Three-reaction model for the anaerobic digestion of microalgae.

Coupling an anaerobic digester to a microalgal culture has received increasing attention as an alternative process for combined bioenergy production and depollution. In this article, a dynamic model for anaerobic digestion of microalgae is developed with the aim of improving the management of such a coupled system. This model describes the dynamics of inorganic nitrogen and volatile fatty acids since both can lead to inhibition and therefore process instability. Three reactions are considered: Two hydrolysis-acidogenesis steps in parallel for sugars/lipids and for proteins, followed by a methanogenesis step. The proposed model accurately reproduces experimental data for anaerobic digestion of the freshwater microalgae Chlorella vulgaris with an organic loading rate of 1 gCOD L(-1) d(-1). In particular, the three-reaction pathway allows to adequately represent the observed decoupling between biogas production and nitrogen release. The reduced complexity of this model makes it suitable for developing advanced, model-based control and monitoring strategies.

Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual-based modelling study.

Plasmid invasion in biofilms is often surprisingly limited in spite of the close contact of cells in a biofilm. We hypothesized that this poor plasmid spread into deeper biofilm layers is caused by a dependence of conjugation on the growth rate (relative to the maximum growth rate) of the donor. By extending an individual-based model of microbial growth and interactions to include the dynamics of plasmid carriage and transfer by individual cells, we were able to conduct in silico tests of this and other hypotheses on the dynamics of conjugal plasmid transfer in biofilms. For a generic model plasmid, we find that invasion of a resident biofilm is indeed limited when plasmid transfer depends on growth, but not so in the absence of growth dependence. Using sensitivity analysis we also find that parameters related to timing (i.e. a lag before the transconjugant can transfer, transfer proficiency and scan speed) and spatial reach (EPS yield, conjugal pilus length) are more important for successful plasmid invasion than the recipients' growth rate or the probability of segregational loss. While this study identifies one factor that can limit plasmid invasion in biofilms, the new individual-based framework introduced in this work is a powerful tool that enables one to test additional hypotheses on the spread and role of plasmids in microbial biofilms.

A new dynamic model for bioavailability and cometabolism of micropollutants during anaerobic digestion.

Organic micropollutants (OMPs) are present in wastewater and sludge. Their possible impact to the environment contributes to their increasing scientific and social interest. Anaerobic digestion has been shown as a potential biological process for removal of these compounds. An accurate description of OMP distribution in the environmental system can be used to better understand which compartment is used for degradation and to improve their depletion in conventional wastewater treatment technologies. In this work, we proposed a dynamical model with a four-compartment distribution to describe the Polycyclic Aromatic Hydrocarbons (PAHs) fate during anaerobic digestion. The model is calibrated and validated using experimental data obtained from two continuous reactors fed with primary and secondary sludge operated under mesophilic conditions. A non-linear least square method was used to optimize the model parameters. The resulted model is in accordance with the experimental data. The PAH biodegradation rate is well modeled when considering the aqueous fraction (including free and sorbed to dissolved/colloidal matter PAHs) as the bioavailable compartment. It was also demonstrated in the simulations that the PAHs biodegradation is linked to a mechanism of cometabolism. The model proposed is potentially useful to better understand the micropollutant distribution, predict the fate of PAHs under anaerobic condition and help to optimize the operation process for their depletion.

Modeling anaerobic digestion of microalgae using ADM1.

The coupling between a microalgal pond and an anaerobic digester is a promising alternative for sustainable energy production by transforming carbon dioxide into methane using solar energy. In this paper, we demonstrate the ability of the original ADM1 model and a modified version (based on Contois kinetics for the hydrolysis steps) to represent microalgae anaerobic digestion. Simulations were compared to experimental data of an anaerobic digester fed with Chlorella vulgaris. The modified ADM1 fits adequately the data for the considered 140 day experiment encompassing a variety of influent load and flow rates. It turns out to be a reliable predictive tool for optimising the coupling of microalgae with anaerobic digestion processes.

iDynoMiCS: next-generation individual-based modelling of biofilms.

Individual-based modelling of biofilms accounts for the fact that individual organisms of the same species may well be in a different physiological state as a result of environmental gradients, lag times in responding to change, or noise in gene expression, which we have become increasingly aware of with the advent of single-cell microbiology. But progress in developing and using individual-based modelling has been hampered by different groups writing their own code and the lack of an available standard model. We therefore set out to merge most features of previous models and incorporate various improvements in order to provide a common basis for further developments. Four improvements stand out: the biofilm pressure field allows for shrinking or consolidating biofilms; the continuous-in-time extracellular polymeric substances excretion leads to more realistic fluid behaviour of the extracellular matrix, avoiding artefacts; the stochastic chemostat mode allows comparison of spatially uniform and heterogeneous systems; and the separation of growth kinetics from the individual cell allows condition-dependent switching of metabolism. As an illustration of the model's use, we used the latter feature to study how environmentally fluctuating oxygen availability affects the diversity and composition of a community of denitrifying bacteria that induce the denitrification pathway under anoxic or low oxygen conditions. We tested the hypothesis that the existence of these diverse strategies of denitrification can be explained solely by assuming that faster response incurs higher costs. We found that if the ability to switch metabolic pathways quickly incurs no costs the fastest responder is always the best. However, if there is a trade-off where faster switching incurs higher costs, then there is a strategy with optimal response time for any frequency of environmental fluctuations, suggesting that different types of denitrifying strategies win in different environments. In a single environment, biodiversity of denitrifiers is higher in biofilms than chemostats, higher with than without costs and higher at intermediate frequency of change. The highly modular nature of the new computational model made this case study straightforward to implement, and reflects the sort of novel studies that can easily be executed with the new model.

Life-cycle assessment of microalgae culture coupled to biogas production.

Due to resource depletion and climate change, lipid-based algal biofuel has been pointed out as an interesting alternative because of the high productivity of algae per hectare and per year and its ability to recycle CO(2) from flue gas. Another option for taking advantage of the energy content of the microalgae is to directly carry out anaerobic digestion of raw algae in order to produce methane and recycle nutrients (N, P and K). In this study, a life-cycle assessment (LCA) of biogas production from the microalgae Chlorella vulgaris is performed and the results are compared to algal biodiesel and to first generation biodiesels. These results suggest that the impacts generated by the production of methane from microalgae are strongly correlated with the electric consumption. Progresses can be achieved by decreasing the mixing costs and circulation between different production steps, or by improving the efficiency of the anaerobic process under controlled conditions. This new bioenergy generating process strongly competes with others biofuel productions.

Experimental study on a coupled process of production and anaerobic digestion of Chlorella vulgaris.

The main goal of this present study is to investigate the feasibility of coupling algae production (Chlorella vulgaris) to an anaerobic digestion unit. An intermediate settling device was integrated in order to adapt the feed-flow concentration and the flow rate. Digestion of C. vulgaris was studied under 16 and 28 days hydraulic retention times (HRT), with a corresponding organic loading rate of 1g(COD)L(-1). Increasing the HRT achieved 51% COD removal with a methane production measured at 240 mL g(VSS)(-1). Performing different HRTs and dynamic monitoring during degradation highlighted differential hydrolysis of microalgae compartments. However, 50% of the biomass did not undergo anaerobic digestion, even under long retention times. This points out the interest for further studies on pre-treatment performances and more generally speaking on the need for intensifying microalgae biomass digestion.

A new extant respirometric assay to estimate intrinsic growth parameters applied to study plasmid metabolic burden.

Start-up phenomena in microbial biokinetic assays are not captured by the most commonly used growth-related equations. In this study we propose a new respirometric experimental design to estimate intrinsic growth parameters that allow us to avoid these limitations without data omission, separate mathematical treatment, or wake-up pulses prior to the analysis. Identifiability and sensitivity analysis were performed to confirm the robustness of the new approach for obtaining unique and accurate estimates of growth kinetic parameters. The new experimental design was applied to establish the metabolic burden caused by the carriage of a pWW0 TOL plasmid in the model organism Pseudomonas putida KT2440. The metabolic burden associated was manifested as a reduction in the yield and the specific growth rate of the host, with both plasmid maintenance and the over-expression of recombinant proteins from the plasmid contributing equally to the overall effect.

Life-cycle assessment of biodiesel production from microalgae.

This paper provides an analysis of the potential environmental impacts of biodiesel production from microalgae. High production yields of microalgae have called forth interest of economic and scientific actors but it is still unclear whether the production of biodiesel is environmentally interesting and which transformation steps need further adjustment and optimization. A comparative LCA study of a virtual facility has been undertaken to assessthe energetic balance and the potential environmental impacts of the whole process chain, from the biomass production to the biodiesel combustion. Two different culture conditions, nominal fertilizing or nitrogen starvation, as well as two different extraction options, dry or wet extraction, have been tested. The best scenario has been compared to first generation biodiesel and oil diesel. The outcome confirms the potential of microalgae as an energy source but highlights the imperative necessity of decreasing the energy and fertilizer consumption. Therefore control of nitrogen stress during the culture and optimization of wet extraction seem to be valuable options. This study also emphasizes the potential of anaerobic digestion of oilcakes as a way to reduce external energy demand and to recycle a part of the mineral fertilizers.

Mass action models describing extant horizontal transfer of plasmids: inferences and parameter sensitivities.

Predicting the fate of horizontally transmissible elements in extant microbial communities might be facilitated by the availability of suitable mathematical models. Since the mid-1970s, mass action models have been introduced to describe the transfer of conjugal and mobilizable genetic elements. This chapter will summarize and explain the assumptions behind spatially homogenous models, and show the predictions by these models under typical scenarios, such as evaluating existence conditions of conjugal plasmids under chemostat or seasonal growth conditions. Special attention is given to the sensitivity of the outcomes to the various plasmid dynamic parameters. For our analysis, we developed a set of user-friendly MatLab routines, which are deposited in the public domain. We hope that the availability of these routines will encourage the computationally untrained microbiologist to make use of these mathematical models. Finally, further permutations, as well as limitations of these mass action models in view of the structured complexity of most microbial systems are addressed.