Investigating biofilm structure developing on carriers from lab-scale moving bed biofilm reactors based on light microscopy and optical coherence tomography

Mass transfer in heterogeneous biofilms: Key issues in biofilm reactors and AI-driven performance prediction

Biofilm reactors, known for utilizing biofilm formation for cell immobilization, offer enhanced biomass concentration and operational stability over traditional planktonic systems. However, the dense nature of biofilms poses challenges for substrate accessibility to cells and the efficient release of products, making mass transfer efficiency a critical issue in these systems. Recent advancements have unveiled the intricate, heterogeneous architecture of biofilms, contradicting the earlier view of them as uniform, porous structures with consistent mass transfer properties. In this review, we explore six biofilm reactor configurations and their potential combinations, emphasizing how the spatial arrangement of biofilms within reactors influences mass transfer efficiency and overall reactor performance. Furthermore, we discuss how to apply artificial intelligence in processing biofilm measurement data and predicting reactor performance. This review highlights the role of biofilm reactors in environmental and energy sectors, paving the way for future innovations in biofilm-based technologies and their broader applications.

Monitoring biofilm thickness using the membrane aerated biofilm reactor (MABR) fingerprint soft sensor to optimize nitrogen removal

The ongoing commercialization and installation of full-scale membrane aerated biofilm reactors (MABRs) stimulate the increasing need to monitor biofilm development. Biofilm thickness in MABRs can be assessed indirectly by plotting the exhaust oxygen purity versus bulk ammonia concentration, defined here as the MABR fingerprint soft sensor. Dynamic simulations with diurnal flow variations of an MABR unit model were implemented over a broad range of biofilm thicknesses and influent conditions consisting of variable C/N ratios and applied ammonia fluxes to assess the utility of the MABR fingerprint. Results show that the continuously decreasing trend of the MABR fingerprint plot slopes can be employed as a useful signal for biofilm thickness control in nitrogen removal processes. This technique is useful in a wide range of influent conditions and is helpful for MABR operators and designers to arrange biofilm thickness control events efficiently and determine where in an overall treatment process the technique can be applied to control biofilm thickness and optimize process performance. PRACTITIONER POINTS: The linear relationship between exhaust oxygen purity and bulk ammonia concentration is defined as the MABR fingerprint plot. MABR fingerprint plots are generated for a given biofilm thickness with diurnal flow or short-term loading variations implemented. Continuously decreasing trends of the MABR fingerprint plot slopes are useful signals for biofilm control in nitrogen removal. The MABR fingerprint is useful over a wide range of influent conditions regarding C/N ratios and applied ammonia fluxes. MABR practitioners can use the fingerprint plots to determine when biofilm control measures should be taken.

Efficiency of various biofilm carriers and microbial interactions with substrate in moving bed-biofilm reactor for environmental wastewater treatment

In a moving bed-biofilm reactor (MBBR), the fluidization efficiency, immobilization of microbial cells, and treatment efficiency are directly influenced by the shape and pores of biofilm carriers. Moreover, the efficacy of bioremediation mainly depends on their interaction interface with microbes and substrate. This review aims to comprehend the role of different carrier properties such as material shapes, pores, and surface area on bioremediation productivity. A porous biofilm carrier with surface ridges containing spherical pores sizes > 1 mm can be ideal for maximum efficacy. It provides diverse environments for cell cultures, develops uneven biofilms, and retains various cell sizes and biomass. Moreover, the thickness of biofilm and controlled scaling shows a significant impact on MBBR performance. Therefore, the effect of these parameters in MBBR is discussed detailed in this review, through which existing literature and technical strategies that focus on the surface area as the primary factor can be critically assessed.

Opportunities for visual techniques to determine characteristics and limitations of electro-active biofilms

Optimization of bio-electrochemical systems (BESs) relies on a better understanding of electro-active biofilms (EABfs). These microbial communities are studied with a range of techniques, including electrochemical, visual and chemical techniques. Even though each of these techniques provides very valuable and wide-ranging information about EABfs, such as performance, morphology and biofilm composition, they are often destructive. Therefore, the information obtained from EABfs development and characterization studies are limited to a single characterization of EABfs and often limited to one time point that determines the end of the experiment. Despite being scarcer and not as commonly reported as destructive techniques, non-destructive visual techniques can be used to supplement EABfs characterization by adding in-situ information of EABfs functioning and its development throughout time. This opens the door to EABfs monitoring studies that can complement the information obtained with destructive techniques. In this review, we provide an overview of visual techniques and discuss the opportunities for combination with the established electrochemical techniques to study EABfs. By providing an overview of suitable visual techniques and discussing practical examples of combination of visual with electrochemical methods, this review aims at serving as a source of inspiration for future studies in the field of BESs.

Characterization of biofilm structure and properties via processing of 2D optical coherence tomography images in BISCAP

MOTIVATION

Processing of Optical Coherence Tomography (OCT) biofilm images is currently restricted to a set of custom-made MATLAB scripts. None of the tools currently available for biofilm image processing (including those developed for Confocal Laser Scanning Microscopy-CLSM) enable a fully automatic processing of 2D OCT images.

RESULTS

A novel software tool entitled Biofilm Imaging and Structure Classification Automatic Processor (BISCAP) is presented. It was developed specifically for the automatic processing of 2D OCT biofilm images. The proposed approach makes use of some of the key principles used in CLSM image processing, and introduces a novel thresholding algorithm and substratum detection strategy. Two complementary pixel continuity checks are executed, enabling very detailed pixel characterizations. BISCAP delivers common structural biofilm parameters and a set of processed images for biofilm analysis. A novel biofilm 'compaction parameter' is suggested. The proposed strategy was tested on a set of 300 images with highly satisfactory results obtained. BISCAP is a Python-based standalone application, not requiring any programming knowledge or property licenses, and where all operations are managed via an intuitive Graphical User Interface. The automatic nature of this image processing strategy decreases biasing problems associated to human-perception and allows a reliable comparison of outputs.

AVAILABILITY AND IMPLEMENTATION

BISCAP and a collection of biofilm images obtained from OCT scans can be found at: https://github.com/diogonarciso/BISCAP.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A Critical Review on Electric Field-Assisted Membrane Processes: Implications for Fouling Control, Water Recovery, and Future Prospects

Electrofiltration, an electric field-assisted membrane process, has been a research topic of growing popularity due to its ability to improve membrane performance by providing in situ antifouling conditions in a membrane system. The number of reports on electrofiltration have increased exponentially over the past two decades. These reports explored many innovations, such as novel configurations of an electric field, engineered membrane materials, and interesting designs of foulant compositions and membrane modules. Recent electrofiltration literature focused mainly on compiling results without a comprehensive comparative analysis across different works. The main objective of this critical review is to, first, organize, compare and contrast the results across various electrofiltration studies; second, discuss various types of mechanisms that could be incorporated into electrofiltration and their effect on membrane system performance; third, characterize electrofiltration phenomenon; fourth, interpret the effects of various operational conditions on the performance of electrofiltration; fifth, evaluate the state-of-the-art knowledge associated with modeling efforts in electrofiltration; sixth, discuss the energy costs related to the implementation of electrofiltration; and finally, identify the current knowledge gaps that hinder the transition of the lab-scale observations to industry-scale electrofiltration as well as the future prospects of electrofiltration.

Contrasting distribution of antibiotic resistance genes and microbial communities in suspended activated sludge versus attached biofilms in an integrated fixed film activated sludge (IFAS) system

Suspended activated sludge (AS) and carrier-attached biofilms simultaneously exist in an integrated fixed film activated sludge (IFAS) system. However, the differentiation of antibiotic resistance genes (ARGs) and microbial communities in different types of biofilms is rarely reported. In this study, successions of ARGs and microbial communities of AS and two types of suspended carrier-attached biofilms over seasons were investigated in the IFAS system of one municipal wastewater treatment plant. Results showed that substantial differences were found in the distribution pattern of ARGs, bacterial communities, and predicted microbial function between AS and attached biofilms. The relative abundances of all detected ARGs in AS were significantly higher than those in attached biofilms. ARGs with higher relative abundances generally existed in K3 carrier (surface area ≥ 800 m²/m³) attached biofilms than those in K1 carrier (surface area ≥ 450 m²/m³) biofilms. The relative abundances of ARGs were negatively correlated with temperature and biochemical oxygen demand (BOD₅) and positively correlated with ammonium nitrogen contents for AS but not for attached biofilms. No significant relationship was found between the extracellular polymeric substance (EPS) content and ARG abundance for all samples. Temperature, BOD₅, and ammonium nitrogen contents were closely connected to microbial communities. The Bray-Curtis distance of bacterial communities between two adjacent sampling seasons for AS was larger than those of two attached biofilms. Network analysis indicated that the AS network had more positive links and intense connections than the attached biofilm networks, potentially facilitating the dissemination of ARGs. The differential distribution of ARGs among the three types of samples was significantly correlated with the microbial co-occurrence network topological properties. Bray-Curtis distance and network analysis suggest that microbial community is more robust in attached biofilms than in suspended AS. This work provides a more in-depth understanding of ARGs and microbial community distributions in wastewater biofilms.

Effect of slow biodegradable substrate addition on biofilm structure and reactor performance in two MBBRs filled with different support media

In this study, two moving-bed biofilm reactors (MBBR₁ and MBBR₂) filled with different size of carrier media (Kaldnes K₁ and Kaldnes K₁ micro, respectively) were subjected to soluble (sugar and sodium acetate (Ac)) substrate and mixture of soluble and particulate (particulate potato starch (PS)) substrate in a very high organic loading rate (12 kgCOD/m³·d) at different temperatures (26 and 15°C, in MBBR₁ and MBBR₂, respectively). The effects of carrier type and substrate on biofilm structure and reactor performance have been studied. Starch was removed by adsorption at the biofilm surface and hydrolyzed which caused substrate gradient in MBBR₁, however, hydrolyzed uniformly within biofilm in MBBR₂. The biofilm of MBBR₁ was irregular due to filamentous structure growth due to the substrate gradient, while, it was regular in MBBR₂ due to uniform distribution of substrate. The performance of both MBBRs in ammonium, COD and TN removal decreased significantly when the amount of small particles in the reactor increased owing to feeding by starch, which led to biomass density decline. The type of media affected the quantity and distribution of attached biomass, which in turn influenced the activity of specific microbial functional groups in the biofilm. The biofilm in MBBR₂ was thicker and consequently nitrogen removal by denitrification was much higher. The lower temperature did not affect negatively the reactor performance in MBBR₂.

3D biofilm visualization and quantification on granular bioanodes with magnetic resonance imaging

The use of microbial fuel cells (MFCs) for wastewater treatment fits in a circular economy context, as they can produce electricity by the removal of organic matter in the wastewater. Activated carbon (AC) granules are an attractive electrode material for bioanodes in MFCs, as they are cheap and provide electroactive bacteria with a large surface area for attachment. The characterization of biofilm growth on AC granules, however, is challenging due to their high roughness and three-dimensional structure. In this research, we show that 3D magnetic resonance imaging (MRI) can be used to visualize biofilm distribution and determine its volume on irregular-shaped single AC granules in a non-destructive way, while being combined with electrochemical and biomass analyses. Ten AC granules with electroactive biofilm (i.e. granular bioanodes) were collected at different growth stages (3 to 21 days after microbial inoculation) from a multi-anode MFC and T₁-weighted 3D-MRI experiments were performed for three-dimensional biofilm visualization. With time, a more homogeneous biofilm distribution and an increased biofilm thickness could be observed in the 3D-MRI images. Biofilm volumes varied from 0.4 μL (day 4) to 2 μL (day 21) and were linearly correlated (R² = 0.9) to the total produced electric charge and total nitrogen content of the granular bioanodes, with values of 66.4 C μL^-1 and 17 μg N μL^-1, respectively. In future, in situ MRI measurements could be used to monitor biofilm growth and distribution on AC granules.

Moving bed biofilm reactor technology in municipal wastewater treatment: A review

The review encompasses the development of municipal wastewater treatment process using MBBR from early stages, established application, and recent advancements. An overview of main drivers leading to the MBBR technology development over its early stage is discussed. Biocarriers types and features together with biofilm development and role of extracellular polymeric substances (EPS) are presented, ultimately, addressing the challenge in decreasing startup time required for full operation. Furthermore, the review investigates the state of the art of MBBR technology for nutrient removal (i.e., COD and BOD, nitrogen and phosphorus) through process functionality and configuration of established (e.g., IFAS) and under development (e.g. PN/A) applications. Reactor operational characteristics such as filling fractions, mixing properties, dissolved oxygen requirements, and loading rates are presented and related to full scale examples. Current literature discussing the most recent studies on MBBR capability in reduction and removal of chemicals of emerging concern (CEC) released is presented. Ultimately, high rate carbon and nitrogen removal through A/B stage process are examined in its main operational parameters and its application towards energy neutrality suggesting novel MBBR application to further reduce energy requirements and plant footprint.

Determination of mechanical properties of biofilms by modelling the deformation measured using optical coherence tomography

The advantage of using non-invasive imaging such as optical coherence tomography (OCT) to asses material properties from deformed biofilm geometries can be compromised by the assumptions made on fluid forces acting on the biofilm. This study developed a method for the determination of elastic properties of biofilms by modelling the biofilm deformation recorded by OCT imaging with poroelastic fluid-structure interaction computations. Two-dimensional biofilm geometries were extracted from OCT scans of non-deformed and deformed structures as a result of hydrodynamic loading. The biofilm geometries were implemented in a model coupling fluid dynamics with elastic solid mechanics and Darcy flow in the biofilm. The simulation results were compared with real deformed geometries and a fitting procedure allowed estimation of the Young's modulus in given flow conditions. The present method considerably improves the estimation of elastic moduli of biofilms grown in mini-fluidic rectangular channels. This superior prediction is based on the relaxation of several simplifying assumptions made in past studies: shear stress is not anymore taken constant over the biofilm surface, total stress including also pressure is accounted for, any biofilm shape can be used in the determinations, and non-linear behavior of mechanical properties can be estimated. Biofilm elastic moduli between 70 and 700 Pa were obtained and biofilm hardening at large applied stress due to increasing flow velocity was quantified. The work performed here opens the way for in-situ determination of other mechanical properties (e.g., viscoelastic properties, relaxation times, plastic yields) and provides data for modelling biofilm deformation and detachment with eventual applications in biofilm control and removal strategies.

Water quality and daily temperature cycle affect biofilm formation in drip irrigation devices revealed by optical coherence tomography

Drip irrigation is a water-saving technology. To date, little is known about how biofilm forms in drippers of irrigation systems. In this study, the internal dripper geometry was recreated in 3-D printed microfluidic devices (MFDs). To mimic the temperature conditions in (semi-) arid areas, experiments were conducted in a temperature controlled box between 20 and 50°C. MFDs were either fed with two different treated wastewater (TWW) or synthetic wastewater. Biofilm formation was monitored non-invasively and in situ by optical coherence tomography (OCT). 3-D OCT datasets reveal the major fouling position and illustrate that biofilm development was influenced by fluid dynamics. Biofilm volumetric coverage of the labyrinth up to 60% did not reduce the discharge rate, whereas a further increase to 80% reduced the discharge rate by 50%. Moreover, the biofilm formation rate was significantly inhibited in daily temperature cycle independent of the cultivation medium used.

Integrated approach to characterize fouling on a flat sheet membrane gravity driven submerged membrane bioreactor

Fouling in membrane bioreactors (MBR) is acknowledged to be complex and unclear. An integrated characterization methodology was employed in this study to understand the fouling on a gravity-driven submerged MBR (GD-SMBR). It involved the use of different analytical tools, including optical coherence tomography (OCT), liquid chromatography with organic carbon detection (LC-OCD), total organic carbon (TOC), flow cytometer (FCM), adenosine triphosphate analysis (ATP) and scanning electron microscopy (SEM). The three-dimensional (3D) biomass morphology was acquired in a real-time through non-destructive and in situ OCT scanning of 75% of the total membrane surface directly in the tank. Results showed that the biomass layer was homogeneously distributed on the membrane surface. The amount of biomass was selectively linked with final destructive autopsy techniques. The LC-OCD analysis indicated the abundance of low molecular weight (LMW) organics in the fouling composition. Three different SEM techniques were applied to investigate the detailed fouling morphology on the membrane.

The inhibitory effects of reject water on nitrifying populations grown at different biofilm thickness

Suppression of nitrite oxidizing bacteria (NOB) is of vital importance to achieve successful, energy efficient, mainstream anammox processes for wastewater treatment. In this study, biofilm carriers from a fully nitrifying MBBR system, fed with mainstream wastewater, were temporarily exposed to reject water from sludge dewatering, to evaluate this as a possible strategy to inhibit NOB and achieve nitrite production under realistic conditions. Two different carrier types were compared, in which biofilm thickness was maintained at approximately 400 and 50 μm, respectively, and reject treatment was tested at different exposure time and loading rates. Reject exposure almost always resulted in an increased nitrite production in the thinner biofilm, and overall, nitrifiers growing in the thin biofilm were more sensitive than those grown in the thicker biofilm. The effect from reject exposure remained in the systems for four days after returning to mainstream operation, with nitrite production gradually increasing for three days. Increased concentrations of free ammonia correlated with reject exposure and may be the cause of inhibition, although other factors cannot be excluded.

Measurement of biofilm growth and local hydrodynamics using optical coherence tomography

We report on localized and simultaneous measurement of biofilm growth and local hydrodynamics in a microfluidic channel using optical coherence tomography. We measure independently with high spatio-temporal resolution the longitudinal flow velocity component parallel to the imaging beam and the transverse flow velocity component perpendicular to the imaging beam. Based on the measured velocities we calculate the shear-rates in the flow channel. We show the relation between the measured biofilm structure and flow velocities as biofilm growth progresses over the course of 48 hours.