Rapid formation of bioaggregates and morphology transition to biofilm streamers induced by pore-throat flows

The mechanism of biofilm detachment in porous medium under flow field

Biofilms are communities formed by bacteria adhering to surfaces, widely present in porous medium, and their growth can lead to clogging. Our experiment finds that under certain flow conditions, biofilms detach in pores and form a dynamically changing flow path. We define detachment that occurs far from the boundary of the flow path (with a distance greater than 200 μm) as internal detachment and detachment that occurs at the boundary of the flow path as external detachment. To understand the mechanism of biofilm detachment, we study the detachment behaviors of the Bacillus subtilis biofilm in a porous medium in a microfluidic device, where Bacillus subtilis strain is triple fluorescent labeled, which can represent three main phenotypes during the biofilm formation: motile cells, matrix-producing cells, and spores. We find that slow small-scale internal detachment occurs in regions with very few motile cells and matrix-producing cells, and bacterial movement in these areas is disordered. The increase in the number of matrix-producing cells induces clogging, and after clogging, the rapid detachment of the bulk internal biofilm occurs due to the increased pressure difference at the inlet and outlet. When both internal and external detachments occur simultaneously, the number of matrix-producing cells in the internal detachment area is 2.5 times that in the external detachment area. The results indicate that biofilm detachment occurs in areas with fewer matrix-producing cells, as matrix-producing cells can help resist detachment by secreting extracellular polymeric substances (EPSs).

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.

The porous structure induced heterogeneous and localized failure of the biofilm in microfluidic channels

Understanding the mechanism of biofilm distribution and detachment is very important to effectively improve water treatment and prevent blockage in porous media. The existing research is more related to the local biofilm evolving around one or few microposts and the lack of the integral biofilm evolution in a micropost array for a longer growth period. This study combines microfluidic experiments and mathematical simulations to study the distribution and detachment of biofilm in porous media. Microfluidic chips with an array of microposts with different sizes are designed to simulate the physical pore structure of soil. The research shows that the initial formation and distribution of biofilm are influenced by bacterial transport velocity gradients within the pore space. Bacteria prefer to aggregate areas with smaller microposts, leading to the development of biofilm in those regions. Consequently, impermeable blockage structures form in this area. By analyzing experimental images of biofilm structures at the later stages, as well as coupling fluid flow and porous medium, and the finite element simulation, we find that the biofilm detachment is correlated with the morphology and permeability (kb) (from 10-15 to 10-9 m2) of the biofilm. The simulations show that there are two modes of biofilm detachment, such as internal detachment and external erosion.

Microfluidic investigation of the impacts of flow fluctuations on the development of Pseudomonas putida biofilms

Biofilms play critical roles in wastewater treatment, bioremediation, and medical-device-related infections. Understanding the dynamics of biofilm formation and growth is essential for controlling and exploiting their properties. However, the majority of current studies have focused on the impact of steady flows on biofilm growth, while flow fluctuations are common in natural and engineered systems such as water pipes and blood vessels. Here, we reveal the effects of flow fluctuations on the development of Pseudomonas putida biofilms through systematic microfluidic experiments and the development of a theoretical model. Our experimental results showed that biofilm growth under fluctuating flow conditions followed three phases: lag, exponential, and fluctuation phases. In contrast, biofilm growth under steady-flow conditions followed four phases: lag, exponential, stationary, and decline phases. Furthermore, we demonstrated that low-frequency flow fluctuations promoted biofilm growth, while high-frequency fluctuations inhibited its development. We attributed the contradictory impacts of flow fluctuations on biofilm growth to the adjustment time (T0) needed for biofilm to grow after the shear stress changed from high to low. Furthermore, we developed a theoretical model that explains the observed biofilm growth under fluctuating flow conditions. Our insights into the mechanisms underlying biofilm development under fluctuating flows can inform the design of strategies to control biofilm formation in diverse natural and engineered systems.

A novel model for biofilm initiation in porous media flow

Bacteria often form biofilms in porous environments where an external flow is present, such as soil or filtration systems. To understand the initial stages of biofilm formation, one needs to study the interactions between cells, the fluid and the confining geometries. Here, we present an agent based numerical model for bacteria that takes into account the planktonic stage of motile cells as well as surface attachment and biofilm growth in a lattice Boltzmann fluid. In the planktonic stage we show the importance of the interplay between complex flow and cell motility when determining positions of surface attachment. In the growth stage we show the applicability of our model by investigating how external flow and biofilm stiffness determine qualitative colony morphologies as well as quantitative measurements of, e.g., permeability.

Microstructural and Rheological Transitions in Bacterial Biofilms

Biofilms are aggregated bacterial communities structured within an extracellular matrix (ECM). ECM controls biofilm architecture and confers mechanical resistance against shear forces. From a physical perspective, biofilms can be described as colloidal gels, where bacterial cells are analogous to colloidal particles distributed in the polymeric ECM. However, the influence of the ECM in altering the cellular packing fraction (ϕ) and the resulting viscoelastic behavior of biofilm remains unexplored. Using biofilms of Pantoea sp. (WT) and its mutant (ΔUDP), the correlation between biofilm structure and its viscoelastic response is investigated. Experiments show that the reduction of exopolysaccharide production in ΔUDP biofilms corresponds with a seven-fold increase in ϕ, resulting in a colloidal glass-like structure. Consequently, the rheological signatures become altered, with the WT behaving like a weak gel, whilst the ΔUDP displayed a glass-like rheological signature. By co-culturing the two strains, biofilm ϕ is modulated which allows us to explore the structural changes and capture a change in viscoelastic response from a weak to a strong gel, and to a colloidal glass-like state. The results reveal the role of exopolysaccharide in mediating a structural transition in biofilms and demonstrate a correlation between biofilm structure and viscoelastic response.