Biophysical controls on cluster dynamics and architectural differentiation of microbial biofilms in contrasting flow environments

Morphogenesis of Biofilms in Porous Media and Control on Hydrodynamics

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

Biophysical properties at patch scale shape the metabolism of biofilm landscapes

Phototrophic biofilms form complex spatial patterns in streams and rivers, yet, how community patchiness, structure and function are coupled and contribute to larger-scale metabolism remains unkown. Here, we combined optical coherence tomography with automated O₂ microprofiling and amplicon sequencing in a flume experiment to show how distinct community patches interact with the hydraulic environment and how this affects the internal distribution of oxygen. We used numerical simulations to derive rates of community photosynthetic activity and respiration at the patch scale and use the obtained parameter to upscale from individual patches to the larger biofilm landscape. Our biofilm landscape approach revealed evidence of parallels in the structure-function coupling between phototrophic biofilms and their streambed habitat.

Influence of the design of fresh-cut food washing tanks on the growth kinetics of Pseudomonas fluorescens biofilms

Mitigation of cross-contamination of fresh-cut food products at the washing step was studied by investigating how the vat design would affect the biofilm contamination surfaces. Hygienic design features such as no horizontal surfaces and only open angles exceeding 100° were proposed. The flow organization (velocity streamlines, wall shear stresses, and dynamics of the flow) was identified by means of computational fluid dynamics (CFD) calculation. Pseudomonas fluorescens PF1 biofilm growth kinetics were then mapped. The change in some geometrical features induced a better flow organization reducing “dead zones”. This significantly changed the biofilm growth kinetics, delaying the detection of biofilms from 20 hr to 24 hr. Critical areas such as welds, corners, and interfaces appeared far less prone to strong bacterial development. This would mean milder or less chemicals required at the washing step and faster and easier cleaning.

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Pseudomonas fluorescens biofilm growth kinetics strongly related to the vat design

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Improved design lead to 24hr lag time before the biofilm exponential growth phase

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Corners, welds, and wetting front areas contamination could be largely mitigated

Exploring flow-biofilm-sediment interactions: Assessment of current status and future challenges

Biofilm activities and their interactions with physical, chemical and biological processes are of great importance for a variety of ecosystem functions, impacting hydrogeomorphology, water quality and aquatic ecosystem health. Effective management of water bodies requires advancing our understanding of how flow influences biofilm-bound sediment and ecosystem processes and vice-versa. However, research on this triangle of flow-biofilm-sediment is still at its infancy. In this Review, we summarize the current state of the art and methodological approaches in the flow-biofilm-sediment research with an emphasis on biostabilization and fine sediment dynamics mainly in the benthic zone of lotic and lentic environments. Example studies of this three-way interaction across a range of spatial scales from cell (nm - µm) to patch scale (mm - dm) are highlighted in view of the urgent need for interdisciplinary approaches. As a contribution to the review, we combine a literature survey with results of a pilot experiment that was conducted in the framework of a joint workshop to explore the feasibility of asking interdisciplinary questions. Further, within this workshop various observation and measuring approaches were tested and the quality of the achieved results was evaluated individually and in combination. Accordingly, the paper concludes by highlighting the following research challenges to be considered within the forthcoming years in the triangle of flow-biofilm-sediment: i) Establish a collaborative work among hydraulic and sedimentation engineers as well as ecologists to study mutual goals with appropriate methods. Perform realistic experimental studies to test hypotheses on flow-biofilm-sediment interactions as well as structural and mechanical characteristics of the bed. ii) Consider spatially varying characteristics of flow at the sediment-water interface. Utilize combinations of microsensors and non-intrusive optical methods, such as particle image velocimetry and laser scanner to elucidate the mechanism behind biofilm growth as well as mass and momentum flux exchanges between biofilm and water. Use molecular approaches (DNA, pigments, staining, microscopy) for sophisticated community analyses. Link varying flow regimes to microbial communities (and processes) and fine sediment properties to explore the role of key microbial players and functions in enhancing sediment stability (biostabilization). iii) Link laboratory-scale observations to larger scales relevant for management of water bodies. Conduct field experiments to better understand the complex effects of variable flow and sediment regimes on biostabilization. Employ scalable and informative observation techniques (e.g., hyperspectral imaging, particle tracking) that can support predictions on the functional aspects, such as metabolic activity, bed stability, nutrient fluxes under variable regimes of flow-biofilm-sediment.

Computational and Experimental Investigation of Biofilm Disruption Dynamics Induced by High-Velocity Gas Jet Impingement

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.

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.

Thickness determines microbial community structure and function in nitrifying biofilms via deterministic assembly

Microbial biofilms are ubiquitous in aquatic environments where they provide important ecosystem functions. A key property believed to influence the community structure and function of biofilms is thickness. However, since biofilm thickness is inextricably linked to external factors such as water flow, temperature, development age and nutrient conditions, its importance is difficult to quantify. Here, we designed an experimental system in a wastewater treatment plant whereby nitrifying biofilms with different thicknesses (50 or 400 µm) were grown in a single reactor, and thus subjected to identical external conditions. The 50 and 400 µm biofilm communities were significantly different. This beta-diversity between biofilms of different thickness was primarily caused by deterministic factors. Turnover (species replacement) contributed more than nestedness (species loss) to the beta-diversity, i.e. the 50 µm communities were not simply a subset of the 400 µm communities. Moreover, the two communities differed in the composition of nitrogen-transforming bacteria and in nitrogen transformation rates. The study illustrates that biofilm thickness alone is a key driver for community composition and ecosystem function, which has implications for biotechnological applications and for our general understanding of biofilm ecology.

Wastewater biofilm formation on self-assembled monolayer surfaces using elastomeric flow cells

In anaerobic wastewater treatment, microbial biofilm is beneficial for efficient substrate utilization and for preventing the wash-out of key microorganisms. By providing solid supports, biofilm formation can be accelerated due to the early initial adhesion of residing microbes. Alteration in surface properties is therefore one such approach that helps us understand microbial interfacial interaction. Here, self-assembled monolayers of alkanethiols with carboxyl (-COOH), hydroxyl (-OH), and amine (-NH₂) terminal moieties on gold (Au) substrates were employed to study the initial adhesion of wastewater microbes. An elastomeric flow cell was also utilized to simulate the environment of wastewater bioreactor. Results from fluorescence in situ hybridization (FISH) portrayed more enhanced microbial adhesion after 2 h on -NH₂ functional group with the calculated surface coverage of 12.8 ± 2.4% as compared to 7.7 ± 1.6% on -COOH, 11.0 ± 2.0% on -OH, and 1.2% on unmodified Au surfaces. This might be because of concomitant electrostatic attraction between negatively-charged bacteria and positively-charged (-NH₃⁺) functional groups. Nevertheless, the average surface coverage by individual biofilm clusters was 28.0 ± 5.0 μm² and 32.0 ± 9.0 μm² on -NH₂ and -OH surfaces, respectively, while -COOH surfaces resulted in higher value (60.0 ± 5.0 μm²) and no significant cluster formation was observed on Au surfaces. Accordingly, the average inter-cluster distance observed on -NH₂ surfaces was relatively smaller (3.0 ± 0.6 μm) as compared to that on other surfaces. Overall, these data suggest favorable initial biofilm growth on more hydrophilic and positively-charged surfaces. Furthermore, the analysis of the mean fluorescence intensity revealed preferred initial adhesion of key microbes (archaea) on -OH and -NH₂ surfaces. Indeed, results obtained from this study would be beneficial in designing selective biointerfaces for certain biofilm carriers in a typical wastewater bioreactor. Importantly, our elastomeric flow cell integrated with SAM-modified surfaces demonstrated an ideal platform for high-throughput investigation of wastewater biofilm under controlled environments.

Cell-gel interactions of in-gel propagating bacteria

Objective

Our immediate objective is to test the data-suggested possibility that in-agarose gel bacterial propagation causes gel fiber dislocation and alteration of cell distribution. We also test the further effect of lowering water activity. We perform these tests with both Gram-negative and Gram-positive bacteria. Data are obtained via electron microscopy of thin sections, which provides the first images of both bacteria and gel fibers in gel-supported bacterial lawns. The long-term objective is analysis of the effects of in-gel propagation on the DNA packaging of phages.

Results

We find that agarose gel-supported cells in lawns of Escherichia coli and Lysinibacillus (1) are primarily in clusters that increase in size with time and are surrounded by gel fibers, and (2) sometimes undergo gel-induced, post-duplication rotation and translation. Bacterial growth-induced dislocation of gel fibers is observed. One reason for clustering is that clustering promotes growth by increasing the growth-derived force applied to the gel fibers. Reactive force exerted by gel on cells explains cell movement. Finally, addition to growth medium of 0.94 M sucrose causes cluster-associated E. coli cells to become more densely packed and polymorphic. Shape is determined, in part, by neighboring cells, a novel observation to our knowledge.

Effects of water flow on submerged macrophyte-biofilm systems in constructed wetlands

The effects of water flow on the leaf-biofilm interface of Vallisneria natans and Hydrilla verticillata were investigated using artificial plants as the control. Water flow inhibited the growth of two species of submerged macrophytes, reduced oxygen concentrations in plant leaves and changed oxygen profiles at the leaf-biofilm interface. The results from confocal laser scanning microscopy and multifractal analysis showed that water flow reduced biofilm thickness, changed biofilm topographic characterization and increased the percentages of single colony-like biofilm patches. A cluster analysis revealed that the bacterial compositions in biofilms were determined mainly by substrate types and were different from those in sediments. However, water flow increased the bacterial diversity in biofilms in terms of operational taxonomic unit numbers and Shannon Indices. Our results indicated that water flow can be used to regulate the biomass, distribution and bacterial diversities of epiphytic biofilms in constructed wetlands dominated by submerged macrophytes.

Geometrical Distribution of Cryptococcus neoformans Mediates Flower-Like Biofilm Development

Microbial biofilms are highly structured and dynamic communities in which phenotypic diversification allows microorganisms to adapt to different environments under distinct conditions. The environmentally ubiquitous pathogen Cryptococcus neoformans colonizes many niches of the human body and implanted medical devices in the form of biofilms, an important virulence factor. A new approach was used to characterize the underlying geometrical distribution of C. neoformans cells during the adhesion stage of biofilm formation. Geometrical aspects of adhered cells were calculated from the Delaunay triangulation and Voronoi diagram obtained from scanning electron microscopy images (SEM). A correlation between increased biofilm formation and higher ordering of the underlying cell distribution was found. Mature biofilm aggregates were analyzed by applying an adapted protocol developed for ultrastructure visualization of cryptococcal cells by SEM. Flower-like clusters consisting of cells embedded in a dense layer of extracellular matrix were observed as well as distinct levels of spatial organization: adhered cells, clusters of cells and community of clusters. The results add insights into yeast motility during the dispersion stage of biofilm formation. This study highlights the importance of cellular organization for biofilm growth and presents a novel application of the geometrical method of analysis.

Modulation of the mechanical properties of bacterial biofilms in response to environmental challenges

In this review, we highlight recent research on the relationship between biofilm matrix composition, biofilm mechanics and environmental stimuli.

Biomechanical Analysis of Infectious Biofilms

The removal of infectious biofilms from tissues or implanted devices and their transmission through fluid transport systems depends in part of the mechanical properties of their polymeric matrix. Linking the various physical and chemical microscopic interactions to macroscopic deformation and failure modes promises to unveil design principles for novel therapeutic strategies targeting biofilm eradication, and provide a predictive capability to accelerate the development of devices, water lines, etc, that minimise microbial dispersal. Here, our current understanding of biofilm mechanics is appraised from the perspective of biophysics , with an emphasis on constitutive modelling that has been highly successful in soft matter. Fitting rheometric data to viscoelastic models has quantified linear and nonlinear stress relaxation mechanisms, how they vary between species and environments, and how candidate chemical treatments alter the mechanical response. The rich interplay between growth, mechanics and hydrodynamics is just becoming amenable to computational modelling and promises to provide unprecedented characterisation of infectious biofilms in their native state.

Modeling the Effects of Hydrodynamic Regimes on Microbial Communities within Fluvial Biofilms: Combining Deterministic and Stochastic Processes

To fully understand the effects of hydrodynamics on a microbial community, the roles of niche-based and neutral processes must be considered in a mathematical model. To this end, a two-dimensional model combining mechanisms of immigration, dispersal, and niche differentiation was first established to describe the effects of hydrodynamics on bacterial communities within fluvial biofilms. Deterministic factors of the model were identified via the calculation of Spearman's rank correlation coefficients between parameters of hydrodynamics and the bacterial community. It was found that turbulent kinetic energy and turbulent intensity were considered as a set of reasonable predictors of community composition, whereas flow velocity and turbulent intensity can be combined together to predict biofilm bacterial biomass. According to the modeling result, the bacterial community could get its favorable assembly condition with a flow velocity ranging from 0.041 to 0.061 m/s. However, the driving force for biofilm community assembly changed with the local hydrodynamics. Individuals reproduction within the biofilm was the main driving force with flow velocity less than 0.05 m/s, while cell migration played a much more important role with velocity larger than 0.05 m/s. The developed model could be considered as a useful tool for improving the technologies of water environment protection and remediation.

Abiotic autumnal organic matter deposition and grazing disturbance effects on epilithic biofilm succession

Stream epilithic biofilm community assembly is influenced in part by environmental factors. Autumn leaf deposition is an annual resource subsidy to streams, but the physical effects of leaves settling on epilithic biofilms has not been investigated.We hypothesized that bacterial and microeukaryotic community assembly would follow a successional sequence that was mediated by abiotic effects that were simulating leaf deposition (reduced light and flow) and by biotic (snail grazing)disturbance. This hypothesis was tested using an in situ experimental manipulation. Ambient biofilms had greater algal biomass and distinct ARISA community profiles compared to biofilms developed under manipulated conditions. There were no significant differences in biofilm characteristics associated with grazing, suggesting that results were driven by reduced light/flow rather than invertebrate disturbance; however, grazing appeared to increase bacterial taxon richness.Interestingly at day 38, all treatments grouped together in ordination space and had similar algal/total biomass ratios. We suggest that algal priming promoted a shift in ambient biofilms but that this effect is dependent upon successional timing of algal establishment. These data demonstrate that abiotic effects were more influential than local grazing disturbance and imply that leaf litter deposition may have bottom-up effects on the stream ecosystem through altered epilithic biofilms.

A mass-spring model unveils the morphogenesis of phototrophic Diatoma biofilms

Diatoms often dominate planktonic communities in the ocean and phototrophic biofilms in streams and rivers, greatly contributing to global biogeochemical fluxes. In pelagic ecosystems, these microscopic algae can form chain-like microcolonies, which seem advantageous for nutrient uptake and protect against grazing, and at the same time reduce sinking. Despite the capability of many diatoms to form chains, their contribution to the architecture of phototrophic biofilms remains elusive. Here we propose a computational model to simulate the growth and behaviour of Diatoma chains in contrasting flow environments. This mass-spring mechanical model captures the natural behaviour of Diatoma chains well, emphasising the relevance of chain growth and entanglement for biofilm morphogenesis. The model qualitatively describes formation of intricate dome-shaped structures and of dreadlock-type streamers as observed in nature in multidirectional and unidirectional flow, respectively. The proposed model is a useful tool to study the effect of fluid dynamics on biofilm morphogenesis.