Spatial structure, chemotaxis and quorum sensing shape bacterial biomass accumulation in complex porous media.

Biological tissues, sediments, or engineered systems are spatially structured media with a tortuous and porous structure that host the flow of fluids. Such complex environments can influence the spatial and temporal colonization patterns of bacteria by controlling the transport of individual bacterial cells, the availability of resources, and the distribution of chemical signals for communication. Yet, due to the multi-scale structure of these complex systems, it is hard to assess how different biotic and abiotic properties work together to control the accumulation of bacterial biomass. Here, we explore how flow-mediated interactions allow the gut commensal Escherichia coli to colonize a porous structure that is composed of heterogenous dead-end pores (DEPs) and connecting percolating channels, i.e. transmitting pores (TPs), mimicking the structured surface of mammalian guts. We find that in presence of flow, gradients of the quorum sensing (QS) signaling molecule autoinducer-2 (AI-2) promote E. coli chemotactic accumulation in the DEPs. In this crowded environment, the combination of growth and cell-to-cell collision favors the development of suspended bacterial aggregates. This results in hot-spots of resource consumption, which, upon resource limitation, triggers the mechanical evasion of biomass from nutrients and oxygen depleted DEPs. Our findings demonstrate that microscale medium structure and complex flow coupled with bacterial quorum sensing and chemotaxis control the heterogenous accumulation of bacterial biomass in a spatially structured environment, such as villi and crypts in the gut or in tortuous pores within soil and filters.

Interstitial flow potentiates TGF-ß/Smad-signaling activity in lung cancer spheroids in a 3D-microfluidic chip.

Within the tumor microenvironment (TME), cancer cells use mechanotransduction pathways to convert biophysical forces to biochemical signals. However, the underlying mechanisms and functional significance of these pathways remain largely unclear. The upregulation of mechanosensitive pathways from biophysical forces such as interstitial flow (IF), leads to the activation of various cytokines, including transforming growth factor-ß (TGF-ß). TGF-ß promotes in part via a Smad-dependent signaling pathway the epithelial-mesenchymal transition (EMT) in cancer cells. The latter process is linked to increased cancer cell motility and invasion. Current research models have limited ability to investigate the combined effects of biophysical forces (such as IF) and cytokines (TGF-ß) in a 3D microenvironment. We used a 3D-matrix based microfluidic platform to demonstrate the potentiating effect of IF on exogenous TGF-ß induced upregulation of the Smad-signaling activity and the expression of mesenchymal marker vimentin in A549 lung cancer spheroids. To monitor this, we used stably integrated fluorescent based reporters into the A549 cancer cell genome. Our results demonstrate that IF enhances exogenous TGF-ß induced Smad-signaling activity in lung cancer spheroids embedded in a matrix microenvironment. In addition, we observed an increased cell motility for A549 spheroids when exposed to IF and TGF-ß. Our 3D-microfluidic model integrated with real-time imaging provides a powerful tool for investigating cancer cell signaling and motility associated with invasion characteristics in a physiologically relevant TME.

Structure induced laminar vortices control anomalous dispersion in porous media.

Natural porous systems, such as soil, membranes, and biological tissues comprise disordered structures characterized by dead-end pores connected to a network of percolating channels. The release and dispersion of particles, solutes, and microorganisms from such features is key for a broad range of environmental and medical applications including soil remediation, filtration and drug delivery. Yet, owing to the stagnant and opaque nature of these disordered systems, the role of microscopic structure and flow on the dispersion of particles and solutes remains poorly understood. Here, we use a microfluidic model system that features a pore structure characterized by distributed dead-ends to determine how particles are transported, retained and dispersed. We observe strong tailing of arrival time distributions at the outlet of the medium characterized by power-law decay with an exponent of 2/3. Using numerical simulations and an analytical model, we link this behavior to particles initially located within dead-end pores, and explain the tailing exponent with a hopping across and rolling along the streamlines of vortices within dead-end pores. We quantify such anomalous dispersal by a stochastic model that predicts the full evolution of arrival times. Our results demonstrate how microscopic flow structures can impact macroscopic particle transport.

Morphogenesis and oxygen dynamics in phototrophic biofilms growing across a gradient of hydraulic conditions.

Biofilms are surface-attached and matrix-enclosed microbial communities that dominate microbial life in numerous ecosystems. Using flumes and automated optical coherence tomography, we studied the morphogenesis of phototrophic biofilms along a gradient of hydraulic conditions. Compact and coalescent biofilms formed under elevated bed shear stress, whereas protruding clusters separated by troughs formed under reduced shear stress. This morphological differentiation did not linearly follow the hydraulic gradient, but a break point emerged around a shear stress of ~0.08 Pa. While community composition did not differ between high and low shear environments, our results suggest that the morphological differentiation was linked to biomass displacement and reciprocal interactions between the biofilm structure and hydraulics. Mapping oxygen concentrations within and around biofilm structures, we provide empirical evidence for biofilm-induced alterations of oxygen mass transfer. Our findings suggest that architectural plasticity, efficient mass transfer, and resistance to shear stress contribute to the success of phototrophic biofilms.