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Whether aggregate carbon is released in the upper ocean or is sequestered at depth depends on its sinking speed and degradation rate. However, little is known about the physical constraints of bacterial colonization and degradation of individual aggregates. Using molecular rotors to measure the nanoscale viscosity field of natural aggregates, we show that aggregates are highly structured microhabitats with less-viscous regions that are accessible for colonization and more-viscous regions that correlate to a barrier to bacterial infiltration. 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