Oxygen deficiency drives drastic pattern transition in algal bioconvection.

Suspensions of motile microorganisms can spontaneously form large-scale fluid motion, known as bio- convection, characterized by dense downwelling plumes separated by broad upwelling regions. In this study, we investigate bioconvection in shallow suspensions of Chlamydomonas reinhardtii confined within spiral-shaped boundaries, combining detailed experiments with three-dimensional simulations. Under open liquid-air interfaces, cells accumulate near the surface via negative gravitaxis, generating spiral-shaped density patterns that subsequently fragment into lattice-like clusters, leading to plume formation. Space-time analyses demonstrate coherent rotational dynamics, with predominantly inward-directed motion near the spiral core and bidirectional motion further out. Introducing confinement by sealing the upper boundary with an air-impermeable wall triggers dramatic pattern transitions due to oxygen depletion: initially stable arrangements reorganize into new structures with significantly reduced wavelengths. Complementary numerical simulations, based on incompressible Navier-Stokes equations incorporating negative buoyancy and active swimmer stress, successfully replicate initial pattern formation, subsequent instability, fragmentation into plumes, and emergence of strong vortical flows-nearly an order of magnitude faster than individual cell swimming. However, these models do not capture oxygen depletion-driven transitions observed experimentally. Our results highlight that geometric confinement, oxygen availability, and metabolic transitions critically regulate bioconvection dynamics, offering novel strategies for controlling microbial self-organization and fluid transport.