Driving factors for bioclogging of pores and porous media

Understanding the interplay between hydrodynamics and biogeochemical processes is of growing importance in environmental applications and studies, especially in the fields of bioremediation and ecology. The majority of the microbial communities living in soil have a surface-attached lifestyle, allowing them to form biofilms. The biofilm growth influences pore geometries by clogging them and thus redirecting the flow, which in return affects biofilm development and local mass transport. After initially clogging single pores, the biofilm structure expands to larger clusters before eventually clogging the porous medium entirely. We study these processes with a soil-born microorganism, Bacillus subtilis, in microfluidic devices mimicking porous media to get a mechanistic understanding of the driving factors of bioclogging of porous media on different scales. Carefully designed porous geometries were used for the experiments to study biofilm growth under different flow conditions. After being seeded with bacteria, devices were exposed to a continuous nutrient flow during several days. Continuously monitoring the pressure evaluation and imaging the biofilm growth using Brightfield microscopy allowed a high temporal resolution of biofilm growth processes. An interplay of hydraulic parameters and geometric features of the porous medium as well as the mass flow rate of nutrients drive the speed of pore clogging. Besides the pore scale clogging, the initiation of biofilm formation as well as the speed of clogging of the entire medium are influenced by the before mentioned parameters. Furthermore, the size and number of the biofilm clusters formed seem to drive the medium scale clogging. This leads to inverting trends concerning the clogging rate in one pore when compared to the porous medium scale for different pore sizes. These results shed light on the pore-scale mechanism as well as driving parameters of biofilm formation and bioclogging and their transferability to the next larger scale, e.g. a porous medium.

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Biofilm formation and permeate quality improvement in Gravity Driven Membrane ultrafiltration

Water Science & Technology Water Supply ◽

10.2166/ws.2013.197 ◽

2013 ◽

Vol 14 (2) ◽

pp. 274-282 ◽

Cited By ~ 8

Author(s):

A. Chomiak ◽

J. Mimoso ◽

S. Koetzsch ◽

B. Sinnet ◽

W. Pronk ◽

...

Keyword(s):

Biofilm Formation ◽

Fine Particles ◽

Packed Bed ◽

Growth Potential ◽

Particle Removal ◽

Permeate Flux ◽

Biofilm Growth ◽

Gravity Driven ◽

Biofilm Development ◽

Biofilm Structure

The effects of biofilm development on ultrafiltration membranes with regard to permeate stability and permeation rates were investigated using Gravity Driven Membrane (GDM) filtration. The first part of the study aimed at evaluating the influence of the biofilm on permeate flux quality and quantity with regard to Assimilable Organic Carbon (AOC) degradation. In addition, two types of biological pre-treatments were evaluated: slow sand filtration and packed bed bio-reactor, compared to a control (no treatment). Biofilm formation helped to decrease the AOC content of permeate water, compared to the influent. Both pre-treatments additionally reduced the AOC level in the permeate and thus increased its biological stability, however none of the systems were able to guarantee microbiologically stable water. Removal of AOC before the GDM filtration reduced the biofilm growth potential, which in turn influenced its physical structure and enhanced the permeation rates. Influence of inorganic particle removal by pre-sedimentation and its effect on biofilm structure were also studied. Pre-sedimentation of particle populations selected fine and homogeneous particle fractions, which led to the formation of a homogeneous biofilm structure characterised by an increased hydraulic resistance. This was clearly visible between horizontally and vertically installed membranes where the latter ones had a significantly reduced flux despite lower deposited particle mass. The presence of larger, heterogeneous particle fractions counterbalanced the negative effects of the fine particles, which overall resulted in enhanced permeation rates.

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Sodium Salicylate Influences the Pseudomonas aeruginosa Biofilm Structure and Susceptibility Towards Silver

International Journal of Molecular Sciences ◽

10.3390/ijms22031060 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1060

Author(s):

Erik Gerner ◽

Sofia Almqvist ◽

Peter Thomsen ◽

Maria Werthén ◽

Margarita Trobos

Keyword(s):

Pseudomonas Aeruginosa ◽

Biofilm Formation ◽

Sodium Salicylate ◽

Treatment Strategies ◽

Cell Aggregation ◽

Wound Fluid ◽

Global Challenge ◽

3D Collagen ◽

Biofilm Development ◽

Biofilm Structure

Hard-to-heal wounds are typically infected with biofilm-producing microorganisms, such as Pseudomonas aeruginosa, which strongly contribute to delayed healing. Due to the global challenge of antimicrobial resistance, alternative treatment strategies are needed. Here, we investigated whether inhibition of quorum sensing (QS) by sodium salicylate in different P. aeruginosa strains (QS-competent, QS-mutant, and chronic wound strains) influences biofilm formation and tolerance to silver. Biofilm formation was evaluated in simulated serum-containing wound fluid in the presence or absence of sodium salicylate (NaSa). Biofilms were established using a 3D collagen-based biofilm model, collagen coated glass, and the Calgary biofilm device. Furthermore, the susceptibility of 48-h-old biofilms formed by laboratory and clinical strains in the presence or absence of NaSa towards silver was evaluated by assessing cell viability. Biofilms formed in the presence of NaSa were more susceptible to silver and contained reduced levels of virulence factors associated with biofilm development than those formed in the absence of NaSa. Biofilm aggregates formed by the wild-type but not the QS mutant strain, were smaller and less heterogenous in size when grown in cultures with NaSa compared to control. These data suggest that NaSa, via a reduction of cell aggregation in biofilms, allows the antiseptic to become more readily available to cells.

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Confinement and activity regulate bacterial motion in porous media

Soft Matter ◽

10.1039/c9sm01735f ◽

2019 ◽

Vol 15 (48) ◽

pp. 9920-9930 ◽

Cited By ~ 8

Author(s):

Tapomoy Bhattacharjee ◽

Sujit S. Datta

Keyword(s):

Porous Medium ◽

Porous Media ◽

Bacterial Motility ◽

Cellular Activity ◽

Direct Visualization ◽

Pore Scale ◽

Active Matter

Direct visualization reveals how bacterial motility in a porous medium is regulated by pore-scale confinement and cellular activity, yielding fundamental insights into the behavior of active matter under confinement.

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Improvement of XTT assay performance for studies involving Candida albicans biofilms

Brazilian Dental Journal ◽

10.1590/s0103-64402008000400014 ◽

2008 ◽

Vol 19 (4) ◽

pp. 364-369 ◽

Cited By ~ 68

Author(s):

Wander José da Silva ◽

Jayampath Seneviratne ◽

Nipuna Parahitiyawa ◽

Edvaldo Antonio Ribeiro Rosa ◽

Lakshman Perera Samaranayake ◽

...

Keyword(s):

Candida Albicans ◽

Biofilm Formation ◽

Cell Activity ◽

Growth Yield ◽

Xtt Assay ◽

Biofilm Growth ◽

Assay Performance ◽

Reduction Assay ◽

Cell Layers ◽

Biofilm Development

2, 3-bis (2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino) carbonyl]-2H-tetrazolium hydroxide (XTT) reduction assay has been used to study Candida biofilm formation. However, considering that the XTT reduction assay is dependent on cell activity, its use for evaluating mature biofilms may lead to inaccuracies since biofilm bottom cell layers tend to be relatively quiescent at later stages of biofilm formation. The aim of this study was to improve XTT reduction assay by adding glucose supplements to the standard XTT formulation. Candida albicans ATCC 90028 was used to form 24-, 48- and 72-h biofilms. The oxidative activity at 90, 180 and 270 min of incubation was evaluated. The control consisted of standard XTT formulation without glucose supplements, and was modified by the addition of 50, 100 and 200 mM of glucose. The XTT assay with 200 mM glucose showed more accurate and consistent readings correlating with biofilm development at 24, 48 and 72 h. Biofilm growth yield after 180 min incubation, when evaluated with the 200 mM glucose supplemented XTT, produced the most consistent readings on repetitive testing. It may be concluded that glucose supplementation of XTT could minimize variation and produce more accurate data for the XTT assay.

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Biofilm formation by a biotechnologically important tropical marine yeast isolate, Yarrowia lipolytica NCIM 3589

Water Science & Technology ◽

10.2166/wst.2008.479 ◽

2008 ◽

Vol 58 (6) ◽

pp. 1221-1229 ◽

Cited By ~ 11

Author(s):

D. H. Dusane ◽

Y. V. Nancharaiah ◽

V. P. Venugopalan ◽

A. R. Kumar ◽

S. S. Zinjarde

Keyword(s):

Yarrowia Lipolytica ◽

Biofilm Formation ◽

Edible Oils ◽

Carbon Sources ◽

Three Dimensional ◽

Ecological Niches ◽

Lag Phase ◽

Biofilm Growth ◽

Water Media ◽

Biofilm Development

Biofilm formation by Yarrowia lipolytica, a biotechnologically important fungus in microtitre plates, on glass slide surfaces and in flow cell was investigated. In microtitre plates, there was a short lag phase of adhesion followed by a period of rapid biofilm growth. The fungus formed extensive biofilms on glass slides, whereas in flow-cells a multicellular, three-dimensional microcolony structure was observed. The isolate formed biofilms in seawater and in fresh water media at neutral pH when grown in microtitre plates. The carbon sources differentially affected formation of biofilms in microtitre plates. Lactic acid, erythritol, glycerol, glucose and edible oils supported the formation of biofilms, while alkanes resulted in sub-optimal biofilm development. A variation in the morphology of the fungus was observed with different carbon sources. The results point to the possible existence of highly structured biofilms in varied ecological niches from where the yeast is isolated.

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Architectural transitions in Vibrio cholerae biofilms at single-cell resolution

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1601702113 ◽

2016 ◽

Vol 113 (14) ◽

pp. E2066-E2072 ◽

Cited By ~ 100

Author(s):

Knut Drescher ◽

Jörn Dunkel ◽

Carey D. Nadell ◽

Sven van Teeffelen ◽

Ivan Grnja ◽

...

Keyword(s):

Single Cell ◽

Vibrio Cholerae ◽

Biofilm Formation ◽

Bacterial Species ◽

Bacterial Biomass ◽

Biofilm Growth ◽

Glass Substrates ◽

Critical Transitions ◽

Cell Shapes ◽

Biofilm Development

Many bacterial species colonize surfaces and form dense 3D structures, known as biofilms, which are highly tolerant to antibiotics and constitute one of the major forms of bacterial biomass on Earth. Bacterial biofilms display remarkable changes during their development from initial attachment to maturity, yet the cellular architecture that gives rise to collective biofilm morphology during growth is largely unknown. Here, we use high-resolution optical microscopy to image all individual cells in Vibrio cholerae biofilms at different stages of development, including colonies that range in size from 2 to 4,500 cells. From these data, we extracted the precise 3D cellular arrangements, cell shapes, sizes, and global morphological features during biofilm growth on submerged glass substrates under flow. We discovered several critical transitions of the internal and external biofilm architectures that separate the major phases of V. cholerae biofilm growth. Optical imaging of biofilms with single-cell resolution provides a new window into biofilm formation that will prove invaluable to understanding the mechanics underlying biofilm development.

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Phenotypic Characterization of Streptococcus pneumoniae Biofilm Development

Journal of Bacteriology ◽

10.1128/jb.188.7.2325-2335.2006 ◽

2006 ◽

Vol 188 (7) ◽

pp. 2325-2335 ◽

Cited By ~ 113

Author(s):

Magee Allegrucci ◽

F. Z. Hu ◽

K. Shen ◽

J. Hayes ◽

Garth D. Ehrlich ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Biofilm Formation ◽

Protein Identification ◽

Development Process ◽

Developmental Stages ◽

Developmental Process ◽

Phenotypic Characterization ◽

Biofilm Growth ◽

Cell Counts ◽

Biofilm Development

ABSTRACT Streptococcus pneumoniae is among the most common pathogens associated with chronic otitis media with effusion, which has been hypothesized to be a biofilm disease. S. pneumoniae has been shown to form biofilms, however, little is known about the developmental process, the architecture, and the changes that occur upon biofilm development. In the current study we made use of a continuous-culture biofilm system to characterize biofilm development of 14 different S. pneumoniae strains representing at least 10 unique serotypes. The biofilm development process was found to occur in three distinct stages, including initial attachment, cluster formation, and biofilm maturation. While all 14 pneumococcal strains displayed similar developmental stages, the mature biofilm architecture differed significantly among the serotypes tested. Overall, three biofilm architectural groups were detected based on biomass, biofilm thickness, and cluster size. The biofilm viable cell counts and total protein concentration increased steadily over the course of biofilm development, reaching ∼8 × 108 cells and ∼15 mg of protein per biofilm after 9 days of biofilm growth. Proteomic analysis confirmed the presence of distinct biofilm developmental stages by the detection of multiple phenotypes over the course of biofilm development. The biofilm development process was found to correlate not only with differential production of proteins but also with a dramatic increase in the number of detectable proteins, indicating that biofilm formation by S. pneumoniae may be a far more complex process than previously anticipated. Protein identification revealed that proteins involved in virulence, adhesion, and resistance were more abundant under biofilm growth conditions. A possible role of the identified proteins in biofilm formation is discussed.

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Biofilm Formation by Candida Species on Silicone Surfaces and Latex Pacifier Nipples: An in vitro Study

Journal of Clinical Pediatric Dentistry ◽

10.17796/jcpd.33.3.7572960tn46837k4 ◽

2009 ◽

Vol 33 (3) ◽

pp. 235-240 ◽

Cited By ~ 15

Author(s):

Luiz Cezar da Silveira ◽

Senda Charone ◽

Lucianne Cople Maia ◽

Rosangela Maria de Araújo Soares ◽

Maristela Barbosa Portela

Keyword(s):

Candida Species ◽

Biofilm Formation ◽

In Vitro Study ◽

Reduction Reaction ◽

Fungal Colonization ◽

Candida Spp ◽

Biofilm Growth ◽

Species Analysis ◽

Biofilm Development

The present study assessed the growth and development of biofilm formation by isolates of C. albicans, C. glabrata and C. parapsilosis on silicone and latex pacifier nipples. The silicone and latex surfaces were evaluated by scanning electronic microscopy (SEM). The plastic component of the nipple also seems to be an important factor regarding the biofilm formation by Candida spp. The biofilm growth was measured using the MTT reduction reaction. C. albicans was found to have a slightly greater capacity of forming biofilm compared to the other Candida species. Analysis of the pattern of biofilm development by C. albicans,C. glabrata and C. parapsilosis on latex and silicon pacifier shields showed an increased biofilm formation regarding the latter substrate. Silicone was shown to be more resistant to fungal colonization, particularly in the case of C. parapsilosis, despite the lack of any statistically significant differences (P > 0.05). In addition, silicone has a smoother surface compared to latex, whose surface was found to be rugose and irregular

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Pore-scale investigation of the displacement fluid mechanics during two-phase flows in natural porous media under the dominance of capillary forces

Georesursy ◽

10.18599/grs.2020.1.4-12 ◽

2020 ◽

Vol 22 (1) ◽

pp. 4-12

Author(s):

Timur R. Zakirov ◽

Maxim G. Khramchenkov

Keyword(s):

Porous Media ◽

Pore Space ◽

Three Dimensional ◽

Capillary Forces ◽

High Temporal Resolution ◽

Pore Scale ◽

Two Phase Flows ◽

Two Phase ◽

Pressure Drops ◽

Mobile Interfaces

This paper presents the results of numerical simulations of two-phase flows in porous media under capillary forces dominance. For modeling of immiscible two-phase flow, the lattice Boltzmann equations with multi relaxation time operator were applied, and the interface phenomena was described with the color-gradient method. The objective of study is to establish direct links between quantitative characteristics of the flow and invasion events, using high temporal resolution when detecting simulation results. This is one of the few works where Haines jumps (rapid invasion event which occurs at meniscus displacing from narrow pore throat to its wide body) are considered in three-dimensional natural pore space, but the focus is also on the displacement mechanics after jumps. It was revealed the sequence of pore scale events which can be considered as a period of drainage process: rapid invasion event during Haines jump; finish of jump and continuation of uniform invasion in current pore; switching of mobile interfaces and displacement in new region. The detected interface change, along with Haines jump, is another distinctive feature of the capillary forces action. The change of the mobile interfaces is manifested in step-like behavior of the front movement. It was obtained that statistical distributions of pressure drops during Haines jumps obey lognormal law. When investigating the flow rate and surface tension effect on the pressure drop statistics it was revealed that these parameters practically don’t affect on the statistical distribution and influence only on the magnitude of pressure drops and the number of individual Haines jumps.

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Comparison of Competing Invasion-Percolation Models for Simulation of Multiphase Flow in Porous Media

10.5194/egusphere-egu21-8826 ◽

2021 ◽

Author(s):

Ishani Banerjee ◽

Anneli Guthke ◽

Kevin Mumford ◽

Wolfgang Nowak

Keyword(s):

Porous Medium ◽

Porous Media ◽

Gas Flow ◽

Flow Regimes ◽

Flow In Porous Media ◽

Invasion Percolation ◽

Pore Scale ◽

Discontinuous Flow ◽

Model Version ◽

Water Saturated

Invasion-Percolation (IP) models are used to simulate multiphase flow in porous media across various scales (from pore-scale IP to Macro-IP). Numerous variations of IP models have emerged; here we are interested in simulating gas flow in a water-saturated porous medium. Gas flow in porous media occurs either as a continuous or as a discontinuous flow, depending on the rate of flow and the nature of the porous medium. A particular IP model version may be well suited for predictions in a specific gas flow regime, but not applicable to other regimes. Our research aims to compare various macro-scale versions of IP models existing in the literature and rank their performance in relevant gas flow regimes.We test the performance of Macro-IP models on a range of gas-injection rates in water-saturated sand experiments, including both continuous and discontinuous flow regimes. The experimental data is obtained as a time series of images using the light transmission technique. To represent pore-scale heterogeneities of sand, we let each model version run on several random realizations of the initial entry pressure field. As a metric for ranking the models, we introduce a diffused version of the so-called Jaccard index (adapted from image analysis and object recognition). We average this metric over time and over all realizations per model version to evaluate each model&#8217;s overall performance. This metric may also be used to calibrate model parameters such as gas saturation.&#160;Our proposed approach evaluates the performance of competing IP model versions in different gas-flow regimes objectively and quantitatively, and thus provides guidance on their applicability under specific conditions. Moreover, our comparison method is not limited to gas-water phase systems in porous media but generalizes to any modelling situation accompanied by spatially and temporally highly resolved data.

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