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.

There is an increasing demand for advanced optical imaging techniques that can detect and resolve nanosize objects at a spatial resolution below the optical diffraction limit, especially in three-dimensional (3D) cellular environments. In this study, using a polarization-activated localization scheme based on the orientation-dependent properties of anisotropic plasmonic metal nanoparticles (MNPs), "photoswitchable" imaging of single gold nanorods (AuNRs) was accomplished not only in two dimensions but also in three dimensions. Moreover, the Rayleigh scattering background arising from the congested subcellular structures was efficiently suppressed. Thus, we obtained the 3D distributions of both the position and the orientation of the AuNRs inside the cells and investigated their internalization kinetics. To our knowledge, this is the first demonstration of the confocal-like 3D imaging of non-fluorescence nanoparticles with a high resolution and almost zero background. This technique is easy to implement and should greatly facilitate MNP studies and applications in biomedicine and biology.