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Biofilms aid bacterial adhesion to surfaces via direct and indirect mechanisms, and formation of biofilms is considered as an important strategy for adaptation and survival in suboptimal environmental conditions. However, the molecular underpinnings of biofilm formation in subsurface sediment/groundwater ecosystems where microorganisms often experience fluctuations in nutrient input, pH, and nitrate or metal concentrations are underexplored. We examined biofilm formation under different nutrient, pH, metal, and nitrate regimens of 16 Rhodanobacter strains isolated from subsurface groundwater wells spanning diverse levels of pH (3.5 to 5) and nitrates (13.7 to 146 mM). Eight Rhodanobacter strains demonstrated significant biofilm growth under low pH, suggesting adaptations for survival and growth at low pH. Biofilms were intensified under aluminum stress, particularly in strains possessing fewer genetic traits associated with biofilm formation, findings warranting further investigation. Through random barcode transposon-site sequencing (RB-TnSeq), proteomics, use of specific mutants, and transmission electron microscopy analysis, we discovered flagellar loss under aluminum stress, indicating a potential relationship between motility, metal tolerance, and biofilm growth. Comparative genomic analyses revealed the absence of flagella and chemotaxis genes and the presence of a putative type VI secretion system in the highly biofilm-forming strain FW021-MT20. In this study we identified genetic determinants associated with biofilm growth under metal stress in a predominant environmental genus, Rhodanobacter, and identified traits aiding survival and adaptation to contaminated subsurface environments.

Abstract The main challenge in the large-scale application of MICP lies in its low efficiency and promoting biofilm growth can effectively address this problem. In the present study, a prediction model was proposed using the response surface method. With the prediction model, optimum concentrations of nutrients in the medium can be obtained. Moreover, the optimized medium was compared with other media via bio-cementation tests. The results show that this prediction model was accurate and effective, and the predicted results were close to the measured results. By using the prediction model, the optimized culture media was determined (20.0 g/l yeast extract, 10.0 g/l polypeptone, 5.0 g/l ammonium sulfate, and 10.0 g/l NaCl). Furthermore, the optimized medium significantly promoted the growth of biofilm compared to other media. In the medium, the effect of polypeptone on biofilm growth was smaller than the effect of yeast extract and increasing the concentration of polypeptone was not beneficial in promoting biofilm growth. In addition, the sand column solidified with the optimized medium had the highest strength and the largest calcium carbonate contents. The prediction model represents a platform technology that leverages culture medium to impart novel sensing, adjustive, and responsive multifunctionality to structural materials in the civil engineering and material engineering fields.

ABSTRACTBackground Streptococcus mutans (S. mutans) is a pivotal cariogenic pathogen contributing to its multiple virulence factors, one of which is synthesizing exopolysaccharides (EPS). VicK, a sensor histidine kinase, plays a major role in regulating genes associated with EPS synthesis and adhesion. Here we first identified an antisense vicK RNA (ASvicK) bound with vicK into double-stranded RNA (dsRNA).Objective This study aims to investigate the effect and mechanism of ASvicK in the EPS metabolism and cariogenesis of S. mutans.Methods The phenotypes of biofilm were detected by scanning electron microscopy (SEM), gas chromatography-mass spectrometery (GC-MS) , gel permeation chromatography (GPC) , transcriptome analysis and Western blot. Co-immunoprecipitation (Co-ip) assay and enzyme activity experiment were adopted to investigate the mechanism of ASvicK regulation. Caries animal models were developed to study the relationship between ASvicK and cariogenicity of S. mutans.Results Overexpression of ASvicK can inhibit the growth of biofilm, reduce the production of EPS and alter genes and protein related to EPS metabolism. ASvicK can adsorb RNase III to regulate vicK and affect the cariogenicity of S. mutans.Conclusions ASvicK regulates vicK at the transcriptional and post-transcriptional levels, effectively inhibits EPS synthesis and biofilm formation and reduces its cariogenicity in vivo.

Concrete cracks have an adverse effect on the strength properties and durability of concrete structures. Therefore, repairing concrete cracks to recover the concrete's strength parameters is an important task in the civil engineering field. For repairing concrete cracks, the MICP technique has been widely analyzed in recent times; however, no research has been conducted to deeply investigate the repair effects of MICP on concrete cracks with a rough surface using a theoretical model. In the current research, MICP with a novel mathematical model was conducted considering the precipitation of calcium carbonate (CaCO3), ureolysis, suspended biomass, geochemistry, transport of solutes, and biofilm growth. Furthermore, crack repair experiments were performed to assess the performance of the new mathematical model. The results revealed that the calculated concentrations of suspended biomass in cracks gradually decreased during the test. The comparison between the experimental results and calculated results verified the precision of the migration behavior of the suspended biomass. At the inlet, the solute concentrations and volume fractions of biofilm were higher, causing an increase in the productive rates of calcium carbonate. The consumed concentrations of solutes were higher for cracks with a smoother surface, eventually leading to smaller values of sonic time; the upper parts of the cracks also had smaller values of sonic time, showing good repair effects. The proposed mathematical model provides a better solution to control the repair time and microbial metabolism process, allowing for adjustive bioremediation and biomineralization of concrete, which could provide a firm basis for the remediation of materials in the civil engineering field. [ABSTRACT FROM AUTHOR]

An implicit Euler finite-volume scheme for a parabolic reaction-diffusion system modeling biofilm growth is analyzed and implemented. The system consists of a degenerate-singular diffusion equation for the biomass fraction, which is coupled to a diffusion equation for the nutrient concentration, and it is solved in a bounded domain with Dirichlet boundary conditions. By transforming the biomass fraction to an entropy-type variable, it is shown that the numerical scheme preserves the lower and upper bounds of the biomass fraction. The existence and uniqueness of a discrete solution and the convergence of the scheme are proved. Numerical experiments in one and two space dimensions illustrate, respectively, the rate of convergence in space of our scheme and the temporal evolution of the biomass fraction and the nutrient concentration. [ABSTRACT FROM AUTHOR]

Biofilms are communities of bacterial cells encased in a self‐produced polymeric matrix that exhibit high tolerance toward environmental stress. Despite the plethora of research on biofilms, most P. aeruginosa biofilm models are cultured on a solid–liquid interface, and the longitudinal growth characteristics of P. aeruginosa biofilm are unclear. This study demonstrates the real‐time and noninvasive monitoring of biofilm growth using a novel dual‐chamber microfluidic device integrated with electrochemical detection capabilities to monitor pyocyanin (PYO). The growth of P. aeruginosa biofilms on the air–liquid interface (ALI) was monitored over 48 h, and its antibiotic susceptibility to 6 h exposure of 50, 400, and 1600 µg/ml of ciprofloxacin solutions was analyzed. The biofilm was treated directly on its surface and indirectly from the substratum by delivering the CIP solution to the top or bottom chamber of the microfluidic device. Results showed that P. aeruginosa biofilm developed on ALI produces PYO continuously, with the PYO production rate varying longitudinally and peak production observed between 24 and 30 h. In addition, this current study shows that the amount of PYO produced by the ALI biofilm is proportional to its viable cell numbers, which has not been previously demonstrated. Biofilm treated with ciprofloxacin solution above 400 µg/ml showed significant PYO reduction, with biofilms being killed more effectively when treatment was applied to their surfaces. The electrochemical measurement results have been verified with colony‐forming unit count results, and the strong correlation between the PYO electrical signal and the viable cell number highlights the usefulness of this approach for fast and low‐cost ALI biofilm study and antimicrobial tests. [ABSTRACT FROM AUTHOR]

This paper presents a comparative study on the effects of the in-situ surface modifications performed on “H” type microfluidic systems obtained via additive manufacturing. The microsystem was printed using a polylactic acid filament on an Ender-5 Pro printer. The surface modification of the main channel was done using chloroform by two different methods: vapor smoothing and flushing. The obtained surface roughness was studied using an optical microscope and the ImageJ software, as well as scanning electron microscopy. The effect of the channel surface treatment upon the characteristics of the fluid flow was assessed. The microfluidic systems were used for the dynamic study of biofilm growth of Candida albicans (ATCC 10231). The influence of the surface roughness of the main channel on the formation and growth of the biofilm was studied using quantitative methods, scanning electron microscopy imaging as well as optical coherence tomography.

Bioclogging is the most crucial operation problem of the constructed wetlands, which reduce its removal efficiency and life span. A strategy through properly increasing hydraulic loading is proposed in this study to alleviate the bioclogging for CWs. The two-dimensional porous media flow cell (2D PMFC) test indicated that a quadratic correlation was found between local biofilms growth rate and the near-wall Reynolds number (r > 0.765, p < 0.05). The biofilm growth rate declined with the flowrate when Re exceeded about 6.0. It was also found that the higher flowrate (6 mL/min) lead to the homogeneous biofilm and velocity distribution in the PMFC. The column test indicated that the highest hydraulic loading (9.2 cm/h) produced the smallest decrease in hydraulic conductivity, which was 80 times more than that of low hydraulic load (3.0 cm/h) at the end (40 days) of experiment. Moreover, the relatively homogenized distribution of biofilm was found along the column with the highest hydraulic loading, which confirmed that the proper increase in hydraulic loading can alleviate bioclogging. [ABSTRACT FROM AUTHOR]

To assess the cytotoxicity of an experimental hybrid-glass-based infiltrant and its effect on biofilm attachment, growth and metabolic activity, and to compare it to the resin-based infiltrant Icon. Cytotoxicity of hybrid-glass-based material (EXP) and resin-based infiltrant Icon (Icon) was tested in direct contact tests on freshly cured (direct_mat) and on materials kept for 24 h in cell culture medium (direct_exmat), and extract test with materials 24-h extracts (extract). Cell viability of L929 mouse fibroblast cell line was measured with MTT assay, according to ISO10993–5:2009. Biofilm attachment (5 h), growth (24 h and 48 h) and lactic-acid production (24 h and 48 h) on glass-disk specimens coated with EXP or Icon , or uncoated (control), were assessed using a microcosm biofilm model and Amsterdam Active Attachment system. At indicated time points, biofilms were harvested, plated, and CFU counts were determined, while lactic-acid production was measured colorimetrically. Cell viability reduction by EXP was below 30%-threshold in direct contact tests, while in extract test an increased cell viability was observed. Icon reduced cell viability substantially in all three tests. Significantly less bacteria attached to the surface of EXP after 5 h compared to Icon and control. Biofilm growth was significantly lower on EXP than on Icon and control after 24 h, but this difference was smaller and statistically insignificant after 48 h. There was no difference in lactic-acid production among groups. Novel hybrid-glass-based infiltrant seems to have a better biocompatibility and accumulates on its surface less bacteria than resin-based infiltrant, which makes it an attractive resin-free alternative. • Hybrid-glass-based infiltrant shows no cytotoxic effect on L929 fibroblasts. • Initial bacterial attachment and early biofilm growth are significantly lower on hybrid-glass-based infiltrant compared to resin-based infiltrant. • Hybrid-glass-based infiltrant is an attractive alternative to resin-based infiltrant. [ABSTRACT FROM AUTHOR]

[Display omitted] • Modelling H 2 production using lattice Boltzmann method and cellular automata. • Capturing biofilm pattern heterogeneity in a two-stage biofilm-based bioreactor. • Addressing the key barrier of increasing H 2 production and scaling-up. • A lag of the biofilm growth and H 2 production at the second part of the bioreactor. • A novel tool to improve bioreactor design, operation, and scale-up H 2 production. Hydrogen production through biochemical reactions is regarded as one of the most potential alternative technologies for producing hydrogen because of its efficacy, renewability, and environmental friendliness. Indirect biophotolysis is one of the most potential biohydrogen production technologies. In this study, a platform based on a coupled lattice Boltzmann method with cellular automata (LBM-CA) was developed to investigate the effects of different illumination intensities and carbon dioxide (CO 2) concentrations on indirect photolysis in a bioreactor. The bioreactor was divided into two distinct parts. The first part as a photobioreactor had a transparent window at the top wall of the bioreactor that allowed solar illumination to enter the domain to generate glucose through the conversion of CO 2 to carbohydrates (such as glucose) while the second was opaque where hydrogen was produced from carbohydrates by microorganisms. The results show that in the first part of the bioreactor, biofilm grew once CO 2 was available. However, there is a lag in the biofilm growth and biohydrogen production between the first and the second part of the bioreactor because they depend on glucose production in the first part. The biofilm concentration increased as illumination increased, especially in the early stages, while the biofilm growth mainly occurred in the first part of the bioreactor. Increasing illumination could increase biofilm concentration by 92.4 % and reduce the lag time. It is also observed that increasing CO 2 concentration changed the normalized biofilm concentration considerably, from − 40.9 % to 18.8 %. This can be attributed to increased nutrient availability for microorganism growth and glucose production in the first part of biophotolysis, resulting in greater concentrations of glucose as the main nutrient in the next part. Changing the inlet concentration leads to variations in the normalized hydrogen concentration in the range of − 72.9 % to 49.5 %. [ABSTRACT FROM AUTHOR]

Women with cystic fibrosis (CF) have a significantly lower life expectancy compared to men, which is indicated by an earlier impairment of lung function due to chronic colonization with biofilm formed by Pseudomonas aeruginosa. There is growing evidence that blood serum concentrations of the steroid sex hormone estradiol (E2) correlate with the occurrence of pulmonary exacerbations in CF but also play a role in the mucoid switch of P. aeruginosa. This study aims to shed light on possible microbiological reasons for sexual dimorphism in CF by investigating the influence of E2 on biofilm formation of P. aeruginosa CF isolates. For this purpose, 10 CF isolates of the respiratory tract derived from different CF patients have been treated with E2 in a microtiter plate biofilm model. Biofilms have been examined by crystal violet assays, field emission scanning electron microscopy (FE-SEM), 3D laser scanning microscopy (LSM), and quorum sensing (QS) reporter assays of the supernatants taken from biofilms. This allowed us to simultaneously investigate the effects of E2 on attached biofilm mass, biofilm ultrastructure, and QS activity. Upon E2 treatment, six out of 10 investigated CF isolates showed an increase of attached biofilm mass, whereas biofilms from two tested non-CF laboratory strains (PAO1 and ATCC19660) did not. Moreover, FE-SEM and 3D LSM analyses of the E2 responsive CF biofilms revealed ultrastructural remodeling of biofilm structure at different scales with increased formation of prominent biofilm spots, enhanced coverage with extracellular polymeric substance (EPS), and extended average surface roughness. QS activity measurements performed in biofilm supernatants via luminescence acyl homoserine lactone (AHL) reporter assays further showed that E2 treatment may also modulate QS signaling, as shown in an E2 sensitive CF isolate. Together, our results suggest the biofilm modulating effects of E2 on various clinical CF isolates that are documented by both biomass and ultrastructural changes of biofilms. The gained new insight into the influence of steroid hormones on P. aeruginosa biofilm phenotypes might pave the way for novel future approaches in personalized medicine based on the patients' sex and hormonal status. [ABSTRACT FROM AUTHOR]

This paper presents a comparative study on the effects of the in-situ surface modifications performed on "H" type microfluidic systems obtained via additive manufacturing. The microsystem was printed using a polylactic acid filament on an Ender-5 Pro printer. The surface modification of the main channel was done using chloroform by two different methods: vapor smoothing and flushing. The obtained surface roughness was studied using an optical microscope and the ImageJ software, as well as scanning electron microscopy. The effect of the channel surface treatment upon the characteristics of the fluid flow was assessed. The microfluidic systems were used for the dynamic study of biofilm growth of Candida albicans (ATCC 10231). The influence of the surface roughness of the main channel on the formation and growth of the biofilm was studied using quantitative methods, scanning electron microscopy imaging as well as optical coherence tomography. [ABSTRACT FROM AUTHOR]

Women with cystic fibrosis (CF) have a significantly lower life expectancy compared to men, which is indicated by an earlier impairment of lung function due to chronic colonization with biofilm formed by Pseudomonas aeruginosa. There is growing evidence that blood serum concentrations of the steroid sex hormone estradiol (E2) correlate with the occurrence of pulmonary exacerbations in CF but also play a role in the mucoid switch of P. aeruginosa. This study aims to shed light on possible microbiological reasons for sexual dimorphism in CF by investigating the influence of E2 on biofilm formation of P. aeruginosa CF isolates. For this purpose, 10 CF isolates of the respiratory tract derived from different CF patients have been treated with E2 in a microtiter plate biofilm model. Biofilms have been examined by crystal violet assays, field emission scanning electron microscopy (FE-SEM), 3D laser scanning microscopy (LSM), and quorum sensing (QS) reporter assays of the supernatants taken from biofilms. This allowed us to simultaneously investigate the effects of E2 on attached biofilm mass, biofilm ultrastructure, and QS activity. Upon E2 treatment, six out of 10 investigated CF isolates showed an increase of attached biofilm mass, whereas biofilms from two tested non-CF laboratory strains (PAO1 and ATCC19660) did not. Moreover, FE-SEM and 3D LSM analyses of the E2 responsive CF biofilms revealed ultrastructural remodeling of biofilm structure at different scales with increased formation of prominent biofilm spots, enhanced coverage with extracellular polymeric substance (EPS), and extended average surface roughness. QS activity measurements performed in biofilm supernatants via luminescence acyl homoserine lactone (AHL) reporter assays further showed that E2 treatment may also modulate QS signaling, as shown in an E2 sensitive CF isolate. Together, our results suggest the biofilm modulating effects of E2 on various clinical CF isolates that are documented by both biomass and ultrastructural changes of biofilms. The gained new insight into the influence of steroid hormones on P. aeruginosa biofilm phenotypes might pave the way for novel future approaches in personalized medicine based on the patients’ sex and hormonal status.

The problem of biofilm formation by clinical strains of opportunistic bacteria is one of the most significant for medicine, because in a state of biofilm bacteria become more resistant to environmental factors, including antibiotics, a situation that can cause failure of treatment. Among opportunistic pathogens staphylococci are of special interest. Knowledge about the peculiarities of biofilm formation of these strains, in particular the polysaccharide biosynthesis, can be used for creation of a strategy of prophylaxis of different lesions that bind with staphylococci. The effect of different concentrations of the most widespread sugars (glucose, sucrose, lactose, galactose) on the activity of biofilm formation by strains of Staphylococcus epidermidis was investigated. Strains of S. epidermidis (n = 7) were isolated from the reproductive tract of women with dysbiosis. The cultures were grown in universal synthetic media with concentration of one of the listed sugars (0.5–3.0%) during 72 h. Results were obtained colorimetrically. We studied the number of cells in biofilm and the index of biofilm formation. The largest number of cells in the biofilm was observed when the culture incubated in a medium with 2.0% of glucose (increase of 25.3 times compared to control). The amount of CFU in the control biofilm was 9.96 lg CFU/mL. The glucose concentration of 3.0% inhibited the biofilm formation: the number of cells in the biofilm was 569 times less compared to the control. The highest value of biofilm formation index was 7.2, which was 1.3 times higher than the control (5.4). In the presence of lactose and galactose in nutrient medium in concentrations from 1.0% a decrease in the number of cells and biofilm formation index were observed. The received data show that process of biofilm formation is significantly dependent on external sources of sugars, which can indicate the possibility of their use as antibiofilm drug compounds, which inhibit membrane transport of sugars in bacteria.

Background and purpose: Household drinking water treatment devices are becoming commonplace to improve the quality of drinking water, remove odor, taste, turbidity and color, pathogenic organisms, toxic chemicals, organic matter, and carcinogenic pollutants. This study aimed at investigating the Heterotrophic plate count (HPC) in drinking water and possibility of biofilm formation in household drinking water treatment devices in sari, Iran. Materials and methods: In a descriptive-analytical study, 100 samples were collected from the inlet and outlet reservoirs of urban drinking water distribution network and household water treatment systems according to the standard method in summer 2019. HPC culture was tested by spread plate method using R2A agar culture. Results: Among the samples studied, HPC was 12% higher than the standard level in 25% of urban water samples and 4% higher than the standard level in 18% of home water treatment system samples. Low residual chlorine in network and effluent of treatment devices and presence of heterotrophic bacteria in these samples, reinforces the possibility of biofilm growth on the network system and devices. The study showed significant relationship between lifetime of the filters, HPC, and residual chlorine (P

Biohydrogen is renewable and has a huge potential to replace fossil fuels. Understanding mechanisms of controlling microbial processes of the dynamic membrane is critical for effective dark fermentative biohydrogen production in a dynamic membrane bioreactor (DMBR). This paper aims to develop a sophisticated model of biofilm growth, dynamic membrane formation, and dark fermentative hydrogen production within a platform of coupled lattice Boltzmann and cellular automata. The model was validated against the experimental data available and then was applied for the investigation of biohydrogen production in bioreactors under different membrane structures and inlet velocities. The results showed that porous twisted channels in the dynamic membrane could significantly affect biohydrogen extraction and biofilm patterns. In all cases, the dynamic membrane formation has three phases: the initial bacteria deposit, stable biofilm growth, and stable maximum biofilm biomass. The biohydrogen production could increase by 16.4% by optimizing the porous structure and increase 30%–40% of the hydrogen extraction. Inlet velocity also affects biohydrogen extraction in a range of −28.3%–71.2%. Both porous structure and inlet velocity would be critical operational parameters for continuous biohydrogen production. The present model demonstrated its capability to investigate dark fermentative hydrogen production and its potential applications to porous bioreactors. • Develop a sophisticated model of dark fermentative biohydrogen production. • Integrate dark fermentation module with lattice Boltzmann-cellular automata model. • Examine the impacts of different porous structures and inlet velocities. • Investigate complex interactions of abiotic spatial heterogeneity and biotic processes. • Provide an integrated modeling tool for optimal design of microbioreactors. [ABSTRACT FROM AUTHOR]

The management of infections caused by Acinetobacter baumannii is hindered by its intrinsic tolerance to a wide variety of biocides. The aim of the study was to analyze the role of different A. baumannii efflux pumps (EPs) in tolerance to chlorhexidine (CHX) and benzalkonium (BZK) and identify non-toxic compounds, which can restore susceptibility to CHX and BZK in A. baumannii. A. baumannii ATCC 19606 strain was tolerant to both CHX and BZK with MIC and MBC value of 32 mg/L. CHX subMIC concentrations increased the expression of adeB and adeJ (RND superfamily), aceI (PACE family) and amvA (MFS superfamily) EP genes. The values of CHX MIC and MBC decreased by eightfold in Δ adeB and twofold in Δ amvA or Δ aceI mutants, respectively, while not affected in Δ adeJ mutant; EPs double and triple deletion mutants showed an additive effect on CHX MIC. CHX susceptibility was restored in double and triple deletion mutants with inactivation of adeB gene. BZK MIC was decreased by fourfold in Δ adeB mutant, and twofold in Δ amvA and Δ aceI mutants, respectively; EPs double and triple deletion mutants showed an additive effect on BZK MIC. BZK susceptibility was recovered in Δ adeB Δ aceI Δ adeJ and Δ amvA Δ adeB Δ adeJ triple mutants. The structural comparison of AdeB and AdeJ protomers showed a more negatively charged entrance binding site and F-loop in AdeB, which may favor the transport of CHX. The carbonyl cyanide m-chlorophenylhydrazine protonophore (CCCP) EP inhibitor reduced dose-dependently CHX MIC in A. baumannii ATCC 19606 and in Δ adeJ , Δ aceI , or Δ amvA mutants, but not in Δ adeB mutant. Either piperine (PIP) or resveratrol (RV) at non-toxic concentrations inhibited CHX MIC in A. baumannii ATCC 19606 parental strain and EPs gene deletion mutants, and CHX-induced EP gene expression. Also, RV inhibited BZK MIC and EP genes expression in A. baumannii ATCC 19606 parental strain and EPs mutants. These results demonstrate that tolerance to CHX and BZK in A. baumannii is mediated by the activation of AdeB, AceI and AmvA EPs, AdeB playing a major role. Importantly, inhibition of EP genes expression by RV restores CHX and BZK susceptibility in A. baumannii. [ABSTRACT FROM AUTHOR]

Photo fermentation is an emerging approach of biohydrogen production as it is energy saving and environmentally friendly. Understanding mechanisms of controlling the bacteria growth and biohydrogen production is critical for effective improvements in energy harvest and waste treatment in photo fermentative bioreactors. In this study a comprehensive three-dimensional numerical platform of photo fermentation was developed, based on lattice Boltzmann method coupled with cellular automata. The model accounts for photosynthetic bacteria growth, illumination energy conversion by photosynthetic bacteria, and light transfer under biofilm growth. The results showed a threshold of illumination intensity. Below this threshold, the bioreactor performance increased as the illumination intensity increased. Above the threshold, the performance declined if the illumination intensity rose. The normalized average biohydrogen production at the illumination intensity of 6000lx, increased about 66.31%, 13.82% and 13.12%, respectively, compared to ones at 4000lx, 5000lx and 7000lx. An increase in inlet glucose concentration could increase biohydrogen concentration and extraction but dwindled biohydrogen yield. It was found that a lower inlet velocity had higher biohydrogen production rate and concentration but lower biohydrogen extraction and yield. The results demonstrate that the present LBM-CA platform can be a tool to study and enhance the photo fermentative production of biohydrogen. • Present a refined model of biohydrogen production during photo fermentation. • Evaluate the effects of illumination, geometry and velocity on photo fermentation. • Accounts for photosynthetic bacteria growth and illumination energy conversion. • Provide an integrated modeling tool to improve design of photo microbioreactors. [ABSTRACT FROM AUTHOR]

To in situ and noninvasively monitor the biofilm development process by low-field nuclear magnetic resonance (NMR), experiments should be made to determine the mechanisms responsible for the T2 signals of biofilm growth. In this paper, biofilms were cultivated in both fluid media and saturated porous media. T2 relaxation for each sample was measured to investigate the contribution of the related processes to T2 relaxation signals. In addition, OD values of bacterial cell suspensions were measured to provide the relative number of bacterial cells. We also obtained SEM photos of the biofilms after vacuum freeze-drying the pure sand and the sand with biofilm formation to confirm the space within the biofilm matrix and identify the existence of biofilm formation. The T2 relaxation distribution is strongly dependent on the density of the bacterial cells suspended in the fluid and the stage of biofilm development. The peak time and the peak percentage can be used as indicators of the biofilm growth states. [ABSTRACT FROM AUTHOR]

The management of infections caused by Acinetobacter baumannii is hindered by its intrinsic tolerance to a wide variety of biocides. The aim of the study was to analyze the role of different A. baumannii efflux pumps (EPs) in tolerance to chlorhexidine (CHX) and benzalkonium (BZK) and identify non-toxic compounds, which can restore susceptibility to CHX and BZK in A. baumannii. A. baumannii ATCC 19606 strain was tolerant to both CHX and BZK with MIC and MBC value of 32 mg/L. CHX subMIC concentrations increased the expression of adeB and adeJ (RND superfamily), aceI (PACE family) and amvA (MFS superfamily) EP genes. The values of CHX MIC and MBC decreased by eightfold in ΔadeB and twofold in ΔamvA or ΔaceI mutants, respectively, while not affected in ΔadeJ mutant; EPs double and triple deletion mutants showed an additive effect on CHX MIC. CHX susceptibility was restored in double and triple deletion mutants with inactivation of adeB gene. BZK MIC was decreased by fourfold in ΔadeB mutant, and twofold in ΔamvA and ΔaceI mutants, respectively; EPs double and triple deletion mutants showed an additive effect on BZK MIC. BZK susceptibility was recovered in ΔadeB ΔaceI ΔadeJ and ΔamvA ΔadeB ΔadeJ triple mutants. The structural comparison of AdeB and AdeJ protomers showed a more negatively charged entrance binding site and F-loop in AdeB, which may favor the transport of CHX. The carbonyl cyanide m-chlorophenylhydrazine protonophore (CCCP) EP inhibitor reduced dose-dependently CHX MIC in A. baumannii ATCC 19606 and in ΔadeJ, ΔaceI, or ΔamvA mutants, but not in ΔadeB mutant. Either piperine (PIP) or resveratrol (RV) at non-toxic concentrations inhibited CHX MIC in A. baumannii ATCC 19606 parental strain and EPs gene deletion mutants, and CHX-induced EP gene expression. Also, RV inhibited BZK MIC and EP genes expression in A. baumannii ATCC 19606 parental strain and EPs mutants. These results demonstrate that tolerance to CHX and BZK in A. baumannii is mediated by the activation of AdeB, AceI and AmvA EPs, AdeB playing a major role. Importantly, inhibition of EP genes expression by RV restores CHX and BZK susceptibility in A. baumannii.

In nature, bacteria usually exist as mixed-species biofilms, where they engage in a range of synergistic and antagonistic interactions that increase their resistance to environmental challenges. Biofilms are a major cause of persistent infections, and dispersal from initial foci can cause new infections at distal sites thus warranting further investigation. Studies of development and spatial interactions in mixed-species biofilms can be challenging due to difficulties in identifying the different bacterial species in situ . Here, we apply CellTrace dyes to studies of biofilm bacteria and present a novel application for multiplex labeling, allowing identification of different bacteria in mixed-species, in vitro biofilm models. Oral bacteria labeled with CellTrace dyes (far red, yellow, violet, and CFSE [green]) were used to create single- and mixed-species biofilms, which were analyzed with confocal spinning disk microscopy (CSDM). Biofilm supernatants were studied with flow cytometry (FC). Both Gram-positive and Gram-negative bacteria were well labeled and CSDM revealed biofilms with clear morphology and stable staining for up to 4 days. Analysis of CellTrace labeled cells in supernatants using FC showed differences in the biofilm dispersal between bacterial species. Multiplexing with different colored dyes allowed visualization of spatial relationships between bacteria in mixed-species biofilms and relative coverage by the different species was revealed through segmentation of the CSDM images. This novel application, thus, offers a powerful tool for studying structure and composition of mixed-species biofilms in vitro .IMPORTANCEAlthough most chronic infections are caused by mixed-species biofilms, much of our knowledge still comes from planktonic cultures of single bacterial species. Studies of formation and development of mixed-species biofilms are, therefore, required. This work describes a method applicable to labeling of bacteria for in vitro studies of biofilm structure and dispersal. Critically, labeled bacteria can be multiplexed for identification of different species in mixed-species biofilms using confocal spinning disk microscopy, facilitating investigation of biofilm development and spatial interactions under different environmental conditions. The study is an important step in increasing the tools available for such complex and challenging studies., Competing Interests: The authors declare no conflict of interest.

This article reports the design and fabrication of open‐cell polyvinylidene fluoride (PVDF) foams as carriers that can promote biofilm growth and organic removal efficiency for biological wastewater treatment in attached growth bioreactors. Open‐cell PVDF foams were fabricated by a manufacturing approach that integrated compression molding and particulate leaching. PVDF carriers were structured with two governing factors of leaching agent types (e.g., sodium chloride [NaCl] and sodium acetate [NaOAc]) and contents (e.g., 80 and 90 wt%). Open‐cell PVDF foams possessed high porosity and high protected surface area (i.e., more than ×10 to ×20 of the areas of commercialized carriers), which promoted biofilm growth in these carriers. As a successful advantage, PVDF carriers used in the moving bed biofilm reactors (MBBR) were entirely covered by biofilm in both interior and exterior parts without clogging. This provides strong evidence of the bacterial compatibility of the fabricated open‐cell PVDF foam carriers. Moreover, the specific morphology of the PVDF carriers in this article provided superior biofilm protection from the detachment in MBBR. Experimental results revealed that PVDF open‐cell foams fabricated by 80 wt% of NaCl demonstrated higher mechanical strength with an organic removal efficiency of 77% ± 7% in the corresponding bioreactor containing them. [ABSTRACT FROM AUTHOR]

• Exogenous inhibitor weakened the biofilm proliferation and live cells dominance. • The control of biofilm proliferation was more pronounced relative to adhesion. • Inhibitor reduce expression of adhesion, virulence, motility and biofilm growth genes. • Stable and long-lasting quorum quenching can be effected at low dosage of inhibitor. • A new avenue for biofilm regulation and control of biofouling was proposed. Biofouling has been a persistent problem hindering the application of membranes in water treatment, and quorum quenching has been identified as an effective method for mitigating biofouling, but surface accumulation of live bacteria still induces biofilm secretion, which poses a significant challenge for sustained prevention of membrane biofouling. In this study, we utilized quercetin, a typical flavonoid with the dual functions of quorum quenching and bacterial inactivation, to evaluate its role in preventing biofilm proliferation and against biofouling. Quercetin exhibited excellent antibacterial activity against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), and the decreased bioactivity was positively correlated with the quercetin concentration, with inhibition rates of 53.1 % and 57.4 %, respectively, at the experimental concentrations. The RT-qPCR results demonstrated that quercetin inhibited AI-2 of E. coli and AGR of S. aureus mediated quorum sensing system, and reduced the expression of genes such as adhesion, virulence, biofilm secretion, and key regulatory proteases. As a result, the bacterial growth cycle was retarded and the biomass and biofilm maturation cycles were alleviated with the synergistic effect of quorum quenching and antibacterial activity. In addition, membrane biofouling was significantly declined in the dynamic operation experiments, dead cells in the biofilm overwhelmingly dominated, and the final normalized water fluxes were increased by more than 49.9 % and 34.5 % for E. coli and S. aureus , respectively. This work demonstrates the potential for mitigating biofouling using protocols that quorum quenching and inactivate bacteria, also provides a unique and long-lasting strategy to alleviate membrane fouling. [Display omitted] [ABSTRACT FROM AUTHOR]

We analysed the relationship between functional and structural variables (leaf litter decomposition, biofilms growth, primary productivity, invertebrate communities' taxonomic structure, and biological traits) and environmental conditions from headwaters into the estuary, which remains under-investigated. Six river sections (headwaters, middle reach, and four large river sections with increasing salinity) and 18 sites were selected in the Mondego river (Central Portugal). Hypotheses of the expected variations were drawn, based on theory (e.g. River Continuum Concept—RCC) and previous studies. Abiotic conditions were strongly associated with macroinvertebrate communities' taxonomic composition, but the relationship with functional parameters was different than the predicted one. Decomposition rates were similar from headwaters to the first large river sections (not expected) but increased in the estuarine sections. The high rates of decomposition were associated with the low salinity and especially with the high densities of the shredder Gammarus sp. Biofilm growth rate peaked in intermediate sections and was lower in the headwaters and in the estuary (not expected). The lower algae productivity in the estuary was not compensated by the heterotrophic component of the biofilm. The use of multiple biological traits indicated an unexpected higher functional similarity among the upper river sections, and differences within large river sections (not evident with taxonomic composition). These results show contradictions to widely accepted river concepts, such as the RCC, and highlight the importance of management practices adjusted to each river section to keep the ecosystem functioning. They also increased the knowledge on the transition zone between fresh and estuarine water which is important in the context of mitigation of climate change effects, considering the expected intrusion of saline water upstream. [ABSTRACT FROM AUTHOR]

Background and purpose:Household drinking water treatment devices are becoming commonplace to improve the quality of drinking water, remove odor, taste, turbidity and color, pathogenic organisms, toxic chemicals,organic matter, and carcinogenic pollutants. This study aimed at investigating the Heterotrophic plate count (HPC)in drinking water and possibility of biofilm formation in household drinking water treatment devices in sari, Iran.Materials and methods:In a descriptive-analytical study, 100 samples were collected from the inlet and outlet reservoirs of urban drinking water distribution network and household water treatment systems according to the standard method in summer 2019. HPC culture was tested by spread plate method using R2A agar culture.Results:Among the samples studied, HPC was 12% higher than the standard level in 25% of urban water samples and 4% higher than the standard level in 18% of home water treatment system samples. Low residual chlorine in network and effluent of treatment devices and presence of heterotrophic bacteria in these samples, reinforces the possibility of biofilm growth on the network system and devices. The study showed significant relationship between lifetime of the filters, HPC, and residual chlorine (P<0.001). Conclusion: Presence of HPC in network and effluent samples of house holddrinking water treatment devices and low residual chlorine in samples increases the rate of biofilm formation in network and devices even by small amounts. [ABSTRACT FROM AUTHOR]

A main challenge in the large-scale application of the microbially induced carbonate precipitation (MICP) technique includes the low efficiency of the cementation of coarse grains. Actually, in the MICP treatment process, the cementation effect of the bonding points was more important than pore filling due to the large porosity for coarse grains. To achieve a better cementation effect at bonding points between coarse particles, the quick formation and growth of a biofilm is necessary. In this study, an optimized medium was proposed to improve the cementation effects for coarse materials. The optimized medium and other different media were used for bio-cementation tests with MICP. The viable cell concentrations, strengths, microscopic characteristics, biofilm contents, and calcium carbonate (CaCO3) contents were used to evaluate the bio-cementation and its effects. In bio-cementation tests, the optimized medium led to increased CaCO3 precipitation at the bonding points and better cementation effects compared to other media. Indeed, the strength of the sample treated with the optimized medium was more than 1.2–4 times higher that of the values for other media. The advantages of the optimized medium were demonstrated via bio-cementation tests.

Abstract Background Several in vitro oral biofilm growth systems can reliably construct oral microbiome communities in culture, yet their stability and reproducibility through time has not been well characterized. Long-term in vitro growth of natural biofilms would enable use of these biofilms in both in vitro and in vivo studies that require complex microbial communities with minimal variation over a period of time. Understanding biofilm community dynamics in continuous culture, and whether they maintain distinct signatures of health and disease, is necessary to determine the reliability and applicability of such models to broader studies. To this end, we performed next-generation sequencing on biofilms grown from healthy and disease-site subgingival plaque for 80 days to assess stability and reliability of continuous oral biofilm growth. Results Biofilms were grown from subgingival plaque collected from periodontitis-affected sites and healthy individuals for ten eight-day long generations, using hydroxyapatite disks. The bacterial community in each generation was determined using Human Oral Microbe Identification by Next-Generation Sequencing (HOMINGS) technology, and analyzed in QIIME. Profiles were steady through the ten generations, as determined by species abundance and prevalence, Spearman’s correlation coefficient, and Faith’s phylogenetic distance, with slight variation predominantly in low abundance species. Community profiles were distinct between healthy and disease site-derived biofilms as demonstrated by weighted UniFrac distance throughout the ten generations. Differentially abundant species between healthy and disease site-derived biofilms were consistent throughout the generations. Conclusions Healthy and disease site-derived biofilms can reliably maintain consistent communities through ten generations of in vitro growth. These communities maintain signatures of health and disease and of individual donors despite culture in identical environments. This subgingival oral biofilm growth and perpetuation model may prove useful to studies involving oral infection or cell stimulation, or those measuring microbial interactions, which require the same biofilms over a period of time.

In this article, we consider a system of two coupled nonlinear diffusion–reaction partial differential equations (PDEs) which model the growth of biofilm and consumption of the nutrient. At the scale of interest the biofilm density is subject to a pointwise constraint, thus the biofilm PDE is framed as a parabolic variational inequality. We derive rigorous error estimates for a finite element approximation to the coupled nonlinear system and confirm experimentally that the numerical approximation converges at the predicted rate. We also show simulations in which we track the free boundary in the domains which resemble the pore scale geometry and in which we test the different modeling assumptions. [ABSTRACT FROM AUTHOR]

The properties of biocarriers significantly influence the performance of a moving bed-biofilm reactor (MBBR). This study aimed to assess the impact of media type, filling ratio, and hydraulic retention time (HRT) on biofilm formation and MBBR performance in both batch and continuous setups using real municipal wastewater. Two different media, high-density polyethylene (HDPE) and polypropylene (PPE), with varying surface area and properties were used. Biofilm growth and MBBR performance were monitored and optimized using response surface methodology. The effect of different media was investigated for three filling ratios of 20%, 40% and 60% and HRT of 4, 6 and 8 h. Results depicted a better biofilm growth on HDPE media in comparison to PPE carriers due to difference in media structure and surface properties. At all the conditions tested, HDPE media showed comparatively better performance for the removal of organic matter and nutrients than PPE media. The maximum organic matter removal efficiency was found as 77% and 75% at an HRT of 6 h and filling ratio of 40% for HDPE and PPE media, respectively. The ammonia removal was also found better for HDPE media due to its geometry and structure favoring the anoxic conditions with maximum removal of 89% achieved at 6-h HRT and 40% filling ratio. Overall, the system with HDPE media indicated more stability in terms of reactor performance than PPE carriers with variations in the operating conditions. • Two types of media were used for the operation of the moving bed biofilm reactor. • High-density polyethylene (HDPE) and polypropylene (PPE) media were used. • HDPE media performed better than the PPE media for the growth of biofilm. • Response surface methodology was used to optimize the operating parameters. • For PPE carrier the efficiency improved with increase in surface area. [ABSTRACT FROM AUTHOR]

Biofilm, a colony forming cooperative response of microorganisms under environmental stress, is a major concern for food safety, water safety and drug resistance. Most current works focus on controlling biofilm growth by targeting single genes. Here, the authors investigated transcriptome-wide expressions of the yeast Saccharomyces cerevisiae biofilm in wildtype, and six previously identified biofilm regulating overexpression strains. Using statistical distributions for low expression filter (TPM > 5), Pearson auto- and cross-correlations reveal a strong transcriptome-wide invariance among all genotypes. The 50 highly expressed genes, however, differ significantly between the genotypes. Principal components analysis shows the global similarity between most overexpression strains. Thus, though single overexpression strains may show significant favourable local and acute expression changes (short-range disorder), the almost unperturbed global and collective structure between the genotypes indicate gradual adaptive response converging to original stable biofilm states (long-range order). Hierarchical clustering and gene ontology show 11 groups of local (e.g. mitochondria processes, amine and nucleotide metabolic processes) and 6 groups of global (e.g. transcription, translation and cell cycle) processes for all genotypes. The overall data indicate that there is a strong global regulatory structure that keeps the overall biofilm stable in all investigated strains.

In this paper, a thermodynamically consistent visco-elastic growth model driven by nutrient diffusion is presented in the finite deformation framework. Growth phenomena usually occur in biological tissues. Systems involving growth are known to be open systems with a continuous injection of mass into the system which results in volume expansion. Here the growth is driven by the diffusion of a nutrient. It implies that the diffusion equation for the nutrient concentration needs to be solved in conjunction with the conservation equation of mass and momentum. Hence, the problem falls into the multi-physics class. Additionally, a viscous rheological model is introduced to account for stress relaxation. Although the emergence of residual stresses is inherent to the growth process, the viscous behaviour of the material determines to what extend such stresses remain in the body. The numerical implementation is performed using the symbolic tool Ace-Gen while employing a fully implicit and monolithic scheme. [ABSTRACT FROM AUTHOR]

Highlights • A complex and sophisticated mathematical model at the pore scale has been developed for simulating biofilm growth, fluid flow, and the dissolution of immobile non-aqueous-phase-liquids (NAPLs). • A series of numerical simulations were conducted to investigate the mechanisms involved in the enhanced dissolution of the NAPLs due to microbial activity. • The model can be used to validate assumptions which are typically invoked to simplify upscaling of NAPL dissolution to larger scales. Abstract In this paper, we introduce a pore-scale model to study the interaction between biofilm growth and non-aqueous-phase-liquid (NAPL) dissolution. Liquid flow and dissolved NAPL transport are coupled with a biofilm growth model to correctly describe the complex dynamics of the processes including fluid flow, NAPL dissolution/biodegradation and biofilm growth. Fluid flow is simulated using an immersed boundary-lattice Boltzmann (IB-LB) model; while solute transport is solved by a cut-cell finite volume method (FVM). A uniform dissolution approach is also adopted to capture the temporal evolution of trapped blobs. Spatio-temporal distributions of the biomass are investigated using a cellular automaton algorithm combined with the immersed boundary method (IBM). Simulations focused on NAPL dissolution in both abiotic and biotic conditions are conducted to assess the capability of the model. In abiotic conditions, we analyze the effects of the hydrodynamic regimes and the spatial distribution of NAPL blobs on the dissolution rate under different assumptions (i.e., blob size and Péclet number). In biotic conditions, a series of impact factors are also investigated (i.e., spatial distribution, reaction kinetics and NAPL-induced toxicity). Finally, the current model is used to evaluate the pore scale relevance of a local equilibrium assumption between fluid phase and biofilm phase in the vicinity of the NAPL source. [ABSTRACT FROM AUTHOR]

Highlights • Glassy carbon electrode is modified with a dispersion of Y zeolite and graphite. • Zeolite changes the electrode surface hydrophobicity favoring the growth of a biofilm. • The modified anodes have an electroactive biofilm with electrochemical activity for acetate oxidation. • The presence of Fe species promotes electron transfer properties of anode. Abstract The performance of microbial fuel cells (MFCs) is highly dependent on the electrode materials. The electrode surface can be modified to provide a favorable environment for biofilms to enhance electron transfer from the bacteria to the anode. In this work, Faujasite zeolite-Y (ZY) was exchanged with iron (Fe) and was used to modify glassy carbon/graphite electrodes (GC/gr-ZY Fe) evaluating its effect in electroactive biofilm development for application in microbial fuel cells. The novel material was evaluated as an anode in MFCs by comparing its performance with GC/gr and GC/gr-ZY electrodes. The results show that when using a GC/gr-ZY Fe electrode, an electroactive biofilm with good electrochemical activity for acetate degradation can be generated on the electrode surface. The maximum current density obtained with a GC/gr-ZY Fe -BF electrode (where BF is biofilm) was 7.7 times higher than that of a GC/gr anode. The modification generates a less hydrophobic electrode surface that facilitates microbial cell attachment, thereby improving bioelectricity production. By using scanning electron microscopy, a homogeneous microbial community with bacteria that had a similar short rod-shaped morphology was observed. Furthermore, electrochemical impedance spectroscopy demonstrated that the charge transfer resistance (R ct) decreased as the biofilm grew, revealing that the presence of the biofilm facilitated the electrochemical reaction. After 7 days of MFC operation, the GC/gr-ZY Fe bioanode showed a reduction in R ct from 212.9 ± 1.81 Ω to 151.5 ± 1.46 Ω, which was 2.4 times lower than that achieved with GC/gr. The biofilm on GC/gr-ZY Fe was characterized using cyclic voltammetry, and the results showed a larger oxidation peak (169.8 μA cm−2) than that of the GC/gr electrode (36.5μA cm−2), further supporting the better electron-transfer properties of the modified electrode. Additionally, this result confirms the capability of biofilms to act as bioelectrocatalysts under acetate-oxidizing conditions. [ABSTRACT FROM AUTHOR]

Abstract The aim of this study was to gain comprehensive insights into the characteristics of antibiotic resistance genes (ARGs) in multiphase samples from drinking water distribution pipelines using a simulated biofilm reactor. During 120 d of continuous operation, common parameters and six ARGs (ermA , ermB , aphA2 , ampC , sulII , and tetO) in samples of three phases (water, particle, and biofilm) from the reactor were investigated, which demonstrated secondary contamination by ARGs. Abundances of the six ARGs in the reactor effluent increased gradually, and in the 120 d effluent, the relative abundances of aphA2 and sulII were the highest, at 9.9 × 10−4 and 1.3 × 10−3, respectively, with a 1.5-fold and 2.8-fold increase, compared with those in the influent. The relative abundances of the six ARGs in the biofilm phase increased significantly (P < 0.05) at 120 d, which was caused by robust bacteria in biofilm that was newly exposed following the detachment of a large piece of aging biofilm. In the particle phase, four of the ARGs did not change significantly during the 120 d period. The six ARGs in the samples of three phases showed a negative correlation with residual chlorine in the pipe water, which demonstrated that low abundance of ARGs in the samples of three phases was related to the improvement of residual chlorine. The proportion of cultivable bacteria illustrated that the robust and active bacteria were negatively correlated with the six ARGs in the biofilm. Total organic carbon (TOC) in the pipeline showed a positive correlation with the proportion of cultivable bacteria in both the water and biofilm phases, which indicated that a TOC reduction in the pipeline contributed to low abundance of ARGs. With low-pressure ultraviolet (LP-UV) irradiation of 20 mJ/cm2, ARGs in the samples of three phases were efficiently controlled, which showed that LP-UV can be used for ARG removal in terminal water for supplemental bactericidal treatment of pipeline effluent. Graphical abstract Unlabelled Image Highlights • A simulated distribution system was used to explore antibiotic resistance genes (ARGs) occurrence. • Six ARGs in effluent increased gradually during the running time. • Six ARGs in samples of three phases have negative correlation with chlorine in pipe. • Reduction of total organic carbon in water contributes to low-abundance of ARGs. • Five ARGs in samples of three phases were controlled by low-pressure ultraviolet. [ABSTRACT FROM AUTHOR]

In this work, we model the biofilm growth at the microscale using a rectangular pore network model in 2D and a cubic network in 3D. For the 2D network, we study the effects of bioclogging on porosity and permeability when we change parameters like the number of nodes in the network, the network size, and the concentration of nutrients at the inlet. We use a 3D cubic network to study the influence of the number of nodes in the z direction on the biofilm growth and on upscalability. We show that the biofilm can grow uniformly or heterogeneously through the network. Using these results, we determine the conditions for upscalability of bioclogging for rectangular and cubic networks. If there is uniform biofilm growth, there is a unique relation between permeability and porosity, K ∼ ϕ2, this relation does not depend on the volume of the network, therefore the system is upscalable. However, if there is preferential biofilm growth, the porosity-permeability relation is not uniquely defined, hence upscalability is not possible. The Damköhler number is used to determine when upscalability is possible. If the Damköhler number is less than 101, the biofilm grows uniformly and therefore the system is upscalable. However, if the Damköhler number is greater than 103, the biofilm growth exhibits a deviation from uniform biofilm growth and heterogeneous growth is observed, therefore upscalability is not possible. There is a transition from uniform growth to preferential growth if the Damköhler number is between 101 and 103. [ABSTRACT FROM AUTHOR]

Highlights • The biomineral flocs in the Belgian coast were investigated during two contrasting periods. • The observed floc size distributions were decomposed to represent microflocs, macroflocs and megaflocs. • A simple flocculation model that can describe the biofilm growth of flocs was developed. • This model was successfully implemented in the open TELEMAC with five passive tracers. Abstract The Floc Size Distributions (FSDs) of biomineral suspended particles are of great importance to understand the dynamics of bio-mediated Suspended Particulate Matters (SPMs). Field observations were investigated at Station MOW1 in Belgian coastal waters (southern North Sea) during two typical periods with abundant and reduced biomass. In addition, the Shen et al. (2018) [Water Res. Vol 145, pp 473–486] multi-class population balance flocculation model was extended to address the occurrence of suspended microflocs, macroflocs and megaflocs during these contrasting periods. The microflocs are treated as elementary particles that constitute macroflocs or megaflocs. The FSD is represented by the size and mass fraction of each particle group, which corresponds to a temporal and spatial varying mass weighted settling velocity. The representative sizes of macroflocs and megaflocs are unfixed and migrated between classes mainly due to the effects of turbulent shear, differential settling and biofilm growth. The growth of an aggregate because of bio-activities is allotted to each elementary particle. It is further hypothesized that the growth kinetics of biomineral particles due to biofilm coating follows the logistic equation. This simple bio-flocculation model has been successfully coupled in the open source TELEMAC modeling system with five passive tracers in a quasi-1D vertical case. Within an intra-tide scale, the settling velocity (w s) is large during slack tides while it is small during maximum current velocities because of variations in turbulence intensities. Nonetheless, the w s may be largely underestimated when the biological effect is neglected. For a seasonal pattern, the w s is higher in biomass-rich periods in May than in biomass-poor periods in October. While the mean sizes of megaflocs are close during the two periods, the macroflocs during algae bloom periods are more abundant with a larger mean size. This study enhances our knowledge on the dynamics of SPMs, especially the biophysical influences on the fate and transport of estuarine aggregates. [ABSTRACT FROM AUTHOR]

The VicRK 2-component system of Streptococcus mutans regulates genes associated with cell wall biogenesis and biofilm formation. A putative RNase III-encoding gene ( rnc) is located downstream from the vicRKX operon. The goals of this study were to investigate the potential role of VicR in the regulation of adjacent downstream genes and evaluate transcription levels of vicR during planktonic and biofilm growth. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to investigate whether vicRKX and adjacent downstream genes were cotranscribed. Binding of purified recombinant VicR protein to promoter regions of vicR, rnc, and syfA genes was confirmed by electrophoretic mobility shift assay and by chromatin immunoprecipitation analyses. VicR antisense (AS vicR) RNA was detected by Northern blotting and qRT-PCR assays. AS vicR overexpression mutants were constructed, and the biofilm biomass was determined by crystal violet microtiter assay. Adjacent downstream genes rnc, smc, syfA, smu.1511, and syfB were cotranscribed with vicRKX. The predicted promoter regions of vicR, rnc, and syfA genes were directly regulated by VicR. An AS vicR RNA transcript was detected upstream of the rnc gene. Expression of the AS vicR RNA transcript was elevated in planktonic cultures and repressed during biofilm growth. In addition, Western blot data showed that expression of the VicR protein decreased by 35% in planktonic as compared with biofilm cultures. Furthermore, we show that overexpression of AS vicR led to a reduction in biofilm formation. The downstream genes rnc, smc, syfA, smu.1511, and syfB are cotranscribed with vicRKX. VicR is autophosphorylated, and rnc and syfA are directly regulated by VicR. Expression of VicR protein correlated inversely with different levels of AS vicR RNA transcript and growth conditions. The biofilm biomass decreased in the AS vicR overexpression mutant. These data suggest a role for the AS vicR RNA transcript in posttranscriptional regulation of VicR protein production in S. mutans. [ABSTRACT FROM AUTHOR]

• A coupling algorithm of flow at pore-scale and porous medium permeability at REV-scale. • Spatial and temporal characteristics of microbial growth at pore-scale. • The equivalent porosity change with time caused by microbial growth. • The linear relationship between clogging periods at REV-scale and pore-scale. In this study, a novel algorithm coupling the flow at the pore and representative elementary volume (REV) scales was developed to analyze the effect of microbial growth at the pore scale on the permeability decay of porous media at the REV scale. This provides a new method for investigating microbial clogging in porous media. At the pore scale, an immersed boundary-lattice Boltzmann model was used to simulate the flow field and solute transportation in porous media, and the cellular automata (CA) model was employed to investigate microbial growth. According to Ergun's empirical relationship, the equivalent porosity change at the pore scale caused by microbial growth was calculated and used in a generalised seepage model describing the fluid flow in the porous medium at the REV scale. First, the microbial growth experiments were conducted to validate the coupling algorithm. Second, the spatial and temporal characteristics of microbial growth at the pore scale were analyzed. Third, we investigated the effects of nutrient inlet concentrations and pH on microbial growth at the pore scale and the macroscopic permeability properties of porous media. The main results are as follows. (1) Microbial growth changes the local porosity and dominant flow path. Spatial non-uniformity in microbial growth depends on the availability of nutrients in the dominant flow path. (2) The discrepancy in microbial growth under different nutrient inlet concentrations was gradually amplified from the pore scale to the REV scale. (3) The microbial clogging period was the shortest at a pH of 6.7. When the pH was >6.7, the microbial clogging period slightly increased at a rate of 6.1 h/pH. When the pH was <6.7, the microbial clogging period increased significantly with decreasing pH at a rate of 20.0 h/pH. (4) A linear relationship was observed between the microbial clogging periods at the REV and pore scales, which enriches the theory about microbial clogging in porous medium. [ABSTRACT FROM AUTHOR]

Biofilm communities of Bacillus subtilis bacteria have recently been shown to exhibit collective growth-rate oscillations mediated by electrochemical signaling to cope with nutrient starvation. These oscillations emerge once the colony reaches a large enough number of cells. However, it remains unclear whether the amplitude of the oscillations, and thus their effectiveness, builds up over time gradually or if they can emerge instantly with a nonzero amplitude. Here we address this question by combining microfluidics-based time-lapse microscopy experiments with a minimal theoretical description of the system in the form of a delay-differential equation model. Analytical and numerical methods reveal that oscillations arise through a subcritical Hopf bifurcation, which enables instant high-amplitude oscillations. Consequently, the model predicts a bistable regime where an oscillating and a nonoscillating attractor coexist in phase space. We experimentally validate this prediction by showing that oscillations can be triggered by perturbing the media conditions, provided the biofilm size lies within an appropriate range. The model also predicts that the minimum size at which oscillations start decreases with stress, a fact that we also verify experimentally. Taken together, our results show that collective oscillations in cell populations can emerge suddenly with nonzero amplitude via a discontinuous transition. [ABSTRACT FROM AUTHOR]

The chemolithoautotrophic biofilm growth of Cupriavidus necator on a platinum cathode is presented. Different current densities from 0 to − 2000 µA/cm2 were investigated. − 500 µA/cm2 was selected as the favourable current density for most optimal hydrogen production for biofilm growth. Lower and higher current densities cause a lower microbial surface coverage due to higher cell death because of nutrient deficiency or due to a fast hydrogen saturation of the medium solution where no impulse is present for the microorganisms to grow at the cathodic surface. The first microbial attachment of Cupriavidus necator and its surface coverage can lead to better understanding of biofilm development and control. [ABSTRACT FROM AUTHOR]

Two non-destructive techniques, confocal laser scanning microscopy (CLSM) and planar optode (VisiSens imaging), were combined to relate the fine-scale spatial structure of biofilm components to real-time images of oxygen decay in aquatic biofilms. Both techniques were applied to biofilms grown for seven days at contrasting light and temperature (10/20°C) conditions. The geo-statistical analyses of CLSM images indicated that biofilm structures consisted of small (~100 μm) and middle sized (~101 μm) irregular aggregates. Cyanobacteria and EPS (extracellular polymeric substances) showed larger aggregate sizes in dark grown biofilms while, for algae, aggregates were larger in light-20°C conditions. Light-20°C biofilms were most dense while 10°C biofilms showed a sparser structure and lower respiration rates. There was a positive relationship between the number of pixels occupied and the oxygen decay rate. The combination of optodes and CLMS, taking advantage of geo-statistics, is a promising way to relate biofilm architecture and metabolism at the micrometric scale. [ABSTRACT FROM AUTHOR]