Estimation of a biofilm-specific reaction rate: kinetics of bacterial urea hydrolysis in a biofilm

Start-up and performance of a downflow fluidised bed reactor for biological treatment of yellow wastewater and nutrient recovery

The treatment of yellow water (human urine) in a downflow fluidised bed reactor (DFFBR) was investigated to evaluate biological ureolysis and nutrient recovery. The reactor was operated at 30±4 °C in batch mode, and reaction time = 1 d. The average immobilised biomass (as volatile solids, IVS) in the reactor was 2.5±0.9 g L^-1_support, and specific ureolytic activity was 121 g Urea-N g^-1 IVS d^-1. The kinetic parameters were 0.152 mol L^-1 (K_m) and 8 mol g^-1 IVS d^-1 (V_max). The ureolysis efficiency was 93.4% and chemical oxygen demand removal efficiency was 31.2%, while total ammonium nitrogen (NH₄⁺-N) production rate was 7 g L^-1 d^-1 and phosphate removal reached 26%. Precipitates recovery during biological treatment was 1.72±0.8 g. These results suggest that the treatment of yellow water in a DFFBR is a viable option for partial recovery of N and P.

Spatiotemporal Distribution of Precipitates and Mineral Phase Transition During Biomineralization Affect Porosity–Permeability Relationships

Enzymatically induced calcium carbonate precipitation is a promising geotechnique with the potential, for example, to seal leakage pathways in the subsurface or to stabilize soils. Precipitation of calcium carbonate in a porous medium reduces the porosity and, consequently, the permeability. With pseudo-2D microfluidic experiments, including pressure monitoring and, for visualization, optical microscopy and X-ray computed tomography, pore-space alterations were reliably related to corresponding hydraulic responses. The study comprises six experiments with two different pore structures, a simple, quasi-1D structure, and a 2D structure. Using a continuous injection strategy with either constant or step-wise reduced flow rates, we identified key mechanisms that significantly influence the relationship between porosity and permeability. In the quasi-1D structure, the location of precipitates is more relevant to the hydraulic response (pressure gradients) than the overall porosity change. In the quasi-2D structure, this is different, because flow can bypass locally clogged regions, thus leading to steadier porosity–permeability relationships. Moreover, in quasi-2D systems, during continuous injection, preferential flow paths can evolve and remain open. Classical porosity–permeability power-law relationships with constant exponents cannot adequately describe this phenomenon. We furthermore observed coexistence and transformation of different polymorphs of calcium carbonate, namely amorphous calcium carbonate, vaterite, and calcite and discuss their influence on the observed development of preferential flow paths. This has so far not been accounted for in the state-of-the-art approaches for porosity–permeability relationships during calcium carbonate precipitation in porous media.

Controlling pore-scale processes to tame subsurface biomineralization

Microorganisms capable of biomineralization can catalyze mineral precipitation by modifying local physical and chemical conditions. In porous media, such as soil and rock, these microorganisms live and function in highly heterogeneous physical, chemical and ecological microenvironments, with strong local gradients created by both microbial activity and the pore-scale structure of the subsurface. Here, we focus on extracellular bacterial biomineralization, which is sensitive to external heterogeneity, and review the pore-scale processes controlling microbial biomineralization in natural and engineered porous media. We discuss how individual physical, chemical and ecological factors integrate to affect the spatial and temporal control of biomineralization, and how each of these factors contributes to a quantitative understanding of biomineralization in porous media. We find that an improved understanding of microbial behavior in heterogeneous microenvironments would promote understanding of natural systems and output in diverse technological applications, including improved representation and control of fluid mixing from pore to field scales. We suggest a range of directions by which future work can build from existing tools to advance each of these areas to improve understanding and predictability of biomineralization science and technology.

Experimental Designs to Study the Aggregation and Colonization of Biofilms by Video Microscopy With Statistical Confidence

The goal of this study was to quantify the variability of confocal laser scanning microscopy (CLSM) time-lapse images of early colonizing biofilms to aid in the design of future imaging experiments. To accomplish this a large imaging dataset consisting of 16 independent CLSM microscopy experiments was leveraged. These experiments were designed to study interactions between human neutrophils and single cells or aggregates of Staphylococcus aureus (S. aureus) during the initial stages of biofilm formation. Results suggest that in untreated control experiments, variability differed substantially between growth phases (i.e., lag or exponential). When studying the effect of an antimicrobial treatment (in this case, neutrophil challenge), regardless of the inoculation level or of growth phase, variability changed as a frown-shaped function of treatment efficacy (i.e., the reduction in biofilm surface coverage). These findings were used to predict the best experimental designs for future imaging studies of early biofilms by considering differing (i) numbers of independent experiments; (ii) numbers of fields of view (FOV) per experiment; and (iii) frame capture rates per hour. A spreadsheet capable of assessing any user-specified design is included that requires the expected mean log reduction and variance components from user-generated experimental results. The methodology outlined in this study can assist researchers in designing their CLSM studies of antimicrobial treatments with a high level of statistical confidence.

Comprehensive Profiling of Microbiologically Induced CaCO3 Precipitation by Ureolytic Bacillus Isolates from Alkaline Soils

Microbiologically induced CaCO3 precipitation (MICP) is a well-known bio-based solution with application in environmental, geotechnical, and civil engineering. The significance of the MICP has increased explorations of process efficiency and specificity via natural bacterial isolates. In this study, comprehensive profiling of five soil ureolytic Bacillus strains was performed through a newly formed procedure that involved six steps from selection and identification, through kinetic study, to the characterization of the obtained precipitates, for the first time. To shorten the whole selection procedure of 43 bioagents with the MICP potential, Standard Score Analysis was performed and five selected bacteria were identified as Bacillus muralis, B. lentus, B. simplex, B. firmus, and B. licheniformis by the MALDI-TOF mass spectrometry. Despite following the targeted activity, kinetic studies were included important aspects of ureolysis and the MICP such as cell concentration, pH profiling, and reduction in calcium ion concentration. At the final step, characterization of the obtained precipitates was performed using FTIR, XRD, Raman, DTA/TGA, and SEM analysis. Although all tested strains showed significant potential in terms of precipitation of calcite or calcite and vaterite phase, the main differences in the MICP behavior can be observed at the bacterial strain level. B. licheniformis showed favorable behavior compared to the reference Sporosarcina pasteurii DSM 33.

A Novel Method to Reveal a Ureolytic Biofilm Attachment and In Situ Growth Monitoring by Electrochemical Impedance Spectroscopy

The formation of biofilms capable of efficiently carrying out ureolysis is of fundamental importance in several biotechnological systems such as urinary tract infections, building materials and municipal wastewater treatment. This work proposes a straightforward method for the formation of a ureolytic biofilm attached to graphite. The proposed strategy reduced the time needed to complete ureolysis to 3 days instead of 16 days required in suspension culture. To confirm the formation of a ureolytic biofilm, scanning electron microscopy and confocal laser scanning microscopy studies were employed ex situ. However, it is imperative to analyse the biofilm by direct non-invasive techniques. Accordingly, open circuit potential (OCP) and electrochemical impedance spectroscopy (EIS) were used as in situ monitoring techniques. The reduction in OCP from - 0.01 to - 0.2 V vs. Ag/AgCl and the increase in capacitance from 200 to 260 μF cm^-2 were related to biofilm attachment. To the best of our knowledge, this is the first time in which a ureolytic biofilm attachment has been analysed by EIS. The increase in the biomass from 0.04 to 2.81 μm³ μm^-2 and in average thickness from 10.19 to 32.78 μm was related to biofilm maturation.

Current insights into the mechanisms and management of infection stones

Infection stones are complex aggregates of crystals amalgamated in an organic matrix that are strictly associated with urinary tract infections. The management of patients who form infection stones is challenging owing to the complexity of the calculi and high recurrence rates. The formation of infection stones is a multifactorial process that can be driven by urine chemistry, the urine microenvironment, the presence of modulator substances in urine, associations with bacteria, and the development of biofilms. Despite decades of investigation, the mechanisms of infection stone formation are still poorly understood. A mechanistic understanding of the formation and growth of infection stones - including the role of organics in the stone matrix, microorganisms, and biofilms in stone formation and their effect on stone characteristics - and the medical implications of these insights might be crucial for the development of improved treatments. Tools and approaches used in various disciplines (for example, engineering, chemistry, mineralogy, and microbiology) can be applied to further understand the microorganism-mineral interactions that lead to infection stone formation. Thus, the use of integrated multidisciplinary approaches is imperative to improve the diagnosis, prevention, and treatment of infection stones.

Pseudomonas aeruginosa β-carbonic anhydrase, psCA1, is required for calcium deposition and contributes to virulence

Calcification of soft tissue leads to serious diseases and has been associated with bacterial chronic infections. However, the origin and the molecular mechanisms of calcification remain unclear. Here we hypothesized that a human pathogen Pseudomonas aeruginosa deposits extracellular calcium, a process requiring carbonic anhydrases (CAs). Transmission electron microscopy confirmed the formation of 0.1-0.2 μm deposits by P. aeruginosa PAO1 growing at 5 mM CaCl₂, and X-ray elemental analysis confirmed they contain calcium. Quantitative analysis of deposited calcium showed that PAO1 deposits 0.35 and 0.75 mM calcium/mg protein when grown at 5 mM and 10 mM CaCl₂, correspondingly. Fluorescent microscopy indicated that deposition initiates at the cell surface. We have previously characterized three PAO1 β-class CAs: psCA1, psCA2, and psCA3 that hydrate CO₂ to HCO₃^-, among which psCA1 showed the highest catalytic activity (Lotlikar et. al. 2013). According to immunoblot and RT-qPCR, growth at elevated calcium levels increases the expression of psCA1. Analyses of the deletion mutants lacking one, two or all three psCA genes, determined that psCA1 plays a major role in calcium deposition and contributes to the pathogen's virulence. In-silico modeling of the PAO1 β-class CAs identified four amino acids that differ in psCA1 compared to psCA2, and psCA3 (T59, A61A, A101, and A108), and these differences may play a role in catalytic rate and thus calcium deposition. A series of inhibitors were tested against the recombinant psCA1, among which aminobenzene sulfonamide (ABS) and acetazolamide (AAZ), which inhibited psCA1 catalytic activity with K_Is of 19 nM and 37 nM, correspondingly. The addition of ABS and AAZ to growing PAO1 reduced calcium deposition by 41 and 78, respectively. Hence, for the first time, we showed that the β-CA psCA1 in P. aeruginosa contributes to virulence likely by enabling calcium salt deposition, which can be partially controlled by inhibiting its catalytic activity.

Real-Time Monitoring and Control of Urea Hydrolysis in Cyber-Enabled Nonwater Urinal System

This research used a cyber-physical system (CPS) to monitor and control the extent of urea hydrolysis in nonwater urinals. Real-time pH and conductivity data were used to control urea hydrolysis inhibition under realistic restroom conditions with acetic acid addition. Variable urination frequencies and urination volumes were used to compare three conditions that affect the progression of urea hydrolysis. Mechanistic and conceptual models were created to evaluate the factors that influence the progression of urea hydrolysis in nonwater urinals. It was found that low urination volumes at low frequencies created ideal conditions for urea hydrolysis to progress. Alternatively, high urination volumes at high frequencies created pseudo-inhibitory conditions because it did not allow for sufficient reaction time or mixing with older urine in the urinal trap. The CPS was used to control urea hydrolysis inhibition by two logics: (1) reactively responding to a pH threshold and (2) predictively responding to past measurements using four lasso regression models. Results from the control logic experiments showed that acid was added once per hour under low use conditions and once in a 4 h experiment for high use conditions. The CPS allowed for full control of urine chemistry in the nonwater urinal, reducing the conditions (i.e., clogging and malodor) that have led to the removal of nonwater urinals in the United States.

Net growth rate of continuum heterogeneous biofilms with inhibition kinetics

Biofilm systems can be modeled using a variety of analytical and numerical approaches, usually by making simplifying assumptions regarding biofilm heterogeneity and activity as well as effective diffusivity. Inhibition kinetics, albeit common in experimental systems, are rarely considered and analytical approaches are either lacking or consider effective diffusivity of the substrate and the biofilm density to remain constant. To address this obvious knowledge gap an analytical procedure to estimate the effectiveness factor (dimensionless substrate mass flux at the biofilm-fluid interface) was developed for a continuum heterogeneous biofilm with multiple limiting-substrate Monod kinetics to different types of inhibition kinetics. The simple perturbation technique, previously validated to quantify biofilm activity, was applied to systems where either the substrate or the inhibitor is the limiting component, and cases where the inhibitor is a reaction product or the substrate also acts as the inhibitor. Explicit analytical equations are presented for the effectiveness factor estimation and, therefore, the calculation of biomass growth rate or limiting substrate/inhibitor consumption rate, for a given biofilm thickness. The robustness of the new biofilm model was tested using kinetic parameters experimentally determined for the growth of Pseudomonas putida CCRC 14365 on phenol. Several additional cases have been analyzed, including examples where the effectiveness factor can reach values greater than unity, characteristic of systems with inhibition kinetics. Criteria to establish when the effectiveness factor can reach values greater than unity in each of the cases studied are also presented.

Ureolytic Activity and Its Regulation in Vibrio campbellii and Vibrio harveyi in Relation to Nitrogen Recovery from Human Urine

Human urine contains a high concentration of nitrogen and is therefore an interesting source for nutrient recovery. Ureolysis is a key requirement in many processes aiming at nitrogen recovery from urine. Although ureolytic activity is widespread in terrestrial and aquatic environments, very little is known about the urease activity and regulation in specific bacteria other than human pathogens. Given the relatively high salt concentration of urine, marine bacteria would be particularly well suited for biotechnological applications involving nitrogen recovery from urine, and therefore, in this study, we investigated ureolytic activity and its regulation in marine vibrios. Thirteen out of 14 strains showed ureolytic activity. The urease activity was induced by urea, since complete and very rapid hydrolysis, up to 4 g L^-1 h^-1 of urea, was observed in synthetic human urine when the bacteria were pretreated with 10 g L^-1 urea, whereas slow hydrolysis occurred when they were pretreated with 1 g L^-1 urea (14-35% hydrolysis after 2 days). There was no correlation between biofilm formation and motility on one hand, and ureolysis on the other hand, and biofilm and motility inhibitors did not affect ureolysis. Together, our data demonstrate for the first time the potential of marine vibrios as fast urea hydrolyzers for biotechnological applications aiming at nutrient recovery from human urine.