Intra-colony channel morphology in Escherichia coli biofilms is governed by nutrient availability and substrate stiffness

Bottura, Beatrice; Rooney, Liam M.; Hoskisson, Paul A.; McConnell, Gail

doi:10.1016/j.bioflm.2022.100084

Cited by 15 publications

(25 citation statements)

References 53 publications

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“…Cell–cell signaling might also be affected by these morphodynamics since different regions of the branched surface of a colony could become decoupled from each other—which in turn, could also affect overall colony function and internal colony morphology ( 133 ). Previous work on 2D growing colonies has shown metabolic cooperation between cells growing at the periphery of the colony and those located in the interior—ion channels enable long-range electric signaling between both regions of the colony, giving rise to spatially propagating metabolic waves ( 134 – 139 ).…”

Section: Discussionmentioning

confidence: 99%

Morphological instability and roughening of growing 3D bacterial colonies

Martínez-Calvo

Bhattacharjee

Bay

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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How do growing bacterial colonies get their shapes? While colony morphogenesis is well studied in two dimensions, many bacteria grow as large colonies in three-dimensional (3D) environments, such as gels and tissues in the body or subsurface soils and sediments. Here, we describe the morphodynamics of large colonies of bacteria growing in three dimensions. Using experiments in transparent 3D granular hydrogel matrices, we show that dense colonies of four different species of bacteria generically become morphologically unstable and roughen as they consume nutrients and grow beyond a critical size—eventually adopting a characteristic branched, broccoli-like morphology independent of variations in the cell type and environmental conditions. This behavior reflects a key difference between two-dimensional (2D) and 3D colonies; while a 2D colony may access the nutrients needed for growth from the third dimension, a 3D colony inevitably becomes nutrient limited in its interior, driving a transition to unstable growth at its surface. We elucidate the onset of the instability using linear stability analysis and numerical simulations of a continuum model that treats the colony as an “active fluid” whose dynamics are driven by nutrient-dependent cellular growth. We find that when all dimensions of the colony substantially exceed the nutrient penetration length, nutrient-limited growth drives a 3D morphological instability that recapitulates essential features of the experimental observations. Our work thus provides a framework to predict and control the organization of growing colonies—as well as other forms of growing active matter, such as tumors and engineered living materials—in 3D environments.

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Section: Discussionmentioning

confidence: 99%

Morphological instability and roughening of growing 3D bacterial colonies

Martínez-Calvo

Bhattacharjee

Bay

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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“…Nutrient availability has also proven to be as important at the initial steps of the biofilm formation e.g. in the layout of the bacteria, 28 as at the later stages in which water channels form for nutrient distribution, 11 and gradients are established. 29 The implication of nutrients at different hierarchical levels of the biofilm architecture can thus explain the effect of their concentration on a broad range of biofilm properties.…”

Section: Discussionmentioning

confidence: 99%

Nutrient availability influencesE. colibiofilm properties and the structure of purified curli amyloid fibers

Siri,

Vázquéz-Dávila,

Bidan

2023

Preprint

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Bacterial biofilms are highly adaptable and resilient to challenges. Nutrient availability can induce changes in biofilm growth, biomass, morphology, architecture and mechanical properties. Bacterial extracellular matrix plays a major role in achieving biofilm stability under different environmental conditions. Curli amyloid fibers are determining for the architecture and stiffness ofE. colibiofilms, but how this major matrix component adapts to different environmental cues remains unclear.Here, we investigated the effect of nutrient availability on both i) biofilm materials properties and ii) the structure and properties of curli amyloid fibers extracted from the biofilms. For this, we culturedE. coliW3110, which main matrix component is curli fibers. We quantified the size, mass and water content of the resulting biofilms and estimated their mechanical properties by microindentation. The curli amyloid fibers were then purified from the biofilms and their molecular structure and properties were studied by spectroscopic techniques. Our results show that the availability of nutrients in the substrate influences the yield of curli fibers, their structural composition and chemical stability, and suggest that these molecular features contribute to the stiffness of the biofilms. Biofilms grown on substrates with high nutrient concentration are softer, contain less curli fibers, and these fibers exhibit low β-sheet content and chemical stability.Our multiscale study sheds new light on the relationship between the molecular structure of bacterial matrix and the macroscopic properties of biofilms. This knowledge will benefit the development of both anti-biofilm strategies and biofilm-based materials.Graphical abstract

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“…Escherichia coli colonies were grown in different nutrient conditions by controlling the carbon and nitrogen concentrations in the growth media and were imaged using fluorescence mesoscopy with the Mesolens (Figure 1B). 9 Using a simple custom image analysis pipeline based on the open-source software FIJI and the Python programming language (Figure 1B), it was possible to measure intra-colony channel width at various positions inside the biofilm. These measurements were used to quantify the effect of nutrient availability on intra-colony channel architecture.…”

Section: Quantifying the Role Of Nutrient Availability On Channel Arc...mentioning

confidence: 99%

“…7 Here we report our progress on the application of the Mesolens and image analysis methods compatible with the large datasets it generates to advance our understanding of single-species and dual-species bacterial colonies growing on agar. 8,9 These microbial communities are notoriously difficult to study by optical microscopy because of their inherent structure; all such biofilms absorb and reflect light because they are densely packed with cell bodies and complex extracellular polymers. Moreover, biofilms exhibit phenotypes which often manifest in morphological changes to overexposure to light or the introduction of aqueous mountants.…”

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confidence: 99%

Addressing multiscale microbial challenges using the Mesolens

Rooney

Bottura

Baxter

et al. 2023

Journal of Microscopy

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We provide a brief review of the development and application of the Mesolens and its impact on microbiology. Microbial specimens such as infected tissue samples, colonies surfaces, and biofilms are routinely collected at the mesoscale. This means that they are relatively large multimillimetre-sized samples which contain microscopic detail that must be observed to answer important questions across various sectors. The Mesolens presents the ideal imaging method to study these specimens as no other optical microscope can thanks to its unique combination of low magnification and high numerical aperture providing large field-of-view, high-resolution imaging. We demonstrate the current applications of the Mesolens to microbial imaging and go on to outline the huge potential of the Mesolens to impact other key areas of microbiology. K E Y W O R D Sbiofilm, high-content imaging, mesoscopic imaging, microbiology From Louis Pasteur's disproof of spontaneous generation to Robert Koch's germ theory, our understanding of microorganisms has crucially depended on optical microscopy. Microscopes, essentially like those used by Pasteur and Koch, are still indispensable today as a complement to biochemical and molecular methods in the diagnosis of infection.However, despite its widespread application in microbiology, the optical microscope has not changed in basic design for over 100 years. The ratio of magnification to numerical aperture (NA) has been set to a fixed value of approximately 40:1 for all microscope objectives. The reason for this is wholly historical: this proportion gives an image in which the detail is suited to the capacity of the human eye. 1 In microbiology, a 4× NA 0.

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Intra-colony channel morphology in Escherichia coli biofilms is governed by nutrient availability and substrate stiffness

Cited by 15 publications

References 53 publications

Morphological instability and roughening of growing 3D bacterial colonies

Morphological instability and roughening of growing 3D bacterial colonies

Nutrient availability influencesE. colibiofilm properties and the structure of purified curli amyloid fibers

Addressing multiscale microbial challenges using the Mesolens

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