M SK AS BC M M SK AS M SK AS BC M SK AS BC
Liberty State Park Marsh J, A J J, A J + + ++ + - + + + 0 ? + ++ 0 ? ++ ++
Cove
Army Corps of Engineers J, A J, A J, A J ++ ++ ++ ++ + + + + ++ ++ + ++ ++ ++ ++ ++
Embayment
SIMS Recycling J, A - - J + 0 0 + - 0 0 0 + 0 0 - 0 0 0 -
Embayment
Embayment North of J, A J, A J, A J ++ ++ + ++ - + + + ++ ++ ++ ++ ++ ++ + ++
Global Marine
Coast Guard Embayment J, A J, A J, A J ++ ++ ++ + - + + + +? ++ ++ + +? ++ ++ +
(North)
Coast Guard Embayment J, A J J, A J ++ + + ++ - + + + ++ ? ? ++ ++ ? ? ++
(South)
Alexan CityView J, A J, A J, A J ++ ++ ++ ++ + + + + ++ ++ ++ ++ ++ ++ ++ ++
Bayonne Golf Club J, A A J, A J + ? ++ + - + ? ? 0 ? ? - 0 ? ? -
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abundance. Some sites lacked evidence of Striped Killifish reproduction and had
low or unmeasured growth and survival. These embayments were likely inadequate
for this species because they lacked shallow water (SIMS Recycling Embayment)
or sandy or protected shorelines (Liberty State Park Marsh Cove, Coast Guard Embayment–
South, Bayonne Golf Club).
For Atlantic Silverside, many embayments provided habitat for abundant juveniles
and adults. The exceptions were the heavily altered site at SIMS Recycling
Embayment, where seine sampling could not occur because of the deeper water and
large boulders, and at the altered site at Coast Guard-South and the naturalized site
at Embayment North of Global Marine, where they were less abundant. Thus, with
these exceptions, the heads of many shallow embayments demonstrated the functional
attributes of Essential Fish Habitat for this species including reproduction,
growth, and survival.
For Blue Crab, many embayments provided habitat and thus critical structural
and functional attributes. Juveniles were present in all embayments, with very
high abundance, growth, and survival of juveniles at several naturalized sites
(Army Corps of Engineers Embayment, Embayment North of Global Marine, Alexan
CityView) and an altered site (Coast Guard Embayment–South), and lower
abundances at another naturalized site (Liberty State Park Marsh Cove). Thus,
shallow water is important to this species as well (Dittel et al. 1995).
The occurrence of a few other species, namely juvenile Limulus polyphemus (L.)
(Horseshoe Crab), Uca spp. (fiddler crabs), Geukensia demissa (Dilwyn) (Ribbed
Mussel), that are common or abundant in estuaries was also assessed based on
qualitative observations. All these species occurred at Liberty State Park Marsh
Cove and Army Corps of Engineers Embayment, whereas both Horseshoe Crab and
Ribbed Mussel occurred at Alexan CityView, and Horseshoe Crab and Uca spp.
occurred at Embayment North of Global Marine. Horseshoe Crab juveniles also
occurred at Coast Guard Embayment–North and Coast Guard Embayment–South.
The heavily altered site at SIMS Recycling Embayment did not have any of these
species due to steeply sloping, rocky edges with deeper water. The occurrence of
these species in an urbanized estuary provides the opportunity for further studies of
Essential Fish Habitat.
Given these findings, it seems clear that the limited shallow, upper portions of
embayments in New York Harbor provide Essential Fish Habitat for the sentinel
species studied here. In a sense, this finding is not surprising since all of these species
spend much of their time in shallow water throughout their life history or at
least as juveniles and, for some species, as eggs and larvae (Able and Fahay 2010).
As a result, these portions of a heavily urbanized estuary may still contribute as
nurseries (see also Courrat et al. 2009, Hajisamae and Chou 2003) although the degree
to which this happens is likely influenced by the reduced spatial availability of
shallow waters in heavily modified habitats, as in New York Harbor (Squires 1992).
Recommendations for restoring habitat value and increasing resilience
These findings indicate that any future restoration or naturalization of New York
Harbor ought to include the restoration or preservation of intertidal and shallow
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2018 No. 16
subtidal habitats. In order to conserve existing habitats, the edges of the harbor
should not be further bulkheaded or hardened. Any activity to fill in the shallow
waters, such as is taking place in the upper margin of the Army Corps of Engineers
Embayment by the Liberty National Golf Course, should be stopped. Where possible,
the margins of the embayments should mimic those of Alexan CityView and
the Bayonne Golf Club, which have extensive fringing salt marsh and shallow
subtidal areas. At these sites and elsewhere, it appears that creeks draining from
culverts, as at the head of Army Corps of Engineers Embayment and at Coast Guard
Embayment–North, may function similarly to marsh creeks based on the abundance
of Mummichog at these sites. Elsewhere, sandy beaches could be restored or created
to provide habitat for such species as Striped Killifish and Horseshoe Crab.
The creation of both of these types of habitats around the periphery of these artificial
embayments would provide additional habitats as well as habitat islands to
provide for the dispersal of these and other species such as Atlantic Silverside and
Blue Crab.
Acknowledgments
Numerous individuals assisted in all aspects of this study. Several RUMFS technicians
helped with sampling/tagging/recapturing including Jenna Rackovan, Thomas Malatesta,
Christine Denisevich, Stacy VanMorter, and Margaret Shaw. Others who assisted with the
initial tagging included Paola Lopez-Duarte and Roland Hagan. Ron D’Argentio provided
access to sites associated with marshes at the Bayonne Golf Club. Robert Rodriguez and
Frank Gallagher assisted with access and background information for the marsh at Liberty
State Park Marsh Cove. Stacy VanMorter and Carol Van Pelt provided organizational and
editorial assistance. Hudson River Foundation provided funding for this research program.
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