Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment

Fungal community shows more variations by season and particle size than bacteria

The global concern regarding the health risk associated with airborne microorganisms has prompted research in this field. However, there is a lack of systematic investigation into the particle-size distribution of airborne bacterial and fungal communities associated with seasons, which determines where they are deposited in the human respiratory tract. To address this gap, we conducted a study in Nanchang, located in central China, where we collected both coarse and fine particles during summer and winter seasons. The results demonstrated that microbial community exhibited obvious seasonal and particle-size variations except bacterial community in fine particles. Certain taxa (e.g., Bacteroidales, Ktedonobacterales, Capnodiales) displayed either seasonal and/or particle-size preferences. Furthermore, airborne microorganisms in coarse particles were more sensitive to season and particle size compared to those in fine particles, with fungal community being more susceptible than bacterial community. The susceptibility can be attributed to their high vulnerability to air pollutants and meteorological conditions, primarily PM2.5 and PM10. Additionally, a greater relative abundance of pathogenic fungi was observed in fine particles, even though microbial diversity in coarse particles was noticeably higher than that in fine particles. Furthermore, some predominant pathogens such as Alternaria, Nigrospora, and Escherichia-Shigella not only had particle size and/or seasonal preferences, but also were strongly correlated with environmental factors. This study advances our understanding of atmospheric pathogenic microorganisms and highlights the fungal health threat.

'Phase transitions' in bacteria - From structural transitions in free living bacteria to phenotypic transitions in bacteria within biofilms

Phase transitions are common in inanimate systems and have been studied extensively in natural sciences. Less explored are the rich transitions that take place at the micro- and nano-scales in biological systems. In conventional phase transitions, large-scale properties of the media change discontinuously in response to continuous changes in external conditions. Such changes play a significant role in the dynamic behaviours of organisms. In this review, we focus on some transitions in both free-living and biofilms of bacteria. Particular attention is paid to the transitions in the flagellar motors and filaments of free-living bacteria, in cellular gene expression during the biofilm growth, in the biofilm morphology transitions during biofilm expansion, and in the cell motion pattern transitions during the biofilm formation. We analyse the dynamic characteristics and biophysical mechanisms of these phase transition phenomena and point out the parallels between these transitions and conventional phase transitions. We also discuss the applications of some theoretical and numerical methods, established for conventional phase transitions in inanimate systems, in bacterial biofilms.

Filamentous morphology of bacterial pathogens: regulatory factors and control strategies

Several studies have demonstrated that when exposed to physical, chemical, and biological stresses in the environment, many bacteria (Gram-positive and Gram-negative) change their morphology from a normal cell to a filamentous shape. The formation of filamentous morphology is one of the survival strategies against environmental stress and protection against phagocytosis or protist predators. Numerous pathogenic bacteria have shown filamentous morphologies when examined in vivo or in vitro. During infection, certain pathogenic bacteria adopt a filamentous shape inside the cell to avoid phagocytosis by immune cells. Filamentous morphology has also been seen in biofilms formed on biotic or abiotic surfaces by certain bacteria. As a result, in addition to protecting against phagocytosis by immune cells or predators, the filamentous shape aids in biofilm adhesion or colonization to biotic or abiotic surfaces. Furthermore, these filamentous morphologies of bacterial pathogens lead to antimicrobial drug resistance. Clinically, filamentous morphology has become one of the most serious challenges in treating bacterial infection. The current review went into great detail about the various factors involved in the change of filamentous morphology and the underlying mechanisms. In addition, the review discussed a control strategy for suppressing filamentous morphology in order to combat bacterial infections. Understanding the mechanism underlying the filamentous morphology induced by various environmental conditions will aid in drug development and lessen the virulence of bacterial pathogens. KEY POINTS: • The bacterial filamentation morphology is one of the survival mechanisms against several environmental stress conditions and protection from phagocytosis by host cells and protist predators. • The filamentous morphologies in bacterial pathogens contribute to enhanced biofilm formation, which develops resistance properties against antimicrobial drugs. • Filamentous morphology has become one of the major hurdles in treating bacterial infection, hence controlling strategies employed for inhibiting the filamentation morphology from combating bacterial infections.

Multi-scale Chimerism: An experimental window on the algorithms of anatomical control

Despite the immense progress in genetics and cell biology, major knowledge gaps remain with respect to prediction and control of the global morphologies that will result from the cooperation of cells with known genomes. The understanding of cooperativity, competition, and synergy across diverse biological scales has been obscured by a focus on standard model systems that exhibit invariant species-specific anatomies. Morphogenesis of chimeric biological material is an especially instructive window on the control of biological growth and form because it emphasizes the need for prediction without reliance on familiar, standard outcomes. Here, we review an important and fascinating body of data from experiments utilizing DNA transfer, cell transplantation, organ grafting, and parabiosis. We suggest that these are all instances (at different levels of organization) of one general phenomenon: chimerism. Multi-scale chimeras are a powerful conceptual and experimental tool with which to probe the mapping between properties of components and large-scale anatomy: the laws of morphogenesis. The existing data and future advances in this field will impact not only the understanding of cooperation and the evolution of body forms, but also the design of strategies for system-level outcomes in regenerative medicine and swarm robotics.

'Chain and running' induced by mechanical interactions among cells of different phenotypes in the Bacillus subtilis biofilm

In either a living system or a non-living system, the interaction among its constituent cells or particles is a fundamental aspect at all scales. For example, during the Bacillus subtilis biofilm formation, cells differentiate into multiple phenotypes to adapt to the environments; few hours after the initial inoculation, we find the phenotype of matrix-producing cells form "chain" structure surrounding the phenotype of the "running" motile cells. We use "chain" to characterize the structure of matrix-producing cells, and "running" to characterize the proliferation and growth of motile cells. Due to a large number of cells in the biofilm, it is impossible to construct a traditional kinetic model to describe the causal link between the single-cell movement and the colony behavior. Here, we obtain cell state information and cell group shape information through experiments; after the image analysis, we get the key interaction rules between cells, and then, we simulate the comparable movement of two cell types and the resulting colony geometry using the multi-agent model. Our work makes a better understanding of the relationship between the macroscopic shape of colonies and microscopic mechanical interactions among cells in the early stage of biofilm growth.

Life, death, and self: Fundamental questions of primitive cognition viewed through the lens of body plasticity and synthetic organisms

Central to the study of cognition is being able to specify the Subject that is making decisions and owning memories and preferences. However, all real cognitive agents are made of parts (such as brains made of cells). The integration of many active subunits into a coherent Self appearing at a larger scale of organization is one of the fundamental questions of evolutionary cognitive science. Typical biological model systems, whether basal or advanced, have a static anatomical structure which obscures important aspects of the mind-body relationship. Recent advances in bioengineering now make it possible to assemble, disassemble, and recombine biological structures at the cell, organ, and whole organism levels. Regenerative biology and controlled chimerism reveal that studies of cognition in intact, "standard", evolved animal bodies are just a narrow slice of a much bigger and as-yet largely unexplored reality: the incredible plasticity of dynamic morphogenesis of biological forms that house and support diverse types of cognition. The ability to produce living organisms in novel configurations makes clear that traditional concepts, such as body, organism, genetic lineage, death, and memory are not as well-defined as commonly thought, and need considerable revision to account for the possible spectrum of living entities. Here, I review fascinating examples of experimental biology illustrating that the boundaries demarcating somatic and cognitive Selves are fluid, providing an opportunity to sharpen inquiries about how evolution exploits physical forces for multi-scale cognition. Developmental (pre-neural) bioelectricity contributes a novel perspective on how the dynamic control of growth and form of the body evolved into sophisticated cognitive capabilities. Most importantly, the development of functional biobots - synthetic living machines with behavioral capacity - provides a roadmap for greatly expanding our understanding of the origin and capacities of cognition in all of its possible material implementations, especially those that emerge de novo, with no lengthy evolutionary history of matching behavioral programs to bodyplan. Viewing fundamental questions through the lens of new, constructed living forms will have diverse impacts, not only in basic evolutionary biology and cognitive science, but also in regenerative medicine of the brain and in artificial intelligence.

Electroactivity of the Gram-positive bacterium Paenibacillus dendritiformis MA-72

Whilst most of the microorganisms recognized as exoelectrogens are Gram-negative bacteria, the electrogenicity of Gram-positive bacteria has not been sufficiently explored. In this study, the putative electroactivity of the Gram-positive Paenibacillus dendritiformis MA-72 strain, isolated from the anodic biofilm of long-term operated Sediment Microbial Fuel Cell (SMFC), has been investigated. SEM observations show that under polarization conditions P. dendritiformis forms a dense biofilm on carbon felt electrodes. A current density, reaching 5 mA m^-2, has been obtained at a prolonged applied potential of -0.195 V (vs. SHE), which represents 35% of the value achieved with the SMFC. The voltammetric studies confirm that the observed Faradaic current is associated with the electrochemical activity of the bacterial biofilm and not with a soluble redox mediator. The results suggest that a direct electron transfer takes place through the conductive extracellular polymer matrix via pili/nanowires and multiple cytochromes. All these findings demonstrate for the first time that the Gram-positive Paenibacillus dendritiformis MA-72 is a new exoelectrogenic bacterial strain.

From Microbial Communities to Distributed Computing Systems

A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tools.

Interaction-dependent effects of surface structure on microbial spatial self-organization

Surface-attached microbial communities consist of different cell types that, at least to some degree, organize themselves non-randomly across space (referred to as spatial self-organization). While spatial self-organization can have important effects on the functioning, ecology and evolution of communities, the underlying determinants of spatial self-organization remain unclear. Here, we hypothesize that the presence of physical objects across a surface can have important effects on spatial self-organization. Using pairs of isogenic strains of Pseudomonas stutzeri, we performed range expansion experiments in the absence or presence of physical objects and quantified the effects on spatial self-organization. We demonstrate that physical objects create local deformities along the expansion frontier, and these deformities increase in magnitude during range expansion. The deformities affect the densities of interspecific boundaries and diversity along the expansion frontier, and thus affect spatial self-organization, but the effects are interaction-dependent. For competitive interactions that promote sectorized patterns of spatial self-organization, physical objects increase the density of interspecific boundaries and diversity. By contrast, for cross-feeding interactions that promote dendritic patterns, they decrease the density of interspecific boundaries and diversity. These qualitatively different outcomes are probably caused by fundamental differences in the orientations of the interspecific boundaries. Thus, in order to predict the effects of physical objects on spatial self-organization, information is needed regarding the interactions present within a community and the general geometric shapes of spatial self-organization that emerge from those interactions. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Cellular heterogeneity results from indirect effects under metabolic tradeoffs

The emergence and maintenance of multicellularity requires the coexistence of diverse cellular populations displaying cooperative relationships. This enables long-term persistence of cellular consortia, particularly under environmental constraints that challenge cell survival. Toxic environments are known to trigger the formation of multicellular consortia capable of dealing with waste while promoting cell diversity as a way to overcome selection barriers. In this context, recent theoretical studies suggest that an environment containing both resources and toxic waste can promote the emergence of complex, spatially distributed proto-organisms exhibiting division of labour and higher-scale features beyond the cell-cell pairwise interactions. Some previous non-spatial models suggest that the presence of a growth inhibitor can trigger the coexistence of competitive species in an antibiotic-resistance context. In this paper, we further explore this idea using both mathematical and computational models taking the most fundamental features of the proto-organisms model interactions. It is shown that this resource-waste environmental context, in which both species are lethally affected by the toxic waste and metabolic tradeoffs are present, favours the maintenance of diverse populations. A spatial, stochastic extension confirms our basic results. The evolutionary and ecological implications of these results are outlined.

Cell-cell communication enhances bacterial chemotaxis toward external attractants

Bacteria are able to coordinate their movement, growth and biochemical activities through cell-cell communication. While the biophysical mechanism of bacterial chemotaxis has been well understood in individual cells, the role of communication in the chemotaxis of bacterial populations is not clear. Here we report experimental evidence for cell-cell communication that significantly enhances the chemotactic migration of bacterial populations, a finding that we further substantiate using numerical simulations. Using a microfluidic approach, we find that E. coli cells respond to the gradient of chemoattractant not only by biasing their own random-walk swimming pattern through the well-understood intracellular chemotaxis signaling, but also by actively secreting a chemical signal into the extracellular medium, possibly through a hitherto unknown communication signal transduction pathway. This extracellular signaling molecule is a strong chemoattractant that attracts distant cells to the food source. The observed behavior may represent a common evolved solution to accelerate the function of biochemical networks of interacting cells.

COLLECTIVE VORTEX BEHAVIORS: DIVERSITY, PROXIMATE, AND ULTIMATE CAUSES OF CIRCULAR ANIMAL GROUP MOVEMENTS

Ant mill, caterpillar circle, bat doughnut, amphibian vortex, duck swirl, and fish torus are different names for rotating circular animal formations, where individuals turn around a common center. These "collective vortex behaviors" occur at different group sizes from pairs to several million individuals and have been reported in a large number of organisms, from bacteria to vertebrates, including humans. However, to date, no comprehensive review and synthesis of the literature on vortex behaviors has been conducted. Here, we review the state of the art of the proximate and ultimate causes of vortex behaviors. The ubiquity of this behavioral phenomenon could suggest common causes or fundamental underlying principles across contexts. However, we find that a variety of proximate mechanisms give rise to vortex behaviors. We highlight the potential benefits of collective vortex behaviors to individuals involved in them. For example, in some species, vortices increase feeding efficiency and could give protection against predators. It has also been argued that vortices could improve collective decision-making and information transfer. We highlight gaps in our understanding of these ubiquitous behavioral phenomena and discuss future directions for research in vortex studies.

A morphospace for synthetic organs and organoids: the possible and the actual

Efforts in evolutionary developmental biology have shed light on how organs are developed and why evolution has selected some structures instead of others. These advances in the understanding of organogenesis along with the most recent techniques of organotypic cultures, tissue bioprinting and synthetic biology provide the tools to hack the physical and genetic constraints in organ development, thus opening new avenues for research in the form of completely designed or merely altered settings. Here we propose a unifying framework that connects the concept of morphospace (i.e. the space of possible structures) with synthetic biology and tissue engineering. We aim for a synthesis that incorporates our understanding of both evolutionary and architectural constraints and can be used as a guide for exploring alternative design principles to build artificial organs and organoids. We present a three-dimensional morphospace incorporating three key features associated to organ and organoid complexity. The axes of this space include the degree of complexity introduced by developmental mechanisms required to build the structure, its potential to store and react to information and the underlying physical state. We suggest that a large fraction of this space is empty, and that the void might offer clues for alternative ways of designing and even inventing new organs.

Symmetry and scale orient Min protein patterns in shaped bacterial sculptures

The boundary of a cell defines the shape and scale of its subcellular organization. However, the effects of the cell's spatial boundaries as well as the geometry sensing and scale adaptation of intracellular molecular networks remain largely unexplored. Here, we show that living bacterial cells can be 'sculpted' into defined shapes, such as squares and rectangles, which are used to explore the spatial adaptation of Min proteins that oscillate pole-to-pole in rod-shaped Escherichia coli to assist cell division. In a wide geometric parameter space, ranging from 2 × 1 × 1 to 11 × 6 × 1 μm(3), Min proteins exhibit versatile oscillation patterns, sustaining rotational, longitudinal, diagonal, stripe and even transversal modes. These patterns are found to directly capture the symmetry and scale of the cell boundary, and the Min concentration gradients scale with the cell size within a characteristic length range of 3-6 μm. Numerical simulations reveal that local microscopic Turing kinetics of Min proteins can yield global symmetry selection, gradient scaling and an adaptive range, when and only when facilitated by the three-dimensional confinement of the cell boundary. These findings cannot be explained by previous geometry-sensing models based on the longest distance, membrane area or curvature, and reveal that spatial boundaries can facilitate simple molecular interactions to result in far more versatile functions than previously understood.

My encounters with bacteria--learning about communication, cooperation and choice

My journey into the physics of living systems began with the most fundamental organisms on Earth, bacteria, that three decades ago were perceived as solitary, primitive creatures of limited capabilities. A decade later this notion had faded away and bacteria came to be recognized as the smart beasts they are, engaging in intricate social life through a sophisticated chemical language. Acting jointly, these tiny organisms can sense the environment, process information, solve problems and make decisions so as to thrive in harsh environments. The bacterial power of cooperation manifests in their ability to develop large colonies of astonishing complexity. The number of bacteria in a colony can amount to many billions, yet they exchange 'chemical tweets' that reach each and every one of them so they all know what they're all doing, each cell being both actor and spectator in the bacterial Game of Life. I share my encounters with bacteria, what I learned about the secrets of their social life and wisdom of the crowd, and why and how, starting as a theoretical physicist, I found myself studying social intelligence of bacteria. The story ends with a bacteria guide to cyber-war on cancer.

From environmental signals to regulators: modulation of biofilm development in Gram-positive bacteria

Bacterial lifestyle is influenced by environmental signals, and many differentiation processes in bacteria are governed by the threshold concentrations of molecules present in their niche. Biofilm is one such example where bacteria in their sessile state adapt to a lifestyle that causes several adaptive alterations in the population. Here, a brief overview is given on a variety of environmental signals that bias biofilm development in Gram-positive bacteria, including nutrient conditions, self- and heterologously produced substances, like quorum sensing and host produced molecules. The Gram-positive model organism, Bacillus subtilis is a superb example to illustrate how distinct signals activate sensor proteins that integrate the environmental signals towards global regulators related to biofilm formation. The role of reduced oxygen level, polyketides, antimicrobials, plant secreted carbohydrates, plant cell derived polymers, glycerol, and osmotic conditions are discussed during the transcriptional activation of biofilm related genes in B. subtilis.

Menaquinone and iron are essential for complex colony development in Bacillus subtilis

Cells of undomesticated species of Bacillus subtilis frequently form complex colonies during spreading on agar surfaces. Given that menaquinone is involved in another form of coordinated behavior, namely, sporulation, we looked for a possible role for menaquinone in complex colony development (CCD) in the B. subtilis strain NCIB 3610. Here we show that inhibition of menaquinone biosynthesis in B. subtilis indeed abolished its ability to develop complex colonies. Additionally some mutations of B. subtilis which confer defective CCD could be suppressed by menaquinone derivatives. Several such mutants mapped to the dhb operon encoding the genes responsible for the biosynthesis of the iron siderophore, bacillibactin. Our results demonstrate that both menaquinone and iron are essential for CCD in B. subtilis.

Identification and characterization of a highly motile and antibiotic refractory subpopulation involved in the expansion of swarming colonies of Paenibacillus vortex

Bacteria often use sophisticated cooperative behaviours, such as the development of complex colonies, elaborate biofilms and advanced dispersal strategies, to cope with the harsh and variable conditions of natural habitats, including the presence of antibiotics. Paenibacillus vortex uses swarming motility and cell-to-cell communication to form complex, structured colonies. The modular organization of P. vortex colony has been found to facilitate its dispersal on agar surfaces. The current study reveals that the complex structure of the colony is generated by the coexistence and transition between two morphotypes – ‘builders’ and ‘explorers’ – with distinct functions in colony formation. Here, we focused on the explorers, which are highly motile and spearhead colonial expansion. Explorers are characterized by high expression levels of flagellar genes, such as flagellin (hag), motA, fliI, flgK and sigD, hyperflagellation, decrease in ATP (adenosine-5′-triphosphate) levels, and increased resistance to antibiotics. Their tolerance to many antibiotics gives them the advantage of translocation through antibiotics-containing areas. This work gives new insights on the importance of cell differentiation and task distribution in colony morphogenesis and adaptation to antibiotics.

Periodic reversals in Paenibacillus dendritiformis swarming

Bacterial swarming is a type of motility characterized by a rapid and collective migration of bacteria on surfaces. Most swarming species form densely packed dynamic clusters in the form of whirls and jets, in which hundreds of rod-shaped rigid cells move in circular and straight patterns, respectively. Recent studies have suggested that short-range steric interactions may dominate hydrodynamic interactions and that geometrical factors, such as a cell's aspect ratio, play an important role in bacterial swarming. Typically, the aspect ratio for most swarming species is only up to 5, and a detailed understanding of the role of much larger aspect ratios remains an open challenge. Here we study the dynamics of Paenibacillus dendritiformis C morphotype, a very long, hyperflagellated, straight (rigid), rod-shaped bacterium with an aspect ratio of ~20. We find that instead of swarming in whirls and jets as observed in most species, including the shorter T morphotype of P. dendritiformis, the C morphotype moves in densely packed straight but thin long lines. Within these lines, all bacteria show periodic reversals, with a typical reversal time of 20 s, which is independent of their neighbors, the initial nutrient level, agar rigidity, surfactant addition, humidity level, temperature, nutrient chemotaxis, oxygen level, illumination intensity or gradient, and cell length. The evolutionary advantage of this unique back-and-forth surface translocation remains unclear.

Hydration dynamics promote bacterial coexistence on rough surfaces

Identification of mechanisms that promote and maintain the immense microbial diversity found in soil is a central challenge for contemporary microbial ecology. Quantitative tools for systematic integration of complex biophysical and trophic processes at spatial scales, relevant for individual cell interactions, are essential for making progress. We report a modeling study of competing bacterial populations cohabiting soil surfaces subjected to highly dynamic hydration conditions. The model explicitly tracks growth, motion and life histories of individual bacterial cells on surfaces spanning dynamic aqueous networks that shape heterogeneous nutrient fields. The range of hydration conditions that confer physical advantages for rapidly growing species and support competitive exclusion is surprisingly narrow. The rapid fragmentation of soil aqueous phase under most natural conditions suppresses bacterial growth and cell dispersion, thereby balancing conditions experienced by competing populations with diverse physiological traits. In addition, hydration fluctuations intensify localized interactions that promote coexistence through disproportional effects within densely populated regions during dry periods. Consequently, bacterial population dynamics is affected well beyond responses predicted from equivalent and uniform hydration conditions. New insights on hydration dynamics could be considered in future designs of soil bioremediation activities, affect longevity of dry food products, and advance basic understanding of bacterial diversity dynamics and its role in global biogeochemical cycles.

Collective navigation of cargo-carrying swarms

Much effort has been devoted to the study of swarming and collective navigation of micro-organisms, insects, fish, birds and other organisms, as well as multi-agent simulations and to the study of real robots. It is well known that insect swarms can carry cargo. The studies here are motivated by a less well-known phenomenon: cargo transport by bacteria swarms. We begin with a concise review of how bacteria swarms carry natural, micrometre-scale objects larger than the bacteria (e.g. fungal spores) as well as man-made beads and capsules (for drug delivery). A comparison of the trajectories of virtual beads in simulations (using different putative coupling between the virtual beads and the bacteria) with the observed trajectories of transported fungal spores implies the existence of adaptable coupling. Motivated by these observations, we devised new, multi-agent-based studies of cargo transport by agent swarms. As a first step, we extended previous modelling of collective navigation of simple bacteria-inspired agents in complex terrain, using three putative models of agent-cargo coupling. We found that cargo-carrying swarms can navigate efficiently in a complex landscape. We further investigated how the stability, elasticity and other features of agent-cargo bonds influence the collective motion and the transport of the cargo, and found sharp phase shifts and dual successful strategies for cargo delivery. Further understanding of such mechanisms may provide valuable clues to understand cargo-transport by smart swarms of other organisms as well as by man-made swarming robots.

Swarm robotics reviewed

We present a review of recent activities in swarm robotic research, and analyse existing literature in the field to determine how to get closer to a practical swarm robotic system for real world applications. We begin with a discussion of the importance of swarm robotics by illustrating the wide applicability of robot swarms in various tasks. Then a brief overview of various robotic devices that can be incorporated into swarm robotic systems is presented. We identify and describe the challenges that should be resolved when designing swarm robotic systems for real world applications. Finally, we provide a summary of a series of issues that should be addressed to overcome these challenges, and propose directions for future swarm robotic research based on our extensive analysis of the reviewed literature.

Modeling collective animal behavior with a cognitive perspective: a methodological framework

The last decades have seen an increasing interest in modeling collective animal behavior. Some studies try to reproduce as accurately as possible the collective dynamics and patterns observed in several animal groups with biologically plausible, individual behavioral rules. The objective is then essentially to demonstrate that the observed collective features may be the result of self-organizing processes involving quite simple individual behaviors. Other studies concentrate on the objective of establishing or enriching links between collective behavior researches and cognitive or physiological ones, which then requires that each individual rule be carefully validated. Here we discuss the methodological consequences of this additional requirement. Using the example of corpse clustering in ants, we first illustrate that it may be impossible to discriminate among alternative individual rules by considering only observational data collected at the group level. Six individual behavioral models are described: They are clearly distinct in terms of individual behaviors, they all reproduce satisfactorily the collective dynamics and distribution patterns observed in experiments, and we show theoretically that it is strictly impossible to discriminate two of these models even in the limit of an infinite amount of data whatever the accuracy level. A set of methodological steps are then listed and discussed as practical ways to partially overcome this problem. They involve complementary experimental protocols specifically designed to address the behavioral rules successively, conserving group-level data for the overall model validation. In this context, we highlight the importance of maintaining a sharp distinction between model enunciation, with explicit references to validated biological concepts, and formal translation of these concepts in terms of quantitative state variables and fittable functional dependences. Illustrative examples are provided of the benefits expected during the often long and difficult process of refining a behavioral model, designing adapted experimental protocols and inversing model parameters.

Genome sequence of the pattern-forming social bacterium Paenibacillus dendritiformis C454 chiral morphotype

Paenibacillus dendritiformis is a Gram-positive, soil-dwelling, spore-forming social microorganism. An intriguing collective faculty of this strain is manifested by its ability to switch between different morphotypes, such as the branching (T) and the chiral (C) morphotypes. Here we report the 6.3-Mb draft genome sequence of the P. dendritiformis C454 chiral morphotype.

Emergence of self-organized amoeboid movement in a multi-agent approximation of Physarum polycephalum

The giant single-celled slime mould Physarum polycephalum exhibits complex morphological adaptation and amoeboid movement as it forages for food and may be seen as a minimal example of complex robotic behaviour. Swarm computation has previously been used to explore how spatio-temporal complexity can emerge from, and be distributed within, simple component parts and their interactions. Using a particle-based swarm approach we explore the question of how to generate collective amoeboid movement from simple non-oscillatory component parts in a model of P. polycephalum. The model collective behaves as a cohesive and deformable virtual material, approximating the local coupling within the plasmodium matrix. The collective generates de-novo and complex oscillatory patterns from simple local interactions. The origin of this motor behaviour distributed within the collective rendering is morphologically adaptive, amenable to external influence and robust to simulated environmental insult. We show how to gain external influence over the collective movement by simulated chemo-attraction (pulling towards nutrient stimuli) and simulated light irradiation hazards (pushing from stimuli). The amorphous and distributed properties of the collective are demonstrated by cleaving it into two independent entities and fusing two separate entities to form a single device, thus enabling it to traverse narrow, separate or tortuous paths. We conclude by summarizing the contribution of the model to swarm-based robotics and soft-bodied modular robotics and discuss the future potential of such material approaches to the field.

Insights from the architecture of the bacterial transcription apparatus

We provide a portrait of the bacterial transcription apparatus in light of the data emerging from structural studies, sequence analysis and comparative genomics to bring out important but underappreciated features. We first describe the key structural highlights and evolutionary implications emerging from comparison of the cellular RNA polymerase subunits with the RNA-dependent RNA polymerase involved in RNAi in eukaryotes and their homologs from newly identified bacterial selfish elements. We describe some previously unnoticed domains and the possible evolutionary stages leading to the RNA polymerases of extant life forms. We then present the case for the ancient orthology of the basal transcription factors, the sigma factor and TFIIB, in the bacterial and the archaeo-eukaryotic lineages. We also present a synopsis of the structural and architectural taxonomy of specific transcription factors and their genome-scale demography. In this context, we present certain notable deviations from the otherwise invariant proteome-wide trends in transcription factor distribution and use it to predict the presence of an unusual lineage-specifically expanded signaling system in certain firmicutes like Paenibacillus. We then discuss the intersection between functional properties of transcription factors and the organization of transcriptional networks. Finally, we present some of the interesting evolutionary conundrums posed by our newly gained understanding of the bacterial transcription apparatus and potential areas for future explorations.

Smart swarms of bacteria-inspired agents with performance adaptable interactions

Collective navigation and swarming have been studied in animal groups, such as fish schools, bird flocks, bacteria, and slime molds. Computer modeling has shown that collective behavior of simple agents can result from simple interactions between the agents, which include short range repulsion, intermediate range alignment, and long range attraction. Here we study collective navigation of bacteria-inspired smart agents in complex terrains, with adaptive interactions that depend on performance. More specifically, each agent adjusts its interactions with the other agents according to its local environment – by decreasing the peers' influence while navigating in a beneficial direction, and increasing it otherwise. We show that inclusion of such performance dependent adaptable interactions significantly improves the collective swarming performance, leading to highly efficient navigation, especially in complex terrains. Notably, to afford such adaptable interactions, each modeled agent requires only simple computational capabilities with short-term memory, which can easily be implemented in simple swarming robots.

Many groups of organisms, from colonies of bacteria and social insects through schools of fish and flocks of birds to herds of mammals exhibit advanced collective navigation. Identifying the minimal features of biologically-inspired interacting agents that can lead to emergence of “intelligent” like collective navigation and decision making is fundamental to our understanding of collective behavior, and is of great interest in artificial intelligence and robotics. Previous models of collective behavior of agents, which relied on static interactions of repulsion, orientation (alignment), and attraction, have shown the emergence of collective swarming. Here we show the advantage of performance adaptable interactions for navigation of groups in complex terrains. Each agent senses the local environment and is then allowed to adjust its interactions with the other agents according to its local environment – by decreasing the peers' influence while navigating in a beneficial direction and vice versa. We found that inclusion of such adaptable interactions dramatically improves the collective swarming performance leading to highly efficient navigation especially in very complex terrains.

Computing with bacterial constituents, cells and populations: from bioputing to bactoputing

The relevance of biological materials and processes to computing-alias bioputing-has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating.

Modeling population patterns of chemotactic bacteria in homogeneous porous media

The spatio-temporal distribution of subsurface microorganisms determines their efficiency in providing essential ecosystem services such as the degradation of organic matter, the remineralization of carbon and nitrogen, or the remediation of anthropogenic contaminants. Populations of motile, chemotactic bacteria have been shown to be capable of pattern formation even in the absence of environmental heterogeneities. Focusing on the water saturated domain of the subsurface (e.g., aquatic sediments, porous aquifers), we analyze this innate capability of bacterial populations in an idealized model of a homogeneous, saturated porous medium. Considering a linear array of connected, identical microhabitats populated by motile, chemotactic bacterial cells, we identify prerequisites for pattern formation, analyze types of patterns, and assess their impact on substrate utilization. In our model, substrate supplied to the microhabitats facilitates bacterial growth, and microbial cells can migrate between neighboring microhabitats due to (i) random motility, (ii) chemotaxis towards substrate, and (iii) self-attraction. A precondition for inhomogeneous population patterns is analytically derived, stating that patterns are possible if the self-attraction exceeds a threshold defined by the random motility and the steady state population density in the microhabitats. An individual-based implementation of the model shows that static and dynamic population patterns can unfold. Degradation efficiency is highest for homogeneous bacterial distributions and decreases as pattern formation commences. If during biostimulation efforts the carrying capacity of the microhabitats is successively increased, simulation results show that degradation efficiency can unexpectedly decrease when the pattern formation threshold is crossed.

Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments

Background

The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced. However, no genomic data is available on the Paenibacillus species with pattern-forming and complex social motility. Here we report the de novo genome sequence of this Gram-positive, soil-dwelling, sporulating bacterium.

Results

The complete P. vortex genome was sequenced by a hybrid approach using 454 Life Sciences and Illumina, achieving a total of 289× coverage, with 99.8% sequence identity between the two methods. The sequencing results were validated using a custom designed Agilent microarray expression chip which represented the coding and the non-coding regions. Analysis of the P. vortex genome revealed 6,437 open reading frames (ORFs) and 73 non-coding RNA genes. Comparative genomic analysis with 500 complete bacterial genomes revealed exceptionally high number of two-component system (TCS) genes, transcription factors (TFs), transport and defense related genes. Additionally, we have identified genes involved in the production of antimicrobial compounds and extracellular degrading enzymes.

Conclusions

These findings suggest that P. vortex has advanced faculties to perceive and react to a wide range of signaling molecules and environmental conditions, which could be associated with its ability to reconfigure and replicate complex colony architectures. Additionally, P. vortex is likely to serve as a rich source of genes important for agricultural, medical and industrial applications and it has the potential to advance the study of social microbiology within Gram-positive bacteria.

Glucose induced fractal colony pattern of Bacillus thuringiensis

Growing colonies of bacteria on the surface of thin agar plates exhibit fractal patterns as a result of nonlinear response to environmental conditions, such as nutrients, solidity of the agar medium and temperature. Here, we examine the effect of glucose on pattern formation by growing colonies of Bacillus thuringiensis isolate KPWP1. We also present the theoretical modeling of the colony growth of KPWP1 and the associated spatio-temporal patterns. Our experimental results are in excellent agreement with simulations based on a reaction-diffusion model that describes diffusion-limited aggregation and branching, in which individual cells move actively in the periphery, but become immotile in the inner regions of the growing colony. We obtain the Hausdorff fractal dimension of the colony patterns: D(H.Expt)=1.1969 and D(H, R.D.=)1.1965, for experiment and reaction-diffusion model, respectively. Results of our experiments and modeling clearly show how glucose at higher concentration can prove to be inhibitory for motility of growing colonies of B. thuringiensis cells on semisolid support and be responsible for changes in the growth pattern.

Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago

The evidence for macroscopic life during the Palaeoproterozoic era (2.5-1.6 Gyr ago) is controversial. Except for the nearly 2-Gyr-old coil-shaped fossil Grypania spiralis, which may have been eukaryotic, evidence for morphological and taxonomic biodiversification of macroorganisms only occurs towards the beginning of the Mesoproterozoic era (1.6-1.0 Gyr). Here we report the discovery of centimetre-sized structures from the 2.1-Gyr-old black shales of the Palaeoproterozoic Francevillian B Formation in Gabon, which we interpret as highly organized and spatially discrete populations of colonial organisms. The structures are up to 12 cm in size and have characteristic shapes, with a simple but distinct ground pattern of flexible sheets and, usually, a permeating radial fabric. Geochemical analyses suggest that the sediments were deposited under an oxygenated water column. Carbon and sulphur isotopic data indicate that the structures were distinct biogenic objects, fossilized by pyritization early in the formation of the rock. The growth patterns deduced from the fossil morphologies suggest that the organisms showed cell-to-cell signalling and coordinated responses, as is commonly associated with multicellular organization. The Gabon fossils, occurring after the 2.45-2.32-Gyr increase in atmospheric oxygen concentration, may be seen as ancient representatives of multicellular life, which expanded so rapidly 1.5 Gyr later, in the Cambrian explosion.

Uniform categorization of biocommunication in bacteria, fungi and plants

This article describes a coherent biocommunication categorization for the kingdoms of bacteria, fungi and plants. The investigation further shows that, besides biotic sign use in trans-, inter- and intraorganismic communication processes, a common trait is interpretation of abiotic influences as indicators to generate an appropriate adaptive behaviour. Far from being mechanistic interactions, communication processes within organisms and between organisms are sign-mediated interactions. Sign-mediated interactions are the precondition for every cooperation and coordination between at least two biological agents such as cells, tissues, organs and organisms. Signs of biocommunicative processes are chemical molecules in most cases. The signs that are used in a great variety of signaling processes follow syntactic (combinatorial), pragmatic (context-dependent) and semantic (content-specific) rules. These three levels of semiotic rules are helpful tools to investigate communication processes throughout all organismic kingdoms. It is not the aim to present the latest empirical data concerning communication in these three kingdoms but to present a unifying perspective that is able to interconnect transdisciplinary research on bacteria, fungi and plants.

Lethal protein produced in response to competition between sibling bacterial colonies

Sibling Paenibacillus dendritiformis bacterial colonies grown on low-nutrient agar medium mutually inhibit growth through secretion of a lethal factor. Analysis of secretions reveals the presence of subtilisin (a protease) and a 12 kDa protein, termed sibling lethal factor (Slf). Purified subtilisin promotes the growth and expansion of P. dendritiformis colonies, whereas Slf is lethal and lyses P. dendritiformis cells in culture. Slf is encoded by a gene belonging to a large family of bacterial genes of unknown function, and the gene is predicted to encode a protein of approximately 20 kDa, termed dendritiformis sibling bacteriocin. The 20 kDa recombinant protein was produced and found to be inactive, but exposure to subtilisin resulted in cleavage to the active, 12 kDa form. The experimental results, combined with mathematical modeling, show that subtilisin serves to regulate growth of the colony. Below a threshold concentration, subtilisin promotes colony growth and expansion. However, once it exceeds a threshold, as occurs at the interface between competing colonies, Slf is then secreted into the medium to rapidly reduce cell density by lysis of the bacterial cells. The presence of genes encoding homologs of dendritiformis sibling bacteriocin in other bacterial species suggests that this mechanism for self-regulation of colony growth might not be limited to P. dendritiformis.

Characteristics of pattern formation and evolution in approximations of Physarum transport networks

Most studies of pattern formation place particular emphasis on its role in the development of complex multicellular body plans. In simpler organisms, however, pattern formation is intrinsic to growth and behavior. Inspired by one such organism, the true slime mold Physarum polycephalum, we present examples of complex emergent pattern formation and evolution formed by a population of simple particle-like agents. Using simple local behaviors based on chemotaxis, the mobile agent population spontaneously forms complex and dynamic transport networks. By adjusting simple model parameters, maps of characteristic patterning are obtained. Certain areas of the parameter mapping yield particularly complex long term behaviors, including the circular contraction of network lacunae and bifurcation of network paths to maintain network connectivity. We demonstrate the formation of irregular spots and labyrinthine and reticulated patterns by chemoattraction. Other Turing-like patterning schemes were obtained by using chemorepulsion behaviors, including the self-organization of regular periodic arrays of spots, and striped patterns. We show that complex pattern types can be produced without resorting to the hierarchical coupling of reaction-diffusion mechanisms. We also present network behaviors arising from simple pre-patterning cues, giving simple examples of how the emergent pattern formation processes evolve into networks with functional and quasi-physical properties including tensionlike effects, network minimization behavior, and repair to network damage. The results are interpreted in relation to classical theories of biological pattern formation in natural systems, and we suggest mechanisms by which emergent pattern formation processes may be used as a method for spatially represented unconventional computation.

Deadly competition between sibling bacterial colonies

Bacteria can secrete a wide array of antibacterial compounds when competing with other bacteria for the same resources. Some of these compounds, such as bacteriocins, can affect bacteria of similar or closely related strains. In some cases, these secretions have been found to kill sibling cells that belong to the same colony. Here, we present experimental observations of competition between 2 sibling colonies of Paenibacillus dendritiformis grown on a low-nutrient agar gel. We find that neighboring colonies (growing from droplet inoculation) mutually inhibit growth through secretions that become lethal if the level exceeds a well-defined threshold. In contrast, within a single colony developing from a droplet inoculation, no growth inhibition is observed. However, growth inhibition and cell death are observed if material extracted from the agar between 2 growing colonies is introduced outside a growing single colony. To interpret the observations, we devised a simple mathematical model for the secretion of an antibacterial compound. Simulations of this model illustrate how secretions from neighboring colonies can be deadly, whereas secretions from a single colony growing from a droplet are not.

Chemotaxis as an emergent property of a swarm

We have characterized and quantified a form of bacterial chemotaxis that manifests only as an emergent property by measuring symmetry breaking in a swarm of Myxococcus xanthus exposed to a two-dimensional nutrient gradient from within an agar substrate. M. xanthus chemotaxis requires cell-cell contact and coordinated motility, as individual motile cells exhibit only nonvectorial movement in the presence of a nutrient gradient. Genes that specifically affect M. xanthus chemotaxis include at least 10 of the 53 that express enhancer binding proteins of the NtrC-like class, an indication that this behavior is controlled through transcription, most likely by a complex signal transduction network.

Swarming and complex pattern formation in Paenibacillus vortex studied by imaging and tracking cells

Background

Swarming motility allows microorganisms to move rapidly over surfaces. The Gram-positive bacterium Paenibacillus vortex exhibits advanced cooperative motility on agar plates resulting in intricate colonial patterns with geometries that are highly sensitive to the environment. The cellular mechanisms that underpin the complex multicellular organization of such a simple organism are not well understood.

Results

Swarming by P. vortex was studied by real-time light microscopy, by in situ scanning electron microscopy and by tracking the spread of antibiotic-resistant cells within antibiotic-sensitive colonies. When swarming, P. vortex was found to be peritrichously flagellated. Swarming by the curved cells of P. vortex occurred on an extremely wide range of media and agar concentrations (0.3 to 2.2% w/v). At high agar concentrations (> 1% w/v) rotating colonies formed that could be detached from the main mass of cells by withdrawal of cells into the latter. On lower percentage agars, cells moved in an extended network composed of interconnected "snakes" with short-term collision avoidance and sensitivity to extracts from swarming cells. P. vortex formed single Petri dish-wide "supercolonies" with a colony-wide exchange of motile cells. Swarming cells were coupled by rapidly forming, reversible and non-rigid connections to form a loose raft, apparently connected via flagella. Inhibitors of swarming (p-Nitrophenylglycerol and Congo Red) were identified. Mitomycin C was used to trigger filamentation without inhibiting growth or swarming; this facilitated dissection of the detail of swarming. Mitomycin C treatment resulted in malcoordinated swarming and abortive side branch formation and a strong tendency by a subpopulation of the cells to form minimal rotating aggregates of only a few cells.

Conclusion

P. vortex creates complex macroscopic colonies within which there is considerable reflux and movement and interaction of cells. Cell shape, flagellation, the aversion of cell masses to fuse and temporary connections between proximate cells to form rafts were all features of the swarming and rotation of cell aggregates. Vigorous vortex formation was social, i.e. required > 1 cell. This is the first detailed examination of the swarming behaviour of this bacterium at the cellular level.

Genetic drift at expanding frontiers promotes gene segregation

Competition between random genetic drift and natural selection play a central role in evolution: Whereas nonbeneficial mutations often prevail in small populations by chance, mutations that sweep through large populations typically confer a selective advantage. Here, however, we observe chance effects during range expansions that dramatically alter the gene pool even in large microbial populations. Initially well mixed populations of two fluorescently labeled strains of Escherichia coli develop well defined, sector-like regions with fractal boundaries in expanding colonies. The formation of these regions is driven by random fluctuations that originate in a thin band of pioneers at the expanding frontier. A comparison of bacterial and yeast colonies (Saccharomyces cerevisiae) suggests that this large-scale genetic sectoring is a generic phenomenon that may provide a detectable footprint of past range expansions.

Wrinkly-Spreader fitness in the two-dimensional agar plate microcosm: maladaptation, compensation and ecological success

Bacterial adaptation to new environments often leads to the establishment of new genotypes with significantly altered phenotypes. In the Wrinkly Spreader (WS), ecological success in static liquid microcosms was through the rapid colonisation of the air-liquid interface by the production of a cellulose-based biofilm. Rapid surface spreading was also seen on agar plates, but in this two-dimensional environment the WS appears maladapted and rapidly reverts to the ancestral smooth (SM)-like colony genotype. In this work, the fitness of WS relative to SM in mixed colonies was found to be low, confirming the WS instability on agar plates. By examining defined WS mutants, the maladaptive characteristic was found to be the expression of cellulose. SM-like revertants had a higher growth rate than WS and no longer expressed significant amounts of cellulose, further confirming that the expression of this high-cost polymer was the basis of maladaptation and the target of compensatory mutation in developing colonies. However, examination of the fate of WS-founded populations in either multiple-colony or single mega-colony agar plate microcosms demonstrated that the loss of WS lineages could be reduced under conditions in which the rapid spreading colony phenotype could dominate nutrient and oxygen access more effectively than competing SM/SM-like genotypes. WS-like isolates recovered from such populations showed increased WS phenotype stability as well as changes in the degree of colony spreading, confirming that the WS was adapting to the two-dimensional agar plate microcosm.

A tunable algorithm for collective decision-making

Complex biological systems are increasingly understood in terms of the algorithms that guide the behavior of system components and the information pathways that link them. Much attention has been given to robust algorithms, or those that allow a system to maintain its functions in the face of internal or external perturbations. At the same time, environmental variation imposes a complementary need for algorithm versatility, or the ability to alter system function adaptively as external circumstances change. An important goal of systems biology is thus the identification of biological algorithms that can meet multiple challenges rather than being narrowly specified to particular problems. Here we show that emigrating colonies of the ant Temnothorax curvispinosus tune the parameters of a single decision algorithm to respond adaptively to two distinct problems: rapid abandonment of their old nest in a crisis and deliberative selection of the best available new home when their old nest is still intact. The algorithm uses a stepwise commitment scheme and a quorum rule to integrate information gathered by numerous individual ants visiting several candidate homes. By varying the rates at which they search for and accept these candidates, the ants yield a colony-level response that adaptively emphasizes either speed or accuracy. We propose such general but tunable algorithms as a design feature of complex systems, each algorithm providing elegant solutions to a wide range of problems.

Modeling vortex swarming in Daphnia

Based on experimental observations in Daphnia, we introduce an agent-based model for the motion of single and swarms of animals. Each agent is described by a stochastic equation that also considers the conditions for active biological motion. An environmental potential further reflects local conditions for Daphnia, such as attraction to light sources. This model is sufficient to describe the observed cycling behavior of single Daphnia. To simulate vortex swarming of many Daphnia, i.e. the collective rotation of the swarm in one direction, we extend the model by considering avoidance of collisions. Two different ansatzes to model such a behavior are developed and compared. By means of computer simulations of a multi-agent system we show that local avoidance - as a special form of asymmetric repulsion between animals - leads to the emergence of a vortex swarm. The transition from uncorrelated rotation of single agents to the vortex swarming as a function of the swarm size is investigated. Eventually, some evidence of avoidance behavior in Daphnia is provided by comparing experimental and simulation results for two animals.