In large-scale syngas fermentation, strong gradients in dissolved gas (CO, H₂) concentrations are very likely to occur due to locally varying mass transfer and convection rates. Using Euler-Lagrangian CFD simulations, we analyzed these gradients in an industrial-scale external-loop gas-lift reactor (EL-GLR) for a wide range of biomass concentrations, considering CO inhibition for both CO and H₂ uptake. Lifeline analyses showed that micro-organisms are likely to experience frequent (5 to 30 s) oscillations in dissolved gas concentrations with one order of magnitude. From the lifeline analyses, we developed a conceptual scale-down simulator (stirred-tank reactor with varying stirrer speed) to replicate industrial-scale environmental fluctuations at bench scale. The configuration of the scale-down simulator can be adjusted to match a broad range of environmental fluctuations. Our results suggest a preference for industrial operation at high biomass concentrations, as this would strongly reduce inhibitory effects, provide operational flexibility and enhance the product yield. The peaks in dissolved gas concentration were hypothesized to increase the syngas-to-ethanol yield due to the fast uptake mechanisms in C. autoethanogenum. The proposed scale-down simulator can be used to validate such results and to obtain data for parametrizing lumped kinetic metabolic models that describe such short-term responses.

Mass transfer limitations in syngas fermentation processes are mostly attributed to poor solubility of CO and H₂ in water. Despite these assumed limitations, a syngas fermentation process has recently been commercialized. Using large-sale external-loop gas-lift reactors (EL-GLR), CO-rich off-gases are converted into ethanol, with high mass transfer performance (7–8.5 g.L^-1.h⁻¹). However, when applying established mass transfer correlations, a much poorer performance is predicted (0.3–2.7 g.L^-1.h⁻¹). We developed a CFD model, validated on pilot-scale data, to provide detailed insights on hydrodynamics and mass transfer in a large-scale EL-GLR. As produced ethanol could increase gas hold-up (+30%) and decrease the bubble diameter (≤2 mm) compared to air–water mixtures, we found with our model that a high volumetric mass transfer coefficient (650–750 h⁻¹) and mass transfer capacity (7.5–8 g.L^-1.h⁻¹) for CO are feasible. Thus, the typical mass transfer limitations encountered in air–water systems can be alleviated in the syngas-to-ethanol fermentation process.

The application of membrane technology for water treatment and reuse is hampered by the development of a microbial biofilm. Biofilm growth in micro-and ultrafiltration (MF/UF) membrane modules, on both the membrane surface and feed spacer, can form a secondary membrane and exert resistance to permeation and crossflow, increasing energy demand and decreasing permeate quantity and quality. In recent years, exhaustive efforts were made to understand the chemical, structural and hydraulic characteristics of membrane biofilms. In this review, we critically assess which specific structural features of membrane biofilms exert resistance to forced water passage in MF/UF membranes systems applied to water and wastewater treatment, and how biofilm physical structure can be engineered by process operation to impose less hydraulic resistance (“below-the-pain threshold”). Counter-intuitively, biofilms with greater thickness do not always cause a higher hydraulic resistance than thinner biofilms. Dense biofilms, however, had consistently higher hydraulic resistances compared to less dense biofilms. The mechanism by which density exerts hydraulic resistance is reported in the literature to be dependant on the biofilms’ internal packing structure and EPS chemical composition (e.g., porosity, polymer concentration). Current reports of internal porosity in membrane biofilms are not supported by adequate experimental evidence or by a reliable methodology, limiting a unified understanding of biofilm internal structure. Identifying the dependency of hydraulic resistance on biofilm density invites efforts to control the hydraulic resistance of membrane biofilms by engineering internal biofilm structure. Regulation of biofilm internal structure is possible by alteration of key determinants such as feed water nutrient composition/concentration, hydraulic shear stress and resistance and can engineer biofilm structural development to decrease density and therein hydraulic resistance. Future efforts should seek to determine the extent to which the concept of “biofilm engineering” can be extended to other biofilm parameters such as mechanical stability and the implication for biofilm control/removal in engineered water systems (e.g., pipelines and/or, cooling towers) susceptible to biofouling.

Coral reefs are constructed by calcifying coral animals that engage in a symbiosis with dinoflagellate microalgae harboured in their tissue. The symbiosis takes place in the presence of steep and dynamic gradients of light, temperature and chemical species that are affected by the structural and optical properties of the coral and their interaction with incident irradiance and water flow. Microenvironmental analyses have enabled quantification of such gradients and bulk coral tissue and skeleton optical properties, but the multi-layered nature of corals and its implications for the optical, thermal and chemical microenvironment remains to be studied in more detail. Here, we present a multiphysics modelling approach, where three-dimensional Monte Carlo simulations of the light field in a simple coral slab morphology with multiple tissue layers were used as input for modelling the heat dissipation and photosynthetic oxygen production driven by photon absorption. By coupling photon, heat and mass transfer, the model predicts light, temperature and O2 gradients in the coral tissue and skeleton, under environmental conditions simulating, for example, tissue contraction/expansion, symbiont loss via coral bleaching or different distributions of coral host pigments. The model reveals basic structure-function mechanisms that shape the microenvironment and ecophysiology of the coral symbiosis in response to environmental change.

The emergence of phenotypic diversity in a population of cells and their arrangement in space and time is one of the most fascinating features of living systems. In fact, understanding multicellularity is unthinkable without explaining the proximate and the ultimate causes of cell differentiation in time and space. Simpler forms of cell differentiation can be found in unicellular organisms, such as bacterial biofilm, where reversible cell differentiation results in phenotypically diverse populations. In this manuscript, we attempt to start with the simple case of reversible nongenetic phenotypic to construct a model of differentiation and pattern formation. Our model, which we refer to as noise-driven differentiation (NDD) model, is an attempt to consider the prevalence of noise in biological systems, alongside what is known about genetic switches and signaling, to create a simple model which generates spatiotemporal patterns from bottom-up. Our simulations indicate that the presence of noise in cells can lead to reversible differentiation and the addition of signaling can create spatiotemporal pattern.

Experimental data showed that high-speed microsprays can effectively disrupt biofilms on their support substratum, producing a variety of dynamic reactions such as elongation, displacement, ripple formation, and fluidization. However, the mechanics underlying the impact of high-speed turbulent flows on biofilm structure is complex under such extreme conditions, since direct measurements of viscosity at these high shear rates are not possible using dynamic testing instruments. Here, we used computational fluid dynamics simulations to assess the complex fluid interactions of ripple patterning produced by high-speed turbulent air jets impacting perpendicular to the surface of Streptococcus mutans biofilms, a dental pathogen causing caries, captured by high-speed imaging. The numerical model involved a two-phase flow of air over a non-Newtonian biofilm, whose viscosity as a function of shear rate was estimated using the Herschel-Bulkley model. The simulation suggested that inertial, shear, and interfacial tension forces governed biofilm disruption by the air jet. Additionally, the high shear rates generated by the jet impacts coupled with shear-thinning biofilm property resulted in rapid liquefaction (within milliseconds) of the biofilm, followed by surface instability and traveling waves from the impact site. Our findings suggest that rapid shear thinning under very high shear flows causes the biofilm to behave like a fluid and elasticity can be neglected. A parametric sensitivity study confirmed that both applied force intensity (i.e., high jet nozzle air velocity) and biofilm properties (i.e., low viscosity and low air-biofilm surface tension and thickness) intensify biofilm disruption by generating large interfacial instabilities.IMPORTANCE Knowledge of mechanisms promoting disruption though mechanical forces is essential in optimizing biofilm control strategies which rely on fluid shear. Our results provide insight into how biofilm disruption dynamics is governed by applied forces and fluid properties, revealing a mechanism for ripple formation and fluid-biofilm mixing. These findings have important implications for the rational design of new biofilm cleaning strategies with fluid jets, such as determining optimal parameters (e.g., jet velocity and position) to remove the biofilm from a certain zone (e.g., in dental hygiene or debridement of surgical site infections) or using antimicrobial agents which could increase the interfacial area available for exchange, as well as causing internal mixing within the biofilm matrix, thus disrupting the localized microenvironment which is associated with antimicrobial tolerance. The developed model also has potential application in predicting drag and pressure drop caused by biofilms on bioreactor, pipeline, and ship hull surfaces.

The economic impact of fouling in spiral wound membranes is not yet well explored. There has been an established assumption that the cost of fouling in membrane processes is significant, but this hypothesis has not been thoroughly evaluated. We conducted an economic analysis on seven full-scale installations, four nanofiltration (NF) and three reverse osmosis (RO), to estimate the cost of fouling in industrial plants. The cost of fouling was calculated in detail, including costs of increase in feed channel pressure drop, water permeability reduction, early membrane replacement, and extensive cleaning-in-place (CIP). The estimated cost of fouling was expressed as a fraction of operational expenses (OPEX) for each plant and the major cost factors in fouling and CIP costs were identified. The selected NF plants were fed with anoxic ground water, while the feed water to RO plants was either surface water or municipal wastewater effluent. All the NF plants produce drinking water, while the RO plants produce demineralized water for industrial applications. We found that the cost of fouling in the RO plants was around 24% of OPEX, while the fouling related costs in NF cases was only around 11% due to the low biofouling potential of the anoxic ground water. The major factor in the cost of fouling is the early membrane replacement cost, followed by additional energy and with only a minor contribution from the cleaning costs. The down-time cost (caused by the interruption of water production during a CIP event) can be the major CIP cost factor for the plants with frequent cleaning events, while the cost of chemicals dominates in the plants with non-frequent CIP. In case of manual cleaning-in-place, the cost of fouling is increased by around 2% for the RO plants with frequent CIP. The manual execution of CIP cleaning is an attention point to reconsider, as the reviewed plants hold an automated CIP cleaning, providing membrane productivity advantages.

Chemical cleaning is vital for the optimal operation of membrane systems. Membrane chemical cleaning protocols are often developed in the laboratory flow cells (e.g., Membrane Fouling Simulator (MFS)) using synthetic feed water (nutrient excess) and short experimental time of typically days. However, full-scale Reverse Osmosis (RO) membranes are usually fed with nutrient limited feed water (due to extensive pre-treatment) and operated for a long-time of typically years. These operational differences lead to significant differences in the efficiency of chemical Cleaning-In-Place (CIP) carried out on laboratory-scale and on full-scale RO systems. Therefore, we investigated the suitability of lab-scale CIP results for full-scale applications. A lab-scale flow cell (i.e., MFSs) and two full-scale RO modules were analysed to compare CIP efficiency in terms of water flux recovery and biofouling properties (biomass content, Extracellular Polymeric Substances (EPS) composition and EPS adherence) under typical lab-scale and full-scale conditions. We observed a significant difference between the CIP efficiency in lab-scale (~50%) and full-scale (9–20%) RO membranes. Typical biomass analysis such as Total Organic Carbon (TOC) and Adenosine triphosphate (ATP) measurements did not indicate any correlation to the observed trend in the CIP efficiency in the lab-scale and full-scale RO membranes. However, the biofilms formed in the lab-scale contains different EPS than the biofilms in the full-scale RO modules. The biofilms in the lab-scale MFS have polysaccharide-rich EPS (Protein/Polysaccharide ratio = 0.5) as opposed to biofilm developed in full-scale modules which contain protein-rich EPS (Protein/Polysaccharide ratio = 2.2). Moreover, EPS analysis indicates the EPS extracted from full-scale biofilms have a higher affinity and rigidity to the membrane surface compared to EPS from lab-scale biofilm. Thus, we propose that CIP protocols should be optimized in long-term experiments using the realistic feed water.

Transporting materials from Earth to Mars is a significant logistical constraint on mission design. Thus, a sustained settlement will be enhanced if it can perform elemental extraction and utilization in situ. In this study, all requirements to test a novel, biological approach for in situ resource utilization (ISRU) are conceptualized. We present designs for two bioreactor systems to be incorporated in a Mars habitat. The first system is a standard algae bioreactor which produces oxygen and biomass. The second bioreactor is capable of taking in Martian regolith and extracting enhanced iron ores from it via biological processes. Additionally, we propose the use of the leftover iron-poor but biomass rich material in a plant compartment. The multiple, different compartments feed into each other, creating an interconnected process enhancing self-sufficiency. In this paper, computational fluid dynamics of mixing behavior under reduced gravity, a breakdown of the process flow for a biological ISRU approach and exploratory in silico evaluation of the feasibility are presented.

Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal, conditions which may not very often match natural ecosystems. We here analyze the impact of cell-to-cell distance on unidirectional cross-feeding in a three-dimensional aqueous system with competition for the exchanged metabolite. Effective interaction distances were computed with a reaction-diffusion model and experimentally verified by growing a synthetic consortium of 1 µm-sized metabolite producer, receiver, and competitor cells in different spatial structures. We show that receivers cannot interact with producers located on average 15 µm away from them, as product concentration gradients flatten close to producer cells. We developed an aggregation protocol and varied the receiver cells’ product affinity, to show that within producer–receiver aggregates even low-affinity receiver cells could interact with producers. These results show that competition or other metabolite-removal of a public good in a three-dimensional system reduces metabolic interaction distances to the low µm-range, highlighting the importance of concentration gradients as physical constraint for cellular interactions.

The H₂-based membrane biofilm reactor (H₂−MBfR) is an emerging technology for removal of nitrate (NO₃⁻) in water supplies. In this research, a lab-scale H₂−MBfR equipped with a separated CO₂ providing system and a microsensor measuring unit was developed for NO₃⁻ removal from synthetic groundwater. Experimental results show that efficient NO₃⁻ reduction with a flux of 1.46 g/(m²⋅d) was achieved at the optimal operating conditions of hydraulic retention time (HRT) 80 min, influent NO₃⁻ concentration 20 mg N/L, H₂ pressure 5 psig and CO₂ addition 50 mg/L. Given the complex counter-diffusion of substrates in the H₂−MBfR, mathematical modeling is a key tool to both understand its behavior and optimize its performance. A sophisticated model was successfully established, calibrated and validated via comparing the measured and simulated system performance and/or substrate gradients within biofilm. Model results indicate that i) even under the optimal operating conditions, denitrifying bacteria (DNB) in the interior and exterior of biofilm suffered low growth rate, attributed to CO₂ and H₂ limitation, respectively; ii) appropriate operating parameters are essential to maintaining high activity of DNB in the biofilm; iii) CO₂ concentration was the decisive factor which matters its dominant role in mediating hydrogenotrophic denitrification process; iv) the predicted optimum biofilm thickness was 650 µm that can maximize the denitrification flux and prevent loss of H₂.

A vital component of spiral-wound membrane modules is the spacer mesh. It not only structurally supports the membranes but also aids in mass-transport enhancement through the membrane surface. Fundamental understanding of hydrodynamics associated with these spacer designs is critical to improve the permeate flux performance by decreasing concentration polarization and minimizing (bio)fouling, as well as minimizing the axial pressure drop. In the present study, time and space resolved Direct Numerical Simulations (DNS) were performed for a commercial spacer geometry. The spacer geometry was reconstructed by measurements using Scanning Electron Microscopy (SEM). Computations were performed for three spacer cells, allowing elimination of stream-wise periodicity that was a major bottleneck in earlier studies. The numerical solver was well checked in terms of boundary layer profiles obtained from Particle Image Velocimetry (PIV) data and with pressure measurements corresponding to various flow channel velocities. Non-dimensional computations were performed for Reynolds Numbers (Re) ranging from 73 to 375 (inlet channel velocity of 0.073–0.375 m/s) covering the flow transition dynamics regime. Results indicate that flow transition from steady to unsteady regime occurs for Re > 250. The flow transition could be primarily attributed to the interaction between vortices attached to the spacer filaments and the screw-vortex that originates along the diagonal of the spacer cells. No turbulent transition was observed even at the highest investigated velocity (Re = 375). The frequency spectra of time-varying velocity signal shows that at Re > 350 a sudden shift of frequency spectra occurs from discrete to continuous mode indicating the onset of advanced instability. Spacer design criteria in terms of maximum principal stress is also proposed, which can potentially aid in minimizing biofilm seeding.

Poroelastic fluid-structure interaction models were coupled to experimental data to determine the effects of biofilm spatial distribution of mechanical and hydraulic properties on the biofilm hydraulic resistance and compressibility in membrane filtration processes. Biofilms were cultivated on ultrafiltration membranes for 20 and 30 days under high (0.28 bar) and low (0.06 bar) transmembrane pressure (TMP), in dead-end filtration mode. Subsequently, biofilms were subjected to a compression/relaxation cycles by step-wise TMP changes. Structural deformation of biofilms during compression was observed in-situ using optical coherence tomography. Experimental results show that the observed increase in the biofilm hydraulic resistance during compression is not necessarily accompanied by a detectable biofilm thickness reduction. A dual-layer biofilm model with a dense base and porous top layer could explain these observed results. Because porosity controls indirectly the mechanical response of biofilms under compression, results could be described without assuming a gradient in mechanical properties within the biofilm. The biofilm surface roughness did not significantly influence the water flux in this study. However, the fraction of biofilm base layer directly exposed to bulk liquid could be a good indicator in the determination of water flux. The main implications of this study for the design and operation of low-pressure membrane systems (e.g., MF and UF with fouling layer being the main filtration resistance) lays in the selection of favorable operational TMP and biofilm morphology.

Groundwater microorganisms hardly ever cover the solid matrix uniformly–instead they form micro-scale colonies. To which extent such colony formation limits the bioavailability and biodegradation of a substrate is poorly understood. We used a high-resolution numerical model of a single pore channel inhabited by bacterial colonies to simulate the transport and biodegradation of organic substrates. These high-resolution 2D simulation results were compared to 1D simulations that were based on effective rate laws for bioavailability-limited biodegradation. We (i) quantified the observed bioavailability limitations and (ii) evaluated the applicability of previously established effective rate concepts if microorganisms are heterogeneously distributed. Effective bioavailability reductions of up to more than one order of magnitude were observed, showing that the micro-scale aggregation of bacterial cells into colonies can severely restrict the bioavailability of a substrate and reduce in situ degradation rates. Effective rate laws proved applicable for upscaling when using the introduced effective colony sizes.

Whole-cell bacterial bioreporters are proposed as alternatives to chemical analysis of, for example, pollutants in environmental compartments. Commonly based on reporter gene induction, bioreporters produce a detectable signal within 30 min to a few hours after exposure to the chemical target, which is impractical for applications aiming at a fast response. In an attempt to attain faster readout but maintain flexibility of chemical targeting, we explored the concept for quantitative chemical sensing by bacterial chemotaxis. Chemotaxis was quantified from enrichment of cells across a 600 µm-wide chemical gradient stabilized by parallel flow in a microfluidic chip, further supported by transport and chemotaxis steady state and kinetic modelling. As proof-of-concept, we quantified Escherichia coli chemotaxis towards serine, aspartate and methylaspartate as a function of attractant concentration and exposure time. E. coli chemotaxis enrichment increased sharply between 0 and 10 µM serine, before saturating at 100 µM. The chemotaxis accumulation rate was maximal at 10 µM serine, leading to observable cell enrichment within 5 min. The potential application for biosensing of environmental toxicants was investigated by quantifying chemotaxis of Cupriavidus pinatubonensis JMP134 towards the herbicide 2,4-dichlorophenoxyacetate. Our results show that bacterial chemotaxis can be quantified on a scale of minutes and may be used for developing faster bioreporter assays.

Biofilm formation in membrane systems negatively impacts the filtration system performances. This study evaluated how biofilm compression driven by permeate flow increases the hydraulic resistance and leads to reduction in permeate flux. We analysed the effect of biofilm compression on hydraulic resistance and permeate flux through computational models supported by experimental data. Biofilms with homogeneous surface structure were subjected to step-wise changes in flux and transmembrane pressure during compression and relaxation tests. Biofilm thickness under applied forces was measured non-invasively in-situ using optical coherence tomography (OCT). A numerical model of poroelasticity, which couples water flow through the biofilm with biofilm mechanics, was developed to correlate the structural deformation with biofilm hydraulics (permeability and resistance). The computational model enabled extracting mechanical and hydrological parameters corresponding to the experimental data. Homogeneous biofilms under elevated compression forces experienced a significant reduction in thickness while only a slight increase in resistance was observed. This shows that hydraulic resistance of homogeneous biofilms was affected more by permeability decrease due to pore closure than by a decrease in thickness. Both viscoelastic and elastoplastic models could describe well the permanent biofilm deformation. However, for biofilms under study, a simpler elastic model could also be used due to the small irreversible deformations. The elastic moduli fitting the measured data were in agreement with other reported values for biofilm under compression. Biofilm stiffening under larger flow-driven compression forces was observed and described numerically by correlating inversely the elastic modulus with biofilm porosity. The importance of this newly developed method lies in estimation of accurate biofilm mechanical parameters to be used in numerical models for both membrane filtration system and biofouling cleaning strategies. Such model can ultimately be used to identify optimal operating conditions for membrane system subjected to biofouling.

The advantage of using non-invasive imaging such as optical coherence tomography (OCT) to asses material properties from deformed biofilm geometries can be compromised by the assumptions made on fluid forces acting on the biofilm. This study developed a method for the determination of elastic properties of biofilms by modelling the biofilm deformation recorded by OCT imaging with poroelastic fluid-structure interaction computations. Two-dimensional biofilm geometries were extracted from OCT scans of non-deformed and deformed structures as a result of hydrodynamic loading. The biofilm geometries were implemented in a model coupling fluid dynamics with elastic solid mechanics and Darcy flow in the biofilm. The simulation results were compared with real deformed geometries and a fitting procedure allowed estimation of the Young's modulus in given flow conditions. The present method considerably improves the estimation of elastic moduli of biofilms grown in mini-fluidic rectangular channels. This superior prediction is based on the relaxation of several simplifying assumptions made in past studies: shear stress is not anymore taken constant over the biofilm surface, total stress including also pressure is accounted for, any biofilm shape can be used in the determinations, and non-linear behavior of mechanical properties can be estimated. Biofilm elastic moduli between 70 and 700 Pa were obtained and biofilm hardening at large applied stress due to increasing flow velocity was quantified. The work performed here opens the way for in-situ determination of other mechanical properties (e.g., viscoelastic properties, relaxation times, plastic yields) and provides data for modelling biofilm deformation and detachment with eventual applications in biofilm control and removal strategies.

This study evaluated the impact of precise representation of spacer geometry on numerical simulations of hydrodynamics and solute transport in feed channels of membrane processes. Three levels of increasing geometry accuracy were assessed: i) cylindrical filaments, ii) filaments with circular sections of variable diameter based on microscopic measurements, and iii) geometries obtained from X-ray computed tomography (CT scans) in three resolutions (22 µm, 11 µm, and 5.5 µm). The three-dimensional CT scans revealed quasi-elliptic, not circular, cross-sections of the filaments. Microscopic measurements fail to account for this ellipticity, resulting in overestimation of pressure drop calculated at industry-typical average velocities (0.07–0.15 m s⁻¹) by a factor of 1.8 compared to CT-based geometries. On the other hand, the cylindrical spacer filaments representation overestimates concentration polarization at the membrane surface compared to CT-based geometries. Experimental results of pressure drop and particle deposition were in close agreement with simulations using CT scanned geometries. This work demonstrates that modeling results depend significantly on the spacer geometry accuracy. Within the investigated CT scan accuracies 20 µm was found sufficient for modeling hydrodynamics and solute transport in spacer-filled feed channels. The results may be useful for reliable investigation and development of novel spacer geometries.