Characterizing the Non-linear Interactions Between Tide, Storm Surge, and River Flow in the Delaware Bay Estuary, United States

Low-lying coastal areas in the mid-Atlantic region are prone to compound flooding resulting from the co-occurrence of river floods and coastal storm surges. To better understand the contribution of non-linear tide-surge-river interactions to compound flooding, the unstructured-grid Finite Volume Community Ocean Model was applied to simulate coastal storm surge and flooding in the Delaware Bay Estuary in the United States. The model was validated with tide gauge data in the estuary for selected hurricane events. Non-linear interactions between tide-surge-river were investigated using a non-stationary tidal analysis method, which decomposes the interactions’ components at the frequency domain. Model results indicated that tide-river interactions damped semidiurnal tides, while the tide-surge interactions mainly influenced diurnal tides. Tide-river interactions suppressed the water level upstream while tide-surge interaction increased the water level downstream, which resulted in a transition zone of damping and enhancing effects where the tide-surge-river interaction was prominent. Evident compound flooding was observed as a result of non-linear tide-surge-river interactions. Furthermore, sensitivity analysis was carried out to evaluate the effect of river flooding on the non-linear interactions. The transition zone of damping and enhancing effects shifted downstream as the river flow rate increased.

Metagenomes, Metatranscriptomes, and Metagenome-Assembled Genomes from Chesapeake and Delaware Bay (USA) Water Samples

Here, we present 36 metagenomes, 59 metatranscriptomes, and 373 metagenome-assembled genomes (MAGs) from Chesapeake and Delaware Bay water samples. This data set will be useful for studying microbial biogeochemical cycling in estuaries.

The Crab House on Oyster Creek: Folkloristic Response to Vernacular Landscape and its Environmental Moorings

The Andersen crab house on Oyster Creek is located on a waterway that is part of the wider estuarine environment consisting of New Jersey’s Great Bay and the Mullica River. It is a building type that has long served oystermen, clammers, crabbers, finfishers, and waterfowlers along New Jersey’s Atlantic Ocean and Delaware Bay coastlines. Having survived for almost ninety years, the building’s siting allows Phil Andersen to effectively tend the adjacent crabbing grounds and prepare the catch for market. The building, along with his boat and harvesting gear organizes the contours of his working landscape, tools that do not simply define the occupation’s environmental fit, but, as an assemblage, continually advance Andersen’s acquisition of traditional ecological knowledge. While its stark presence on the salt marsh punctuates its environmental fit and role as the axis of Andersen’s occupational map, its enduring function as a working landscape resonates widely throughout the community. The work and social life of the building speak to its capacity to be broadly affiliative, its features, use, and siting laden with aesthetic and performative depth that make it a touchstone of environmental experience and sense of place. These attributes—specifically their role in curating memory and affirming a community’s environmental moorings—show how the Andersen crab house, and similar buildings that preceded it, have engendered folkloristic response for over one hundred and fifty years.

Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale

ABSTRACT Viruses are ubiquitous and abundant in the oceans, and viral metagenomes (viromes) have been investigated extensively via several large-scale ocean sequencing projects. However, there have not been any systematic viromic studies in estuaries. Here, we investigated the viromes of the Delaware Bay and Chesapeake Bay, two Mid-Atlantic estuaries. Deep sequencing generated a total of 48,190 assembled viral sequences (>5 kb) and 26,487 viral populations (9,204 virus clusters and 17,845 singletons), including 319 circular viral contigs between 7.5 kb and 161.8 kb. Unknown viruses represented the vast majority of the dominant populations, while the composition of known viruses, such as pelagiphage and cyanophage, appeared to be relatively consistent across a wide range of salinity gradients and in different seasons. A difference between estuarine and ocean viromes was reflected by the proportions of Myoviridae, Podoviridae, Siphoviridae, Phycodnaviridae, and a few well-studied virus representatives. The difference in viral community between the Delaware Bay and Chesapeake Bay is significantly more pronounced than the difference caused by temperature or salinity, indicating strong local profiles caused by the unique ecology of each estuary. Interestingly, a viral contig similar to phages infecting Acinetobacter baumannii (“Iraqibacter”) was found to be highly abundant in the Delaware Bay but not in the Chesapeake Bay, the source of which is yet to be identified. Highly abundant viruses in both estuaries have close hits to viral sequences derived from the marine single-cell genomes or long-read single-molecule sequencing, suggesting that important viruses are still waiting to be discovered in the estuarine environment. IMPORTANCE This is the first systematic study about spatial and temporal variation of virioplankton communities in estuaries using deep metagenomics sequencing. It is among the highest-quality viromic data sets to date, showing remarkably consistent sequencing depth and quality across samples. Our results indicate that there exists a large pool of abundant and diverse viruses in estuaries that have not yet been cultivated, their genomes only available thanks to single-cell genomics or single-molecule sequencing, demonstrating the importance of these methods for viral discovery. The spatiotemporal pattern of these abundant uncultivated viruses is more variable than that of cultured viruses. Despite strong environmental gradients, season and location had surprisingly little impact on the viral community within an estuary, but we saw a significant distinction between the two estuaries and also between estuarine and open ocean viromes.

Prime Hook National Wildlife Refuge Marsh Restoration & Shoreline Resilience Project – A Carbon Sequestration Case Study in the Coastal Zone

<p>Prime Hook National Wildlife Refuge and its adjacent water bodies are important natural features along western Delaware Bay, USA. Historically salt and brackish marsh habitats, portions of the Refuge were diked and managed as freshwater impoundments starting in the early 1980s. Over the past decade, some of these impoundments have reverted to saline conditions, largely due to several storm events (including Hurricane Sandy in 2012) that have caused flooding, erosion, and opened several breaches between the Refuge and Delaware Bay. Because of these significant morphologic changes, the United States Fish and Wildlife Service (USFWS) completed a series of surveys, numerical modeling using Delft3D and coastal engineering analyses to aid in developing restoration alternatives for managing the Refuge and its marshlands. This work will review the results of the strategic planning used to recommend a preferred restoration alternative for managing the Refuge under the new environmental regime aimed at resilience. As a result of this effort, a project for restoring and managing the Refuge was recommended and constructed in 2018. Total cost of the project was $40 million US and was the largest restoration/recovery project authorized to address the impacts of Hurricane Sandy.</p><p>The project included two major components: 1) shoreline reconstruction and 2) marsh restoration.  The shoreline reconstruction portion of the project included placing approximately 1.2 million cubic meters of sand from an offshore borrow area along the shoreline to reconstruction a 12 m wide dune, 45 m beach berm and 30 m back-bay marsh platform (essentially rebuilding the entire barrier island). In addition, the project included a major marsh restoration effort including dredging 48 km of conveyance channels and “thin layer” disposal of 460,000 cubic meters of sediment to create 2,000 hectares of salt marsh.</p><p>Herein will present findings from an analysis using monitoring data and observations to evaluate converting freshwater wetlands to saltwater marshes and the resulting increase in carbon sequestration. As tidal marshes are restored, harmful emissions decline as the project site transforms from a freshwater to a saltwater environment. Therefore, carbon is stored in the soils more readily under tidal marsh conditions. The findings will show the increase in carbon sequestration as a result of the vegetation community response and discuss future projections.  Methodologies used for identifying vegetation community response included:</p><ul><li>Salt Marsh Integrity (SMI) and Saltmarsh Habitat & Avian Research Program (SHARP)</li> <li>Mid-Atlantic Tidal Rapid Assessment Method (MidTRAM)</li> <li>Normalized Difference Vegetation Index (NDVI)</li> </ul><p>This work will show the importance of incorporating coastal restoration projects and carbon sequestration into policies and management in the coastal zone.</p>

Assessment of Vibrio parahaemolyticus levels in oysters (Crassostrea virginica) and seawater in Delaware Bay in relation to environmental conditions and the prevalence of molecular markers to identify pathogenic Vibrio parahaemolyticus strains

This study identified Vibrio parahaemolyticus in oyster and seawater samples collected from Delaware Bay from June through October of 2016. Environmental parameters including water temperature, salinity, dissolved oxygen, pH, and chlorophyll a were measured per sampling event. Oysters homogenate and seawater samples were 10-fold serially diluted and directly plated on CHROMagarᵀᴹ Vibrio medium. Presumptive V. parahaemolyticus colonies were counted and at least 20% of these colonies were selected for molecular chracterization. V. parahaemolyticus isolates (n = 165) were screened for the presence of the species-specific thermolabile hemolysin (tlh) gene, the pathogenic thermostable direct hemolysin (tdh)/ thermostable related hemolysin (trh) genes, the regulatory transmembrane DNA-binding gene (toxR), and V. parahaemolyticus metalloprotease (vpm) gene using a conventional PCR. The highest mean levels of the presumptive V. parahaemolyticus were 9.63×103 CFU/g and 1.85×103 CFU/mL in the oyster and seawater samples, respectively, during the month of July. V. parahaemolyticus levels in oyster and seawater samples were significantly positively correlated with water temperature. Of the 165 isolates, 137 (83%), 110 (66.7%), and 108 (65%) were tlh+, vpm+, and toxR+, respectively. Among the V. parahaemolyticus (tlh+) isolates, 7 (5.1%) and 15 (10.9%) were tdh+ and trh+, respectively, and 24 (17.5%), only oyster isolates, were positive for both genes. Potential pathogenic strains that possessed tdh and/or trh were notably higher in oyster (39%) than seawater (15.6%) isolates. The occurrence of total V. parahaemolyticus (tlh+) was not necessarily proportional to the potential pathogenic V. parahaemolyticus. Co-occurrence of the five genetic markers were observed only among oyster isolates. The co-occurrence of the gene markers showed a relatedness potential of tdh occurrence with vpm. We believe exploring the role of V. parahaemolyticus metalloprotease and whether it is involved in the toxic activity of the thermostable direct hemolysin (TDH) protein can be of significance. The outcomes of this study will provide some foundation for future studies regarding pathogenic Vibrio dynamics in relation to environmental quality.