Bacterial hopping and trapping in porous media.
Ontology highlight
ABSTRACT:
SUBMITTER: Bhattacharjee T
PROVIDER: S-EPMC6502825 | biostudies-other | 2019 May
REPOSITORIES: biostudies-other
Publications
Bacterial hopping and trapping in porous media.
Bhattacharjee Tapomoy T Datta Sujit S SS
Nature communications 20190506 1
Diverse processes-e.g. bioremediation, biofertilization, and microbial drug delivery-rely on bacterial migration in disordered, three-dimensional (3D) porous media. However, how pore-scale confinement alters bacterial motility is unknown due to the opacity of typical 3D media. As a result, models of migration are limited and often employ ad hoc assumptions. Here we reveal that the paradigm of run-and-tumble motility is dramatically altered in a porous medium. By directly visualizing individual E ...[more]
Similar Datasets
Project description:The chemotaxis signal transduction network regulates the biased random walk of many bacteria in favorable directions and away from harmful ones through modulating the frequency of directional reorientations. In mutants of diverse bacteria lacking the chemotaxis response, migration in classic motility agar, which constitutes a fluid-filled porous medium, is compromised; straight-swimming cells unable to tumble become trapped within the agar matrix. Spontaneous mutations that restore spreading have been previously observed in the enteric bacterium Escherichia coli, and recent work in other bacterial species has isolated and quantified different classes of nonchemotacting mutants exhibiting the same spreading phenotype. We present a theoretical description of bacterial diffusion in a porous medium-the natural habitat for many cell types-which elucidates how diverse modifications of the motility apparatus resulting in a nonzero tumbling frequency allows for unjamming of otherwise straight-swimming cells at internal boundaries and leads to net migration. A unique result of our analysis is increasing diffusive spread with increasing tumbling frequency in the small pore limit, consistent with earlier experimental observations but not captured by previous models. Our theoretical results, combined with a simple model of bacterial diffusion and growth in agar, are compared with our experimental measurements of swim ring expansion as a function of time, demonstrating good quantitative agreement. Our results suggest that the details of the cellular tumbling process may be adapted to enable bacteria to propagate efficiently through complex environments. For engineered, self-propelled microswimmers that navigate via alternating straight runs and changes in direction, these results suggest an optimal reorientation strategy for efficient migration in a porous environment with a given microarchitecture.
| S-EPMC4805881 | biostudies-other
Project description:The complexity of natural soils presents a challenge to the systematic identification and disentanglement of governing processes that shape natural bacterial communities. Studies have highlighted the critical role of the soil aqueous phase in shaping interactions among soil bacterial communities. To quantify and improve the attributability of soil aqueous-phase effects, we introduced a synthetic and traceable bacterial community to simple porous microcosms and subjected the community to constant or dynamic hydration conditions. The results were expressed in terms of absolute abundance and show species-specific responses to hydration and nutrient conditions. Hydration dynamics exerted a significant influence on the fraction of less-abundant species, especially after extended incubation periods. Phylogenetic relationships did not explain the group of most abundant species. The ability to quantify species-level dynamics in a bacterial community offers an important step toward deciphering the links between community composition and functions in dynamic terrestrial environments.IMPORTANCE The composition and activity of soil bacteria are central to various ecosystem services and soil biogeochemical cycles. A key factor for soil bacterial activity is soil hydration, which is in a constant state of change due to rainfall, drainage, plant water uptake, and evaporation. These dynamic changes in soil hydration state affect the structure and function of soil bacterial communities in complex ways often unobservable in natural soil. We designed an experimental system that retains the salient features of hydrated soil yet enables systematic evaluation of changes in a representative bacterial community in response to cycles of wetting and drying. The study shows that hydration cycles affect community abundance, yet most changes in composition occur with the less-abundant species (while the successful ones remain dominant). This research offers a new path for an improved understanding of bacterial community assembly in natural environments, including bacterial growth, maintenance, and death, with a special focus on the role of hydrological factors.
| S-EPMC6912082 | biostudies-literature
Project description:We present plasmonic optical trapping of micron-sized particles in biologically relevant buffer media with varying ionic strength. The media consist of 3 cell-growth solutions and 2 buffers and are specifically chosen due to their widespread use and applicability to breast-cancer and angiogenesis studies. High-precision rheological measurements on the buffer media reveal that, in all cases excluding the 8.0 pH Stain medium, the fluids exhibit Newtonian behavior, thereby enabling straightforward measurements of optical trap stiffness from power-spectral particle displacement data. Using stiffness as a trapping performance metric, we find that for all media under consideration the plasmonic nanotweezers generate optical forces 3-4x a conventional optical trap. Further, plasmonic trap stiffness values are comparable to those of an identical water-only system, indicating that the performance of a plasmonic nanotweezer is not degraded by the biological media. These results pave the way for future biological applications utilizing plasmonic optical traps.
| S-EPMC3977964 | biostudies-literature
Project description:An approach for the preparation of an oxidized porous silicon microparticle drug delivery system that can provide efficient trapping and sustained release of various drugs is reported. The method uses the contraction of porous silicon's mesopores, which occurs during oxidation of the silicon matrix, to increase the loading and retention of drugs within the particles. First, a porous Si (pSi) film is prepared by electrochemical etching of p-type silicon with a resistivity of >0.65 Ω cm in a 1:1 (v/v) HF/ethanol electrolyte solution. Under these conditions, the pore walls are sufficiently thin to allow for complete oxidation of the silicon skeleton under mild conditions. The pSi film is then soaked in an aqueous solution containing the drug (cobinamide or rhodamine B test molecules were used in this study) and sodium nitrite. Oxidation of the porous host by nitrite results in a shrinking of the pore openings, which physically traps the drug in the porous matrix. The film is subsequently fractured by ultrasonication into microparticles. Upon comparison with commonly used oxidizing agents for pSi such as water, peroxide, and dimethyl sulfoxide, nitrite is kinetically and thermodynamically sufficient to oxidize the pore walls of the pSi matrix, precluding reductive (by Si) or oxidative (by nitrite) degradation of the drug payload. The drug loading efficiency is significantly increased (by up to 10-fold), and the release rate is significantly prolonged (by 20-fold) relative to control samples in which the drug is loaded by infiltration of pSi particles postoxidation. We find that it is important that the silicon skeleton be completely oxidized to ensure the drug is not reduced or degraded by contact with elemental silicon during the particle dissolution-drug release phase.
| S-EPMC4311935 | biostudies-literature
Project description:Geoenergy and geoengineering applications usually involve fluid injection into and production from fractured media. Accounting for fractures is important because of the strong poromechanical coupling that ties pore pressure changes and deformation. A possible approach to the problem uses equivalent porous media to reduce the computational cost and model complexity instead of explicitly including fractures in the models. We investigate the validity of this simplification by comparing these two approaches. Simulation results show that pore pressure distribution significantly differs between the two approaches even when both are calibrated to predict identical values at the injection and production wells. Additionally, changes in fracture stability are not well captured with the equivalent porous medium. We conclude that explicitly accounting for fractures in numerical models may be necessary under some circumstances to perform reliable coupled thermohydromechanical simulations, which could be used in conjunction with other tools for induced seismicity forecasting.
| S-EPMC8243940 | biostudies-literature
Project description:ABSTRACT Porous media filters are used widely to remove bacteria from contaminated water, such as stormwater runoff. Biofilms that colonize filter media during normal function can significantly alter performance, but it is not clear how characteristics of individual populations colonizing porous media combine to affect bacterial retention. We assess how four bacterial strains isolated from stormwater and a laboratory strain, Pseudomonas aeruginosa PAO1, alter Escherichia coli retention in experimental sand columns under conditions of stormwater filtration relative to a clean-bed control. Our results demonstrate that these strains differentially affect E. coli retention, as was previously shown for a model colloid. To determine whether E. coli retention could be influenced by changes in relative abundance of strains within a microbial community, we selected two pairs of biofilm strains with the largest observed differences in E. coli retention and tested how changes in relative abundance of strain pairs in the biofilm affected E. coli retention. The results demonstrate that E. coli retention efficiency is influenced by the retention characteristics of the strains within biofilm microbial community, but individual strain characteristics influence retention in a manner that cannot be determined from changes in their relative abundance alone. This study demonstrates that changes in the relative abundance of specific members of a biofilm community can significantly alter filter performance, but these changes are not a simple function of strain-specific retention and the relative abundance. Our results suggest that the microbial community composition of biofilms should be considered when evaluating factors that influence filter performance. IMPORTANCE The retention efficiency of bacterial contaminants in biofilm-colonized biofilters is highly variable. Despite the increasing number of studies on the impact of biofilms in filters on bacterial retention, how individual bacterial strains within a biofilm community combine to influence bacterial retention is unknown. Here, we studied the retention of an E. coli K-12 strain, as a model bacterium, in columns colonized by four bacterial strains isolated from stormwater and P. aeruginosa, a model biofilm-forming strain. Simplified two-strain biofilm communities composed of combinations of the strains were used to determine how relative abundance of biofilm strains affects filter performance. Our results provide insight into how biofilm microbial composition influences bacterial retention in filters and whether it is possible to predict bacterial retention efficiency in biofilm-colonized filters from the relative abundance of individual members and the retention characteristics of cultured isolates.
| S-EPMC8549730 | biostudies-literature
Project description:Finger-like protrusions that form along fluid-fluid displacement fronts in porous media are often excited by hydrodynamic instability when low-viscosity fluids displace high-viscosity resident fluids. Such interfacial instabilities are undesirable in many natural and engineered displacement processes. We report a phenomenon whereby gradual and monotonic variation of pore sizes along the front path suppresses viscous fingering during immiscible displacement, that seemingly contradicts conventional expectation of enhanced instability with pore size variability. Experiments and pore-scale numerical simulations were combined with an analytical model for the characteristics of displacement front morphology as a function of the pore size gradient. Our results suggest that the gradual reduction of pore sizes act to restrain viscous fingering for a predictable range of flow conditions (as anticipated by gradient percolation theory). The study provides insights into ways for suppressing unwanted interfacial instabilities in porous media, and provides design principles for new engineered porous media such as exchange columns, fabric, paper, and membranes with respect to their desired immiscible displacement behavior.
| S-EPMC5948996 | biostudies-literature
Project description:In geologic, biologic, and engineering porous media, bubbles (or droplets, ganglia) emerge in the aftermath of flow, phase change, or chemical reactions, where capillary equilibrium of bubbles significantly impacts the hydraulic, transport, and reactive processes. There has previously been great progress in general understanding of capillarity in porous media, but specific investigation into bubbles is lacking. Here, we propose a conceptual model of a bubble's capillary equilibrium associated with free energy inside a porous medium. We quantify the multistability and hysteretic behaviors of a bubble induced by multiple state variables and study the impacts of pore geometry and wettability. Surprisingly, our model provides a compact explanation of counterintuitive observations that bubble populations within porous media can be thermodynamically stable despite their large specific area by analyzing the relationship between free energy and bubble volume. This work provides a perspective for understanding dispersed fluids in porous media that is relevant to CO2 sequestration, petroleum recovery, and fuel cells, among other applications.
| S-EPMC8092930 | biostudies-literature
Project description:We investigate, by means of pore-scale lattice Boltzmann simulations, the mechanisms of interception of respiratory droplets within fibrous porous media composing face masks. We simulate the dynamics, coalescence, and collection of droplets of the size comparable with the fiber and pore size in typical fluid-dynamic conditions that represent common expiratory events. We discern the fibrous microstructure into three categories of pores: small, large, and medium-sized pores, where we find that within the latter, the incoming droplets tend to be more likely intercepted. The size of the medium-sized pores relative to the fiber size is placed between the droplet-to-fiber size ratio and a porosity-dependent microstructural parameter Lϵ*=ϵ/(1-ϵ) , with ϵ being the porosity. In larger pores, droplets collection is instead inhibited by the small pore-throat-to-fiber size ratio that characterizes the pore perimeter, limiting their access. The efficiency of the fibrous media in intercepting droplets without compromising breathability, for a given droplet-to-fiber size ratio, can be estimated by knowing the parameter Lϵ* . We propose a simple model that predicts the average penetration of droplets into the fibrous media, showing a sublinear growth with Lϵ* . Permeability is shown also to scale well with Lϵ* but following a superlinear growth, which indicates the possibility of increasing the medium permeability at a little cost in terms of interception efficiency for high values of porosity. As a general design guideline, the results also suggest that a fibrous layer thickness relative to the fiber size should exceed the value Lϵ* in order to ensure effective droplets filtration.
| S-EPMC8404382 | biostudies-literature
Project description:The removal of ethane (C2H6) from its analogous ethylene (C2H4) is of paramount importance in the petrochemical industry, but highly challenging due to their similar physicochemical properties. The use of emerging porous organic cage (POC) materials for C2H6/C2H4 separation is still in its infancy. Here, we report the benchmark example of a truncated octahedral calix[4]resorcinarene-based POC adsorbent (CPOC-301), preferring to adsorb C2H6 than C2H4, and thus can be used as a robust absorbent to directly separate high-purity C2H4 from the C2H6/C2H4 mixture. Molecular modelling studies suggest the exceptional C2H6 selectivity is due to the suitable resorcin[4]arene cavities in CPOC-301, which form more multiple C-H···π hydrogen bonds with C2H6 than with C2H4 guests. This work provides a fresh avenue to utilize POC materials for highly selective separation of industrially important hydrocarbons.
| S-EPMC8211788 | biostudies-literature