Automated 3D Optical Coherence Tomography to Elucidate Biofilm Morphogenesis Over Large Spatial Scales

Depetris, Anna; Wiedmer, Antoine; Wagner, Michael; Schäfer, Sebastian; Battin, Tom J.; Peter, Hannes

doi:10.3791/59356

Cited by 5 publications

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“…Numerical simulations further showed that the bed shear stress increased from 0.04 Pa to 0.13 Pa ( Figure 1 B). We used an automated OCT system ( Depetris et al, 2019 ) to characterize the biofilm surface topology at high resolution (40 μm, 40 μm, and 2.18 μm in x , y , z dimensions) across several spatial scales — ranging from patches formed by multicellular clusters (~100 μm) to the higher-order patterns emerging at the scale of the entire biofilm landscape (0.4 m in length) ( Figures 1 C–1G). The OCT scans did not evidence the presence of voids below the biofilm surface and were processed to obtain DEMs of the biofilm surface topology ( Depetris et al, 2019 ).…”

Section: Resultsmentioning

confidence: 99%

“…Here we applied an experimental and multi-scale approach to relate the structure and function of phototrophic biofilms to their hydraulic environment. We used an automated optical coherence tomography (OCT) system ( Depetris et al, 2019 ) to quantify the topography of the biofilm as a digital elevation model (DEM) over a large rectangular surface (0.025 m × 0.4 m). This approach is analogous to the in situ 3D imaging of forests and coral reefs providing quantitative and detailed structural information to test hypotheses relating structure to function of these ecosystems ( Calders et al., 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Morphogenesis and oxygen dynamics in phototrophic biofilms growing across a gradient of hydraulic conditions

et al. 2021

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Biofilms are surface-attached and matrix-enclosed microbial communities that dominate microbial life in numerous ecosystems. Using flumes and automated optical coherence tomography, we studied the morphogenesis of phototrophic biofilms along a gradient of hydraulic conditions. Compact and coalescent biofilms formed under elevated bed shear stress, whereas protruding clusters separated by troughs formed under reduced shear stress. This morphological differentiation did not linearly follow the hydraulic gradient, but a break point emerged around a shear stress of~0.08 Pa. While community composition did not differ between high and low shear environments, our results suggest that the morphological differentiation was linked to biomass displacement and reciprocal interactions between the biofilm structure and hydraulics. Mapping oxygen concentrations within and around biofilm structures, we provide empirical evidence for biofilm-induced alterations of oxygen mass transfer. Our findings suggest that architectural plasticity, efficient mass transfer, and resistance to shear stress contribute to the success of phototrophic biofilms.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Morphogenesis and oxygen dynamics in phototrophic biofilms growing across a gradient of hydraulic conditions

et al. 2021

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“…Biofilm development 25 mm downstream of the inlet was monitored daily for ten consecutive days by means of OCT using the EvoBot platform [20,49]. Briefly, the EvoBot platform allows the automated positioning of the OCT scanning probe as well as the acquisition of threedimensional OCT datasets similar to the platform described by Depetris et al [50]. Thereby, operator-related errors during dataset acquisition are reduced.…”

Section: Biofilm Cultivationmentioning

confidence: 99%

Impact of Fe2+ and Shear Stress on the Development and Mesoscopic Structure of Biofilms—A Bacillus subtilis Case Study

2022

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Bivalent cations are known to affect the structural and mechanical properties of biofilms. In order to reveal the impact of Fe2+ ions within the cultivation medium on biofilm development, structure and stability, Bacillus subtilis biofilms were cultivated in mini-fluidic flow cells. Two different Fe2+ inflow concentrations (0.25 and 2.5 mg/L, respectively) and wall shear stress levels (0.05 and 0.27 Pa, respectively) were tested. Mesoscopic biofilm structure was determined daily in situ and non-invasively by means of optical coherence tomography. A set of ten structural parameters was used to quantify biofilm structure, its development and change. The study focused on characterizing biofilm structure and development at the mesoscale (mm-range). Therefore, biofilm replicates (n = 10) were cultivated and analyzed. Three hypotheses were defined in order to estimate the effect of Fe2+ inflow concentration and/or wall shear stress on biofilm development and structure, respectively. It was not the intention to investigate and describe the underlying mechanisms of iron incorporation as this would require a different set of tools applied at microscopic levels as well as the use of, i.e., omic approaches. Fe2+ addition influenced biofilm development (e.g., biofilm accumulation) and structure markedly. Experiments revealed the accumulation of FeO(OH) within the biofilm matrix and a positive correlation of Fe2+ inflow concentration and biofilm accumulation. In more detail, independent of the wall shear stress applied during cultivation, biofilms grew approximately four times thicker at 2.5 mg Fe2+/L (44.8 µmol/L; high inflow concentration) compared to the low Fe2+ inflow concentration of 0.25 mg Fe2+/L (4.48 µmol/L). This finding was statistically verified (Scheirer–Ray–Hare test, ANOVA) and hints at a higher stability of Bacillus subtilis biofilms (e.g., elevated cohesive and adhesive strength) when grown at elevated Fe2+ inflow concentrations.

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“…However, 3D printers and CNC systems are delivered with specific software and it still takes much efforts converting hard-and software from 3D printing or routing/milling applications into an automated OCT-based monitoring setup for biofilms. However, if one is willing to accept these challenges, Depetris et al 19 recently presented their approach on a modified CNC machine 19 .…”

Section: Introductionmentioning

confidence: 99%

An open-source robotic platform that enables automated monitoring of replicate biofilm cultivations using optical coherence tomography

Gierl

Støy

Faina

et al. 2020

npj Biofilms Microbiomes

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The paper introduces a fully automated cultivation and monitoring tool to study biofilm development in replicate experiments operated in parallel. To gain a fundamental understanding of the relation between cultivation conditions and biofilm characteristics (e.g., structural, mechanical) a monitoring setup allowing for the standardization of methods is required. Optical coherence tomography (OCT) is an imaging modality ideal for biofilms since it allows for the monitoring of structure in real time. By integrating an OCT device into the open-source robotic platform EvoBot, a fully automated monitoring platform for investigating biofilm development in several flow cells at once was realized. Different positioning scenarios were tested and revealed that the positioning accuracy is within the optical resolution of the OCT. On that account, a reliable and accurate monitoring of biofilm development by means of OCT has become possible. With this robotic platform, reproducible biofilm experiments including a statistical analysis are achievable with only a small investment of operator time. Furthermore, a number of structural parameters calculated within this study confirmed the necessity to perform replicate biofilm cultivations.npj Biofilms and Microbiomes (2020) 6:18 ; https://doi.

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Automated 3D Optical Coherence Tomography to Elucidate Biofilm Morphogenesis Over Large Spatial Scales

Cited by 5 publications

References 0 publications

Morphogenesis and oxygen dynamics in phototrophic biofilms growing across a gradient of hydraulic conditions

Morphogenesis and oxygen dynamics in phototrophic biofilms growing across a gradient of hydraulic conditions

Impact of Fe2+ and Shear Stress on the Development and Mesoscopic Structure of Biofilms—A Bacillus subtilis Case Study

An open-source robotic platform that enables automated monitoring of replicate biofilm cultivations using optical coherence tomography

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