This multi-reserve catalyst project compared established and emerging methods for assessing intertidal oyster reef community structure and ecosystem function. With their partners, the project catalyzed a strong community of practice in the Southeastern U.S. to support management efforts related to oyster reef conservation and the advancement of monitoring protocol. The Project Intertidal oyster reefs provide key habitat for a diverse and productive community of estuarine fauna, yet have declined drastically due to overfishing and disease outbreaks. With increased conservation and restoration efforts for intertidal oyster reefs, there is a need for more efficient ways of assessing oyster reefs as well as more holistic understandings of how oyster reefs function as habitats for other estuarine animals. However, assessing the ecosystem benefits of intertidal oyster reefs is challenging because the reefs occupy a dynamic tidal environment characterized by highly turbid water. Established sampling techniques for assessing intertidal oyster reefs are labor intensive and therefore difficult to replicate at multiple sites, limiting the ecological information they can provide, especially at large scales. In contrast, emerging techniques prove promising for examining intertidal oyster reef community structure and ecosystem function. Collaborating with four reserves and five universities, this project compared established sampling techniques for assessing intertidal oyster reefs with four emerging methods that each provide unique ecological information: 1. High-Resolution Acoustic Imaging 2. Stable Isotope Analysis 3. eDNA Metabarcoding 4. Oyster Disease Assays The project team applied these methods alongside traditional methods for collection of free-swimming marine organisms via nets/traps at four reserves in the southeastern U.S. Afterwards, the team convened with their partners and intended users to examine the results and evaluate the potential utility and feasibility of incorporating the emerging methods into their research and monitoring programs. Users overwhelmingly expressed that expanded application of these emerging techniques could improve the assessment of the function of multiple different oyster reef types. The results of this Catalyst project, along with the collaborative network that project has built, bolsters technical capacity at reserves and state agencies to understand the function of critical habitats.

These data represent oyster reefs in Georgia's coastal waterways, extending from Chatham County south to Glynn County. A pilot project for certain coastal regions was completed in 2013, with the remaining project areas finished in 2015. This mapping project was conducted under contract to the Georgia Department of Natural Resources with the goal of inventorying oyster reefs in Georgia's coastal waterways. Oyster reef extent polygons were created through heads-up digitization using 4-band, 6-inch resolution DMC digital aerial imagery as the source. This imagery was collected between November 2012 and February 2013. The minimum mapping unit is 5 square meters, though discretion was used to collect features smaller than this. Partners: Georgia Department of Natural Resources

Coastal researchers, fishermen, fishery managers and educators teamed up to understand changes in shrimp populations in response to shifting environmental conditions in estuaries. The Project Shrimping has deep cultural and economic ties to the South Carolina and Georgia coasts, and the southeast US Atlantic coast region as a whole. However, over the past two decades, commercial shrimp landings have been highly variable. Fishery management agencies, extension offices, and several southeastern Reserves have identified the need to better understand how shrimp populations are responding to changing environmental conditions, including warmer winters and altered salinity regimes. To do this work, a diverse team with members from universities, fishery management agencies, fisheries extension offices, and Reserves came together to form the Lowcountry Shrimp Collaborative. The Lowcountry Shrimp Collaborative used a comprehensive approach to examine how environmental conditions in estuaries are affecting abundance and timing of shrimp populations throughout the region through examination of each stage of the shrimp life cycle. Together, the Collaborative: Analyzed and synthesized numerous ongoing, long-term (30+ years) datasets on multiple shrimp life history stages (postlarval, juvenile, sub-adult, adult, commercially harvested) and environmental conditions (water quality, including System-Wide Monitoring Program data); Conducted field sampling targeting shrimp and their prey in salt marsh creeks during spring and summer seasons, over two years, at three southeast Reserves; Ran controlled seawater laboratory experiments to understand the impacts of competition for limited resources between shrimp species during their overlapping periods of estuarine residency; and, Interviewed commercial shrimpers based in Georgia and South Carolina, to better understand historical changes in, and perceptions of environmental impacts on, the shrimp industry in the southeast US. The project found that estuarine water temperature is rising across the region, mainly driven by increases during winter months. Warming temperatures can alter the life histories of shrimp, including shifting body size, altering the timing of migratory cues, and modifying habitat use. These warmer temperatures are also resulting in longer shrimping seasons with shrimpers often able to continue harvesting well into January. These results were confirmed by observations shared by shrimpers, who joined for a project wrap-up event where the team presented results and engaged in lively discussions about research needs and opportunities for collaboration between researchers, managers, and the industry.

We examined the distribution of nekton across the marsh landscape using a 1-m2 drop sampler to compare nekton densities across three different salinity zones (intermediate, brackish, saline), three pond sizes (diameter 40 msmall, 250300 mmedium, 750 mlarge), and two habitat types (pond, adjacent marsh) in the Barataria Bay Estuary, Louisiana. Nekton assemblages of ponds and the adjacent marsh appeared to be structured by the responses of individual species to the estuarine salinity gradient at the landscape scale and to pond habitat attributes locally. Our results indicate that ponds in the brackish and saline zones are more important nursery areas for most fishery species than ponds in the intermediate zone. Medium and large ponds supported higher densities of most species than small ponds. Most species of nekton were associated with vegetation structure, and individuals of these species were either concentrated among plant stems at the marsh edge or within submerged aquatic vegetation in ponds.

The Eastern oyster (Crassostrea virginica) is a keystone species in northeast Florida estuaries, including the Guana Tolomato Matanzas (GTM) Reserve. However, scientists, managers and oyster harvesters are concerned about the long-term persistence and viability of local populations. In the GTM Reserve, water quality issues are causing some areas to be closed for harvesting, which could be intensifying harvesting pressure in remaining open areas. Other factors, such as predation, disease, and increased salinity, can also slow growth or kill oysters. This complicated situation recently led stakeholders and reserve staff to establish the GTM Oyster Water Quality Task Force in order to identify causes and collaboratively address the region’s oyster challenges.

This project will assess the ecosystem services of shellfish farming by measuring impacts of newly established farms in the North Carolina Research Reserve. Because there is an opportunity to assess conditions before farm installation, North Carolina estuaries provide an ideal place to measure these effects. Two years of intensive sampling in and adjacent to oyster farms, concentrating on wild shellfish resources and the physical and chemical environment, will aim to link small-scale changes with larger-scale ecosystem-level alterations. Coastal managers, state agencies, and shellfish farmers will provide input throughout the course of the project to ensure that the study parameters align with decision-making needs. The project will culminate with the production of visualization tools and models to allow resource managers, culturists, and reserve staff members to make better decisions when determining the locations and scales of shellfish farming operations.

The project team established an experiment that mimicked commercial aquaculture practices and allowed for a robust comparison of nitrogen removal rates from three commonly used gear types: floating bags of oysters, oyster condos suspended in midwater, and bottom cages of oysters. All gear was deployed in the same environmental setting (Waquoit Bay, Falmouth, MA) and maintained by the Town of Falmouth in a manner that a typical grower would follow. The growing systems were maintained for two full growing seasons (2018 and 2019) and compared to a nearby control site. Every two weeks during the growing season, the team conducted a series of measurements to provide a robust estimate of nitrogen fluxes and microbial activity below each of the aquaculture operations. Measurements included: (1) nutrient analyses of sediment, porewater and bottom water samples, (2) genetic sequencing of RNA and DNA extracted from sediment samples to determine the presence and activity level of certain bacteria; and 3) measurements of N2 fluxes from sediment cores placed in flux chambers to measure N2 production rates. All three oyster growing methods enhanced nitrogen removal relative to the control site. However, gene expression data indicate that nitrogen retention may be induced under some gear, particularly after the end of July under bottom cages, and to a lesser extent other gear types.

The Northern Shrimp Survey was initiated in 1983 by the Atlantic States Marine Fisheries Commission (ASMFC) and monitors the relative abundance (number of shrimp), biomass (weight of shrimp), and composition of the northern shrimp stock throughout the Gulf of Maine. The data give an understanding of year class strength and sex stage and maturity of shrimp in the population. The survey focuses its efforts in offshore waters (in depths greater than 50 meters) and is timed to sample both males and females during the summer when they are expected to be offshore. The data it collects forms the basis of the annual northern shrimp assessment, which in turn, is used by fishery managers from Maine, New Hampshire and Massachusetts to set each year’s fishing regulations.

Scientists at NOAA Northeast Fisheries Science Center (NEFSC) are using environmental DNA (eDNA) to identify fish communities and monitor ecosystems by collecting a water sample and analyzing the DNA found in it, identifying the species that left it behind without capturing a single animal. As animals swim, they shed scales, tissue, and waste, leaving traces of DNA in the water. A water sample is first collected from the ocean and filtered to concentrate DNA in it. NOAA scientists then make millions of copies of a target DNA region through polymerase chain reaction (PCR) to make enough genetic material for high throughput sequencing. The metabarcoding process described above for eDNA analysis allows scientists to look for many species in the same sample. The final step is like a matching game, in which the DNA sequences are compared with a reference library of known species to find a match. The eDNA method is particularly useful for detecting species that are not easily captured, including rare or migratory species. It can also help in areas that are difficult to sample because of challenging ocean conditions, sensitive habitats, or a rugged seafloor. An eDNA analysis provides a snapshot of the community of species at the time of sampling and over time. This can help us detect shifts in marine ecosystems. eDNA samples have been collected on NOAA Ecosystem Monitoring (EcoMon) surveys since 2019. These samples will help develop best eDNA practices using metabarcoding, an innovative way to determine what fish species live in what parts of the ocean without actually seeing any fish.

Scientists at NOAA's Northeast Fisheries Science Center (NEFSC) are using environmental DNA (eDNA) to identify fish communities and monitor ecosystems by collecting a water sample and analyzing the DNA found in it, identifying the species that left it behind without capturing a single animal. As animals swim, they shed scales, tissue, and waste, leaving traces of DNA in the water. A water sample is first collected from the ocean and filtered to concentrate DNA in it. NOAA scientists then make millions of copies of a target DNA region through polymerase chain reaction (PCR) to make enough genetic material for high throughput sequencing. The metabarcoding process described above for eDNA analysis allows scientists to look for many species in the same sample. The final step is like a matching game, in which the DNA sequences are compared with a reference library of known species to find a match. The eDNA method is particularly useful for detecting species that are not easily captured, including rare or migratory species. It can also help in areas that are difficult to sample because of challenging ocean conditions, sensitive habitats, or a rugged seafloor. An eDNA analysis provides a snapshot of the community of species at the time of sampling and over time. This can help us detect shifts in marine ecosystems. eDNA samples have been collected on NOAA Ecosystem Monitoring (EcoMon) surveys since 2019. These samples will help develop best eDNA practices using metabarcoding, an innovative way to determine what fish species live in what parts of the ocean without actually seeing any fish.