Skip Navigation
Search

School of Marine and Atmospheric Sciences

The School of Marine and Atmospheric SciencesPeopleSoMAS PeopleBassem Allam

img 

Office: Dana Hall 149

Phone: 631-632-8745



Bassem Allam

Marinetics Endowed Professor in Marine Sciences

Education:

Ph.D.1998

- European Institute of Marine Sciences, University of Western Brittany, Brest, France

Research Topics:

Marine invertebrate physiology and health, Shellfish Genomics, Aquaculture

Visit our Lab Site

rays

  • Bio/Research

    Bio/Research

    My research focuses on interactions between benthic invertebrates and waterborne microbes in the framework of host-pathogen or predator-prey (filter-feeding) interactions. This includes the mechanisms of resistance to pathogens and the effect of environmental factors (e.g. ocean acidification) on host-pathogen interactions. My current projects encompass animal-microbe interactions at molecular, cellular and organismal scales, and my approach to addressing these issues involves field studies and laboratory experiments. Because of the specific service responsibilities of our laboratory (reference lab for shellfish diseases in New York State), my research also includes a strong applied component aimed at enhancing knowledge and development of mitigation strategies for diseases affecting local shellfish species. Taken together, our activities use a diverse range of experimental and technical approaches ranging from ecological physiology, pathology and immunology to modern “omics” (genomics, transcriptomics and proteomics) tools and methods to answer a broad range of basic and applied questions (the publication list below provides a rapid overview of the diversity of our research activities). Current funding in my lab derives from the NSF (mucosal immunity and mechanisms of food particle recognition in suspension-feeding bivalves), NOAA (mechanisms and costs of resilience to ocean acidification in bivalve mollusks, ecological physiology of economically-important bivalve species and adaptation to changing environments, selective breeding), the USDA (genetic markers -e.g. SNPs- associated with disease resistance and development of marker-assisted selection for disease resistance in bivalves) and the New York State Department of Environmental Conservation (biosecurity, shellfish restoration, marine diseases and human health). For more information about these projects and other activities, please visit: http://you.stonybrook.edu/madl

    Note to Prospective Students

    There are often openings for different types of positions ranging from post-doctoral positions to high school internships. Please contact Bassem Allam for information about current availabilities.

    Recent Seminars

    NECAN Industry Webinar: Climate Change Impacts on the Health of Commercially Important Species (YouTube)

  • Publications

    Publications

    Recent publications (since 2020):

    Schwaner C, Barbosa M, Pales Espinosa E, Allam B. (2024). Probing the role of carbonic anhydrase in shell repair mechanisms in the eastern oyster Crassostrea virginica under experimental acidification stress. Journal of Experimental Marine Biology and Ecology. In Press.

    Schwaner C, Barbosa M, Haley J, Pales Espinosa E, Allam B. (2024). Transcriptomics, proteomics, and physiological assays reveal immunosuppression in the eastern oyster Crassostrea virginica exposed to acidification stress. Fish and Shellfish Immunology 146: 109366.

    Geraci-Yee S, Collier JL, Allam B. (2024). A microcosm experiment reveals the temperature-sensitive release of Mucochytrium quahogii (=QPX) from hard clams and pallial fluid as a stable QPX reservoir. Microorganisms 12: 241.

    Schwaner C, Farhat S, Boutet I, Tanguy A, Barbosa M, Grouzdev D, Pales Espinosa E, Allam B. (2023). Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica). Marine Biotechnology. In Press. https://doi.org/10.1007/s10126-023-10255-y

    Czaja R, Beal B, Pepperman K, Pales Espinosa E, Munroe D, Cerrato R, Busch E, Allam B. (2023). Interactive roles of temperature and food availability in predicting habitat suitability for marine invertebrates. Estuarine, Coastal and Shelf Science, 293: 108515. 

    Brianik C, Bouallegui Y, Allam B. (2023). Triploid animals, a potential model for ETosis research: Influence of polyploidy on the formation and efficacy of extracellular traps in the eastern oyster. Fish and Shellfish Immunology, 140: 108992.

    Czaja R, Pales Espinosa E, Cerrato R, Lwiza K, Allam B. (2023). Using meta-analysis to explore the roles of global upwelling exposure and experimental design in bivalve responses to low pH. Science of The Total Environment, 902: 165900.

    Brianik CJ, Allam B. (2023). The need for more information on the resistance to biological and environmental stressors in triploid oysters. Aquaculture, 577: 739913.

    Czaja Jr R, Holmberg R, Pales Espinosa E, Hennen D, Cerrato R, Lwiza K, O’Dwyer J, Beal B, Root K, Zuklie H, Allam, B. (2023). Behavioral and physiological effects of ocean acidification and warming on larvae of a continental shelf bivalve. Marine Pollution Bulletin, 192, 115048.

    Brianik CJ, Bopp J, Piechocki C, Liang N, O’Reilly S, Cerrato RM, Allam B. (2023). Infection prevalence, intensity, and gill coverage by the parasitic flatworm, Bdelloura candida, in the American horseshoe crab (Limulus polyphemus). Hydrobiologia 850: 3655-3669.

    Pales Espinosa E, Bouallegui Y, Grouzdev D, Brianik C, Czaja R, Geraci-Yee S, Kristmundsson A, Muehl M, Schwaner C, Tettelbach ST, Tobi H, Allam B. (2023). An apicomplexan parasite drives the collapse of the bay scallop population in New York. Scientific Reports, 13(1), 6655.

    Tettelbach ST, Czaja R, Tobi H, Hughes S, Peterson BJ, Heck S, MacGregor J, DeLany F, Scannell B, Pales Espinosa E, Allam B. (2023). Collapse of the New York Bay Scallop Fishery Despite Sustained Larval and Juvenile Recruitment. Marine Ecology Progress Series 714, 45-56.

    Schwaner C, Barbosa M, Schwemmer T, Pales Espinosa E,  Allam B. (2023). Increased food resources help eastern oyster mitigate the negative impacts of coastal acidification. Invited Research Paper. Animals 13(7): 1161.

    Schwaner C, Pales Espinosa E,  Allam B. (2023). RNAi silencing of the biomineralization gene Perlucin impairs oyster ability to cope with ocean acidification. International Journal of Molecular Sciences, 24(4), 3661; https://doi.org/10.3390/ijms24043661

    Czaja R, Hennen R, Cerrato R, Lwiza K, Pales Espinosa E, O’Dwyer J, Allam B. (2023). Using LASSO regularization to project recruitment under CMIP6 climate scenarios in a coastal fishery with spatial oceanographic gradients. Canadian Journal of Fisheries and Aquatic Sciences 80(6): 1032-1046. https://doi.org/10.1139/cjfas-2022-0091

    Guo X, Puritz J , Wang Z, Proestou D, Allen S, Small J, Verbyla K, Zhao H, Haggard J, Chriss N, Zeng D, Lundgren K, Allam B, et al. (2023). Development and evaluation of high-density SNP arrays for the eastern oyster Crassostrea virginica. Marine Biotechnology 25(1): 174-191. https://rdcu.be/c24XS

    Tomasetti S, Hallinan B, Tettelbach S, Doherty O, Allam B, Gobler C. (2023). Warming and hypoxia reduce performance and survival of northern bay scallops Argopecten irradians irradians amid a fishery collapse. Global Change Biology 29(8): 2092-2107. doi.org: 10.1111/gcb.16575

    Schwaner C, Farhat S, Barbosa M, Boutet I, Tanguy A, Pales Espinosa E, Allam B. (2023). Molecular features associated with resilience to ocean acidification in the northern quahog, Mercenaria mercenaria. Marine Biotechnology 25(1): 83-99.

    Schwaner C, Farhat S, Haley J, Pales Espinosa E, Allam B. (2022). Proteomic and transcriptomic responses enable clams to correct the pH of calcifying fluids and sustain biomineralization in acidified environments. International Journal of Molecular Sciences 23, 16066.

    Geraci-Yee S, Collier JL, Allam B. (2022). Mucochytrium quahogii (=QPX) Is a Commensal, Opportunistic Pathogen of the Hard Clam (Mercenaria mercenaria): Evidence and Implications for QPX Disease Management. Journal of Fungi 8: 1128.

    Geraci-Yee S, Allam B, Collier JL. (2022). A nested, quantitative PCR assay for detection of the hard clam pathogen, Mucochytrium quahogii (=QPX), in environmental samples. Frontiers in Marine Science: 2215. doi: 10.3389/fmars.2022.988918.

    Barbosa M, Schwaner C, Pales Espinosa E, Allam B. (2022). A transcriptomic analysis of phenotypic plasticity in Crassostrea virginica larvae under experimental acidification. Genes 22(13): 1529.

    Boutet I., Monteiro HJA, Takeuchi T, Baudry L, Bonnivard E, Billoud B, Farhat S, Gonzales-Haraya R, Salaun B, Andersen A, Toullec J-Y, Lallier F, Flot J-F, Guiglielmoni N, Guo X, Cui L, Allam B, Pales Espinosa E, Hemmer-Hansen J, Marbouty M, Koszul R, & Tanguy A. (2022). Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic ressource for aquaculture. Evolutionary Applications DOI: 10.1111/eva.13462

    El-Sayed H, Elshobary M, Barakat K, Khairy H, El-Sheikh M, Czaja R, Allam B, Senousy H. (2022). Ocean acidification induced changes in Ulva fasciata biochemistry may improve Dicentrarchus labrax aquaculture via enhanced antimicrobial activity. Aquaculture 560: 738474. https://doi.org/10.1016/j.aquaculture.2022.738474

    Pales Espinosa E, Eckstein M, Allam B. (2022). Density of compatible ligands on the surface of food particles modulates sorting efficiency in the blue mussel Mytilus edulis. Frontiers in Marine Sciences 9: 882356. https://doi.org/10.3389/fmars.2022.882356

    Geraci-Yee S, Allam B, Collier J. (2022). Keeping up with advances in qPCR pathogen detection: an example for QPX disease in hard clams. Diseases of Aquatic Organisms 148: 127-144.

    Schwaner C, Farhat S, Haley J, Pales Espinosa E, Allam B. (2022). Transcriptomic, proteomic, and functional assays underline the dual role of extrapallial hemocytes in immunity and biomineralization in the hard clam Mercenaria mercenaria. Frontiers in Immunology 13: 838530. doi: 10.3389/fimmu.2022.838530

    Farhat S, Bonnivard E, Pales Espinosa E, Tanguy A, Boutet I, Guiglielmoni N, Flot J-F, Allam B. (2022). Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks. BMC Genomics 23:192. doi: 10.1186/s12864-021-08262-1

    Kim S-H, Nam K-W, Allam B, Choi K-S, Park K-H, Park K-I. (2021). Quantification of the Inflammatory Responses to Pro-and Anti-Inflammatory Agents in Manila clam, Ruditapes philippinarum. Fish & Shellfish Immunology 115: 22-26.

    Geraci-Yee S, Brianik CJ, Rubin E, Collier JL, Allam B. (2021). Erection of a New Genus and Species for the Pathogen of Hard Clams ‘Quahog Parasite Unknown’(QPX): Mucochytrium quahogii gen. nov., sp. nov. Protist 172(1): 125793. Open access: https://doi.org/10.1016/j.protis.2021.125793

    Pales Espinosa E, Allam B. (2021). High spatial resolution mapping of the mucosal proteome of the gills of Crassostrea virginica: implication in particle processing. Journal of Experimental Biology 224, jeb233361. doi:10.1242/jeb.233361

    Cerullo A, Lai T-Y, Allam B, Baer A, Barnes J, Barrientos Z, Deheyn D, Fudge D, Gould J, Harrington M, Holford M, Hung C-S, Jain G, Mayer G, Medina-Munoz M, Monge J, Napolitano T, Pales Espinosa E, Schmidt S, Thompson E, Braunschweig A. (2020). Comparative animal mucomics: Inspiration for functional materials from ubiquitous and understudied biopolymers. ACS Biomaterials Science & Engineering 6(10): 5377-5398.

    Farhat S, Tanguy A, Pales Espinosa E, Guo X, Boutet I, Smolowitz R, Murphy D, Rivara G, Allam B. (2020). Identification of variants associated with hard clam, Mercenaria mercenaria, resistance to Quahog Parasite Unknown disease. Genomics 112(6): 4887-4896.

    Allam S, Allam B, Pales Espinosa E. (2020). Regulation of mucosal lectins in the oyster Crassostrea virginica in response to food availability and environmental factors. Journal of Molluscan Studies 87(1): eyaa037.

    Zuykov M, Allam B, Gosselin M, Archambault P, Spiers G, Schindler M. (2020). First report of signs of infection by Coccomyxa-like algae in wild blue mussels, Mytilus spp., in the Gulf of Maine (USA, Maine). Journal of Fish Diseases 43: 775-778.

    Jones J, Allam B, Pales Espinosa E. (2020). Particle selection in suspension-feeding bivalves: Does one model fit all? Biological Bulletin 238: 41-53.

    Schwaner C, Barbosa M, Connors P, Park TJ, de Silva D, Griffith A, Gobler CJ, Pales Espinosa E, Allam B. (2020). Experimental acidification increases susceptibility of Mercenaria mercenaria to infection by Vibrio species. Marine Environmental Research 154: 104872
  • Links