Cooperative organization of bacterial colonies: from genotype to morphotype

Bacterial stigmergy: an organising principle of multicellular collective behaviours of bacteria

The self-organisation of collective behaviours often manifests as dramatic patterns of emergent large-scale order. This is true for relatively "simple" entities such as microbial communities and robot "swarms," through to more complex self-organised systems such as those displayed by social insects, migrating herds, and many human activities. The principle of stigmergy describes those self-organised phenomena that emerge as a consequence of indirect communication between individuals of the group through the generation of persistent cues in the environment. Interestingly, despite numerous examples of multicellular behaviours of bacteria, the principle of stigmergy has yet to become an accepted theoretical framework that describes how bacterial collectives self-organise. Here we review some examples of multicellular bacterial behaviours in the context of stigmergy with the aim of bringing this powerful and elegant self-organisation principle to the attention of the microbial research community.

Laser-induced speckle scatter patterns in Bacillus colonies

Label-free bacterial colony phenotyping technology called BARDOT (Bacterial Rapid Detection using Optical scattering Technology) provided successful classification of several different bacteria at the genus, species, and serovar level. Recent experiments with colonies of Bacillus species provided strikingly different characteristics of elastic light scatter (ELS) patterns, which were comprised of random speckles compared to other bacteria, which are dominated by concentric rings and spokes. Since this laser-based optical sensor interrogates the whole volume of the colony, 3-D information of micro- and macro-structures are all encoded in the far-field scatter patterns. Here, we present a theoretical model explaining the underlying mechanism of the speckle formation by the colonies from Bacillus species. Except for Bacillus polymyxa, all Bacillus spp. produced random bright spots on the imaging plane, which presumably dependent on the cellular and molecular organization and content within the colony. Our scatter model-based analysis revealed that colony spread resulting in variable surface roughness can modify the wavefront of the scatter field. As the center diameter of the Bacillus spp. colony grew from 500 to 900 μm, average speckles area decreased two-fold and the number of small speckles increased seven-fold. In conclusion, as Bacillus colony grows, the average speckle size in the scatter pattern decreases and the number of smaller speckle increases due to the swarming growth characteristics of bacteria within the colony.

Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics

The interspecies exchange of metabolites plays a key role in the spatiotemporal dynamics of microbial communities. This raises the question of whether ecosystem-level behavior of structured communities can be predicted using genome-scale metabolic models for multiple organisms. We developed a modeling framework that integrates dynamic flux balance analysis with diffusion on a lattice and applied it to engineered communities. First, we predicted and experimentally confirmed the species ratio to which a two-species mutualistic consortium converges and the equilibrium composition of a newly engineered three-member community. We next identified a specific spatial arrangement of colonies, which gives rise to what we term the "eclipse dilemma": does a competitor placed between a colony and its cross-feeding partner benefit or hurt growth of the original colony? Our experimentally validated finding that the net outcome is beneficial highlights the complex nature of metabolic interactions in microbial communities while at the same time demonstrating their predictability.

Crude oil treatment leads to shift of bacterial communities in soils from the deep active layer and upper permafrost along the China-Russia Crude Oil Pipeline route

The buried China-Russia Crude Oil Pipeline (CRCOP) across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision) being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs). The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils.

Laser optical sensor, a label-free on-plate Salmonella enterica colony detection tool

We investigated the application capabilities of a laser optical sensor, BARDOT (bacterial rapid detection using optical scatter technology) to generate differentiating scatter patterns for the 20 most frequently reported serovars of Salmonella enterica. Initially, the study tested the classification ability of BARDOT by using six Salmonella serovars grown on brain heart infusion, brilliant green, xylose lysine deoxycholate, and xylose lysine tergitol 4 (XLT4) agar plates. Highly accurate discrimination (95.9%) was obtained by using scatter signatures collected from colonies grown on XLT4. Further verification used a total of 36 serovars (the top 20 plus 16) comprising 123 strains with classification precision levels of 88 to 100%. The similarities between the optical phenotypes of strains analyzed by BARDOT were in general agreement with the genotypes analyzed by pulsed-field gel electrophoresis (PFGE). BARDOT was evaluated for the real-time detection and identification of Salmonella colonies grown from inoculated (1.2 × 10(2) CFU/30 g) peanut butter, chicken breast, and spinach or from naturally contaminated meat. After a sequential enrichment in buffered peptone water and modified Rappaport Vassiliadis broth for 4 h each, followed by growth on XLT4 (~16 h), BARDOT detected S. Typhimurium with 84% accuracy in 24 h, returning results comparable to those of the USDA Food Safety and Inspection Service method, which requires ~72 h. BARDOT also detected Salmonella (90 to 100% accuracy) in the presence of background microbiota from naturally contaminated meat, verified by 16S rRNA sequencing and PFGE. Prolonged residence (28 days) of Salmonella in peanut butter did not affect the bacterial ability to form colonies with consistent optical phenotypes. This study shows BARDOT's potential for nondestructive and high-throughput detection of Salmonella in food samples.

IMPORTANCE

High-throughput screening of food products for pathogens would have a significant impact on the reduction of food-borne hazards. A laser optical sensor was developed to screen pathogen colonies on an agar plate instantly without damaging the colonies; this method aids in early pathogen detection by the classical microbiological culture-based method. Here we demonstrate that this sensor was able to detect the 36 Salmonella serovars tested, including the top 20 serovars, and to identify isolates of the top 8 Salmonella serovars. Furthermore, it can detect Salmonella in food samples in the presence of background microbiota in 24 h, whereas the standard USDA Food Safety and Inspection Service method requires about 72 h.

Collective motion of spherical bacteria

A large variety of motile bacterial species exhibit collective motions while inhabiting liquids or colonizing surfaces. These collective motions are often characterized by coherent dynamic clusters, where hundreds of cells move in correlated whirls and jets. Previously, all species that were known to form such motion had a rod-shaped structure, which enhances the order through steric and hydrodynamic interactions. Here we show that the spherical motile bacteria Serratia marcescens exhibit robust collective dynamics and correlated coherent motion while grown in suspensions. As cells migrate to the upper surface of a drop, they form a monolayer, and move collectively in whirls and jets. At all concentrations, the distribution of the bacterial speed was approximately Rayleigh with an average that depends on concentration in a non-monotonic way. Other dynamical parameters such as vorticity and correlation functions are also analyzed and compared to rod-shaped bacteria from the same strain. Our results demonstrate that self-propelled spherical objects do form complex ordered collective motion. This opens a door for a new perspective on the role of cell aspect ratio and alignment of cells with regards to collective motion in nature.

Development of an integrated optical analyzer for characterization of growth dynamics of bacterial colonies

In order to understand the biophysics behind collective behavior of a bacterial colony, a confocal displacement meter was used to measure the profiles of the bacterial colonies, together with a custom built optical density circuits. The system delivered essential information related to the quantitative growth dynamics (height, diameter, aspect ratio, optical density) of the bacterial colony. For example, the aspect ratio of S. aureus was approximately two times higher than that of E. coli O157 : H7, while the OD of S. aureus was approximately 1/3 higher than that of E. coli O157 : H7.

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.

A hydration-based biophysical index for the onset of soil microbial coexistence

Mechanistic exploration of the origins of the unparalleled soil microbial biodiversity represents a vast and uncharted scientific frontier. Quantification of candidate mechanisms that promote and sustain such diversity must be linked with microbial functions and measurable biophysical interactions at appropriate scales. We report a novel microbial coexistence index (CI) that links macroscopic soil hydration conditions with microscale aquatic habitat fragmentation that impose restrictions on cell dispersion and growth rates of competing microbial populations cohabiting soil surfaces. The index predicts a surprisingly narrow range of soil hydration conditions that suppress microbial coexistence; and for most natural conditions found in soil hydration supports coexistence. The critical hydration conditions and relative abundances of competing species are consistent with limited experimental observations and with individual-based model simulations. The proposed metric offers a means for systematic evaluation of factors that regulate microbial coexistence in an ecologically consistent fashion.

Non-contiguous finished genome sequence and description of Paenibacillus senegalensis sp. nov

Paenibacillus senegalensis strain JC66(T), is the type strain of Paenibacillus senegalensis sp. nov., a new species within the genus Paenibacillus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. P. senegalensis strain JC66(T) is a facultative Gram-negative anaerobic rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,581,254 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 48.2% and contains 5,008 protein-coding and 51 RNA genes, including 9 rRNA genes.

BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology

Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI) recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.

Developmental plasticity of bacterial colonies and consortia in germ-free and gnotobiotic settings

Background

Bacteria grown on semi-solid media can build two types of multicellular structures, depending on the circumstances. Bodies (colonies) arise when a single clone is grown axenically (germ-free), whereas multispecies chimeric consortia contain monoclonal microcolonies of participants. Growth of an axenic colony, mutual interactions of colonies, and negotiation of the morphospace in consortial ecosystems are results of intricate regulatory and metabolic networks. Multicellular structures developed by Serratia sp. are characteristically shaped and colored, forming patterns that reflect their growth conditions (in particular medium composition and the presence of other bacteria).

Results

Building on our previous work, we developed a model system for studying ontogeny of multicellular bacterial structures formed by five Serratia sp. morphotypes of two species grown in either "germ-free" or "gnotobiotic" settings (i.e. in the presence of bacteria of other conspecific morphotype, other Serratia species, or E. coli). Monoclonal bodies show regular and reproducible macroscopic appearance of the colony, as well as microscopic pattern of its growing margin. Standard development can be modified in a characteristic and reproducible manner in close vicinity of other bacterial structures (or in the presence of their products). Encounters of colonies with neighbors of a different morphotype or species reveal relationships of dominance, cooperation, or submission; multiple interactions can be summarized in "rock – paper – scissors" network of interrelationships. Chimerical (mixed) plantings consisting of two morphotypes usually produced a “consortium” whose structure is consistent with the model derived from interaction patterns observed in colonies.

Conclusions

Our results suggest that development of a bacterial colony can be considered analogous to embryogenesis in animals, plants, or fungi: to proceed, early stages require thorough insulation from the rest of the biosphere. Only later, the newly developing body gets connected to the ecological interactions in the biosphere. Mixed “anlagen” cannot accomplish the first, germ-free phase of development; hence, they will result in the consortium of small colonies. To map early development and subsequent interactions with the rest of the biospheric web, simplified gnotobiotic systems described here may turn to be of general use, complementing similar studies on developing multicellular eukaryots under germ-free or gnotobiotic conditions.

Liquid-infused structured surfaces with exceptional anti-biofouling performance

Bacteria primarily exist in robust, surface-associated communities known as biofilms, ubiquitous in both natural and anthropogenic environments. Mature biofilms resist a wide range of antimicrobial treatments and pose persistent pathogenic threats. Treatment of adherent biofilm is difficult, costly, and, in medical systems such as catheters or implants, frequently impossible. At the same time, strategies for biofilm prevention based on surface chemistry treatments or surface microstructure have been found to only transiently affect initial attachment. Here we report that Slippery Liquid-Infused Porous Surfaces (SLIPS) prevent 99.6% of Pseudomonas aeruginosa biofilm attachment over a 7-d period, as well as Staphylococcus aureus (97.2%) and Escherichia coli (96%), under both static and physiologically realistic flow conditions. In contrast, both polytetrafluoroethylene and a range of nanostructured superhydrophobic surfaces accumulate biofilm within hours. SLIPS show approximately 35 times the reduction of attached biofilm versus best case scenario, state-of-the-art PEGylated surface, and over a far longer timeframe. We screen for and exclude as a factor cytotoxicity of the SLIPS liquid, a fluorinated oil immobilized on a structured substrate. The inability of biofilm to firmly attach to the surface and its effective removal under mild flow conditions (about 1 cm/s) are a result of the unique, nonadhesive, "slippery" character of the smooth liquid interface, which does not degrade over the experimental timeframe. We show that SLIPS-based antibiofilm surfaces are stable in submerged, extreme pH, salinity, and UV environments. They are low-cost, passive, simple to manufacture, and can be formed on arbitrary surfaces. We anticipate that our findings will enable a broad range of antibiofilm solutions in the clinical, industrial, and consumer spaces.

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.

Towards an integrated experimental-theoretical approach for assessing the mechanistic basis of hair and feather morphogenesis

In his seminal 1952 paper, 'The Chemical Basis of Morphogenesis', Alan Turing lays down a milestone in the application of theoretical approaches to understand complex biological processes. His deceptively simple demonstration that a system of reacting and diffusing chemicals could, under certain conditions, generate spatial patterning out of homogeneity provided an elegant solution to the problem of how one of nature's most intricate events occurs: the emergence of structure and form in the developing embryo. The molecular revolution that has taken place during the six decades following this landmark publication has now placed this generation of theoreticians and biologists in an excellent position to rigorously test the theory and, encouragingly, a number of systems have emerged that appear to conform to some of Turing's fundamental ideas. In this paper, we describe the history and more recent integration between experiment and theory in one of the key models for understanding pattern formation: the emergence of feathers and hair in the skins of birds and mammals.

Control of bacterial biofilm growth on surfaces by nanostructural mechanics and geometry

Surface-associated communities of bacteria, called biofilms, pervade natural and anthropogenic environments. Mature biofilms are resistant to a wide range of antimicrobial treatments and therefore pose persistent pathogenic threats. The use of surface chemistry to inhibit biofilm growth has been found to only transiently affect initial attachment. In this work, we investigate the tunable effects of physical surface properties, including high-aspect-ratio (HAR) surface nanostructure arrays recently reported to induce long-range spontaneous spatial patterning of bacteria on the surface. The functional parameters and length scale regimes that control such artificial patterning for the rod-shaped pathogenic species Pseudomonas aeruginosa are elucidated through a combinatorial approach. We further report a crossover regime of biofilm growth on a HAR nanostructured surface versus the nanostructure effective stiffness. When the 'softness' of the hair-like nanoarray is increased beyond a threshold value, biofilm growth is inhibited as compared to a flat control surface. This result is consistent with the mechanoselective adhesion of bacteria to surfaces. Therefore by combining nanoarray-induced bacterial patterning and modulating the effective stiffness of the nanoarray--thus mimicking an extremely compliant flat surface--bacterial mechanoselective adhesion can be exploited to control and inhibit biofilm growth.

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.

Cellular decision making and biological noise: from microbes to mammals

Cellular decision making is the process whereby cells assume different, functionally important and heritable fates without an associated genetic or environmental difference. Such stochastic cell fate decisions generate nongenetic cellular diversity, which may be critical for metazoan development as well as optimized microbial resource utilization and survival in a fluctuating, frequently stressful environment. Here, we review several examples of cellular decision making from viruses, bacteria, yeast, lower metazoans, and mammals, highlighting the role of regulatory network structure and molecular noise. We propose that cellular decision making is one of at least three key processes underlying development at various scales of biological organization.

Surviving bacterial sibling rivalry: inducible and reversible phenotypic switching in Paenibacillus dendritiformis

Natural habitats vary in available nutrients and room for bacteria to grow, but successful colonization can lead to overcrowding and stress. Here we show that competing sibling colonies of Paenibacillus dendritiformis bacteria survive overcrowding by switching between two distinct vegetative phenotypes, motile rods and immotile cocci. Growing colonies of the rod-shaped bacteria produce a toxic protein, Slf, which kills cells of encroaching sibling colonies. However, sublethal concentrations of Slf induce some of the rods to switch to Slf-resistant cocci, which have distinct metabolic and resistance profiles, including resistance to cell wall antibiotics. Unlike dormant spores of P. dendritiformis, the cocci replicate. If cocci encounter conditions that favor rods, they secrete a signaling molecule that induces a switch to rods. Thus, in contrast to persister cells, P. dendritiformis bacteria adapt to changing environmental conditions by inducible and reversible phenotypic switching.

In favorable environments, species may face space and nutrient limits due to overcrowding. Bacteria provide an excellent model for analyzing principles underlying overcrowding and regulation of density in nature, since their population dynamics can be easily and accurately assessed under controlled conditions. We describe a newly discovered mechanism for survival of a bacterial population during overcrowding. When competing with sibling colonies, Paenibacillus dendritiformis produces a lethal protein (Slf) that kills cells at the interface of encroaching colonies. Slf also induces a small proportion of the cells to switch from motile, rod-shaped cells to nonmotile, Slf-resistant, vegetative cocci. When crowding is reduced and nutrients are no longer limiting, the bacteria produce a signal that induces cocci to switch back to motile rods, allowing the population to spread. Genes encoding components of this phenotypic switching pathway are widespread among bacterial species, suggesting that this survival mechanism is not unique to P. dendritiformis.

On the sensitivity of forward scattering patterns from bacterial colonies to media composition

Morphology of colonies is important for taxonomy and diagnostics in microbiology where the response to environmental factors is sensitive enough to support discrimination. In this research, we analyzed the forward scattering patterns of individual Escherichia coli K12 colonies when agar hardness and nutrition levels were varied from the control sample. As the agar concentration increased from 1.2% to 1.8%, the diameter of the forward scattering patterns also increased for the same experimental condition which reflects that the colony thickness at the apex is greater for increased agar concentrations. Regarding nutrition, increasing dextrose resulted in smaller mean colony diameters while the mean diameters of the colonies were proportional to the yeast extract concentration up to 0.5%. The result reveals that ±0.3% agar concentration from the control sample is sufficient to create variations in the scattering patterns. For nutrition -0.25% of yeast extract showed significant variations while +0.25% from control sample showed minimal variations.

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.

Bacteria pattern spontaneously on periodic nanostructure arrays

Surface-associated bacteria typically form self-organizing communities called biofilms. Spatial segregation is important for various bacterial processes associated with cellular and community development. Here, we demonstrate bacterial ordering and oriented attachment on the single-cell level induced by nanometer-scale periodic surface features. These surfaces cause spontaneous and distinct patterning phases, depending on their periodicity, which is observed for several strains, both gram positive and negative. This patterning is a general phenomenon that can control natural biofilm organization on the cellular level.

General factors important for the formation of structured biofilm-like yeast colonies

The lifestyle of wild and laboratory yeast strains significantly differs. In contrast to the smooth colonies of laboratory strains, wild Saccharomyces cerevisiae strains form biofilm-like, strikingly structured colonies possessing distinctive traits enabling them to better survive in hostile environments in the wild. Here, comparing three sets of strains forming differently structured colonies (fluffy, semi-fluffy and smooth), each derived from ancestors with distinct genetic backgrounds isolated from natural settings (BR-88, BR-99 and BR-103), we specified the factors essential for the formation of structured colonies, i.e. for the lifestyle most likely to be preferred in the wild. The ability to form an abundant extracellular matrix (ECM) is one of the features typical for structured colonies. ECM influences colony architecture and many other physiological properties, such as the capability to retain water in a 2-fold surplus to wet cell biomass. ECM composition, however, differs among distinct strains, depending on their particular genetic background. We further show that the expression of certain genes (AQY1, FLO11) is also strictly related to the particular colony morphology, being highest in the most structured colonies. Flo11p adhesin, important for cell-cell and cell-surface adhesion, is essential for the formation of fluffy colonies and thus significantly contributes to the phenotype variability of wild yeast strains. On the other hand, surprisingly, neither the cell shape nor budding pattern nor the ability to form pseudohyphae directly influences the formation of three-dimensional fluffy colony architecture.

Bacterial chemotaxis and entropy production

Entropy production is calculated for bacterial chemotaxis in the case of a migrating band of bacteria in a capillary tube. It is found that the speed of the migrating band is a decreasing function of the starting concentration of the metabolizable attractant. The experimentally found dependence of speed on the starting concentration of galactose, glucose and oxygen is fitted with power-law functions. It is found that the corresponding exponents lie within the theoretically predicted interval. The effect of the reproduction of bacteria on band speed is considered, too. The acceleration of the band is predicted due to the reproduction rate of bacteria. The relationship between chemotaxis, the maximum entropy production principle and the formation of self-organizing structure is discussed.

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.

Population context determines cell-to-cell variability in endocytosis and virus infection

Single-cell heterogeneity in cell populations arises from a combination of intrinsic and extrinsic factors. This heterogeneity has been measured for gene transcription, phosphorylation, cell morphology and drug perturbations, and used to explain various aspects of cellular physiology. In all cases, however, the causes of heterogeneity were not studied. Here we analyse, for the first time, the heterogeneous patterns of related cellular activities, namely virus infection, endocytosis and membrane lipid composition in adherent human cells. We reveal correlations with specific cellular states that are defined by the population context of a cell, and we derive probabilistic models that can explain and predict most cellular heterogeneity of these activities, solely on the basis of each cell's population context. We find that accounting for population-determined heterogeneity is essential for interpreting differences between the activity levels of cell populations. Finally, we reveal that synergy between two molecular components, focal adhesion kinase and the sphingolipid GM1, enhances the population-determined pattern of simian virus 40 (SV40) infection. Our findings provide an explanation for the origin of heterogeneity patterns of cellular activities in adherent cell populations.

Paenibacillus dendritiformis bacterial colony growth depends on surfactant but not on bacterial motion

Most research on growing bacterial colonies on agar plates has concerned the effect of genetic or morphotype variation. Some studies have indicated that there is a correlation between microscopic bacterial motion and macroscopic colonial expansion, especially for swarming strains, but no measurements have been obtained for a single strain to relate the microscopic scale to the macroscopic scale. We examined here a single strain (Paenibacillus dendritiformis type T; tip splitting) to determine both the macroscopic growth of colonies and the microscopic bacterial motion within the colonies. Our multiscale measurements for a variety of growth conditions revealed that motion on the microscopic scale and colonial growth are largely independent. Instead, the growth of the colony is strongly affected by the availability of a surfactant that reduces surface tension.

A simple model for the early events of quorum sensing in Pseudomonas aeruginosa: modeling bacterial swarming as the movement of an "activation zone"

Background

Quorum sensing (QS) is a form of gene regulation based on cell-density that depends on inter-cellular communication. While there are a variety of models for bacterial colony morphology, there is little work linking QS genes to movement in an open system.

Results

The onset of swarming in environmental P. aeruginosa PUPa3 was described with a simplified computational model in which cells in random motion communicate via a diffusible signal (representing N-acyl homoserine lactones, AHL) as well as diffusible, secreted factors (enzymes, biosurfactans, i.e. "public goods") that regulate the intensity of movement and metabolism in a threshold-dependent manner. As a result, an "activation zone" emerges in which nutrients and other public goods are present in sufficient quantities, and swarming is the spontaneous displacement of this high cell-density zone towards nutrients and/or exogenous signals. The model correctly predicts the behaviour of genomic knockout mutants in which the QS genes responsible either for the synthesis (lasI, rhlI) or the sensing (lasR, rhlR) of AHL signals were inactivated. For wild type cells the model predicts sustained colony growth that can however be collapsed by the overconsumption of nutrients.

Conclusion

While in more complex models include self-orienting abilities that allow cells to follow concentration gradients of nutrients and chemotactic agents, in this model, displacement towards nutrients or environmental signals is an emergent property of the community that results from the action of a few, well-defined QS genes and their products. Still the model qualitatively describes the salient properties of QS bacteria, i.e. the density-dependent onset of swarming as well as the response to exogenous signals or cues.

Reviewers

This paper was reviewed by Gáspár Jékely, L. Aravind, Eugene V. Koonin and Artem Novozhilov (nominated by Eugene V. Koonin).

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.

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.

Spatial-temporal modelling of bacterial colony growth on solid media

The enormous diversity among bacterial colonies of different species, and among colonies of the same species under different environmental conditions, has long interested microbiologists. Yet it is only comparatively recently that quantitative, rather than merely conceptual, models have been developed to explain the dynamics of bacterial colony formation and growth. Understanding the fundamental processes that drive these dynamics is still at a rudimentary level, though a number of advances have been made. This review traces the history of bacterial colony growth modelling, from the pioneering work of Pirt in the late 1960s, through experimental investigations by Wimpenny and his colleagues in the 1970s, and further models extending from that work to understand complex bacterial colony formations. It concludes with recent results which find that both diameter and height of the colony follow simple power-law behaviour over the entire active growth period (from a few hours to several days old), and that the results of Pirt, Wimpenny and their contemporaries can be re-interpreted.

Stress-induced mutagenesis in bacteria

Bacteria spend their lives buffeted by changing environmental conditions. To adapt to and survive these stresses, bacteria have global response systems that result in sweeping changes in gene expression and cellular metabolism. These responses are controlled by master regulators, which include: alternative sigma factors, such as RpoS and RpoH; small molecule effectors, such as ppGpp; gene repressors such as LexA; and, inorganic molecules, such as polyphosphate. The response pathways extensively overlap and are induced to various extents by the same environmental stresses. These stresses include nutritional deprivation, DNA damage, temperature shift, and exposure to antibiotics. All of these global stress responses include functions that can increase genetic variability. In particular, up-regulation and activation of error-prone DNA polymerases, down-regulation of error-correcting enzymes, and movement of mobile genetic elements are common features of several stress responses. The result is that under a variety of stressful conditions, bacteria are induced for genetic change. This transient mutator state may be important for adaptive evolution.

Stability analysis of a hybrid cellular automaton model of cell colony growth

Cell colonies of bacteria, tumor cells, and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell colony growth. In the model the growth of the colony is limited by a nutrient that is consumed by the cells and which inhibits cell division if it falls below a certain threshold. Using this model we have investigated how the nutrient consumption rate of the cells affects the growth dynamics of the colony. We found that for low consumption rates the colony takes on an Eden-like morphology, while for higher consumption rates the morphology of the colony is branched with a fractal geometry. These findings are in agreement with previous results, but the simplicity of the model presented here allows for a linear stability analysis of the system. By observing that the local growth of the colony is proportional to the flux of the nutrient we derive an approximate dispersion relation for the growth of the colony interface. This dispersion relation shows that the stability of the growth depends on how far the nutrient penetrates into the colony. For low nutrient consumption rates the penetration distance is large, which stabilizes the growth, while for high consumption rates the penetration distance is small, which leads to unstable branched growth. When the penetration distance vanishes the dispersion relation is reduced to the one describing Laplacian growth without ultra-violet regularization. The dispersion relation was verified by measuring how the average branch width depends on the consumption rate of the cells and shows good agreement between theory and simulations.

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.

Self-engineering capabilities of bacteria

Under natural growth conditions, bacteria can utilize intricate communication capabilities (e.g. quorum-sensing, chemotactic signalling and plasmid exchange) to cooperatively form (self-organize) complex colonies with elevated adaptability-the colonial pattern is collectively engineered according to the encountered environmental conditions. Bacteria do not genetically store all the information required for creating all possible patterns. Instead, additional information is cooperatively generated as required for the colonial self-organization to proceed. We describe how complex colonial forms (patterns) emerge through the communication-based singular interplay between individual bacteria and the colony. Each bacterium is, by itself, a biotic autonomous system with its own internal cellular informatics capabilities (storage, processing and assessment of information). These afford the cell plasticity to select its response to biochemical messages it receives, including self-alteration and the broadcasting of messages to initiate alterations in other bacteria. Hence, new features can collectively emerge during self-organization from the intracellular level to the whole colony. The cells thus assume newly co-generated traits and abilities that are not explicitly stored in the genetic information of the individuals.

A mechanical role for the chemotaxis system in swarming motility

The chemotaxis system, but not chemotaxis, is essential for swarming motility in Salmonella enterica serovar Typhimurium. Mutants in the chemotaxis pathway exhibit fewer and shorter flagella, downregulate class 3 or 'late' motility genes, and appear to be less hydrated when propagated on a surface. We show here that the output of the chemotaxis system, CheY approximately P, modulates motor bias during swarming as it does during chemotaxis, but for a distinctly different end. A constitutively active form of CheY was found to promote swarming in the absence of several upstream chemotaxis components. Two point mutations that suppressed the swarming defect of a cheY null mutation mapped to FliM, a protein in the motor switch complex with which CheY approximately P interacts. A common property of these suppressors was their increased frequency of motor reversal. These and other data suggest that the ability to switch motor direction is important for promoting optimal surface wetness. If the surface is sufficiently wet, exclusively clockwise or counterclockwise directions of motor rotation will support swarming, suggesting also that the bacteria can move on a surface with flagellar bundles of either handedness.

Symmetry-breaking in mammalian cell cohort migration during tissue pattern formation: role of random-walk persistence

Coordinated, cohort cell migration plays an important role in the morphogenesis of tissue patterns in metazoa. However, individual cells intrinsically move in a random walk-like fashion when studied in vitro. Hence, in the absence of an external orchestrating influence or template, the emergence of cohort cell migration must involve a symmetry-breaking event. To study this process, we used a novel experimental system in which multiple capillary endothelial cells exhibit spontaneous and robust cohort migration in the absence of chemical gradients when cultured on micrometer-scale extracellular matrix islands fabricated using microcontact printing. A computational model suggested that directional persistence of random-walk and dynamic mechanical coupling of adjacent cells are the critical control parameters for this symmetry-breaking behavior that is induced in spatially-constrained cell ensembles. The model predicted our finding that fibroblasts, which exhibit a much shorter motility persistence time than endothelial cells, failed to undergo symmetry breaking or produce cohort migration on the matrix islands. These findings suggest that cells have intrinsic motility characteristics that are tuned to match their role in tissue patterning. Our results underscore the importance of studying cell motility in the context of cell populations, and the need to address emergent features in multicellular organisms that arise not only from cell-cell and cell-matrix interactions, but also from properties that are intrinsic to individual cells.

Complex pattern formation of marine gradient bacteria explained by a simple computer model

We report on the formation of conspicuous patterns by the sulfide-oxidizing bacterium Thiovulum majus and a recently described vibrioid bacterium. These microaerophilic bacteria form mucus veils on top of sulfidic marine sediment exhibiting regular spaced bacterial patterns (honeycombs, interwoven bands, or inverse honeycombs). A simple qualitative computer model, based on chemotaxis towards oxygen and the ability of the bacteria to induce water advection when attached, can explain the formation of the observed patterns. Our study shows that complex bacterial patterns in nature can be explained in terms of chemotaxis and resource optimisation without involvement of cell-cell signalling or social behavior amongst bacteria.

Bacterial linguistic communication and social intelligence

Bacteria have developed intricate communication capabilities (e.g. quorum-sensing, chemotactic signaling and plasmid exchange) to cooperatively self-organize into highly structured colonies with elevated environmental adaptability. We propose that bacteria use their intracellular flexibility, involving signal transduction networks and genomic plasticity, to collectively maintain linguistic communication: self and shared interpretations of chemical cues, exchange of chemical messages (semantic) and dialogues (pragmatic). Meaning-based communication permits colonial identity, intentional behavior (e.g. pheromone-based courtship for mating), purposeful alteration of colony structure (e.g. formation of fruiting bodies), decision-making (e.g. to sporulate) and the recognition and identification of other colonies - features we might begin to associate with a bacterial social intelligence. Such a social intelligence, should it exist, would require going beyond communication to encompass unknown additional intracellular processes to generate inheritable colonial memory and commonly shared genomic context.

Emergence of phenotypic variants upon mismatch repair disruption in Pseudomonas aeruginosa

MutS is part of the bacterial mismatch repair system that corrects point mutations and small insertions/deletions that fail to be proof-read by DNA polymerase activity. In this work it is shown that the disruption of theP. aeruginosa mutSgene generates the emergence of diverse colony morphologies in contrast with its parental wild-type strain that displayed monomorphic colonies. Interestingly, two of themutSmorphotypes emerged at a high frequency and in a reproducible way and were selected for subsequent characterization. One of them displayed a nearly wild-type morphology while the other notably showed, compared with the wild-type strain, increased production of pyocyanin and pyoverdin, lower excretion of LasB protease and novel motility characteristics, mainly related to swarming. Furthermore, it was reproducibly observed that, after prolonged incubation in liquid culture, the pigmented variant consistently emerged from themutSwild-type-like variant displaying a reproducible event. It is also shown that theseP. aeruginosa mutSmorphotypes not only displayed an increase in the frequency of antibiotic-resistant mutants, as described for clinicalP. aeruginosamutator isolates, but also generated mutants whose antibiotic-resistant levels were higher than those measured from spontaneous resistant mutants derived from wild-type cells. It was also found that both morphotypes showed a decreased cytotoxic capacity compared to the wild-type strain, leading to the emergence of invasive variants. By using mutated versions of a tetracycline resistance gene, themutSmutant showed a 70-fold increase in the reversion frequency of a +1 frameshift mutation with respect to its parental wild-type strain, allowing the suggestion that the phenotypical diversity generated in themutSpopulation could be produced in part by frameshift mutations. Finally, since morphotypical diversification has also been described in clinical isolates, the possibility that thismutSdiversification was related to the high frequency hypermutability observed inP. aeruginosaCF isolates is discussed.

Bacterial motility on a surface: many ways to a common goal

When free-living bacteria colonize biotic or abiotic surfaces, the resultant changes in physiology and morphology have important consequences on their growth, development, and survival. Surface motility, biofilm formation, fruiting body development, and host invasion are some of the manifestations of functional responses to surface colonization. Bacteria may sense the growth surface either directly through physical contact or indirectly by sensing the proximity of fellow bacteria. Extracellular signals that elicit new gene expression include autoinducers, amino acids, peptides, proteins, and carbohydrates. This review focuses mainly on surface motility and makes comparisons to features shared by other surface phenomenon.