An official website of the United States government
Abstract Background The hard clam Mercenaria mercenaria is a major marine resource along the Atlantic coasts of North America and has been introduced to other continents for resource restoration or aquaculture activities. Significant mortality events have been reported in the species throughout its native range as a result of diseases (microbial infections, leukemia) and acute environmental stress. In this context, the characterization of the hard clam genome can provide highly needed resources to enable basic (e.g., oncogenesis and cancer transmission, adaptation biology) and applied (clam stock enhancement, genomic selection) sciences. Results Using a combination of long and short-read sequencing technologies, a 1.86 Gb chromosome-level assembly of the clam genome was generated. The assembly was scaffolded into 19 chromosomes, with an N50 of 83 Mb. Genome annotation yielded 34,728 predicted protein-coding genes, markedly more than the few other members of the Venerida sequenced so far, with coding regions representing only 2% of the assembly. Indeed, more than half of the genome is composed of repeated elements, including transposable elements. Major chromosome rearrangements were detected between this assembly and another recent assembly derived from a genetically segregated clam stock. Comparative analysis of the clam genome allowed the identification of a marked diversification in immune-related proteins, particularly extensive tandem duplications and expansions in tumor necrosis factors (TNFs) and C1q domain-containing proteins, some of which were previously shown to play a role in clam interactions with infectious microbes. The study also generated a comparative repertoire highlighting the diversity and, in some instances, the specificity of LTR-retrotransposons elements, particularly Steamer elements in bivalves. Conclusions The diversity of immune molecules in M. mercenaria may allow this species to cope with varying and complex microbial and environmental landscapes. The repertoire of transposable elements identified in this study, particularly Steamer elements, should be a prime target for the investigation of cancer cell development and transmission among bivalve mollusks.
more »
« less
This content will become publicly available on November 1, 2026
Bottom-Use Conflicts in Shallow Coastal Zones: Hard Clam (Mercenaria mercenaria) Aquaculture and Restored Seagrass (Zostera marina)
Abstract Multiple-use conflicts of the marine benthos (“bottom-use conflicts”) are increasing as humans expand use of the coastal zone. These conflicts necessitate balanced policies that consider the economic and ecological benefits of different bottom uses. In the Virginia coastal lagoons on the US east coast, there is a potential bottom-use conflict between hard clam (Mercenaria mercenaria) aquaculture and seagrass (Zostera marina) meadows. We leveraged two decades (2001–2021) of aerial imagery and environmental data to quantify historic trends in bottom use, assess the realized niche of seagrass and clam aquaculture across depth, sand fraction, root mean square (RMS) velocity, fetch, and sea surface temperature (SST) anomaly, and used random forest models to predict the potential extent of seagrass, clam aquaculture, and bottom-use conflict. We found growth in the coverage of both seagrass (+ 3373%) and clam aquaculture (+ 140%) over the past 20 years with a corresponding increase in bottom-use conflict (+ 2579%), though conflict area remained relatively minor. Seagrass occurred in deeper areas with higher fetch, a higher frequency of SST anomalies, lower sand fraction, and similar RMS velocities to areas containing clam aquaculture. Our random forest models predicted potential for the expansion of seagrass (+ 62%) and clam aquaculture (+ 263.9%) with a relatively small area of predicted spatial overlap (12.3%) under current conditions. These results illustrate how species distribution models can help us understand the spatial impacts of aquaculture on natural ecosystems and inform managers and policy makers to create objective policies that balance socioeconomic and ecologic needs.
more »
« less
- Award ID(s):
- 1832221
- PAR ID:
- 10634271
- Publisher / Repository:
- Springer
- Date Published:
- Journal Name:
- Estuaries and Coasts
- Volume:
- 48
- Issue:
- 6
- ISSN:
- 1559-2723
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
The exposure of ecologically critical invertebrates to pharmaceutically active compounds in aquatic environments has been one of the major concerns over the past decade, which also adds serious risk to the aquatic ecosystem. However, the metabolic level perturbations in invertebrates in response to sub-lethal doses of pharmaceuticals are still rarely studied, especially in the marine coastal environment. In this study, the diclofenac regulation of southern hard clam Mercenaria campechiensis metabolites at different time points and concentrations was investigated using NMR-based metabolomics. As a result, clam metabolic profile perturbations were observed under both low and high concentrations of diclofenac exposure in one week according to principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA); however, the potential influenced metabolic pathways were distinctly different. The low-concentration group showed significant taurine upregulation, which indicated self-protection from osmotic stress. However, the metabolites succinate, alanine, and glutamate were significantly upregulated at the relatively high concentration of diclofenac, which was a sign of anaerobic activities. The metabolic profile perturbations in week 2 showed high similarity in both low- and high-concentration groups, and the osmotic protectants betaine and taurine were significantly downregulated. The study indicated the early markers of diclofenac exposure in M. campechiensis , which provided pioneering results for monitoring the toxicity of pharmaceuticals to marine coastal water.more » « less
-
Circulating hemocytes in the hemolymph represent the backbone of innate immunity in bivalves. Hemocytes are also found in the extrapallial fluid (EPF), the space delimited between the shell and the mantle, which is the site of shell biomineralization. This study investigated the transcriptome, proteome, and function of EPF and hemolymph in the hard clam Mercenaria mercenaria . Total and differential hemocyte counts were similar between EPF and hemolymph. Overexpressed genes in the EPF were found to have domains previously identified as being part of the “biomineralization toolkit” and involved in bivalve shell formation. Biomineralization related genes included chitin-metabolism genes, carbonic anhydrase, perlucin, and insoluble shell matrix protein genes. Overexpressed genes in the EPF encoded proteins present at higher abundances in the EPF proteome, specifically those related to shell formation such as carbonic anhydrase and insoluble shell matrix proteins. Genes coding for bicarbonate and ion transporters were also overexpressed, suggesting that EPF hemocytes are involved in regulating the availability of ions critical for biomineralization. Functional assays also showed that Ca 2+ content of hemocytes in the EPF were significantly higher than those in hemolymph, supporting the idea that hemocytes serve as a source of Ca 2+ during biomineralization. Overexpressed genes and proteins also contained domains such as C1q that have dual functions in biomineralization and immune response. The percent of phagocytic granulocytes was not significantly different between EPF and hemolymph. Together, these findings suggest that hemocytes in EPF play a central role in both biomineralization and immunity.more » « less
-
Restoration of coastal dunes following tropical storm events often requires renourishment of sand substrate dredged from offshore sources, although dredging has well‐described negative ecological impacts and high economic costs. As a potential solution, recycled glass sand (cullet) made from crushed glass bottles has been proposed as a potential replacement for dredging. However, glass sand substrates may have limited ability to provide support to coastal plant communities due to the absence of native soil microbial communities. To explore the potential use of glass sand as a substrate for dune plants in the Northern Gulf of Mexico, we compared the growth of Sea oats (Uniola paniculata), Beach morning‐glory (Ipomoea imperati), and Railroad vine (I. pes‐caprae) in glass sand to growth in live beach sand. To determine if inoculation of glass sand with native soil microbial communities improved survival, growth, and biomass production, we also tested plant growth in glass sand with native microbial amendments. Overall, we found no difference in the survival of the three dune species across three soil treatments and weak differences in plant growth and biomass production across our soil substrates. Our results suggest that glass sand substrates may be a viable option for coastal dune restoration, with limited differences between live beach sand, glass sand, and glass sand inoculated with native soil microbes. Restoration and replenishment of coastal dunes using glass sand as a substrate following tropical storms or sea‐level rise may allow coastal managers to reduce the economic and ecological damage associated with offshore sediment dredging.more » « less
