Research Article: Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network

Date Published: June 27, 2019

Publisher: Public Library of Science

Author(s): Jayde A. Aufrecht, Jason D. Fowlkes, Amber N. Bible, Jennifer Morrell-Falvey, Mitchel J. Doktycz, Scott T. Retterer, Robert Nerenberg.


Bacteria occupy heterogeneous environments, attaching and growing within pores in materials, living hosts, and matrices like soil. Systems that permit high-resolution visualization of dynamic bacterial processes within the physical confines of a realistic and tractable porous media environment are rare. Here we use microfluidics to replicate the grain shape and packing density of natural sands in a 2D platform to study the flow-induced spatial evolution of bacterial biofilms underground. We discover that initial bacterial dispersal and grain attachment is influenced by bacterial transport across pore space velocity gradients, a phenomenon otherwise known as rheotaxis. We find that gravity-driven flow conditions activate different bacterial cell-clustering phenotypes depending on the strain’s ability to product extracellular polymeric substances (EPS). A wildtype, biofilm-producing bacteria formed compact, multicellular patches while an EPS-defective mutant displayed a linked-cell phenotype in the presence of flow. These phenotypes subsequently influenced the overall spatial distribution of cells across the porous media network as colonies grew and altered the fluid dynamics of their microenvironment.

Partial Text

Microbial communities are complex systems that shape, and are shaped by, their local microenvironments. Bacteria often inhabit heterogeneous microenvironments with hydrodynamic flows that influence local nutrient transport and chemical gradients, creating specialized niches for microorganisms[1–3]. Likewise, the spatial confinement of some bacteria can influence emergent phenomena like quorum sensing, intercellular communication, and biofilm formation[4–6]. These microenvironment factors and complexities contribute to microbial community diversity and synergism, which hinders their isolation and culture in bulk laboratory conditions[7,8].




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