Soft Biological Matter in the Ocean: Emerging Measurement Tools and Model Systems

The living world contains striking examples of how complex structure and function emerge from simple local interactions. The ocean, the largest biosphere, is a natural laboratory for studying how soft biological matter organizes and evolves under non-equilibrium conditions. Across this vast environment, evolution in a unique physical setting has generated a stunning range of cellular forms, materials, and collective behaviors. Marine microbes drive half of global carbon fixation, and their interactions generate sinking aggregates that transfer carbon to depth. How the structure, mechanics, and transport of these soft-matter systems emerge from interactions between active biological matter and a fluctuating fluid environment remains a central open question. Addressing this problem requires tools that connect microscopic interactions to emergent material behavior across scales. In this talk I will discuss Scale-free Vertical Tracking Microscopy, a system I co-invented for measuring cells, organisms, and sinking aggregates with microscopic resolution across depths spanning tens to hundreds of meters. This approach has enabled new measurements of microbial motility, plankton behavior, and flow-mediated transport around sinking aggregates, revealing how single-cell processes shape ocean particle dynamics. I will also discuss loricate choanoflagellates, an emerging model system for soft and active matter. These organisms solve a challenging assembly problem: a single cell rapidly and reliably constructs intricate extracellular baskets from hundreds of rod-like biosilica strips, each about 5 microns long and 100 nanometers wide, despite strong chemical and mechanical noise. The resulting structures are ordered, resilient, and mechanically robust, pointing to a dynamically regulated adhesion landscape patterned in space and time. I will highlight emerging evidence that surface glycans and their associated biophysical properties, including charge, polymeric interactions, and adhesion specificity, regulate selective adhesion and, together with active cell-generated stresses, guide mesoscale assembly. Together, these tools and organisms position ocean microbes as tractable model systems for uncovering how soft, active matter assembles and functions in fluctuating environments.