Cooperative organization of bacterial colonies: from genotype to morphotype

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

During colonial development, bacteria generate a wealth of patterns, some of which are reminiscent of those occurring in abiotic systems. They can exhibit rich behaviour, reflecting informative communication capabilities that include exchange of genetic materials and the fact that the colony's building blocks are biotic. Each has internal degrees of freedom, informatic capabilities and freedom to respond by altering itself and others via emission of signals in a self-regulated manner. To unravel the special secrets of bacterial self-organization, we conducted an integrative (experimental and theoretical) study of abiotic and biotic systems. Guided by the notion of general biotic motives and principles, I propose that the informative communication between individuals makes possible the enhancement of the individuals' regulated freedom, while increasing their cooperation. This process is accomplished via cooperative complexification of the colony through self-organization of hierarchical spatio-temporal patterning. The colonial higher complexity provides the degree of plasticity and flexibility required for better colonial adaptability and endurability in a dynamic environment. The biotic system can modify the environment and obtain environmental information for further self-improvement. I reflect on the potential applications of the new understanding on 'engineered self-organization of systems too complex to design' and other issues.

Modeling the early stages of vascular network assembly

In vertebrates, networks of capillary vessels supply tissues with nutrients. Capillary patterns are closely mimicked by endothelial cells cultured on basement membrane proteins that allow single randomly dispersed cells to self-organize into vascular networks. Here we provide a model including chemoattraction as the fundamental mechanism for cell-to-cell communication in order to identify key parameters in the complexity of the formation of vascular patterns. By flanking biological experiments, theoretical insights and numerical simulations, we provide strong evidence that endothelial cell number and the range of activity of a chemoattractant factor regulate vascular network formation and size. We propose a mechanism linking the scale of formed endothelial structures to the range of cell-to-cell interaction mediated by the release of chemoattractants.

Colony shape as a genetic trait in the pattern-forming Bacillus mycoides

BACKGROUND

Bacillus mycoides Flügge, a Gram-positive, non-motile soil bacterium assigned to Bacillus cereus group, grows on agar as chains of cells linked end to end, forming radial filaments curving clock- or counter-clockwise (SIN or DX morphotypes). The molecular mechanism causing asymmetric curving is not known: our working hypothesis considers regulation of filamentous growth as the prerequisite for these morphotypes.

RESULTS

SIN and DX strains isolated from the environment were classified as B. mycoides by biochemical and molecular biology tests. Growth on agar of different hardness and nutrient concentration did not abolish colony patterns, nor was conversion between SIN and DX morphotypes ever noticed. A number of morphotype mutants, all originating from one SIN strain, were obtained. Some lost turn direction becoming fluffy, others became round and compact. All mutants lost wild type tight aggregation in liquid culture. Growth on agar was followed by microscopy, exploring the process of colony formation and details of cell divisions. A region of the dcw (division cell wall) cluster, including ftsQ, ftsA, ftsZ and murC, was sequenced in DX and SIN strains as a basis for studying cell division. This confirmed the relatedness of DX and SIN strains to the B. cereus group.

CONCLUSIONS

DX and SIN asymmetric morphotypes stem from a close but not identical genomic context. Asymmetry is established early during growth on agar. Wild type bacilli construct mostly uninterrupted filaments with cells dividing at the free ends: they "walk" longer distances compared to mutants, where enhanced frequency of cell separation produces new growing edges resulting in round compact colonies.

[Evolutionary epidemiological thought on infections]

The objective of the study is to analyse the main aspects of current epidemiological knowledge on the evolutionary status of infections. Living organisms in the biosphere are part of dynamic systems of variable intensities. Some of these systems are on the surface while others take place inside the genome core. Parasitism is a phenomenon commonly seen in nature. Infective parasites relate to each other through several mechanisms, such as genetic DNA exchange, and because of the connections established communities of infectious agents are not isolated. The internalization process allows the parasites to get into their hosts' cells, which is accomplished through the phagocytosis of infectious agents or other more sophisticated mechanisms such as pill production. To leave the intracellular medium, some organisms make use of apoptosis, a highly specialized genetic mechanism that makes possible to destroy macrophages. It is currently accepted that molecular DNA can flow into the blood stream as the so-called infectrons. Thus it is hypothesized the existence of infection networks that allows the coadaptability of parasites and their hosts, and creates coevolutionary forces between hosts and their parasites facilitating the emergence of new pathogens.

Anatomical analysis of Saccharomyces cerevisiae stalk-like structures reveals spatial organization and cell specialization

Recently we reported an unusual multicellular organization in yeast that we termed stalk-like structures. These structures are tall (0.5 to 3 cm long) and narrow (1 to 3 mm in diameter). They are formed in response to UV radiation of cultures spread on high agar concentrations. Here we present an anatomical analysis of the stalks. Microscopic inspection of cross sections taken from stalks revealed that stalks are composed of an inner core in which cells are dense and vital and a layer of cells (four to six rows) that surrounds the core. This outer layer is physically separated from the core and contains many dead cells. The outer layer may form a protective shell for the core cells. Through electron microscopy analysis we observed three types of cells within the stalk population: (i) cells containing many unusual vesicles, which might be undergoing some kind of cell death; (ii) cells containing spores (usually one or two spores only); and (iii) familiar rounded cells. We suggest that stalk cells are not only spatially organized but may undergo processes that induce a certain degree of cell specialization. We also show that high agar concentration alone, although not sufficient to induce stalk formation, induces dramatic changes in a colony's morphology. Most striking among the agar effects is the induction of growth into the agar, forming peg-like structures. Colonies grown on 4% agar or higher are reminiscent of stalks in some aspects. The agar concentration effects are mediated in part by the Ras pathway and are related to the invasive-growth phenomenon.

Coevolutionary networks: a novel approach to understanding the relationships of humans with the infectious agents

Human organism is interpenetrated by the world of microorganisms, from the conception until the death. This interpenetration involves different levels of interactions between the partners including trophic exchanges, bi-directional cell signaling and gene activation, besides genetic and epigenetic phenomena, and tends towards mutual adaptation and coevolution. Since these processes are critical for the survival of individuals and species, they rely on the existence of a complex organization of adaptive systems aiming at two apparently conflicting purposes: the maintenance of the internal coherence of each partner, and a mutually advantageous coexistence and progressive adaptation between them. Humans possess three adaptive systems: the nervous, the endocrine and the immune system, each internally organized into subsystems functionally connected by intraconnections, to maintain the internal coherence of the system. The three adaptive systems aim at the maintenance of the internal coherence of the organism and are functionally linked by interconnections, in such way that what happens to one is immediately sensed by the others. The different communities of infectious agents that live within the organism are also organized into functional networks. The members of each community are linked by intraconnections, represented by the mutual trophic, metabolic and other influences, while the different infectious communities affect each other through interconnections. Furthermore, by means of its adaptive systems, the organism influences and is influenced by the microbial communities through the existence of transconnections. It is proposed that these highly complex and dynamic networks, involving gene exchange and epigenetic phenomena, represent major coevolutionary forces for humans and microorganisms.

The evolution of social behavior in microorganisms

Recent studies of microorganisms have revealed diverse complex social behaviors, including cooperation in foraging, building, reproducing, dispersing and communicating. These microorganisms should provide novel, tractable systems for the analysis of social evolution. The application of evolutionary and ecological theory to understanding their behavior will aid in developing better means to control the many pathogenic bacteria that use social interactions to affect humans.

Relation of capsular polysaccharide production and colonial cell organization to colony morphology in Vibrio parahaemolyticus

Vibrio parahaemolyticus is a ubiquitous, gram-negative marine bacterium that undergoes phase variation between opaque and translucent colony morphologies. The purpose of this study was to determine the factor(s) responsible for the opaque and translucent phenotypes and to examine cell organization within both colony types. Examination of thin sections of ruthenium red-stained bacterial cells by electron microscopy revealed a thick, electron-dense layer surrounding the opaque cells that was absent in preparations from translucent strains. Extracellular polysaccharide (EPS) material was extracted from both opaque and translucent strains, and the opaque strain was shown to produce abundant levels of polysaccharide, in contrast to the translucent strain. Compositional analysis of the EPS identified four major sugars: glucose, galactose, fucose, and N-acetylglucosamine. Confocal scanning laser microscopy was used to investigate cell organization within opaque and translucent colonies. Cells within both types of colonies exhibited striking organization; rod-shaped cells were aligned parallel to one another and perpendicular to the agar surface throughout the depth of the colony. Cells within translucent colonies appeared more tightly packed than cells in opaque colonies. In addition, a dramatic difference in the structural integrity of these two colony types was observed. When colonies were perturbed, the cell organization of the translucent colonies was completely disrupted while the organization of the opaque colonies was maintained. To our knowledge, this study represents the first description of how cells are organized in the interior of a viable bacterial colony. We propose that the copious amount of EPS produced by the opaque strain fills the intercellular space within the colony, resulting in increased structural integrity and the opaque phenotype.

Differentiation of chitinase-active and non-chitinase-active subpopulations of a marine bacterium during chitin degradation

The ability of marine bacteria to adhere to detrital particulate organic matter and rapidly switch on metabolic genes in an effort to reproduce is an important response for bacterial survival in the pelagic marine environment. The goal of this investigation was to evaluate the relationship between chitinolytic gene expression and extracellular chitinase activity in individual cells of the marine bacterium Pseudoalteromonas sp. strain S91 attached to solid chitin. A green fluorescent protein reporter gene under the control of the chiA promoter was used to evaluate chiA gene expression, and a precipitating enzyme-linked fluorescent probe, ELF-97-N-acetyl-beta-D-glucosaminide, was used to evaluate extracellular chitinase activity among cells in the bacterial population. Evaluation of chiA expression and ELF-97 crystal location at the single-cell level revealed two physiologically distinct subpopulations of S91 on the chitin surface: one that was chitinase active and remained associated with the surface and another that was non-chitinase active and released daughter cells into the bulk aqueous phase. It is hypothesized that the surface-associated, non-chitinase-active population is utilizing chitin degradation products that were released by the adjacent chitinase-active population for cell replication and dissemination into the bulk aqueous phase.

Yeast colonies synchronise their growth and development

The ability to emit and receive signals over long distances is one of the characteristic attributes of multicellular organisms. Such communication can be mediated in different manners (by chemical compounds, light waves, acoustic waves etc.) and usually is reflected in the behaviour of the communicating organisms. Recently, we reported that individual yeast colonies, organised multicellular structures, can also communicate at long distance by means of volatile ammonia, which is produced by colonies in pulses separated by acidification of the medium. Here, we demonstrate that the colony that first reached the stage of intense ammonia production induces ammonia production response in surrounding colonies regardless of their age, causing the synchronisation of their NH(3) pulses and, consequently, the mutual affection of their growth. Also an artificial source of ammonia (but neither NH(4)(+) nor NaOH gradients) can immediately induce the ammonia production even in the colony starting its acidic stage of the development. The repeated transition of Candida mogii colonies from the acidic phase to the phase of intensive ammonia production is accompanied by dramatic changes in colony morphology and also in cell morphology and growth. Relatively smooth colonies in the acidic phase are formed by growing pseudohyphae. After ammonia induction, pseudohyphae decompose into non-dividing yeast-like cells, which rearrange themselves into ruffled spaghetti-like structures. The synchronisation of colony growth, that also exists between yeast colonies of different genera, could be important in establishing their optimal distribution in a natural habitat.

Lubricating bacteria model for branching growth of bacterial colonies

Various bacterial strains (e.g., strains belonging to the genera Bacillus, Paenibacillus, Serratia, and Salmonella) exhibit colonial branching patterns during growth on poor semisolid substrates. These patterns reflect the bacterial cooperative self-organization. A central part of the cooperation is the collective formation of a lubricant on top of the agar which enables the bacteria to swim. Hence it provides the colony means to advance towards the food. One method of modeling the colonial development is via coupled reaction-diffusion equations which describe the time evolution of the bacterial density and the concentrations of the relevant chemical fields. This idea has been pursued by a number of groups. Here we present an additional model which specifically includes an evolution equation for the lubricant excreted by the bacteria. We show that when the diffusion of the fluid is governed by a nonlinear diffusion coefficient, branching patterns evolve. We study the effect of the rates of emission and decomposition of the lubricant fluid on the observed patterns. The results are compared with experimental observations. We also include fields of chemotactic agents and food chemotaxis and conclude that these features are needed in order to explain the observations.

Chemotactic-like response of Escherichia coli cells lacking the known chemotaxis machinery but containing overexpressed CheY

We describe a chemotactic-like response of Escherichia coli strains lacking most of the known chemotaxis machinery but containing high levels of the response regulator CheY. The bacteria accumulated in aspartate-containing capillaries, they formed rings on tryptone-containing semisolid agar, and the probability of counterclockwise flagellar rotation transiently increased in response to stimulation with aspartate (10(-10)-10(-5) M; the response was inverted at > 10(-4) M). The temporal response was partial and delayed, as was the response of a control wild-type strain having a high CheY level. alpha-Methyl-DL-aspartate, a non-metabolizable analogue of aspartate as well as other known attractants of E. Coli, glucose and, to a lesser extent, galactose, maltose and serine caused a similar response. So did low concentrations of acetate and benzoate (which, at higher concentrations, act as repellents for wild-type E. coli). Other tested repellents such as indole, Ni2+ and CO2+ increased the clockwise bias. These observations raise the possibility that, at least when the conventional signal transduction components are missing, a non-conventional chemotactic signal transduction pathway might be functional in E. coli. Potential molecular mechanisms are discussed.