How encounters at the microscale prime microbial ecosystems

Microorganisms control the global biogeochemistry of the oceans through interactions between individual cells and between cells and particles of organic matter. Prominent examples include marine snow formation by phytoplankton following a phytoplankton bloom or bacterial degradation of marine snow responsible for carbon export from the upper ocean in the biological pump. A variety of physical mechanisms can drive these interactions, including diffusion, active swimming, gravitational settling and turbulent mixing, and the concept of encounter rates provide a unifying framework to describe them. However, the corresponding collision kernels, which map the physical mechanisms to the frequency of encounters, have been traditionally computed for inanimate particles. Here, we first describe the impact of elongation, sinking and turbulence on marine snow formation, and later we describe the impact of elongation and fluid shear on the encounters between motile bacteria and sinking particles of organic matter. Overall, our results demonstrate that microbial traits must be taken into account to accurately predict encounter rates at the microscale, which govern the large carbon flux in the ocean's biological pump.