Experimental and simulation analysis of community structure of nitrifying bacteria in a membrane-aerated biofilm

Organic matter removal in a simultaneous nitrification-denitrification process using fixed-film system

Swine wastewater treatment is a complex challenge, due to the high organic matter (OM) and nitrogen (N) concentrations which require an efficient process. This study focused on evaluating two different support media for OM and N removal from an Upflow Anaerobic Sludge Blanket (UASB) reactor fed with swine wastewater. Maximum specific nitrification (MSNA) and denitrification (MSDA) activity test for both biofilm and suspended biomass were carried out using as supports: polyurethane foam (R1) and polyethylene rings (R2). The results showed that R2 system was more efficiently than R1, reaching OM removal of 77 ± 8% and N of 98 ± 4%, attributed to higher specific denitrifying activity recorded (5.3 ± 0.34 g NO₃-N/g TVS∙h). Furthermore, 40 ± 5% of the initial N in the wastewater could have been transformed into molecular nitrogen through SND, of which only 10 ± 1% was volatilized. In this sense, MSDA tests indicated that suspended biomass was responsible for at least 70% of N removal and only 20% can be attributed to biofilm. SND could be confirmed with the analysis of microbial diversity, due to the presence of the genus Pseudomonas dominated the prokaryotic community of the system in 54.4%.

Long-term operation assessment of a full-scale membrane-aerated biofilm reactor under Nordic conditions

Membrane-aerated biofilm reactor (MABR) technology is an exciting alternative to conventional activated sludge, with promising results in bench and pilot-scale systems. Nevertheless, there is still a lack of long-term and full-scale data under different operational conditions. This study aims to report the performance of a full-scale hybrid MABR located in the North of Europe. Influent, effluent, and exhaust data were collected for 1 year (September 2019 to September 2020) using online sensors/gas-analyzers and off-line laboratory analysis. Next, oxygen transfer rate (OTR), oxygen transfer efficiency (OTE), and nitrification rates (NR) were quantified as process indicators. Finally, multivariate methods were used to find patterns among monitored variables. Observations revealed that lower airflows achieved higher OTE at the same values of OTR and OTR was strongly correlated to ammonia/um concentration in the MABR tank (NH_x,eff). The dynamics between oxygen concentration in the exhaust (O_2,exh) and NH_x,eff indicated that a nitrifying biofilm was established within 3 weeks. Average NR were calculated using four different methods and ranged between 1 and 2 g N m^-2d^-1. Principal component analysis (PCA) explained 81.4% of the sample variance with the first three components and cluster analysis (CA) divided the yearly data into five distinctive periods. Hence, it was possible to identify typical Nordic episodes with high frequency of heavy rain, low temperature, and high variations in pollution load. The study concludes that nitrification capacity obtained with MABR is robust during cold weather conditions, and its volumetric value is comparable to other well-established biofilm-based technologies. Moreover, the aeration efficiency (AE) obtained in this study, 5.8 kg O₂ kW h^-1, would suppose an average reduction in energy consumption of 55% compared to fine pore diffused aeration and 74% to the existing surface aeration at the facility.

Nitrifying biofilms deprived of organic carbon show higher functional resilience to increases in carbon supply

In nitrifying biofilms, the organic carbon to ammonia nitrogen (C/N) supply ratio can influence resource competition between heterotrophic and nitrifying bacteria for oxygen and space. We investigated the impact of acute and chronic changes in carbon supply on inter-guild competition in two moving bed biofilm reactors (MBBR), operated with (R1) and without (R0) external organic carbon supply. The microbial and nitrifying community composition of the reactors differed significantly. Interestingly, acute increases in the dissolved organic carbon inhibited nitrification in R1 ten times more than in R0. A sustained increase in the carbon supply decreased nitrification efficiency and increased denitrification activity to a greater extent in R1, and also increased the proportion of potential denitrifiers in both bioreactors. The findings suggest that autotrophic biofilms subjected to increases in carbon supply show higher nitrification and lower denitrification activity than carbon-fed biofilms. This has significant implications for the design of nitrifying bioreactors. Specifically, efficient removal of organic matter before the nitrification unit can improve the robustness of the bioreactor to varying influent quality. Thus, maintaining a low C/N ratio is important in nitrifying biofilters when acute carbon stress is expected or when anoxic activity (e.g. denitrification or H₂S production) is undesirable, such as in recirculating aquaculture systems (RAS).

Predation creates unique void layer in membrane-aerated biofilms

The membrane-aerated biofilm reactor (MABR) is a novel wastewater treatment technology based on oxygen-supplying membranes. The counter diffusion of oxygen and electron donors in MABRs leads to unique behavior, and we hypothesized it also could impact predation. We used optical coherence tomography (OCT), microsensor analyses, and mathematical modeling to investigate predation in membrane-aerated biofilms (MABs). When protozoa were excluded from the inoculum, the MAB's OCT-observable void fraction was around 5%. When protozoa were included, the void fraction grew to nearly 50%, with large, continuous voids at the base of the biofilm. Real-time OCT imaging showed highly motile protozoa in the voids. MABs with protozoa and a high bulk COD (270 mg/L) only had 4% void fraction. DNA sequencing revealed a high relative abundance of amoeba in both high and low-COD MABs. Flagellates were only abundant in the low-COD MAB. Modeling also suggested a relationship between substrate concentrations, diffusion mode (co- or counter-diffusion), and biofilm void fraction. Results suggest that amoeba proliferate in the biofilm interior, especially in the aerobic zones. Voids form once COD limitation at the base of MABs allows predation rates to exceed microbial growth rates. Once formed, the voids provide a niche for motile protozoa, which expand the voids into a large, continuous gap. This increases the potential for biofilm sloughing, and may have detrimental effects on slow-growing, aerobic microorganisms such as nitrifying bacteria.

Periodic venting of MABR lumen allows high removal rates and high gas-transfer efficiencies

The membrane-aerated biofilm reactor (MABR) is a novel treatment technology that employs gas-supplying membranes to deliver oxygen directly to a biofilm growing on the membrane surface. When operated with closed-end membranes, the MABR provides 100-percent oxygen transfer efficiencies (OTE), resulting in significant energy savings. However, closed-end MABRs are more sensitive to back-diffusion of inert gases, such as nitrogen. Back-diffusion reduces the average oxygen transfer rates (OTR), consequently decreasing the average contaminant removal fluxes (J). We hypothesized that venting the membrane lumen periodically would increase the OTR and J. Using an experimental flow cell and mathematical modeling, we showed that back-diffusion gas profiles developed over relatively long timescales. Thus, very short ventings could re-establish uniform gas profiles for relatively long time periods. Using modeling, we systematically explored the effect of the venting interval (time between ventings). At moderate venting intervals, opening the membrane for 20 s every 30 min, the venting significantly increased the average OTR and J without substantially impacting the OTEs. When the interval was short enough, in this case shorter than 20 min, the OTR was actually higher than for continuous open-end operation. Our results show that periodic venting is a promising strategy to combine the advantages of open-end and closed end operation, maximizing both the OTR and OTE.

Continuum and discrete approach in modeling biofilm development and structure: a review

The scientific community has recognized that almost 99% of the microbial life on earth is represented by biofilms. Considering the impacts of their sessile lifestyle on both natural and human activities, extensive experimental activity has been carried out to understand how biofilms grow and interact with the environment. Many mathematical models have also been developed to simulate and elucidate the main processes characterizing the biofilm growth. Two main mathematical approaches for biomass representation can be distinguished: continuum and discrete. This review is aimed at exploring the main characteristics of each approach. Continuum models can simulate the biofilm processes in a quantitative and deterministic way. However, they require a multidimensional formulation to take into account the biofilm spatial heterogeneity, which makes the models quite complicated, requiring significant computational effort. Discrete models are more recent and can represent the typical multidimensional structural heterogeneity of biofilm reflecting the experimental expectations, but they generate computational results including elements of randomness and introduce stochastic effects into the solutions.

Advancing microbial sciences by individual-based modelling

Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage-CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE).

Impact of oxygen on the coexistence of nitrification, denitrification, and sulfate reduction in oxygen-based membrane aerated biofilm

Membrane aerated biofilms (MABs) are subject to "counter diffusion" of oxygen and substrates. In a membrane aerated biofilm reactor, gases (e.g., oxygen) diffuse through the membrane into the MAB, and liquid substrates pass from the bulk liquid into the MAB. This behavior can result in a unique biofilm structure in terms of microbial composition, distribution, and community activity in the MAB. Previous studies have shown simultaneous aerobic oxidation, nitrification, and denitrification within a single MAB. Using molecular techniques, we investigated the growth of sulfate-reducing bacteria (SRB) in the oxygen-based MAB attached to a flat sheet membrane. Denaturing gradient gel electrophoresis of the amplified 16S rRNA gene fragments and functional gene fragments specific for ammonia-oxidizing bacteria (amoA), denitrifying bacteria (nirK), and SRB (dsrB) demonstrated the coexistence of nitrifiers, denitrifiers, and SRB communities within a single MAB. The functional diversities of SRB and denitrifiers decreased with an increase in the oxygen concentration in the bulk water of the reactor.

Nitrifying moving bed biofilm reactor (MBBR) biofilm and biomass response to long term exposure to 1 °C

This study aims to investigate moving bed biofilm reactor (MBBR) nitrification rates, nitrifying biofilm morphology, biomass viability as well as bacterial community shifts during long-term exposure to 1 °C. Long-term exposure to 1 °C is the key operational condition for potential ammonia removal upgrade units to numerous northern region treatment systems. The average laboratory MBBR ammonia removal rate after long-term exposure to 1 °C was measured to be 18 ± 5.1% as compared to the average removal rate at 20 °C. Biofilm morphology and specifically the thickness along with biomass viability at various depths in the biofilm were investigated using variable pressure electron scanning microscope (VPSEM) imaging and confocal laser scanning microscope (CLSM) imaging in combination with viability live/dead staining. The biofilm thickness along with the number of viable cells showed significant increases after long-term exposure to 1 °C. Hence, this study observed nitrifying bacteria with higher activities at warm temperatures and a slightly greater quantity of nitrifying bacteria with lower activities at cold temperatures in nitrifying MBBR biofilms. Using DNA sequencing analysis, Nitrosomonas and Nitrosospira (ammonia oxidizers) as well as Nitrospira (nitrite oxidizer) were identified and no population shift was observed between 20 °C and after long-term exposure to 1 °C.

A model-based approach to detect interspecific interactions during biofilm development

A model-based approach was developed to detect interspecific interactions during biofilm development. This approach relied on the comparison of experimental data with a simple null model of biofilm growth dynamics where individual species grew independently of one another, except that they competed for space. Such a model was directly parameterized with a 4D confocal image series of biofilms and then used as a null model to detect interspecific interactions between pairs of bacterial species. This approach was tested in two bispecific competitive trials. In the first trial, the progressive exclusion of Pseudomonas fluorescens by Pseudomonas putida appeared to be due solely to the different intrinsic growth rates of the two strains. In contrast, modelling results suggested the presence of interference competition between Pseudomonas aeruginosa and P. putida in mixed biofilms. The authors' approach enables the detection of ecologically relevant interactions which constitute a prerequisite to building a comprehensive view of the dynamics and functioning of spatially structured bacterial communities.

Multidimensional modeling of biofilm development and fluid dynamics in a hydrogen-based, membrane biofilm reactor (MBfR)

A two-dimensional, particle-based biofilm model coupled with mass transport and computational fluid dynamics was developed to simulate autotrophic denitrification in a spiral-wound membrane biofilm reactor (MBfR), where hydrogen is supplied via hollow-fiber membrane fabric. The spiral-wound configuration consists of alternating layers of plastic spacer net and membrane fabric that create rows of flow channels, with the top and bottom walls comprised of membranes. The transversal filaments of the spacer partially obstruct the channel flow, producing complex mixing and shear patterns that require multidimensional representation. This study investigated the effect of hydrogen and nitrate concentrations, as well as spacer configuration, on biofilm development and denitrification fluxes. The model results indicate that the cavity spacer filaments, which rest on the bottom membranes, cause uneven biofilm growth. Most biofilm resided on the bottom membranes, only in the wake of the filaments where low shear zones formed. In this way, filament configuration may help achieve a desired biofilm thickness. For the conditions tested in this study, the highest nitrate fluxes were attained by minimizing the filament diameter and maximizing the filament spacing. This lowered the shear stress at the top membranes, allowing for more biofilm growth. For the scenarios studied, biomass limitation at the top membranes hindered performance more significantly than diffusion limitation in the thick biofilms at the bottom membranes. The results also highlighted the importance of two-dimensional modeling to capture uneven biofilm growth on a substratum with geometrical complexity.

Challenges for complex microbial ecosystems: combination of experimental approaches with mathematical modeling

In the past couple of decades, molecular ecological techniques have been developed to elucidate microbial diversity and distribution in microbial ecosystems. Currently, modern techniques, represented by meta-omics and single cell observations, are revealing the incredible complexity of microbial ecosystems and the large degree of phenotypic variation. These studies propound that microbiological techniques are insufficient to untangle the complex microbial network. This minireview introduces the application of advanced mathematical approaches in combination with microbiological experiments to microbial ecological studies. These combinational approaches have successfully elucidated novel microbial behaviors that had not been recognized previously. Furthermore, the theoretical perspective also provides an understanding of the plasticity, robustness and stability of complex microbial ecosystems in nature.

The membrane biofilm reactor (MBfR) for water and wastewater treatment: principles, applications, and recent developments

The membrane biofilm reactor (MBfR), an emerging technology for water and wastewater treatment, is based on pressurized membranes that supply a gaseous substrate to a biofilm formed on the membrane's exterior. MBfR biofilms behave differently from conventional biofilms due to the counter-diffusion of substrates. MBfRs are uniquely suited for numerous treatment applications, including the removal of carbon and nitrogen when oxygen is supplied, and reduction of oxidized contaminants when hydrogen is supplied. Major benefits include high gas utilization efficiency, low energy consumption, and small reactor footprints. The first commercial MBfR was recently released, and its success may lead to the scale-up of other applications. MBfR development still faces challenges, including biofilm management, the design of scalable reactor configurations, and the identification of cost-effective membranes. If future research and development continue to address these issues, the MBfR may play a key role in the next generation of sustainable treatment systems.

Shear-induced detachment of biofilms from hollow fiber silicone membranes

A suite of techniques was utilized to evaluate the correlation between biofilm physiology, fluid-induced shear stress, and detachment in hollow fiber membrane aerated bioreactors. Two monoculture species biofilms were grown on silicone fibers in a hollow fiber membrane aerated bioreactors (HfMBR) to assess detachment under laminar fluid flow conditions. Both physiology (biofilm thickness and roughness) and nutrient mass transport data indicated the presence of a steady state mature biofilm after 3 weeks of development. Surface shear stress proved to be an important parameter for predicting passive detachment for the two biofilms. The average shear stress at the surface of Nitrosomonas europaea biofilms (54.5 ± 3.2 mPa) was approximately 20% higher than for Pseudomonas aeruginosa biofilms (45.8 ± 7.7 mPa), resulting in higher biomass detachment. No significant difference in shear stress was measured between immature and mature biofilms of the same species. There was a significant difference in detached biomass for immature vs. mature biofilms in both species. However, there was no difference in detachment rate between the two species.

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.

Spatial Architecture of Nitrifying Bacteria Biofilm Immobilized on Polyurethane Foam in an Automatic Biodetector for Water Toxicity

We describe the architecture of nitrifying bacteria biofilms immobilized on a three-dimensional (3D) polyurethane foam that permits efficient water flow through a bioreactor. The 3D spatial organization of immobilized bacterial colonies is characterized on three resolution levels with X-ray tomography, light confocal microscopy, and scanning electron microscopy (SEM). Using these techniques we demonstrate biofilm distribution in the foam and the existence of several modes of binding of bacteria to the foam. Computed X-ray tomography permits observation of the distribution of the biofilm in the whole open cellular polyurethane material volume and estimation of biofilm volume. SEM and confocal laser scanning microscopy techniques permit 3D visualization of biofilm structure. Three distinct immobilization patterns could be observed in the open cellular polyurethane material: (1) large irregular aggregates of bacterial biofilm that exist as irregular biofilm fragments, rope-like structures, or biofilm layers on the foam surface; (2) spherical (pom-pom) aggregates of bacteria localized on the external surface of biofilm; and (3) biofilm threads adherent to the surface of polyurethane foam. Finally, we demonstrate that immobilized bacteria exhibit metabolic activity and growth.

Inoculum effects on community composition and nitritation performance of autotrophic nitrifying biofilm reactors with counter-diffusion geometry

The link between nitritation success in a membrane-aerated biofilm reactor (MABR) and the composition of the initial ammonia- and nitrite-oxidizing bacterial (AOB and NOB) population was investigated. Four identically operated flat-sheet type MABRs were initiated with two different inocula: from an autotrophic nitrifying bioreactor (Inoculum A) or from a municipal wastewater treatment plant (Inoculum B). Higher nitritation efficiencies (NO(2)(-)-N/NH(4)(+)-N) were obtained in the Inoculum B- (55.2-56.4%) versus the Inoculum A- (20.2-22.1%) initiated reactors. The biofilms had similar oxygen penetration depths (100-150 µm), but the AOB profiles [based on 16S rRNA gene targeted real-time quantitative PCR (qPCR)] revealed different peak densities at or distant from the membrane surface in the Inoculum B- versus A-initiated reactors, respectively. Quantitative fluorescence in situ hybridization (FISH) revealed that the predominant AOB in the Inoculum A- and B-initiated reactors were Nitrosospira spp. (48.9-61.2%) versus halophilic and halotolerant Nitrosomonas spp. (54.8-63.7%), respectively. The latter biofilm displayed a higher specific AOB activity than the former biofilm (1.65 fmol cell(-1) h(-1) versus 0.79 fmol cell(-1) h(-1) ). These observations suggest that the AOB and NOB population compositions of the inoculum may determine dominant AOB in the MABR biofilm, which in turn affects the degree of attainable nitritation in an MABR.

Intertwined interspecies relationships: approaches to untangle the microbial network

In nature, microorganisms live by interacting with each other. Microbiological studies that only consider pure cultures are not sufficient to adequately describe the natural behaviour of microbes. Several microbial interactions have been recognized to affect the growth or metabolism of others; e.g. syntrophic cometabolism, competition, production of inhibitors or activators, and predation. It is believed that third-party organisms easily affect the two-species relationships and these relationships form the basis of interspecies networks within microbial communities. A microbial network contributes to 'functional redundancy' or 'structural diversity' and the microbial communities effectively act as a multicellular organism. It is necessary to understand not only the physiological activity of members within microbial communities but also their roles to regulate the activity or population of others. To access the microbial network, we require (i) comprehensive determination of all possible interspecies relationships among microbes, (ii) knock-out experiments by which certain members can be removed or suppressed, and (iii) supplemental addition of microbes or activation of certain members. Microbial network studies have started using defined microbial communities, i.e. a mixed culture that is composed of three or four species. In order to expand these studies to microflora in nature, microbial ecology requires the help of mathematical biology.

Is gas-discharge plasma a new solution to the old problem of biofilm inactivation?

Conventional disinfection and sterilization methods are often ineffective with biofilms, which are ubiquitous, hard-to-destroy microbial communities embedded in a matrix mostly composed of exopolysaccharides. The use of gas-discharge plasmas represents an alternative method, since plasmas contain a mixture of charged particles, chemically reactive species and UV radiation, whose decontamination potential for free-living, planktonic micro-organisms is well established. In this study, biofilms were produced using Chromobacterium violaceum, a Gram-negative bacterium present in soil and water and used in this study as a model organism. Biofilms were subjected to an atmospheric pressure plasma jet for different exposure times. Our results show that 99.6 % of culturable cells are inactivated after a 5 min treatment. The survivor curve shows double-slope kinetics with a rapid initial decline in c.f.u. ml(-1) followed by a much slower decline with D values that are longer than those for the inactivation of planktonic organisms, suggesting a more complex inactivation mechanism for biofilms. DNA and ATP determinations together with atomic force microscopy and fluorescence microscopy show that non-culturable cells are still alive after short plasma exposure times. These results indicate the potential of plasma for biofilm inactivation and suggest that cells go through a sequential set of physiological and morphological changes before inactivation.

Membrane-aerated biofilms for high rate biotreatment: performance appraisal, engineering principles, scale-up, and development requirements

Diffusion of the electron acceptor is the rate controlling step in virtually all biofilm reactors employed for aerobic wastewater treatment. The membrane-aerated biofilm reactor (MABR) is a technology that can deliver oxygen at high rates and transfer efficiencies, thereby enhancing the biofilm activity. This paper provides a comparative performance rate analysis of the MABR in terms of its application for carbonaceous pollutant removal, nitrification/denitrification and xenobiotic biotreatment. We also describe the mechanisms influencing process performance in the MABR and the inter-relationships between these factors. The challenges involved in scaling-up the process are discussed with recommendations for prioritization of research needs.