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Abstract The bay scallop, Argopecten irradians , represents a commercially, culturally and ecologically important species found along the United States’ Atlantic and Gulf coasts. Since 2019, scallop populations in New York have been suffering large-scale summer mortalities resulting in 90–99% reduction in biomass of adult scallops. Preliminary investigations of these mortality events showed 100% prevalence of an apicomplexan parasite infecting kidney tissues. This study was designed to provide histological, ultrastructural and molecular characteristics of a non-described parasite, member of the newly established Marosporida clade (Apicomplexa) and provisionally named BSM (Bay Scallop Marosporida). Molecular diagnostics tools (quantitative PCR, in situ hybridization) were developed and used to monitor disease development. Results showed that BSM disrupts multiple scallop tissues including kidney, adductor muscle, gill, and gonad. Microscopy observations allowed the identification of both intracellular and extracellular stages of the parasite. Field surveys demonstrated a strong seasonal signature in disease prevalence and intensity, as severe cases and mortality increase as summer progresses. These results strongly suggest that BSM infection plays a major role in the collapse of bay scallop populations in New York. In this framework, BSM may synergistically interact with stressful environmental conditions to impair the host and lead to mortality. 

Mass mortality events, due to a variety of natural and anthropogenic causes, usually result in population (and associated fishery) crashes. Recovery from such events may not occur for many years, if at all. We have witnessed a mass die-off of adult (1+ yr) bay scallops Argopecten irradians irradians in the Peconic Bays, New York, USA, from 2019-2022, with declines in population density from spring to fall of 90-99%. Similar declines in commercial landings have occurred since 2018, with severe economic consequences for fishermen. Observed mortality levels are well above those seen prior to 2019. However, since die-offs of adult scallops have been occurring after the first seasonal spawning cycle, larval and benthic juvenile (0+ yr) recruitment have remained robust through 2021. Nevertheless, with lower numbers of adults surviving to spawn in September-October, resulting in fewer fall recruits, potential buffering of marked annual fluctuations in abundance is now less likely for this short-lived species. Peconic bay scallops are again in a precarious state as these recurring die-offs, likely driven by changing environmental conditions, present further challenges to the persistence of robust populations and the likelihood of successful restoration efforts.