Kin discrimination between sympatric Bacillus subtilis isolates

Harnessing microbial biofilms in soil ecosystems: Enhancing nutrient cycling, stress resilience, and sustainable agriculture

Soil ecosystems are complex networks of microorganisms that play pivotal roles in nutrient cycling, stress resilience, and the provision of ecosystem services. Among these microbial communities, soil biofilms, and complex aggregations of microorganisms embedded within extracellular polymeric substances (EPS) exert significant influence on soil health and function. This review delves into the dynamics of soil biofilms, highlighting their structural intricacies and the mechanisms by which they facilitate nutrient cycling, and discusses how biofilms enhance the degradation of pollutants through the action of extracellular enzymes and horizontal gene transfer, contributing to soil detoxification and fertility. Furthermore, the role of soil biofilms in stress resilience is underscored, as they form symbiotic relationships with plants, bolstering their growth and resistance to environmental stressors. The review also explores the ecological functions of biofilms in enhancing soil structure stability by promoting aggregate formation, which is crucial for water retention and aeration. By integrating these insights, we aim to provide a comprehensive understanding of the multifaceted benefits of biofilms in soil ecosystems. This knowledge is essential for developing strategies to manipulate soil biofilms to improve agricultural productivity and ecological sustainability. This review also identifies research gaps and emphasizes the need for practical applications of biofilms in sustainable agriculture.

Insights into the genomic and phenotypic characteristics of Bacillus spp. strains isolated from biofilms in broiler farms

The characterization of surface microbiota living in biofilms within livestock buildings has been relatively unexplored, despite its potential impact on animal health. To enhance our understanding of these microbial communities, we characterized 11 spore-forming strains isolated from two commercial broiler chicken farms. Sequencing of the strains revealed them to belong to three species Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis. Genomic analysis revealed the presence of antimicrobial resistance genes and genes associated with antimicrobial secretion specific to each species. We conducted a comprehensive characterization of the biofilm formed by these strains under various conditions, and we revealed significant structural heterogeneity across the different strains. A macro-colony interaction model was employed to assess the compatibility of these strains to coexist in mixed biofilms. We identified highly competitive B. velezensis strains, which cannot coexist with other Bacillus spp. Using confocal laser scanning microscopy along with a specific dye for extracellular DNA, we uncovered the importance of extracellular DNA for the formation of B. licheniformis biofilms. Altogether, the results highlight the heterogeneity in both genome and biofilm structure among Bacillus spp. isolated from biofilms present within livestock buildings.IMPORTANCELittle is known about the microbial communities that develop on farms in direct contact with animals. Nonpathogenic strains of Bacillus velezensis, Bacillus subtilis, and Bacillus licheniformis were found in biofilm samples collected from surfaces in contact with animals. Significant genetic and phenotypic diversity was described among these Bacillus strains. The strains do not possess mobile antibiotic resistance genes in their genomes and have a strong capacity to form structured biofilms. Among these species, B. velezensis was noted for its high competitiveness compared with the other Bacillus spp. Additionally, the importance of extracellular DNA in the formation of B. licheniformis biofilms was observed. These findings provide insights for the management of these surface microbiota that can influence animal health, such as the use of competitive strains to minimize the establishment of undesirable bacteria or enzymes capable of specifically deconstructing biofilms.

The Utilization of Bacillus subtilis to Design Environmentally Friendly Living Paints with Anti-Mold Properties

The anti-fungal properties of the probiotic bacterium Bacillus subtilis have been studied extensively in agriculture and ecology, but their applications in the built environment remain to be determined. Our work aims to utilize this biological component to introduce new diverse anti-mold properties into paint. "Mold" refers to the ubiquitous fungal species that generate visible multicellular filaments commonly found in household dust. The development of mold leads to severe health problems for occupants, including allergic response, hypersensitivity pneumonitis, and asthma, which have significant economic and clinical outcomes. We here demonstrate the robust effect of a commercial paint enhanced with Bacillus subtilis cells against the common mold agent, Aspergillus niger, and identify three biosynthetic clusters essential for this effect. Our results lay the foundation for bio-convergence and synthetic biology approaches to introduce renewable and environmentally friendly bio-anti-fungal agents into the built environment.

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.

The effect of cooperator recognition on competition among clones in spatially structured microbial communities

In spatially structured microbial communities, clonal growth of stationary cells passively generates clusters of related individuals. This can lead to stable cooperation without the need for recognition mechanisms. However, recent research suggests that some biofilm-forming microbes may have mechanisms of kin recognition. To explore this unexpected observation, we studied the effects of different types of cooperation in a microbial colony using spatially explicit, agent-based simulations of two interacting strains. We found scenarios that favor a form of kin recognition in spatially structured microbial communities. In the presence of a "cheater" strain, a strain with greenbeard cooperation was able to increase in frequency more than a strain with obligate cooperation. This effect was most noticeable in high density colonies and when the cooperators were not as abundant as the cheaters. We also studied whether a polychromatic greenbeard, in which cells only cooperate with their own type, could provide a numerical benefit beyond a simple, binary greenbeard. We found the greatest benefit to a polychromatic greenbeard when cooperation is highly effective. These results suggest that in some ecological scenarios, recognition mechanisms may be beneficial even in spatially structured communities.

Using kin discrimination to construct synthetic microbial communities of Bacillus subtilis strains impacts the growth of black soldier fly larvae

Using synthetic microbial communities to promote host growth is an effective approach. However, the construction of such communities lacks theoretical guidance. Kin discrimination is an effective means by which strains can recognize themselves from non-self, and construct competitive microbial communities to produce more secondary metabolites. However, the construction of cooperative communities benefits from the widespread use of beneficial microorganisms. We used kin discrimination to construct synthetic communities (SCs) comprising 13 Bacillus subtilis strains from the surface and gut of black soldier fly (BSF) larvae. We assessed larval growth promotion in a pigeon manure system and found that the synthetic community comprising 4 strains (SC 4) had the most profound effect. Genomic analyses of these 4 strains revealed that their complementary functional genes underpinned the robust functionality of the cooperative synthetic community, highlighting the importance of strain diversity. After analyzing the bacterial composition of BSF larvae and the pigeon manure substrate, we observed that SC 4 altered the bacterial abundance in both the larval gut and pigeon manure. This also influenced microbial metabolic functions and co-occurrence network complexity. Kin discrimination facilitates the rapid construction of synthetic communities. The positive effects of SC 4 on larval weight gain resulted from the functional redundancy and complementarity among the strains. Furthermore, SC 4 may enhance larval growth by inducing shifts in the bacterial composition of the larval gut and pigeon manure. This elucidated how the SC promoted larval growth by regulating bacterial composition and provided theoretical guidance for the construction of SCs.

Mechanical constraints to unbound expansion of B. subtilis on semi-solid surfaces

IMPORTANCE

How bacterial cells colonize new territory is a problem of fundamental microbiological and biophysical interest and is key to the emergence of several phenomena of biological, ecological, and medical relevance. Here, we demonstrate how bacteria stuck in a colony of finite size can resume exploration of new territory by aquaplaning and how they fine tune biofilm viscoelasticity to surface material properties that allows them differential mobility. We show how changing local interfacial forces and colony viscosity results in a plethora of bacterial morphologies on surfaces with different physical and mechanical properties.

Nonkin interactions between Bacillus subtilis soil isolates limit the spread of swarming deficient cheats

Cooperative behaviours in human, animal, and even microbial societies are vulnerable to exploitation. Kin discrimination has been hypothesized to help stabilize cooperation. However, the mechanisms that sustain cooperative behaviour remain poorly understood. Here, we investigate the role of kin discrimination in limiting the spread of cheats in adjoining populations during surfactant-dependent cooperative swarming over surfaces using the bacterium Bacillus subtilis as a model organism. We show that mixing surfactant secreting cooperators and cheats that do not produce surfactants at 1:1 initial ratio quickly leads to cooperation collapse. However, when such common swarms encounter nonkin B. subtilis swarms, the proportion of the surfactant nonproducers decreases, suggesting that kinship dependent interactions may limit cheats' advantage in an adjoining population. To further validate this finding, we subjected wild-type cooperators to multiple transient encounters with kin and nonkin swarms over 20 cycles of experimental evolution. The evolved populations exposed to nonkin swarms less frequently contained defective swarming phenotypes compared to those encountering kin swarms. Altogether, our results support the prediction that the spread of cheats in an adjoining bacterial population is impeded by kin discrimination interactions, which might have a role in stabilizing cooperative behaviour in evolving populations.

Multiscale spatial segregation analysis in digital images of biofilms

Quantifying the degree of spatial segregation of two bacterial strains in mixed biofilms is an important topic in microbiology. Spatial segregation is dependent on spatial scale as two strains may appear to be well mixed if observed from a distance, but a closer look can reveal strong separation. Typically, this information is encoded in a digital image that represents the binary system, e.g., a microscopy image of a two species biofilm. To decode spatial segregation information, we have developed quantitative measures for evaluating the degree of the spatial scale-dependent segregation of two bacterial strains in a digital image. The constructed algorithm is based on the new segregation measures and overcomes drawbacks of existing approaches for biofilm segregation analysis. The new approach is implemented in a freely available software and was successfully applied to biofilms of two strains and bacterial suspensions for detection of the different spatial scale-dependent segregation levels.

EAM highlights in FEMS 2023: from the Petri dish to planet Earth

On 9-13 July 2023, the 10th FEMS Congress took place in Hamburg, Germany. As part of this major event in European microbiology, the European Academy of Microbiology (EAM) organized two full sessions. One of these sessions aimed to highlight the research of four recently elected EAM fellows and saw presentations on bacterial group behaviours and development of resistance to antibiotics, as well as on new RNA viruses including bacteriophages and giant viruses of amoebae. The other session included five frontline environmental microbiologists who showcased real-world examples of how human activities have disrupted the balance in microbial ecosystems, not just to assess the current situation but also to explore fresh approaches for coping with external disturbances. Both sessions were very well attended, and no doubt helped to gain the EAM and its fellows more visibility.

Signatures of kin selection in a natural population of the bacteria Bacillus subtilis

Laboratory experiments have suggested that bacteria perform a range of cooperative behaviors, which are favored because they are directed toward relatives (kin selection). However, there is a lack of evidence for cooperation and kin selection in natural bacterial populations. Molecular population genetics offers a promising method to study natural populations because the theory predicts that kin selection will lead to relaxed selection, which will result in increased polymorphism and divergence at cooperative genes. Examining a natural population of Bacillus subtilis, we found consistent evidence that putatively cooperative traits have higher polymorphism and greater divergence than putatively private traits expressed at the same rate. In addition, we were able to eliminate alternative explanations for these patterns and found more deleterious mutations in genes controlling putatively cooperative traits. Overall, our results suggest that cooperation is favored by kin selection, with an average relatedness of r = .79 between interacting individuals.

DegQ is an important policing link between quorum sensing and regulated adaptative traits in Bacillus subtilis

Quorum sensing (QS) is a widespread bacterial communication system that controls important adaptive traits in a cell density-dependent manner. However, mechanisms by which QS-regulated traits are linked within the cell and mechanisms by which these links affect adaptation are not well understood. In this study, Bacillus subtilis was used as a model bacterium to investigate the link between the ComQXPA QS system, DegQ, surfactin and protease production in planktonic and biofilm cultures. The work tests two alternative hypotheses predicting that hypersensitivity of the QS signal-deficient mutant (comQ::kan) to exogenously added ComX, resulting in increased surfactin production, is linked to an additional genetic locus, or alternatively, to overexpression of the ComX receptor ComP. Results are in agreement with the first hypothesis and show that the P srfAA hypersensitivity of the comQ::kan mutant is linked to a 168 strain-specific mutation in the P degQ region. Hence, the markerless ΔcomQ mutant lacking this mutation is not overresponsive to ComX. Such hyper-responsiveness is specific for the P srfAA and not detected in another ComX-regulated promoter, the P aprE , which is under the positive control by DegQ. Our results suggest that DegQ by exerting differential effect on P srfAA and P aprE acts as a policing mechanism and the intracellular link, which guards the cell from an overinvestment into surfactin production. IMPORTANCE DegQ levels are known to regulate surfactin synthesis and extracellular protease production, and DegQ is under the control of the ComX-dependent QS. DegQ also serves as an important policing link between these QS-regulated processes, preventing overinvestment in these costly processes. This work highlights the importance of DegQ, which acts as the intracellular link between ComX production and the response by regulating extracellular degradative enzyme synthesis and surfactin production.

The putative role of the epipeptide EpeX in Bacillus subtilis intra-species competition

Bacteria engage in competitive interactions with neighbours that can either be of the same or different species. Multiple mechanisms are deployed to ensure the desired outcome and one tactic commonly implemented is the production of specialised metabolites. The Gram-positive bacterium Bacillus subtilis uses specialized metabolites as part of its intra-species competition determinants to differentiate between kin and non-kin isolates. It is, however, unknown if the collection of specialized metabolites defines competitive fitness when the two isolates start as a close, interwoven community that grows into a densely packed colony biofilm. Moreover, the identity of specialized metabolites that have an active role in defining the outcome of an intra-species interaction has not been revealed. Here, we determine the competition outcomes that manifest when 21 environmental isolates of B. subtilis are individually co-incubated with the model isolate NCIB 3610 in a colony biofilm. We correlated these data with the suite of specialized metabolite biosynthesis clusters encoded by each isolate. We found that the epeXEPAB gene cluster was primarily present in isolates with a strong competitive phenotype. This cluster is responsible for producing the epipeptide EpeX. We demonstrated that EpeX is a competition determinant of B. subtilis in an otherwise isogenic context for NCBI 3610. However, when we competed the NCIB 3610 EpeX-deficient strain against our suite of environmental isolates we found that the impact of EpeX in competition is isolate-specific, as only one of the 21 isolates showed increased survival when EpeX was lacking. Taken together, we have shown that EpeX is a competition determinant used by B. subtilis that impacts intra-species interactions but only in an isolate-specific manner.

Rhizosphere bacterial interactions and impact on plant health

The rhizosphere is a chemically complex environment that harbors a strikingly diverse microbial community. The past few decades have seen a rapid growth in the body of literature on plant-microbe-microbe interactions and plant health. Thus, the aim of this paper is to review current knowledge on plant-microbe-microbe (specifically bacteria) interactions in the rhizosphere and how these influence rhizosphere microbiomes and impact plant health. This article discusses (i) how the plant recruits beneficial rhizosphere bacteria and ii) how competition between rhizosphere bacteria and mechanisms/weapons employed in bacteria-bacteria competition shapes rhizosphere microbiome and in turn affects plant heath. The discussion mainly focuses on interference competition, characterized by production of specialized metabolites (antibacterial compounds) and exploitative competition where a bacterial strain restricts the competitor's access to nutrients such as through secretion of siderophores that could allude to cooperation. Understanding mechanisms employed in bacteria-bacteria and plant-bacteria interactions could provide insights into how to manipulate microbiomes for improved agricultural outcomes.

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.

Nutrient Availability and Biofilm Polysaccharide Shape the Bacillaene-Dependent Antagonism of Bacillus subtilis against Salmonella Typhimurium

Salmonella enterica is one of the most common foodborne pathogens and, due to the spread of antibiotic resistance, new antimicrobial strategies are urgently needed to control it. In this study, we explored the probiotic potential of Bacillus subtilis PS-216 and elucidated the mechanisms that underlie the interactions between this soil isolate and the model pathogenic strain S. Typhimurium SL1344. The results reveal that B. subtilis PS-216 inhibits the growth and biofilm formation of S. Typhimurium through the production of the pks cluster-dependent polyketide bacillaene. The presence of S. Typhimurium enhanced the activity of the PpksC promoter that controls bacillaene production, suggesting that B. subtilis senses and responds to Salmonella. The level of Salmonella inhibition, overall PpksC activity, and PpksC induction by Salmonella were all higher in nutrient-rich conditions than in nutrient-depleted conditions. Although eliminating the extracellular polysaccharide production of B. subtilis via deletion of the epsA-O operon had no significant effect on inhibitory activity against Salmonella in nutrient-rich conditions, this deletion mutant showed an enhanced antagonism against Salmonella in nutrient-depleted conditions, revealing an intricate relationship between exopolysaccharide production, nutrient availability, and bacillaene synthesis. Overall, this work provides evidence on the regulatory role of nutrient availability, sensing of the competitor, and EpsA-O polysaccharide in the social outcome of bacillaene-dependent competition between B. subtilis and S. Typhimurium. IMPORTANCE Probiotic bacteria represent an alternative for controlling foodborne disease caused by Salmonella enterica, which constitutes a serious concern during food production due to its antibiotic resistance and resilience to environmental stress. Bacillus subtilis is gaining popularity as a probiotic, but its behavior in biofilms with pathogens such as Salmonella remains to be elucidated. Here, we show that the antagonism of B. subtilis is mediated by the polyketide bacillaene and that the production of bacillaene is a highly dynamic trait which depends on environmental factors such as nutrient availability and the presence of competitors. Moreover, the production of extracellular polysaccharides by B. subtilis further alters the influence of these factors. Hence, this work highlights the inhibitory effect of B. subtilis, which is condition-dependent, and the importance of evaluating probiotic strains under conditions relevant to the intended use.

Involvement of Flagellin in Kin Recognition between Bacillus velezensis Strains

Kin discrimination in nature is an effective way for bacteria to stabilize population cooperation and maintain progeny benefits. However, so far, the research on kin discrimination for Bacillus still has concentrated on "attack and defense" between cells and diffusion-dependent molecular signals of quorum sensing, kin recognition in Bacillus, however, has not been reported. To determine whether flagellar is involve in the kin recognition of Bacillus, we constructed Bacillus velezensis SQR9 assembled with flagellin of its kin and non-kin strains, and performed a swarm boundary assay with SQR9, then analyzed sequence variation of flagellin and other flagellar structural proteins in B. velezensis genus. Our results showed that SQR9 assembled with flagellin of non-kin strains was more likely to form a border phenotype with wild-type strain SQR9 in swarm assay than that of kin strains, and that non-kin strains had greater variation in flagellin than kin strains. In B. velezensis, these variations in flagellin were prevalent and had evolved significantly faster than other flagellar structural proteins. Therefore, we proposed that flagellin is an effective tool partly involved in the kin recognition of B. velezensis strains. IMPORTANCE Kin selection plays an important role in stabilizing population cooperation and maintaining the progeny benefits for bacteria in nature. However, to date, the role of flagellin in kin recognition in Bacillus has not been reported. By using rhizospheric Bacillus velezensis SQR9, we accomplished flagellin region interchange among its related strains, and show that flagellin acts as a mediator to distinguish kin from non-kin in B. velezensis. We demonstrated the polymorphism of flagellin in B. velezensis through alignment analysis of flagellin protein sequences. Therefore, it was proposed that flagellin was likely to be an effective tool for mediating kin recognition in B. velezensis.

Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study

Bacillus is a genus of microorganisms (bacteria) and contains many important commercial species used in industry, agriculture and healthcare. Many different Bacilli are relatively well understood at the single-cell level; however, molecular tools that determine the diversity and ecology of Bacillus community are limited, which limits our understanding of how the Bacillus community works. In the present study, we investigated the potential of the housekeeping gene gyrA as a molecular marker for determining the diversity of Bacillus species. The amplification efficiency for Bacillus species diversity could be greatly improved by primer design. Therefore, we designed a novel primer pair gyrA3 that can detect at least 92 Bacillus species and related species. For B. amyloliquefaciens, B. pumilus, and B. megaterium, we observed that the high variability of the gyrA gene allows for more detailed clustering at the subspecies level that cannot be achieved by the 16S rRNA gene. Since gyrA provides better phylogenetic resolution than 16S rRNA and informs on the diversity of the Bacillus community, we propose that the gyrA gene may have broad application prospects in the study of Bacillus ecology.

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.

Kin Discrimination Modifies Strain Distribution, Spatial Segregation, and Incorporation of Extracellular Matrix Polysaccharide Mutants of Bacillus subtilis Strains into Mixed Floating Biofilms

Microorganisms in nature form multicellular groups called biofilms. In biofilms, bacteria embedded in the extracellular matrix (ECM) interact intensely due to their proximity. Most studies have investigated genetically homogeneous biofilms, leaving a gap in knowledge on genetically heterogeneous biofilms. Recent insights show that a Gram-positive model bacterium, Bacillus subtilis, discriminates between strains of high (kin) and low (nonkin) genetic similarity, reflected in merging (kin) and boundaries (nonkin) between swarms. However, it is unclear how kinship between interacting strains affects their fitness, the genotype assortment, and incorporation of the mutant lacking the main structural ECM polysaccharide (EpsA-O) into floating biofilms (pellicles). We cultivated Bacillus subtilis strains as mixtures of isogenic, kin, and nonkin strain combinations in the biofilm-promoting minimal medium under static conditions, allowing them to form pellicles. We show that in nonkin pellicles, the dominant strain strongly reduced the frequency of the other strain. Segregation of nonkin mixtures in pellicles increased and invasion of nonkin EpsA-O-deficient mutants into pellicles decreased compared to kin and isogenic floating biofilms. Kin and isogenic strains had comparable relative frequencies in pellicles and showed more homogenous cell mixing. Overall, our results emphasize kin discrimination as a social behavior that shapes strain distribution, spatial segregation, and ECM mutant ability to incorporate into genetically heterogenous biofilms of B. subtilis. IMPORTANCE Biofilm communities have beneficial and harmful effects on human societies in natural, medical, and industrial environments. Bacillus subtilis is a biotechnologically important bacterium that serves as a model for studying biofilms. Recent studies have shown that this species engages in kin discriminatory behavior during swarming, which may have implications for community assembly, thus being of fundamental importance. Effects of kin discrimination on fitness, genotype segregation, and success of extracellular matrix (ECM) polysaccharide (EpsA-O) mutant invasion into biofilms are not well understood. We provide evidence that kin discrimination depends on the antagonism of the dominant strain against nonkin by using environmental strains with determined kin types and integrated fluorescent reporters. Moreover, this antagonism has important implications for genotype segregation and for when the bacteria are mixed with ECM producers. The work advances the understanding of kin-discrimination-dependent bacterial sociality in biofilms and its role in the assembly of multicellular groups.

Nutritional stress induced intraspecies competition revealed by transcriptome analysis in Sphingomonas melonis TY

Bacteria have developed various mechanisms by which they can compete or cooperate with other bacteria. This study showed that in the cocultures of wild-type Sphingomonas melonis TY and its isogenic mutant TYΔndpD grow with nicotine, the former can outcompete the latter. TYΔndpD undergoes growth arrest after four days when cocultured with wild-type TY, whereas the coculture has just entered a stationary phase and the substrate was nearly depleted, and the interaction between the two related strains was revealed by transcriptomic analysis. Analysis of the differential expression genes indicated that wild-type TY inhibited the growth of TYΔndpD mainly through toxin-antitoxin (TA) systems. The four upregulated antitoxin coding genes belong to type II TA systems in which the bactericidal effect of the cognate toxin was mainly through inhibition of translation or DNA replication, whereas wild-type TY with upregulated antitoxin genes can regenerate cognate immunity protein continuously and thus prevent the lethal action of toxin to itself. In addition, colicin-mediated antibacterial activity against closely related species may also be involved in the competition between wild-type TY and TYΔndpD under nutritional stress. Moreover, upregulation of carbon and nitrogen catabolism related-, stress response related-, DNA repair related-, and DNA replication-related genes in wild-type TY showed that it triggered a series of response mechanisms when facing dual stress of competition from isogenic mutant cells and nutritional limitation. Thus, we proposed that S. melonis TY employed the TA systems and colicin to compete with TYΔndpD under nutritional stress, thereby maximally acquiring and exploiting finite resources. KEY POINTS: • Cross-feeding between isogenic mutants and the wild-type strain. • Nutrition stress caused a shift from cooperation to competition. • TYΔndpD undergo growth arrest by exogenous and endogenous toxins.

Bacteria grow swiftly and live thriftily

Bacteria have evolved numerous strategies to use resources efficiently. However, bacterial economies depend on both the physiological context of the organisms as well as their growth state - whether they are growing, non-growing or reinitiating growth. In this essay, we discuss some of the features that make bacteria efficient under these different conditions and during the transitions between them. We also highlight the many outstanding questions regarding the physiology of non-growing bacterial cells. Lastly, we examine how efficiency is apparent in both the mode and tempo of bacterial evolution.

Founder cell configuration drives competitive outcome within colony biofilms

Bacteria can form dense communities called biofilms, where cells are embedded in a self-produced extracellular matrix. Exploiting competitive interactions between strains within the biofilm context can have potential applications in biological, medical, and industrial systems. By combining mathematical modelling with experimental assays, we reveal that spatial structure and competitive dynamics within biofilms are significantly affected by the location and density of the founder cells used to inoculate the biofilm. Using a species-independent theoretical framework describing colony biofilm formation, we show that the observed spatial structure and relative strain biomass in a mature biofilm comprising two isogenic strains can be mapped directly to the geographical distributions of founder cells. Moreover, we define a predictor of competitive outcome that accurately forecasts relative abundance of strains based solely on the founder cells' potential for radial expansion. Consequently, we reveal that variability of competitive outcome in biofilms inoculated at low founder density is a natural consequence of the random positioning of founding cells in the inoculum. Extension of our study to non-isogenic strains that interact through local antagonisms, shows that even for strains with different competition strengths, a race for space remains the dominant mode of competition in low founder density biofilms. Our results, verified by experimental assays using Bacillus subtilis, highlight the importance of spatial dynamics on competitive interactions within biofilms and hence to related applications.

Systems view of Bacillus subtilis pellicle development

In this study, we link pellicle development at the water-air interface with the vertical distribution and viability of the individual B. subtilis PS-216 cells throughout the water column. Real-time interfacial rheology and time-lapse confocal laser scanning microscopy were combined to correlate mechanical properties with morphological changes (aggregation status, filament formation, pellicle thickness, spore formation) of the growing pellicle. Six key events were identified in B. subtilis pellicle formation that are accompanied by a major change in viscoelastic and morphology behaviour of the pellicle. The results imply that pellicle development is a multifaceted response to a changing environment induced by bacterial growth that causes population redistribution within the model system, reduction of the viable habitat to the water-air interface, cell development, and morphogenesis. The outcome is a build-up of mechanical stress supporting structure that eventually, due to nutrient deprivation, reaches the finite thickness. After prolonged incubation, the formed pellicle collapses, which correlates with the spore releasing process. The pellicle loses the ability to support mechanical stress, which marks the end of the pellicle life cycle and entry of the system into the dormant state.

Annulment of Bacterial Antagonism Improves Plant Beneficial Activity of a Bacillus velezensis Consortium

Bacillus sp. strains that are beneficial to plants are widely used in commercial biofertilizers and biocontrol agents for sustainable agriculture. Generally, functional Bacillus strains are applied as single-strain communities since the principles of synthetic microbial consortia constructed with Bacillus strains remain largely unclear. Here, we demonstrated that the mutual compatibility directly affects the survival and function of two-member consortia composed of Bacillus velezensis SQR9 and FZB42 in the rhizosphere. A mutation in the global regulator Spo0A of SQR9 markedly reduced the boundary phenotype (appearance of a visible boundary line at the meeting point of two swarms) with wild-type FZB42, and the combined use of the SQR9(△spo0A) mutant and FZB42 improved biofilm formation, root colonization, and the production of secondary metabolites that are beneficial to plants. Furthermore, alleviation of antagonistic interactions of two-member Bacillus consortia improved its beneficial effects to cucumber in a greenhouse experiment. Our results provide evidence that social interactions among bacteria could be an influencing factor for achieving a desired community-level function. IMPORTANCE Bacillus velezensis is one of the most widely applied bacteria in biofertilizers in China and Europe. Additionally, the molecular mechanisms of plant growth promotion and disease suppression by representative model strains are well established, such as B. velezensis SQR9 and FZB42. However, it remains extremely challenging to design efficient consortia based on these model strains. Here, we showed that swarm encounter phenotype is one of the major determinants that affects the performance of two-member Bacillus consortia in vitro and in the rhizosphere. Deletion in global regulatory gene spo0A of SQR9 reduced the strength of boundary formation with FZB42 and resulted in the improved plant growth promotion performance of the dual consortium. This knowledge provides new insights into efficient probiotics consortia design in Bacillus spp.

Kin discrimination drives territorial exclusion during Bacillus subtilis swarming and restrains exploitation of surfactin

Swarming is the collective movement of bacteria across a surface. It requires the production of surfactants (public goods) to overcome surface tension and provides an excellent model to investigate bacterial cooperation. Previously, we correlated swarm interaction phenotypes with kin discrimination between B. subtilis soil isolates, by showing that less related strains form boundaries between swarms and highly related strains merge. However, how kin discrimination affects cooperation and territoriality in swarming bacteria remains little explored. Here we show that the pattern of surface colonization by swarming mixtures is influenced by kin types. Closely related strain mixtures colonize the surface in a mixed swarm, while mixtures of less related strains show competitive exclusion as only one strain colonizes the surface. The outcome of nonkin swarm expansion depends on the initial ratio of the competing strains, indicating positive frequency-dependent competition. We find that addition of surfactin (a public good excreted from cells) can complement the swarming defect of nonkin mutants, whereas close encounters in nonkin mixtures lead to territorial exclusion, which limits the exploitation of surfactin by nonkin nonproducers. The work suggests that kin discrimination driven competitive territorial exclusion may be an important determinant for the success of cooperative surface colonization.

Biosynthetic gene cluster profiling predicts the positive association between antagonism and phylogeny in Bacillus

Understanding the driving forces and intrinsic mechanisms of microbial competition is a fundamental question in microbial ecology. Despite the well-established negative correlation between exploitation competition and phylogenetic distance, the process of interference competition that is exemplified by antagonism remains controversial. Here, we studied the genus Bacillus, a commonly recognized producer of multifarious antibiotics, to explore the role of phylogenetic patterns of biosynthetic gene clusters (BGCs) in mediating the relationship between antagonism and phylogeny. Comparative genomic analysis revealed a positive association between BGC distance and phylogenetic distance. Antagonistic tests demonstrated that the inhibition phenotype positively correlated with both phylogenetic and predicted BGC distance, especially for antagonistic strains possessing abundant BGCs. Mutant-based verification showed that the antagonism was dependent on the BGCs that specifically harbored by the antagonistic strain. These findings highlight that BGC-phylogeny coherence regulates the positive correlation between congeneric antagonism and phylogenetic distance, which deepens our understanding of the driving force and intrinsic mechanism of microbial interactions.

Resolving the conflict between antibiotic production and rapid growth by recognition of peptidoglycan of susceptible competitors

Microbial communities employ a variety of complex strategies to compete successfully against competitors sharing their niche, with antibiotic production being a common strategy of aggression. Here, by systematic evaluation of four non-ribosomal peptides/polyketide (NRPs/PKS) antibiotics produced by Bacillus subtilis clade, we revealed that they acted synergistically to effectively eliminate phylogenetically distinct competitors. The production of these antibiotics came with a fitness cost manifested in growth inhibition, rendering their synthesis uneconomical when growing in proximity to a phylogenetically close species, carrying resistance against the same antibiotics. To resolve this conflict and ease the fitness cost, antibiotic production was only induced by the presence of a peptidoglycan cue from a sensitive competitor, a response mediated by the global regulator of cellular competence, ComA. These results experimentally demonstrate a general ecological concept - closely related communities are favoured during competition, due to compatibility in attack and defence mechanisms.

Bacillus subtilis biofilm formation and social interactions

Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.

Adaptive evolution of hybrid bacteria by horizontal gene transfer

Horizontal gene transfer (HGT) is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer and about its effects on the recipient organism's physiology and fitness. Here, we address these questions in a parallel evolution experiment with two Bacillus subtilis lineages of 7% sequence divergence. We observe rapid evolution of hybrid organisms: gene transfer swaps ∼12% of the core genome in just 200 generations, and 60% of core genes are replaced in at least one population. By genomics, transcriptomics, fitness assays, and statistical modeling, we show that transfer generates adaptive evolution and functional alterations in hybrids. Specifically, our experiments reveal a strong, repeatable fitness increase of evolved populations in the stationary growth phase. By genomic analysis of the transfer statistics across replicate populations, we infer that selection on HGT has a broad genetic basis: 40% of the observed transfers are adaptive. At the level of functional gene networks, we find signatures of negative, positive, and epistatic selection, consistent with hybrid incompatibilities and adaptive evolution of network functions. Our results suggest that gene transfer navigates a complex cross-lineage fitness landscape, bridging epistatic barriers along multiple high-fitness paths.

Diverse LXG toxin and antitoxin systems specifically mediate intraspecies competition in Bacillus subtilis biofilms

Biofilms are multispecies communities, in which bacteria constantly compete with one another for resources and niches. Bacteria produce many antibiotics and toxins for competition. However, since biofilm cells exhibit increased tolerance to antimicrobials, their roles in biofilms remain controversial. Here, we showed that Bacillus subtilis produces multiple diverse polymorphic toxins, called LXG toxins, that contain N-terminal LXG delivery domains and diverse C-terminal toxin domains. Each B. subtilis strain possesses a distinct set of LXG toxin–antitoxin genes, the number and variation of which is sufficient to distinguish each strain. The B. subtilis strain NCIB3610 possesses six LXG toxin–antitoxin operons on its chromosome, and five of the toxins functioned as DNase. In competition assays, deletion mutants of any of the six LXG toxin–antitoxin operons were outcompeted by the wild-type strain. This phenotype was suppressed when the antitoxins were ectopically expressed in the deletion mutants. The fitness defect of the mutants was only observed in solid media that supported biofilm formation. Biofilm matrix polymers, exopolysaccharides and TasA protein polymers were required for LXG toxin function. These results indicate that LXG toxin-antitoxin systems specifically mediate intercellular competition between B. subtilis strains in biofilms. Mutual antagonism between some LXG toxin producers drove the spatial segregation of two strains in a biofilm, indicating that LXG toxins not only mediate competition in biofilms, but may also help to avoid warfare between strains in biofilms. LXG toxins from strain NCIB3610 were effective against some natural isolates, and thus LXG toxin–antitoxin systems have ecological impact. B. subtilis possesses another polymorphic toxin, WapA. WapA had toxic effects under planktonic growth conditions but not under biofilm conditions because exopolysaccharides and TasA protein polymers inhibited WapA function. These results indicate that B. subtilis uses two types of polymorphic toxins for competition, depending on the growth mode.

Biofilms are surface-associated multispecies communities, in which bacteria are protected by self-produced extracellular polymeric substances. In biofilms, bacteria constantly engage in intra- and interspecies competition. To minimize exploitation by competitors, bacteria produce a variety of antibiotics and toxins for competition. However, since biofilm cells exhibit increased tolerance to antimicrobials, the function of antibiotics and toxins in biofilms remains controversial. Therefore, the mechanisms underlying bacterial competition in biofilms remain to be investigated. We found that the soil bacterium B. subtilis produces polymorphic toxins, termed LXG toxins. LXG toxins are highly diversified among B. subtilis strains, and each B. subtilis strain possesses three to nine different LXG toxins. LXG toxins specifically mediate intraspecies competition in biofilms. Competition between some LXG toxin producers resulted in the spatial segregation of strains in biofilms, indicating that LXG toxins not only mediate competition, but also help to minimize warfare in biofilms. LXG toxins were effective against natural isolates of B. subtilis, suggesting that LXG toxin–antitoxin systems have ecological impact. Our results provide new insights into how bacteria survive competition in biofilms.

Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis

Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, resulting in killing of one of the strains. This process is mediated by a fast-evolving kin discrimination (KD) system consisting of cellular attack and defence mechanisms. Here, we show that these swarm antagonisms promote transformation-mediated horizontal gene transfer between strains of low relatedness. Gene transfer between interacting non-kin strains is largely unidirectional, from killed cells of the donor strain to surviving cells of the recipient strain. It is associated with activation of a stress response mediated by sigma factor SigW in the donor cells, and induction of competence in the recipient strain. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, do not upregulate transformation upon encounter. This result indicates that social interactions can override mechanistic barriers to horizontal gene transfer. We hypothesize that KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context.

Bacillaene Mediates the Inhibitory Effect of Bacillus subtilis on Campylobacter jejuni Biofilms

Biofilms are the predominant bacterial lifestyle and can protect microorganisms from environmental stresses. Multispecies biofilms can affect the survival of enteric pathogens that contaminate food products, and thus, investigating the underlying mechanisms of multispecies biofilms is essential for food safety and human health. In this study, we investigated the ability of the natural isolate Bacillus subtilis PS-216 to restrain Campylobacter jejuni biofilm formation and adhesion to abiotic surfaces as well as to disrupt preestablished C. jejuni biofilms. Using confocal laser scanning microscopy and colony counts, we demonstrate that the presence of B. subtilis PS-216 prevents C. jejuni biofilm formation, decreases growth of the pathogen by 4.2 log₁₀, and disperses 26-h-old preestablished C. jejuni biofilms. Furthermore, the coinoculation of B. subtilis and C. jejuni interferes with the adhesion of C. jejuni to abiotic surfaces, reducing it by 2.4 log₁₀. We also show that contact-independent mechanisms contribute to the inhibitory effect of B. subtilis PS-216 on C. jejuni biofilm. Using B. subtilis mutants in genes coding for nonribosomal peptides and polyketides revealed that bacillaene significantly contributes to the inhibitory effect of B. subtilis PS-216. In summary, we show a strong potential for the use of B. subtilis PS-216 against C. jejuni biofilm formation and adhesion to abiotic surfaces. Our research could bring forward novel applications of B. subtilis in animal production and thus contribute to food safety. IMPORTANCE Campylobacter jejuni is an intestinal commensal in animals (including broiler chickens) but also the most frequent cause of bacterial foodborne infection in humans. This pathogen forms biofilms which enhance survival of C. jejuni in food processing and thus threaten human health. Probiotic bacteria represent a potential alternative in the prevention and control of foodborne infections. The beneficial bacterium Bacillus subtilis has an excellent probiotic potential to reduce C. jejuni in the animal gastrointestinal tract. However, data on the effect of B. subtilis on C. jejuni biofilms are scarce. Our study shows that the B. subtilis natural isolate PS-216 prevents adhesion to the abiotic surfaces and the development of submerged C. jejuni biofilm during coculture and destroys the preestablished C. jejuni biofilm. These insights are important for development of novel applications of B. subtilis that will reduce the use of antibiotics in human and animal health and increase productivity in animal breeding.

Surfactin Facilitates Horizontal Gene Transfer in Bacillus subtilis

Genetic competence for the uptake and integration of extracellular DNA is a key process in horizontal gene transfer (HGT), one of the most powerful forces driving the evolution of bacteria. In several species, development of genetic competence is coupled with cell lysis. Using Bacillus subtilis as a model bacterium, we studied the role of surfactin, a powerful biosurfactant and antimicrobial lipopeptide, in genetic transformation. We showed that surfactin itself promotes cell lysis and DNA release, thereby promoting HGT. These results, therefore, provide evidence for a fundamental mechanism involved in HGT and significantly increase our understanding of the spreading of antibiotic resistance genes and diversification of microbial communities in the environment.

Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome

A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.

Molecular Aspects of Plant Growth Promotion and Protection by Bacillus subtilis

Bacillus subtilis is one of the most widely studied plant growth-promoting rhizobacteria. It is able to promote plant growth as well as control plant pathogens through diverse mechanisms, including the improvement of nutrient availability and alteration of phytohormone homeostasis as well as the production of antimicrobials and triggering induced systemic resistance, respectively. Even though its benefits for crop production have been recognized and studied extensively under laboratory conditions, the success of its application in fields varies immensely. It is widely accepted that agricultural application of B. subtilis often fails because the bacteria are not able to persist in the rhizosphere. Bacterial colonization of plant roots is a crucial step in the interaction between microbe and plant and seems, therefore, to be of great importance for its growth promotion and biocontrol effects. A successful root colonization depends thereby on both bacterial traits, motility and biofilm formation, as well as on a signal interplay with the plant. This review addresses current knowledge about plant-microbial interactions of the B. subtilis species, including the various mechanisms for supporting plant growth as well as the necessity for the establishment of the relationship.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.

Pervasive prophage recombination occurs during evolution of spore-forming Bacilli

Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.

Ecological Advantages and Evolutionary Limitations of Aggregative Multicellular Development

All multicellular organisms develop through one of two basic routes: they either aggregate from free-living cells, creating potentially chimeric multicellular collectives, or they develop clonally via mother-daughter cellular adhesion. Although evolutionary theory makes clear predictions about trade-offs between these developmental modes, these have never been experimentally tested in otherwise genetically identical organisms. We engineered unicellular baker's yeast (Saccharomyces cerevisiae) to develop either clonally ("snowflake"; Δace2) or aggregatively ("floc"; GAL1p::FLO1) and examined their fitness in a fluctuating environment characterized by periods of growth and selection for rapid sedimentation. When cultured independently, aggregation was far superior to clonal development, providing a 35% advantage during growth and a 2.5-fold advantage during settling selection. Yet when competed directly, clonally developing snowflake yeast rapidly displaced aggregative floc. This was due to unexpected social exploitation: snowflake yeast, which do not produce adhesive FLO1, nonetheless become incorporated into flocs at a higher frequency than floc cells themselves. Populations of chimeric clusters settle much faster than floc alone, providing snowflake yeast with a fitness advantage during competition. Mathematical modeling suggests that such developmental cheating may be difficult to circumvent; hypothetical "choosy floc" that avoid exploitation by maintaining clonality pay an ecological cost when rare, often leading to their extinction. Our results highlight the conflict at the heart of aggregative development: non-specific cellular binding provides a strong ecological advantage-the ability to quickly form groups-but this very feature leads to its exploitation.

Inhibitions Dominate but Stimulations and Growth Rescues Are Not Rare Among Bacterial Isolates from Grains of Forest Soil

Soil is a complex environment made of multiple microhabitats in which a wide variety of microorganisms co-exist and interact to form dynamic communities. While the abiotic factors that regulate the structure of these communities are now quite well documented, our knowledge of how bacteria interact with each other within these communities is still insufficient. Literature reveals so far contradictory results and is mainly focused on antagonistic interactions. To start filling this gap, we isolated 35 different bacterial isolates from grains of soil assuming that, at this scale, these bacteria would have been likely interacting in their natural habitat. We tested pairwise interactions between all isolates from each grain and scored positive and negative interactions. We compared the effects of simultaneous versus delayed co-inoculations, allowing or not to a strain to modify first its environment. One hundred fifty-seven interactions, either positive or negative, were recorded among the 525 possible one's. Members of the Bacillus subtilis, Pseudomonas and Streptomyces genera were responsible for most inhibitions, while positive interactions occurred between isolates of the Bacillales order and only in delayed inoculation conditions. Antagonist isolates had broad spectral abilities to acquire nutrients from organic and inorganic matter, while inhibited isolates tended to have little potentials. Despite an overall domination of antagonistic interactions (87%), a third of the isolates were able to stimulate or rescue the growth of other isolates, suggesting that cooperation between bacteria may be underestimated.

Coaggregation properties of trimeric autotransporter adhesins

Trimeric autotransporter adhesins (TAAs) comprise a group of virulence‐related proteins in Gram‐negative bacteria. Members of this family bind to extracellular matrix components such as collagen and fibronectin, but also they exhibit several other functions, such as conferring serum resistance and autoaggregation. Autoaggregation promoted by TAAs is homotypic and mediated by the sticky, globular head domains of these lollipop‐like molecules. However, whether TAAs mediate heterotypic interactions (i.e., coaggregation) has not been studied. To address this question, we investigated the coaggregation of two model TAA groups: YadA from the enteropathogenic Yersiniae and the immunoglobulin‐binding Eib proteins from Escherichia coli. To study TAA coaggregation, we coexpressed a fluorescent label together with a particular TAA and followed the aggregative interactions using fluorescence microscopy and quantified the interactions using a novel script implemented in Fiji. Our results show that there is coaggregation between some populations expressing different TAAs, which can be explained by relatively high sequence similarity between the interacting TAAs. Generally, the level of coaggregation correlated with the sequence similarity. However, some TAAs did not interact despite high sequence similarity, showing exclusion of bacteria producing a noncompatible TAA. These data demonstrate that TAAs can mediate bacterial coaggregation, but in some cases prevent coaggregation of bacteria with disparate TAAs. Our results have implications for the ecology of TAA‐producing bacteria, where coaggregation may promote co‐operation whereas exclusion might be an indication of competition.

Privatization of Biofilm Matrix in Structurally Heterogeneous Biofilms

The self-produced biofilm provides beneficial protection for the enclosed cells, but the costly production of matrix components makes producer cells susceptible to cheating by nonproducing individuals. Despite detrimental effects of nonproducers, biofilms can be heterogeneous, with isogenic nonproducers being a natural consequence of phenotypic differentiation processes. For instance, in Bacillus subtilis biofilm cells differ in production of the two major matrix components, the amyloid fiber protein TasA and exopolysaccharides (EPS), demonstrating different expression levels of corresponding matrix genes. This raises questions regarding matrix gene expression dynamics during biofilm development and the impact of phenotypic nonproducers on biofilm robustness. Here, we show that biofilms are structurally heterogeneous and can be separated into strongly and weakly associated clusters. We reveal that spatiotemporal changes in structural heterogeneity correlate with matrix gene expression, with TasA playing a key role in biofilm integrity and timing of development. We show that the matrix remains partially privatized by the producer subpopulation, where cells tightly stick together even when exposed to shear stress. Our results support previous findings on the existence of "weak points" in seemingly robust biofilms as well as on the key role of linkage proteins in biofilm formation. Furthermore, we provide a starting point for investigating the privatization of common goods within isogenic populations.IMPORTANCE Biofilms are communities of bacteria protected by a self-produced extracellular matrix. The detrimental effects of nonproducing individuals on biofilm development raise questions about the dynamics between community members, especially when isogenic nonproducers exist within wild-type populations. We asked ourselves whether phenotypic nonproducers impact biofilm robustness, and where and when this heterogeneity of matrix gene expression occurs. Based on our results, we propose that the matrix remains partly privatized by the producing subpopulation, since producing cells stick together when exposed to shear stress. The important role of linkage proteins in robustness and development of the structurally heterogeneous biofilm provides an entry into studying the privatization of common goods within isogenic populations.

The ComX Quorum Sensing Peptide of Bacillus subtilis Affects Biofilm Formation Negatively and Sporulation Positively

Quorum sensing (QS) is often required for the formation of bacterial biofilms and is a popular target of biofilm control strategies. Previous studies implicate the ComQXPA quorum sensing system of Bacillus subtilis as a promoter of biofilm formation. Here, we report that ComX signaling peptide deficient mutants form thicker and more robust pellicle biofilms that contain chains of cells. We confirm that ComX positively affects the transcriptional activity of the PepsA promoter, which controls the synthesis of the major matrix polysaccharide. In contrast, ComX negatively controls the PtapA promoter, which drives the production of TasA, a fibrous matrix protein. Overall, the biomass of the mutant biofilm lacking ComX accumulates more monosaccharide and protein content than the wild type. We conclude that this QS phenotype might be due to extended investment into growth rather than spore development. Consistent with this, the ComX deficient mutant shows a delayed activation of the pre-spore specific promoter, PspoIIQ, and a delayed, more synchronous commitment to sporulation. We conclude that ComX mediated early commitment to sporulation of the wild type slows down biofilm formation and modulates the coexistence of multiple biological states during the early stages of biofilm development.

Stress signalling in acellular slime moulds and its detection by conspecifics

Unicellular organisms live in unpredictable environments. Therefore, they need to continuously assess environmental conditions and respond appropriately to survive and thrive. When subjected to rapid changes in their environment or to cellular damages, unicellular organisms such as bacteria exhibit strong physiological reactions called stress responses that can be sensed by conspecifics. The ability to detect and use stress-related cues released by conspecifics to acquire information about the environment constitutes an adaptive survival response by prompting the organism to avoid potential dangers. Here, we investigate stress signalling and its detection by conspecifics in a unicellular organism, Physarum polycephalum. Slime moulds were subjected to either biotic (i.e. nutritional) or abiotic (i.e. chemical and light) stressors or left undisturbed while they were exploring a homogeneous environment. Then, we observed the responses of slime moulds facing a choice between cues released by stressed clone mates and cues released by undisturbed ones. We found that slime moulds actively avoided environments previously explored by stressed clone mates. These results suggest that slime moulds, like bacteria or social amoeba, exhibit physiological responses to biotic and abiotic stresses that can be sensed by conspecifics. Our results establish slime moulds as a promising new model to investigate the use of social information in unicellular organisms. This article is part of the theme issue 'Signal detection theory in recognition systems: from evolving models to experimental tests'.

Mining the Biosynthetic Potential for Specialized Metabolism of a Streptomyces Soil Community

The diversity and distribution of specialized metabolite gene clusters within a community of bacteria living in the same soil habitat are poorly documented. Here we analyzed the genomes of 8 Streptomyces isolated at micro-scale from a forest soil that belong to the same species or to different species. The results reveal high levels of diversity, with a total of 261 biosynthesis gene clusters (BGCs) encoding metabolites such as terpenes, polyketides (PKs), non-ribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs) with potential bioactivities. A significant part of these BGCs (n = 53) were unique to only one strain when only 5 were common to all strains. The metabolites belong to very diverse chemical families and revealed that a large diversity of metabolites can potentially be produced in the community. Although that analysis of the global metabolome using GC-MS revealed that most of the metabolites were shared between the strains, they exhibited a specific metabolic pattern. We also observed that the presence of these accessory pathways might result from frequent loss and gain of genes (horizontal transfer), showing that the potential of metabolite production is a dynamic phenomenon in the community. Sampling Streptomyces at the community level constitutes a good frame to discover new biosynthetic pathways and it appears as a promising reservoir for the discovery of new bioactive compounds.

Environment Shapes the Intra-species Diversity of Bacillus subtilis Isolates

Cosmopolitan bacteria are those that are found practically everywhere in the world. One of them is Bacillus subtilis, which can travel around the world through dust storms rising from various deserts. Upon landing, bacterial survival is determined by the ability to adjust to the heterogonous environments and bacteria isolated from extremely different environments, such as desert and riverbank soil, are expected to be less related due to the environmental pressure of each region. However, little is known about the influence of soil and habitat on B. subtilis evolution. Here, we show that desert and riverbank B. subtilis strains differ in genetic relatedness and physiological traits, such as biofilm morphology and utilisation of carbon sources. Desert strains showed more diversity at the genetic level and were able to utilise more carbon sources than riverbank strains which were highly genetically conserved. Biofilm morphologies of desert and riverbank strains generally segregated and both groups formed different morphology clusters despite the astonishing diversity observed among riverbank strains. We also show that relatedness of B. subtilis strains does not decrease with distance inside the same habitat, which, together with diversity data implies that the difference in environmental selection pressures plays a fundamental role in the evolution of this species.

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.

Sexual Selection in Bacteria?

A main mechanism of lateral gene transfer in bacteria is transformation, where cells take up free DNA from the environment which subsequently can be recombined into the genome. Bacteria are also known to actively release DNA into the environment through secretion or lysis, which could aid uptake via transformation. Various evolutionary benefits of DNA uptake and DNA release have been proposed but these have all been framed in the context of natural selection. Here, we interpret bacterial DNA uptake and release in the context of sexual selection theory, which has been central to our understanding of the bewildering diversity of traits associated with sexual reproduction in the eukaryote world but has never been applied to prokaryotes. Specifically, we explore potential scenarios where bacteria releasing DNA into the environment could compete for successful uptake by other cells, or where bacteria could selectively take up DNA to enhance their fitness. We conclude that there is potential for sexual selection to act in bacteria, and that this might in part explain the considerable diversity in transformation-related behaviours.

Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics

Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods.

In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations.