Gary H. Wikfors

The eastern oyster Crassostrea virginica is a major aquaculture species for the USA. The sustainable development of eastern oyster aquaculture depends upon the continued improvement of cultured stocks through advanced breeding technologies. The Eastern Oyster Breeding Consortium (EOBC) was formed to advance the genetics and breeding of the eastern oyster. To facilitate efficient genotyping needed for genomic studies and selection, the consortium developed two single-nucleotide polymorphism (SNP) arrays for the eastern oyster: one screening array with 566K SNPs and one breeders’ array with 66K SNPs. The 566K screening array was developed based on whole-genome resequencing data from 292 oysters from Atlantic and Gulf of Mexico populations; it contains 566,262 SNPs including 47K from protein-coding genes with a marker conversion rate of 48.34%. The 66K array was developed using best-performing SNPs from the screening array, which contained 65,893 oyster SNPs including 22,984 genic markers with a calling rate of 99.34%, a concordance rate of 99.81%, and a much-improved marker conversion rate of 92.04%. Null alleles attributable to large indels were found in 13.1% of the SNPs, suggesting that copy number variation is pervasive. Both arrays provided easy identification and separation of selected stocks from wild progenitor populations. The arrays contain 31 mitochondrial SNPs that allowed unambiguous identification of Gulf mitochondrial genotypes in some Atlantic populations. The arrays also contain 756 probes from 13 oyster and human pathogens for possible detection. Our results show that marker conversion rate is low in high polymorphism species and that the two-step process of array development can greatly improve array performance. The two arrays will advance genomic research and accelerate genetic improvement of the eastern oyster by delineating genetic architecture of production traits and enabling genomic selection. The arrays also may be used to monitor pedigree and inbreeding, identify selected stocks and their introgression into wild populations, and assess the success of oyster restoration.

One hitherto unstudied aspect of differences between sexual and asexual life stages in large‐scale transport and accumulation is density (mass per unit volume) of cells in each life stage. The specific density was determined for Scrippsiella lachrymosa cells in medium with and without nitrogen (N) enrichment through density gradient centrifugation. Growth medium without N addition is often called “encystment medium” when used for the purpose of resting cyst formation in cyst‐forming dinoflagellates; mating gametes are usually seen after two to three days. Significant differences in specific density were found after two days in encystment medium simultaneously with the observation of typical gamete swimming behavior and mating. The specific density of cells in encystment medium was 1.06 g · cm^‐3; whereas, the specific density of cells in growth medium was 1.11 g · cm^‐3. Cells in encystment medium were found to have significantly increased lipid content, reduced chlorophyll content, and reduced internal complexity. The findings may explain differential transport of less dense and chemotactically aggregating gametes into surface blooms in contrast to denser vegetative cells which perform daily vertical migration and do not aggregate. Passive accumulation of non‐migrating gametes into layers in stagnant water also can be explained, as well as sinking of zygotes when the storage of highly‐dense starch increases. Resting cysts had a density of over 1.14 g · cm^‐3 and would sink to become part of the silt fraction of the sediment. We suggest that differences in behavior and buoyancy between sexual and asexual life stages cause differences in cell accumulation, and therefore large‐scale, environmental transport could be directly dependent upon life‐cycle transitions.

Eutrophication is a challenge to coastal waters around the globe. In many places, nutrient reductions from land-based sources have not been sufficient to achieve desired water quality improvements. Bivalve shellfish have shown promise as an in-water strategy to complement land-based nutrient management. A local-scale production model was used to estimate oyster (Crassostrea virginica) harvest and bioextraction of nitrogen (N) in Great Bay Piscataqua River Estuary (GBP), New Hampshire, USA, because a system-scale ecological model was not available. Farm-scale N removal results (0.072 metric tons acre⁻¹year⁻¹) were up-scaled to provide a system-wide removal estimate for current (0.61 metric tons year⁻¹), and potential removal (2.35 metric tons year⁻¹) at maximum possible expansion of licensed aquaculture areas. Restored reef N removal was included to provide a more complete picture. Nitrogen removal through reef sequestration was ~ 3 times that of aquaculture. Estimated reef-associated denitrification, based on previously reported rates, removed 0.19 metric tons N year⁻¹. When all oyster processes (aquaculture and reefs) were included, N removal was 0.33% and 0.54% of incoming N for current and expanded acres, respectively. An avoided cost approach, with wastewater treatment as the alternative management measure, was used to estimate the value of the N removed. The maximum economic value for aquaculture-based removal was $105,000 and $405,000 for current and expanded oyster areas, respectively. Combined aquaculture and reef restoration is suggested to maximize N reduction capacity while limiting use conflicts. Comparison of removal based on per oyster N content suggests much lower removal rates than model results, but model harvest estimates are similar to reported harvest. Though results are specific to GBP, the approach is transferable to estuaries that support bivalve aquaculture but do not have complex system-scale hydrodynamic or ecological models.

As mariculture progresses offshore in the US Exclusive Economic Zone, technical and ecological challenges need to be overcome, such as the choice of suitable sites that favor the production of target species. The offshore culture of blue mussels, Mytilus edulis, is performed with submerged longlines and mussels need to withstand more motion than on coastal sites. Temperature affects the ability of the byssus to adhere to farming rope, while chlorophyll concentration provides an estimation of food availability. Together, these are important factors in predicting the suitability of offshore mussel farms. To identify suitable depth of submersion for mussel ropes in New England federal waters, historical oceanographic data of temperature and chlorophyll a from 2005 to 2012 were used. The results suggest that mussel ropes were submerged during summer to a minimum depth of 15 m in northern and a 20-m depth in southern areas of New England where temperature is at a species-optimum and phytoplankton biomass is abundant. For the site offshore Massachusetts, in situ biodeposition measurements validated predicted depth, confirming satisfactory mussel performance. Promising local areas have shallow thermoclines, such as offshore Long Island, Cape Ann and New Hampshire. Recommended depths can be adjusted to future temperature increases associated with climate change.

As shellfish aquaculture moves from coastal embayments and estuaries to offshore locations, the need to quantify ecosystem interactions of farmed bivalves (i.e., mussels, oysters, and clams) presents new challenges. Quantitative data on the feeding behavior of suspension-feeding mollusks is necessary to determine important ecosystem interactions of offshore shellfish farms, including their carrying capacity, the competition with the zooplankton community, the availability of trophic resources at different depths, and the deposition to the benthos. The biodeposition method is used to quantify feeding variables in suspension-feeding bivalves in a natural setting and represents a more realistic proxy than laboratory experiments. This method, however, relies upon a stable platform to satisfy the requirements that water flow rates supplied to the shellfish remain constant and the bivalves are undisturbed. A flow-through device and process for using the biodeposition method to quantify the feeding of bivalve mollusks were modified from a land-based format for shipboard use by building a two-dimensional gimbal table around the device. Planimeter data reveal a minimal pitch and yaw of the chambers containing the test shellfish despite boat motion, the flow rates within the chambers remain constant, and operators are able to collect the biodeposits (feces and pseudofeces) with sufficient consistency to obtain accurate measurements of the bivalve clearance, filtration, selection, ingestion, rejection, and absorption at offshore shellfish aquaculture sites.