Modeling Biofilms in Water Systems with New Variables: A Review

Validated In Silico Model for Biofilm Formation in Escherichia coli

Using Escherichia coli as the representative biofilm former, we report here the development of an in silico model built by simulating events that transform a free-living bacterial entity into self-encased multicellular biofilms. Published literature on ∼300 genes associated with pathways involved in biofilm formation was curated, static maps were created, and suitably interconnected with their respective metabolites using ordinary differential equations. Precise interplay of genetic networks that regulate the transitory switching of bacterial growth pattern in response to environmental changes and the resultant multicomponent synthesis of the extracellular matrix were appropriately represented. Subsequently, the in silico model was analyzed by simulating time-dependent changes in the concentration of components by using the R and python environment. The model was validated by simulating and verifying the impact of key gene knockouts (KOs) and systematic knockdowns on biofilm formation, thus ensuring the outcomes were comparable with the reported literature. Similarly, specific gene KOs in laboratory and pathogenic E. coli were constructed and assessed. MiaA, YdeO, and YgiV were found to be crucial in biofilm development. Furthermore, qRT-PCR confirmed the elevation of expression in biofilm-forming clinical isolates. Findings reported in this study offer opportunities for identifying biofilm inhibitors with applications in multiple industries. The application of this model can be extended to the health care sector specifically to develop novel adjunct therapies that prevent biofilms in medical implants and reduce emergence of biofilm-associated resistant polymicrobial-chronic infections. The in silico framework reported here is open source and accessible for further enhancements.

An improved ASM-GDA approach to evaluate the production kinetics of loosely bound and tightly bound extracellular polymeric substances in biological phosphorus removal process

This study established an extended activated sludge model no. 2 (ASM2) for providing a new recognition of the contributions of both loosely-bound EPS (LB-EPS) and tightly-bound EPS (TB-EPS) into phosphorus (P) removal by incorporating their formation and degradation processes during the anaerobic-aerobic cycle. For determining the best-fit values for the new model parameters (k _h,TB-EPS, k _h,LB-EPS, f _PP,TB-EPS, and f _PP,LB-EPS) in this extended ASM2, a novel and convenient gradient descent algorithm (GDA) based ASM (ASM-GDA) method was developed. Sensitivity analysis of f _PP,TB-EPS, f _PP,LB-EPS, k _h,TB-EPS, and k _h,LB-EPS on the model target outputs of S _PO4 , X _TB-EPS, X _LB-EPS, and X _PP proved the accuracy of the chosen parameters. Eight batch experiments conducted under different influential chemical oxygen demand (COD) and P conditions were quantitatively and qualitatively analyzed. Respectively, 9.37-9.64% and 4.17-4.29% of P removal by TB-EPS and LB-EPS were achieved. Self-Organizing Map (SOM) has shown its high performance for visualization and abstraction for exhibiting the high correlations of the influential COD/P concentrations and the P% removal by TB-EPS (and LB-EPS). Comprehensive analyses of the influences of influential COD and P concentration on the biological phosphorus removal process help us in successfully establishing the mechanism kinetics of production and degradation of P in a dynamic P biological-treatment model.

Mitigating biofouling with a vanillin coating on thin film composite reverse osmosis membranes

Several methods, such as pretreatment, membrane surface modification, feed water chlorination, and chemical cleaning, have recently been applied to control biofouling on reverse osmosis (RO) membranes-with limited success. As an alternative, compounds that inhibit bacterial quorum sensing can be used to disrupt formation of bacterial colonies. In this study, anti-biofouling using vanillin, which is a natural substance among quorum sensing inhibitor compounds, was trialed, by modifying RO membrane surfaces with vanillin, at various concentrations. We then reviewed consequential changes to membrane surface characteristics and vanillin anti-biofouling properties. A long-term RO membrane simulator was used to analyze permeability, contact angle was measured for hydrophilicity evaluation, and membrane surface morphology was analyzed, through atomic force microscopy and scanning electron microscopy. A quorum quenching effect was confirmed by utilizing Petrifilm to count bacteria on the surface of a modified membrane. As a result, the permeability of the surface modified membranes was slightly decreased compared to the pristine membrane, but the hydrophilicity was increased, and the number of colonies decreased remarkably, the membrane modified with 0.5 M vanillin outperforming that modified with 0.25 M vanillin.

Biofilm research within irrigation water distribution systems: Trends, knowledge gaps, and future perspectives

Biofilms in irrigation water distribution systems (IWDSs) play an essential role in spreading pathogens, chemical pollutants, and environmental pollutants into downstream irrigated crops and thus should be considered a potential threat to food safety. Although the role of biofilms in drinking water distribution systems has been extensively studied in the last decade, the research on IWDS biofilms in this period has been limited. This review identifies research gaps in the field of IWDS biofilms, provides perspectives on experimental designs for investigating IWDS biofilms, and suggests potential strategies worth pursuing in IWDS management. The current state of the art of IWDS biofilms is discussed, and an analysis of the challenges in IWDS biofilm research is presented. Furthermore, this review proposes useful advanced technologies that allow a practical, in-depth fundamental understanding of IWDS biofilms. In a nutshell, this article provides future directions and insights into detailed experimental designs on a relatively under-reported research topic: "IWDS biofilms."

Microbial Interaction as a Determinant of the Quality of Supply Drinking Water: A Conceptual Analysis

This conceptual analysis elucidates the microbial interaction inside municipal distribution pipes, subsequent deterioration in the quality of the supply water, and its impacts on public health. Literature review involved a total of 21 original reports on microbiological events inside the water distribution system were studied, summarizing the current knowledge about the build-up of microbes in treated municipal water at various points of the distribution system. Next, original reports from the microbiological analysis of supply water from Bangladesh were collected to enlist the types of bacteria found growing actively. A schematic diagram of microbial interaction among the genera was constructed with respect to the physical, chemical, and microbiological quality of the supply water. Finally latest guidelines and expert opinions from public health authorities around the world are reviewed to keep up with using cutting-edge molecular technology to ensure safe and good quality drinking water for municipal supply.

Low-level concentrations of aminoglycoside antibiotics induce the aggregation of cyanobacteria

The interactions between antibiotics and microorganisms have attracted enormous research attentions. In this study, we investigated the effects of two typical aminoglycoside antibiotics on the aggregation of the model cyanobacterium, Synechococcus elongatus, and the dominating strain in algal blooms, Microcystis aeruginosa, via the analysis of zeta potentials, hydrophobicity, and extracellular polymeric substances (EPS) secretion. The results showed that low-level antibiotics promoted the aggregation of S. elongatus and M. aeruginosa by 40 and 18% under 0.10 and 0.02 μg/mL of kanamycin, respectively, which was mainly attributed to the combined effects of increased zeta potentials and the ratio between extracellular proteins and polysaccharides. Tobramycin exerted similar effects. Additionally, we discovered that at low pH (pH 5) and ionic strength (1 mM Na⁺ and 2 mM Mg²⁺), the inducing effects of antibiotics would be even larger than those with higher pH and ionic strength. As aggregation is important to cyanobacteria in either the basic physiology of biofilm formation or the algal bloom, our study demonstrated that low-level antibiotics exert ecological impacts via interfered aggregation. We believe this study will shed light on the mechanisms underlying antibiotic-induced biofilm formation and help with the evaluation of the environmental and ecological risks of antibiotics and other emerging pollutants.

Influences of graphene oxide on biofilm formation of gram-negative and gram-positive bacteria

In this study, we evaluated the influences of graphene oxide (GO) on biofilm formation. Escherichia coli MG1655 and Bacillus subtilis 168 were used as models for Gram-negative and Gram-positive bacteria. The growth profiles and viability assays indicated that GO exhibited a high antibacterial activity, of which the negative effects on bacteria growth raised with the increasing GO concentration. The antibacterial activity of GO was mainly attributed to the membrane stress and ROS-independent oxidative stress. Moreover, it was worthy to note that the biofilm formation was enhanced in the presence of GO at low dosage whereas inhibited in the high-concentration GO environment. These results could be explained by the roles of the dead cells, which were inactivated by GO. When the concentration of GO was limited, only a part of the cells would be inactivated, which may then serve as a protection barrier as well as the necessary nutrient to the remaining living cells for the formation of biofilm. In contrast, with a sufficient presence of GO, almost all cells can be inactivated completely and thus the formation of biofilm could no longer be triggered. Overall, the present work provides significant new insights on the influence of carbon nanomaterials towards biofilm formation, which has far-reaching implications in the field of biofouling and membrane bioreactor. Graphical abstract ᅟ.