Coupled flow and biomass-nutrient growth at pore-scale with permeable biofilm, adaptive singularity and multiple species

Microscale advection governs microbial growth and oxygen consumption in macroporous aggregates

Most microbial life on Earth is found in localized microenvironments that collectively exert a crucial role in maintaining ecosystem health and influencing global biogeochemical cycles. In many habitats such as biofilms in aquatic systems, bacterial flocs in activated sludge, periphyton mats, or particles sinking in the ocean, these microenvironments experience sporadic or continuous flow. Depending on their microscale structure, pores and channels through the microenvironments permit localized flow that shifts the relative importance of diffusive and advective mass transport. How this flow alters nutrient supply, facilitates waste removal, drives the emergence of different microbial niches, and impacts the overall function of the microenvironments remains unclear. Here, we quantify how pores through microenvironments that permit flow can elevate nutrient supply to the resident bacterial community using a microfluidic experimental system and gain further insights from coupled population-based and computational fluid dynamics simulations. We find that the microscale structure determines the relative contribution of advection vs diffusion, and even a modest flow through a pore in the range of 10 µm s-1 can increase the carrying capacity of a microenvironment by 10%. Recognizing the fundamental role that microbial hotspots play in the Earth system, developing frameworks that predict how their heterogeneous morphology and potential interstitial flows change microbial function and collectively alter global scale fluxes is critical.IMPORTANCEMicrobial life is a key driver of global biogeochemical cycles. Similar to the distribution of humans on Earth, they are often not homogeneously distributed in nature but occur in dense clusters that resemble microbial cities. Within and around these clusters, diffusion is often assumed as the sole mass-transfer process that dictates nutrient supply and waste removal. In many natural and engineered systems such as biofilms in aquatic environments, aggregates in bioremediation, or flocs in wastewater treatment plants, these clusters are exposed to flow that elevates mass transfer, a process that is often overlooked. In this study, we show that advective fluxes can increase the local growth of bacteria in a single microenvironment by up to 50% and shape their metabolism by disrupting localized anoxia or supplying nutrients at different rates. Collectively, advection-enhanced mass transport may thus regulate important biogeochemical transformations in both natural and engineered environments.

Reduced Model for Properties of Multiscale Porous Media with Changing Geometry

In this paper, we consider an important problem for modeling complex coupled phenomena in porous media at multiple scales. In particular, we consider flow and transport in the void space between the pores when the pore space is altered by new solid obstructions formed by microbial growth or reactive transport, and we are mostly interested in pore-coating and pore-filling type obstructions, observed in applications to biofilm in porous media and hydrate crystal formation, respectively. We consider the impact of these obstructions on the macroscopic properties of the porous medium, such as porosity, permeability and tortuosity, for which we build an experimental probability distribution with reduced models, which involves three steps: (1) generation of independent realizations of obstructions, followed by, (2) flow and transport simulations at pore-scale, and (3) upscaling. For the first step, we consider three approaches: (1A) direct numerical simulations (DNS) of the PDE model of the actual physical process called BN which forms the obstructions, and two non-DNS methods, which we call (1B) CLPS and (1C) LP. LP is a lattice Ising-type model, and CLPS is a constrained version of an Allen–Cahn model for phase separation with a localization term. Both LP and CLPS are model approximations of BN, and they seek local minima of some nonconvex energy functional, which provide plausible realizations of the obstructed geometry and are tuned heuristically to deliver either pore-coating or pore-filling obstructions. Our methods work with rock-void geometries obtained by imaging, but bypass the need for imaging in real-time, are fairly inexpensive, and can be tailored to other applications. The reduced models LP and CLPS are less computationally expensive than DNS, and can be tuned to the desired fidelity of the probability distributions of upscaled quantities.