The effects of extrinsic factors on the structural and mechanical properties of Pseudomonas fluorescens biofilms: A combined study of nutrient concentrations and shear conditions

Bacterial biofilm growth and perturbation by serine protease from Bacillus sp

In nature, bacteria are ubiquitous and can be categorized as beneficial or harmless to humans, but most bacteria have one thing in common which is their ability to produce biofilm. Biofilm is encased within an extracellular polymeric substance (EPS) which provides resistance against antimicrobial agents. Protease enzymes have the potential to degrade or promote the growth of bacterial biofilms. In this study, the effects of a recombinant intracellular serine protease from Bacillus sp. (SPB) on biofilms from Staphylococcus aureus, Acinetobacter baumannii, and Pseudomonas aeruginosa were analyzed. SPB was purified using HisTrap HP column and concentrated using Amicon 30 ultra-centrifugal filter. SPB was added with varying enzyme activity and assay incubation period after biofilms were formed in 96-well plates. SPB was observed to have contrasting effects on different bacterial biofilms, where biofilm degradations were observed for both 7-day-old A. baumannii (37.26%) and S. aureus (71.51%) biofilms. Meanwhile, SPB promoted growth of P. aeruginosa biofilm up to 176.32%. Compatibility between protein components in S. aureus biofilm with SPB as well as a simpler membrane structure morphology led to higher biofilm degradation for S. aureus compared to A. baumannii. However, SPB promoted growth of P. aeruginosa biofilm due likely to its degrading protein factors that are responsible for biofilm detachment and dispersion, thus resulting in more multi-layered biofilm formation. Commercial protease Savinase which was used as a comparison showed degradation for all three bacterial biofilms. The results obtained are unique and will expand our understanding on the effects that bacterial proteases have toward biofilms.

Probing the reduction of adhesion forces between biofilms and anti-biofouling filtration membrane surfaces using FluidFM technology

Biofouling is a persistent problem in many sectors (healthcare, medicine, marine, and membrane filtration processes). To control the biofouling of surfaces, it is essential to overcome or reduce the adhesion forces between biofilms and surfaces. To access and understand the molecular basis of these interactions, atomic force microscopy (AFM) is a well-suited technology that can measure adhesion forces at the piconewton level. However, AFM-based existing methods only probe interactions between individual cells and surfaces, which is not representative of realistic conditions given that bacteria mainly exist in biofilms. We develop here an original method using FluidFM, a combination of AFM and microfluidics, to probe the adhesion forces between biofilms and filtration membranes modified with an anti-biofouling agent, vanillin. This strategy involves i) growing bacterial biofilms on micrometer-sized polystyrene beads, ii) aspirating these biofilm beads at the aperture of microfluidic cantilevers and iii) using them as probes in force spectroscopy experiments. The results obtained first showed that COOH-functionalized polystyrene beads are more suitable for bacterial growth, and that biofilms obtained after 3 h of incubation could be used with FluidFM. Then, biofilm-scale force spectroscopy experiments showed a significant decrease in adhesion forces, adhesion work, and adhesion events after membrane modification, demonstrating the potential of vanillin-coated membranes to reduce biofouling. In addition, the comparison between results at the individual cell and biofilm scales highlighted the complexity of polymeric matrix unbinding and/or unfolding in the biofilm, showing that individual cells behave differently from biofilms. Overall, this method could have implications in the fields of materials science, chemical engineering, health, and the environment.

Genome Analysis and Physiology of Pseudomonas sp. Strain OVF7 Degrading Naphthalene and n-Dodecane

The complete genome of the naphthalene- and n-alkane-degrading strain Pseudomonas sp. strain OVF7 was collected and analyzed. Clusters of genes encoding enzymes for the degradation of naphthalene and n-alkanes are localized on the chromosome. Based on the Average Nucleotide Identity and digital DNA-DNA Hybridization compared with type strains of the group of fluorescent pseudomonads, the bacterium studied probably belongs to a new species. Using light, fluorescent, and scanning electron microscopy, the ability of the studied bacterium to form biofilms of different architectures when cultured in liquid mineral medium with different carbon sources, including naphthalene and n-dodecane, was demonstrated. When grown on a mixture of naphthalene and n-dodecane, the strain first consumed naphthalene and then n-dodecane. Cultivation of the strain on n-dodecane was characterized by a long adaptation phase, in contrast to cultivation on naphthalene and a mixture of naphthalene and n-dodecane.

Evaluation of Disinfectant Efficacy against Biofilm-Residing Wild-Type Salmonella from the Porcine Industry

Salmonella enterica is a causative pathogen of Salmonellosis, a zoonosis causing global disease and financial losses every year. Pigs may be carriers of Salmonella and contribute to the spread to humans and food products. Salmonella may persist as biofilms. Biofilms are bacterial aggregates embedded in a self-produced matrix and are known to withstand disinfectants. We studied the effect of glutaraldehyde and peracetic acid, two active substances frequently used in disinfectant formulations in the pig industry, on representative biofilm-residing wild-type Salmonella collected from pig housings in the United Kingdom (UK). We screened biofilm production of strains using the microtiter plate (MTP) assay and Congo Red Coomassie Blue (CRCB) agar method. Previously published stainless-steel coupon (SSCA), polyvinylchloride coupon (PCA), and glass bead (GBA) assays were used for disinfection studies. The mean reduction in the tested wild-type strains met the criterion of ≥4 log₁₀ CFU at a disinfectant concentration of 0.05% with SSCA and GBA, and 0.005% with PCA for peracetic acid, along with 0.5% for glutaraldehyde with all three assays on the mean. At these concentrations, both tested disinfectants are suitable for disinfection of pig housings against Salmonella. When evaluating the efficacy of disinfectants, biofilms should be included, as higher disinfectant concentrations are necessary compared to planktonic bacteria.

Inhibiting bacterial biofilm formation by stimulating c-di-GMP regulation using citrus peel extract from Jeju Island

Biofilms consist of single or multiple species of bacteria embedded in extracellular polymeric substances (EPSs), which affect the increase in antibiotic resistance by restricting the transport of antibiotics to the bacterial cells. An alternative approach to treatment with antimicrobial agents is using biofilm inhibitors that regulate biofilm development without inhibiting bacterial growth. In this study, we found that citrus peel extract from Jeju Island (CPEJ) can inhibit bacterial biofilm formation. According to the results, CPEJ concentration-dependently reduces biofilm formation without affecting bacterial growth. Additionally, CPEJ decreased the production of extracellular polymeric substances but increased bacterial swarming motility. These results led to the hypothesis that CPEJ can reduce intracellular bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) concentration. The results showed that CPEJ significantly reduced the c-di-GMP level through increased phosphodiesterase activity. Altogether, these findings suggest that CPEJ as a biofilm inhibitor has new potential for pharmacological (e.g. drug and medication) and industrial applications (e.g. ship hulls, water pipes, and membrane processes biofouling control).

Effects of phosphate and silicate on stiffness and viscoelasticity of mature biofilms developed with simulated drinking water

Biofilms, a porous matrix of cells aggregated with extracellular polymeric substances under the influence of chemical constituents in the feed water, can develop a viscoelastic response to mechanical stresses. In this study, the roles of phosphate and silicate, common additives in corrosion control and meat processing, on the stiffness, viscoelasticity, porous structure networks, and chemical properties of biofilm were investigated. Three-year biofilms on PVC coupons were grown from sand-filtered groundwater with or without one of the non-nutrient (silicate) or nutrient additives (phosphate or phosphate blends). Compared with non-nutrient additives, the phosphate and phosphate-blend additives led to a biofilm with the lowest stiffness, most viscoelastic, and more porous structure, including more connecting throats with greater equivalent radii. The phosphate-based additives also led to more organic species in the biofilm matrix than the silicate additive did. This work demonstrated that nutrient additives could promote biomass accumulation but also reduce mechanical stability.

Impact of Fe2+ and Shear Stress on the Development and Mesoscopic Structure of Biofilms-A Bacillus subtilis Case Study

Bivalent cations are known to affect the structural and mechanical properties of biofilms. In order to reveal the impact of Fe²⁺ ions within the cultivation medium on biofilm development, structure and stability, Bacillus subtilis biofilms were cultivated in mini-fluidic flow cells. Two different Fe²⁺ inflow concentrations (0.25 and 2.5 mg/L, respectively) and wall shear stress levels (0.05 and 0.27 Pa, respectively) were tested. Mesoscopic biofilm structure was determined daily in situ and non-invasively by means of optical coherence tomography. A set of ten structural parameters was used to quantify biofilm structure, its development and change. The study focused on characterizing biofilm structure and development at the mesoscale (mm-range). Therefore, biofilm replicates (n = 10) were cultivated and analyzed. Three hypotheses were defined in order to estimate the effect of Fe²⁺ inflow concentration and/or wall shear stress on biofilm development and structure, respectively. It was not the intention to investigate and describe the underlying mechanisms of iron incorporation as this would require a different set of tools applied at microscopic levels as well as the use of, i.e., omic approaches. Fe²⁺ addition influenced biofilm development (e.g., biofilm accumulation) and structure markedly. Experiments revealed the accumulation of FeO(OH) within the biofilm matrix and a positive correlation of Fe²⁺ inflow concentration and biofilm accumulation. In more detail, independent of the wall shear stress applied during cultivation, biofilms grew approximately four times thicker at 2.5 mg Fe²⁺/L (44.8 µmol/L; high inflow concentration) compared to the low Fe²⁺ inflow concentration of 0.25 mg Fe²⁺/L (4.48 µmol/L). This finding was statistically verified (Scheirer-Ray-Hare test, ANOVA) and hints at a higher stability of Bacillus subtilis biofilms (e.g., elevated cohesive and adhesive strength) when grown at elevated Fe²⁺ inflow concentrations.

Impact of Growth Conditions on Pseudomonas fluorescens Morphology Characterized by Atomic Force Microscopy

This work is dedicated to the characterization by Atomic Force Microscopy (AFM) of Pseudomonas fluorescens, bacteria having high potential in biotechnology. They were first studied first in optimal conditions in terms of culture medium and temperature. AFM revealed a more-or-less elongated morphology with typical dimensions in the micrometer range, and an organization of the outer membrane characterized by the presence of long and randomly distributed ripples, which are likely related to the organization of lipopolysaccharides (LPS). The outer membrane also presents invaginations, some of them showing a reorganization of ripples, which could be the first sign of a bacterial stress response. In a second step, bacteria grown under unfavorable conditions were characterized. The choice of the medium appeared to be more critical in the case of the second generation of cells, the less adapted medium inducing not only changes in the membrane organization but also larger damages in bacteria. An increased growth temperature affected both the usual “swollen” morphology and the organization of the outer membrane. Here also, LPS likely contribute to membrane remodelling, which makes them potential markers to track cell state changes.

Wetting properties of dehydrated biofilms under different growth conditions

Biofilms are resilient to environmental conditions and often resistant even to strong disinfectants. It is crucial to investigate their interfacial properties, which can be effectively characterized by wetting analysis. Wetting phenomena on biofilm surfaces have been poorly investigated in literature, in particular a systematic study of wetting on real biofilm-coated substrates including the application of external body forces (forced wetting, i.e.: centrifugal and gravitational forces) is missing. The aim of this work is to study the role of nutrient and shear flow conditions on wetting properties of Pseudomonas fluorescens dehydrated biofilms, grown on glass substrates. An innovative device (Kerberos®), capable to study spreading/sliding behavior under the application of external body forces, is used here for a systematic analysis of wetting/de-wetting liquid droplets on horizontal substrates under the action of tangential forces. Results prove that, under different growth conditions, (i.e., nutrients and imposed flow), biofilms exhibit different wetting properties. At lower nutrient/shear flow conditions, biofilms show spreading/sliding behavior close to that of pure glass. At higher nutrient and shear flow conditions, droplets on biofilms show spreading followed by imbibition soon after deposition, which leads to peculiar droplet depinning during the rotation test. Wetting properties are derived as a function of the rotation speed from both top and side views videoframes through a dedicated image analysis technique. A detailed analysis of biofilm formation and morphology/topography is also provided here.

The role of antibiotics and heavy metals on the development, promotion, and dissemination of antimicrobial resistance in drinking water biofilms

Antimicrobial resistance (AMR), as well as the development of biofilms in drinking water distribution systems (DWDSs), have become an increasing concern for public health and management. As bulk water travels from source to tap, it may accumulate contaminants of emerging concern (CECs) such as antibiotics and heavy metals. When these CECs and other selective pressures, such as disinfection, pipe material, temperature, pH, and nutrient availability interact with planktonic cells and, consequently, DWDS biofilms, AMR is promoted. The purpose of this review is to highlight the mechanisms by which AMR develops and is disseminated within DWDS biofilms. First, this review will lay a foundation by describing how DWDS biofilms form, as well as their basic intrinsic and acquired resistance mechanisms. Next, the selective pressures that further induce AMR in DWDS biofilms will be elaborated. Then, the pressures by which antibiotic and heavy metal CECs accumulate in DWDS biofilms, their individual resistance mechanisms, and co-selection are described and discussed. Finally, the known human health risks and current management strategies to mitigate AMR in DWDSs will be presented. Overall, this review provides critical connections between several biotic and abiotic factors that influence and induce AMR in DWDS biofilms. Implications are made regarding the importance of monitoring and managing the development, promotion, and dissemination of AMR in DWDS biofilms.

Nano- and Macroscale Imaging of Cholesterol Linoleate and Human Beta Defensin 2-Induced Changes in Pseudomonas aeruginosa Biofilms

The biofilm production of Pseudomonas aeruginosa (PA) is central to establishing chronic infection in the airways in cystic fibrosis. Epithelial cells secrete an array of innate immune factors, including antimicrobial proteins and lipids, such as human beta defensin 2 (HBD2) and cholesteryl lineolate (CL), respectively, to combat colonization by pathogens. We have recently shown that HBD2 inhibits biofilm production by PA, possibly linked to interference with the transport of biofilm precursors. Considering that both HBD2 and CL are increased in airway fluids during infection, we hypothesized that CL synergizes with HBD2 in biofilm inhibition. CL was formulated in phospholipid-based liposomes (CL-PL). As measured by atomic force microscopy of single bacteria, CL-PL alone and in combination with HBD2 significantly increased bacterial surface roughness. Additionally, extracellular structures emanated from untreated bacterial cells, but not from cells treated with CL-PL and HBD2 alone and in combination. Crystal violet staining of the biofilm revealed that CL-PL combined with HBD2 effected a significant decrease of biofilm mass and increased the number of larger biofilm particles consistent with altered cohesion of formed biofilms. These data suggest that CL and HBD2 affect PA biofilm formation at the single cell and community-wide level and that the community-wide effects of CL are enhanced by HBD2. This research may inform future novel treatments for recalcitrant infections in the airways of CF patients.

Self-Adaptation of Pseudomonas fluorescens Biofilms to Hydrodynamic Stress

In some conditions, bacteria self-organize into biofilms, supracellular structures made of a self-produced embedding matrix, mainly composed of polysaccharides, DNA, proteins, and lipids. It is known that bacteria change their colony/matrix ratio in the presence of external stimuli such as hydrodynamic stress. However, little is still known about the molecular mechanisms driving this self-adaptation. In this work, we monitor structural features of Pseudomonas fluorescens biofilms grown with and without hydrodynamic stress. Our measurements show that the hydrodynamic stress concomitantly increases the cell density population and the matrix production. At short growth timescales, the matrix mediates a weak cell-cell attractive interaction due to the depletion forces originated by the polymer constituents. Using a population dynamics model, we conclude that hydrodynamic stress causes a faster diffusion of nutrients and a higher incorporation of planktonic bacteria to the already formed microcolonies. This results in the formation of more mechanically stable biofilms due to an increase of the number of crosslinks, as shown by computer simulations. The mechanical stability also relies on a change in the chemical compositions of the matrix, which becomes enriched in carbohydrates, known to display adhering properties. Overall, we demonstrate that bacteria are capable of self-adapting to hostile hydrodynamic stress by tailoring the biofilm chemical composition, thus affecting both the mesoscale structure of the matrix and its viscoelastic properties that ultimately regulate the bacteria-polymer interactions.

Biofilm mechanics: Implications in infection and survival

It has long been recognized that biofilms are viscoelastic materials, however the importance of this attribute to the survival and persistence of these microbial communities is yet to be fully realized. Here we review work, which focuses on understanding biofilm mechanics and put this knowledge in the context of biofilm survival, particularly for biofilm-associated infections. We note that biofilm viscoelasticity may be an evolved property of these communities, and that the production of multiple extracellular polymeric slime components may be a way to ensure the development of biofilms with complex viscoelastic properties. We discuss viscoelasticity facilitating biofilm survival in the context of promoting the formation of larger and stronger biofilms when exposed to shear forces, promoting fluid-like behavior of the biofilm and subsequent biofilm expansion by viscous flow, and enabling resistance to both mechanical and chemical methods of clearance. We conclude that biofilm viscoelasticity contributes to the virulence of chronic biofilm infections.

Evaluating a new injection method of liquid/gas mixture spray injection via performing long-term in situ bioremediation tests

During in situ bioremediation, continuous injection of growth substrates such as carbon sources, electron donors, or electron acceptors inevitably results in microbial growth, resulting in biological clogging in an aquifer. Therefore, for successful bioremediation, development of a new injection method is needed to reduce or alleviate this clogging problem. In this study, we carried out field tracer tests using single-well push-pull tests (SWPPTs), single-well natural gradient drift tests (SWNGDTs), and long-term in situ well-to-well tests to develop and evaluate a new method of liquid/gas mixture spray injection. The effectiveness of the new method was evaluated by estimating the factors as follow: longitudinal dispersivity (α_L), radius of influence (RI), shear stress on the surface of aquifer particles (σ), biofilm-shear-loss rate (R_s), and the ratio of volume occupied by cells grown to the original pore volume. At the tested site, the liquid/gas mixture spray injection method turned out to have several advantages compared to the traditional solution injection method: 1) transport of solute to a larger proportion of an aquifer by a factor of 1.3-1.7, 2) application of higher shear stress onto the surface of soil particles by a factor of 4.2-5.0, 3) faster biofilm sloughing rates by a factor of 2.3-2.6, 4) reduction in the ratio of the volume occupied by microorganisms to total pore volume (Vol_microbes/Vol_pore), and 5) efficient trichloroethylene (TCE) dechlorination for a period of 550 days without any injection problems. This new injection method showed positive effects on the hydrogeological and physical characteristics of the system, thus alleviating the biological clogging problem.

Characterization of planktonic and biofilm cells from two filamentous cyanobacteria using a shotgun proteomic approach

Cyanobacteria promote marine biofouling with significant impacts. A qualitative proteomic analysis, by LC-MS/MS, of planktonic and biofilm cells from two cyanobacteria was performed. Biofilms were formed on glass and perspex at two relevant hydrodynamic conditions for marine environments (average shear rates of 4 s^-1 and 40 s^-1). For both strains and surfaces, biofilm development was higher at 4 s^-1. Biofilm development of Nodosilinea sp. LEGE 06145 was substantially higher than Nodosilinea sp. LEGE 06119, but no significant differences were found between surfaces. Overall, 377 and 301 different proteins were identified for Nodosilinea sp. LEGE 06145 and Nodosilinea sp. LEGE 06119. Differences in protein composition were more noticeable in biofilms formed under different hydrodynamic conditions than in those formed on different surfaces. Ribosomal and photosynthetic proteins were identified in most conditions. The characterization performed gives new insights into how shear rate and surface affect the planktonic to biofilm transition, from a structural and proteomics perspective.

pH responsive superporogen combined with PDT based on poly Ce6 ionic liquid grafted on SiO2 for combating MRSA biofilm infection

Background: Biofilm infection caused by multidrug-resistant bacteria is difficult to eradicate by conventional therapies. Photodynamic therapy (PDT) is an effective antibacterial method for fighting against biofilm infection. However, the blocked photosensitizers outside of biofilm greatly limit the efficacy of PDT.

Methods: Herein, a novel acid-responsive superporogen and photosensitizer (SiO₂-P_Ce6-IL) was developed. Because of the protonation of the photosensitizer and the high binding energy of the polyionic liquid, SiO₂-P_Ce6-IL changed to positive SiO₂-P_IL⁺ in an acidic microenvironment of biofilm infection. SiO₂-P_IL⁺ could combine with negatively charged extracellular polymeric substances (EPS) and create holes to remove the biofilm barrier. To strengthen the interaction between SiO₂-P_IL⁺ and EPS, SiO₂-P_IL⁺ of high charge density was prepared by grafting the high-density initiation site of ATRP onto the surface of the SiO₂ base.

Results: Due to the rapid protonation rate of COO^- and the strong binding energy of SiO₂-P_IL⁺ with EPS, SiO₂-P_Ce6-IL could release 90% of Ce6 in 10 s. With the stronger electrostatic and hydrophobic interaction of SiO₂-P_IL⁺ with EPS, the surface potential, hydrophobicity, adhesion and mechanical strength of biofilm were changed, and holes in the biofilm were created in 10 min. Combining with the release of photosensitizers and the porous structure of the biofilm, Ce6 was efficiently concentrated in the biofilm. The in vitro and in vivo antibacterial experiments proved that SiO₂-P_Ce6-IL dramatically improved the PDT efficacy against MRSA biofilm infection.

Conclusion: These findings suggest that SiO₂-P_Ce6-IL could rapidly increase the concentration of photosensitizer in biofilm and it is an effective therapy for combating biofilm infection.

Role of feed water biodegradable substrate concentration on biofouling: Biofilm characteristics, membrane performance and cleanability

Biofouling severely impacts operational performance of membrane systems increasing the cost of water production. Understanding the effect of critical parameters of feed water such as biodegradable substrate concentration on the developed biofilm characteristics enables development of more effective biofouling control strategies. In this study, the effect of substrate concentration on the biofilm characteristics was examined using membrane fouling simulators (MFSs). A feed channel pressure drop (PD) increase of 200 mbar was used as a benchmark to study the developed biofilm. The amount and characteristics of the formed biofilm were analysed in relation to membrane performance indicators: feed channel pressure drop and permeate flux. The effect of the characteristics of the biofilm developed at three substrate concentrations on the removal efficiency of the different biofilms was evaluated applying acid/base cleaning. Results showed that a higher feed water substrate concentration caused a higher biomass amount, a faster PD increase, but a lower permeate flux decline. The permeate flux decline was affected by the spatial location and the physical characteristics of the biofilm rather than the total amount of biofilm. The slower growing biofilm developed at the lowest substrate concentration was harder to remove by NaOH/HCl cleanings than the biofilm developed at the higher substrate concentrations. Effective biofilm removal is essential to prevent a fast biofilm regrowth after cleaning. While substrate limitation is a generally accepted biofouling control strategy delaying biofouling, development of advanced cleaning methods to remove biofilms formed under substrate limited conditions is of paramount importance.