Quantitative 3D comparison of biofilm imaged by X-ray micro-tomography and two-photon laser scanning microscopy

Nondestructive and three-dimensional visualization by identifying elements using synchrotron radiation microscale X-ray CT reveals microbial and cavity distributions in anaerobic granular sludge

We developed a nondestructive three-dimensional microbial visualization method utilizing synchrotron radiation X-ray microscale computed tomography to better understand the relationship between microorganisms and their surrounding habitats. The method was tested and optimized using a mixture of axenic Escherichia coli and Comamonas testosteroni. The osmium-thiocarbohydrazide-osmium method was used to stain all the microbial cells, and gold in situ hybridization was used to detect specific phylogenetic microbial groups. The stained samples were embedded in epoxy resin for microtomographic analysis. Differences in X-ray absorbances were calculated by subtracting the pre-L3-edge images from the post-L3-edge images to visualize the osmium and gold signals. Although we successfully detected cells stained with osmium, those labeled with gold were not detected, probably because of the insufficient density of gold atoms in the microbial cells. We then applied the developed technique to anaerobic granules and visualized the distribution of microbial cells and extracellular polymeric substances. Empty spaces were highlighted to determine the cavity distribution in granules. Numerous independent cavities of different sizes were identified in the granules. The developed method can be applied to various environmental samples for deeper insights into microbial life in their habitats.

IMPORTANCE

Microorganisms inhabit diverse environments and often form biofilms. One factor that affects their community structure is the surrounding physical environment. The arrangement of residential space within the formed biofilm plays a crucial role in the supply and transportation of substances, as well as the discharge of metabolites. Conventional approaches, such as scanning electron microscopy and confocal laser scanning microscopy combined with fluorescence in situ hybridization, have limitations as they provide information primarily from the biofilm surface and cross-sections. In this study, we developed a method for detecting microorganisms in biofilms using synchrotron radiation X-ray microscale computer tomography. The developed method allows nondestructive three-dimensional observation of biofilms at a single-cell resolution (voxel size of approximately 200 nm), facilitating an understanding of the relationship between microorganisms and their physical habitats.

A versatile micromodel technology to explore biofilm development in porous media flows

Bacterial biofilms that grow in porous media are critical to ecosystem processes and applications ranging from soil bioremediation to bioreactors for treating wastewater or producing value-added products. However, understanding and engineering the complex phenomena that drive the development of biofilms in such systems remains a challenge. Here we present a novel micromodel technology to explore bacterial biofilm development in porous media flows. The technology consists of a set of modules that can be combined as required for any given experiment and conveniently tuned for specific requirements. The core module is a 3D-printed micromodel where biofilm is grown into a perfusable porous substrate. High-precision additive manufacturing, in particular stereolithography, is used to fabricate porous scaffolds with precisely controlled architectures integrating flow channels with diameters down to several hundreds of micrometers. The system is instrumented with: ultraviolet-C light-emitting diodes; on-line measurements of oxygen consumption and pressure drop across the porous medium; camera and spectrophotometric cells for the detection of biofilm detachment events at the outlet. We demonstrate how this technology can be used to study the development of Pseudomonas aeruginosa biofilm for several days within a network of flow channels. We find complex dynamics whereby oxygen consumption reaches a steady-state but not the pressure drop, which instead features a permanent regime with large fluctuations. We further use X-ray computed microtomography to image the spatial distribution of biofilms and computational fluid dynamics to link biofilm development with local flow properties. By combining the advantages of additive manufacturing for the creation of reproducible 3D porous microarchitectures with the flow control and instrumentation accuracy of microfluidics, our system provides a platform to study the dynamics of biofilm development in 3D porous media and to rapidly test new concepts in process engineering.

Natural Source Zone Depletion (NSZD) Quantification Techniques: Innovations and Future Directions

Natural source zone depletion (NSZD) is an emerging technique for sustainable and cost-effective bioremediation of light non-aqueous phase liquid (LNAPL) in oil spill sites. Depending on regulatory objectives, NSZD has the potential to be used as either the primary or sole LNAPL management technique. To achieve this goal, NSZD rate (i.e., rate of bulk LNAPL mass depletion) should be quantified accurately and precisely. NSZD has certain characteristic features that have been used as surrogates to quantify the NSZD rates. This review highlights the most recent trends in technology development for NSZD data collection and rate estimation, with a focus on the operational and technical advantages and limitations of the associated techniques. So far, four principal techniques are developed, including concentration gradient (CG), dynamic closed chamber (DCC), CO2 trap and thermal monitoring. Discussions revolving around two techniques, “CO2 trap” and “thermal monitoring”, are expanded due to the particular attention to them in the current industry. The gaps of knowledge relevant to the NSZD monitoring techniques are identified and the issues which merit further research are outlined. It is hoped that this review can provide researchers and practitioners with sufficient information to opt the best practice for the research and application of NSZD for the management of LNAPL impacted sites.

First visualisation of bacterial biofilms in 3D porous media with neutron microtomography without contrast agent

Characterising bacterial biofilm growth in porous media is important for developing reliable numerical models of biofouling in industrial biofilters. One of the promising imaging methods to do that has been a recent successful application of X-ray microtomography. However, this technique requires a contrast agent (1-chloronaphtalene, for example) to distinguish biofilm from the liquid phase, which raises concern about biofilm disruption and impaired image interpretation. To overcome these drawbacks, we tested a new approach based on neutron tomography (NT), which does not need a contrast agent, by imaging two types of porous media (polytetrafluoroethylene - PTFE - and clay beads of various diameters) in glass or PTFE tubes in which bacterial biofilms were grown for 7 days and by comparing these images with the ones obtained with X-ray microtomography. NT images showed that the biofilm formed preferentially around the beads and at bead/bead interface. Visual comparison of both imaging techniques showed consistent biofilm spatial distributions and that the contrasting agent did not significantly disrupt the biofilm. NT images, on the other hand, were still too noisy to allow quantitative measurements. Therefore, X-ray microtomography (provided it uses non-disruptive contrast agents) seems to provide more reliable microstructural descriptors.

Insights into the Development of Phototrophic Biofilms in a Bioreactor by a Combination of X-ray Microtomography and Optical Coherence Tomography

As productive biofilms are increasingly gaining interest in research, the quantitative monitoring of biofilm formation on- or offline for the process remains a challenge. Optical coherence tomography (OCT) is a fast and often used method for scanning biofilms, but it has difficulty scanning through more dense optical materials. X-ray microtomography (μCT) can measure biofilms in most geometries but is very time-consuming. By combining both methods for the first time, the weaknesses of both methods could be compensated. The phototrophic cyanobacterium Tolypothrix distorta was cultured in a moving bed photobioreactor inside a biocarrier with a semi-enclosed geometry. An automated workflow was developed to process µCT scans of the biocarriers. This allowed quantification of biomass volume and biofilm-coverage on the biocarrier, both globally and spatially resolved. At the beginning of the cultivation, a growth limitation was detected in the outer region of the carrier, presumably due to shear stress. In the later phase, light limitations could be found inside the biocarrier. µCT data and biofilm thicknesses measured by OCT displayed good correlation. The latter could therefore be used to rapidly measure the biofilm formation in a process. The methods presented here can help gain a deeper understanding of biofilms inside a process and detect any limitations.

Light-Sheet Microscopy for Surface Topography Measurements and Quantitative Analysis

A novel light-sheet microscopy (LSM) system that uses the laser triangulation method to quantitatively calculate and analyze the surface topography of opaque samples is discussed. A spatial resolution of at least 10 μm in z-direction, 10 μm in x-direction and 25 μm in y-direction with a large field-of-view (FOV) is achieved. A set of sample measurements that verify the system′s functionality in various applications are presented. The system has a simple mechanical structure, such that the spatial resolution is easily improved by replacement of the objective, and a linear calibration formula, which enables convenient system calibration. As implemented, the system has strong potential for, e.g., industrial sample line inspections, however, since the method utilizes reflected/scattered light, it also has the potential for three-dimensional analysis of translucent and layered structures.

The case for examining fluid flow in municipal solid waste at the pore-scale - A review

In this paper, we discuss recent efforts from the last 20 years to describe transport in municipal solid waste (MSW). We first discuss emerging themes in the field to draw the reader's attention to a series of significant challenges. We then examine contributions regarding the modelling of leachate flow to study transport via mechanistic and stochastic approaches, at a variety of scales. Since MSW is a multiphase, biogeochemically active porous medium, and with the aim of providing a picture of transport phenomena in a wider context, we then discuss a selection of studies on leachate flow incorporating some of the complex landfill processes (e.g. biodegradation and settlement). It is clear from the literature survey that our understanding of transport phenomena exhibited by landfilled waste is far from complete. Attempts to model transport have largely consisted of applying representative elementary-scale models (the smallest volume which can be considered representative of the entire waste mass). Due to our limited understanding of fluid flow through landfilled waste, and the influence of simultaneously occurring biogeomechanical processes within the waste mass, elementary-scale models have been unable to fully describe the flow behaviour of MSW. Pore-scale modelling and experimental studies have proven to be a promising approach to study fluid flow through complex porous media. Here, we suggest that pore-scale modelling and experimental work may provide valuable insights into transport phenomena exhibited by MSW, which could then be used to revise elementary-scale models for improved representation of field-scale problems.