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

Self-growth suppression in Bradyrhizobium diazoefficiens is caused by a diffusible antagonist

Microbes in soil navigate interactions by recognizing kin, forming social groups, exhibiting antagonistic behavior, and engaging in competitive kin rivalry. Here, we investigated a novel phenomenon of self-growth suppression (sibling rivalry) observed in Bradyrhizobium diazoefficiens USDA 110. Swimming colonies of USDA 110 developed a distinct demarcation line and inter-colony zone when inoculated adjacent to each other. In addition to self, USDA 110 suppressed growth of other Bradyrhizobium strains and several other soil bacteria. We demonstrated that the phenomenon of sibling rivalry is due to growth suppression but not cell death. The cells in the inter-colony zone were culturable but have reduced respiratory activity, ATP levels and motility. The observed growth suppression was due to the presence of a diffusible effector compound. This effector was labile, preventing extraction, and identification, but it is unlikely a protein or a strong acid or base. This counterintuitive phenomenon of self-growth suppression suggests a strategic adaptation for conserving energy and resources in competitive soil environments. Bradyrhizobium's utilization of antagonism including self-growth suppression likely provides a competitive advantage for long-term success in soil ecosystems.

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.

Social Diversification Driven by Mobile Genetic Elements

Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.

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.

Mixed-species bacterial swarms show an interplay of mixing and segregation across scales

Bacterial swarms are a highly-researched example of natural active matter. In particular, the interplay between biological interactions and the physics underlying the swarming dynamics is of both biological and physical interest. In this paper, we study mixed swarms of Bacillus subtilis and Pseudomonas aeruginosa. We find intricate interactions between the species, showing both cooperation and segregation across different spatial and temporal scales. On one hand, even though axenic colonies grow on disparate time scale, an order of magnitude apart, the two-species swarm together, forming a single, combined colony. However, the rapidly moving populations are locally segregated, with different characteristic speeds and lengths (or cluster sizes) that depend on the ratio between the species. Comparison with controlled mutant strains suggest that both the physical and known biological differences in species characteristics may not be enough to explain the segregation between the species in the mixed swarm. We hypothesize that the heterogeneous spatial distribution is due to some mechanism that enables bacteria to recognize their own kind, whose precise origin we could not identify.

Rapid diversification of wild social groups driven by toxin-immunity loci on mobile genetic elements

Many species form distinct social groups that provide fitness advantages to individuals. However, the evolutionary processes that generate new social groups are not well understood. Here we examined recently diverged natural isolates of the model social bacterium, Myxococcus xanthus, to probe the genetic mechanisms and evolutionary processes of kin discrimination that occurred naturally in soil. We show that social incompatibilities were formed from horizontal gene transfer of effectors belonging to three distinct polymorphic toxin systems; outer membrane exchange, type VI secretion and rearrangement hotspot systems. Strikingly, the unique toxin effectors and their respective immunity genes that are responsible for social incompatibilities reside on mobile genetic elements, which make up nearly all of the genotypic variation between isolates within clades. By disrupting these three toxin systems, we engineered social harmony between strains that were originally incompatible. In addition, a horizontal allele swap of a single kin recognition receptor changed social interactions and competition outcomes. Our results provide a case study for how horizontal gene transfer led to social diversification in a natural context. Finally, we show how genomic information of kin discriminatory loci can be used to predict social interactions.

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.

Kin discrimination and outer membrane exchange in Myxococcus xanthus: Experimental analysis of a natural population

In some species of myxobacteria, adjacent cells sufficiently similar at the adhesin protein TraA can exchange components of their outer membranes. The primary benefits of such outer membrane exchange (OME) in natural populations are unclear, but in some OME interactions, transferred OM content can include SitA toxins that kill OME participants lacking an appropriate immunity gene. Such OME-dependent toxin transfer across Myxococcus xanthus strains that differ only in their sitBAI toxin/antitoxin cassette can mediate inter-strain killing and generate colony-merger incompatibilities (CMIs)–inter-colony border phenotypes between distinct genotypes that differ from respective self-self colony interfaces. Here we ask whether OME-dependent toxin transfer is a common cause of prevalent CMIs and antagonisms between M. xanthus natural isolates identical at TraA. We disrupted traA in eleven isolates from a cm-scale soil population and assayed whether traA disruption eliminated or reduced CMIs between swarming colonies or antagonisms between strains in mixed cultures. Among 33 isolate pairs identical at traA that form clear CMIs, in no case did functional disruption of traA in one partner detectably alter CMI phenotypes. Further, traA disruption did not alleviate strong antagonisms observed during starvation-induced fruiting-body development in seven pairs of strains identical at traA. Collectively, our results suggest that most mechanisms of interference competition and inter-colony kin discrimination in natural populations of myxobacteria do not require OME. Finally, our experiments also indicate that several closely related laboratory reference strains kill some natural isolates by toxins delivered by a shared, OME-independent type VI secretion system (T6SS), suggesting that some antagonisms between sympatric natural isolates may also involve T6SS toxins.

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].

Omics Studies Revealed the Factors Involved in the Formation of Colony Boundary in Myxococcus xanthus

Two unrecognizable strains of the same bacterial species form a distinct colony boundary. During growth as colonies, Myxococcus xanthus uses multiple factors to establish cooperation between recognized strains and prevent interactions with unrecognized strains of the same species. Here, ΔMXAN_0049 is a mutant strain deficient in immunity for the paired nuclease gene, MXAN_0050, that has a function in the colony-merger incompatibility of Myxococcus xanthus DK1622. With the aim to investigate the factors involved in boundary formation, a proteome and metabolome study was employed. Visualization of the boundary between DK1622 and ΔMXAN_0049 was done scanning electron microscope (SEM), which displayed the presence of many damaged cells in the boundary. Proteome analysis of the DK1622- boundary disclosed many possible proteins, such as cold shock proteins, cell shape-determining protein MreC, along with a few pathways, such as RNA degradation, phenylalanine, tyrosine and tryptophan biosynthesis, and Type VI secretion system (T6SS), which may play major roles in the boundary formation. Metabolomics studies revealed various secondary metabolites that were significantly produced during boundary formation. Overall, the results concluded that multiple factors participated in the boundary formation in M. xanthus, leading to cellular damage that is helpful in solving the mystery of the boundary formation mechanism.