Coupling between distant biofilms and emergence of nutrient time-sharing

Heterogeneity in respiratory electron transfer and adaptive iron utilization in a bacterial biofilm

In Bacillus subtilis, robust biofilm formation requires large quantities of ferric iron. Here we show that this process requires preferential production of a siderophore precursor, 2,3-dihydroxybenzoate, instead of the siderophore bacillibactin. A large proportion of iron is associated extracellularly with the biofilm matrix. The biofilms are conductive, with extracellular iron potentially acting as electron acceptor. A relatively small proportion of ferric iron is internalized and boosts production of iron-containing enzymes involved in respiratory electron transfer and establishing strong membrane potential, which is key to biofilm matrix production. Our study highlights metabolic diversity and versatile energy generation strategies within B. subtilis biofilms.

Biofilm formation in Bacillus subtilis requires high levels of ferric iron. Here, Qin et al. show that iron accumulation requires production of dihydroxybenzoate (a precursor in siderophore biosynthesis), and matrix-associated iron may be acting as extracellular electron acceptor during respiratory electron transfer.

Metabolic basis of brain-like electrical signalling in bacterial communities

Information processing in the mammalian brain relies on a careful regulation of the membrane potential dynamics of its constituent neurons, which propagates across the neuronal tissue via electrical signalling. We recently reported the existence of electrical signalling in a much simpler organism, the bacterium Bacillus subtilis. In dense bacterial communities known as biofilms, nutrient-deprived B. subtilis cells in the interior of the colony use electrical communication to transmit stress signals to the periphery, which interfere with the growth of peripheral cells and reduce nutrient consumption, thereby relieving stress from the interior. Here, we explicitly address the interplay between metabolism and electrophysiology in bacterial biofilms, by introducing a spatially extended mathematical model that combines the metabolic and electrical components of the phenomenon in a discretized reaction-diffusion scheme. The model is experimentally validated by environmental and genetic perturbations, and confirms that metabolic stress is transmitted through the bacterial population via a potassium wave. Interestingly, this behaviour is reminiscent of cortical spreading depression in the brain, characterized by a wave of electrical activity mediated by potassium diffusion that has been linked to various neurological disorders, calling for future studies on the evolutionary link between the two phenomena. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.

Electrical Polarization Enables Integrative Quality Control during Bacterial Differentiation into Spores

Quality control of offspring is important for the survival of cells. However, the mechanisms by which quality of offspring cells may be checked while running genetic programs of cellular differentiation remain unclear. Here we investigated quality control during sporulating in Bacillus subtilis by combining single-cell time-lapse microscopy, molecular biology, and mathematical modeling. Our results revealed that the quality control via premature germination is coupled with the electrical polarization of outer membranes of developing forespores. The forespores that accumulate fewer cations on their surface are more likely to be aborted. This charge accumulation enables the projection of multi-dimensional information about the external environment and morphological development of the forespore into one-dimensional information of cation accumulation. We thus present a paradigm of cellular regulation by bacterial electrical signaling. Moreover, based on the insight we gain, we propose an electrophysiology-based approach of reducing the yield and quality of Bacillus endospores.

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Quality control during bacterial sporulation is coupled with cation accumulation

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Cation accumulation prevents premature germination

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Cation accumulation integrates information on morphological defects and environments

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Spores are less fit when sporulated with Thioflavin T

Emergence of active nematics in chaining bacterial biofilms

Growing tissue and bacterial colonies are active matter systems where cell divisions and cellular motion generate active stress. Although they operate in the non-equilibrium regime, these biological systems can form large-scale ordered structures. How mechanical instabilities drive the dynamics of active matter systems and form ordered structures are not well understood. Here, we use chaining Bacillus subtilis, also known as a biofilm, to study the relation between mechanical instabilities and nematic ordering. We find that bacterial biofilms have intrinsic length scales above which a series of mechanical instabilities occur. Localized stress and friction drive buckling and edge instabilities which further create nematically aligned structures and topological defects. We also observe that topological defects control stress distribution and initiate the formation of sporulation sites by creating three-dimensional structures. In this study we propose an alternative active matter platform to study the essential roles of mechanics in growing biological tissue.

Metabolic Remodeling during Biofilm Development of Bacillus subtilis

Bacterial biofilms are ubiquitous in natural environments and play an important role in many clinical, industrial, and ecological settings. Although much is known about the transcriptional regulatory networks that control biofilm formation in model bacteria such as Bacillus subtilis, very little is known about the role of metabolism in this complex developmental process. To address this important knowledge gap, we performed a time-resolved analysis of the metabolic changes associated with bacterial biofilm development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. Here, we report a widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. This report serves as a unique hypothesis-generating resource for future studies on bacterial biofilm physiology. Outside the biofilm research area, this work should also prove relevant to any investigators interested in microbial physiology and metabolism.

Biofilms are structured communities of tightly associated cells that constitute the predominant state of bacterial growth in natural and human-made environments. Although the core genetic circuitry that controls biofilm formation in model bacteria such as Bacillus subtilis has been well characterized, little is known about the role that metabolism plays in this complex developmental process. Here, we performed a time-resolved analysis of the metabolic changes associated with pellicle biofilm formation and development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. We report surprisingly widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. Most of these metabolic alterations were hitherto unrecognized as biofilm associated. For example, we observed increased activity of the tricarboxylic acid (TCA) cycle during early biofilm growth, a shift from fatty acid biosynthesis to fatty acid degradation, reorganization of iron metabolism and transport, and a switch from acetate to acetoin fermentation. Close agreement between metabolomic, transcriptomic, and proteomic measurements indicated that remodeling of metabolism during biofilm development was largely controlled at the transcriptional level. Our results also provide insights into the transcription factors and regulatory networks involved in this complex metabolic remodeling. Following upon these results, we demonstrated that acetoin production via acetolactate synthase is essential for robust biofilm growth and has the dual role of conserving redox balance and maintaining extracellular pH. This report represents a comprehensive systems-level investigation of the metabolic remodeling occurring during B. subtilis biofilm development that will serve as a useful road map for future studies on biofilm physiology.

Synchronization of Bioelectric Oscillations in Networks of Nonexcitable Cells: From Single-Cell to Multicellular States

Biological networks use collective oscillations for information processing tasks. In particular, oscillatory membrane potentials have been observed in nonexcitable cells and bacterial communities where specific ion channel proteins contribute to the bioelectric coordination of large populations. We aim at describing theoretically the oscillatory spatiotemporal patterns that emerge at the multicellular level from the single-cell bioelectric dynamics. To this end, we focus on two key questions: (i) What single-cell properties are relevant to multicellular behavior? (ii) What properties defined at the multicellular level can allow an external control of the bioelectric dynamics? In particular, we explore the interplay between transcriptional and translational dynamics and membrane potential dynamics in a model multicellular ensemble, describe the spatiotemporal patterns that arise when the average electric potential allows groups of cells to act as a coordinated multicellular patch, and characterize the resulting synchronization phenomena. The simulations concern bioelectric networks and collective communication across different scales based on oscillatory and synchronization phenomena, thus shedding light on the physiological dynamics of a wide range of endogenous contexts across embryogenesis and regeneration.

Emergence of three-dimensional order and structure in growing biofilms

Surface-attached bacterial biofilms are self-replicating active liquid crystals and the dominant form of bacterial life on earth (1-4). In conventional liquid crystals and solid-state materials, the interaction potentials between the molecules that comprise the system determine the material properties. However, for growth-active biofilms it is unclear whether potential-based descriptions can account for the experimentally observed morphologies, and which potentials would be relevant. Here, we overcame previous limitations of single-cell imaging techniques (5,6) to reconstruct and track all individual cells inside growing three-dimensional (3D) biofilms with up to 10,000 individuals. Based on these data, we identify, constrain, and provide a microscopic basis for an effective cell-cell interaction potential, which captures and predicts the growth dynamics, emergent architecture, and local liquid crystalline order of Vibrio cholerae biofilms. Furthermore, we show how external fluid flows control the microscopic structure and 3D morphology of biofilms. Our analysis implies that local cellular order and global biofilm architecture in these active bacterial communities can arise from mechanical cell-cell interactions, which cells can modulate by regulating the production of particular matrix components. These results establish an experimentally validated foundation for improved continuum theories of active matter and thereby contribute to solving the important problem of controlling biofilm growth.

From molecules to multispecies ecosystems: the roles of structure in bacterial biofilms

Biofilms are communities of sessile microbes that are bound to each other by a matrix made of biopolymers and proteins. Spatial structure is present in biofilms on many lengthscales. These range from the nanometer scale of molecular motifs to the hundred-micron scale of multicellular aggregates. Spatial structure is a physical property that impacts the biology of biofilms in many ways. The molecular structure of matrix components controls their interaction with each other (thereby impacting biofilm mechanics) and with diffusing molecules such as antibiotics and immune factors (thereby impacting antibiotic tolerance and evasion of the immune system). The size and structure of multicellular aggregates, combined with microbial consumption of growth substrate, give rise to differentiated microenvironments with different patterns of metabolism and gene expression. Spatial association of more than one species can benefit one or both species, while distances between species can both determine and result from the transport of diffusible factors between species. Thus, a widespread theme in the biological importance of spatial structure in biofilms is the effect of structure on transport. We survey what is known about this and other effects of spatial structure in biofilms, from molecules up to multispecies ecosystems. We conclude with an overview of what experimental approaches have been developed to control spatial structure in biofilms and how these and other experiments can be complemented with computational work.

Magnesium Flux Modulates Ribosomes to Increase Bacterial Survival

Bacteria exhibit cell-to-cell variability in their resilience to stress, for example, following antibiotic exposure. Higher resilience is typically ascribed to "dormant" non-growing cellular states. Here, by measuring membrane potential dynamics of Bacillus subtilis cells, we show that actively growing bacteria can cope with ribosome-targeting antibiotics through an alternative mechanism based on ion flux modulation. Specifically, we observed two types of cellular behavior: growth-defective cells exhibited a mathematically predicted transient increase in membrane potential (hyperpolarization), followed by cell death, whereas growing cells lacked hyperpolarization events and showed elevated survival. Using structural perturbations of the ribosome and proteomic analysis, we uncovered that stress resilience arises from magnesium influx, which prevents hyperpolarization. Thus, ion flux modulation provides a distinct mechanism to cope with ribosomal stress. These results suggest new approaches to increase the effectiveness of ribosome-targeting antibiotics and reveal an intriguing connection between ribosomes and the membrane potential, two fundamental properties of cells.

Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations

BACKGROUND

Microbial communities are susceptible to the public goods dilemma, whereby individuals can gain an advantage within a group by utilizing, but not sharing the cost of producing, public goods. In bacteria, the development of quorum sensing (QS) can establish a cooperation system in a population by coordinating the production of costly and sharable extracellular products (public goods). Cooperators with intact QS system and robust ability in producing public goods are vulnerable to being undermined by QS-deficient defectors that escape from QS but benefit from the cooperation of others. Although microorganisms have evolved several mechanisms to resist cheating invasion in the public goods game, it is not clear why cooperators frequently coexist with defectors and how they form a relatively stable equilibrium during evolution.

RESULTS

We show that in Pseudomonas aeruginosa, QS-directed social cooperation can select a conditional defection strategy prior to the emergence of QS-mutant defectors, depending on resource availability. Conditional defectors represent a QS-inactive state of wild type (cooperator) individual and can invade QS-activated cooperators by adopting a cheating strategy, and then revert to cooperating when there are abundant nutrient supplies irrespective of the exploitation of QS-mutant defector. Our mathematical modeling further demonstrates that the incorporation of conditional defection strategy into the framework of iterated public goods game with sound punishment mechanism can lead to the coexistence of cooperator, conditional defector, and defector in a rock-paper-scissors dynamics.

CONCLUSIONS

These findings highlight the importance of behavioral heterogeneity in stabilizing the population structure and provide a potential reasonable explanation for the maintenance and evolution of cooperation in microbial communities.

Biological Engineered Living Materials: Growing Functional Materials with Genetically Programmable Properties

Natural biological materials exhibit remarkable properties: self-assembly from simple raw materials, precise control of morphology, diverse physical and chemical properties, self-repair, and the ability to sense-and-respond to environmental stimuli. Despite having found numerous uses in human industry and society, the utility of natural biological materials is limited. But, could it be possible to genetically program microbes to create entirely new and useful biological materials? At the intersection between microbiology, material science, and synthetic biology, the emerging field of biological engineered living materials (ELMs) aims to answer this question. Here we review recent efforts to program cells to produce living materials with novel functional properties, focusing on microbial systems that can be engineered to grow materials and on new genetic circuits for pattern formation that could be used to produce the more complex systems of the future.

Cell-cell bioelectrical interactions and local heterogeneities in genetic networks: a model for the stabilization of single-cell states and multicellular oscillations

Genetic networks operate in the presence of local heterogeneities in single-cell transcription and translation rates. Bioelectrical networks and spatio-temporal maps of cell electric potentials can influence multicellular ensembles. Could cell-cell bioelectrical interactions mediated by intercellular gap junctions contribute to the stabilization of multicellular states against local genetic heterogeneities? We theoretically analyze this question on the basis of two well-established experimental facts: (i) the membrane potential is a reliable read-out of the single-cell electrical state and (ii) when the cells are coupled together, their individual cell potentials can be influenced by ensemble-averaged electrical potentials. We propose a minimal biophysical model for the coupling between genetic and bioelectrical networks that associates the local changes occurring in the transcription and translation rates of an ion channel protein with abnormally low (depolarized) cell potentials. We then analyze the conditions under which the depolarization of a small region (patch) in a multicellular ensemble can be reverted by its bioelectrical coupling with the (normally polarized) neighboring cells. We show also that the coupling between genetic and bioelectric networks of non-excitable cells, modulated by average electric potentials at the multicellular ensemble level, can produce oscillatory phenomena. The simulations show the importance of single-cell potentials characteristic of polarized and depolarized states, the relative sizes of the abnormally polarized patch and the rest of the normally polarized ensemble, and intercellular coupling.

Learning the space-time phase diagram of bacterial swarm expansion

Most living systems, from individual cells to tissues and swarms, display collective self-organization on length scales that are much larger than those of the individual units that drive this organization. A fundamental challenge is to understand how properties of microscopic components determine macroscopic, multicellular biological function. Our study connects intracellular physiology to macroscale collective behaviors during multicellular development, spanning five orders of magnitude in length and six orders of magnitude in time, using bacterial swarming as a model system. This work is enabled by a high-throughput adaptive microscopy technique, which we combined with genetics, machine learning, and mathematical modeling to reveal the phase diagram of bacterial swarming and that cell–cell interactions within each swarming phase are dominated by mechanical interactions.

Coordinated dynamics of individual components in active matter are an essential aspect of life on all scales. Establishing a comprehensive, causal connection between intracellular, intercellular, and macroscopic behaviors has remained a major challenge due to limitations in data acquisition and analysis techniques suitable for multiscale dynamics. Here, we combine a high-throughput adaptive microscopy approach with machine learning, to identify key biological and physical mechanisms that determine distinct microscopic and macroscopic collective behavior phases which develop as Bacillus subtilis swarms expand over five orders of magnitude in space. Our experiments, continuum modeling, and particle-based simulations reveal that macroscopic swarm expansion is primarily driven by cellular growth kinetics, whereas the microscopic swarming motility phases are dominated by physical cell–cell interactions. These results provide a unified understanding of bacterial multiscale behavioral complexity in swarms.

Flavin-based metabolic cycles are integral features of growth and division in single yeast cells

The yeast metabolic cycle (YMC) is a fascinating example of biological organization, in which cells constrain the function of specific genetic, protein and metabolic networks to precise temporal windows as they grow and divide. However, understanding the intracellular origins of the YMC remains a challenging goal, as measuring the oxygen oscillations traditionally associated with it requires the use of synchronized cultures growing in nutrient-limited chemostat environments. To address these limitations, we used custom-built microfluidic devices and time-lapse fluorescence microscopy to search for metabolic cycling in the form of endogenous flavin fluorescence in unsynchronized single yeast cells. We uncovered robust and pervasive metabolic cycles that were synchronized with the cell division cycle (CDC) and oscillated across four different nutrient conditions. We then studied the response of these metabolic cycles to chemical and genetic perturbations, showing that their phase synchronization with the CDC can be altered through treatment with rapamycin, and that metabolic cycles continue even in respiratory deficient strains. These results provide a foundation for future studies of the physiological importance of metabolic cycles in processes such as CDC control, metabolic regulation and cell aging.

Social behaviours by Bacillus subtilis: quorum sensing, kin discrimination and beyond

Here, we review the multiple mechanisms that the Gram‐positive bacterium Bacillus subtilis uses to allow it to communicate between cells and establish community structures. The modes of action that are used are highly varied and include routes that sense pheromone levels during quorum sensing and control gene regulation, the intimate coupling of cells via nanotubes to share cytoplasmic contents, and long‐range electrical signalling to couple metabolic processes both within and between biofilms. We explore the ability of B. subtilis to detect ‘kin’ (and ‘cheater cells’) by looking at the mechanisms used to potentially ensure beneficial sharing (or limit exploitation) of extracellular ‘public goods’. Finally, reflecting on the array of methods that a single bacterium has at its disposal to ensure maximal benefit for its progeny, we highlight that a large future challenge will be integrating how these systems interact in mixed‐species communities.

Intercellular Connectivity and Multicellular Bioelectric Oscillations in Nonexcitable Cells: A Biophysical Model

Bioelectricity is emerging as a crucial mechanism for signal transmission and processing from the single-cell level to multicellular domains. We explore theoretically the oscillatory dynamics that result from the coupling between the genetic and bioelectric descriptions of nonexcitable cells in multicellular ensembles, connecting the genetic prepatterns defined over the ensemble with the resulting spatio-temporal map of cell potentials. These prepatterns assume the existence of a small patch in the ensemble with locally low values of the genetic rate constants that produce a specific ion channel protein whose conductance promotes the cell-polarized state (inward-rectifying channel). In this way, the short-range interactions of the cells within the patch favor the depolarized membrane potential state, whereas the long-range interaction of the patch with the rest of the ensemble promotes the polarized state. The coupling between the local and long-range bioelectric signals allows a binary control of the patch membrane potentials, and alternating cell polarization and depolarization states can be maintained for optimal windows of the number of cells and the intercellular connectivity in the patch. The oscillatory phenomena emerge when the feedback between the single-cell bioelectric and genetic dynamics is coupled at the multicellular level. In this way, the intercellular connectivity acts as a regulatory mechanism for the bioelectrical oscillations. The simulation results are qualitatively discussed in the context of recent experimental studies.

Dissipative structures in biological systems: bistability, oscillations, spatial patterns and waves

The goal of this review article is to assess how relevant is the concept of dissipative structure for understanding the dynamical bases of non-equilibrium self-organization in biological systems, and to see where it has been applied in the five decades since it was initially proposed by Ilya Prigogine. Dissipative structures can be classified into four types, which will be considered, in turn, and illustrated by biological examples: (i) multistability, in the form of bistability and tristability, which involve the coexistence of two or three stable steady states, or in the form of birhythmicity, which involves the coexistence between two stable rhythms; (ii) temporal dissipative structures in the form of sustained oscillations, illustrated by biological rhythms; (iii) spatial dissipative structures, known as Turing patterns; and (iv) spatio-temporal structures in the form of propagating waves. Rhythms occur with widely different periods at all levels of biological organization, from neural, cardiac and metabolic oscillations to circadian clocks and the cell cycle; they play key roles in physiology and in many disorders. New rhythms are being uncovered while artificial ones are produced by synthetic biology. Rhythms provide the richest source of examples of dissipative structures in biological systems. Bistability has been observed experimentally, but has primarily been investigated in theoretical models in an increasingly wide range of biological contexts, from the genetic to the cell and animal population levels, both in physiological conditions and in disease. Bistable transitions have been implicated in the progression between the different phases of the cell cycle and, more generally, in the process of cell fate specification in the developing embryo. Turing patterns are exemplified by the formation of some periodic structures in the course of development and by skin stripe patterns in animals. Spatio-temporal patterns in the form of propagating waves are observed within cells as well as in intercellular communication. This review illustrates how dissipative structures of all sorts abound in biological systems.This article is part of the theme issue 'Dissipative structures in matter out of equilibrium: from chemistry, photonics and biology (part 1)'.

What are the advantages of living in a community? A microbial biofilm perspective!

Biofilm formation is the preferred mode of growth lifestyle for many microorganisms, including bacterial and fungal human pathogens. Biofilm is a strong and dynamic structure that confers a broad range of advantages to its members, such as adhesion/cohesion capabilities, mechanical properties, nutritional sources, metabolite exchange platform, cellular communication, protection and resistance to drugs (e.g., antimicrobials, antiseptics, and disinfectants), environmental stresses (e.g., dehydration and ultraviolet light), host immune attacks (e.g., antibodies, complement system, antimicrobial peptides, and phagocytes), and shear forces. Microbial biofilms cause problems in the hospital environment, generating high healthcare costs and prolonged patient stay, which can result in further secondary microbial infections and various health complications. Consequently, both public and private investments must be made to ensure better patient management, as well as to find novel therapeutic strategies to circumvent the resistance and resilience profiles arising from biofilm-associated microbial infections. In this work, we present a general overview of microbial biofilm formation and its relevance within the biomedical context.

Signal Percolation within a Bacterial Community

Signal transmission among cells enables long-range coordination in biological systems. However, the scarcity of quantitative measurements hinders the development of theories that relate signal propagation to cellular heterogeneity and spatial organization. We address this problem in a bacterial community that employs electrochemical cell-to-cell communication. We developed a model based on percolation theory, which describes how signals propagate through a heterogeneous medium. Our model predicts that signal transmission becomes possible when the community is organized near a critical phase transition between a disconnected and a fully connected conduit of signaling cells. By measuring population-level signal transmission with single-cell resolution in wild-type and genetically modified communities, we confirm that the spatial distribution of signaling cells is organized at the predicted phase transition. Our findings suggest that at this critical point, the population-level benefit of signal transmission outweighs the single-cell level cost. The bacterial community thus appears to be organized according to a theoretically predicted spatial heterogeneity that promotes efficient signal transmission.

Microfluidics and single-cell microscopy to study stochastic processes in bacteria

Bacteria have molecules present in low and fluctuating numbers that randomize cell behaviors. Understanding these stochastic processes and their impact on cells has, until recently, been limited by the lack of single-cell measurement methods. Here, we review recent developments in microfluidics that enable following individual cells over long periods of time under precisely controlled conditions, and counting individual fluorescent molecules in many cells. We showcase discoveries that were made possible using these devices in various aspects of microbiology, such as antibiotic tolerance/persistence, cell-size control, cell-fate determination, DNA damage response, and synthetic biology.

Information transmission in microbial and fungal communication: from classical to quantum

Microbes have their own communication systems. Secretion and reception of chemical signaling molecules and ion-channels mediated electrical signaling mechanism are yet observed two special ways of information transmission in microbial community. In this article, we address the aspects of various crucial machineries which set the backbone of microbial cell-to-cell communication process such as quorum sensing mechanism (bacterial and fungal), quorum sensing regulated biofilm formation, gene expression, virulence, swarming, quorum quenching, role of noise in quorum sensing, mathematical models (therapy model, evolutionary model, molecular mechanism model and many more), synthetic bacterial communication, bacterial ion-channels, bacterial nanowires and electrical communication. In particular, we highlight bacterial collective behavior with classical and quantum mechanical approaches (including quantum information). Moreover, we shed a new light to introduce the concept of quantum synthetic biology and possible cellular quantum Turing test.

Metabolic interactions between dynamic bacterial subpopulations

Individual microbial species are known to occupy distinct metabolic niches within multi-species communities. However, it has remained largely unclear whether metabolic specialization can similarly occur within a clonal bacterial population. More specifically, it is not clear what functions such specialization could provide and how specialization could be coordinated dynamically. Here, we show that exponentially growing Bacillus subtilis cultures divide into distinct interacting metabolic subpopulations, including one population that produces acetate, and another population that differentially expresses metabolic genes for the production of acetoin, a pH-neutral storage molecule. These subpopulations exhibit distinct growth rates and dynamic interconversion between states. Furthermore, acetate concentration influences the relative sizes of the different subpopulations. These results show that clonal populations can use metabolic specialization to control the environment through a process of dynamic, environmentally-sensitive state-switching.

The chemical reactions that occur within a living organism are collectively referred to as its metabolism. Many metabolic reactions produce byproducts that will poison the cells if they are not dealt with: fermenting bacteria, for example, release harmful organic acids and alcohols. How the bacteria respond to these toxins has been most studied at the level of entire microbial populations, meaning the activities of individual cells are effectively “averaged” together. Yet, even two bacteria with the same genes and living in the same environment can behave in different ways. This raises the question: do bacterial populations specialize into distinct subpopulations that play distinct roles when dealing with metabolic products, or do all cells in the community act in unison?

Rosenthal et al. set out to answer this question for a community of Bacillus subtilis, a bacterium that is commonly studied in the laboratory and used for the industrial production of enzymes. The analysis focused on genes involved in fundamental metabolic processes, known as the TCA cycle, which the bacteria use to generate energy and build biomass. The experiments revealed that, even when all the cells are genetically identical, different Bacillus subtilis cells do indeed specialize into metabolic subpopulations with distinct growth rates.

Time-lapse movies of bacteria that made fluorescent markers of different colors whenever certain metabolic genes became active showed cells switching different colors on and off, indicating that they switch between metabolic subpopulations. Further biochemical studies and measures of gene activity revealed that the different subpopulations produce and release distinct metabolic products, including toxic byproducts. Notably, the release of these metabolites by one subpopulation appeared to activate other subpopulations within the community.

This example of cells specializing into unique interacting metabolic subpopulations provides insight into several fundamental issues in microbiology and beyond. It is relevant to evolutionary biologists, since the fact that fractions of the population can switch in and out of a metabolic state, instead of evolving into several inflexible specialists, may provide an evolutionary advantage in fluctuating natural environments by reducing the risk of extinction. It also has implications for industrial fermentation processes and metabolic engineering, and may help biotechnologists design more efficient ways to harness bacterial metabolism to produce useful products.

Sequential pretreatment for cell disintegration of municipal sludge in a neutral Bio-electro-Fenton system

Sludge cell disruption was generally considered as the rate-limiting step for the anaerobic digestion of waste activated sludge (WAS). Advanced oxidation processes and bio-electro-chemical systems were recently reported to enhance the hydrolysis of WAS and sludge cell disruption, while the cell-breaking processes of these systems remain unclear yet. In this study, an innovative Bio-electro-Fenton system was developed to pretreat the WAS sequentially with cathode Fenton process and anode anaerobic digestion. Significant cell disruption and dissolution intracellular organics were founded after the treatment. X-ray photoelectron spectroscopy (XPS) analysis and fourier transform infrared spectroscopy (FT-IR) spectra indicated that Gram-negative bacteria were more sensitive to free radicals yielded in cathode to induce a chain reaction that destroyed the lipid-contained outer membrane, while Gram-positive bacteria with thick peptidoglycan layer were liable to be biologically decomposed in the anode. Compared with the oxidation of organic matters in the cathode Fenton, the secretion of enzyme increased in the anode which was beneficial to break down the complex matters (peptidoglycans) into simples that were available for anode oxidation by exoelectrogens. The results also showed a possible prospect for the application of this sequential pretreatment in bio-electro-Fenton systems to disrupt sludge cells and enhance the anaerobic digestion.

Multigenerational memory and adaptive adhesion in early bacterial biofilm communities

Using multigenerational, single-cell tracking we explore the earliest events of biofilm formation by Pseudomonas aeruginosa During initial stages of surface engagement (≤20 h), the surface cell population of this microbe comprises overwhelmingly cells that attach poorly (∼95% stay <30 s, well below the ∼1-h division time) with little increase in surface population. If we harvest cells previously exposed to a surface and direct them to a virgin surface, we find that these surface-exposed cells and their descendants attach strongly and then rapidly increase the surface cell population. This "adaptive," time-delayed adhesion requires determinants we showed previously are critical for surface sensing: type IV pili (TFP) and cAMP signaling via the Pil-Chp-TFP system. We show that these surface-adapted cells exhibit damped, coupled out-of-phase oscillations of intracellular cAMP levels and associated TFP activity that persist for multiple generations, whereas surface-naïve cells show uncorrelated cAMP and TFP activity. These correlated cAMP-TFP oscillations, which effectively impart intergenerational memory to cells in a lineage, can be understood in terms of a Turing stochastic model based on the Pil-Chp-TFP framework. Importantly, these cAMP-TFP oscillations create a state characterized by a suppression of TFP motility coordinated across entire lineages and lead to a drastic increase in the number of surface-associated cells with near-zero translational motion. The appearance of this surface-adapted state, which can serve to define the historical classification of "irreversibly attached" cells, correlates with family tree architectures that facilitate exponential increases in surface cell populations necessary for biofilm formation.

Ecological suicide in microbes

The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification of the environment. Examples are the cooperative breakdown of complex nutrients in microbes or the construction of elaborate architectures in social insects, where the individual profits from the collective actions of her peers. However, organisms can similarly display negative interactions by changing the environment in ways that are detrimental for them, for example by resource depletion or the production of toxic byproducts. Here we find an extreme type of negative interactions, in which Paenibacillus sp. bacteria modify the environmental pH to such a degree that it leads to a rapid extinction of the whole population, a phenomenon we call ecological suicide. Modification of the pH is more pronounced at higher population densities, and thus ecological suicide is more likely with increasing bacterial density. Correspondingly, promoting bacterial growth can drive populations extinct whereas inhibiting bacterial growth by the addition of harmful substances – like antibiotics – can rescue them. Moreover, ecological suicide can cause oscillatory dynamics, even in single-species populations. We find ecological suicide in a wide variety of microbes, suggesting that it could play a significant role in microbial ecology and evolution.

Role of metabolic spatiotemporal dynamics in regulating biofilm colony expansion

Cell fate determination is typically regulated by biological networks, yet increasing evidences suggest that cell-cell communication and environmental stresses play crucial roles in the behavior of a cell population. A recent microfluidic experiment showed that the metabolic codependence of two cell populations generates a collective oscillatory dynamic during the expansion of a Bacillus subtilis biofilm. We develop a modeling framework for the spatiotemporal dynamics of the associated metabolic circuit for cells in a colony. We elucidate the role of metabolite diffusion and the need of two distinct cell populations to observe oscillations. Uniquely, this description captures the onset and thereafter stable oscillatory dynamics during expansion and predicts the existence of damping oscillations under various environmental conditions. This modeling scheme provides insights to understand how cells integrate the information from external signaling and cell-cell communication to determine the optimal survival strategy and/or maximize cell fitness in a multicellular system.

Combining a Toggle Switch and a Repressilator within the AC-DC Circuit Generates Distinct Dynamical Behaviors

Although the structure of a genetically encoded regulatory circuit is an important determinant of its function, the relationship between circuit topology and the dynamical behaviors it can exhibit is not well understood. Here, we explore the range of behaviors available to the AC-DC circuit. This circuit consists of three genes connected as a combination of a toggle switch and a repressilator. Using dynamical systems theory, we show that the AC-DC circuit exhibits both oscillations and bistability within the same region of parameter space; this generates emergent behaviors not available to either the toggle switch or the repressilator alone. The AC-DC circuit can switch on oscillations via two distinct mechanisms, one of which induces coherence into ensembles of oscillators. In addition, we show that in the presence of noise, the AC-DC circuit can behave as an excitable system capable of spatial signal propagation or coherence resonance. Together, these results demonstrate how combinations of simple motifs can exhibit multiple complex behaviors.

Application of Microfluidics in Experimental Ecology: The Importance of Being Spatial

Microfluidics is an emerging technology that is used more and more in biology experiments. Its capabilities of creating precisely controlled conditions in cellular dimensions make it ideal to explore cell-cell and cell-environment interactions. Thus, a wide spectrum of problems in microbial ecology can be studied using engineered microbial habitats. Moreover, artificial microfluidic ecosystems can serve as model systems to test ecology theories and principles that apply on a higher level in the hierarchy of biological organization. In this mini review we aim to demonstrate the versatility of microfluidics and the diversity of its applications that help the advance of microbiology, and in more general, experimental ecology.

Porin self-association enables cell-to-cell contact in Providencia stuartii floating communities

The gram-negative pathogen Providencia stuartii forms floating communities within which adjacent cells are in apparent contact, before depositing as canonical surface-attached biofilms. Because porins are the most abundant proteins in the outer membrane of gram-negative bacteria, we hypothesized that they could be involved in cell-to-cell contact and undertook a structure-function relationship study on the two porins of P. stuartii, Omp-Pst1 and Omp-Pst2. Our crystal structures reveal that these porins can self-associate through their extracellular loops, forming dimers of trimers (DOTs) that could enable cell-to-cell contact within floating communities. Support for this hypothesis was obtained by studying the porin-dependent aggregation of liposomes and model cells. The observation that facing channels are open in the two porin structures suggests that DOTs could not only promote cell-to-cell contact but also contribute to intercellular communication.

Microbial mutualism at a distance: The role of geometry in diffusive exchanges

The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry of many natural microbial habitats, including in the soil or on the surfaces of plants or animals. Here we address the important question of how such geometry may control diffusive exchanges and microbial interaction. We model mathematically mutualistic interactions within a minimal unit of structure: two growing reservoirs linked by a diffusive channel through which metabolites are exchanged. The model is applied to study a synthetic mutualism, experimentally parametrized on a model algal-bacterial co-culture. Analytical and numerical solutions of the model predict conditions for the successful establishment of remote mutualisms, and how this depends, often counterintuitively, on diffusion geometry. We connect our findings to understanding complex behavior in synthetic and naturally occurring microbial communities.

Single-cell Microfluidic Analysis of Bacillus subtilis

Microfluidic technology overcomes many of the limitations to traditional analytical methods in microbiology. Unlike bulk-culture methods, it offers single-cell resolution and long observation times spanning hundreds of generations; unlike agarose pad-based microscopy, it has uniform growth conditions that can be tightly controlled. Because the continuous flow of growth medium isolates the cells in a microfluidic device from unpredictable variations in the local chemical environment caused by cell growth and metabolism, authentic changes in gene expression and cell growth in response to specific stimuli can be more confidently observed. Bacillus subtilis is used here as a model bacterial species to demonstrate a "mother machine"-type method for cellular analysis. We show how to construct and plumb a microfluidic device, load it with cells, initiate microscopic imaging, and expose cells to a stimulus by switching from one growth medium to another. A stress-responsive reporter is used as an example to reveal the type of data that may be obtained by this method. We also briefly discuss further applications of this method for other types of experiments, such as analysis of bacterial sporulation.

Heterogeneous absorption of antimicrobial peptide LL37 in Escherichia coli cells enhances population survivability

Antimicrobial peptides (AMPs) are broad spectrum antibiotics that selectively target bacteria. Here we investigate the activity of human AMP LL37 against Escherichia coli by integrating quantitative, population and single-cell level experiments with theoretical modeling. We observe an unexpected, rapid absorption and retention of a large number of LL37 peptides by E. coli cells upon the inhibition of their growth, which increases population survivability. This transition occurs more likely in the late stage of cell division cycles. Cultures with high cell density exhibit two distinct subpopulations: a non-growing population that absorb peptides and a growing population that survive owing to the sequestration of the AMPs by others. A mathematical model based on this binary picture reproduces the rather surprising observations, including the increase of the minimum inhibitory concentration with cell density (even in dilute cultures) and the extensive lag in growth introduced by sub-lethal dosages of LL37 peptides.

Interplay between Antibiotic Efficacy and Drug-Induced Lysis Underlies Enhanced Biofilm Formation at Subinhibitory Drug Concentrations

Subinhibitory concentrations of antibiotics have been shown to enhance biofilm formation in multiple bacterial species. While antibiotic exposure has been associated with modulated expression of many biofilm-related genes, the mechanisms of drug-induced biofilm formation remain a focus of ongoing research efforts and may vary significantly across species. In this work, we investigate antibiotic-induced biofilm formation in Enterococcus faecalis, a leading cause of nosocomial infections. We show that biofilm formation is enhanced by subinhibitory concentrations of cell wall synthesis inhibitors but not by inhibitors of protein, DNA, folic acid, or RNA synthesis. Furthermore, enhanced biofilm is associated with increased cell lysis, increases in extracellular DNA (eDNA) levels, and increases in the density of living cells in the biofilm. In addition, we observe similar enhancement of biofilm formation when cells are treated with nonantibiotic surfactants that induce cell lysis. These findings suggest that antibiotic-induced biofilm formation is governed by a trade-off between drug toxicity and the beneficial effects of cell lysis. To understand this trade-off, we developed a simple mathematical model that predicts changes in antibiotic-induced biofilm formation due to external perturbations, and we verified these predictions experimentally. Specifically, we demonstrate that perturbations that reduce eDNA (DNase treatment) or decrease the number of living cells in the planktonic phase (a second antibiotic) decrease biofilm induction, while chemical inhibitors of cell lysis increase relative biofilm induction and shift the peak to higher antibiotic concentrations. Overall, our results offer experimental evidence linking cell wall synthesis inhibitors, cell lysis, increased eDNA levels, and biofilm formation in E. faecalis while also providing a predictive quantitative model that sheds light on the interplay between cell lysis and antibiotic efficacy in developing biofilms.

Applications of Microfluidics in Quantitative Biology

Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, the authors present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future.

Habits of Highly Effective Biofilms: Ion Signaling

How do neighboring bacterial biofilms sense and communicate with each other? In a recent paper, Liu et al. (2017) demonstrate how electrical signaling allows communication of metabolic states between adjacent B. subtilis biofilms, providing a possible generalizable mechanism for communication in multispecies biofilms with interdependent metabolism.

Bacterial intelligence: imitation games, time-sharing, and long-range quantum coherence

Bacteria are far more intelligent than we can think of. They adopt different survival strategies to make their life comfortable. Researches on bacterial communication to date suggest that bacteria can communicate with each other using chemical signaling molecules as well as using ion channel mediated electrical signaling. Though in past few decades the scopes of chemical signaling have been investigated extensively, those of electrical signaling have received less attention. In this article, we present a novel perspective on time-sharing behavior, which maintains the biofilm growth under reduced nutrient supply between two distant biofilms through electrical signaling based on the experimental evidence reported by Liu et al., in 2017. In addition, following the recent work by Humphries et al. Cell 168(1):200-209, in 2017, we highlight the consequences of long range electrical signaling within biofilm communities through spatially propagating waves of potassium. Furthermore, we address the possibility of two-way cellular communication between artificial and natural cells through chemical signaling being inspired by recent experimental observation (Lentini et al. 2017) where the efficiency of artificial cells in imitating the natural cells is estimated through cellular Turing test. These three spectacular observations lead us to envisage and devise new classical and quantum views of these complex biochemical networks that have never been realized previously.

Papers of note in Science (6338)

This week’s articles demonstrate how T cells search for ligands; a role for the endoplasmic reticulum in the nonclathrin-mediated endocytosis of a growth factor receptor; and growth coupling between distant bacterial colonies that enables the cells to share limited resources.