Biofilms in 3D porous media: Delineating the influence of the pore network geometry, flow and mass transfer on biofilm development

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.

Influence of phosphate on bacterial release from activated carbon point-of-use filters and on biofilm characteristics

Point-of-use (POU) filters certified to remove lead are often composed of activated carbon and have been shown to release high concentrations of bacteria, including opportunistic pathogens. In this study, we examine the impacts of the common corrosion inhibitor phosphate on biofilm characteristics and the relationship between biofilm structure and bacterial release from POU filters. This knowledge is essential for understanding how best to use the filters and where these filters fit in a system where other lead contamination prevention measures may be in place. We measured the bacterial release from activated carbon POU filters fed with groundwater - a common source of drinking water - with and without phosphate. We used optical coherence tomography (OCT) to quantitatively characterize biofilm growing on activated carbon filter material in which the biofilms were fed groundwater with and without phosphate. Phosphate filters released significantly less (57-87 %) bacteria than groundwater filters, and phosphate biofilms (median thickness: 82-331 μm) grew to be significantly thicker than groundwater biofilms (median thickness: 122-221 μm). The phosphate biofilm roughness ranged from 97 to 142 % of the groundwater biofilm roughness and was significantly greater in most weeks. Phosphate biofilms also had fewer pores per biofilm volume and shorter channels connecting those pores.

Geometry-Dependent Elastic Flow Dynamics in Micropillar Arrays

Regular device-scale DNA waves for high DNA concentrations and flow velocities have been shown to emerge in quadratic micropillar arrays with potentially strong relevance for a wide range of microfluidic applications. Hexagonal arrays constitute another geometry that is especially relevant for the microfluidic pulsed-field separation of DNA. Here, we report on the differences at the micro and macroscopic scales between the resulting wave patterns for these two regular array geometries and one disordered array geometry. In contrast to the large-scale regular waves visible in the quadratic array, in the hexagonal arrays, waves occur in a device-scale disordered zig-zag pattern with fluctuations on a much smaller scale. We connect the large-scale pattern to the microscopic flow and observe flow synchronization that switches between two directions for both the quadratic and hexagonal arrays. We show the importance of order using the disordered array, where steady-state stationary and highly fluctuating flow states persist in seemingly random locations across the array. We compare the flow dynamics of the arrays to that in a device with sparsely distributed pillars. Here, we observe similar vortex shedding, which is clearly observable in the quadratic and disordered arrays. However, the shedding of these vortices couples only in the flow direction and not laterally as in the dense, ordered arrays. We believe that our findings will contribute to the understanding of elastic flow dynamics in pillar arrays, helping us elucidate the fundamental principles of non-Newtonian fluid flow in complex environments as well as supporting applications in engineering involving e.g., transport, sorting, and mixing of complex fluids.

A versatile micromodel technology to explore biofilm development in porous media flows

Bacterial biofilms that grow in porous media are critical to ecosystem processes and applications ranging from soil bioremediation to bioreactors for treating wastewater or producing value-added products. However, understanding and engineering the complex phenomena that drive the development of biofilms in such systems remains a challenge. Here we present a novel micromodel technology to explore bacterial biofilm development in porous media flows. The technology consists of a set of modules that can be combined as required for any given experiment and conveniently tuned for specific requirements. The core module is a 3D-printed micromodel where biofilm is grown into a perfusable porous substrate. High-precision additive manufacturing, in particular stereolithography, is used to fabricate porous scaffolds with precisely controlled architectures integrating flow channels with diameters down to several hundreds of micrometers. The system is instrumented with: ultraviolet-C light-emitting diodes; on-line measurements of oxygen consumption and pressure drop across the porous medium; camera and spectrophotometric cells for the detection of biofilm detachment events at the outlet. We demonstrate how this technology can be used to study the development of Pseudomonas aeruginosa biofilm for several days within a network of flow channels. We find complex dynamics whereby oxygen consumption reaches a steady-state but not the pressure drop, which instead features a permanent regime with large fluctuations. We further use X-ray computed microtomography to image the spatial distribution of biofilms and computational fluid dynamics to link biofilm development with local flow properties. By combining the advantages of additive manufacturing for the creation of reproducible 3D porous microarchitectures with the flow control and instrumentation accuracy of microfluidics, our system provides a platform to study the dynamics of biofilm development in 3D porous media and to rapidly test new concepts in process engineering.

Monitoring biofilm thickness using the membrane aerated biofilm reactor (MABR) fingerprint soft sensor to optimize nitrogen removal

The ongoing commercialization and installation of full-scale membrane aerated biofilm reactors (MABRs) stimulate the increasing need to monitor biofilm development. Biofilm thickness in MABRs can be assessed indirectly by plotting the exhaust oxygen purity versus bulk ammonia concentration, defined here as the MABR fingerprint soft sensor. Dynamic simulations with diurnal flow variations of an MABR unit model were implemented over a broad range of biofilm thicknesses and influent conditions consisting of variable C/N ratios and applied ammonia fluxes to assess the utility of the MABR fingerprint. Results show that the continuously decreasing trend of the MABR fingerprint plot slopes can be employed as a useful signal for biofilm thickness control in nitrogen removal processes. This technique is useful in a wide range of influent conditions and is helpful for MABR operators and designers to arrange biofilm thickness control events efficiently and determine where in an overall treatment process the technique can be applied to control biofilm thickness and optimize process performance. PRACTITIONER POINTS: The linear relationship between exhaust oxygen purity and bulk ammonia concentration is defined as the MABR fingerprint plot. MABR fingerprint plots are generated for a given biofilm thickness with diurnal flow or short-term loading variations implemented. Continuously decreasing trends of the MABR fingerprint plot slopes are useful signals for biofilm control in nitrogen removal. The MABR fingerprint is useful over a wide range of influent conditions regarding C/N ratios and applied ammonia fluxes. MABR practitioners can use the fingerprint plots to determine when biofilm control measures should be taken.

Controlling biofilm transport with porous metamaterials designed with Bayesian learning

Biofilm growth and transport in confined systems frequently occur in natural and engineered systems. Designing customizable engineered porous materials for controllable biofilm transportation properties could significantly improve the rapid utilization of biofilms as engineered living materials for applications in pollution alleviation, material self-healing, energy production, and many more. We combine Bayesian optimization (BO) and individual-based modeling to conduct design optimizations for maximizing different porous materials' (PM) biofilm transportation capability. We first characterize the acquisition function in BO for designing 2-dimensional porous membranes. We use the expected improvement acquisition function for designing lattice metamaterials (LM) and 3-dimensional porous media (3DPM). We find that BO is 92.89% more efficient than the uniform grid search method for LM and 223.04% more efficient for 3DPM. For all three types of structures, the selected characterization simulation tests are in good agreement with the design spaces approximated with Gaussian process regression. All the extracted optimal designs exhibit better biofilm growth and transportability than unconfined space without substrates. Our comparison study shows that PM stimulates biofilm growth by taking up volumetric space and pushing biofilms' upward growth, as evidenced by a 20% increase in bacteria cell numbers in unconfined space compared to porous materials, and 128% more bacteria cells in the target growth region for PM-induced biofilm growth compared with unconfined growth. Our work provides deeper insights into the design of substrates to tune biofilm growth, analyzing the optimization process and characterizing the design space, and understanding biophysical mechanisms governing the growth of biofilms.

Using symmetry to control viscoelastic waves in pillar arrays

Solutions of macromolecules exhibit viscoelastic properties and unlike Newtonian fluids, they may break time-reversal symmetry at low Reynolds numbers resulting in elastic turbulence. Furthermore, under some conditions, instead of the chaotic turbulence, the result is large-scale waves in the form of cyclic spatial and temporal concentration variations, as has been shown for macromolecular DNA flowing in microfluidic pillar arrays. We here demonstrate how altering the symmetry of the individual pillars can be used to influence the symmetry of these waves. We control the extent of instabilities in viscoelastic flow by leveraging the effects of the symmetry of the pillars on the waves, demonstrating suppressed viscoelastic fluctuations with relevance for transport and sorting applications, or conversely opening up for enhanced viscoelasticity-mediated mixing. The onset of waves, which changes flow resistance, occurs at different Deborah numbers for flow in different directions through the array of triangular pillars, thus breaking the symmetry of the flow resistance along the device, opening up for using the occurrence of the waves to construct a fluidic diode.

Spatial-temporal clogging development in leachate collection systems of landfills: Insight into chemical and biological clogging characteristics

The clogging of leachate collection systems (LCSs) is a typical challenge for landfills operation. Although clogging occurs in different LCS components, its spatial-temporal distributions remain unclear. This study aimed to systematically investigate the dynamic clogging development in simulated LCSs by monitoring changes in clogging characteristics over time. Results revealed that clogging accumulated in all components of the simulated LCS during a 215-day period, including chemical clogging and bio-clogging. Distinct spatial variations in clogging components were observed along the leachate flow of the simulated LCS, with the geotextile being severely clogged due to bio-clogging (70.1 ± 3.0%-80.0 ± 0.5%). Additionally, chemical clogging mainly occurred at the top (85.4 ± 0.8%-95.0 ± 0.9%) and middle (91.2 ± 0.8%-94.9 ± 1.1%) gravel layers. Nevertheless, the percentage of chemical clogging decreased from 72.0 ± 2.1% (day 42) to 42.5 ± 2.7% (day 215) at the bottom gravel layer. Chemical clogging was the main type in the pipe, accounting for 69.6 ± 0.5% (day 215). In addition, the ratios of bio-clogging to chemical clogging changed over time in all LCS components. The spatial-temporal characteristics of clogging across LCS components can enhance the understanding of clogging mechanisms, facilitate the design optimization of LCSs, and promote the formulation of effective control strategies.

Fluid-Solid Reaction in Porous Media as a Chaotic Restart Process

Chemical and biological reactions at fluid-solid interfaces are central to a broad range of porous material applications and research. Pore-scale solute transport limitations can reduce reaction rates, with marked consequences for a wide spectrum of natural and engineered processes. Recent advances show that chaotic mixing occurs spontaneously in porous media, but its impact on surface reactions is unknown. We show that pore-scale chaotic mixing significantly increases reaction efficiency compared to nonchaotic flows. We find that reaction rates are well described in terms of diffusive first-passage times of reactants to the solid interface subjected to a stochastic restart process resulting from Lagrangian chaos. Under chaotic mixing, the shear layer at no-slip interfaces sets the restart rate and leads to a characteristic scaling of reaction efficiency with Péclet number, in excellent agreement with numerical simulations. Reaction rates are insensitive to the flow topology as long as flow is chaotic, suggesting the relevance of this process to a broad range of porous materials.

Internal Biofilm Heterogeneities Enhance Solute Mixing and Chemical Reactions in Porous Media

Bacterial biofilms can form in porous media that are of interest in industrial applications ranging from medical implants to biofilters as well as in environmental applications such as in situ groundwater remediation, where they can be critical locations for biogeochemical reactions. The presence of biofilms modifies porous media topology and hydrodynamics by clogging pores and consequently solutes transport and reactions kinetics. The interplay between highly heterogeneous flow fields found in porous media and microbial behavior, including biofilm growth, results in a spatially heterogeneous biofilm distribution in the porous media as well as internal heterogeneity across the thickness of the biofilm. Our study leverages highly resolved three-dimensional X-ray computed microtomography images of bacterial biofilms in a tubular reactor to numerically compute pore-scale fluid flow and solute transport by considering multiple equivalent stochastically generated internal permeability fields for the biofilm. We show that the internal heterogeneous permeability mainly impacts intermediate velocities when compared with homogeneous biofilm permeability. While the equivalent internal permeability fields of the biofilm do not impact fluid-fluid mixing, they significantly control a fast reaction. For biologically driven reactions such as nutrient or contaminant uptake by the biofilm, its internal permeability field controls the efficiency of the process. This study highlights the importance of considering the internal heterogeneity of biofilms to better predict reactivity in industrial and environmental bioclogged porous systems.

Morphogenesis of Biofilms in Porous Media and Control on Hydrodynamics

The functioning of natural and engineered porous media, like soils and filters, depends in many cases on the interplay between biochemical processes and hydrodynamics. In such complex environments, microorganisms often form surface-attached communities known as biofilms. Biofilms can take the shape of clusters, which alter the distribution of fluid flow velocities within the porous medium, subsequently influencing biofilm growth. Despite numerous experimental and numerical efforts, the control of the biofilm clustering process and the resulting heterogeneity in biofilm permeability is not well understood, limiting our predictive abilities for biofilm-porous medium systems. Here, we use a quasi-2D experimental model of a porous medium to characterize biofilm growth dynamics for different pore sizes and flow rates. We present a method to obtain the time-resolved biofilm permeability field from experimental images and use the obtained permeability field to compute the flow field through a numerical model. We observe a biofilm cluster size distribution characterized by a spectrum slope evolving in time between -2 and -1, a fundamental measure that can be used to create spatio-temporal distributions of biofilm clusters for upscaled models. We find a previously undescribed biofilm permeability distribution, which can be used to stochastically generate permeability fields within biofilms. An increase in velocity variance for a decrease in physical heterogeneity shows that the bioclogged porous medium behaves differently than expected from studies on heterogeneity in abiotic porous media.

Poly(vinylidene fluoride) membrane with immobilized TiO2 for degradation of steroid hormone micropollutants in a photocatalytic membrane reactor

The lack of effective technologies to remove steroid hormones (SHs) from aquatic systems is a critical issue for both environment and public health. The performance of a flow-through photocatalytic membrane reactor (PMR) with TiO₂ immobilized on a photostable poly(vinylidene fluoride) membrane (PVDF-TiO₂) was evaluated in the context of SHs degradation at concentrations from 0.05 to 1000 µg/L under UV exposure (365 nm). A comprehensive investigation into the membrane preparation approach, including varying the surface Ti content and distribution, and membrane pore size, was conducted to gain insights on the rate-limiting steps for the SHs degradation. Increasing surface Ti content from 4 % to 6.5 % enhanced the 17β-estradiol (E2) degradation from 46 ± 12-81 ± 6 %. Apparent degradation kinetics were independent of both TiO₂ homogeneity and membrane pore size (0.1-0.45 µm). With optimized conditions, E2 removal was higher than 96 % at environmentally relevant feed concentration (100 ng/L), a flux of 60 L/m²h, 25 mW/cm², and 6.5 % Ti. These results indicated that the E2 degradation on the PVDF-TiO₂ membrane was limited by the catalyst content and light penetration depth. Further exploration of novel TiO₂ immobilization approach that can offer a larger catalyst content and light penetration is required to improve the micropollutant removal efficiency in PMR.

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

Bioaggregates are condensed porous materials comprising microbes, organic and inorganic matters, and water. They are commonly found in natural and engineered porous media and often cause clogging. Despite their importance, the formation mechanism of bioaggregates in porous media systems is largely unknown. Through microfluidic experiments and direct numerical simulations of fluid flow, we show that the rapid bioaggregation is driven by the interplay of the viscoelastic nature of biomass and hydrodynamic conditions at pore throats. At an early stage, unique flow structures around a pore throat promote the biomass attachment at the throat. Then, the attached biomass fluidizes when the shear stress at the partially clogged pore throat reaches a critical value. After the fluidization, the biomass is displaced and accumulated in the expansion region of throats forming bioaggregates. We further find that such criticality in shear stress triggers morphological changes in bioaggregates from rounded- to streamer-like shapes. This knowledge was used to control the clogging of throats by tuning the flow conditions: When the shear stress at the throat exceeded the critical value, clogging was prevented. The bioaggregation process did not depend on the detailed pore-throat geometry, as we reproduced the same dynamics in various pore-throat geometries. This study demonstrates that pore-throat structures, which are ubiquitous in porous media systems, induce bioaggregation and can lead to abrupt disruptions in flow.

Fluid transport in porous media based on differences in filter media morphology and biofilm growth in bioreactors

To elucidate the effect of pore structure on bioclogging and seepage flow in bioreactors, we used X-ray computed tomography (X-CT) to investigate the changes in seepage flow of porous media in zeolite, gravel and ceramsite bioreactors with biofilm growth by injecting a non-ionic contrast medium iohexol. Based on the X-CT images using a ball-and-stick model, the highest average pore radius (R‾) and the average pore throat radius (r‾) in the ceramsite column were found under the initial conditions, which facilitated its permeability. The pore and throat of the gravel column were small and homogeneous relatively. Biofilm growth decreased the pore and pore throat in the columns. The total throat area of zeolite, gravel and ceramsite columns declined by 74%, 73% and 79% respectively. The zeolite column had the highest average pore throat, which contributed to its maximum conductivity subsequently after biofilm growth. Further, the fractal dimensions of the pore structure increased with biofilm growth, especially in the zeolite and ceramsite columns. The heterogeneity of the porous media was reinforced by the biofilm growth in the zeolite and ceramsite columns due to their higher heterogeneity initially. We also observed that an increase in heterogeneity of porous medium amplified the preferential flow and flow heterogeneities, especially in the zeolite and ceramsite columns.

Role of surface physicochemical properties of pipe materials on bio-clogging in leachate collection systems from a thermodynamic perspective

Bio-clogging in pipes poses a significant threat to the operation of leachate collection systems. Bio-clogging formation is influenced by the pipe materials. However, the relationship between bio-clogging and the physicochemical properties of different pipe materials has not been clarified yet, especially from a thermodynamic aspect. In this study, the dynamic bio-clogging processes in pipes of different materials (high-density polyethylene (HDPE), polyvinyl chloride (PVC), polypropylene (PP), and polyethylene (PE)) were compared, and their correlation with the physicochemical properties was investigated. Results showed that the bio-clogging in HDPE and PVC pipes was more severe than that in PP and PE pipes. In bio-clogging development, the predominant factor changed from the surface roughness to the electron donator parameter (γ^-). In the initial phase, the most severe bio-clogging was observed in the HDPE pipe, which exhibited the highest roughness (432 ± 76 nm). In the later phase, the highest γ^- (2.2 mJ/m²) and protein content (2623.1 ± 33.2 μg/cm²) were observed in the PVC simultaneously. Moreover, the interaction energy indicated that the bacteria could irreversibly and reversibly adhere to the HDPE, whereas irreversible adhesion was observed in the PVC, PP, and PE cases. The findings clarify the thermodynamic mechanism underlying bio-clogging behaviors and provide novel insights into the bio-clogging behaviors in pipes of different materials, which can facilitate the development of effective bio-clogging control strategies.

Morphology and Size of Bacterial Colonies Control Anoxic Microenvironment Formation in Porous Media

Bacterial metabolisms using electron acceptors other than oxygen (e.g., methanogenesis and fermentation) largely contribute to element cycling and natural contaminant attenuation/mobilization, even in well-oxygenated porous environments, such as shallow aquifers. This paradox is commonly explained by the occurrence of small-scale anoxic microenvironments generated by the coupling of bacterial respiration and dissolved oxygen (O₂) transport by pore water. Such microenvironments allow facultative anaerobic bacteria to proliferate in oxic environments. Microenvironment dynamics are still poorly understood due to the challenge of directly observing biomass and O₂ distributions at the microscale within an opaque sediment matrix. To overcome these limitations, we integrated a microfluidic device with transparent O₂ planar optical sensors to measure the temporal behavior of dissolved O₂ concentrations and biomass distributions with time-lapse videomicroscopy. Our results reveal that bacterial colony morphology, which is highly variable in flowing porous systems, controls the formation of anoxic microenvironments. We rationalize our observations through a colony-scale Damköhler number comparing dissolved O₂ diffusion and a bacterial O₂ uptake rate. Our Damköhler number enables us to predict the pore space fraction occupied by anoxic microenvironments in our system for a given bacterial organization.

Upstream wall vortices in viscoelastic flow past a cylinder

We report a novel inertia-less, elastic flow instability for a viscoelastic, shear-thinning wormlike micellar solution flowing past a microcylinder in a channel with blockage ratio B_R = 2R/W = 0.5 and aspect ratio α = H/W ≈ 5, where R ≈ 100 μm is the cylinder radius, W is the channel width, and H is the channel height. The instability manifests upstream of the cylinder and changes form with increasing Weissenberg number over the range 0.5 ≲ Wi = Uλ/R ≲ 900, where U is the average flow velocity and λ is the terminal relaxation time of the fluid. Beyond a first critical Wi, the instability begins as a bending of the streamlines near the upstream pole of the cylinder that breaks the symmetry of the flow. Beyond a second critical Wi, small, time-steady, and approximately symmetric wall-attached vortices form upstream of the cylinder. Beyond a third critical Wi, the flow becomes time dependent and pulses with a characteristic frequency commensurate with the breakage timescale of the wormlike micelles. This is accompanied by a breaking of the symmetry of the wall-attached vortices, where one vortex becomes considerably larger than the other. Finally, beyond a fourth critical Wi, a vortex forms attached to the upstream pole of the cylinder whose length fluctuates in time. The flow is highly time dependent, and the cylinder-attached vortex and wall-attached vortices compete dynamically for space and time in the channel. Our results add to the rapidly growing understanding of viscoelastic flow instabilities in microfluidic geometries.

Opportunities for visual techniques to determine characteristics and limitations of electro-active biofilms

Optimization of bio-electrochemical systems (BESs) relies on a better understanding of electro-active biofilms (EABfs). These microbial communities are studied with a range of techniques, including electrochemical, visual and chemical techniques. Even though each of these techniques provides very valuable and wide-ranging information about EABfs, such as performance, morphology and biofilm composition, they are often destructive. Therefore, the information obtained from EABfs development and characterization studies are limited to a single characterization of EABfs and often limited to one time point that determines the end of the experiment. Despite being scarcer and not as commonly reported as destructive techniques, non-destructive visual techniques can be used to supplement EABfs characterization by adding in-situ information of EABfs functioning and its development throughout time. This opens the door to EABfs monitoring studies that can complement the information obtained with destructive techniques. In this review, we provide an overview of visual techniques and discuss the opportunities for combination with the established electrochemical techniques to study EABfs. By providing an overview of suitable visual techniques and discussing practical examples of combination of visual with electrochemical methods, this review aims at serving as a source of inspiration for future studies in the field of BESs.

Temporal Evolution of Erosion in Pore Networks: From Homogenization to Instability

We study the dynamics of flow networks in porous media using two and three dimensional pore-network models. We consider a class of erosion dynamics for a single phase flow with no deposition, chemical reactions, or topology changes assuming a constitutive law depending on flow rate, local velocities, or shear stress at the walls. We show that depending on the erosion law, the flow may become uniform and homogenized or become unstable and develop channels. By defining an order parameter capturing these different behaviors we show that a phase transition occurs depending on the erosion dynamics. Using a simple model, we identify quantitative criteria to distinguish these regimes and correctly predict the fate of the network, and discuss the experimental relevance of our result.

Modular configurations of living biomaterials incorporating nano-based artificial mediators and synthetic biology to improve bioelectrocatalytic performance: A review

Currently, the industrial application of bioelectrochemical systems (BESs) that are incubated with natural electrochemically active microbes (EABs) is limited due to inefficient extracellular electron transfer (EET) by natural EABs. Notably, recent studies have identified several novel living biomaterials comprising highly efficient electron transfer systems allowing unparalleled proficiency of energy conversion. Introduction of these biomaterials into BESs could fundamentally increase their utilization for a wide range of applications. This review provides a comprehensive assessment of recent advancements in the design of living biomaterials that can be exploited to enhance bioelectrocatalytic performance. Further, modular configurations of abiotic and biotic components promise a powerful enhancement through integration of nano-based artificial mediators and synthetic biology. Herein, recent advancements in BESs are synthesized and assessed, including heterojunctions between conductive nanomaterials and EABs, in-situ hybrid self-assembly of EABs and nano-sized semiconductors, cytoprotection in biohybrids, synthetic biological modifications of EABs and electroactive biofilms. Since living biomaterials comprise a broad range of disciplines, such as molecular biology, electrochemistry and material sciences, full integration of technological advances applied in an interdisciplinary framework will greatly enhance/advance the utility and novelty of BESs. Overall, emerging fundamental knowledge concerning living biomaterials provides a powerful opportunity to markedly boost EET efficiency and facilitate the industrial application of BESs to meet global sustainability challenges/goals.

Insight into the effect of calcium on bio-clogging behavior via quartz crystal microbalance with dissipation monitoring

Bio-clogging of leachate collection systems has attracted much attention because of its threat to landfill slope stability and landfill landslide events. Calcium in leachate plays a vital role in the formation of bio-clogging. However, the influence of calcium on bio-clogging remains unclear. This study examined the effects of calcium concentration on bio-clogging, including 0, 1.25, 5, 25, and 75 mM CaCl₂ groups. A technique involving quartz crystal microbalance with dissipation monitoring (QCM-D) was applied to evaluate the bacteria adhesion behaviors in real time. The results showed that the presence of Ca²⁺ accelerated the bacterial attachment and increased the viscoelasticity of deposited layers. The deposition mass for 75 mM CaCl₂ was 1442 ± 260 ng/cm², which is 1.5 times that for 1.25 mM CaCl₂. The Derjaguin-Landau-Verwey-Overbeek (DLVO) theory could explain the bacterial adhesion behaviors in low calcium concentrations (<25 mM). In comparison, the effect of calcium bridge was shown in high calcium concentrations (>25 mM). The development of biofilms was a dynamic process, and the Ca²⁺ concentration was positively related to the amount of biofilm generated. In low CaCl₂ concentration (less than 5 mM) groups, the degree of bio-clogging increased from the exponential growth phase to the decline phase; in contrast, in high CaCl₂ concentration (above 25 mM) groups, the degree of bio-clogging increased and later declined. Therefore, the calcium concentration should be controlled at a low level in leachate to mitigate bio-clogging in LCSs.

Contributions of biofilm-induced flow heterogeneities to solute retention and anomalous transport features in porous media

Microbial biofilms are ubiquitous within porous media and the dynamics of their growth influence surface and subsurface flow patterns which impacts the physical properties of porous media and large-scale transport of solutes. A two-dimensional pore-scale numerical model was used to evaluate the impact of biofilm-induced flow heterogeneities on conservative transport. Our study integrates experimental biofilm images of Paenibacillus 300A strain in a microfluidic device packed with cylindrical grains in a hexagonal distribution, with mathematical modeling. Biofilm is represented as a synthetic porous structure with locally varying physical properties that honors the impact of biofilm on the porous medium. We find that biofilm plays a major role in shaping the observed conservative transport dynamics by enhancing anomalous characteristics. More specifically, when biofilm is present, the pore structure in our geometry becomes more spatially correlated. We observe intermittent behavior in the Lagrangian velocities that switches between fast transport periods and long trapping events. Our results suggest that intermittency enhances solute spreading in breakthrough curves which exhibit extreme anomalous slope at intermediate times and very marked late solute arrival due to solute retention. The efficiency of solute retention by the biofilm is controlled by a transport regime which can extend the tailing in the concentration breakthrough curves. These results indicate that solute retention by the biofilm exerts a strong control on conservative solute transport at pore-scale, a role that to date has not received enough attention.

Low-Field Nuclear Magnetic Resonance Characteristics of Biofilm Development Process

To in situ and noninvasively monitor the biofilm development process by low-field nuclear magnetic resonance (NMR), experiments should be made to determine the mechanisms responsible for the T₂ signals of biofilm growth. In this paper, biofilms were cultivated in both fluid media and saturated porous media. T₂ relaxation for each sample was measured to investigate the contribution of the related processes to T₂ relaxation signals. In addition, OD values of bacterial cell suspensions were measured to provide the relative number of bacterial cells. We also obtained SEM photos of the biofilms after vacuum freeze-drying the pure sand and the sand with biofilm formation to confirm the space within the biofilm matrix and identify the existence of biofilm formation. The T₂ relaxation distribution is strongly dependent on the density of the bacterial cells suspended in the fluid and the stage of biofilm development. The peak time and the peak percentage can be used as indicators of the biofilm growth states.

New directions and challenges in engineering biologically-enhanced biochar for biological water treatment

Cost-effective, efficient, and sustainable water treatment solutions utilising existing materials and technology will make it easier for low and middle-income countries to adopt them, improving public health. The ability of biochar to mediate and support microbial degradation of contaminants, combined with its carbon-sequestration potential, has attracted attention in recent years. Biochar is a possible candidate for use in cost-effective and sustainable biological water treatment, especially in agrarian economies with easy access to abundant biomass in the form of crop residues and organic wastes. This review evaluates the scope, potential benefits (economic and environmental) and challenges of sustainable biological water treatment using 'Biologically-Enhanced Biochar' or BEB. We discuss the various processes occurring in BEB systems and demonstrate the urgent need to investigate microbial degradation mechanisms. We highlight the need to correlate biochar properties to biofilm development, which can eventually determine process efficiency. We also demonstrate the various opportunities in adopting BEB as a cheaper and more viable alternative in Low and Middle Income Countries and compare it to the current benchmark, 'Biological Activated Carbon'. We focus on the recent advances in the areas of data science, mathematical modelling and molecular biology to systematically and sustainably design BEB filters, unlike the largely empirical design approaches seen in water treatment. 'Sequential biochar systems' are introduced as specially designed end-of-life techniques to lower the environmental impact of BEB filters and examples of their integration into biological water treatment that can fulfil zero waste criteria for BEBs are given.

Insights into the Development of Phototrophic Biofilms in a Bioreactor by a Combination of X-ray Microtomography and Optical Coherence Tomography

As productive biofilms are increasingly gaining interest in research, the quantitative monitoring of biofilm formation on- or offline for the process remains a challenge. Optical coherence tomography (OCT) is a fast and often used method for scanning biofilms, but it has difficulty scanning through more dense optical materials. X-ray microtomography (μCT) can measure biofilms in most geometries but is very time-consuming. By combining both methods for the first time, the weaknesses of both methods could be compensated. The phototrophic cyanobacterium Tolypothrix distorta was cultured in a moving bed photobioreactor inside a biocarrier with a semi-enclosed geometry. An automated workflow was developed to process µCT scans of the biocarriers. This allowed quantification of biomass volume and biofilm-coverage on the biocarrier, both globally and spatially resolved. At the beginning of the cultivation, a growth limitation was detected in the outer region of the carrier, presumably due to shear stress. In the later phase, light limitations could be found inside the biocarrier. µCT data and biofilm thicknesses measured by OCT displayed good correlation. The latter could therefore be used to rapidly measure the biofilm formation in a process. The methods presented here can help gain a deeper understanding of biofilms inside a process and detect any limitations.

Visualizing, quantifying, and controlling local hydrodynamic effects on biofilm accumulation in complex flow paths

Complex flow paths (CFPs) are commonly applied in precision equipment to accurately supply controllable fluids with designed structures. However, the presence of biofilms in CFPs causes quite a few unwanted issues, such as bio-erosion, clogging, or even health risks. To date, visualizing and quantifying the interaction between biofilm distribution and local hydrodynamics remains difficult, and the mechanism during the process is unclear. In this paper, the remodeling simulation method (3D industrial computed tomography scanning-inverse modeling-numerical simulation) and 16S rRNA high-throughput sequencing were integrated. The results indicated that local hydrodynamic characteristics significantly affected biofilm thicknesses on CFP surfaces (relative differences of 41.3-71.2%), which inversely influenced the local turbulence intensity. The average biofilm thicknesses exhibited a significant quadratic correlation with the near-wall hydraulic shear forces (r > 0.72, p < 0.05), and the biofilm reached a maximum thickness at 0.36-0.45 Pa. On the other hand, the near-wall hydraulic shear forces not only affected microbial community characteristics of biofilms, but they also influenced the number of microorganisms involved, which determined the biofilm accumulation thereafter. The PHYLUM Firmicutes and Proteobacteria were the dominant bacteria during the process. The results obtained in this paper could provide practical conceptions for the targeted control of biofilms and put forward more efficient controlling methods in commonly applied CFP systems.

Characterizing the Shearing Stresses within the CDC Biofilm Reactor Using Computational Fluid Dynamics

Shearing stresses are known to be a critical factor impacting the growth and physiology of biofilms, but the underlying fluid dynamics within biofilm reactors are rarely well characterized and not always considered when a researcher decides which biofilm reactor to use. The CDC biofilm reactor is referenced in validated Standard Test Methods and US EPA guidance documents. The driving fluid dynamics within the CDC biofilm reactor were investigated using computational fluid dynamics. An unsteady, three-dimensional model of the CDC reactor was simulated at a rotation rate of 125 RPM. The reactor showed turbulent structures, with shear stresses averaging near 0.365 ± 0.074 Pa across all 24 coupons. The pressure variation on the coupon surfaces was found to be larger, with a continuous 2–3 Pa amplitude, coinciding with the baffle passage. Computational fluid dynamics was shown to be a powerful tool for defining key fluid dynamic parameters at a high fidelity within the CDC biofilm reactor. The consistency of the shear stresses and pressures and the unsteadiness of the flow within the CDC reactor may help explain its reproducibility in laboratory studies. The computational model will enable researchers to make an informed decision whether the fluid dynamics present in the CDC biofilm reactor are appropriate for their research.

Bio-clogging mitigation in the leachate collection system of municipal solid waste landfill using graphene oxide-coated geotextiles

In this study, graphene oxide (GO) was coated in geotextiles (GO-GT) to evaluate its potential for bio-clogging mitigation in the leachate collection system (LCS) of a landfill. Results showed that GO coating enhanced the surface hydrophilicity of geotextile. Bacterial experiments revealed that dead cells in the bio-clogging increased to 68.7% with GO-GT, compared to that in the GT (44.0%). After 136 days of operation, the GO-GT reduced the bio-clogging by decreasing the total amount of bacteria and the percentage of living bacteria. The total amount of extracellular polymeric substances in the GO-GT and GT was 22.8 ± 4.4 and 52.8 ± 4.8 mg/g of volatile suspended solids, respectively. Microbial analysis showed that Limnochordia and Symbiobacteriia were the most sensitive groups, with a decreased percentage in the GO-GT. Electrostatic repulsion and surface wrinkling were attributed to the attenuation effect on the GO-GT. These results imply the potential application of GO-coated geotextile for reducing bio-clogging in landfill LCS.

Non-Invasive Measurement, Mathematical Simulation and In Situ Detection of Biofilm Evolution in Porous Media: A Review

The development of biofilms and the related changes in porous media in the subsurface cannot be directly observed and evaluated. The primary reason that the mechanism of biofilm clogging in porous media cannot be clearly demonstrated is due to the opacity and structural complexity of three-dimensional pore space. Interest in exploring methods to overcome this limitation has been increasing. In the first part of this review, we introduce the underlying characteristics of biofilm in porous media. Then, we summarize two approaches, non-invasive measurement methods and mathematical simulation strategies, for studying fluid–biofilm–porous medium interaction with spatiotemporal resolution. We also discuss the advantages and limitations of these approaches. Lastly, we provide a perspective on opportunities for in situ monitoring at the field site.

Comparison of bio-clogging characteristics of geotextiles in MSW and bottom ash co-disposal landfills

Bio-clogging of geotextile is a big challenge for the leachate collection system in landfills. It is important to understand the characteristics of geotextile bio-clogging to develop control technologies. This study investigated the characteristics of geotextile bio-clogging in municipal solid waste landfill (MSW_G) and bottom ash (BA) co-disposal landfill (BA_G). Results showed that the bio-clogging mass of per area in MSW_G and BA_G was 49 ± 5 g/m² and 57 ± 3 g/m², respectively. Bio-clogging was dominated by live cells in both MSW_G and BA_G. The confocal laser scanning microscopy images revealed that live cells percentage was 46% in MSW_G, while it increased to 77% in BA_G. In contrast, the percentage of the dead cells was 47% and 9% in MSW_G and BA_G, respectively. The biofilm formed in BA _G was thinner and denser than that in MSW_G. Based on the microbial analysis, the biofilms of BA_G had a higher genetic amount and diversity than these of MSW_G. The total amount of extracellular polymeric substances in BA_G was 45.29 ± 4.52 mg/g volatile suspended solids, which was 1.5 times of that in MSW_G. The co-disposal of BA increased the microbial diversity and accelerated bio-clogging due to the high calcium concentration. These findings provide a better understanding of the bio-clogging characteristics, which is helpful to control bio-clogging in co-disposal landfills.

Modeling the impact of evolving biofilms on flow in porous media inside a microfluidic channel

This study integrates microfluidic experiments and mathematical modeling to study the impacts of biofilms on flow in porous media and to explore approaches to simplify modeling permeability with complicated biofilm geometries. E. coli biofilms were grown in a microfluidic channel packed with a single layer of glass beads to reach three biofilm levels: low, intermediate, and high, with biofilm ratios (β_r) of 2.7%, 17.6%, and 55.2%, respectively. Two-dimensional biofilm structures and distributions in the porous medium were modeled by digitizing confocal images and considering broad ranges of biofilm permeability (k_b) (from 10^-15 m² to 10^-7 m²) and biofilm porosity (ε_b) (from 0.2 to 0.8). The overall permeability of the porous medium (k), the flow pathways and the overall/local pressure gradients were found to be highly dependent on β_r and k_b but were moderately impacted by ε_b when the biofilm levels were high and intermediate with k_b>10^-11 m². When biofilm structures are well developed, simplified biofilm geometries, such as uniform coating and symmetric contact filling, can provide reasonable approximations of k.

Effect of Nonphosphorus Corrosion Inhibitors on Biofilm Pore Structure and Mechanical Properties

Understanding the effects of biofilm structural and mechanical properties, which can influence biofilm cohesiveness and detachment under physical stress, is critical for biofilm and biofilm-associated pathogen control. In this study, we used optical coherence tomography (OCT) and nanoindentation to determine the role of silicate and tin (two experimental nonphosphate corrosion inhibitors) on the porous structure and stiffness of three types of multispecies biofilms. These biofilms were grown from groundwater (a drinking water source), and this groundwater was amended with either tin or silicate corrosion inhibitor (0.5 mg/L as Sn and 20 mg/L as SiO₂). Based on the elastic moduli of these biofilms, tin biofilms and groundwater biofilms were the stiffest, followed by silicate biofilms. The thickness normalized by the growth time for silicate biofilms was highest at 38 ± 7.1 μm/month, compared to 21 ± 3.2 and 11 ± 2.4 μm/month for tin biofilms and groundwater biofilms, respectively. The silicate biofilms had the greatest overall porosities and were thickest among the three biofilms. Based on the pore network modeling (PNM) of OCT images, larger pores and connections were found in the silicate biofilms compared to those in tin and groundwater biofilms. Our analysis showed that the thicker and more porous biofilms (silicate biofilms) were potentially less resistant to deformation than the thinner and denser biofilms (tin and groundwater biofilms).

Visualization study on aniline-degrading bacteria AN-1 transport in the aquifer with the low-permeability lens

The geological conditions of the contaminated sites will affect the migration of microorganisms in the underground environment. In order to study the effect of low-permeability lens on bacterial transport, green fluorescent protein labeling combined with light transmission method was used to reveal the bacterial transport in the heterogeneous aquifer. The experiment has the advantages of real-time monitoring and no disturbance. The results showed that the bacteria gave priority to bypass the lens to flow away. The lens had a significant effect on hindering the bacterial transport due to adsorption and straining. The larger permeability coefficient ratio between the bulk media and the low-permeability lens was, the more obvious the obstruction was. AN-1 cannot enter the lens until the ratio decreased to the order of 10². With the increase of the flow velocity, the bacterial plume changed a lot. The higher flow velocity reduced the adsorption and retention of AN-1 to the media, resulting in some microorganisms remaining in the pores washed down. When the flow came to 2.0 m·d^-1, AN-1 cannot adhere to the media due to the excessive fluid shear stress.

Numerical investigation of microbial quorum sensing under various flow conditions

Microorganisms efficiently coordinate phenotype expressions through a decision-making process known as quorum sensing (QS). We investigated QS amongst distinct, spatially distributed microbial aggregates under various flow conditions using a process-driven numerical model. Model simulations assess the conditions suitable for QS induction and quantify the importance of advective transport of signaling molecules. In addition, advection dilutes signaling molecules so that faster flow conditions require higher microbial densities, faster signal production rates, or higher sensitivities to signaling molecules to induce QS. However, autoinduction of signal production can substantially increase the transport distance of signaling molecules in both upstream and downstream directions. We present empirical approximations to the solutions of the advection–diffusion–reaction equation that describe the concentration profiles of signaling molecules for a wide range of flow and reaction rates. These empirical relationships, which predict the distribution of dissolved solutes along pore channels, allow to quantitatively estimate the effective communication distances amongst multiple microbial aggregates without further numerical simulations.

Visualization and characterization of Enterococcus faecalis biofilm structure in bovine dentin using 2D and 3D microscopic techniques

Bacterial biofilms are related to various dental and periodontal infectious diseases, and the characterization of this biological structure with micro-computed tomography (micro-CT) may offer valuable information for clinical and research applications. In this study, we aimed to develop a model to visualize three-dimensionally the biofilm structure on dentin using micro-CT. Dentin blocks were prepared and incubated in tryptic soy broth with Enterococcus faecalis (ATCC 29212). The control group did not receive any staining procedure, while groups 1 and 2 were stained with 100% and 50% barium sulfate, respectively. Transmission electron microscopy (TEM) and confocal laser scanning microscopy (CLSM) were used to detect biofilm formation, barium sulfate penetration, and microbial cell density in the biofilm. Micro-computed tomography (micro-CT) (SkyScan 1172, Bruker Co., Belgium) was used to visualize biofilm formation on the dentin blocks. Biofilm thicknesses were measured from 10 different locations on the specimen surfaces, using CTAn v.1.14.4 software. Obtained data were statistically analyzed using Kruskal-Wallis and Dunn's tests. TEM photomicrographs showed that barium sulfate could penetrate the biofilm structure. CLSM analysis showed that viable and total cell densities were similar between the control and barium sulfate-treated groups (P > 0.05), indicating barium sulfate had no significant influence on cell density. In barium sulfate-treated blocks, biofilm could be discriminated from the dentin, and its thickness could be measured with micro-CT. This study showed that bacterial biofilm on dentin could be characterized by micro-CT after barium sulfate staining without causing any significant side effect on viable and total cell densities.

Trait-specific dispersal of bacteria in heterogeneous porous environments: from pore to porous medium scale

The dispersal of organisms controls the structure and dynamics of populations and communities, and can regulate ecosystem functioning. Predicting dispersal patterns across scales is important to understand microbial life in heterogeneous porous environments such as soils and sediments. We developed a multi-scale approach, combining experiments with microfluidic devices and time-lapse microscopy to track individual bacterial trajectories and measure the overall breakthrough curves and bacterial deposition profiles: we, then, linked the two scales with a novel stochastic model. We show that motile cells of Pseudomonas putida disperse more efficiently than non-motile mutants through a designed heterogeneous porous system. Motile cells can evade flow-imposed trajectories, enabling them to explore larger pore areas than non-motile cells. While transported cells exhibited a rotation in response to hydrodynamic shear, motile cells were less susceptible to the torque, maintaining their body oriented towards the flow direction and thus changing the population velocity distribution with a significant impact on the overall transport properties. We also found, in a separate set of experiments, that if the suspension flows through a porous system already colonized by a biofilm, P. putida cells are channelled into preferential flow paths and the cell attachment rate is increased. These two effects were more pronounced for non-motile than for motile cells. Our findings suggest that motility coupled with heterogeneous flows can be beneficial to motile bacteria in confined environments as it enables them to actively explore the space for resources or evade regions with unfavourable conditions. Our study also underlines the benefit of a multi-scale approach to the study of bacterial dispersal in porous systems.

Mass transfer of nanobubble aeration and its effect on biofilm growth: Microbial activity and structural properties

It is necessary to improve the performance and reduce the aeration cost is of wastewater treatment by aerobic biofilm systems. Nanobubble aeration is supposed to be a promising method to achieve these goals. Compared with coarse bubbles, dissolved oxygen profiling showed that the nanobubbles provided more oxygen to biofilms, offering superior oxygen supply capacity and 1.5 times higher oxygen transfer efficiency. Nanobubble aeration accelerated the growth of the biofilm and achieved better removal efficiencies of chemical oxygen demand and ammonia, with as maximum as six times higher dehydrogenase activity, and more extracellular polymeric substance content than when using the traditional aeration mode. This is attributed to the enhancement of metabolism and the proliferation of microorganisms. Confocal laser-scanning microscopy imaging confirmed that nanobubble aeration affected the components of biofilm by shifting the microbial community and changing its metabolic pathways of biofilms, such as carbohydrate synthesis. Nanobubble aeration resulted in an energy saving of approximately 80%. The assessment of nanobubble aerated biofilm growth suggests that this technique can offer a rapid-initiation, high efficiency, and low-cost strategy for aerobic biofilm systems in wastewater treatment.

Visualizing the macroscale spatial distributions of biofilms in complex flow channels using industrial computed tomography

The presence of biofilms in enclosed pipelines can lead to numerous deleterious issues. To date, it has been difficult to use optical imaging techniques to monitor the macroscale spatial distributions of biofilms. To address this concern, a combination of industrial computed tomography (ICT) and a contrast agent was explored to noninvasively visualize biofilms in three types of drip irrigation emitters. The results showed that ICT successfully observed and quantified the macroscale spatial distributions of biofilms. The complex hydrodynamic characteristics in the emitter channels affected the local distributions of biofilms. Biofilms were mainly attached to the lateral and medial faces and biomass decreased along the flow directions. Based on the distributions of biofilms, some emitter structural design defects were further diagnosed. Applying ICT in combination with the contrast agent could potentially provide a visual and effective way to reveal the formation mechanisms of biofilms and to optimize flow channel structures to avoid biofilm accumulations.

In-situ monitoring AHL-mediated quorum-sensing regulation of the initial phase of wastewater biofilm formation

Initial attachment plays an important role in biofilm formation in wastewater treatment processes. However, the initial attachment process mediated by N-acyl-homoserine lactones (AHLs) is difficult to be fully understood due to the lack of non-invasive and on-line investigation techniques. In this study, the AHL-regulated wastewater biofilm attachment was quantified using ultrasonic time-domain reflectometry (UTDR) as an in-situ and non-invasive monitoring technique. Results demonstrated that the reversible adhesion time in municipal and industrial wastewaters was significantly decreased in the presence of exogenous AHLs. Biofilm thickness in municipal and industrial wastewaters increased significantly with the addition of exogenous AHLs. Also, the addition of acylase delayed the initial biofilm formation (lengthened reversible adhesion time and decreased biofilm thickness and density). Compared with biofilm behavior in the presence of low concentrations of AHLs (4.92 ± 0.17 μg/L), both reversible adhesion time and biofilm thickness were not significantly increased (p > 0.05) with an increase in AHL concentration (9.75 ± 0.41 μg/L). Furthermore, the addition of exogenous AHLs resulted in significant changes in the attached bacterial community structures, in which both QS and quorum-quenching (QQ) bacteria were stimulated. The current work presents an effective approach to in-situ monitoring of the regulation of AHL-mediated QS in the initial attachment of biofilms, especially in the reversible adhesion process, which may provide a potential strategy to facilitate biofilm establishment in wastewater treatment processes.

Enhanced hydrolyzed polyacrylamide removal from water by an aerobic biofilm reactor-ozone reactor-aerobic biofilm reactor hybrid treatment system: Performance, key enzymes and functional microorganisms

Degradation of hydrolyzed polyacrylamide-containing (HPAM-containing) wastewater was investigated in a lab-scale aerobic-ozonic-aerobic hybrid treatment system. When the HPAM concentration was 500 mg L^-1 and the ozone dose was 25 g O₃/g TOC, the HPAM removal rate reached 90.79%. Experimental results obtained from gel permeation chromatography (GPC) and rheometer indicated that the refractory HPAM was decomposed into small-molecule compounds. High performance liquid chromatography (HPLC) analysis showed that there was no acrylamide (AM) in the effluent of the system. Microbial communities in two aerobic biofilm reactors (ABRs) were analyzed by Illumina MiSeq Sequencing, which indicated that norank_f_Cytophagaceae, Meiothermus, Bacillus, etc. were keystone functional bacterial genera and Methanobacterium, norank_p_Bathyarchaeota, norank_c_Marine_Group_Ⅰ, etc. were dominant functional archaeal groups. To our knowledge, this is the first study to treat HPAM-containing wastewater using an aerobic-ozonic-aerobic hybrid process. Good removal efficiencies and presence of functional microorganisms demonstrated that the hybrid treatment system was practical for treating HPAM-containing wastewater.

Potential use of high-throughput sequencing of bacterial communities for postmortem submersion interval estimation

Microorganisms play vital roles in the natural decomposition of carcasses in aquatic systems. Using high-throughput sequencing techniques, we evaluated the composition and succession of microbial communities throughout the decomposition of rat carcasses in freshwater. A total of 4,428,781 high-quality 16S rRNA gene sequences and 2144 operational taxonomic units were obtained. Further analysis revealed that the microbial composition differed significantly between the epinecrotic (rat skins) and the epilithic (rocks) samples. During the carcass decomposition process, Proteobacteria became the dominant phylum in the epinecrotic, epilithic, and environmental (water) samples, followed by Firmicutes in the epinecrotic samples and Bacteroidetes in the epilithic and water samples. Microbial communities were influenced by numerous environmental factors, such as dissolved oxygen content and conductivity. Our study provides new insight about postmortem submersion interval (PMSI) estimation in aquatic environments.

Upscaling of microbially driven first-order reactions in heterogeneous porous media

Reactions mediated by microorganisms determine the fate of many chemicals in natural porous media. At the pore scale, the distribution of chemicals and microorganisms is not homogeneous, leading to heterogeneous distribution of microbial activities at the pore scale. We conducted pore scale reactive transport simulations to investigate the scaling of microbially mediated consumption reaction rates under a range of flow and reaction conditions. The results reveal that the scaling effects largely depended on Péclet and Damköhler numbers. Consumption rate estimates based on volume-averaged concentrations and reaction kinetics overestimated the true volumetric reaction rates, and large-sized biomass aggregates intensified these scaling errors. In contrast, the macroscopic rates estimated via flux-weighted concentrations underestimated the true volumetric reaction rates, with large microbial aggregates reducing scaling errors. This study also demonstrated that macroscopic rate estimates can be improved by combining information on the reaction kinetics with the flux-weighted concentrations.

Challenges of biofilm control and utilization: lessons from mathematical modelling

This article reviews modern applications of mathematical descriptions of biofilm formation. The focus is on theoretically obtained results which have implications for areas including the medical sector, food industry and wastewater treatment. Examples are given as to how models have contributed to the overall knowledge on biofilms and how they are used to predict biofilm behaviour. We conclude that the use of mathematical models of biofilms has demonstrated over the years the ability to significantly contribute to the vast field of biofilm research. Among other things, they have been used to test various hypotheses on the nature of interspecies interactions, viability of biofilm treatment methods or forces behind observed biofilm pattern formations. Mathematical models can also play a key role in future biofilm research. Many models nowadays are analysed through computer simulations and continue to improve along with computational capabilities. We predict that models will keep on providing answers to important challenges involving biofilm formation. However, further strengthening of the ties between various disciplines is necessary to fully use the tools of collective knowledge in tackling the biofilm phenomenon.

Colonization and growth of dehalorespiring biofilms on carbonaceous sorptive amendments

Removal of polychlorinated biphenyls (PCBs) from contaminated sediments is a priority due to accumulation in the food chain. Recent success with reduction of PCB bioavailability due to adsorption onto activated carbon led to the recognition of in situ treatment as a remediation approach. In this study, reduced bioavailability and subsequent break-down of PCBs in dehalorespiring biofilms was investigated using Dehalobium chlorocoercia DF1. DF1 formed a patchy biofilm ranging in thickness from 3.9 to 6.7 µm (average 4.6 ± 0.87 µm), while the biofilm coverage varied from 5.5% (sand) to 20.2% (activated carbon), indicating a preference for sorptive materials. Quantification of DF1 biofilm bacteria showed 1.2-15.3 × 10⁹ bacteria per gram of material. After 22 days, coal activated carbon, bone biochar, polyoxymethylene, and sand microcosms had dechlorinated 73%, 93%, 100%, and 83%, respectively. These results show that a biofilm-based inoculum for bioaugmentation of PCBs in sediment can be an efficient approach.

Acinetobacter baumannii biofilms: effects of physicochemical factors, virulence, antibiotic resistance determinants, gene regulation, and future antimicrobial treatments

Acinetobacter baumannii is a leading cause of nosocomial infections due to its increased antibiotic resistance and virulence. The ability of A. baumannii to form biofilms contributes to its survival in adverse environmental conditions including hospital environments and medical devices. A. baumannii has undoubtedly propelled the interest of biomedical researchers due to its broad range of associated infections especially in hospital intensive care units. The interplay among microbial physicochemistry, alterations in the phenotype and genotypic determinants, and the impact of existing ecological niche and the chemistry of antimicrobial agents has led to enhanced biofilm formation resulting in limited access of drugs to their specific targets. Understanding the triggers to biofilm formation is a step towards limiting and containing biofilm-associated infections and development of biofilm-specific countermeasures. The present review therefore focused on explaining the impact of environmental factors, antimicrobial resistance, gene alteration and regulation, and the prevailing microbial ecology in A. baumannii biofilm formation and gives insights into prospective anti-infective treatments.

Impact of biological clogging on the barrier performance of landfill liners

The durability of landfill mainly relies on the anti-seepage characteristic of liner system. The accumulation of microbial biomass is effective in reducing the hydraulic conductivity of soils. This study aimed at evaluating the impact of the microorganism on the barrier performance of landfill liners. According to the results, Escherichia coli. produced huge amounts of extracellular polymeric substances and coalesced to form a confluent plugging biofilm. This microorganism eventually resulted in the decrease of soil permeability by 81%-95%. Meanwhile, the increase of surface roughness inside the internal pores improved the adhesion between microorganism colonization and particle surface. Subsequently, an extensive parametric sensitivity analysis was undertaken for evaluating the contaminant transport in landfill liners. Decreasing the hydraulic conductivity from 1 × 10^-8 m/s to 1 × 10^-10 m/s resulted in the increase of the breakthrough time by 345.2%. This indicates that a low hydraulic conductivity was essential for the liner systems to achieve desirable barrier performance.