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{"Abstract":["This is an archive of model output from the Regional Ocean Modeling System (ROMS) with two grids and two-way nesting. The parent grid resolution (referred to as Doppio) is 7 km and spans the Atlantic Ocean off the northeast United States from Cape Hatteras to Nova Scotia. The refinement grid (referred to as Snaildel) focuses on Delaware Bay and the adjacent coastal ocean at 1 km resolution. This ROMS configuration uses turbulence kinetic energy flux and significant wave height from Simulating Waves Nearshore (SWAN) as surface boundary conditions for turbulence closure.Ocean state variables computed are sea level, velocity, temperature, and salinity. Also inclued are surface and bottom stresses, as well as vertical diffusivity of tracer and momentum. \nThe files uploaded here are examples of one time record from each of this dataset. Outputs for the full reanalysis, which comprises 14 Terabytes of data, are made available for download via a THREDDS (Thematic Real-time Environmental Distributed Data Services) web service to facilitate user geospatial or temporal sub-setting.\nThe THREDDS catalog URLs and example filenames available here, for the respective collections, are:\n\t- 12 minute snapshots of the Doppio domain 2009-2015:\nhttps://tds.marine.rutgers.edu/thredds/roms/snaildel/catalog.html?dataset=snaildel_doppio_history\n\t- 12 minute snapshots of the Snaildel domain 2009-2015:\nhttps://tds.marine.rutgers.edu/thredds/roms/snaildel/catalog.html?dataset=snaildel_snaildel_history\n \nGarwood, J. C., H. L. Fuchs, G. P. Gerbi, E. J. Hunter, R. J. Chant and J. L. Wilkin (2022). "Estuarine retention of larvae: Contrasting effects of behavioral responses to turbulence and waves." Limnol. Oceanogr. 67: 992-1005.\nHunter, E. J., H. L. Fuchs, J. L. Wilkin, G. P. Gerbi, R. J. Chant and J. C. Garwood (2022). "ROMSPath v1.0: Offline Particle Tracking for the Regional Ocean Modeling System (ROMS)." Geosci. Model Dev. 15: 4297-4311."]} 

Marine coccolithophores are globally distributed, unicellular phytoplankton that produce nanopatterned, calcite biominerals (coccoliths). These biominerals are synthesized internally, deposited into an extracellular coccosphere, and routinely released into the external medium, where they profoundly affect the global carbon cycle. The cellular costs and benefits of calcification remain unresolved. Here, we show observational and experimental evidence, supported by biophysical modeling, that free coccoliths are highly adsorptive biominerals that readily interact with cells to form chimeric coccospheres and with viruses to form “viroliths,” which facilitate infection. Adsorption to cells is mediated by organic matter associated with the coccolith base plate and varies with biomineral morphology. Biomineral hitchhiking increases host-virus encounters by nearly an order of magnitude and can be the dominant mode of infection under stormy conditions, fundamentally altering how we view biomineral-cell-virus interactions in the environment. 

Abstract. Offline particle tracking (OPT) is a widely used tool for theanalysis of data in oceanographic research. Given the output of ahydrodynamic model, OPT can provide answers to a wide variety of researchquestions involving fluid kinematics, zooplankton transport, the dispersionof pollutants, and the fate of chemical tracers, among others. In thispaper, we introduce ROMSPath, an OPT model designed to complement theRegional Ocean Modeling System (ROMS). Based on the Lagrangian TRANSport(LTRANS) model (North et al., 2008), ROMSPath is written in Fortran90 and provides advancements in functionality and efficiency compared toLTRANS. First, ROMSPath calculates particle trajectories using the ROMSnative grid, which provides advantages in interpolation, masking, andboundary interaction while improving accuracy. Second, ROMSPath enablessimulated particles to pass between nested ROMS grids, which is anincreasingly popular scheme to simulate the ocean over multiple scales.Third, the ROMSPath vertical turbulence module enables the turbulent(diffusion) time step and advection time step to be specified separately,adding flexibility and improving computational efficiency. Lastly, ROMSPathincludes new infrastructure which enables inputting of auxiliary parameters for addedfunctionality. In particular, Stokes drift can be input and added toparticle advection. Here we describe the details of these updates andperformance improvements. 

Abstract The blooming cosmopolitan coccolithophore Emiliania huxleyi and its viruses (EhVs) are a model for density-dependent virulent dynamics. EhVs commonly exhibit rapid viral reproduction and drive host death in high-density laboratory cultures and mesocosms that simulate blooms. Here we show that this system exhibits physiology-dependent temperate dynamics at environmentally relevant E. huxleyi host densities rather than virulent dynamics, with viruses switching from a long-term non-lethal temperate phase in healthy hosts to a lethal lytic stage as host cells become physiologically stressed. Using this system as a model for temperate infection dynamics, we present a template to diagnose temperate infection in other virus–host systems by integrating experimental, theoretical, and environmental approaches. Finding temperate dynamics in such an established virulent host–virus model system indicates that temperateness may be more pervasive than previously considered, and that the role of viruses in bloom formation and decline may be governed by host physiology rather than by host–virus densities.