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

Abstract

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 particle 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 particle attachment is a stochastic process driven by bacterial rheotactic transport across pore space velocity gradients. Over time, we find that gravity-driven flow conditions activate different cell-clustering phentoypes in EPS producing and EPS defective bacteria strains, which subsequently changes the overall spatial distribution of cells across the porous media network as colonies grow and alter the fluid dynamics of their microenvironment.

Microfluidic devices for studying bacterial taxis, drug testing and biofilm formation

“…Both tended to choose a preferential route until the accumulated bacteria blocked this route, so the fluid flow redirected to other routes, supplying nutrients to slow-growing bacteria. The only difference noticed between the wild-type and EPS mutant was that the mutant bacteria associated in long chains in the presence of a flow stimulus, whereas, they remained independent in static zones (Aufrecht et al, 2019).…”

“…from the rhizosphere of Populus deltoides and grew it on an agar plate. On the other hand, Aufrecht et al, after isolating Pantoea sp., cultured it on a surface with heterogeneous pores that simulate a more realistic soil distribution (Aufrecht et al, 2019). In addition, Aufretch applied a flow stream over the system to recreate rainwater filtration.…”

“…While Pantoea sp. grew homogeneously on the agar plate and formed colonies (Bible et al, 2016), in the microfluidic device, it tended to grow by selecting preferential routes depending on the availability of nutrients provided by the stream flows (Aufrecht et al, 2019). Altogether, it is tempting to conclude that microfluidics offers the possibility of replicating more realistic environments than those offered by traditional methods.…”

The first open channel for yield-stress fluids in porous media

“…2008), fermentation (Pandey 2003; Aufrecht et al. 2019), soil sequestration (Schlesinger 1999), energy storage (Duduta et al. 2011; Sun et al.…”

“…Fluid flows in porous media have been studied for more than a century due to their high relevance to several engineering applications such as enhanced oil recovery (Green & Willhite 1998;Sahimi 2011;Farajzadeh et al 2012;Fraggedakis et al 2015), filtration and separation (Herzig, Leclerc & Goff 1970;Tien & Payatakes 1979;Jaisi et al 2008), fermentation (Pandey 2003;Aufrecht et al 2019), soil sequestration (Schlesinger † Email address for correspondence: dimfraged@gmail.com 1999), energy storage (Duduta et al 2011;Sun et al 2019) and food processing (Greenkorn 1983). In most cases, the fluids involved in these applications exhibit yield stress/viscoplastic behaviour (Bonn & Denn 2009;Balmforth, Frigaard & Ovarlez 2014).…”