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The phytoplankton genus Phaeocystis has well-documented, spatially and temporally extensive blooms of gelatinous colonies; these are associated with release of copious amounts of dimethyl sulphide (an important climate-cooling aerosol) and alterations of material flows among trophic levels and export from the upper ocean. A potentially salient property of the importance of Phaeocystis in the marine ecosystem is its physiological capability to transform between solitary cell and gelatinous colonial life cycle stages, a process that changes organism biovolume by 6–9 orders of magnitude, and which appears to be activated or stimulated under certain circumstances by chemical communication. Both life-cycle stages can exhibit rapid, phased ultradian growth. The colony skin apparently confers protection against, or at least reduces losses to, smaller zooplankton grazers and perhaps viruses. There are indications that Phaeocystis utilizes chemistry and/or changes in size as defenses against predation, and its ability to create refuges from biological attack is known to stabilize predator–prey dynamics in model systems. Thus the life cycle form in which it occurs, and particularly associated interactions with viruses, determines whether Phaeocystis production flows through the traditional “great fisheries” food chain, the more regenerative microbial food web, or is exported from the mixed layer of the ocean. Despite this plethora of information regarding the physiological ecology of Phaeocystis , fundamental interactions between life history traits and system ecology are poorly understood. Research summarized here, and described in the various papers in this special issue, derives from a central question: how do physical (light, temperature, particle distributions, hydrodynamics), chemical (nutrient resources, infochemistry, allelopathy), biological (grazers, viruses, bacteria, other phytoplankton), and self-organizational mechanisms (stability, indirect effects) interact with life-cycle transformations of Phaeocystis to mediate ecosystem patterns of trophic structure, biodiversity, and biogeochemical fluxes? Ultimately the goal is to understand and thus predict why Phaeocystis occurs when and where it does, and the bio-feedbacks between this keystone species and the multitrophic level ecosystem.