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Billion Oyster Project Living Breakwaters Oyster Enhancement Monitoring and Adaptive Management Plan

Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Version 5 Submission Date: June 16, 2025

Revised: July 3, 2025

Plan Overview The purpose of this Monitoring and Adaptive Management Plan is to describe Billion Oyster Project’s methods and analytical approaches for understanding oyster health and performance and the success of restoration on the Living Breakwaters (Figure 1).

Oysters will be introduced to the breakwaters in two phases and use two restoration techniques:

1) three in situ (direct setting) trials in 2025 and 2026, and 2) the introduction of 4,494 ECOncrete Disks set with spat (juvenile oysters) into armor units in 2026. Complete descriptions of these restoration activities are included in the permit application. Summaries are provided below (see “In Situ Setting Trials” and ”Seeded ECOncrete Disks”).

Monitoring is organized into two areas: (1) oyster health & performance, and (2) estuarine community utilization (Table 1). Monitoring will be conducted for five years following the installation of each phase (Table 2).

An annual monitoring report will be prepared and submitted to the permitting agencies by December 31 of each year. These reports will contain data, analyses, and observations on the relevant parameters measured each year and propose management recommendations to guide ongoing restoration at this site (see “Deliverables” below).

This plan was updated in June 2025 and resubmitted to regulatory agencies to reflect changes to the project scope, timeline, and reporting requirements. The following changes are reflected:

● Adjustment of the project years to 2025 and 2026. No installation will occur in 2027.

● Removal of Droplocks from the Monitoring Plan per the revised permit application.

● Adjustment of the in situ trials’ sequencing so that the first trial occurs in 2025.

● Inclusion of a revised protocol to assess recruitment along the breakwaters.

● Discussion on the statistical reporting and analysis to be performed for each oyster performance parameter.

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Figure 1. Proposed overall site plan as per the Joint Permit Application showing the location of breakwater structures. Oysters will be installed on breakwaters D, F, G, and H. Sheets referenced in this diagram are not included in this Monitoring Plan, but can be found in the complete Joint Permit Application.

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Table 1. Monitoring Protocols and Timeline

Table 2. Timeline of Restoration and Monitoring Activities

Approach 2025 2026 2027 2028 2029 2030 2031

In Situ Setting Breakwater D

Year 0 / Installation

Year 1 Year 2 Year 3 Year 4 Year 5 -

In Situ Setting Breakwaters F, G

- Year 0 / Installation

Year 1 Year 2 Year 3 Year 4 Year 5

Seeded Disks - Year 0 / Installation

Year 1 Year 2 Year 3 Year 4 Year 5

Research Area Protocol Parameter(s) Substrate Frequency (Per phase)

Sample size (Per event)

Oyster Health & Performance

Growth, Mortality, & Recruitment

Shell Height Survival Rate Mortality Rate Predation Recruitment

Seeded Disks

Annually Years 1-5

At least one disk from ~30% of armor units

(41 of 137)

Growth, Mortality, & Recruitment

Shell Height Survival Rate Mortality Rate Predation Recruitment

Armor units and core stone from in situ trials and control breakwater

Annually Year 0

Years 1-5

Two 150’ transects per breakwater

Reproduction Gonad Condition Sex Ratio Condition Index

Summer Year 3 Year 5 n = 40 oysters stratified across 4 breakwaters

Disease Disease Intensity & Prevalence

Summer Year 3 Year 5 n = 40 oysters stratified across 4 breakwaters

Research Area Protocol Parameter(s) Substrate Frequency Sample size

Estuarine Community Utilization

Epibenthic Characterization

Biodiversity Abundance

Seeded Disks Year 1 Year 3 Year 5

At least one disk from ~30% of armor units

(41 of 137)

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

In Situ Setting Trials A complete description of the In Situ Setting Trials can be found in the In Situ (Direct Setting) with a Turbidity Curtain and Contingency Plans Protocol. In brief, BOP will deploy a Type-III turbidity curtain to enclose a 100-150’ section of a breakwater and directly set approximately 30 million pediveliger-stage spat to the leeward sides of Breakwaters D, F, and G (each) in three separate trials in 2025 or 2026 (Table 3, Figure 2). This approach will seed juvenile oysters onto both the intertidal and subtidal granite core stone and ECOncrete armor units of the breakwaters. Based on literature reviews, BOP anticipates an in situ trial to yield an 8-10% setting rate: to set 30 million spat, this requires approximately 300 million larvae. This setting rate and spat count will be verified through post-trial monitoring.

Table 3. Summary of In Situ Trials to be conducted in 2025 and 2026

Breakwater Year No. Larvae

D 2025 70 M

F, G 2026 230 M

Figure 2. Schematic of turbidity curtain deployment during in situ setting trial.

https://docs.google.com/document/d/1EpV25gfuVd7P3RKJAOgMV-5m2-D2g-GEbIWTvgqzHuQ/edit?usp=sharing https://docs.google.com/document/d/1EpV25gfuVd7P3RKJAOgMV-5m2-D2g-GEbIWTvgqzHuQ/edit?usp=sharing

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Seeded ECOncrete Disks The permit application provides a complete description of the ECOncrete Disks and armor units, but a brief description follows. Each ECOncrete disk weighs approximately 10-12 lbs and has a diameter of approximately 10 inches. When stacked on top of each other, ECOncrete disks can interlock, which is then stabilized by placing a shaft anchor through the middle of each disk (molds include this design feature).

BOP will install approximately 4,500 ECOncrete disks to 137 armor units on Breakwaters D, F, G, and H (Table 4, Figure 3). Each armor unit houses 14 disks. The oyster disks will be seeded with spat (juvenile oysters) prior to installation.

Table 4. Summary of Seeded ECOncrete Disks to be installed in 137 armor units in 2026

Breakwater # Disks

D 980

F 1,582

G 938

H 994

TOTAL 4,494

Figure 3. Schematic of seeded ECOncrete disks installed in armor units of breakwaters.

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Protocols Billion Oyster Project will follow relevant research protocols used in similar habitat enhancement projects within New York Harbor and the Hudson River, such as the Hudson River Park Sanctuary projects, Soundview Oyster Habitat Restoration Project, and Governor Mario M.

Cuomo (Tappan Zee) oyster restoration projects, to allow for collection of comparable data across the region (Grizzle et al. 2013, Lodge et al. 2017, Fitzgerald et al. 2020). This Monitoring Plan that follows below details Billion Oyster Project’s approach and protocols for each research area.

Deliverables All data will be provided to the regulatory agencies in an annual report in compliance with all permit conditions and requirements. Some parameters are not measured annually and will be included in reports as appropriate. Table 6 provides a summary of the statistical analysis that will be reported for each variable.

Year 0 Post-Installation Report

By September 30, 2025, Billion Oyster Project will submit a post-installation report summarizing the preliminary results, data, and lessons learned from the first in situ trial, which will be conducted in early July 2025. This report will also include baseline recruitment data from pre-trial surveys of Breakwater D.

Annual Report

From 2026 to 2031, Billion Oyster Project’s Annual Report will include data and analysis of oyster growth, mortality, and recruitment at the Living Breakwaters. Data and analysis of oyster reproduction and disease will be included in years 3 and 5 for the seeded disks (2029 and 2031).

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Growth, Mortality, & Recruitment - Seeded Disks

Objectives

Each year, a random subset of seeded ECOncrete disks on Breakwaters D, F, G, and H will be monitored to assess oyster density, shell height (i.e., growth), evidence of predation, and survival/mortality. The presence of juvenile oysters (i.e., spat) is an indicator of a reproductive oyster community, and while the origin of newly settled spat cannot be directly attributed to the installed oysters from this project without genetic testing, it can speak to the habitat function of the oysters as a desirable substrate for settlement. Similar oyster measurements have been made by Lodge et al. (2017) on gabions and reef balls as part of the Tappan Zee Bridge mitigation/restoration project.

Field Methods

ECOncrete disks will be retrieved and measured onshore or on the deck of a small vessel, in situ at low tide, or in situ by divers or snorkelers taking pictures of quadrats using a Go-Pro® attached to a Clearwater Box®.

● Density: The entire disk surface area will be assessed for oyster density (i.e., number of live and dead box oysters per unit and per square meter).

● Growth: Using calipers, all live and dead box (i.e., dead oysters with both valves still intact) oysters on a disk will be measured along the longest point of shell height (bill to umbo) in millimeters. If the number of oysters to measure on a disk exceeds 50, a quadrat of known area will be used to subsample remaining oysters on fixed locations of the top, bottom, and sides of the disks.

● Mortality: Oyster mortality is measured by visual assessment of dead box oysters. Shell height of dead box oysters will be measured and the upper valve will be removed after measuring so the oyster is not remeasured on subsequent sampling events.

● Predation: Visual assessment for evidence of oyster drills, boring sponges, or other predators will be noted. Counts of these common predators will also be recorded if seen on the disks during monitoring.

● Recruitment: The number of spat on the disks or attached to oysters on the disks will be recorded when the disks are monitored. Oysters introduced by BOP typically grow to a shell height of more than 25 mm after one year of installation, which means any oysters that are smaller than 25 mm are likely recruits at the site.

Sampling Plan

BOP will finalize and submit a sampling plan post-installation in 2026 once an “as-built” record of installed disks and quantities is prepared. Before Year 1 monitoring begins in 2027, BOP will

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan randomly select a subset of disks from a randomly selected subset of armor units from each of the four breakwaters. The randomization will be stratified to ensure samples are taken representative of potential covariates (e.g., water depth, position of disk within armor units, or linear position of armor unit along breakwater). BOP will aim to sample at least one disk from 30% of the armor units on each breakwater (41 of the 137 total armor units) at each sampling event.

Lab Methods

Not applicable.

Analysis & Reporting

● Density: For each sampling event, the average and standard deviation of live oysters per disk will be reported for each breakwater and across all breakwaters. Oysters per disk can be converted to oysters per square meter, based on the known surface area of a disk.

● Growth: For each sampling event, size frequency distributions (i.e., histograms) of oyster shell height across all disks on each breakwater will be reported. The average shell height and standard deviation will be reported for each breakwater and across all breakwaters. An annual growth rate can be calculated by comparing changes in the average shell height across years.

● Annual Mortality: For each sampling event, the average and standard deviation of percent dead oysters per disk will be reported for each breakwater and across all breakwaters.

● Annual Survival: For each sampling event, the average and standard deviation of percent live oysters per disk will be reported for each breakwater and across all breakwaters.

● Predation: For each sampling event, the presence and total abundance of predators will be reported for each breakwater and across all breakwaters. The percentage of disks per breakwater with predators present or identifiable marks of predation will be reported.

● Recruitment: For each sampling event, the average and standard deviation of the number of oysters with shell height less than 25 mm per disk will be reported for each breakwater and across all breakwaters. The size-frequency distributions of oyster shell height will also be examined visually for the presence of bimodal patterns(e.g., one peak above 25 mm and another peak below 25 mm) to confirm recruitment, but if recruitment is low, a distinct peak of smaller oysters may not be apparent through visual inspection.

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Growth, Mortality, & Recruitment - In Situ Trials

The armor units and granite core stone of breakwaters will be surveyed to monitor the oysters that were established as a result of the in situ setting trials in 2025 and 2026 and any that recruited naturally. Potential breakwaters to be surveyed will be those where in situ trials were performed - D, F, and G - and breakwaters where no oysters were installed (e.g., Breakwater C).

The goal of the surveys is to assess growth (i.e., shell height), density, predation, mortality/survival, and recruitment of oysters on substrates other than disks.

Field Methods

BOP will establish approximately 150’ transects on the lee and ocean sides of the breakwater that is being surveyed. The transect will be established between Mean High Water (MHW, +2.08’ NAVD88) and MLW and run parallel to the breakwater structure at an approximately fixed elevation. BOP will aim to establish the transects to span the area where the turbidity curtain is deployed for the in situ trial (i.e., a 150’ transect will be centered around the 50’ turbidity curtain deployment area with ~50’ on either side). Start and end points of the transects will be recorded with a handheld GPS unit. Sampling protocols will be similar to those in BOP’s Wild Oyster Survey Protocol and adapted to be conducted via kayak.

Sampling Plan

The oyster performance parameters measured along the transect are similar to those measured on the seeded ECOncrete disks and include:

● Density: The number of oysters (both live and dead box) along the transect will be counted.

● Growth: Using calipers, all live and dead box (i.e., dead oysters with both valves still intact) oysters along the transect will be measured along the longest point of shell height (bill to umbo) in millimeters.

● Mortality: Oyster mortality is measured by visual assessment of dead box oysters. Shell height of dead box oysters will be measured and the upper valve will be removed after measuring so the oyster is not remeasured on subsequent sampling events.

● Predation: Visual assessment for evidence of oyster drills, boring sponges, or other predators will be noted. Counts of these common predators will also be recorded if seen on the disks during monitoring.

If oyster densities along a transect are high and the entire length cannot be surveyed, this monitoring approach may be modified to subsample with randomly-selected quadrats or reduce the overall transect length.

https://docs.google.com/document/d/1dZGLaVxli-ES7WldyPqfvqGWEVqvhdjFxEhz6yEeuWE/edit?usp=sharing https://docs.google.com/document/d/1dZGLaVxli-ES7WldyPqfvqGWEVqvhdjFxEhz6yEeuWE/edit?usp=sharing

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Lab Methods

Not Applicable.

Analysis & Reporting

● Density: For each sampling event, the total number of live oysters per transect will be reported for each breakwater and across all breakwaters.

● Growth: For each sampling event, size frequency distributions (i.e., histograms) of oyster shell height along each transect will be reported. The average shell height and standard deviation will be reported for each breakwater and across all breakwaters. An annual growth rate can be calculated by comparing changes in the average shell height across years.

● Annual Mortality: For each sampling event, the average and standard deviation of percent dead oysters per transect will be reported for each breakwater and across all breakwaters.

● Annual Survival: For each sampling event, the average and standard deviation of percent live oysters per transect will be reported for each breakwater and across all breakwaters.

● Predation: For each sampling event, the presence and total abundance of predators will be reported for each transect, each breakwater, and across all breakwaters.

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Reproduction, Condition Index, & Disease - Seeded Disks

Reproduction As oysters mature, they allocate energy toward growth, maintenance, and, once fully developed, reproduction. A key indicator of an oyster's reproductive potential is the maturity of its gonads, which produce gametes—eggs or sperm—during the warmer months in preparation for spawning. Oysters have separate sexes but can switch between male and female after reaching sexual maturity, typically around two years post-settlement. Assessing gonad condition involves evaluating sexual maturity and the readiness for spawning. Determining the sex ratio is also important, as balanced proportions of male and female oysters increase the likelihood of successful reproduction. Similar methods for evaluating reproduction, condition index, and disease have been used by Levinton et al. (2013) and are regularly used at BOP’s other restoration sites throughout the region.

Condition Index An indicator of oyster health is the condition index, calculated as the dry weight of its tissues (in grams) divided by the dry weight of its shell (in grams), multiplied by 100.

Disease MSX (Haplosporidium nelsoni) and Dermo (Perkinsus marinus) are two diseases known to infect oysters in NY/NJ Harbor, negatively affecting oyster health and potentially leading to mortality.

Field Methods

Oysters will be carefully removed from the disks to prevent any shell damage that could compromise internal tissues. Once collected, they will be placed in a cooler with ice packs to maintain a low temperature during transport. To avoid freezing or tissue damage, oysters will be kept cool but not in direct contact with the ice. All samples will be delivered to the disease testing facility within 24 hours of collection.

Sampling Plan

In August of Years 3 and 5 (2029 and 2031), adult oysters from the seeded disks will be sampled to assess reproduction, condition index, and disease. The Marine Animal Disease Lab at Stony Brook University recommends a minimum sample of 30 oysters. A total of 40 oysters will be collected approximately evenly across the four breakwaters (10 oysters per breakwater)

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan and randomly stratified to ensure representation along the length of each structure. Each oyster will be analyzed for all three parameters: reproduction, condition index, and disease.

Lab Methods - Reproduction

Tissue will be dissected from oysters and slides will be prepared to analyze under a microscope to determine sex and gonad condition as described by Fisher et al. (1996). See below for a description of the gametogenic characteristics associated with different stages of sexual development that can be determined through this histological analysis.

Lab Methods - Condition Index

Oysters will be shucked, weighed, and dried for condition index. Condition Index = (tissue dry weight (g) / dry shell weight (g)) x 100 (Filgueira et al. 2013).

Lab Methods - Disease

The disease testing facility will use standard industry protocols. Ray’s fluid thioglycollate medium will be used on the mantle and rectal tissues for Dermo diagnosis. The remaining tissues will be fixed in a buffered formalin solution for histopathology, with one slide from each paraffin block. Hemotoxylin and eosin staining will be used for MSX diagnosis.

Analysis & Reporting - Reproduction

For sex ratio, the ratio of male to female oysters will be reported based on a sample of 40 oysters. As this is a single observed ratio, no measure of variance will be provided. For the stage of sexual development, the number of oysters observed in each developmental stage will be summarized, and variance will not be reported, as it is not applicable. Developmental stages will be categorized as follows:

● I: Inactive (no gonadal activity, resting)

● G1: Gametogenic I stage; gametogenesis has begun; no ripe gametes visible

● G2: Gametogenic II stage; first ripe gametes appeared; gonad developed to about one-third of its final size

● D1: Developing I stage; Gonad increased in mass to about half the full ripe condition;

each follicle contains about equal proportions of ripe and developing gametes

● D2: Developing II stage; Gametogenesis still progressing; follicles mainly contain ripe gametes

● R: Ripe stage; Gonad fully ripe, early stages of gametogenesis rare; follicles distended with ripe gametes; ova compacted into polygonal configurations; sperm with visible tails

● S1: Spawning stage I; Active emission of gametes has begun; gametes density reduced

● S2: Spawning stage II; Gonad about half empty

● S3: Spawning stage III; Gonadal area reduced; follicles about one-third full of ripe gametes

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

● S4: Spawning stage IV; Only residual gametes remain; some may be undergoing cytolysis

● Undetermined: these are oysters where gonad tissue was rudimentary (completely undeveloped as is the case in very young oysters) or absent

Analysis & Reporting - Condition Index

For each sampling event, the average and standard deviation of condition index will be reported for sampled oysters on each breakwater and across all breakwaters.

Analysis & Reporting - Disease

Outputs will include both disease prevalence (percentage of samples that tested positive for a given disease) and intensity (degree to which an individual oyster is infected with a given disease) for both MSX and Dermo. For each sampled oyster, Dermo intensity will be reported on the Mackin Scale of 0, 0.5 (rare), 1.0 (light), 2 (light-to-moderate), 3 (moderate), 4 (moderate-to-heavy), and 5 (heavy) and MSX intensity will be reported as low, medium, or high (qualitative scoring based on the Standard Operating Procedures of the Marine Animal Disease Laboratory at Stony Brook University). Categorical data from all sampled oysters will be reported in either tabular and graphical formats, so no measure of variance for disease prevalence or intensity is possible.

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Epibenthic Community Utilization - Seeded Disks

ECOncrete Disks provide a surface area to which other sessile organisms and vegetation colonize. BOP will survey the epibenthic community composition on the disks in Years 1, 3, and 5 (2027, 2029, and 2031) by retrieval of disks or in situ photos and/or video captured by divers.

This monitoring will document the community composition of vegetation (e.g., Fucus sp., Ulva sp.), sessile colonial organisms (e.g., sponges, hydroids), sessile individuals (e.g., barnacles, mussels, sea squirts, slipper snails, polychaete worms), and mobile individuals (e.g., oyster drills, polychaetes, flatworms, and portunid crabs).

Field Methods

Disks may be retrieved and monitored on a vessel or on shore or monitored in situ depending on site conditions. If in situ monitoring is required, snorkelers or divers from a boat may operate a Clearwater Box® with an affixed Go-Pro® camera and methodically take photos and/or video along the armor units and seeded disks. If sedimentation has obscured visibility on the surface of the disks, divers will brush mud with their hands and pause until the epibenthic organisms are visible. Mobile species, if present, will also be recorded. All flora and fauna will be identified to the lowest practical taxon (species when possible) and enumerated through non-destructive means. If retrieved, the disks will be redeployed to the armor units after monitoring. Similar methods have been used by Fitzgerald et al. (2020) to monitor the epibenthic community on reef balls as part of Hudson River Park Trust’s Tribeca Habitat Enhancement.

Sampling Plan

BOP will finalize and submit an epibenthic sampling plan post-installation in 2026 once an “as-built” record of installed disks and quantities is prepared. Before Year 1 monitoring begins in 2027, BOP will randomly select a subset of disks from a randomly selected subset of armor units from each of the four breakwaters. The randomization will be stratified to ensure samples are taken representative of potential covariates (e.g., water depth, position of disk within armor units, or linear position of armor unit along breakwater). BOP will aim to sample at least one disk from 30% of the armor units on each breakwater (41 of the 137 total armor units) at each sampling event.

Lab Methods

If photos and/or videos are captured of disks, they will be analyzed to identify all flora and fauna to the lowest practical taxon (species when possible). For clonal, colonial and encrusting organisms, surface area will be calculated with image analysis software (e.g., ImageJ).

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Analysis & Reporting

For each sampling event, the following values will be reported at the level of each disk, each breakwater, and the overall site (i.e., across all breakwaters):

● List of taxa observed

● Taxonomic richness

● Abundance of each taxa (for individual organisms) - including average and standard deviation when reported at the breakwater or site level.

● Percent cover of each taxa (for colonial organisms) - including average and standard deviation when reported at the breakwater or site level.

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Performance Criteria Monitoring data will be compared with the Performance Criteria presented in Table 5 and reported in the Annual Report.

Table 5. Performance criteria for Living Breakwaters

Topic Protocol Parameter(s) Performance Metric Explanation Oyster Health Performance

Size/Growth & Mortality

Height Density Annual Survival Annual Mortality Predation

Continued increase in average shell height after Year 1

Average oyster density stabilizes years 3-5 after initial mortality

Growth rates typically slow down in year 2+, but oysters should continue to increase their shell height.

Reproduction Gonad Condition Assessment of gonad condition shows the gonads ripe and ready to spawn in years 2-5

Oysters switch sexes, with smaller and younger oysters typically being males.

Sex Ratio

Sex ratios near or at 50:50 (40:60 is acceptable) in years 2-5

Even sex ratios will increase the odds of successful reproduction.

Disease Disease Intensity & Prevalence

Disease prevalence of Dermo MSX are moderate (<60%)

No more than 25% High on the MSX intensity scale

No more than 25% at stages 4 or 5 on the Dermo intensity scale

Prevalence and intensity of oyster disease (Dermo, MSX) should be low.

Recruitment Spat Counts >1 size class of oysters present After 3 or more years, more than one size class of oysters should be present through reseeding interventions or natural recruitment.

Oysters with a shell height of <25mm are considered recruits.

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Table 6. Analysis and statistical reporting of parameters

Parameter Analysis & Measure of variance

Shell height

For each sampling event, size frequency distributions (i.e., histograms) of oyster shell height across all units (disks or quadrats) on each breakwater will be reported. The average shell height and standard deviation will be reported for each breakwater and across all breakwaters. An annual growth rate can be calculated by comparing changes in the average shell height across years.

Oyster density

For each sampling event, the average and standard deviation of live oysters per unit will be reported for each breakwater and across all breakwaters. Oysters per unit can be converted to oysters per square meter, based on the known surface area of a disk or quadrat.

For transect-based surveys, average and standard deviation of oyster density will be reported separately for breakwaters with in situ setting (D, F, G) and control (C) and diss only/control (H).

Annual survival For each sampling event, the average and standard deviation of percent live oysters per unit will be reported for each breakwater and across all breakwaters.

Annual mortality For each sampling event, the average and standard deviation of percent dead oysters per unit will be reported for each breakwater and across all breakwaters.

Predation For each sampling event, the presence and total abundance of predators will be reported for each breakwater and across all breakwaters. The percentage of units per breakwater with predators present or identifiable marks of predation will be reported.

Recruitment

For each sampling event, the average and standard deviation of number oysters with shell height <25 mm per disk will be reported for each breakwater and across all breakwaters. The size-frequency distributions of oyster shell height one year post-installation will also be examined visually for the presence of two peaks (e.g., one <25 mm and one >25 mm) to confirm recruitment, but if recruitment is low, a peak of smaller oysters may not be visible through visual inspection.

Gonad condition # of oysters per developmental stage from n = 40 oysters. Counts of oysters in each development stage will be reported, so no measure of variance for any sexual development stage is possible.

Sex ratio Ratio of male/female from n = 40 oysters. No measure of variance.

Condition index For each sampling avent, average and standard deviation of condition index from n = 40 oysters

Disease prevalence % of oysters infected from n = 40 oysters. No measure of variance.

Disease intensity # of oysters per disease stage (Mackin Scale of stages 0-5 for Dermo; qualitative ranking of low, medium, or high for MSX). No measure of variance.

% of oysters w/ potentially lethal intensity (for Dermo) from n = 40 oysters. No measure of variance

Epibenthic richness Average # of species (or taxa) present per unit Total # of species (or taxa) present across all units

Epibenthic abundance

Average and standard deviation of individuals of each species (or taxa) per unit Total # of individuals of each species (or taxa) across all units

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

Adaptive Management Strategies Adaptive management strategies ensure that insights gained from monitoring activities guide both current and future restoration efforts. This iterative approach allows the Billion Oyster Project to continuously refine its methods, respond to changing environmental conditions, and enhance ecological and restoration outcomes. Data collected during the reporting period—including oyster performance, associated biodiversity, and observations on the condition of the ECOncrete disks—will help determine whether adaptive management actions are needed. While the following section outlines potential scenarios and corresponding responses, unforeseen challenges may also arise. In such cases, the Billion Oyster Project will communicate field observations and emerging challenges to regulatory agencies to coordinate appropriate responses.

Re-seeding in Response to Oyster Performance

Re-seeding, a targeted strategy involving the introduction of a new cohort of oyster spat to the breakwaters, is a practical and widely accepted best management practice when mortality rate exceeds recruitment. Techniques to re-seed the breakwaters may include:

● The addition of seeded ECOncrete disks to unfilled ECOncrete armor units: Billion Oyster Project will contact SCAPE and ECOncrete to identify the unfilled, appropriate armor units in which seeded ECOncrete disks may be added.

● In situ setting trials: Billion Oyster Project will plan and implement additional in situ trials directly on the breakwaters.

Disk Replacement

If Billion Oyster Project observes any missing, broken, or cracked ECOncrete disks during annual monitoring activities, the condition, location of the Armor Unit, and quantity will be documented and reported. Billion Oyster Project may plan to replace the affected disk(s) with new seeded disks during the next setting season.

Revising Oyster Performance Monitoring on ECOncrete Disks

As oysters grow out on the ECOncrete disks, the disks may become difficult to remove from the armor units without risking oyster mortality. Should this occur, BOP may revise its monitoring methods to assess oyster performance on the disks without removal.

Additional Adaptive Management Measures If excessive disease or predation impede restoration success, other adaptive management measures (e.g., use of disease-resistant oyster strains, use predator cues during setting to induce stronger shell morphology) could be investigated in coordination with regulatory agencies, but most of these approaches have not been successfully deployed at scales large enough for this project and would increase project costs.

Billion Oyster Project Living Breakwaters Oyster Enhancements Monitoring and Adaptive Management Plan

References

Filgueira, R., L. Comeau, T. Landry, and J. Grant. 2013. Bivalve condition index as an indicator of aquaculture intensity: A meta-analysis. Ecological Indicators 25: 215-229.

Fitzgerald, A.M., C. Roble, M. Krupitsky, M. Ramirez, and C. Giraldo. 2020. Invertebrate colonization of pier pilings in the Hudson River. Final Report to Hudson River Park Trust.

Fisher, W.S., J.T. Winstead, L.M. Oliver, H.L. Edmiston, and G.O. Bailey. 1996. Physiologic Variability of Eastern Oysters from Apalachicola Bay. Florida. J. Shellfish Res. 15:543-553.

Levinton, J., Doall, M. and Allam, B. 2013. Growth and mortality patterns of the eastern oyster Crassostrea virginica in impacted waters in coastal waters in New York, USA. J. Shellfish Res.

32(2):417-427.

Lodge, J., R. Grizzle, K. Ward, P. Malinowski, and K. Mosher Smith. 2017. Tier 3 Tappan Zee Bridge Oyster Restoration Pilot Study. Final Report to AKRF, Inc. and The New York State Thruway Authority.

https://bpb-us-e1.wpmucdn.com/you.stonybrook.edu/dist/3/599/files/2014/10/Jeff-JSR-1-xzln04.pdf

TO: Chelsea Miller, NYSDEC FROM: Cate Collinson, Billion Oyster Project DATE: May 2, 2025 RE: LCP-Scientific #1143, 2025 Modification Request - Living Breakwaters Project

The following memorandum outlines Billion Oyster Project’s (BOP) request to add proposed off-bottom oyster recruitment enhancement activities for the Living Breakwaters Project to License to Collect and Possess- Scientific (LCP) #1143. As part of the enhancement activities, BOP seeks authorization to directly seed 7 million oysters onto the Breakwater D via in situ setting in July 2025. Additional in situ trials on Breakwaters F and G are planned for 2026 and BOP will submit a separate LCP modification request for those activities once the details are finalized.

Background The Living Breakwaters Project is designed to reduce or reverse shoreline erosion along the Tottenville shoreline of Staten Island and to enhance habitat diversity through the establishment of new structural habitats using eco-enhancing materials and structures that provide interstitial habitat. Oyster restoration at the Breakwaters Project would restore a complex oyster reef habitat at the Living Breakwaters segments. Permit approvals for the addition of structures set with live oysters onto the Breakwaters is pending (Application ID: 2-6405-00610/00007). During a meeting with New York State Department of Environmental Conservation (NYSDEC) Region 2, Department of Marine Resources (DMR) along with the Project Applicant, Resilient Homes and Communities, and BOP on April 23rd, 2025, NYSDEC Region 2 and DMR agreed that in light of the pending approvals to add additional set structure on to the Breakwaters, BOP could apply for an LCP modification to conduct the in situ setting (direct seeding) scope of the proposed project beginning in 2025 with a second in situ event occurring in the summer of 2026.

Proposed Activities For Approval BOPs proposes a series of in situ oyster larval setting trials to enhance oyster recruitment on three breakwaters of the larger Living Breakwaters system: Breakwaters D, F, and G. The trials will directly release pediveliger-stage larvae onto granite core stone and ECOncrete armor units along the leeward sides of the breakwaters. A Type-III turbidity curtain will retain larvae within the target area, minimize dispersal by currents, and support conditions for settlement.

The 2025 trial involves receiving, holding, and releasing approximately 70 million oyster larvae over a weeklong window. BOP assumes a 10% setting rate1, which would result in the installation of 7 million oyster spat (Table 1). BOP will deploy a Type-III turbidity curtain to enclose a 100-150’ section of the breakwater during high tide, releasing larvae inside the curtain

1 Steppe CN, Fredriksson DW, Wallendorf L, Nikolov M, Mayer R (2016) Direct setting of Crassostrea virginica larvae in a tidal tributary: applications for shellfish restoration and aquaculture. Marine Ecology Progress Series 546:97-112.

to encourage settlement onto the hard substrate. The curtain will remain in place for 48-72 hours post-release and will be monitored daily. Similar studies using containment structures utilized a Type III curtain for 72 hours to maximize larval settlement and survival on the targeted substrates. All equipment will be removed once the setting period concludes.

A detailed protocol for in situ setting on the Living Breakwater Project is included in Appendix A. If severe weather is forecast within 48 hours of larval receipt, BOP will activate a contingency plan to address the inherent weather sensitivity of in situ trials (see Contingency Planning).

Table 1. For Approval - Summary of Proposed in situ Setting Activities in 2025

Enhance ment

Treatment

QTY Year Breakwat er

Total Larvae Required

Total Spat Expected based on 10% Setting

Rate in situ 1 2025 D 70,000,000 7,000,000

Totals 70,000,000 7,000,000

Contingency Planning If severe weather is forecast within 24 hours of larval receipt, 40 million of the 70 million larvae would be set to 16 cubic yards of clean shell at BOP’s remote setting facility for installation at the Head of Bay site in Jamaica Bay, New York. Unused larvae would be disposed of in an upland facility. Assuming a ~24% setting rate in the repmore setting facility, the resultant 10 million spat-on-shell (SOS) would be taken to the Head of Bay site to be installed on Reefs 1 and 4 as part of the Town of Hempstead’s Head of Bay Oyster Enhancement Project (NYSDEC Permit No. 1-2820-06812/00005; USACE Permit NAN-2024-00155). This installation of 10 million SOS, along with the BOP”s planned installation of 10 million SOS at the Head of Bay site in 2025 on Reefs 1 and 4 would fulfill the permitted maximum (20,000,000 spat oysters on 32 CY of shell) under the Town of Hempstead Project. BOP would coordinate with NYSDEC Region 1 and the Department of Marine Resources if the contingency plan is needed.

Please note that this contingency plan would not be needed in 2026 if inclement weather impacts the remaining two in situ trials on the LBW sites. Should unfavourable weather prevent in situ setting in 2026, BOP would divert the oyster larvae to set the permitted oyster disk structures.

Importation Requests Previous Requests On March 27th, 2025 BOP submitted importation permit requests for our May and June sets.

The importation requests for June included the following:

● June 30th to July 3rd:

○ 50.37 million eyed larvae from Mook Sea Farm with final disposition in Raritan

Bay at the Living Breakwaters site (Richmond County), and recycled in an upland facility at BOP’s shell pile.

Eyed oyster larvae imported from Mook Sea Farm were to be used to set ECOncrete disks for the LBW Project (48.37 million) and for BOP’s planned small scale in situ setting experiment approved for Bush Terminal Park (2 million).

Updated Requests With the verbal understanding from NYSDEC that BOP would no longer be setting ECOncrete disks for LWBs in 2025 and would instead conduct the in situ trial on Breakwater D, BOP is no longer planning to conduct the small scale in situ trail at Bush Terminal Park. Final disposition of all 50 million oyster larvae requested from Mook Sea Farms will be on the Breakwater D. In addition, BOP is requesting to import another 20 million eyed larvae from Mobjack Bay Lease Holdings with final disposition planned for Breakwater D. The updated importation requests for June 2025 for the LBW in situ activities are as follows included in Appendix B:

● June 30th to July 3rd:

○ 50 million eyed larvae from Mook Sea Farm with final disposition in Raritan Bay at the Living Breakwaters site (Richmond County).

○ 20 million eyed larvae from Mobjack Bay Lease Holdings with final disposition in

Raritan Bay at the Living Breakwaters site (Richmond County).

Appendix A

Living Breakwaters Oyster Restoration In Situ (Direct Setting) Protocol

Living Breakwaters Oyster Restoration Protocol: In Situ (Direct Setting) with a Turbidity Curtain and Contingency Plans

Summary Billion Oyster Project (BOP) proposes a series of in situ oyster larval setting trials to enhance oyster recruitment on three breakwaters of the larger Living Breakwaters system: Breakwaters D, F, and G. The trials will directly release pediveliger-stage larvae onto granite core stone and ECOncrete armor units along the leeward sides of the breakwaters. A Type-III turbidity curtain will retain larvae within the target area, minimize dispersal by currents, and support conditions for settlement.

Each trial involves receiving, holding, and releasing oyster larvae to a targeted location on the breakwaters. BOP will deploy a Type-III turbidity curtain to enclose a 100-150’ section of the breakwater during high tide, releasing larvae inside the curtain to encourage settlement onto the hard substrate. The curtain will remain in place for 48-72 hours post-release and will be monitored daily. Similar studies using containment structures utilized a Type III curtain for 72 hours to maximize larval settlement and survival on the targeted substrates (Frederiksson et al., 2016, and Steppe et al., 2016). All equipment will be removed once the setting period concludes.

Three trials are planned in 2025 and 2026. BOP developed a contingency plan to address the inherent weather sensitivity of in situ trials. If severe weather is forecast within 24 hours of larval receipt, larvae will instead be set onto an alternative substrate (cured shell or ECOncrete disks). Their final disposition to a permitted location will be determined in coordination with NYSDEC and RHC.

Application To enhance oyster recruitment and early survival by directly setting oyster larvae onto subtidal granite, armor units, and bay balls along the leeward side of breakwaters. A turbidity curtain will retain larvae within the target zone, minimize dispersal by currents, and reduce sediment disturbance during settlement.

Variables Measured Oyster shell heights to determine growth rate Oyster mortality by assessing oyster status (live or dead) Oyster density (i.e., spat counts or live oysters per quadrat)

Datasheet(s): Spat Monitoring_Quadrat_Datasheet

Key Equipment Not including basic field supplies and personal protection equipment (first aid kit, hand sanitizer, waders, gloves, etc.)

Turbidity curtain Caliper(s) Datasheet(s), pencils Clipboard

Phone (with camera) Go-Pro camera on a pyramid quadrat (0.04 m2) Hand Counters (spat size dependent) https://docs.google.com/document/d/1uRMjAigrMKyzBQimfKba6_uCxZmzr8fSC5mLTyJPUFQ/edit?usp=sharing

Turbidity Curtain BOP will deploy a 100’ x 20’ Type III Turbidity curtain. This curtain will be anchored with a chain that rests along the substrate and several danforth anchors across the length to ensure the curtain stays in place.

Curtain specifications will be confirmed at the time of procurement.

1. Site Preparation

● Site Selection: BOP will conduct in situ trials at three breakwaters (D, F, G), focusing on the leeward side where conditions favor larval settlement. See Attachment A for breakwater layouts.

Trials are sequenced by year, as outlined in Table 3.

● Baseline Monitoring: In 2025, BOP will conduct a series of wild oyster surveys along breakwaters D, F, and G using a photo-quadrat method along 160-200’ transects. Presence, abundance, and shell height will be documented and reported. Before each trial, BOP will visit the breakwaters by boat to confirm the specific setting location and note it using GPS points.

○ Water chemistry will be recorded before the larvae are released using a handheld sonde or, in the event of equipment failure, reference NYC DEP Water Quality station K5A-Raritan River. Parameters will include salinity, temperature, turbidity, and dissolved oxygen.

● Substrate: Setting will target the granite core stone and the ECOncrete armor units along the leeward breakwater slope.

● Project Team: A team of five to seven people is needed to set up and break down the turbidity curtain. A minimum of two people are needed to complete the mid-trial and post-trial monitoring:

one to record data, and one to observe and measure oysters.

2. Turbidity Curtain Deployment

● Scheduling: 10 days before the trial, begin monitoring the 10-day National Weather Service forecast and report anticipated trial status to RHC and NYSDEC.

● 5 days before the trial window, continue monitoring the National Weather Service forecast and report anticipated trial status to RHC and NYSDEC.

● If no weather issues are present within 48 hours of the trial, BOP will confirm to RHC and NYSDEC that the trial is a go. If weather issues are present, see Section 6.

● Curtain Type: Type-III turbidity curtain with a 20-foot skirt designed to sit vertically in the water column, stabilized with floats, weighted with ⅜” chain, and secured at the bottom to the bay floor.

● Installation:

○ The curtain will be manually deployed one day before the trial during high tide or the slack tide immediately following high tide with vessel support.

○ The sides of the curtain will be secured directly to the breakwater core stone using ⅜” chain and weighted sandbags.

● Design Considerations: A Type III curtain features mesh with openings approximately 0.2 mm to manage silt particulate matter. Oyster larvae are approximately 0.240 mm at this stage and will thus be successfully contained within the enclosure. The small size of the mesh openings should also prevent entrapment or entanglement issues for mobile marine species. BOP staff will be on-site daily during the trial to monitor conditions and will respond to any issues should they arise.

3. Larval Seeding

● Larvae Preparation:

○ Hatchery-supplied larvae will primarily be in the pediveliger stage, ready for immediate settlement.

○ Larvae will be received chilled on ice, stored briefly in refrigeration, and released within 24 hours.

● Seeding Method:

○ Water chemistry will be recorded before the larvae are released using a handheld sonde or from the NYC DEP Water Quality station K5A-Raritan River (salinity, temperature, turbidity, dissolved oxygen).

○ Larvae will be gently broadcast by hand into the enclosed area during high tide.

○ Larvae will be released as close to the armor units and breakwater core stone as possible.

● Seeding Density: In 2025, BOP will introduce 70 million larvae to yield approximately 7 million spat (see Table 3). Based on literature reviews, BOP anticipates an in situ trial to yield an 8-10% setting rate, but will verify this rate through spat counts.

4. Post-Seeding Retention Period

● Curtain Duration: The turbidity curtain will remain in place for 2-3 days post-seeding.

● Daily Monitoring: BOP staff will check curtain integrity daily during the retention period, addressing any issues as needed. Water chemistry will be recorded each day using a handheld sonde or from the NYC DEP Water Quality station K5A-Raritan River (salinity, temperature, turbidity, dissolved oxygen).

● Curtain Removal: The curtain and all materials will be removed carefully during low tide to minimize disturbance.

5. Data Collection and Reporting

● Monitoring:

○ BOP will return to the site approximately 1 month after seeding to conduct spat counts and calculate setting rates.

○ Biannual monitoring will document oyster survival, growth, and environmental parameters for five to six years post-installation. The recommended quadrat size for sampling is 0.04 m² (0.20 m × 0.20 m), though adjustments may be made based on oyster density.

● Sampling Intensity: Biannual sampling intensity requires appropriate tide times, safe weather conditions, and adequate field support.

● Sampling Frequency:

○ Year 0: BOP will attempt a spat count at the end of the trial, but the small size of the spat may affect accuracy. BOP will return to the site approximately one month after the trial to repeat spat counts and calculate an estimated setting rate. The spat will be larger and easier to see, but the assumed setting rate will be affected by expected mortality within the first month since introduction, so additional inference may be required to understand the true setting rate.

○ Year 1+:…