Cristian Picioreanu

The membrane bioreactor: A novel tool to grow anammox bacteria as free cells

In a membrane bioreactor (MBR), fast growth of anammox bacteria was achieved with a sludge residence time (SRT) of 12 days. This relatively short SRT resulted in a—for anammox bacteria—unprecedented purity of the enrichment of 97.6%. The absence of a selective pressure for settling, and dedicated cultivation conditions led to growth in suspension as free cells and the complete absence of flocs or granules. Fast growth, low levels of calcium and magnesium, and possibly the presence of yeast extract and a low shear stress are critical for the obtainment of a completely suspended culture consisting of free anammox cells. During cultivation, a population shift was observed from Candidatus “Brocadia” to Candidatus “Kuenenia stuttgartiensis.” It is hypothesized that the reason for this shift is the higher affinity for nitrite of “Kuenenia.” The production of anammox bacteria in suspension with high purity and productivity makes the MBR a promising tool for the cultivation and study of anammox bacteria. Biotechnol. Bioeng. 2008;101: 286–294.

Individual-based modelling of biofilms.

Understanding the emergence of the complex organization of biofilms from the interactions of its parts, individual cells and their environment, is the aim of the individual-based modelling (IbM) approach. This IbM is version 2 of BacSim, a model of Escherichia coli colony growth, which was developed into a two-dimensional multi-substrate, multi-species model of nitrifying biofilms. It was compared with the established biomass-based model (BbM) of Picioreanu and others. Both models assume that biofilm growth is due to the processes of diffusion, reaction and growth (including biomass growth, division and spreading). In the IbM, each bacterium was a spherical cell in continuous space and had variable growth parameters. Spreading of biomass occurred by shoving of cells to minimize overlap between cells. In the BbM, biomass was distributed in a discrete grid and each species had uniform growth parameters. Spreading of biomass occurred by cellular automata rules. In the IbM, the effect of random variation of growth parameters of individual bacteria was negligible in contrast to the E. coli colony model, because the heterogeneity of substrate concentrations in the biofilm was more important. The growth of a single cell into a clone, and therefore also the growth of the less abundant species, depended on the randomly chosen site of attachment, owing to the heterogeneity of substrate concentrations in the biofilm. The IbM agreed with the BbM regarding the overall growth of the biofilm, due to the same diffusion-reaction processes. However, the biofilm shape was different due to the different biomass spreading mechanisms. The IbM biofilm was more confluent and rounded due to the steady, deterministic and directionally unconstrained spreading of the bacteria. Since the biofilm shape is influenced by the spreading mechanism, it is partially independent of growth, which is driven by diffusion-reaction. Chance in initial attachment events modifies the biofilm shape and the growth of single cells because of the high heterogeneity of substrate concentrations in the biofilm, which again results from the interaction of diffusion-reaction with spreading. This stresses the primary importance of spreading and chance in addition to diffusion-reaction in the emergence of the complexity of the biofilm community.

Particle-Based Multidimensional Multispecies Biofilm Model

ABSTRACT In this paper we describe a spatially multidimensional (two-dimensional [2-D] and three-dimensional [3-D]) particle-based approach for modeling the dynamics of multispecies biofilms growing on multiple substrates. The model is based on diffusion-reaction mass balances for chemical species coupled with microbial growth and spreading of biomass represented by hard spherical particles. Effectively, this is a scaled-up version of a previously proposed individual-based biofilm model. Predictions of this new particle-based model were quantitatively compared with those obtained with an established one-dimensional (1-D) multispecies model for equivalent problems. A nitrifying biofilm containing aerobic ammonium and nitrite oxidizers, anaerobic ammonium oxidizers, and inert biomass was chosen as an example. The 2-D and 3-D models generally gave the same results. If only the average flux of nutrients needs to be known, 2-D and 1-D models are very similar. However, the behavior of intermediates, which are produced and consumed in different locations within the biofilm, is better described in 2-D and 3-D models because of the multidirectional concentration gradients. The predictions of 2-D or 3-D models are also different from those of 1-D models for slowly growing or minority species in the biofilm. This aspect is related to the mechanism of biomass spreading or advection implemented in the models and should receive more attention in future experimental studies.

Influence of biomass production and detachment forces on biofilm structures in a biofilm airlift suspension reactor

The influence of process conditions (substrate loading rate and detachment force) on the structure of biofilms grown on basalt particles in a Biofilm Airlift Suspension (BAS) reactor was studied. The structure of the biofilms (density, surface shape, and thickness) and microbial characteristics (biomass yield) were investigated at substrate loading rates of 5, 10, 15, and 20 kg COD/m3. day with basalt concentrations of 60 g/L, 150 g/L, and 250 g/L. The basalt concentration determines the number of biofilm particles in steady state, which is the main determining factor for the biofilm detachment in these systems. In total, 12 experimental runs were performed. A high biofilm density (up to 67 g/L) and a high biomass concentration was observed at high detachment forces. The higher biomass content is associated with a lower biomass substrate loading rate and therefore with a lower biomass yield (from 0.4 down to 0.12 gbiomass/gacetate). Contrary to general beliefs, the observed biomass detachment decreased with increasing detachment force. In addition, smoother (fewer protuberances), denser and thinner compact biofilms were obtained when the biomass surface production rate decreased and/or the detachment force increased. These observations confirmed a hypothesis, postulated earlier by Van Loosdrecht et al. (1995b), that the balance between biofilm substrate surface loading (proportional to biomass surface production rate, when biomass yield is constant) and detachment force determines the biofilm structure. When detachment forces are relatively high only a patchy biofilm will develop, whereas at low detachment forces, the biofilm becomes highly heterogeneous with many pores and protuberances. With the right balance, smooth, dense and stable biofilms can be obtained. Copyright 1998 John Wiley & Sons, Inc.

A new combined differential-discrete cellular automaton approach for biofilm modeling : Application for growth in gel beads

The theoretical basis and quantitative evaluation of a new approach for modeling biofilm growth are presented here. Soluble components (e.g., substrates) are represented in a continuous field, whereas discrete mapping is used for solid components (e.g., biomass). The spatial distribution of substrate is calculated by applying relaxation methods to the reaction-diffusion mass balance. A biomass density map is determined from direct integration in each grid cell of a substrate-limited growth equation. Spreading and distribution of biomass is modeled by a discrete cellular automaton algorithm. The ability of this model to represent diffusion-reaction-microbial growth systems was tested for a well-characterized system: immobilized cells growing in spherical gel beads. Good quantitative agreement with data for global oxygen consumption rate was found. The calculated concentration profiles of substrate and biomass in gel beads corresponded to those measured. Moreover, it was possible, using the discrete spreading algorithm, to predict the spatial two- and three-dimensional distribution of microorganisms in relation to, for example, substrate flux and inoculation density. The new technique looks promising for modeling diffusion-reaction-microbial growth processes in heterogeneous systems as they occur in biofilms.

Effect of Diffusive and Convective Substrate Transport on Biofilm Structure Formation: A Two-Dimensional Modeling Study

A two-dimensional model for quantitative evaluation of the effect of convective and diffusive substrate transport on biofilm heterogeneity was developed. The model includes flow computation around the irregular biofilm surface, substrate mass transfer by convection and diffusion, biomass growth, and biomass spreading. It was found that in the absence of detachment, biofilm heterogeneity is mainly determined by internal mass transfer rate of substrates and by the initial percentage of carrier-surface colonization. Model predictions show that biofilm structures with highly irregular surface develop in the mass transfer-limited regime. As the nutrient availability increases, there is a gradual shift toward compact and smooth biofilms. A smaller fraction of colonized carrier surface leads to a patchy biofilm. Biofilm surface irregularity and deep vertical channels are, in this case, caused by the inability of the colonies to spread over the whole substratum surface. The maximum substrate flux to the biofilm was greatly influenced by both internal and external mass transfer rates, but not affected by the inoculation density. In general, results of the present model were similar to those obtained by a simple diffusion-reaction-growth model.

Mathematical modelling of biofilm structures

The morphology of biofilms received much attention in the last years. Several concepts to explain the development of biofilm structures have been proposed. We believe that biofilm structure formation depends on physical as well as general and specific biological factors. The physical factors (e.g. governing substrate transport) as well as general biological factors such as growth yield and substrate conversion rates are the basic factors governing structure formation. Specific strain dependent factors will modify these, giving a further variation between different biofilm systems. Biofilm formation seems to be primarily dependent on the interaction between mass transport and conversion processes. When a biofilm is strongly diffusion limited it will tend to become a heterogeneous and porous structure. When the conversion is the rate-limiting step, the biofilm will tend to become homogenous and compact. On top of these two processes, detachment processes play a significant role. In systems with a high detachment (or shear) force, detachment will be in the form of erosion, giving smoother biofilms. Systems with a low detachment force tend to give a more porous biofilm and detachment occurs mainly by sloughing. Biofilm structure results from the interplay between these interactions (mass transfer, conversion rates, detachment forces) making it difficult to study systems taking only one of these factors into account.

A three-dimensional numerical study on the correlation of spatial structure, hydrodynamic conditions, and mass transfer and conversion in biofilms

Abstract A three-dimensional model for convection, diffusion, and reaction in a porous, heterogeneous system has been implemented. It is used to analyse the influence of hydrodynamics and structural heterogeneities on mass transfer and conversion processes of solutes in biofilm systems. The mathematical model comprises the full incompressible Navier–Stokes equations and mass transfer with nonlinear reactions in the biofilm. It is found that increased biofilm surface roughness means decreased mass conversion in the solid biofilm. Secondly, a correlation between bulk flow Reynolds number and the Sherwood number for mass transfer across the irregular liquid/solid interface is formulated. In a further study the contribution of convective transport to overall mass transfer from bulk liquid into the biofilm was analysed. The main result was that the experimental observation of high convective flux of solutes in biofilm channels not necessarily is coupled with an equally high net convective contribution to mass transfer from bulk liquid into biofilm.

Challenges in microbial ecology: building predictive understanding of community function and dynamics

The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth’s soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model–experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved.

Modelling the effect of oxygen concentration on nitrite accumulation in a biofilm airlift suspension reactor

For an integrated nitrification-denitrification processes, nitrite formation in the aerobic stage leads to big savings. Recently experimental observations (Garrido et al., 1996) have shown that it is possible to obtain full ammonium conversion with approximately 50 % nitrate and 50 % nitrite in the effluent of a biofilm airlift suspension reactor. With oxygen concentrations between 1 and 2 mg/l a maximum nitrite accumulation of 50 % was reached. Here we give a simple diffusion-reaction model describing these results. All the kinetic and mass transfer parameters were taken from the literature, except the mass transfer coefficient around the biofilm surface, which was fitted. The proposed model describes very well the measured data, despite the assumptions made. Using this model the influence of operational parameters was evaluated in order to establish ways to affect the NO2 concentration. None of these (surface loading, kl, pH) had a significant effect on NO2 accumulation. Controlling the oxygen concentration seems to be the most practical method to obtain optimal nitrification to nitrite in BAS reactors since this can be done simply by varying the superficial gas velocity or by partial recirculation of the off-gas.