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Abstract Essential to life on Earth, assessment of marine photosynthesis is of paramount importance. Photosynthesis occurs in spatially discrete microscopic entities at various levels of biological organization, from subcellular chloroplasts to symbiotic microalgae and macroalgae, and is influenced by the surrounding conditions.As such, in situ photosynthetic efficiency mapping on appropriate scales holds great promise for learning about these processes.To achieve this goal, we designed, fabricated, and tested an underwater microscope that incorporates standard colour, epifluorescence, and variable chlorophyllafluorescence imaging with nearly micron spatial resolution that resolves the structure and photosynthetic efficiency of benthic organisms.Our results highlight coral observations with high‐resolution photosynthetic spatial variability and detailed morphology. Our imaging system therefore enables research never before possible on the health and physiology of benthic aquatic organisms in situ, placing it in the context of their physical and biological environment. 

Abstract Coastal physical processes are essential for the cross‐shore transport of meroplanktonic larvae to their benthic adult habitats. To investigate these processes, we released a swarm of novel, trackable, subsurface vehicles, the Mini‐Autonomous Underwater Explorers (M‐AUEs), which we programmed to mimic larval depth‐keeping behavior. The M‐AUE swarm measured a sudden net onshore transport of 30–70 m over 15–20 min, which we investigated in detail. Here, we describe a novel transport mechanism of depth‐keeping plankton revealed by these observations. In situ measurements and models showed that, as a weakly nonlinear internal wave propagated through the swarm, it deformed surface‐intensified, along‐isopycnal background velocities downward, accelerating depth‐keeping organisms onshore. These higher velocities increased both the depth‐keepers' residence time in the wave and total cross‐shore displacement, leading to wave‐induced transports twice those of fully Lagrangian organisms and four times those associated with the unperturbed background currents. Our analyses also show that integrating velocity time series from virtual larvae or mimics moving with the flow yields both larger and more accurate transport estimates than integrating velocity time series obtained at a point (Eulerian). The increased cross‐shore transport of organisms capable of vertical swimming in this wave/background‐current system is mathematically analogous to the increase in onshore transport associated with horizontal swimming in highly nonlinear internal waves. However, the mechanism described here requires much weaker swimming speeds (mm s⁻¹vs. cm s⁻¹) to achieve significant onshore transports, and meroplanktonic larvae only need to orient themselves vertically, not horizontally.