Repulsion and metabolic switches in the collective behavior of bacterial colonies

Escherichia coli has an undiscovered ability to inhibit the growth of both Gram-negative and Gram-positive bacteria

The ability for bacteria to form boundaries between neighboring colonies as the result of intra-species inhibition has been described for a limited number of species. Here, we report that intra-species inhibition is more common than previously recognized. We demonstrated that swimming colonies of four Escherichia coli strains and six other bacteria form inhibitory zones between colonies, which is not caused by nutrient depletion. This phenomenon was similarly observed with non-flagellated bacteria. We developed a square-streaking pattern assay which revealed that Escherichia coli BW25113 inhibits the growth of other E. coli, and surprisingly, other Gram-positive and negative bacteria, including multi-drug resistant clinical isolates. Altogether, our findings demonstrate intra-species inhibition is common and might be used by E. coli to inhibit other bacteria. Our findings raise the possibility for a common mechanism shared across bacteria for intra-species inhibition. This can be further explored for a potential new class of antibiotics.

Mechanisms driving spatial distribution of residents in colony biofilms: an interdisciplinary perspective

Biofilms are consortia of microorganisms that form collectives through the excretion of extracellular matrix compounds. The importance of biofilms in biological, industrial and medical settings has long been recognized due to their emergent properties and impact on surrounding environments. In laboratory situations, one commonly used approach to study biofilm formation mechanisms is the colony biofilm assay, in which cell communities grow on solid-gas interfaces on agar plates after the deposition of a population of founder cells. The residents of a colony biofilm can self-organize to form intricate spatial distributions. The assay is ideally suited to coupling with mathematical modelling due to the ability to extract a wide range of metrics. In this review, we highlight how interdisciplinary approaches have provided deep insights into mechanisms causing the emergence of these spatial distributions from well-mixed inocula.

In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology

Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.

Influence of the Microbiota of the Cryolithozone Paleoecosystems on the Behavioral Functions of the Nervous System of Chickens Gallus gallus

We studied the influence of microorganisms isolated from permafrost on the psychophysiological parameters of birds. Significant effect of the microbiota of the paleoecosystems of the cryolithozone on locomotor activity, psycho-emotional state, and psychophysiological lateralization of brain function of Gallus gallus chickens. The involvement of both the autonomic and the higher central nervous systems in this regulatory process via synthesis of neuropeptides by symbionts is discussed.

Loss of Motility as a Non-Lethal Mechanism for Intercolony Inhibition ("Sibling Rivalry") in Marinobacter

Bacteria from the genus Marinobacter are ubiquitous throughout the worlds' oceans as "opportunitrophs" capable of surviving a wide range of conditions, including colonization of surfaces of marine snow and algae. To prevent too many bacteria from occupying this ecological niche simultaneously, some sort of population dependent control must be operative. Here, we show that while Marinobacter do not produce or utilize an acylhomoserine lactone (AHL)-based quorum sensing system, "sibling" colonies of many species of Marinobacter exhibit a form of non-lethal chemical communication that prevents colonies from overrunning each other's niche space. Evidence suggests that this inhibition is the result of a loss in motility for cells at the colony interfaces. Although not the signal itself, we have identified a protein, glycerophosphoryl diester phosphodiesterase, that is enriched in the inhibition zone between the spreading colonies that may be part of the overall response.

Probiotics and Psychobiotics: the Role of Microbial Neurochemicals

In light of recent data, microorganisms should be construed as organisms that are capable of communication and collective behaviors. Microbial communication signals are involved both in interactions among microbial cells within microbial social systems, including the human body-inhabiting microconsortium, and the dialog between the microbiota and the host organism. The microbiota inhabits various niches of the host organism, especially the gastrointestinal (GI) tract. Microorganisms release diverse signal molecules and, in addition, specifically respond to host signals. This enables them to constantly interact with the nervous system including the brain and the immune system of the host organism. Evolutionarily conserved signals that are involved in the communication between microbiota and the host include neuroactive substances (neurochemicals) such as peptides, amino acids, biogenic amines, short-chain fatty acids, and gaseous substances. This ongoing dialog may either stabilize the host's physical and mental health state or, alternatively, cause serious health problems. Attempts are made to correct imbalances in the brain-gut-microbiota axis with probiotics including their subgroup called psychobiotics that release neuroactive substances directly influencing the human brain, psyche, and behavior. A number of recent review works address the microbiota-host system and its communication signals. Some of the publications focus on the involvement of neurochemicals in the bidirectional communication within the host-microbiota system. However, this work concentrates on the impact of bacterial cell components, metabolites, and signal molecules as promising alternatives to the currently widespread probiotics that have both advantages and disadvantages. Such biologically active agents of microbial origin are referred to as postbiotics or, alternatively, metabiotics (the term preferred in this work).

Reply to the comment on "Rivalry in Bacillus subtilis colonies: enemy or family?"

Sibling Bacillus subtilis colony merging phenomenon at the microscopic length scale has revealed interesting dynamics which depends on the strain and the composition of the growth medium.

Comment on "Rivalry in Bacillus subtilis colonies: enemy or family?"

It is well known that biofilms are one of the most widespread forms of life on Earth, capable of colonising almost any environment from humans to metals.

Rivalry in Bacillus subtilis colonies: enemy or family?

Two colonies of Bacillus subtilis of identical strains growing adjacent to each other on an agar plate exhibit two distinct types of interactions: they either merge as they grow or demarcation occurs leading to formation of a line of demarcation at the colony fronts. The nature of this interaction depends on the agar concentration in the growth medium and the initial separation between the colonies. When the agar concentration was 0.67% or lower, the two sibling colonies were found to always merge. At 1% or higher concentrations, the colonies formed a demarcation line only when their initial separation was 20 mm or higher. Interactions of a colony with solid structures and liquid drops have indicated that biochemical factors rather than the presence of physical obstacles are responsible for the demarcation line formation. A reaction diffusion model has been formulated to predict if two sibling colonies will form a demarcation line under given agar concentration and initial separation. The model prediction agrees well with experimental findings and generates a dimensionless phase diagram containing merging and demarcation regimes. The phase diagram is in terms of a dimensionless initial separation, d[combining macron], and a dimensionless diffusion coefficient, D[combining macron], of the colonies. The phase boundary between the two interaction regimes can be described by a power law relation between d[combining macron] and D[combining macron].

Mechanism of Kin-Discriminatory Demarcation Line Formation between Colonies of Swarming Bacteria

Swarming bacteria use kin discrimination to preferentially associate with their clonemates for certain cooperative behaviors. Kin discrimination can manifest as an apparent demarcation line (a region lacking cells or with much lower cell density) between antagonist strains swarming toward each other. In contrast, two identical strains merge with no demarcation. Experimental studies suggest contact-dependent killing between different strains as a mechanism of kin discrimination, but it is not clear whether this killing is sufficient to explain the observed patterns. Here, we investigate the formation of demarcation line with a mathematical model. First, using data from competition experiments between kin discriminating strains of Myxococcus xanthus and Proteus mirabilis, we found the rates of killing between the strains to be highly asymmetric, i.e., one strain kills another at a much higher rate. Then, to investigate how such asymmetric interactions can lead to a stable demarcation line, we construct reaction-diffusion models for colony expansion of kin-discriminatory strains. Our results demonstrate that a stable demarcation line can form when both cell movement and cell growth cease at low nutrient levels. Further, our study suggests that, depending on the initial separation between the inoculated colonies, the demarcation line may move transiently before stabilizing. We validated these model predictions by observing dynamics of merger between two M. xanthus strains, where one strain expresses a toxin protein that kills a second strain lacking the corresponding antitoxin. Our study therefore provides a theoretical understanding of demarcation line formation between kin-discriminatory populations, and can be used for analyzing and designing future experiments.

Physical Forces Shape Group Identity of Swimming Pseudomonas putida Cells

The often striking macroscopic patterns developed by motile bacterial populations on agar plates are a consequence of the environmental conditions where the cells grow and spread. Parameters such as medium stiffness and nutrient concentration have been reported to alter cell swimming behavior, while mutual interactions among populations shape collective patterns. One commonly observed occurrence is the mutual inhibition of clonal bacteria when moving toward each other, which results in a distinct halt at a finite distance on the agar matrix before having direct contact. The dynamics behind this phenomenon (i.e., intolerance to mix in time and space with otherwise identical others) has been traditionally explained in terms of cell-to-cell competition/cooperation regarding nutrient availability. In this work, the same scenario has been revisited from an alternative perspective: the effect of the physical mechanics that frame the process, in particular the consequences of collisions between moving bacteria and the semi-solid matrix of the swimming medium. To this end, we set up a simple experimental system in which the swimming patterns of Pseudomonas putida were tested with different geometries and agar concentrations. A computational analysis framework that highlights cell-to-medium interactions was developed to fit experimental observations. Simulated outputs suggested that the medium is compressed in the direction of the bacterial front motion. This phenomenon generates what was termed a compression wave that goes through the medium preceding the swimming population and that determines the visible high-level pattern. Taken together, the data suggested that the mechanical effects of the bacteria moving through the medium created a factual barrier that impedes to merge with neighboring cells swimming from a different site. The resulting divide between otherwise clonal bacteria is thus brought about by physical forces—not genetic or metabolic programs.

Patterning of mutually interacting bacterial bodies: close contacts and airborne signals

Background

Bacterial bodies (colonies) can develop complex patterns of color and structure. These patterns may arise as a result of both colony-autonomous developmental and regulatory processes (self-patterning) and environmental influences, including those generated by neighbor bodies. We have studied the interplay of intra-colony signaling (self-patterning) and inter-colony influences in related clones of Serratia rubidaea grown on rich media.

Results

Colonies are shaped by both autonomous patterning and by signals generated by co-habitants of the morphogenetic space, mediating both internal shaping of the body, and communication between bodies sharing the same living space. The result of development is affected by the overall distribution of neighbors in the dish. The neighbors' presence is communicated via at least two putative signals, while additional signals may be involved in generating some unusual patterns observed upon encounters of different clones. A formal model accounting for some aspects of colony morphogenesis and inter-colony interactions is proposed.

Conclusions

The complex patterns of color and texture observed in Serratia rubidaea colonies may be based on at least two signals produced by cells, one of them diffusing through the substrate (agar) and the other carried by a volatile compound and absorbed into the substrate. Differences between clones with regard to the interpretation of signals may result from different sensitivity to signal threshold(s).