This project synthesized Sentinel Site data for four New England National Estuarine Research Reserves (Great Bay, Narragansett, Waquoit Bay, and Wells), which have been individually monitoring salt marsh vegetation and elevation changes since at least 2011. The project team developed statistics-ready data packages linking vegetation change with surface elevation and other data, including output from an inundation tool. This project equipped New England reserves and coastal managers with new information to inform and improve the management, protection, and restoration of salt marshes. It produced an improved Sentinel Site monitoring protocol and established a methodology for analysis of marsh condition that can be used across the reserve system and by coastal managers nationwide. This catalyst project was funded by NOAA through the National Estuarine Research Reserve System Science Collaborative to advance collaborative science. It did not produce any new data.

The National Estuarine Research Reserve System has developed a consistent protocol for monitoring vegetation across the nations estuaries. Eventually, the goal is to be monitoring vegetation regularly at every Reserve, allowing for robust spatial and temporal analyses of estuarine vegetation trends. To date, 18 Reserves have implemented this vegetation monitoring protocol. The vegetation community that is assessed varies by reserve. The protocol has been implemented for submerged aquatic vegetation such as eelgrass and algae, as well as for emergent vegetation such as salt marshes and mangroves. The vegetation monitoring protocol involves permanent sampling plots along fixed transects. Parameters monitored include percent cover of all plant species, as well as stem density and canopy height of the common species. Elevation is also assessed for each plot when feasible. The complete monitoring protocol provides more details. These data will be valuable for tracking changes in abundance of particular species of interest, or in species composition over time. For instance, the transects can be used to detect landward migration of vegetation communities in the face of projected sea level rise. The National Estuarine Research Reserves is a network of 30 reserves protected for long-term research, ecosystem monitoring, education, and coastal stewardship. Established by the Coastal Zone Management Act, the reserve system is a partnership program between NOAA and the coastal states. NOAA provides funding, national guidance, and technical assistance. Each reserve is managed on daily basis by a lead state agency or university with input from local partners. These data are collected as part of the NERRS System-Wide Monitoring Program (SWMP), which includes (1) abiotic indicators of water quality and weather; (2) biological monitoring; and (3) watershed, habitat, and land use mapping. Data were collected under individual Reserve NOAA grant/cooperative agreements and managed by the CDMO under NOAA grant/cooperative agreement #NA23NOS4200321 (2023) and prior grants. For more information on Reserve locations and programs, please visit www.nerrsdata.org or https://coast.noaa.gov/nerrs/.

A team of collaborators from the Tijuana River National Estuarine Research Reserve, Southwest Wetlands Interpretive Association, and University of California-Davis are exploring the environmental consequences of managing the opening and closing of lagoon mouths. The project approach includes the following elements: Collaboration with Users: The project team will regularly engage members of the Southern California Wetlands Recovery Project, which coordinates and funds restoration projects throughout the region. Data Synthesis: Long-term water quality and vegetation data will be analyzed from three estuary systems: San Diego Bay, Los Peasquitos Lagoon, and Tijuana Estuary. The team will look at how mouth closures influence factors such as dissolved oxygen and salinity, which in turn affect plants and animals. Literature Review: The project team will pull together relevant scientific articles and reports to guide its interpretation of monitoring data and development of management recommendations. This science transfer project was funded by NOAA through the National Estuarine Research Reserve System Science Collaborative to promote the use of science. It did not produce any new data.

A new tool has been developed, the Climate Change Vulnerability Assessment Tool for Coastal Habitats (CCVATCH), to help land managers, decision makers, and researchers develop conservation, management, and restoration plans for coastal habitats. This assessment tool identifies primary sources of vulnerability to assist with prioritizing coastal habitat management actions. As part of this project, four estuarine reserves in New England will conduct assessments of their areas, demonstrating the utility of the tool to support adaptive management in response to climate change. This science transfer project was funded by NOAA through the National Estuarine Research Reserve System Science Collaborative to promote the use of science. It did not produce any new data.

The reserve system has identified a need to increase its collective capacity to process and synthesize Surface Elevation Table data and to create visualizations and educational tools for scientists, managers, and the public. This project addresses these needs by developing standardized tools to quality-check Surface Elevation Table data, perform trend analyses, and generate informative visualizations for a variety of technical and non-technical audiences. The team’s collaborative approach to developing statistical methods and outreach products will build both technical expertise and broader understanding of how the data can be used to better understand how sea level rise is impacting marshes.

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.

This project evaluated ecosystem damage and recovery by developing a time series of habitat maps for the Rookery Bay National Estuarine Research Reserve. Habitat maps were created based on WorldView-2 and Landsat-8 satellite imagery from 2010-2018 using an automated technique and validated with a field campaign. Landsat images were mapped using the Support Vector Machine machine learning method in ENVI, and WorldView images were mapped using a preliminary version of the SOALCHI decision tree algorithm. Habitats mapped include healthy mangrove, degraded mangrove, marsh, upland vegetation, soil, and water. Habitat change maps document the damage caused by Hurricane Irma in September of 2017 as it made landfall in the reserve as a Category 4 storm. Project outputs include field-survey results with GPS points, a baseline habitat map, annual habitat seasons for 2016-2018, and habitat change assessments. Outcomes include the development of new research collaborations, quantitative characterization of reserve habitat change, improved understanding of critical habitat change dynamics, and assessment of chronic and extreme-event disturbance and recovery.

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.

This project will implement monitoring programs for the endangered southern cassowary, Casuarisus casuarius, and the vulnerable spectacled flying-fox, Pteropus conspicillatus. Cassowary monitoring will be based on regular surveys to collect dung. DNA fingerprinting of the bird dung will provide data on cassowary abundance and distribution, the influence of habitat type and the structure and phylogeography of cassowary populations across the region. For spectacled flying-fox monthly surveys of all known spectacled flying-fox camps in the Wet Tropics Region will be conducted. Resulting data will be used to describe population distribution, population size and trends to build upon the long term database already established.