Habitat benefits of restored oyster reefs and aquaculture to fish and invertebrates in a coastal pond in Rhode Island, US

Abstract

Oyster habitat restoration seeks to recover lost ecosystem services including increased provisioning of refuge and foraging habitat for fish and invertebrate communities. The goal of this study was to quantify the ecosystem service benefit of habitat provisioning in Ninigret Pond, RI following oyster restoration. We measured four metrics, abundance, biomass, species richness and diversity, as well as isotopic composition in fish and invertebrates collected seasonally from restored oyster, aquaculture, and bare sediment sites, to examine whether the oyster habitat outperformed the bare sediment habitat. Sampling locations were chosen in Foster’s Cove north and south, Grassy Point, South Sanctuary, and an Aquaculture lease; each had two restored oyster sites and one bare sediment site. Each site was sampled using a box trap, seine net, shrimp trap, and minnow trap. Oyster habitats had significantly greater metrics than did bare sediment habitats in some comparisons from the box trap and seine net samples. Restored oyster sites at South Sanctuary had lower metric values than the other oyster sites. Metrics from the Aquaculture sites were comparable to the Foster’s Cove and Grassy Point restored oyster sites and often outperformed South Sanctuary restored oyster sites. Seasonally, spring and autumn samples tended to have higher abundance and biomass values than summer. Isotopic composition of five species occurring at both restored oyster and bare sediment sites demonstrated some differences in the trophic levels between species but not between habitat types. In Ninigret Pond, fish and invertebrate abundance, biomass, species richness, and diversity benefit from the use of oyster and bare sediment habitats. Coastal zone managers interested in restoring the ecological function of oyster reefs to support fish and invertebrate communities should consider strategically locating restoration projects within the mosaic of structured habitats and monitoring them for selected ecosystem services.

Introduction

During the past century, degradation of habitats and the ecosystem services they provide in coastal and marine environments has resulted from multiple stressors including nutrient pollution, over-exploitation of resources, invasive species, and climate change (Jackson et al. 2001, Millennium Ecosystem Assessment Report 2005, Duarte et al. 2020). In the extreme, these stressors, dubbed ‘ocean calamities’ by Duarte and colleagues (2015), are the result of human disturbances and mismanagement of the coastal and marine resources. Jackson et al. (2001) considered human exploitation of marine fisheries resources across temporal and spatial scales as the first disturbance to impact coastal ecosystem health.

Overfishing and subsequent collapse of oyster fisheries globally provides an example of the consequences of the degradation of an ecosystem (Beck et al. 2011, zu Ermgassen et al. 2012, Gillies et al. 2018, Pogoda et al. 2019). Beck et al. (2011) documents that an average of 85% of oyster reefs have been lost globally despite their historic dominance in estuarine systems and their ecological and economic importance, and subsequent regional assessments indicate even higher rates of loss. Therefore, over time, diminished oyster habitat has led to the loss of the ecosystem services they once provided in coastal waters (Coen et al. 2007, Grabowski & Peterson 2007).

As ecosystem engineers, the eastern oyster (Crassostrea virginica Gmelin, 1791) can create three-dimensional biogenic reefs that provide valuable non-extractive ecosystem services, independent of the socio-economic value of a commercial fishery. The creation of sustainable, preferred habitat for valuable fish and invertebrate production and enhanced biodiversity are key services which have driven much of the rationale for oyster reef restoration (Arve 1960, Breitburg 1999, Peterson et al. 2003, Humphries et al. 2011, Quan et al. 2012, see Table 4 therein, Pierson & Eggleston 2014, zu Ermgassen et al. 2016, see References therein). Additionally, oyster reefs are credited with providing erosion control through the stabilization of sediment and dissipation of wave energy (Meyer et al. 1997, Coen & Luckenback 2000, La Peyre et al. 2015) and water quality improvements, particularly nutrient removal and water clarity through filtration (Newell 2004, Grizzle et al. 2008, Piehler & Smyth 2011, Kellogg et al. 2013 and 2014, zu Ermgassen et al. 2013, Humphries et al. 2016).

Table 4.

Four-factor ANOVA for all species collected by seine net with location (SS, AQ, FC, GP), habitat type (oyster habitat vs. bare habitat), and season (SP, SU, AU) as fixed effects and site nested within the habitat type/location interaction term.

Seine Net		Interaction Terms				Overall Differences for Terms			Pairwise Differences
Taxa	Metric	Location × Habitat Type × Season	Location × Habitat Type	Location × Season	Habitat Type × Season	Location	Habitat Type	Season	Location	Habitat Type	Season
Crab	Density	-	-	-	-	-	F=6.127 p=0.043	-	-	O>B	-
	Biomass	-	-	-	-	F=9.761 p=0.007	-	F=9.424 p=0.003	GP,AQ>SS	-	SP,AU>SU
Fish	Density	-	-	-	-	F=5.712 p=0.027	-	-	GP>SS	-	-
	Biomass	-	-	F=3.125 p=0.037	-	-	-	-	AU:FC>SS; SU:GP>SS	-	GP:SU>AU
Mollusc	Density	-	-	F=3.549 p=0.024	-	-	-	-	SP:FC>GP, SS	-	FC:SP>SU,AU
	Biomass	-	-	-	-	F=7.01 p=0.016	-	F=7.172 p=0.007	FC>GP,SS	-	SP>SU,AU
Shrimp	Density	-	-	-	F=4.256 p=0.036	F=5.367 p=0.031	-	-	FC>SS	AU:O>B	B:SP>SU; O:AU,SP>SU
	Biomass	-	-	-	-	F=7.991 p=0.012	F=11.840 p=0.011	F=24.011 p<0.001	AQ,FC>SS	O>B	SP,AU>SU

All data were normal-score transformed prior to analyses.

Significance reported at p<0.05.

^**Not all habitat type/location/seasons were sampled so pairwise comparisons could not be fully assessed when significant interactions occurred.

Nonsignificant relationships and overall comparisons that are not applicable due to significant interactions denoted by −.

Attributes of oyster reefs have been compared to those of seagrass and saltmarsh habitats for functional equivalence to provide foraging and shelter habitat for nekton and invertebrates, and have value as habitat for secondary production of fish and invertebrates (Heck et al. 2003, Minello et al. 2003, Peterson et al. 2003, zu Ermgassen et al. 2016). Breitburg (1999) contends that oyster reef is an essential habitat for resident fish and crab population in the Chesapeake Bay. Glancy et al. (2003) determined that along the central coast of Florida, decapod assemblages associated with oyster reefs were distinct from seagrass and salt marsh decapod assemblages. Conversely, transient fish species presence along a gradient from oyster reef to sand bottom demonstrated no definitive pattern of habitat utilization in Virginia (Harding & Mann 2001). Heck et al. (2003) meta-analysis of studies which compared seagrass meadows to other habitat types as nursery habitat for nekton indicated that seagrass meadows met predictions that growth, abundance and survival of fishes were greater in vegetated habitat than in unstructured habitats. When seagrass meadows were compared to oyster reefs, however, there were few significant differences between these habitats. In contrast, meta-analysis of salt marsh studies conducted by Minello et al. (2003) concluded that fish and crustacean density ranked poorly at oyster reefs compared to seagrass, vegetated and non-vegetated marsh edge, open water, and macroalgae habitats. Other studies have shown that restored oyster reef positioned near other biogenic habitats (seagrass and saltmarsh) did not increase production of small resident fish species (Grabowski et al. 2005, Geraldi et al. 2009, Pfirrmann & Seitz 2019). Substantial differences in fish and invertebrate growth and diversity have been recorded when restored oyster reef is compared to bare sediment habitat (Tolley & Volety 2005, Gregalis et al. 2009, Humphries et al. 2011, Quan et al. 2012, Pierson & Eggleston 2014).

In the state of Rhode Island oyster stocks are greatly depleted due to the combined influences of disease, environmental conditions, a lack of recruits, and fishing pressure (Oviatt et al. 1998). Both aquaculture and restoration have increased in recent years. Between 2010 and 2018 the number of farm leases increased from 38 to 76, and there was a three-fold increase in the harvest value from $2.1 mil to $6.1 mil (R. Rheault pers. comm. January 2020). Between 2000 and 2015 restoration of oyster habitat in Rhode Island has seeded 6.6 acres representing 26 million oysters (Griffin 2016), although less than 1 acre has been seeded since 2015. Mortality generally outpaces recruitment in RI waters, which has contributed to declines in populations despite restoration actions.

There is limited information on the influence of restored oyster reefs and oyster aquaculture on the fish and invertebrate populations in RI coastal ponds. This represents challenges to future decision-making regarding oyster aquaculture and oyster restoration and conservation projects. Understanding the value of these oyster habitats to fishes and invertebrates can better inform the planning and implementation of restoration projects. The current research aims to assess the contributions of four habitat types; restored oyster reef, an aquaculture lease, and associated bare sediment sites, to fish and invertebrate abundance, biomass, and diversity in Ninigret Pond, Rhode Island. The study also aimed to examine the isotopic signature of fish and invertebrate fauna to comment on trophic structure in the pond.

Methods

Locations and Sites

Ninigret Pond (41.3° N, −71.6° W) is a shallow lagoonal systems along the southern coast of RI, US (Figure 1). The 2356 ha pond has an average depth of 1.2 m (Stolgitis et al. 1976, Lee 1980) and a water residence time of approximately 10 days (Hougham & Moran 2007). Historically, Ninigret Pond supported thriving oyster reefs, but these have declined to functional extinction since the 1960s (Lee 1980). Restoration of Ninigret Pond oyster habitat to regain key ecosystem services has involved collaborative efforts between multiple federal and state agencies, non-governmental organizations and shellfish aquaculturists. Griffin (2016) has detailed the initiation and monitoring of these restored reefs. The footprint of the restored oyster reef from this effort is approximately 0.0266 ha or 0.001% of the total area in Ninigret Pond.

Figure 1.

Map of sampling design in Ninigret Pond, RI. Four locations were sampled, Aquaculture (3sites), South Sanctuary (3 sites), Foster’s Cove (6 sites) and Grassy Point (3 sites). Restored reef habitat= * and bare sediment habitat= •.

Between 2010 and 2012, Rhode Island The Nature Conservancy (RI TNC) and collaborators constructed oyster reefs in several locations in the pond. In 2014 the US Environmental Protection Agency (US EPA) and the RI TNC formed a partnership to study five locations comprising 15 sites. The sampling methodology, sampling protocol, and monitoring were designed and implemented collaboratively. The US EPA study locations were the oyster restoration reefs constructed within a RI Department of Environmental Management (DEM) Spawner Sanctuary (SS), and an oyster aquaculture lease (AQ). Oyster reefs at SS averaging 20–38 m² were created as oyster spat on shell set on top of a 15–20 cm layer of surf clam and oyster shell cultch creating a complex and three-dimensional reef structure on an unstructured sandy bottom. Two restored reef sites (SS1 and SS2) and one bare sediment site (SSB) each measuring approximately 6 m by 5 m and each separated by 50 m were sampled. The average density of live oysters on these reef sites was 54 m⁻² (SD ± 15). The AQ site used rack and bag grow out gear and was designed as 15 m long PVC racks situated about 0.40 m above the sediment with plastic mesh bags (75 cm × 40 cm) attached. The density of oysters and their size varied throughout the season as the oysters obtained legal size and were harvested. Generally, there were a minimum of 200 oysters per mesh bag. Two aquaculture sites (AQ1 and AQ2) approximately 6 m × 5 m were situated among the aquaculture rack and bag gear on unstructured sediment. A bare sediment site (AQB) of the same dimensions was established in an area without aquaculture gear, within the leased area. Sites were approximately 50 m from one another.

The RI TNC locations were restored oyster reefs at Foster’s Cove north (FCN), Foster’s Cove south (FCS), and Grassy Point (GP). Each reef was constructed in subtidal areas as 3 m wide by 9 m length plots parallel to shore using a 50:50 mixture of surf clam and cured oyster shell enhanced with oyster castles, (four sided stackable blocks measuring 30 cm by 30 cm by 20 cm made of crushed oyster shell and cement) designed to provide preferential larval settlement substrate. Four restored oyster sites (FCN1, FCN2, and FCS3, FCS4) paired with two bare sediment (FCNB and FCSB, respectively) were sampled. At GP two restored oyster sites (GP1 and GP2) and one bare sediment (GPB) were sampled. Sites were separated by approximately 50 m.

Environmental variables

Water temperature (°C), salinity (PSU), and dissolved oxygen (DO, mg l⁻¹) were measured during each collection period at each site with a Hach probe (HQD portable meter with 4-pole conductivity probe and luminescent dissolved oxygen probe). At SS and AQ sites, sediment grain size, sediment chlorophyll a (chl a) and molar carbon:nitrogen (C:N) ratios were measured. Sediment grain size was determined from each site using a Malvern Hydro 2000S/Mastersizer 2000 System. Duplicate sediment cores were collected each month to measure sediment chl a and C:N ratios. Sediment chl a sample were analyzed on a Turner Model AU-10 Digital Fluorometer with Optical Kit P/N 10–040R (Arar & Collins 1997). The C:N sediment samples were processed on a ThermoFinnigan Flash EA 112 (Katz et al. 2013). All samples were processed and analyzed at the US EPA laboratory in Narragansett, RI.

Fish and invertebrate collections

Fish and invertebrates were sampled with four gear types monthly from May through October 2014 at each of the 15 shallow, subtidal sites. May and June constituted spring samples, July and August were the summer samples, and September and October were the autumn samples.

A box trap, seine net, minnow trap, and shrimp trap were used to provide estimates of fish and invertebrate abundance, biomass and diversity (Kushlan 1981, Rozas & Minello 1997, Grabowski et al. 2005). Our box trap (60 cm × 60 cm) was haphazardly set at each of the sites. A fine mesh scoop net, which fit the inside dimensions of the trap, removed fish and macroinvertebrates. Collections were considered complete after five empty scoops of the net. The seine net (6 m long × 1.2 m tall with 0.6 cm mesh) was hauled approximately 20 m around the perimeter of each restored reef and associated bare habitat, and between the rack and bag aquaculture grow out gear, and an equivalent distance on the bare habitat within the aquaculture lease area. All attempts were made to sample during the incoming tide. The areas sampled by the box trap and seine net were used in the calculation of density (individuals m⁻²) and biomass m⁻² (g wet weight m⁻²).

One unbaited minnow trap (44.5 cm long by 24.5 cm diameter with a 5.0 mm mesh and a 2.5 cm opening on each side) and one unbaited shrimp trap (25.4 cm wide by 25.4 cm wide by 43.2 cm long with a 3.2 mm mesh and a 5.1 cm opening on each side) were deployed monthly for 24 hours to determine the abundance (number of individuals) and biomass (g wet weight ) of fish and invertebrate species at each site. Transient fish species were sampled with a 10 m monofilament gill net. However, during the spring 2014 this proved unsuccessful as the nets caught only large blue crabs, Callinectes sapidus (Rathbun, 1896) which became entangled, destroying the mesh of the gill nets, subsequently this gear was discontinued. As each gear type has a different fishing efficiency (Rotherham & Gray 2005), all statistical comparisons were conducted separately by gear type.

Samples were stored on ice and returned to the laboratory where they were kept frozen until processing. Fish and invertebrates were identified to species level whenever possible. Within a sample all individuals of a species were weighed (nearest 0.1 g wet weight) to obtain biomass and enumerated. Oysters were counted and returned to the site. Each season five oysters from SS were returned to the laboratory for C:N ratio analysis of the tissue and shell.

At SS and AQ sites, two replicate infauna cores (6.5 cm D by 14 cm H) were collected haphazardly within each box trap to a depth of 10 cm after the box trap had been cleared of macrofauna (N = 12 samples/month × 6 months - May through October). The sample material was washed over a 250 μm mesh sieve in the laboratory. Organisms retained on the screen were frozen at −18° C before processing. After thawing the organisms were sorted and identified to the lowest practical taxonomic level under a stereomicroscope (magnification range 10X-60X), enumerated, and weighed at the lowest taxonomical level (to the nearest 0.1 g) (Pollock 1998, Patricio et al. 2009).

Stable Isotope Analysis

Post identification fish and invertebrates from SS and AQ collections were washed in deionized water, placed in aluminum trays and dried in an oven at 60°C for at least 24 hours to obtain dry weight (nearest 0.1 g). Individual bivalves, crabs, and gastropods over 10 mm in total length were removed from their shells prior to drying. After drying each organism was ground to a fine powder with a mortar and pestle. Shells were dried and pulverized in a SPEX Sample Prep Shatterbox 8530. Approximately 4–5 mg of tissue and shell from each species in a sample was weighed for analysis. Carbon and nitrogen isotope analysis were conducted on an elemental analyzer (Carlo Erba NA1500) coupled to an isotope ratio mass spectrometer (Finnigan MAT 252) via a continuous flow interface at the Northern Arizona University’s Colorado Plateau Stable Isotope Laboratory. Isotopic composition was expressed in standard delta notation (δ) as parts per thousand (‰) difference between the sample and the reference material as: δ¹⁵N or δ¹³C sample = [(R_sample− R_standard)/(R_standard) − 1] × 1000, where R= (¹⁵N/¹⁴R) or (¹³C/¹²C). Reproducibility between instrument replicates was typically <0.2‰, and certified standard reference material from National Institute of Standards and Technologies was analyzed routinely for quality assurance of the instrument.

Statistical methods

Statistical comparisons of the metrics of density (number of individuals m⁻²; box trap and seine net) or abundance (number of individuals; minnow trap and shrimp trap), biomass m⁻² (wet weight m⁻²; box trap and seine net) or biomass (wet weight; minnow trap and shrimp trap), Simpson’s diversity index (D) and species richness between fauna collected at oyster sites (restored oyster or aquaculture) and bare sediment sites were performed using General Linear Models (GLMs), using SAS Version 9.4 (2013). Oysters were removed from all analyses. Prior to fitting the models, the results for the four metrics were standardized using the normal scores transformation, to meet assumptions of normality and homoscedasticity. Comparisons used metrics summarized across all individual species and summarized across specific taxa by gear type. For these analyses, the taxa used were crabs, non-crab crustaceans, fish, molluscs, polychaetes, and shrimp. Comparisons were statistically significant at the p<0.05 level. For all GLMs, tests of significance were designed to account for the mix of fixed and random effects and of potential pseudoreplication by using the appropriate nested term (for habitat type and location main effects and their interaction) or site-by-season interaction (for the season main effect and all interaction terms including season) rather than the model MSE as the denominator of the F-ratio and pairwise comparison significance tests.

Comparisons of each metric were performed using a single model for each gear type that included four factors: location (AQ, SS, FC, [FCN and FCS were combined], and GP), site within a location (an individual sampling site e.g. SS1, AQ2, FCNB, GP2), habitat type (oyster [reef or aquaculture] vs. bare), and season (spring, summer, autumn). Site was considered as a nested factor within the habitat type × location interaction term. All interaction terms involving the habitat type, location, and season terms were evaluated. The inadequate number of monthly samples collected with box trap gear from FC and GP meant the pairwise comparisons of site differences were specific to AQ versus SS only.

When there were significant interactions, pairwise comparisons were made using Bonferroni correction for the individual comparisons of combinations of the two interacting variables (e.g., if season and location interacted significantly, the seasonal comparisons are performed separately for each location, and location comparisons were performed separately for each season). If there were no interactions, pairwise comparisons were performed to identify specific location or season differences using the Tukey-Kramer method.

Results

Environmental variables

Water temperatures in Ninigret Pond during 2014 ranged from 15–23°C in spring, 21–25°C in the summer and 10–20°C in the fall. Salinity ranged between 18–32, with most values between 24–27. Dissolved oxygen varied between 4.7 mg l⁻¹ (55.7% saturation) and 10.6 mg l⁻¹ (116.2% saturation). Average seasonal values of physical and chemical variables from AQ and SS, demonstrated relatively consistent sediment grain size values, with AQ1 and AQ2 having a lower average percentage of sand and greater percentage of silt than SS sites. Similarly, average sediment molar C:N ratios varied little between sites. Average sediment chl a values ranged from a 2.6 ug g⁻¹ (SD ± 2.4) at SSB to 12.58 ug g-¹ (SD ± 6.28) at AQ1 and AQ2 (Table 1).

Table 1.

Average values (± SD) of physical-chemical variables of grain size, sediment chlorophyll a, and sediment molar C:N ratio recorded from the top 0–1 cm of sediment from the Aquaculture and South Sanctuary sites in Ninigret Pond in 2014.

		Grain Size							Sediment chlorophyll a (μg g-1)			Sediment C:N, molar mass
			% Clay		% Silt		% Sand
Location	Treatment	n	Ave	± SD	Ave	± SD	Ave	± SD	n	Ave	± SD	n	Ave	± SD
Aquaculture	AQ Bare	2	0		0.05		99.95		9	4.87	2.43	6	12.37	0.64
	AQ 1 and 2	4	0.02	0.02	5.55	1.03	94.44	1.04	18	12.58	6.28	12	10.45	1.31
South Sanctuary	SS Bare	2	0		0		100		9	2.6	0.83	6	12.24	1.73
	SS 1 and 2	4	0		0.26	0.52	99.74	0.52	18	3.87	2.4	12	14.59	1.87

Fish and invertebrate collections

There were 30,392 individual fish and invertebrates with a total biomass of 19.24 kg collected from all 15 sites from May through October 2014 using the four gear types (Appendices 1–4). Dominant fauna were distributed between Bivalvia, Crustacea, Gastropoda, Osteichthyes, and Polychaeta.

Box Trap Collections

Fish and invertebrates from 37 samples at 14 sites (FC4 not sampled) were collected monthly between May and October (except September) and produced a density of 40,023.2 individuals m⁻² with a biomass of 18.83 kg m⁻² from 96 species. Oysters were collected occasionally in the process of scoop netting. They accounted for <1% of the total density but 87.2% of the total biomass m⁻². Amphipods accounted for 71.5% and P. pugio accounted for 7.7% of the total density; however, ubiquitous and abundant, P. pugio contributed only 2.7% to the biomass m⁻². The mud crab, Panopeus herbstii (Milne-Edwards, 1834), was collected at nearly all sites (2.8% of the biomass m⁻²) with higher abundances in oyster habitat. Amphipod and finfish species were abundant at AQ1 and AQ2. Many small invertebrate specimens were collected as a result of the fine mesh scoop scraping the top layer of sediment (Appendix 1a and 1b).

Four-way ANOVA (Table 2) of box trap biomass m⁻² for all species produced statistically significant location by habitat type (F_(3,6)=6.220; p<0.05) and location by season (F_(4,5)=9.411; p<0.05) interactions, indicating that differences between oyster and bare habitat sites, and seasonal differences, were location-specific. A statistically significant interaction (Table 3) between location and season was observed when evaluating the crab biomass (F_(4,5)=7.935; p<0.05), and a significant interaction between location and habitat type was observed for mollusc biomass (F_(3,5)=6.567; p<0.05). Despite the interaction, significant pairwise differences between oyster and bare habitat sites were observed for mollusc biomass at both SS and AQ (in both cases oyster habitat was greater than bare habitat, but with the magnitude of the difference more pronounced at SS than for AQ). Significant differences were observed only for the shrimp biomass (F_(1,5)=12.507; p<0.05), with oyster habitat greater than bare habitat. An overall significant difference between locations was observed for fish biomass (F_(3,6)=5.634; p<0.05) with AQ greater than SS and GP. Significant seasonal differences were observed for only polychaete taxa biomass with autumn greater than summer (F_(2,4)=15.209; p<0.05).

Table 2.

Four-factor ANOVA for all species collected by gear types with location (SS, AQ, FC, GP), habitat type (oyster (O) vs. bare (B)), and season (SP, SU, AU) as fixed effects and site nested within the habitat type/location interaction term.

		Interaction Terms				Overall Differences for Terms			Pairwise Differences
Gear	Metric	Location × Habitat Type × Season	Location × Habitat Type	Location × Season	Habitat Type × Season	Location	Habitat Type	Season	Location	Habitat Type	Season
Box Trap**	Density	-	-	-	F=13.041 p=0.010	-	-	-	None found	Could not be evaluated	None found
	Biomass	-	F=6.220 p=0.029	F=9.411 p=0.015	-	-	-	-	None found	AQ:O>B SS:O>B	AQ:SU>SP
	Richness	-	-	-	-	-	-	-	-	-	-
	Diversity (H)	-	F=10.687 p=0.013	-	-	-	-	F=12.879 p=0.011	None found	SS:O>B	None found
Seine Net	Density	-	-	-	-	F=8.739 p=0.009	F=12.944 p=0.009	F=14.661 p<0.05	SS<all others	O>B	SP,AU>SU
	Biomass	-	-	-	-	F=8.798 p=0.009	-	F=3.859 p=0.046	SS<all others	-	SP,AU>SU
	Richness	-	-	-	-	F=6.698 p=0.018	-	F=18.795 p<0.001	SS<all others	-	SP,AU>SU
	Diversity (H)	-	-	-	-	F=16.116 p=0.002	-	F=5.765 p=0.015	SS<all others	-	SP,SU>AU
Minnow Trap	Abundance	-	-	-	-	-	-	F=6.688 p=0.009	-	-	AU>SP,SU
	Biomass	-	-	-	-	-	-	-	-	-	-
	Richness	-	-	-	-	-	-	-	-	-	-
	Diversity (H)	-	-	F=5.220 p=0.006	-	-	-	-	AU:AQ>SS; SP:GP>AQ; SU:AQ>FC,SS*	-	AQ:AU,SU>SP; FC:AU>SU*
Shrimp Trap	Abundance	-	-	-	-	-	-	-	-	-	-
	Biomass	-	-	-	-	-	-	-	-	-	-
	Richness	-	-	-	-	-	-	-	-	-	-
	Diversity (H)	-	-	-	-	-	-	-	-	-	-

All data were normal-score transformed prior to analyses.

Statistical significance reported at p<0.05.

^*FC-spring could not be evaluated for MT Diversity.

^**Not all habitat type/location/seasons were sampled so pairwise comparisons could not be fully assessed when significant interactions occurred.

FC and GP sites could not be included in site comparisons due to insufficient sample size.

Nonsignificant relationships and overall comparisons that are not applicable due to significant interactions denoted by −.

Table 3.

Four-factor ANOVA for major taxa collected by box trap with location (SS, AQ, FC, GP), habitat type (oyster (O) vs. bare (B)), and season (SP, SU, AU) as fixed effects and site nested within the habitat type/location interaction term.

Box Trap		Interaction Terms				Overall Differences for Terms			Pairwise Differences
Taxa	Metric	Location × Habitat Type × Season	Location × Habitat Type	Location × Season	Habitat Type × Season	Location	Habitat Type	Season	Location **	Habitat Type**	Season**
Crab	Density	-	-	F=8.256 p=0.033	-	-	F=8.216 p=0.029	-	SU: SS>AQ;	O>B	None found
	Biomass	-	-	F=7.935 p=0.022	-	-	-	-	None found	-	None found
Fish	Density	-	-	-	-	-	-	-	-	-	-
	Biomass	-	-	-	-	F=5.634 p=0.035	-	-	AQ>SS,GP	-	-
Mollusc	Density	-	-	-	-	-	-	-	-	-	-
	Biomass	-	F=6.567 p=0.035	-	-	-	-	-	None found	AQ: O>B; SS: O>B	-
Shrimp	Density	-	-	F=8.941 p=0.028	-	-	F=16.904 p=0.006	-	None found	O>B	AQ: SU>SP;
	Biomass	-	-	-	-	-	F=12.507 p=0.017	-	-	O>B	-
Crustacean	Density	-	-	-	-	-	-	-	-	-	-
	Biomass	-	-	-	-	-	-	-	-	-	-
Polychaete	Density	F=11.363 p=0.019	-	-	-	-	-	-	None found	None found	None found
	Biomass	-	-	-	-	-	-	F=15.209 p=0.014	-	-	AU>SU

All data were normal-score transformed prior to analyses.

Significance reported at p<0.05.

^**Not all habitat type/location/seasons were sampled so pairwise comparisons could not be fully assessed when significant interactions occurred.

FC and GP sites could not be included in site comparisons due to insufficient sample size.

Nonsignificant relationships and overall comparisons that are not applicable due to significant interactions denoted by −.

Box trap density data (Table 2) demonstrated a statistically significant habitat type by season (F_(2,5)=13.041; p<0.05) interaction. While pairwise comparisons of habitat type by season-specific means of densities could not be evaluated directly, due to the imbalance in the study design, results tended to be much higher for oyster habitat than bare habitat sites during the spring, but showed little difference, (or in some cases greater bare habitat means), during the other seasons. Significant differences between oyster and bare habitat sites were observed for crab density (F_(1,6)=8.216; p<0.05) and shrimp density (F_(1,6)=16.904; p<0.05), with oyster habitat sites yielding significantly higher densities for both taxa (Table 3). Significant interactions between location and season also were observed for these same taxa (F_(4,4)=8.256; p<0.05 and F_(4,4)=8.941; p<0.05, for crab and shrimp, respectively); densities were significantly higher at SS during the summer only for crab, while no individual significant pairwise location differences could be found for shrimp. Shrimp, however, did exhibit a seasonal difference at AQ, with summer densities significantly exceeding the spring densities. No location or seasonal effects were observed for any other taxa. Polychaetes had a three-factor interaction between habitat type, location, and season (F_(4,4)=11.363; p<0.05). Due to the complexity of the interactions, the interrelationship among these three variables was difficult to discern; however, it appeared that polychaete densities from bare sediment tended to be higher than those of the corresponding oyster habitat. The exception was for the SS oyster habitat sites during the spring and summer, which yielded higher polychaete densities than its associated bare sediment site.

The species richness metric (Table 2) showed no statistically significant relationships, while the diversity metric had a significant location by habitat type (F_(3,5)=10.687; p<0.05) interaction with oyster habitat greater than bare habitat at SS. There was a difference in diversity between seasons (F_(2,5)=12.879; p<0.05). No statistically significant pairwise differences were observed between seasons; however, diversity tended to be higher during the spring than for the other seasons.

Seine Net Collections

Twenty-nine species were identified from 74 seine net hauls at all sites totaling 98.30 individuals m⁻² with a biomass of 51.63 g m⁻². Twenty-one finfish species were collected with 11 of these species limited to one location. There were representatives of pelagic (e.g., bluefish, Pomatomus saltatrix (Linnaeus, 1766), and M. menidia), benthic (e.g., winter flounder, Pseudopleuronectes americanus (Walbaum, 1792), and oyster toadfish, Opsanus tau (Linnaeus, 1766)) and opportunistic (e.g., trevally jack, Caranx hippos (Linnaeus, 1766)) finfish life histories. The shrimp, P. pugio contributed the greatest density (74.78 individuals m⁻²) and biomass m⁻² (17.07 g m⁻²) to the collection. Finfish contributed 15.37 g m⁻² and the four species of crab 14.73 g m⁻² to the total biomass (Appendix 2a and 2b).

Seine net biomass data (Table 2) did not exhibit any statistically significant interactions between habitat type, location, or season when evaluated across all species. Taxa-specific evaluations resulted in a statistically significant location by season interaction for fish biomass (F_(6,14) =3.125; p<0.05) with SS lower than FC in autumn, and SS lower than GP in the summer (Table 4). No overall habitat type effect was observed when evaluating across all species, and only shrimp exhibited a significant difference (F_(1,7)=11.840, p<0.05) with oyster habitats having a significantly greater biomass than bare habitat (Table 4). Location differences yielded statistically significant lower biomass of all species at SS than all other locations (F_(3,7)=8.798, p<0.05) (Table 2). South Sanctuary also yielded lower biomass by location for most of the individual taxa (Table 4). Biomass was significantly lower at SS than GP and AQ for crabs (F_(3,7)=9.761), GP and SS were significantly lower than FC for molluscs (F_(3,7)=7.010; p<0.05), and SS was significantly lower than from AQ and FC for shrimp (F_(3,7)=7.991; p<0.05). Significant seasonal differences in biomass were observed for all species (F_(2,14)=3.859, p<0.05) and across most taxa, with biomass significantly lower during the summer than for other seasons [crabs (F_(2,14)=9.424; p<0.05), mollusc (F_(2,14)=7.172; p<0.05), shrimp (F_(2,14)=24.011; p<0.001)] (Tables 2 and 4).

No factors interacted significantly for seine net density when evaluated across all species (Table 2). Among specific taxa, a significant habitat type by season interaction was observed for shrimp (F_(2,14)=4.256, p<0.05) (Table 4), with oyster habitat sites yielding significantly higher density than bare sediment sites during the autumn only. Statistically significant overall habitat differences were observed when evaluating across species (F_(1,7)=12.944, p<0.05) (Table 2), and for the crab taxa (F_(1,7)=6.127, p<0.05) (Table 4), with oyster habitat sites significantly higher in both cases. Location and season interacted significantly for mollusc density (F_(6,14)=3.549, p<0.05) (Table 4); with FC higher than GP and SS during the spring only. South Sanctuary yielded significantly lower densities than other sites when evaluated across all species (F_(3,7)=8.739, p<0.05) (Table 2). South Sanctuary was also significantly lower than GP for fish (F_(3,7)=5.712, p<0.05) and significantly lower than FC for shrimp (F_(3,7)=5.367, p<0.05) (Table 4). Seasonal differences were observed across all species (F_(2,14)=14.661, p<0.001) (Table2), with densities lower in the summer.

Both diversity and richness exhibited similar patterns to biomass when evaluated across all species. No significant differences were observed between oyster and bare sediment sites for either metric. Location differences were observed for diversity and richness (F_(3,7)=16.116, p<0.05 and F_(3,7)=6.698, p<0.05, respectively), with SS significantly lower than all other sites (Table 2). Seasonal differences were statistically significant (F_(2,14)=5.765, p<0.05 and F_(2,14)=18.8795, p<0.001 for diversity and richness, respectively), with diversity significantly lower during the autumn while richness was significantly lower during the summer.

Minnow Trap and Shrimp Trap Collections

The total abundance from 86 trap sets was 1,994 fish and invertebrates with a biomass of 5.10 kg from 25 species. The minnow, F. heteroclitus comprised 50% of the abundance. Minnow trap biomass was greatest at GP1 which was influenced by catches of the American eel, Anguilla rostrata (Lesueur, 1821) (Appendix 3a and 3b).

Biomass data for all species combined were not statistically significant for any individual variable or interaction (Table 2). A three-factor significant interaction (F_(6,14)=4.521, p<0.05) was observed for crab biomass. Statistically significant location (F_(3,7)=5.773, p<0.05) and seasonal (F_(2,14)=4.539, p<0.05) differences were observed for fish biomass, with SS lower than GP and FC, and autumn biomass greater than the spring.

Abundance data for all species showed no statistically significant habitat type or location effects but did exhibit a significant season effect (F_(2,14)=6.688, p<0.05) with autumn abundance greater than spring and summer (Table 2). Fish abundance had a statistically significant three-factor interaction term (F_(6,14)= 4.219; p<0.05); while specific differences could not be evaluated statistically, the results did indicate that the largest habitat differences occurred for FC during the summer and AQ during the spring and autumn. No other significant differences were observed for abundance for the other taxa. The species diversity metric did not differ significantly between oyster and bare habitat sites but did produce a significant location by season interaction (F_(6,13)=5.220; p<0.05). Seasonally, the diversity metric for GP was greater than that for AQ in the spring, AQ was greater than SS in the summer and autumn, and FC in the summer. There were also seasonal differences at AQ (summer and autumn greater than spring) and at FC (autumn greater than summer).

Shrimp trap total abundance was 5,269 fish and invertebrates with a biomass of 4.13 kg. Palaemonetes pugio represented 80.9% of the abundance and 33.7% of the biomass. Catches at FC and GP sites were dominated by the mud snail, Ilyanassa obsoleta (Say, 1822), blue crab, C. sapidus, and C. maenas (Appendix 4a and b). ANOVA results from the shrimp trap data for all species abundance, biomass, species richness and diversity data produced no statistically significant relationships (Table 2). Crab abundance showed a significant location by season interaction (F_(6,14)=3.062; p<0.05). While no season-specific significant pairwise differences between locations were observed, there was a significant seasonal effect observed at AQ with crab abundance in the autumn greater than the summer.

Infauna collections

Duplicate infauna samples (Appendix 5) collected seasonally from AQ and SS sites (N = 68 infauna cores) produced 327 invertebrates representing five invertebrate classes with the Malacostraca and Polychaeta being the most prevalent. Six species comprised 45% of the total abundance with the polychaete worm, Capitella capitata (Fabricius, 1780), and the amphipod, Microdeutopus gryllotalpa (Costa, 1853), comprising 20% of the total density.

Isotopic analysis

Differences between the δ¹³C and δ ¹⁵N signatures of three fish (F. heteroclitus, M. menidia, and L. parva), one crab (C. maenas), and one shrimp (P. pugio) species collected in sufficient numbers at FC and GP restored oyster and associated bare habitat were used for statistical comparisons. None of these five generalist species demonstrated a statistically significant relationship for either δ¹³C or δ¹⁵N signatures by habitat type. Both P. pugio and C. maenas had δ ¹⁵N values about 9.5‰ while benthic fish F. heteroclitus and L. parva had slightly higher values about 10.4‰. Menidia menidia, a pelagic species, had the highest δ ¹⁵N values of 11.5‰. The four benthic associated species, F. heteroclitus, L. parva, C. maenas and P. pugio, clustered together with δ¹³C values around −14‰, and M. menidia had a lower δ¹³C about −17‰ (Figure 2).

Figure 2.

Average isotopic values for δ¹³C and δ¹⁵N (± SD) for species common to both the restored oyster reef and bare habitats at Foster’s Cove and Grassy Point sites combined. Restored oyster reef= ◊ and bare habitats=▪. Carcinus maenas=Cm, Fundulus heteroclitus=Fh, Lucania parva=Lp, Menidia spp.=M, Palaemonetes pugio=P.

Discussion

This study offered an opportunity to compare and quantify fish and invertebrate communities in restored oyster reef, aquaculture, and associated bare sediment habitats in a shallow water marine system in southern New England. These findings support previous observations from other geographies of the foraging and refugia benefits of restored oyster habitat (Breitburg 1999, Grabowski et al. 2005, Tolley & Volety 2005, Shervette & Gelwick 2008, Gregalis et al. 2009, Humphries et al. 2011, Kellogg et al. 2013), aquaculture grow-out gear (Kilpatrick 2002, Dealteris et al. 2004, Tallman et al. 2011) and unstructured bare sediment (Geraldi et al. 2009) to finfish and invertebrate assemblages as measured by the four performance metrics.

Determining the optimal sampling gear can be confounded by many biological and physical factors (Rotherham & Gray 2005 and references therein). Four types of sampling gear were chosen for this study. Box traps and seine nets were selected as quantitative sampling techniques which scale to estimate density and biomass of the fauna (Kushlan 1981). Box traps worked efficiently to sample sessile and slow-moving fauna but did not adequately capture finfish. While seine net hauls caught finfish species, the small net did not catch representative pelagic and piscivorous fish species (only one bluefish and one striped bass were recorded), indicating this may not be the most efficacious sampling method (Steele et al. 2006, Hallett & Hall 2012). The passive samplers, minnow and shrimp traps, were used to provide additional information on a variety of benthic species not readily collected with the other gear types (Grabowski et al. 2005). Gill nets have been used to catch large transient and piscivorous fish (Humphries et al. 2011), but this was not a feasible technique as nets were quickly destroyed by large blue crabs.

Oyster reef dependent finfish species have not been well described in the New England region, despite on-going oyster restoration efforts. During this study, six of the 17 fish species described as reliant on reef habitat for some portion of their life history at a Chesapeake Bay location (Breitburg 1999) were collected at one or more Ninigret Pond sites. The reef resident oyster toadfish, O. tau, was collected nearly exclusively at the Aquaculture sites, while the naked goby, Gobiosoma bosc (Lacepede, 1800), was ubiquitous across sites. The northern pipefish, Syngnathus fuscus (Storer, 1839), considered a facultative species was collected in small numbers from all sites. Three transient species were collected in this study. The American eel, A. rostrata, had limited distribution at the Aquaculture and Grassy Point sites, while juvenile winter flounder, P. americanus, and the silverside, M. menidia were found at all sites.

Examination of the performance metrics indicate the results were highly dependent on the sampling gear used. Although not all metrics demonstrated significant differences, the box trap and seine net results suggest that restored oyster habitats at Foster’s Cove, Grassy Point and the Aquaculture site produced a greater density, biomass, species richness and diversity of species than their associated bare sediment habitats. The minnow and shrimp trap results demonstrated no statistically significant distinctions between the habitat types for the abundance or biomass metric for all species combined. Crab, finfish, mollusc, and shrimp taxa were important in discriminating between habitat types. Broadly, these results indicated greater abundance and biomass at oyster habitats than bare habitat. The results support previous studies such as Gregalis et al. (2009) findings of increased abundance of small demersal fish and sessile invertebrate species on restored oyster reef compared to unstructured bottom sediment in coastal Alabama. In Louisiana, Humphries et al. (2011b) reported a different assemblage of nekton at oyster reef sites with a greater abundance, biomass, and diversity compared to mud bottom sites. Newly created oyster reefs supported more unique species than unstructured habitat suggesting their importance as valued refugia in North Carolina (Pierson & Eggleston 2014). Crab and fish density, biomass, and diversity were all greater at reefs with live shell or cleaned and articulated shell as compared to an unstructured sand bottom at a Florida location (Tolley & Volety 2005).

South Sanctuary restored oyster habitat did not perform as well as the Foster’s Cove and Grassy Point oyster sites. A possible explanation for our findings relies on the physical context of the restoration sites (Grabowski et al. 2005). Foster’s Cove restored oyster sites abutted fringing smooth cordgrass, Spartina alterniflora (Loisel) and other marsh vegetation and benefitted from oyster recruitment from local remnant native populations. Grassy Point restored oyster sites were located within a small cove and the restored reef and bare sediment habitats were adjacent to fringing S. alterniflora along the shoreline and subtidal eelgrass beds, (Zostera marina; Linnaeus, 1753). In contrast to these productive habitats, the noncontiguous spatial configuration and small footprint of the Spawner Sanctuary restored oyster reefs, located on a sandy outwash, and 10’s of meters to adjacent shoreline habitats suggests fragmentation of habitat between the reefs and shoreline which may reduce the value of the reefs to attract and retain resident and transient fish and invertebrates. This emphasizes the need to assess site suitability prior to restoration efforts to maximize the potential for reef sustainability and enhance the ecosystem service of habitat provisioning for fish and invertebrate species.

Aquaculture oyster site metrics were comparable to Foster’s Cove and Grassy Point restored oyster reef habitat, and often outperformed the South Sanctuary restored reef. Aquaculture leases cover 3.9 % of the bottom area of Ninigret Pond (D. Beutel, Aquaculture and Fisheries Coordinator at RI Coastal Resources Management Council, pers. comm. June 2017). In Rhode Island, rack and bag grow-out gear is a commonly deployed aquaculture method in the shallow subtidal waters. Hundreds of juvenile finfish from RI oyster aquaculture grow-out cages were collected when cages were removed from the water for cleaning (Kilpatrick 2002). Dealteris et al. (2004) contends that rack and bag aquaculture gear has greater habitat value than unvegetated substrate for density and species diversity, and is at least equivalent to submerged aquatic vegetation (Z. marina) within Point Judith Pond, RI. Hosack et al. (2006) suggests that aquaculture grow out gear might act as a substitute for seagrass habitats which had increased density and biomass as compared to mudflats. Similarly, Tallman & Forrester (2007) examined oyster aquaculture grow-out cages compared to natural, and artificial reef habitats in Narragansett Bay, RI and determined the cages provide preferred habitat for juvenile tautog and scup. These studies demonstrate the functional equivalence of oyster aquaculture rack and bag grow-out gear compared with restored oyster reef to provide habitat for nekton. A possible explanation may be the increased structural complexity of the aquaculture grow out gear with dense mats of filamentous macroalgae attached to the grow-out gear during summer months enhancing the refuge and foraging habitat for small resident fish and invertebrate species (Heck & Wetstone 1977). It is noteworthy that sediment at the Aquaculture site had a higher average N load (lower C:N ratio) than South Sanctuary sites and a higher average primary productivity (chl a). This is likely due to the higher oyster biomass at the Aquaculture site. A higher total biodeposit load at the Aquaculture site would drive the higher sediment primary productivity.

The lack of significant metrics results from the minnow and shrimp trap fish and invertebrate collections indicate unstructured bare sediment habitats also support fish and invertebrate assemblages. This is not an anomalous finding. Grabowski et al. (2005) investigated fish and invertebrate habitat utilization on oyster reefs constructed on mudflats, and next to saltmarsh, and seagrass habitats. Abundances of polychaetes, bivalves, and some decapods, were augmented on oyster reefs within each habitat type, while resident juvenile finfish abundance was enhanced exclusively on restored reefs constructed on mudflat. The authors attribute this to habitat complexity and functional redundancy, and lower abundance of piscivorous adult fishes on the mudflat areas. Functional redundancy of oyster reef habitat restored near salt marsh in tidal creeks at Dauphin Island, AL, explained a lack of significant results for enhanced abundance of fish and mobile macroinvertebrate communities (Geraldi et al. 2009), leading the authors to argue the response of nekton to oyster restoration is not automatic but must be considered in the context of the entire seascape. Fish abundance on large restored reefs in a tributary of the Chesapeake Bay more than eight years post-construction had significantly lower abundance compared to associated unstructured bottom (Pfirrmann & Seitz 2019). In Ninigret Pond, unstructured bare sediment may also serve as valuable foraging habitat for fish and invertebrates.

In the present study, seine net collections produced seasonally significant results for metrics during the spring and autumn compared to the summer. While size distribution data are not presented here, spring samples often contained the juveniles of species such as M. menidia, F. heteroclitus, and various crab species. This result is in contrast with other studies from southern New England which demonstrated peak abundance during the summer season (Ayvazian et al. 1992, Deegan et al. 1997, Meng & Powell 1999).

The lack of a significant relationship between the isotopic composition and habitat type for the five generalist species from Foster’s Cove and Grassy Point suggests they may be foraging at both oyster and bare habitats, or that the food resources in the two habitats are similar. There was a weak trophic dynamic in δ ¹⁵N values. The scavengers/omnivores P. pugio and C. maenas consume microalgae, small worms, and crustaceans, and they showed the lowest isotopic N values. Benthic fish species F. heteroclitus and L. parva had higher values and consume crustaceans and small worms as well as some algae. These species had δ ¹³C values indicative of a salt marsh or aquatic vegetation resource base which agrees with their location of capture. The pelagic M. menidia had the highest δ ¹⁵N values and the δ ¹³C values are suggestive of a marine resource base consistent with their zooplankton feeding. This study was unable to collect multiple species at multiple trophic levels to determine the value of the restored reefs and aquaculture as foraging areas compared to bare sediment sites. In other studies, Abeels et al. (2012) modeled trophic relationships which indicated that reef-residents consume other reef organisms and transient species also feed on reef organisms demonstrating the functionality of the restored reef as a foraging area. Rezek et al. (2017) compared food web dynamics between natural and restored reefs in the Gulf of Mexico and found the restored reef supports food web dynamics like that provided by the naturally occurring reefs.

This study is among the first in coastal New England to document responses of the fish and invertebrate communities to restored oyster reefs, aquaculture leases, and associated bare sediment habitats. Despite comprehensive sampling the expected relationships were not as pronounced as hypothesized. Where performance metrics were significant for habitat type, oyster habitats out-performed bare sediment. These results can be applied to the development of guidelines for the placement of oyster restoration sites in southern New England. This would include an understanding of the biophysical conditions necessary to ensure self-sustaining oyster reef habitat. Additionally, a strategic focus on a management paradigm to optimize aquaculture leases for their habitat value to benefit the conservation of important fish and invertebrate species, i.e. ‘conservation aquaculture’ (Froehlich et al. 2017) or ‘restorative aquaculture’ (Theuerkauf et al. 2019), would align restoration and aquaculture practices. Future work would include determination of increased survivorship and enhanced productivity of fish and invertebrates using these salt pond oyster habitats to contribute quantifiable estimates to fisheries production to estimate ecosystem service benefits (zu Ermgassen et al. 2016).

Appendix 1a.

Box trap species biomass m⁻² collected from sampling sites in Ninigret Pond during 2014. AQB=Aquaculture Bare, AQ1 and AQ2=Aquaculture sites 1 and 2, FCNB=Foster’s Cove North Bare, FCSB=Foster’s Cove South Bare, FC1, 2, 3, and 4=Foster’s Cove sites 1, 2, 3 and 4, GPB=Grassy Point Bare, GP1 and 2=Grassy Point sites 1 and 2, SSB=South Sanctuary Bare, SS1 and 2=South Sanctuary sites 1 and 2. See Figure 1 for locations.

	Site Number of Samples
	AQB	AQ1	AQ2	FCNB	FC1	FC2	FCSB	FC3	GPB	GP1	GP2	SSB	SS1	SS2
Species Name	4	4	4	2	1	2	2	1	2	1	2	4	4	4
Acanthohaustoris millsi	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Acartia spp.	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Alitta succinea	0.06	2.92	0	0.03	0.19	0	0.97	0	0.27	0.70	0.60	0	1.60	0.89
Alitta virens	0	0	0	0	0	1.40	0	0	0	0	0	0	0	0
Ampelisca abdita	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Amphipoda spp.	0.30	36.12	13.54	0	0	0	0	0	0	0	0	1.83	35.05	22.58
Amphiporeia virginiana	0	0	0.08	0	0	0	0	0	0	0	0	0	0	0
Ampithoe longimana	6.20	0	1.73	0	0	0	0.07	0	0.02	0	0	0	0	0
Ampithoe valida	0	0	0.95	0	0	0.16	0	0	0	0.05	0.27	0	2.68	0
Apeltes quadracus	0	7.36	0.68	0	0	0	0	0	0	0	0	0	0	0
Arabella iricolor	0.06	0.05	3.10	0	0	0	0	0	0	0	0	0	0	2.08
Argopecten irradians	0	0	0	0	0	0	0	0	0	0	0	0	6.76	0
Boreotrophon truncatus	0.73	0.57	4.08	0	0	0	0	0	0	0	0	0	0	0
Byblis serrata	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Callinectes sapidus	0.87	0	0	0	0	0	0	0	0	0	0	0	0	0
Capitella capitata	0.14	0.28	0.05	0	0	0	0	0	0	0	0	0	0.18	0.07
Capitella spp.	0	0	0	0	0	0	0	0	0	0	0	0	0	0.01
Caprella equilibra	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Carcinus maenas	0	0	26.81	0	0	0	0	0	0	0	0	0	0	0
Centropages spp.	0	0	0	0	0	0	0	0	0	0	0	0.01	0	0
Cirratulidae	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Cirratulus cirratus	0	0	0	0	0.02	0	0	0	0	0	0	0	0	0
Cliona spp.	0	0	0	0	0	0	0	0	0	0	0	0	226.75	0
Corophium volutator	0.01	0	0	0	0	0	0	0	0	0	0	0	0	0
Crangon septemspinosa	18.85	0.84	3.78	0	0	0	0.25	0	5.00	0	0	0	0	0
Crassostrea virginica	0	0	1041.77	0.00	9787.79	0	0	0	2051.76	0	0	0	590.24	2954.98
Crepidula convexa	0	0	0	0	0	0	0	0	0.10	0	0	0	0.37	0.72
Crepidula fornicata	0	0.22	0.02	0	0	6.61	4.00	3.44	0	0	0.51	0	59.29	32.40
Crepidula plana	0	0	0	0	0	0	0	0	0	0	0	0	3.67	7.64
Drilonereis longa	0	0	0	0	0	0	0	0	0	0	0	0	2.28	0
Edotia triloba	0.01	0	0	0	0	0	0	0	0	0	0	0	0	0
Eteone spp.	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Eurypanopeus depressus	0	0	0	0	0	0	2.15	0	2.71	0	0.04	0	0	0
Exogone spp.	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Filograna implexa	2.81	0	0	0	0	0	0	0	0	0	0	0	0	0
Fundulus heteroclitus	0	37.81	0	0	0	0	0	0	0	0	0	0	0	0
Fundulus majalis	0	0	0.59	0	0	0	0	0	0	0	0	0	0	0
Gammarus mucronatus	0	0.01	0.17	1.35	0	0	0	0.34	0.61	0	0	0	0	0
Gasterosteus aculeatus	0.18	0	3.52	0	0	0	0	0	0	0	0	0	0	0
Gemma gemma	0.01	0	0.02	0	0	0	0	0	0.40	0	0	0.02	0	0
Geukensia demissa	0	0.01	0.08	0	0	0	0	0	0	0	0	0	0	0
Glycera americana	0.01	0.02	0.01	0	0	0	0	0	0	0	0	0.15	0	0
Gobiosoma bosc	0	1.54	0.22	0	0	0	1.99	1.86	0	0	0	0	0	1.36
Goniada maculata	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Haminoea solitaria	0	0	0	1.18	0	11.90	22.95	4.39	0	0	0	0	0	0
Harpinia propinqua	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Hemigrapsus sanguineus	0	0	0	0	0	0	0.02	0	0	3.26	0	0	0	0
Heteromastus filiformis	0.01	0	0	0.05	0	0	0.01	0	0	0	0	0	0	0
Hypereteone heteropoda	0	0.01	0.01	0	0	0	0.01	0	0	0	0	0	0	0
Ilyanassa obsoleta	0.45	0	1.70	110.33	0	0	0	6.50	0	0	0	0	0	0
Ilyanassa trivittata	0	0.10	0.03	0	0	0	0	0	0	0	0	0	0.06	0
Lacuna vincta	0	8.56	0.06	0	0	0	0	0	0	0	0	0	0	0
Leitoscoloplos fragilis	0	0.25	0	0	0	0	0	0	0	0	0	0.97	0	0
Lembros smithi	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Lembros websteri	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Leptocheirus pinguis	0	0	0	0.25	0	0	0	0	0	0	0	0.03	0	0
Leucon americanus	0.01	0	0	0	0	0	0	0	0.02	0	0	0.01	0	0
Libinia emarginata	0	0	4.73	0	0	0	0	0	0	0	0	0	32.76	0
Listriella clymenellae	0.01	0	0.03	0	0	0	0	0	0	0	0	0	0	0
Littorina littorea	0	0.16	0.11	0	0	0	0	0	0	53.41	0	0	0.06	0
Lucania parva	0.94	0	1.45	0	0	0	0	0	0	0	0	0	0	0
Lysianopsis alba	0.04	0.01	0.01	0	0	0	0	0	0	0	0	0	0	0.01
Melita dentata	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Menidia menidia	27.45	50.78	107.02	0	0	0	0	0	0	0	0	0	0	0
Mercenaria mercenaria	0	0	0.03	0	0	0	0	0	0.02	47.62	151.23	0	0	0
Microdeutopus gryllotalpa	0.05	0.04	0.07	1.18	0	0	0.18	0	0.24	0	0.02	0	0	0.01
Monoculodes edwardsi	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Mytilus edulis	0	5.68	0.02	0	0	0	0	0	0	0	0	0	0	0
Neanthes arenaceodentata	0	0	0.01	0	0	0	0	0	0	0	0	0	0	0
Nematode	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Neomysis americana	0.03	0	0	0.87	0	0	0	0	0	0	0	0	0	0
Oligochaeta	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Opsanus tau	1.31	0	7.55	0	0	0	0	0	0	0	0	0	0	0
Orbinia ornata	0.11	0	0.13	0	0	0	0	0	0	0	0	0.20	0	0
Ostracod	0.02	0.01	0	0	0	0	0	0	0	0	0	0	0	0
Oxydromus obscura	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Palaemonetes pugio	11.88	52.32	81.20	1.89	0	78.68	3.52	59.86	2.02	40.73	10.21	13.61	72.66	79.62
Panopeus herbstii	0.14	10.82	31.29	0	0	38.61	43.99	26.92	2.99	73.25	59.88	0	184.15	57.65
Pherusa affinis	0	0	0	0	0	0	0	0	0	0	0	0	0.13	0
Pleusymtes glaber	0	0.01	0	0	0	0	0	0	0	0	0	0	0	0
Polychaeta	0	0	0.05	0	0	0	0	0	0	0	0	0.01	0.01	4.77
Polydora cornuta	0.01	0.07	0	0	0	0	0	0	0	0	0	0	0	0
Prionospio spp.	0.18	0	0	0	0	0	0	0	0	0	0	0	0	0
Pseudopleuronectes americanus	9.82	42.71	0	0.62	0	0	0	0	0	0	0	0	0	0
Rhepoxynius epistomus	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Scoletoma spp.	0.01	0	0	0	0	0	0	0	0	0	0	0	0	0
Scoloplos armiger	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Solemya velum	0	0.99	0.84	0	0	0	0	0	0	0	0	0	0	0
Streblospio benedicti	0.14	0.01	0	0	0	0	0	0	0	0	0	0	0	0
Syllidae	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Syngnathus fuscus	0	3.44	0	0	0	0	0	0	0	0	0	0	0.19	7.86
Tellina agilis	0	0	0	0	0	0	0	0	0	0	0	0.56	0	0
Tharyx acutus	0	0	0	0	0.03	0	0	0	0	0	0	0	0	0
Unciola irrorata	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Unciola serrata	0	0	0	0.04	0	0	0	0	0	0	0	0	0	0
Upogebia affinis	0	0	0	0	0	0	0.83	0	0	0	0	0	0	0

Appendix 1b.

Box trap species density collected from sampling sites in Ninigret Pond during 2014. AQB=Aquaculture Bare, AQ1 and AQ2=Aquaculture sites 1 and 2, FCNB=Foster’s Cove North Bare, FCSB=Foster’s Cove South Bare, FC1, 2, 3, and 4=Foster’s Cove sites 1, 2, 3 and 4, GPB=Grassy Point Bare, GP1 and 2=Grassy Point sites 1 and 2, SSB=South Sanctuary Bare, SS1 and 2=South Sanctuary sites 1 and 2. See Figure 1 for locations.

	Site Number of Samples
	AQB	AQ1	AQ2	FCNB	FC1	FC2	FCSB	FC3	GPB	GP1	GP2	SSB	SS1	SS2
Species Name	4	4	4	2	2	1	1	2	2	1	2	4	4	4
Acanthohaustoris millsi	2.80	0	0	0	0	0	0	0	0	0	0	0	0	0
Acartia spp.	0	0	0	0	0	0	0	0	0	2.80	0	0	0	0
Alitta succinea	2.80	11.20	2.80	2.80	5.60	0	30.80	0	14.00	8.40	5.60	0	58.80	8.40
Alitta virens	0	0	0	0	0	22.40	0	19.60	0	0	0	0	0	0
Ampelisca abdita	5.60	2.80	0	0	0	0	0	0	0	0	0	0	0	0
Amphipoda spp.	131.60	18600.40	3203.20	0	0	0	0	0	0	0	0	333.20	4317.60	1758.40
Amphiporeia virginiana	0	0	14.00	0	0	0	0	0	0	0	0	0	0	0
Ampithoe longimana	372.40	30.80	243.60	0	0	0	2.80	0	2.80	0	0	0	0	0
Ampithoe valida	0	19.60	240.80	0	0	5.60	0	0	0	8.40	14.00	0	221.20	0
Apeltes quadracus	0	16.80	8.40	0	0	0	0	0	0	0	0	0	0	0
Arabella iricolor	11.20	16.80	16.80	0	0	0	0	0	0	0	0	0	0	8.40
Argopecten irradians	0	0	0	0	0	0	0	0	0	0	0	0	2.80	0
Boreotrophon truncatus	5.60	2.80	22.40	0	0	0	0	0	0	0	0	0	0	0
Byblis serrata	5.60	0	0	0	0	0	2.80	0	0	0	0	0	0	0
Callinectes sapidus	2.80	0	0	0	0	0	0	0	0	0	0	0	0	0
Capitella capitata	28.00	72.80	313.60	0	0	0	0	0	0	0	2.80	2.80	16.80	11.20
Capitella spp.	0	0	0	0	0	0	0	0	0	0	0	0	0	5.60
Caprella equilibra	0	0	0	0	0	0	0	0	0	0	2.80	0	0	0
Carcinus maenas	0	0	8.40	0	0	0	0	0	0	0	0	0	0	0
Centropages spp.	0	0	0	0	0	0	0	0	0	0	0	2.80	0	0
Cirratulidae	0	0	0	0	0	0	0	0	0	0	2.80	0	0	0
Cirratulus cirratus	0	0	0	0	5.60	0	0	0	0	0	0	0	0	0
Cliona spp.	0	0	0	0	0	0	0	0	0	0	0	0	2.80	0
Corophium volutator	2.80	0	0	5.60	2.80	0	0	0	0	0	0	0	0	2.80
Crangon septemspinosa	56.00	2.80	2.80	0	0	0	5.60	0	11.20	0	0	0	0	0
Crassostrea virginica	0	0	28.00	0	285.60	0	0	0	56.00	0	0	0	16.80	11.20
Crepidula convexa	0	0	0	0	0	0	0	0	2.80	0	0	0	8.40	8.40
Crepidula fornicata	0	14.00	2.80	0	0	42.00	22.40	14.00	0	0	14.00	0	114.80	30.80
Crepidula plana	0	0	0	0	0	0	0	0	0	0	0	0	2.80	2.80
Drilonereis longa	0	0	0	0	0	0	0	0	0	0	0	0	2.80	0
Edotia triloba	2.80	2.80	0	0	0	0	2.80	0	0	0	0	0	0	0
Eteone spp.	0	2.80	0	0	0	0	0	0	2.80	0	0	0	2.80	2.80
Eurypanopeus depressus	0	0	0	0	0	0	5.60	0	2.80	0	2.80	0	0	0
Exogone spp.	30.80	8.40	11.20	0	0	0	0	0	14.00	0	0	14.00	0	2.80
Filograna implexa	5.60	0	0	0	0	0	0	0	0	0	0	0	0	0
Fundulus heteroclitus	0	5.60	0	0	0	0	0	0	0	0	0	0	0	0
Fundulus majalis	0	0	8.40	0	0	0	0	0	0	0	0	0	0	0
Gammarus mucronatus	2.80	5.60	16.80	67.20	0	0	0	5.60	22.40	0	0	0	0	0
Gasterosteus aculeatus	2.80	0	5.60	0	0	0	0	0	0	0	0	0	0	0
Gemma gemma	2.80	0	8.40	0	0	0	0	0	2.80	0	0	5.60	0	0
Geukensia demissa	0	8.40	25.20	0	0	0	0	0	0	0	0	0.0	0.0	0.0
Glycera americana	5.60	2.80	2.80	0	0	0	0	0	0	0	0	2.80	0	0
Gobiosoma bosc	0	5.60	2.80	0	0	0	25.20	2.80	0	0	0	0	0	2.80
Goniada maculata	0	0	0	0	0	0	0	0	0	0	0	2.80	0	0
Haminoea solitaria	0	0	0	5.60	0	58.80	187.60	28.00	0	0	0	0	0	0
Harpinia propinqua	0	0	0	0	0	0	0	0	0	0	0	2.80	0	0
Hemigrapsus sanguineus	0	0	0	0	5.60	0	2.80	0	0	11.20	0	0	0	0
Heteromastus filiformis	8.40	0	0	5.60	0	0	5.60	0	0	0	0	2.80	0	0
Hypereteone heteropoda	30.80	16.80	25.20	2.80	0	0	8.40	0	5.60	0	0	0	2.80	2.80
Ilyanassa obsoleta	2.80	0	8.40	53.20	0	0	0	2.80	0	0	0	0	0	0
Ilyanassa trivittata	0	8.40	8.40	0	0	0	0	0	0	0	0	0	2.80	0
Lacuna vincta	0	1005.20	11.20	0	0	0	0	0	0	0	0	0	0	0
Leitoscoloplos fragilis	0	5.60	0	0	0	0	0	0	0	0	0	98.0	0	0
Lembros smithi	0	0	0	0	0	0	0	0	0	0	5.60	0	0	0
Lembros websteri	0	0	2.80	0	0	0	0	0	0	0	0	0	0	0
Leptocheirus pinguis	14.00	0	0	78.40	0	0	0	0	0	0	0	14.0	0	0
Leucon americanus	11.20	0	0	0	0	0	0	0	2.80	0	0	5.60	0	0
Libinia emarginata	0	0	5.60	0	0	0	0	0	0	0	0	0	5.60	0
Listriella clymenellae	2.80	0	19.60	0	0	0	0	0	0	0	0	0	2.80	0
Littorina littorea	0	92.40	36.40	0	0	0	0	0	0	11.20	0	0	0	0
Lucania parva	5.60	0	16.80	0	0	0	0	0	0	0	0	0	0	0
Lysianopsis alba	8.40	8.40	5.60	0	0	0	0	0	0	0	0	0	0	5.60
Melita dentata	0	30.80	0	0	0	0	0	0	0	0	0	0	0	0
Menidia menidia	42.00	56.00	100.80	0	0	0	0	0	0	0	0	0	0	0
Mercenaria mercenaria	0.0	0	5.60	0	0	0	0	0	5.60	2.80	5.60	0	0	0
Microdeutopus gryllotalpa	84.00	44.80	61.60	512.40	0	0	39.20	0	42.00	0	2.80	0	0	14.00
Monoculodes edwardsi	0	0	0	0	0	0	0	0	0	0	0	2.80	0	0
Mytilus edulis	0	394.80	5.60	0	0	0	0	0	0	0	0	0	0	0
Neanthes arenaceodentata	2.80	0	2.80	0	0	0	0	0	0	0	0	0	0	0
Nematode	0	0	0	0	0	0	0	0	22.40	0	0	0	0	0
Neomysis americana	5.60	0	0	5.60	0	0	0	0	0	0	0	0	0	0
Oligochaeta	0	2.80	0	0	0	0	2.80	0	0	2.80	0	0	0	0
Opsanus tau	2.80	0	5.60	0	0	0	0	0	0	0	0	0	0	0
Orbinia ornata	28.00	0	2.80	0	0	0	0	0	0	0	0	11.20	0	0
Ostracod	22.40	47.60	8.40	0	0	0	2.80	0	0	0	0	14.00	0	2.80
Oxydromus obscura	0	2.80	0	0	0	0	0	0	0	0	0	0	0	0
Palaemonetes pugio	100.80	358.40	761.60	5.60	0	246.40	14.00	193.20	14.00	218.40	75.60	117.60	442.40	490.00
Panopeus herbstii	2.80	22.40	50.40	0	0	75.60	420.00	44.80	2.80	131.60	58.80	0	501.20	218.40
Pherusa affinis	0	0	0	0	0	0	0	0	0	0	0	0	5.60	0
Pleusymtes glaber	0	2.80	0	0	0	0	0	0	0	0	0	0	0	0
Polychaeta	5.60	2.80	5.60	0	2.80	0	0	0	2.80	0	0	5.60	2.80	22.40
Polydora cornuta	11.20	16.80	2.80	0	0	0	2.80	0	0	0	0	2.80	0	0
Prionospio spp.	39.20	0	0	0	0	0	0	0	2.80	0	0	0	0	0
Pseudopleuronectes americanus	2.80	11.20	0	2.80	0	0	0	0	0	0	0	0	0	0
Rhepoxynius epistomus	0	5.60	0	0	0	0	0	0	0	0	0	0	0	0
Scoletoma spp.	11.20	0	0	0	0	0	0	0	0	0	0	0	0	0
Scoloplos armiger	0	0	2.80	0	0	0	0	0	0	0	0	0	0	0
Solemya velum	0	16.80	16.80	0	0	0	0	0	0	0	0	0	0	0
Streblospio benedicti	53.20	2.80	2.80	0	0	0	0	0	0	0	0	0	0	0
Syllidae	2.80	0	0	0	0	0	0	0	0	0	0	0	0	0
Syngnathus fuscus	0	2.80	0	0	0	0	0	0	0	0	0	0	2.80	5.60
Tellina agilis	0	0	0	0	0	0	0	0	0	0	0	2.80	0	0
Tharyx acutus	0	0	0	0	5.60	0	8.40	0	0	0	0	0	0	0
Unciola irrorata	0	0	30.80	0	0	0	0	0	0	0	0	0	0	0
Unciola serrata	0	0	0	8.40	0	0	0	0	0	0	0	0	0	0
Upogebia affinis	0	0	0	0	0	0	8.40	0	0	0	0	0	0	0

Appendix 2a.

Seine net species biomass m⁻² collected from sampling sites in Ninigret Pond during 2014. AQB=Aquaculture Bare, AQ1 and AQ2=Aquaculture sites 1 and 2, FCNB=Foster’s Cove North Bare, FCSB=Foster’s Cove South Bare, FC1, 2, 3, and 4=Foster’s Cove sites 1, 2, 3 and 4, GPB=Grassy Point Bare, GP1 and 2=Grassy Point sites 1 and 2, SSB=South Sanctuary Bare, SS1 and 2=South Sanctuary sites 1 and 2. See Figure 1 for locations.

	Site Number of Samples
	AQB	AQ1	AQ2	FCNB	FC3	FC4	FCSB	FC1	FC2	GPB	GP1	GP2	SSB	SS1	SS2
Species	4	6	5	4	5	4	5	5	6	6	6	5	4	5	4
Alosa pseudoharengus	0	0	0	0	0	0	0	0	0	0	0	0.05	0	0	0
Apeltes quadracus	0.06	0.01	0.01	0	0	0	0	0.03	0.04	0	0	0	0	0	0
Callinectes sapidus	0.32	0	0.38	0.86	1.47	0.17	0.06	1.26	0.00	0.03	0.77	0.60	0.00	0.00	0.00
Caranx hippos	0	0	0	0	0	0	0.23	0	0	0	0	0	0	0	0
Carcinus maenas	0.24	0.48	0.45	0	0	0.03	0.03	0	0.17	1.42	0.59	3.08	0	0	0.01
Centropristis striata	0	0	0	0	0	0	0	0	0	0	0.02	0.04	0	0	0
Crangon septemspinosa	0.12	0.22	0.05	0	0	0	0.03	0	0	0	0	0	0.04	0	0
Cyprinodon variegatus	0	0	0	0.23	0.04	0.04	0	0.19	0.29	0	0	0	0	0	0
Eucinostomus havana	0	0	0	0	0	0	0	0	0	0	0.18	0.04	0	0	0
Fundulus heteroclitus	0.90	0.04	0	1.03	0.08	0.02	0.03	0.05	0.17	0.02	0.19	0.49	0	0	0
Fundulus majalis	0	0	0	0	0	0	0	0.08	0	0	0	0	0	0	0
Gasterosteus aculeatus	0	0.01	0	0	0	0	0	0	0.01	0	0	0	0	0	0
Gobiosoma bosc	0.04	0	0.04	0	0.07	0	0.03	0	0.03	0.01	0	0.03	0	0	0
Haminoea solitaria	0	0	0	0.09	0.08	0.13	0.04	0.05	0.01	0	0	0	0	0	0
Ilyanassa obsoleta	0	0	0	1.65	0.48	0.31	0	0.05	0.33	0	0	0	0	0	0
Libinia emarginata	0.09	0.03	0.21	0.00	0.03	0.15	0.03	0.05	0.06	0	0.33	0	0	0.39	0
Lucania parva	0.04	0.06	0.04	0.07	0.06	0	0.10	0.18	0.24	0.07	0.37	0.10	0	0	0
Menidia menidia	0.64	0.20	0	0.82	0.95	0.36	0.11	0.26	0.99	1.27	0.70	0.13	0	0.88	0.86
Morone saxitilis	0	0	0	0	0	0	0	0	0	0	0.02	0	0	0	0
Opsanus tau	0	0.14	0	0	0	0	0	0	0	0	0	0	0	0	0
Palaemonetes pugio	0.23	2.52	1.97	1.37	1.46	1.19	0.87	2.26	2.23	0.24	0.83	1.47	0.01	0.28	0.13
Panopeus herbstii	0.03	0.14	0.05	0.04	0.08	0	0.07	0.11	0.12	0.09	0.03	0	0.00	0.18	0
Paralichthys dentatus	0.03	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Prionotus evolans	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Pseudopleuronectes americanus	0.03	0	0.06	0	0.09	0.01	0.04	0.02	0.02	0.04	0.15	0.07	0	0	0
Pomatomus saltatrix	0	0	0	0	0.01	0	0	0	0	0	0	0	0	0	0
Strongylura marina	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Syngnathus fuscus	0	0	0.01	0	0.03	0	0.03	0	0.01	0	0.04	0.04	0	0	0
Tautoga onitis	0	0.10	0	0	0	0	0	0	0	0	0	0	0	0	0

Appendix 2b.

Seine net species density collected from sampling sites in Ninigret Pond during 2014. AQB=Aquaculture Bare, AQ1 and AQ2=Aquaculture sites 1 and 2, FCNB=Foster’s Cove North Bare, FCSB=Foster’s Cove South Bare, FC1, 2, 3, and 4=Foster’s Cove sites 1, 2, 3 and 4, GPB=Grassy Point Bare, GP1 and 2=Grassy Point sites 1 and 2, SSB=South Sanctuary Bare, SS1 and 2=South Sanctuary sites 1 and 2. See Figure 1 for locations.

	Site Number of Samples
	AQB	AQ1	AQ2	FCNB	FC1	FC2	FCSB	FC3	FC4	GPB	GP1	GP2	SSB	SS1	SS2
Species	4	6	5	4	5	6	5	5	4	6	6	5	4	5	4
Alosa pseudoharengus	0	0	0	0	0	0	0	0	0	0	0	0.02	0	0	0
Apeltes quadracus	0.03	0.02	0.03	0	0.20	0.14	0	0	0	0	0	0	0	0	0.01
Callinectes sapidus	0.02	0	0.02	0.04	0.02	0	0.01	0.04	0.09	0.02	0.04	0.02	0	0	0
Caranx hippos	0	0	0	0	0	0	0.08	0	0	0	0	0	0	0	0
Carcinus maenas	0.02	0.27	0.07	0.01	0.10	0.27	0.04	0	0.01	0.08	0.10	0.28	0	0	0.02
Centropristis striata	0	0	0	0	0	0	0	0	0	0	0.01	0.02	0	0	0
Crangon septemspinosa	0.13	0.44	0.11	0	0	0	0.01	0	0	0	0	0	0.01	0	0
Cyprinodon variegatus	0	0	0	0.09	0.17	0.29	0	0.01	0.02	0	0	0	0	0	0
Eucinostomus havana	0	0	0	0	0	0	0	0	0	0	0.08	0.06	0	0	0
Fundulus heteroclitus	0.26	0.03	0	0.27	0.08	0.07	0.01	0.01	0.04	0.01	0.16	0.22	0	0	0
Fundulus majalis	0	0	0	0	0.01	0	0	0	0	0	0	0	0	0	0
Gasterosteus aculeatus	0.02	0.01	0	0	0	0.03	0	0	0	0	0	0.01	0	0	0
Gobiosoma bosc	0.01	0	0.01	0	0.01	0.01	0.01	0.07	0	0.01	0.01	0.01	0	0	0
Haminoea solitaria	0	0	0	0.36	0.32	0.07	0.69	0.57	0.92	0	0	0	0	0	0
Ilyanassa obsoleta	0	0.09	0	0.71	0.03	0.13	0	0.19	0.12	0	0	0	0	0	0
Libinia emarginata	0.03	0.01	0.06	0	0.01	0.01	0.01	0.01	0.01	0	0.01	0	0	0.02	0
Lucania parva	0.03	0.03	0.03	0.06	0.28	0.54	0.19	0.02	0.02	0.23	1.23	0.21	0	0	0
Menidia menidia	0.24	0.07	0	0.34	0.73	0.88	0.06	0.54	0.14	0.99	0.80	0.07	0	2.66	2.29
Morone saxitilis	0	0	0	0	0	0	0	0	0	0	0.01	0	0	0	0
Opsanus tau	0	0.03	0	0	0	0	0	0	0	0	0	0	0	0	0
Palaemonetes pugio	0.83	9.04	6.16	5.57	9.91	14.82	3.64	6.94	7.22	0.87	2.79	5.70	0.03	0.82	0.43
Panopeus herbstii	0.01	0.08	0.07	0.01	0.24	0.30	0.07	0.07	0	0.01	0.01	0	0	0.13	0
Paralichthys dentatus	0.02	0	0	0.01	0	0	0	0	0	0	0	0	0	0	0
Prionotus evolans	0	0	0	0	0	0	0	0	0	0	0	0.01	0	0	0
Pseudopleuronectes americanus	0.02	0	0.02	0	0.01	0.01	0.01	0.02	0.04	0.02	0.02	0.01	0	0	0
Pomatomus saltatrix	0	0	0	0	0	0	0	0.01	0	0	0	0	0	0	0
Strongylura marina	0	0	0	0	0	0	0	0	0	0.02	0	0	0	0	0
Syngnathus fuscus	0	0	0.01	0	0.01	0.01	0.01	0.01	0	0	0.01	0.01	0	0	0
Tautoga onitis	0	0.02	0	0	0	0	0	0	0	0	0	0	0	0	0

Appendix 3a.

Minnow trap species biomass^{−24 hours} collected from sampling sites in Ninigret Pond during 2014. AQB=Aquaculture Bare, AQ1 and AQ2=Aquaculture sites 1 and 2, FCNB=Foster’s Cove North Bare, FCSB=Foster’s Cove South Bare, FC1, 2, 3, and 4=Foster’s Cove sites 1, 2, 3 and 4, GPB=Grassy Point Bare, GP1 and 2=Grassy Point sites 1 and 2, SSB=South Sanctuary Bare, SS1 and 2=South Sanctuary sites 1 and 2. See Figure 1 for locations.

	Site Number of Samples
	AQB	AQ1	AQ 2	FCNB	FC1	FC2	FCSB	FC3	FC4	GPB	GP1	GP2	SSB	SS1	SS2
Species	6	5	6	6	5	6	6	6	4	6	6	6	6	6	6
Alosa pseudoharengus	0	0	0	0	0	0	0	0	0	0	4.18	0.67	0	0	0
Anguilla rostrata	0	560.52	210.33	0	0	0	0	0	0	0	467.91	0	0	0	0
Apeltes quadracus	0.78	9.16	6.52	0	0	0	0	0	0	3	0	0	0	0	0
Callinectes sapidus	5.45	0	0	0	0	0	0	0	0	0	0	0	0	0	123.19
Caranx hippos	0	0	0	0	0	0	0	0	2.03	1.26	0	0	0	0	0
Carcinus maenas	3.44	5.33	6.64	0	0	0.25	0	0.50	0	0	11.78	10.8	1.62	0	4.89
Crangon septemspinosa	0	0	0	0	0	0	0	2.31	0	0	0	0	0	0	0
Cyprinodon variegatus	0	0	0	85.13	43.13	31.3	0	22.48	18.20	0	0	4.46	0	0	0
Eucinostomus havana	0	0	0	0	0	0	0	0	0	0	0	0.57	0	0	0
Fundulus heteroclitus	0	24.15	44.50	584.85	351.03	418.07	56.46	339.69	293.94	272.76	273.91	116.48	0	0	0
Fundulus majalis	0	0	0	11.60	0	0	0	17.00	20.47	0	44.31	0	0	0	0
Gasterosteus aculeatus	1.17	1.02	1.27	0	0	0	0	0	0	2.92	0.91	0	0	0	0
Gobiosoma bosc	0	0	0	0	4.70	3.28	0	3.21	0	0	0	0	0	0	0
Haminoea solitaria	0	0	0	0	0	0	0.52	0	0	0	0	0	0	0	0
Libinia emarginata	0	0	0	0	0	0	0	0	0	0	0	0	0	0	56.23
Lucania parva	2.33	0	6.21	0	0	0	0	0	0	2.98	7.43	1.14	0	0	0
Menidia menidia	1.57	0	0	5.75	0	0	0	5.91	0	1.8	14.04	1.36	0	0	5.08
Palaemonetes pugio	27.22	11.63	13.58	28.61	11.30	32.35	12.20	40.35	0	10.64	25.73	31.26	35.78	40.90	25.30
Panopeus herbstii	0	0	6.9	0	6.15	3.07	0	6.44	0	0	17.24	1.11	1.33	2.29	2.04
Pseudopleuronectes americanus	0	3.15	10.48	0	0	0	0	0	0	0	0	1.13	0	0	0
Syngnathus fuscus	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0
Tautogolabrus adspersus	0	0	0	0	0	0	0	0	0	10.24	0	0	0	0	0
Tautoga onitis	0	0.85	0	0	0	0	0	0	0	13.09	0	0	0	0	0
Uca pugilator	0	0	0	0	0	0	0	0	0	0	11.39	0	0	0	0

Appendix 3b.

Minnow trap species abundance^{−24 hours} collected from sampling sites in Ninigret Pond during 2014. AQB=Aquaculture Bare, AQ1 and AQ2= Aquaculture sites 1 and 2, FCNB=Foster’s Cove North Bare, FCSB=Foster’s Cove South Bare, FC1, 2, 3, and 4=Foster’s Cove sites 1, 2, 3 and 4, GPB=Grassy Point Bare, GP1 and 2=Grassy Point sites 1 and 2, SSB=South Sanctuary Bare, SS1 and 2=South Sanctuary sites 1 and 2. See Figure 1 for locations.

	Site Number of Samples
	AQB	AQ1	AQ2	FCNB	FC1	FC2	FCSB	FC3	FC4	GPB	GP1	GP2	SSB	SS1	SS2
Species	6	5	6	6	5	6	6	6	4	6	6	6	6	6	6
Alosa pseudoharengus	0	0	0	0	0	0	0	0	0	0	3	1	0	0	0
Anguilla rostrata	0	6	3	0	0	0	0	0	0	0	3	0	0	0	0
Apeltes quadracus	1	10	2	0	0	0	0	0	0	1	0	0	0	0	0
Callinectes sapidus	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1
Caranx hippos	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0
Carcinus maenas	1	1	1	0	0	1	0	1	0	0	1	3	2	0	1
Crangon septemspinosa	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
Cyprinodon variegatus	0	0	0	60	39	34	0	17	18	0	0	1	0	0	0
Eucinostomus havana	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
Fundulus heteroclitus	0	6	26	140	104	160	92	159	67	80	108	58	0	0	0
Fundulus majalis	0	0	0	1	0	0	0	1	5	0	3	0	0	0	0
Gasterosteus aculeatus	1	1	1	0	0	0	0	0	0	3	1	0	0	0	0
Gobiosoma bosc	0	0	0	0	2	1	0	1	0	0	0	0	0	0	0
Haminoea solitaria	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0
Libinia emarginata	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3
Lucania parva	2	0	3	0	0	0	0	0	0	1	2	1	0	0	0
Menidia menidia	1	0	0	3	0	0	0	1	0	1	6	1	0	0	1
Palaemonetes pugio	71	15	29	49	19	61	19	74	0	9	33	53	116	81	69
Panopeus herbstii	0	0	2	0	2	1	0	2	0	0	2	1	1	1	2
Pseudopleuronectes americanus	0	1	2	0	0	0	0	0	0	0	0	1	0	0	0
Syngnathus fuscus	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
Tautogolabrus adspersus	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0
Tautoga onitis	0	1	0	1	0	0	0	0	0	2	0	0	0	0	0
Uca pugilator	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0

Appendix 4a.

Shrimp trap species biomass^{−24 hours} collected from sampling sites in Ninigret Pond during 2014. AQB=Aquaculture Bare, AQ1 and AQ2=Aquaculture sites 1 and 2, FCNB=Foster’s Cove North Bare, FCSB=Foster’s Cove South Bare, FC1, 2, 3, and 4=Foster’s Cove sites 1, 2, 3 and 4, GPB=Grassy Point Bare, GP1 and 2=Grassy Point sites 1 and 2, SSB=South Sanctuary Bare, SS1 and 2=South Sanctuary sites 1 and 2. See Figure 1 for locations.

	Site Number of Samples
	AQB	AQ1	AQ2	F FCNB	FC1	FC2	FCSB	FC3	FC4	GPB	GP1	GP2	SSB	SS1	SS2
Species	6	6	6	5	5	4	6	6	4	6	6	6	6	6	6
Apeltes quadracus	3.71	3.81	4.69	2.83	0	0	0.3	0	0	0	0	0	0	0	0
Callinectes sapidus	16.52	0	0	71.94	241.18	40.29	130.33	112.70	32.97	0.86	94.40	87.68	72.86	40.99	53.15
Carcinus maenas	0	14.12	31.60	0	0	18.54	51.36	0.03	0	66.04	255.86	69.78	0	26.90	0
Crangon septemspinosa	0	0	3.95	0	0	0	0	0	0	0	0	0	0.89	0	0
Cyprinodon variegatus	0	0	0	0	10.16	8.93	2.93	0	0	0	0	0	0	0	0
Fundulus heteroclitus	4.39	16.44	31.98	135.89	140.32	91.66	49.76	27.24	7.13	6.73	0	57.40	0	0.07	0
Gasterosteus aculeatus	2.34	0.07	0	0	0	3.20	0	0	0	0.78	1.25	0	0	0	0
Gobiosoma bosc	0.89	0.43	5.82	3.44	3.89	5.86	3.17	14.81	13.45	0	0	0	0.39	3.09	2.64
Haminoea solitaria	0	0	0	0	0	0	0.73	0	0	0	0	0	0	0	0
Ilyanassa obsoleta	0	0	0	474.45	0	0	10.92	2.61	0	0	0	0	0	0	0
Libinia emarginata	49.37	0	21.08	0	0	0	0	0	0	109.77	0	0	0	55.95	0
Lucania parva	7.81	1.40	21.16	0	10.86	7.24	24.18	5.25	2.62	0.72	0.06	1.71	3.43	7.85	0
Menidia menidia	0	0.56	0	0	0	0	0	0	0	0	2.92	0	0	0	0
Opsanus tau	0	0	0	0.43	0	0	0	0	0	0	0	0	0	0	0
Palaemonetes pugio	51.29	27.03	46.30	106.53	64.31	116.24	68.36	166.75	33.97	57.93	36.89	65.14	47.13	96.40	108.12
Panopeus herbstii	4.77	0	9.96	3.53	15.60	9.11	3.85	4.69	0	0	87.22	5.48	2.83	4.87	3.37
Pseudopleuronectes americanus	0	0	14.10	0	0	0	2.66	0	0	0	0	0	0	5.21	0
Syngnathus fuscus	0	1.79	0	0	0	0	0	0	0	0.19	4.34	0.30	0	0	0
Tautogolabrus adspersus	0	0	4.48	0	0	0	0	0	0	0	0	0	0	0	0
Tautoga onitis	0	0	0	0	0	0	0	0	0	0	1.29	0	0	0	0
Uca pugilator	0	0	0	0	0	0	0	0	0	0.86	0	0	0	0	0

Appendix 4b.

Shrimp trap species abundance^{−24 hours} collected from sampling sites in Ninigret Pond during 2014. AQB=Aquaculture Bare, AQ1 and AQ2=Aquaculture sites 1 and 2, FCNB=Foster’s Cove North Bare, FCSB=Foster’s Cove South Bare, FC1, 2, 3, and 4=Foster’s Cove sites 1, 2, 3 and 4, GPB=Grassy Point Bare, GP1 and 2=Grassy Point sites 1 and 2, SSB=South Sanctuary Bare, SS1 and 2=South Sanctuary sites 1 and 2. See Figure 1 for locations.

	Site Number of Samples
	AQB	AQ1	AQ2	FCNB	FC1	FC2	FCSB	FC3	FC4	GPB	GP1	GP2	SSB	SS1	SS2
Species	6	6	6	5	5	4	6	6	4	6	6	6	6	6	6
Apeltes quadracus	3	3	5	2	0	0	2	0	0	0	0	0	0	0	0
Callinectes sapidus	2	0	0	2	4	1	2	2	1	1	3	2	3	1	1
Carcinus maenas	0	1	7	0	0	8	1	1	0	3	8	4	0	2	0
Crangon septemspinosa	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0
Cyprinodon variegatus	0	0	0	0	16	11	2	0	0	0	0	0	0	0	0
Fundulus heteroclitus	6	27	68	21	63	54	35	23	1	4	0	51	0	1	0
Gasterosteus aculeatus	2	1	0	0	0	5	0	0	0	1	1	0	0	0	0
Gobiosoma bosc	1	1	2	6	3	13	1	13	11	0	0	0	1	2	1
Haminoea solitaria	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0
Ilyanassa obsoleta	0	0	0	211	0	0	3	1	0	0	0	0	0	0	0
Libinia emarginata	2	0	1	0	0	0	0	0	0	3	0	0	0	2	0
Lucania parva	22	6	52	0	10	8	65	2	1	1	1	2	5	34	0
Menidia menidia	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0
Opsanus tau	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
Palaemonetes pugio	163	91	158	393	252	507	300	640	170	144	136	220	199	413	474
Panopeus herbstii	3	0	3	1	8	3	1	3	0	0	4	2	1	1	1
Pseudopleuronectes americanus	0	0	2	0	0	0	1	0	0	0	0	0	0	1	0
Syngnathus fuscus	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0
Tautogolabrus adspersus	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
Tautoga onitis	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0
Uca pugilator	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0

Appendix 5.

Total annual biomass (g m⁻²) and density (individuals m⁻²) of infauna collected monthly between May through October 2014 at the Aquaculture and South Sanctuary sites in Ninigret Pond using a 6.5 cm D × 14 cm H corer. AQB=Aquaculture Bare, AQ1 and AQ2=Aquaculture sites 1 and 2, and SSB=South Sanctuary Bare, and SS1 and SS2=South Sanctuary sites 1 and 2.

	Site Biomass (g m−2)						Site Density (individuals m−2)
Species	AQB	AQ1	AQ2	SSB	SS1	SS2	AQB	AQ1	AQ2	SSB	SS1	SS2
Acanthohaustoris millsi	<0.01	0	0	0	0	0	11.58	0	0	0	0	0
Alitta succinea	0	0.50	<0.01	0	0	0	0	11.58	11.58	0	0	0
Ameritella agilis	0	0	0	5.21	0	0	0	0	0	19.80	0	0
Ampelisca abdita	0.01	0	0	0	0	0	19.80	0	0	0	0	0
Arabella iricolor	0.28	0.20	1.50	0	0	0.89	31.39	19.80	35.79	0	0	19.80
Byblis serrata	0.01	0	0	0	0	0	19.80	0	0	0	0	0
Capitella capitata	0.74	1.38	0.24	0	0.88	0.34	59.41	85.59	31.39	11.58	39.61	31.30
Capitella spp.	0	0	0	0	0	0.03	0	0	0	0	0	19.80
Centropages spp.	0	0	0	0.04	0	0	0	0	0	11.58	0	0
Corophium volutator	0.03	0	0	0	0	0	11.58	0	0	0	0	11.58
Drilonereis longa	0	0	0	0	9.73	0	0	0	0	0	11.58	0
Edotia triloba	0.04	0	0	0	0	0	11.58	0	0	0	0	0
Eteone lactea	0	0	0	0	0	0	0	0	0	0	0	11.58
Eteone trilineata	0	0	0	0	0.07	0	0	0	0	0	11.58	0
Exogone spp.	0.02	<0.01	0.02	<0.01	0	<0.01	62.79	26.18	31.39	48.71	0	11.58
Gemma gemma	0.07	0	0.05	0.21	0	0	11.58	0	19.80	26.18	0	0
Glycera americana	0	0.09	0.03	0	0	0	0	11.58	11.58	0	0	0
Glyceridae	0	0	0	0.76	0	0	0	0	0	11.58	0	0
Goniada maculata	0	0	0	<0.01	0	0	0	0	0	11.58	0	0
Harpinia propinqua	0	0	0	0	0	0	0	0	0	11.58	0	0
Heteromastus filiformis	0.11	0	0	<0.01	0	0	39.61	0	0	11.58	0	0
Hypereteone heteropoda	0.01	0.06	0.04	0	0	<0.01	48.71	39.61	48.71	0	11.58	11.58
Idunella clymenellae	0.06	0	0	0	0	0	11.58	0	0	0	0	0
Leitoscoloplos fragilis	0	1.24	0	4.65	0	0	0	11.58	0	42.97	0	0
Lembos websteri	0	0	0	0	0	0	0	0	11.58	0	0	0
Leptocheirus pinguis	0.03	0	0	0.08	0	0	39.61	0	0	35.79	0	0
Leucon americana	0.01	0	0	0.07	0	0	31.39	0	0	31.39	0	0
Lumbrineris acicularum	0.05	0	0	0	0	0	31.39	0	0	0	0	0
Lysianopsis alba	0.36	0	0	0	0	0.05	39.61	0	11.58	0	0	19.80
Microdeutopus gryllotalpa	0.06	0.09	0.03	0	0	0.03	64.32	35.79	72.16	0	0	35.79
Monoculodes edwardsi	0	0	0	0.03	0	0	0	0	0	19.80	0	0
Neanthes arenaceodentata	<0.01	0	0	0	0	0	19.80	0	0	0	0	0
Oligochaeta	0	<0.01	0	0	0	0	0	11.58	0	0	0	0
Orbinia ornata	0.55	0	0.67	0.99	0	0	48.71	0	11.58	31.39	0	0
Ostracod	0.09	0.02	0.01	0.01	0	<0.01	48.71	26.18	26.18	39.61	0	11.58
Oxydromus obscura		0.02	0	0	0	0	0	11.58	0	0	0	0
Polychaeta	<0.01	<0.01	0	0.03	0	0	31.39	11.58	0	19.80	0	0
Polydora cornuta	0.05	0.34	0.02	0	0	0	45.98	35.79	11.58	11.58	0	0
Polydora spp.	0	0	0	0	0	0	0	0	0	0	0	0
Prionospio spp.	0.86	0	0	0	0	0	57.57	0	0	0	0	0
Scoloplos armiger	0	0	<0.01	0	0	0	0	0	11.58	0	0	0
Solemya velum	0	4.66	3.99	0	0	0	0	39.61	39.61	0	0	0
Streblospio benedicti	0.69	0.03	0.02	0	0	0	68.51	19.81	11.58	0	0	0