Activity-driven emergence of genealogical enclaves in growing bacterial colonies

E-print/Working paper (2023)

Bacterial dispersal, the movement of cells spanning diverse physical scales and environments, has been long investigated owing to its far-reaching ramifications in the ecology and evolution of bacterial ... [more ▼]

Bacterial dispersal, the movement of cells spanning diverse physical scales and environments, has been long investigated owing to its far-reaching ramifications in the ecology and evolution of bacterial species and their consortia. A major proportion of bacterial species are surface associated, yet if and how they disperse, specifically during the early stages of biofilm formation, remains to be understood. While physical vectors like fluid flow drive dispersal across large scales, surface-associated cells may benefit from the active biomechanical forces to navigate locally within a colony. Here, by analyzing sessile bacterial colonies, we study how cells disperse over generations due to the growth-induced forces under different conditions. A custom-built label-free algorithm, developed to track the progeny cells as they grow and divide, reveals the emergence of distinct self-similar genealogical enclaves which intermix over time. Biological activity, indicated by the division times, is a key determinant of the intermixing dynamics; while topological defects appearing at the interface of the enclaves mediate the morphology of finger-like interfacial domains. By quantifying the Shannon entropy, we show that dividing bacterial cells have spatial affinity to close relatives, at the cost of the entropically favourable option of intermixing, wherein faster growing colonies show higher drop in the Shannon entropy over time. A coarse-grained lattice modelling of such colonies, combined with insights from the thermodynamics of phase separation, suggest that the emergence of genealogical enclaves results from an interplay of growth-induced cell dispersal within the colony (which promotes intermixing) and stochasticity of cell division, alongwith the cell-cell interactions at a given growth condition. Our study uncovers the evolution of so-far hidden emergent self-organising features within growing bacterial colonies, which while displaying a high degree of self-similarity on a range of phenotypic traits, point at competing roles of growth-induced forces and entropic landscapes which ultimately shape the genealogical distance of cells to their kith and kin within growing colonies. [less ▲]

Phytoplankton tune local pH to actively modulate circadian swimming behavior

E-print/Working paper (2023)

Diel vertical migration (DVM), the diurnal exodus of motile phytoplankton between the light- and nutrient-rich aquatic regions, is governed by endogenous biological clocks. Many species exhibit irregular ... [more ▼]

Diel vertical migration (DVM), the diurnal exodus of motile phytoplankton between the light- and nutrient-rich aquatic regions, is governed by endogenous biological clocks. Many species exhibit irregular DVM patterns wherein out-of-phase gravitactic swimming–relative to that expected due to the endogenous rhythm–is observed. How cells achieve and control this irregular swimming behavior remains poorly understood. Combining local environmental monitoring with behavioral and physiological analyses of motile bloom-forming Heterosigma akaswhiwo cells, we report that phytoplankton species modulate their DVM pattern by progressively tuning local pH, yielding physiologically equivalent yet behaviorally distinct gravitactic sub-populations which remain separated vertically within a visibly homogeneous cell distribution. Individual and population-scale tracking of the isolated top and bottom sub-populations revealed similar gravitactic (swimming speed and stability) and physiological traits (growth rate and maximum photosynthetic yield), suggesting that the sub-populations emerge due to mutual co-existence. Exposing the top (bottom) sub-population to the spent media of the bottom (top) counterpart recreates the emergent vertical distribution, while no such phenomenon was observed when the sub-populations were exposed to their own spent media. A model of swimming mechanics based on the quantitative analysis of cell morphologies confirms that the emergent sub-populations represent distinct swimming stabilities, resulting from morphological transformations after the cells are exposed to the spent media. Together with the corresponding night-time dataset, we present an integrated picture of the circadian swimming, wherein active chemo-regulation of the local environment underpins motility variations for potential ecological advantages via intraspecific division of labor over the day-night cycle. This chemo-regulated migratory trait offers mechanistic insights into the irregular diel migration, relevant particularly for modelling phytoplankton transport, fitness and adaptation as globally, ocean waters see a persistent drop in the mean pH. [less ▲]

Spatio-temporal programming of lyotropic phase transition in nanoporous microfluidic confinements

in Journal of Colloid and Interface Science (2023)

The nanoporous polydimethylsiloxane (PDMS) surfaces of a rectangular microfluidic channel, selectively uptakes water molecules, concentrating the solute molecules in an aqueous phase, that could drive ... [more ▼]

The nanoporous polydimethylsiloxane (PDMS) surfaces of a rectangular microfluidic channel, selectively uptakes water molecules, concentrating the solute molecules in an aqueous phase, that could drive phase transitions. Factors such as surface wettability, channel geometry, the surface-to-volume ratio, and surface topography of the confinements could play a key role in tuning the phase transitions spatio-temporally. Here, using a lyotropic chromonic liquid crystal as model biological material, confined within nanoporous microfluidic environments, we study molecular assembly driven by nanoporous substrates. Using a combination of timelapse polarized imaging, quantitative image processing, and a simple mathematical model, we analyze the phase transitions and construct a master diagram capturing the role of surface wettability, channel geometry and embedded topography on programmable lyotropic phase transitions. Intrinsic PDMS nanoporosity and confinement cross-section, together with the imposed wettability regulate the rate of the N-M phase transition; whereas the microfluidic geometry and embedded topography enable phase transition at targeted locations. We harness the emergent long-range order during N-M transition to actuate elasto-advective transport of embedded micro-cargo, demonstrating particle manipulation concepts governed by tunable phase transitions. Our results present a programmable physical route to material assembly in microfluidic environment, and offer a new paradigm for assembling genetic components, biological cargo, and minimal synthetic cells. [less ▲]

Drying of Bio-colloidal Sessile Droplets: Advances, Applications, and Perspectives

in Advances in Colloid and Interface Science (2023)

Drying of biologically-relevant sessile droplets, including passive systems (like DNA and proteins), as well as active microbial systems comprising bacteria and algae, has garnered considerable attention ... [more ▼]

Drying of biologically-relevant sessile droplets, including passive systems (like DNA and proteins), as well as active microbial systems comprising bacteria and algae, has garnered considerable attention over the last decades. Distinct morphological patterns emerge when bio-colloids undergo drying, with significant potential in a range of biomedical applications, spanning bio-sensing, medical diagnostics, drug delivery, and antimicrobial resistance. This review presents a comprehensive overview of bio-colloidal droplets drying on solid substrates, focusing on the experimental progress during the last ten years. We provide a summary of the relevant properties of bio-colloids and link their composition (constituent particles, solvent, and concentrations) to the patterns emerging due to drying. We examined the drying patterns generated by passive bio-colloids (DNA, globular, fibrous, and composite proteins, plasma, serum, blood, urine, tears, saliva). This article highlights how morphological patterns are influenced by the nature of the biological entities and the solvent, micro- and global environmental conditions. Correlations between emergent patterns and the initial droplet compositions enable the detection of potential clinical abnormalities when compared with the patterns of drying droplets of healthy control samples, offering a diagnostic blueprint. Recent experimental investigations of pattern formation in the bio-mimetic and salivary drying droplets, relevant to COVID-19 are also presented. Finally, we summarize the role of biologically active agents in drying process, including bacteria and algae during the drying process. The review concludes with a perspective on the next generation of research and applications based on drying droplets, enabling potential innovations and tools to study this exciting interface of physics, biology, data sciences, and machine learning. [less ▲]

Planktonic Active Matter

E-print/Working paper (2023)

Planktonic active matter represents an emergent system spanning different scales: individual, population and community; and complexity arising from sub-cellular and cellular to collective and ecosystem ... [more ▼]

Planktonic active matter represents an emergent system spanning different scales: individual, population and community; and complexity arising from sub-cellular and cellular to collective and ecosystem scale dynamics. This cross-scale active matter system responds to a range of abiotic (temperature, fluid flow and light conditions) and biotic factors (nutrients, pH, secondary metabolites) characteristic to the relevant ecosystems they are part of. Active modulation of cell phenotypes, including morphology, motility, and intracellular organization enable planktonic microbes to dynamically interact with other individuals and species; and adapt - often rapidly - to the changes in their environment. In this chapter, I discuss both traditional and contemporary approaches to study the dynamics of this multi-scale active matter system from a mechanistic standpoint, with specific references to their local settings and their ability to actively tune the behaviour and physiology, and the emergent structures and functions they elicit under natural ecological constraints as well as due to the shifting climatic trends. [less ▲]

Curvature in Biological Systems: Its quantification, Emergence and Implications Across the Scales

in Advanced Materials (2022)

Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature ... [more ▼]

Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology has been supported by numerous recent experimental and theoretical investigations in recent years. In this review, we first give a brief introduction to the key ideas of surface curvature in the context of biological systems and discuss the challenges that arise when measuring surface curvature. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, we address the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological and mechanical processes but that curvature acts also as a signal that co-determines these processes. [less ▲]

Spatio-temporal programming of lyotropic phase transition in nanoporous microfluidic confinements

E-print/Working paper (2022)

Self-assembly of simple molecules into complex phases can be driven by physical constraints, for instance, due to selective molecular uptake by nanoporous surfaces. Despite the significance of surface ... [more ▼]

Self-assembly of simple molecules into complex phases can be driven by physical constraints, for instance, due to selective molecular uptake by nanoporous surfaces. Despite the significance of surface-mediated assembly in evolution of life, physical routes to molecular enrichment and assembly have remained overlooked. Here, using a lyotropic chromonic liquid crystal as model biological material, confined within nanoporous microfluidic environments, we study molecular assembly driven by nanoporous substrates. We demonstrate that nanoporous polydimethylsiloxane (PDMS) surfaces, due to selective permeation of water molecules, drive transition of disordered isotropic phase to ordered nematic, and higher order columnar phases under isothermal conditions. Synergistically, by tailoring the wettability, the surface-to-volume ratio, and surface topography of the confinements, we program the lyotropic phase transitions with a high degree of spatial and temporal control. Using a combination of timelapse polarized imaging, quantitative image processing, and a simple mathematical model, we analyze the phase transitions, and construct a master diagram capturing the role of surface wettability and channel geometry on programmable lyotropic phase transitions. Intrinsic PDMS nanoporosity and confinement cross-section, together with the imposed wettability regulate the rate of the N-M phase transition; whereas the microfluidic geometry and embedded topography enable phase transition at targeted locations. We harness the emergent long-range order during N-M transition to actuate elasto-advective transport of embedded micro-cargo, demonstrating particle manipulation concepts governed by tunable phase transitions. Our results present a programmable physical route to material assembly, and offer a new paradigm for assembling genetic components, biological cargo, and minimal synthetic cells. [less ▲]

Complex Dance of Light-Seeking Algae in Light Gradients

Article for general public (2022)

A population of photosynthetic algae has been shown to exhibit a highly nonlinear response to light, forming dynamic structures in light-intensity gradients. Two longstanding questions about this light ... [more ▼]

A population of photosynthetic algae has been shown to exhibit a highly nonlinear response to light, forming dynamic structures in light-intensity gradients. Two longstanding questions about this light response regard how light-seeking cells move in a light-intensity gradient and whether this motion depends on cell concentration. Aina Ramamonjy and colleagues investigated the dynamics of dilute and semi dilute suspensions of these algae in a light-intensity gradient (varying from darkness to bright green light). The results could improve our understanding of how groups of photosynthetic organisms arrange themselves into dynamic patterns to control the amount of light that they receive. [less ▲]

Active reconfiguration of cytoplasmic lipid droplets governs migration of nutrient-limited phytoplankton

E-print/Working paper (2021)

As open oceans continue to warm, modified currents and enhanced stratification exacerbate nitrogen and phosphorus limitation, constraining primary production. The ability to migrate vertically bestows ... [more ▼]

As open oceans continue to warm, modified currents and enhanced stratification exacerbate nitrogen and phosphorus limitation, constraining primary production. The ability to migrate vertically bestows motile phytoplankton a crucial–albeit energetically expensive–advantage toward vertically redistributing for optimal growth, uptake and resource storage in nutrient-limited water columns. However, this traditional view discounts the possibility that the phytoplankton migration strategy may be actively selected by the storage dynamics when nutrients turn limiting. Here we report that storage and migration in phytoplankton are coupled traits, whereby motile species harness energy storing lipid droplets (LDs) to biomechanically regulate migration in nutrient limited settings. LDs grow and translocate–directionally–within the cytoplasm to accumulate below the cell nucleus, tuning the speed, trajectory and stability of swimming cells. Nutrient reincorporation reverses the LD translocation, restoring the homeostatic migratory traits measured in population-scale millifluidic experiments. Combining intracellular LD tracking and quantitative morphological analysis of red-tide forming alga, Heterosigma akashiwo, along with a model of cell mechanics, we discover that the size and spatial localization of growing LDs govern the ballisticity and orientational stability of migration. The strain-specific shifts in migration which we identify here are amenable to a selective emergence of mixotrophy in nutrient-limited phytoplankton. We rationalize these distinct behavioral acclimatization in an ecological context, relying on concomitant tracking of the photophysiology and reactive oxygen species (ROS) levels, and propose a dissipative energy budget for motile phytoplankton alleviating nutrient limitation. The emergent resource acquisition strategies, enabled by distinct strain-specific migratory acclimatizing mechanisms, highlight the active role of the reconfigurable cytoplasmic LDs in guiding vertical movement. By uncovering the mechanistic coupling between dynamics of intracellular changes to physiologically-governed migration strategies, this work offers a tractable framework to delineate diverse strategies which phytoplankton may harness to maximize fitness and resource pool in nutrient-limited open oceans of the future. [less ▲]

Trade-offs in phenotypic noise synchronize emergent topology to actively enhance transport in microbial environments

E-print/Working paper (2021)

Phenotypic noise underpins homeostasis and fitness of individual cells. Yet, the extent to which noise shapes cell-to-population properties in microbial active matter remains poorly understood. By ... [more ▼]

Phenotypic noise underpins homeostasis and fitness of individual cells. Yet, the extent to which noise shapes cell-to-population properties in microbial active matter remains poorly understood. By quantifying variability in confluent \textit{E.coli} strains, we catalogue noise across different phenotypic traits. The noise, measured over different temperatures serving as proxy for cellular activity, spanned more than two orders of magnitude. The maximum noise was associated with the cell geometry and the critical colony area at the onset of mono-to-multilayer transition (MTMT), while the lower bound was set by the critical time of the MTMT. Our results, supported by a hydrodynamic model, suggest that a trade-off between the noise in the cell geometry and the growth rate can lead to the self-regulation of the MTMT timing. The MTMT cascades synchronous emergence of hydrodynamic fields, actively enhancing the micro-environmental transport. Our results highlight how interplay of phenotypic noise triggers emergent deterministic properties, and reveal the role of multifield topology--of the colony structure and hydrodynamics--to insulate confluent systems from the inherent noise associated with natural cell-environment settings. [less ▲]