Bassem Allam

Ocean warming (OW) and ocean acidification (OA) are expected to have wide-ranging consequences for populations in marine systems caused by organism-level responses at a range of life history...

Forecasts of whether marine species can evolve fast enough to survive climate change rely largely on single-stage tolerance assays, tacitly assuming that tolerance measured at one developmental stage reflects adaptive capacity across the organism’s life cycle. We test this assumption in a common marine bivalve ( Mercenaria mercenaria ) and find that it fails in sign, not degree: larval and post-metamorphic tolerance to end-century ocean acidification are strongly negatively correlated ( r = −0.53, 95% CI [−0.69, −0.33]) across family-level, pedigree-conditioned and animal model estimates, with pervasive rank reversals among the top performers of each stage. A multivariate analysis of the among-family covariance matrix G shows why: under acidification, 57% of the among-family variance collapses onto a single dominant axis that loads positively on every larval trait and negatively on every post-metamorphic trait, whereas under ambient conditions the same families show no cross-stage covariance at all. Acidification therefore does not merely depress performance—it reorganizes the genetic architecture into a cross-stage conflict. Under ramping RCP 8.5 forcing this conflict geometry dictates the direction—not merely the magnitude—of adaptation: only balanced multi-stage selection preserves family diversity, whereas single-stage selection systematically erodes the opposite axis. In complex life cycles, resilience is a geometric property of ontogeny that forecasts cannot compress into a single-stage without inverting the sign of the answer.

Eastern oyster aquaculture has increased steadily over the last three decades, but the industry has not achieved its full potential. In the Northeast USA, production is limited in part by a lack of high performing stocks suited to geographically broad and heterogenous growing environments. Hatchery lines from Maine, New York, and New Jersey and their crosses were evaluated at oyster farms in Rhode Island and New Jersey. Replicate bags of each line were maintained according to standard husbandry practices, and survival, growth and final yield were monitored for 16 months. During the second summer of the evaluation period, subsamples from each line were tested for parasites Perkinsus marinus (Dermo) and Haplosporidium nelsoni (MSX) to assess disease acquisition at both sites. Significant site, line, and line by site (GxE) interaction effects were detected for growth and mortality. Differences in growth between sites reflect food availability while differences in mortality coincide with disease and potential heat stress. Trait differences observed among lines within sites are consistent with selection history and local adaptation. Top performing lines were not consistent across sites, suggesting advantages of long-term selection/local adaptation may not transfer when lines are grown outside their site of origin. Our results highlight the role of GxE interactions in the expression of commercially important traits and can contribute to the development of future breeding strategies and more informed on-farm seed deployments that will augment eastern oyster aquaculture production in the Northeast USA.

As the microbiome becomes increasingly recognized for its role in driving animal health and disease, accurate characterization of microbial community composition is essential. With this research comes the critical need for standardized sampling methods along with an understanding of the biases inherent to these methods. In oysters, hemolymph is a valuable system for microbiome research due to its diverse physiological functions, role as an indicator of health, and ease of collection. Unfortunately, much of the current literature regarding oyster hemolymph microbiome composition is opaque in its description of tissue collection methods. When these methods are clearly described, investigators often collect hemolymph via a needle inserted into the adductor muscle through a notch cut in the shell. However, due to the needle’s movement through soft tissues and mucous membranes exposed to the surrounding seawater, this notch method carries significant risk of sample contamination. An alternative hemolymph sampling method, hereafter referred to as the hole method, minimizes this potential contamination as the needle is inserted through a hole drilled in the shell directly above the adductor muscle, circumventing other soft tissues. Here, we tested whether notch and hole hemolymph collection methods produce different 16S rRNA bacterial community profiles in C. virginica . To compare these two sampling methods and evaluate the potential method-specific biases, particularly biases that may result from tissue contamination, oysters had hemolymph collected through both a notch and hole while alternating method order. Following taxonomic classification and differential abundance analysis of the resultant 16S rRNA sequences, the presence of disproportionate Vibrio spp. enrichment in notch-associated samples was evident. Notch-collected samples yielded significantly higher 16S rRNA gene copy numbers ( p = 0.037) and a 16-fold higher relative abundance of Vibrio spp. compared to hole-collected samples (52.6% vs. 3.2%, p _adj = 0.006) despite no significant change in absolute counts of the dominant genus Poseidonibacter . Overall, this analysis demonstrates both the potential of the hole sampling method and the need for microbiome researchers to account for biases in bacterial community composition associated with their chosen sampling method.

Margolisiella madlensis , previously known as bay scallop Marosporida (BSM), is an apicomplexan parasite implicated in recurrent summer mortality of the bay scallop Argopecten irradians in the Northeastern United States. It is a member of the class Marosporida, a major apicomplexan lineage that has so far lacked nuclear genomic resources. Here we report the draft nuclear genome of M. madlensis 23004-MA1, assembled from PacBio HiFi and Illumina sequencing data. The assembly comprises 41.0 Mb in 6,697 scaffolds. Interspersed repeats accounted for 40.3% of the assembly, while repetitive and low-complexity sequences together accounted for 45.8%. To our knowledge, this is the first nuclear genome available for the class Marosporida. Therefore, this genome provides an essential reference for comparative studies of apicomplexan evolution and establishes a basis for future work on parasite biology, molecular detection, and host-parasite interactions in marine invertebrates.

Since 2019, outbreaks of an apicomplexan parasite caused catastrophic mortalities of adult northern bay scallops (Argopecten irradians irradians) in New York, USA. Anecdotal observations suggested different levels of mortality between different scallop stocks and mortality outbreaks appeared to occur in years displaying positive temperature anomalies. In this study, field and laboratory experiments were designed to evaluate the effect of environmental conditions and host (scallop) background on disease susceptibility and mortality. Wild and aquacultured scallops originally sourced from the same area were deployed in lantern nets (suspended in the water column) or oyster culture bags (on bottom) at two different enzootic sites showing contrasting environmental conditions. Subsets of wild and aquacultured stocks were also used in laboratory experiments exposing scallops to different temperatures and dissolved oxygen levels, mimicking different environmental scenarios. Results showed higher mortality in aquacultured scallops compared to wild scallops, especially in the more stressful conditions. Laboratory experiments showed that the trajectories of disease development and mortality were significantly affected by initial disease levels and environmental factors. For instance, high temperature and low dissolved oxygen were shown to favor disease development when initial disease levels were low (wild scallops) but also appear to lead to an overall reduction in disease via culling of the most heavily infected scallops when initial disease levels and mortality during the experiment were high (aquacultured scallops). Altogether, these findings underline the impact of environmental conditions, in particular temperature, on host-parasite interactions and suggest the potential existence of more resilient scallop stocks.

Substantial progress has been made in understanding hemocytes within the hemolymph (herein referred to as circulatory hemocytes), which are essential for immune defense and various physiological functions in bivalve mollusks. Yet, our knowledge of peripheral immunity, particularly the role of hemocytes associated with mucosal surfaces covering pallial (gills, mantle) organs (herein referred to as mucosal hemocytes), remains limited. While mucosal and circulatory hemocytes share similar morphologies, they exhibit distinct functional profiles and cell surface epitopes. The molecular mechanisms underlying these functional differences remain poorly understood. To address this knowledge gap, we characterized gene expression profiles (using RNA sequencing) in granulocytes and agranulocytes isolated via flow cytometry from hemolymph and mucus covering pallial tissues of the eastern oyster, Crassostrea virginica . Mucosal hemocytes showed overexpression of genes related to cell motility, cytokine activity, signaling, and cell adhesion, supporting the hypothesis that they may have sentinel functions. Despite a consistent dichotomy in gene expression between granulocytes and agranulocytes across both body fluids, it was more pronounced in circulatory hemocytes. Circulatory granulocytes showed functions linked to phagocytosis and pathogen killing, whereas circulatory agranulocytes overexpressed genes associated with mitosis and early inflammation compared to their mucosal counterparts. To our knowledge, this is the first study combining flow cytometry sorting and transcriptomic methods to characterize hemocytes from different body fluids in a marine invertebrate. Results underline the potential role of mucosal hemocytes as immune sentinels, although more studies, possibly using single-cell transcriptomic methods and functional assays associated with pathogen challenge experiments, are needed to probe their specific functions.

Understanding the genetic basis of resilience in marine organisms is critical for conservation and management, particularly in the face of escalating environmental stress and disease outbreaks. The bay scallop Argopecten irradians is a commercially and recreationally important shellfish species found in estuarine and coastal environments of the United States from New England to the Gulf of Mexico. In New York, adult bay scallop populations have been decimated every summer since 2019 leading to the collapse of their fishery. These mortality events were associated with annual outbreaks of an undescribed apicomplexan parasite recently named Bay Scallop Marosporida (BSM) that disrupts scallop kidneys. This study investigates host–pathogen interactions and assesses changes in population structure during BSM-associated mortality events. The research compared wild and aquacultured scallops used for stock enhancement in New York, revealing significant change in population structures throughout the mortality outbreak. The results underscore the selective pressures exerted by BSM infection and environmental stressors, as evidenced by shifts in genetic divergence and allele frequencies particularly in genes associated with kidney function, stress and infection response. Through a detailed genomic and population genetic approach, this research represents a unique case study highlighting the impact of disease on marine biodiversity and advances our understanding of the impact of summer mortality events on the scallop population in NY. This study highlights changes in the genomic structure of bay scallops during a BSM-associated mortality event. Identified mutations (such as the one in the nephrocystin-3-like gene) represent prime candidates for specific targeted investigations to link genotypes to phenotypes. By integrating genomic and epidemiological data, the research provides a basis for understanding the impact of disease on scallop biodiversity. These findings may help guide conservation strategies for sustainable fisheries in the face of environmental change and disease outbreaks.

The bay scallop, Argopecten irradians, is a species of major commercial, cultural, and ecological importance. It is endemic to the eastern coast of the United States, but has also been introduced to China, where it supports a significant aquaculture industry. Here, we provide an annotated chromosome-level reference genome assembly for the bay scallop, assembled using PacBio and Hi-C data. The total genome size is 845.9 Mb, distributed over 1,503 scaffolds with a scaffold N50 of 44.3 Mb. The majority (92.9%) of the assembled genome is contained within the 16 largest scaffolds, corresponding to the 16 chromosomes confirmed by Hi-C analysis. The assembly also includes the complete mitochondrial genome. Approximately 36.2% of the genome consists of repetitive elements. The BUSCO analysis showed a completeness of 96.2%. We identified 33,772 protein-coding genes. This genome assembly will be a valuable resource for future research on evolutionary dynamics, adaptive mechanisms, and will support genome-assisted breeding, contributing to the conservation and management of this iconic species in the face of environmental and pathogenic challenges.

The hard clam (Mercenaria mercenaria), a marine bivalve distributed along the U.S. eastern seaboard, supports a significant shellfish industry. Overharvest in the 1970s and 1980s led to a reduction in landings. While the transition of industry from wild harvest to aquaculture since that time has enhanced production, it has also exacerbated challenges such as disease outbreaks. In this study, we developed and validated a 66K SNP array designed to advance genetic studies and improve breeding programs in the hard clam, focusing particularly on the development of markers that could be useful in understanding disease resistance and environmental adaptability. Whole-genome resequencing of 84 individual clam samples and 277 pooled clam libraries yielded over 305 million SNPs, which were filtered down to a set of 370,456 SNPs that were used as input for the design of a 66K SNP array. This medium-density array features 66,543 probes targeting coding and non-coding regions, including 70 mitochondrial SNPs, to capture the extensive genetic diversity within the species. The SNPs were distributed evenly throughout the clam genome, with an average interval of 25,641 bp between SNPs. The array incorporates markers for detecting the clam pathogen Mucochytrium quahogii (formerly QPX), enhancing its utility in disease management. Performance evaluation on 1,904 samples demonstrated a 72.7% pass rate with stringent quality control. Concordance testing affirmed the array's repeatability, with an average agreement of allele calls of 99.64% across multiple tissue types, highlighting its reliability. The tissue-specific analysis demonstrated that some tissue types yield better genotyping results than others. Importantly, the array, including its embedded mitochondrial markers, effectively elucidated complex genetic relationships across different clam groups, both wild populations and aquacultured stocks, showcasing its utility for detailed population genetics studies. The 66K SNP array is a powerful and robust genotyping tool that offers unprecedented insights into the species’ genomic architecture and population dynamics and that can greatly facilitate hard clam selective breeding. It represents an important resource that has the potential to transform clam aquaculture, thereby promoting industry sustainability and ecological and economic resilience.