Naturphilosophie unfolding in bacterial microcolony revealed by global single-cell/fluid-nanotracer tracking

Abstract Nature, viewed philosophically, is an inherent principle of self-constitution and dynamic unfolding. Here, we explore these profound principles not by contemplating the vastness of the cosmos, but within the confines of Bacillus subtilis microcolony—a tractable micro-Entity where individual-collective interplay becomes observable under a microscope. By tracking the complete spatiotemporal evolution at single-cell/particle resolution, we reveal multi-stage self-organization driven by sequential evolutionary pressures (environmental, peer, differentiation, boundary), manifesting the essential dynamism of the active fluid medium (Copula) that co-evolves with individual bacterial behaviors. In the sparse earliest stage, initial environmental constraints amplify subtle individual variations, triggering a behavioral bifurcation (near-linear traversal vs. large-radius circulation). As cell density increases, heterogeneous intercellular structures emerge, including a dynamic partitioning of “motile” and “static” regions. Notably, even in the highly crowded late stage, a large population of bacteria maintain superdiffusion rather than dynamical arrest. Synchronous tracking of passive fluid nanotracers (~ 200 nm oil-droplets) demonstrates how bacterial activity generates intercellular fluid field and transforms near-Brownian transport into superdiffusive flows, unveiling collective coordination mediated by the bacterial Copula. This comprehensive picture of multi-step dynamic transitions establishes bacterial microcolony evolution as a compelling model system for deciphering the emergence of forms and functions in a living micro-Entity, bridging scientific and philosophical perspectives.