Bacterial swarms recruit cargo bacteria to pave the way in toxic environments

Protocol for isolating single species of bacteria with swarming ability from human feces

Understanding the specific movements of bacteria isolated from human feces can serve as a novel diagnostic and therapeutic tool for inflammatory bowel disease. Here, we present a protocol for a microbial swarming assay and to isolate the bacteria responsible for swarming activity. We describe steps for identifying bacteria using MALDI-TOF mass spectrometry and whole-genome sequencing. We then detail procedures for validating findings by observing the same swarming phenotype upon reperforming the swarming assay. For complete details on the use and execution of this protocol, please refer to De et al.1.

Hitching a Ride in the Phyllosphere: Surfactant Production of Pseudomonas spp. Causes Co-swarming of Pantoea eucalypti 299R

Here, we demonstrate the beneficial effect of surfactant-producing pseudomonads on Pantoea eucalypti 299R. We conducted a series of experiments in environments of increasing complexity. P. eucalypti 299R (Pe299R), and Pseudomonas sp. FF1 (Pff1) or Pe299R and surfactant-production deficient Pseudomonas sp. FF1::ΔviscB (Pff1ΔviscB) were co-inoculated in broth, on swarming agar plates, and on plants. In broth, there were no differences in the growth dynamics of Pe299R when growing in the presence of Pff1 or Pff1ΔviscB. By contrast, on swarming agar plates, Pe299R was able to co-swarm with Pff1 which led to a significant increase in Pe299R biomass compared to Pe299R growing with Pff1ΔviscB or in monoculture. Finally in planta, and using the single-cell bioreporter for reproductive success (CUSPER), we found a temporally distinct beneficial effect of Pff1 on co-inoculated Pe299R subpopulations that did not occur in the presence of Pff1ΔviscB. We tested three additional surfactant-producing pseudomonads and their respective surfactant knockout mutants on PE299R on swarming agar showing similar results. This led us to propose a model for the positive effect of surfactant production during leaf colonization. Our results indicate that co-motility might be common during leaf colonization and adds yet another facet to the already manyfold roles of surfactants.

Multi-population dissolution in confined active fluids

Autonomous out-of-equilibrium agents or cells in suspension are ubiquitous in biology and engineering. Turning chemical energy into mechanical stress, they generate activity in their environment, which may trigger spontaneous large-scale dynamics. Often, these systems are composed of multiple populations that may reflect the coexistence of multiple species, differing phenotypes, or chemically varying agents in engineered settings. Here, we present a new method for modeling such multi-population active fluids subject to confinement. We use a continuum multi-scale mean-field approach to represent each phase by its first three orientational moments and couple their evolution with those of the suspending fluid. The resulting coupled system is solved using a parallel adaptive level-set-based solver for high computational efficiency and maximal flexibility in the confinement geometry. Motivated by recent experimental work, we employ our method to study the spatiotemporal dynamics of confined bacterial suspensions and swarms dominated by fluid hydrodynamic effects. Our in silico explorations reproduce observed emergent collective patterns, including features of active dissolution in two-population active-passive swarms, with results clearly suggesting that hydrodynamic effects dominate dissolution dynamics. Our work lays the foundation for a systematic characterization and study of collective phenomena in natural or synthetic multi-population systems such as bacteria colonies, bird flocks, fish schools, colloid swimmers, or programmable active matter.

Interplay Between Antimicrobial Resistance and Global Environmental Change

Antibiotic resistance genes predate the therapeutic uses of antibiotics. However, the current antimicrobial resistance crisis stems from our extensive use of antibiotics and the generation of environmental stressors that impose new selective pressure on microbes and drive the evolution of resistant pathogens that now threaten human health. Similar to climate change, this global threat results from human activities that change habitats and natural microbiomes, which in turn interact with human-associated ecosystems and lead to adverse impacts on human health. Human activities that alter our planet at global scales exacerbate the current resistance crisis and exemplify our central role in large-scale changes in which we are both protagonists and architects of our success but also casualties of unanticipated collateral outcomes. As cognizant participants in this ongoing planetary experiment, we are driven to understand and find strategies to curb the ongoing crises of resistance and climate change.

Hitchhiking motility of Staphylococcus aureus involves the interaction between its wall teichoic acids and lipopolysaccharide of Pseudomonas aeruginosa

Staphylococcus aureus, which lacks pili and flagella, is nonmotile. However, it hitchhikes motile bacteria, such as Pseudomonas aeruginosa, to migrate in the environment. This study demonstrated that the hitchhiking motility of S. aureus SA113 was reduced after the tagO, which encodes an enzyme for wall teichoic acids (WTA) synthesis, was deleted. The hitchhiking motility was restored after the mutation was complemented by transforming a plasmid expressing TagO into the mutant. We also showed that adding purified lipopolysaccharide (LPS) to a culture that contains S. aureus SA113 and P. aeruginosa PAO1, reduced the movement of S. aureus, showing that WTA and LPS are involved in the hitchhiking motility of S. aureus. This study also found that P. aeruginosa promoted the movement of S. aureus in the digestive tract of Caenorhabditis elegans and in mice. In conclusion, this study reveals how S. aureus hitchhikes P. aeruginosa for translocation in an ecosystem. The results from this study improve our understanding on how a nonmotile pathogen moves in the environment and spreads in animals.

Design and construction of 3D printed devices to investigate active and passive bacterial dispersal on hydrated surfaces

Background

To disperse in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such “fungal highways” may be driven both by mycelial physical properties and by interactions between bacteria and fungi. However, we still do not have a way to disentangle the biotic and abiotic elements.

Results

We designed and 3D printed two devices establishing stable liquid films that support bacteria dispersal in the absence of biotic interactions. The thickness of the liquid film determined the presence of hydraulic flow capable of transporting non-motile cells. In the absence of flow, only motile cells can disperse in the presence of an energy source. Non-motile cells could not disperse autonomously without flow but dispersed as “hitchhikers” when co-inoculated with motile cells.

Conclusions

The 3D printed devices can be used as an abiotic control to study bacterial dispersal on hydrated surfaces, such as plant roots and fungal hyphae networks in the soil. By teasing apart the abiotic and biotic dimensions, these 3D printed devices will stimulate further research on microbial dispersal in soil and other water-unsaturated environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01406-z.

Surface Motility Favors Codependent Interaction between Pseudomonas aeruginosa and Burkholderia cenocepacia

Interactions between different bacterial species shape bacterial communities and their environments. The opportunistic pathogens Pseudomonas aeruginosa and Burkholderia cenocepacia both can colonize the lungs of individuals affected by cystic fibrosis. Using the social surface behavior called swarming motility as a study model, we noticed intricate interactions between B. cenocepacia K56-2 and P. aeruginosa PA14. While strain K56-2 does not swarm under P. aeruginosa favorable swarming conditions, co-inoculation with a nonmotile PA14 flagellum-less ΔfliC mutant restored spreading for both strains. We show that P. aeruginosa provides the wetting agent rhamnolipids allowing K56-2 to perform swarming motility, while aflagellated PA14 appears to “hitchhike” along with K56-2 cells in the swarming colony.

IMPORTANCEPseudomonas aeruginosa and Burkholderia cenocepacia are important opportunistic pathogens often found together in the airways of persons with cystic fibrosis. Laboratory cocultures of both species often ends with one taking over the other. We used a surface motility assay to study the social interactions between populations of these bacterial species. Under our conditions, B. cenocepacia cannot swarm without supplementation of the wetting agent produced by P. aeruginosa. In a mixed colony of both species, an aflagellated mutant of P. aeruginosa provides the necessary wetting agent to B. cenocepacia, allowing both bacteria to swarm and colonize a surface. We highlight this peculiar interaction where both bacteria set aside their antagonistic tendencies to travel together.

Physical characteristics of mixed-species swarming colonies

In nature, bacterial collectives typically consist of multiple species, which are interacting both biochemically and physically. Nonetheless, past studies on the physical properties of swarming bacteria were focused on axenic (single-species) populations. In bacterial swarming, intricate interactions between the individuals lead to clusters, rapid jets, and vortices that depend on cell characteristics such as speed and length. In this work, we show the first results of rapidly swarming mixed-species populations of Bacillus subtilis and Serratia marcescens, two model swarm species that are known to swarm well in axenic situations. In mixed liquid cultures, both species have higher reproduction rates. We show that the mixed population swarms together well and that the fraction between the species determines all dynamical scales-from the microscopic (e.g., speed distribution), mesoscopic (vortex size), and macroscopic (colony structure and size). Understanding mixed-species swarms is essential for a comprehensive understanding of the bacterial swarming phenomenon and its biological and evolutionary implications.

Dynamic proteome allocation regulates the profile of interaction of auxotrophic bacterial consortia

Microbial ecosystems are composed of multiple species in constant metabolic exchange. A pervasive interaction in microbial communities is metabolic cross-feeding and occurs when the metabolic burden of producing costly metabolites is distributed between community members, in some cases for the benefit of all interacting partners. In particular, amino acid auxotrophies generate obligate metabolic inter-dependencies in mixed populations and have been shown to produce a dynamic profile of interaction that depends upon nutrient availability. However, identifying the key components that determine the pair-wise interaction profile remains a challenging problem, partly because metabolic exchange has consequences on multiple levels, from allocating proteomic resources at a cellular level to modulating the structure, function and stability of microbial communities. To evaluate how ppGpp-mediated resource allocation drives the population-level profile of interaction, here we postulate a multi-scale mathematical model that incorporates dynamics of proteome partition into a population dynamics model. We compare our computational results with experimental data obtained from co-cultures of auxotrophic Escherichia coli K12 strains under a range of amino acid concentrations and population structures. We conclude by arguing that the stringent response promotes cooperation by inhibiting the growth of fast-growing strains and promoting the synthesis of metabolites essential for other community members.

Flagella at the Host-Microbe Interface: Key Functions Intersect With Redundant Responses

Many bacteria and other microbes achieve locomotion via flagella, which are organelles that function as a swimming motor. Depending on the environment, flagellar motility can serve a variety of beneficial functions and confer a fitness advantage. For example, within a mammalian host, flagellar motility can provide bacteria the ability to resist clearance by flow, facilitate access to host epithelial cells, and enable travel to nutrient niches. From the host’s perspective, the mobility that flagella impart to bacteria can be associated with harmful activities that can disrupt homeostasis, such as invasion of epithelial cells, translocation across epithelial barriers, and biofilm formation, which ultimately can decrease a host’s reproductive fitness from a perspective of natural selection. Thus, over an evolutionary timescale, the host developed a repertoire of innate and adaptive immune countermeasures that target and mitigate this microbial threat. These countermeasures are wide-ranging and include structural components of the mucosa that maintain spatial segregation of bacteria from the epithelium, mechanisms of molecular recognition and inducible responses to flagellin, and secreted effector molecules of the innate and adaptive immune systems that directly inhibit flagellar motility. While much of our understanding of the dynamics of host-microbe interaction regarding flagella is derived from studies of enteric bacterial pathogens where flagella are a recognized virulence factor, newer studies have delved into host interaction with flagellated members of the commensal microbiota during homeostasis. Even though many aspects of flagellar motility may seem innocuous, the host’s redundant efforts to stop bacteria in their tracks highlights the importance of this host-microbe interaction.

Dynamics and removal mechanisms of antibiotic and antibiotic resistance genes during the fermentation process of spectinomycin mycelial dregs: An integrated meta-omics study

Antibiotic mycelial dregs (AMDs) have been listed as industrial hazardous wastes. With the aim of reducing the environmental risk, the integrated-omics and qPCR approaches were used to reveal the dynamics and removal mechanisms of antibiotic and antibiotic resistance genes (ARGs) during the fermentation of different spectinomycin mycelial dregs (SMDs). The results showed that the removal efficiency of antibiotic in the fermentation of high moisture SMDs reached up to 98%. The high abundance of aadA1 gene encoded by Streptomyces, Lactobacillus, and Pseudomonas was associated with the efficient degradation of spectinomycin, and the inactivating enzymes secreted by degradative bacteria were identified. Furthermore, the dominant microbiota was impacted by moisture content significantly under high temperature environments. In the fermentation of low moisture SMDs, Saccharopolyspora was the dominant microbiota which secreted S8 endopeptidase, M14, M15, S10, S13 carboxypeptidases, M1, M28, S15 aminopeptidases, and antioxidant enzymes, while in the fermentation of high moisture SMDs, Bacillus and Cerasibacillus were dominant genera which mainly secreted S8 endopeptidase and antioxidant enzymes. The abundance of ARGs and mobile genetic elements decreased significantly at thermophilic phase, with maximum drops of 93.7% and 99.9%, respectively. Maintaining moisture content below 30% at the end phase could prevent the transmission of ARGs effectively.

Surveying a Swarm: Experimental Techniques to Establish and Examine Bacterial Collective Motion

The survival and successful spread of many bacterial species hinges on their mode of motility. One of the most distinct of these is swarming, a collective form of motility where a dense consortium of bacteria employ flagella to propel themselves across a solid surface. Surface environments pose unique challenges, derived from higher surface friction/tension and insufficient hydration. Bacteria have adapted by deploying an array of mechanisms to overcome these challenges. Beyond allowing bacteria to colonize new terrain in the absence of bulk liquid, swarming also bestows faster speeds and enhanced antibiotic resistance to the collective. These crucial attributes contribute to the dissemination, and in some cases pathogenicity, of an array of bacteria. This mini-review highlights; 1) aspects of swarming motility that differentiates it from other methods of bacterial locomotion. 2) Facilitatory mechanisms deployed by diverse bacteria to overcome different surface challenges. 3) The (often difficult) approaches required to cultivate genuine swarmers. 4) The methods available to observe and assess the various facets of this collective motion, as well as the features exhibited by the population as a whole.

Microbial hitchhiking: how Streptomyces spores are transported by motile soil bacteria

Streptomycetes are sessile bacteria that produce metabolites that impact the behavior of microbial communities. Emerging studies have demonstrated that Streptomyces spores are distributed through various mechanisms, but it remains unclear how spores are transported to their preferred microenvironments, such as plant roots. Here, we show that Streptomyces spores are capable of utilizing the motility machinery of other soil bacteria. Motility assays and microscopy studies reveal that Streptomyces spores are transported to plant tissues by interacting directly with the flagella of both gram-positive and gram-negative bacteria. Genetics experiments demonstrate that this form of motility is facilitated by structural proteins on the spore coat. These results demonstrate that nonmotile bacteria are capable of utilizing the motility machinery of other microbes to complete necessary stages of their lifecycle.

Proliferation of antibiotic-resistant microorganisms and associated genes during composting: An overview of the potential impacts on public health, management and future

Antibiotic residues together with non-antibiotic drugs and heavy metals act as a selective pressure for the spread of antibiotic-resistant microorganisms (ARMs), antibiotic-resistant genes (ARGs), and mobile genetic elements (MGEs) during composting of livestock manure. ARMs, ARGs and MGEs have become emerging contaminants since they are regularly implicated in the majority of compost produced from livestock manure. The prevalence of these contaminants in agricultural soil receiving compost has drawn huge attention globally due to the risks they pose to the total environment. Although a large body of literature exists on the application of composting methods in minimizing the relative abundance of these contaminants, there is a paucity of information on the robustness, limitations and opportunities and threats of various composting protocols currently deployed. To address this knowledge gap, the current review compiled literature on the origin and mechanisms of the proliferation of ARMs, ARGs, and MGEs during composting of livestock manure. The effectiveness of current composting protocols in the reduction or removal of emerging contaminants was evaluated. Furthermore, the potential environmental impacts and human health risks of these contaminants following land application of compost were also presented. Finally, we propose some strategic approaches for the reduction of ARGs and MGEs during composting of livestock manure.

Scattered migrating colony formation in the filamentous cyanobacterium, Pseudanabaena sp. NIES-4403

Background

Bacteria have been reported to exhibit complicated morphological colony patterns on solid media, depending on intracellular, and extracellular factors such as motility, cell propagation, and cell-cell interaction. We isolated the filamentous cyanobacterium, Pseudanabaena sp. NIES-4403 (Pseudanabaena, hereafter), that forms scattered (discrete) migrating colonies on solid media. While the scattered colony pattern has been observed in some bacterial species, the mechanism underlying such a pattern still remains obscure.

Results

We studied the morphology of Pseudanabaena migrating collectively and found that this species forms randomly scattered clusters varying in size and further consists of a mixture of comet-like wandering clusters and disk-like rotating clusters. Quantitative analysis of the formation of these wandering and rotating clusters showed that bacterial filaments tend to follow trajectories of previously migrating filaments at velocities that are dependent on filament length. Collisions between filaments occurred without crossing paths, which enhanced their nematic alignments, giving rise to bundle-like colonies. As cells increased and bundles aggregated, comet-like wandering clusters developed. The direction and velocity of the movement of cells in comet-like wandering clusters were highly coordinated. When the wandering clusters entered into a circular orbit, they turned into rotating clusters, maintaining a more stable location. Disk-like rotating clusters may rotate for days, and the speed of cells within a rotating cluster increases from the center to the outmost part of the cluster. Using a mathematical modeling with simplified assumption we reproduced some features of the scattered pattern including migrating clusters.

Conclusion

Based on these observations, we propose that Pseudanabaena forms scattered migrating colonies that undergo a series of transitions involving several morphological patterns. A simplified model is able to reproduce some features of the observed migrating clusters.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02183-5.

The spatial organization of microbial communities during range expansion

Microbes in nature often live in dense and diverse communities exhibiting a variety of spatial structures. Microbial range expansion is a universal ecological process that enables populations to form spatial patterns. It can be driven by both passive and active processes, for example, mechanical forces from cell growth and bacterial motility. In this review, we provide a taste of recent creative and sophisticated efforts being made to address basic questions in spatial ecology and pattern formation during range expansion. We especially highlight the role of motility to shape community structures, and discuss the research challenges and future directions.

Exploration of social spreading reveals behavior is prevalent among Pedobacter and P. fluorescens isolates, and shows variations in induction of phenotype

Within soil, bacteria are found in multi-species communities, where interactions can lead to emergent community properties. Studying bacteria in a social context is critical for investigation of community-level functions. We previously showed that co-cultured Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48 engage in interspecies social spreading (ISS) on a hard agar surface, a behavior which required close contact and depended on the nutritional environment. Here, we investigate whether social spreading is widespread among P. fluorescens and Pedobacter isolates, and whether the requirements for interaction vary. We find that this phenotype is not restricted to the interaction between P. fluorescens Pf0-1 and Pedobacter sp. V48, but is a prevalent behavior found in one clade in the P. fluorescens group and two clades in the Pedobacter genus. We show that the interaction with certain Pedobacter isolates occurred without close contact, indicating induction of spreading by a putative diffusible signal. As with ISS by Pf0-1+V48, motility of interacting pairs is influenced by the environment, with no spreading behaviors (or induction of motility) observed under high nutrient conditions. While Pf0-1+V48 require low nutrient but high NaCl conditions, in the broader range of interacting pairs the high salt influence was variable. The prevalence of motility phenotypes observed here and found within the literature indicates that community-induced locomotion in general, and social spreading in particular, is likely important within the environment. It is crucial that we continue to study microbial interactions and their emergent properties to gain a fuller understanding of the functions of microbial communities. Importance Interspecies social spreading (ISS) is an emergent behavior observed when P. fluorescens Pf0-1 and Pedobacter sp. V48 interact, during which both species move together across a surface. Importantly, this environment does not permit movement of either individual species. This group behavior suggests that communities of microbes can function in ways not predictable by knowledge of the individual members. Here we have asked whether ISS is widespread and thus potentially of importance in soil microbial communities. The significance of this research is the demonstration that surface spreading behaviors are not unique to the Pf0-1-V48 interaction, but rather is a more widespread phenomenon observed among members of distinct clades of both P. fluorescens and Pedobacter isolates. Further, we identify differences in mechanism of signaling and nutritional requirements for ISS. Emergent traits resulting from bacterial interactions are widespread and their characterization is necessary for a complete understanding of microbial community function.

Bacterial Swarmers Enriched During Intestinal Stress Ameliorate Damage

BACKGROUND AND AIMS

Bacterial swarming, a collective movement on a surface, has rarely been associated with human pathophysiology. This study aims to define a role for bacterial swarmers in amelioration of intestinal stress.

METHODS

We developed a polymicrobial plate agar assay to detect swarming and screened mice and humans with intestinal stress and inflammation. From chemically induced colitis in mice, as well as humans with inflammatory bowel disease, we developed techniques to isolate the dominant swarmers. We developed swarm-deficient but growth and swim-competent mutant bacteria as isogenic controls. We performed bacterial reinoculation studies in mice with colitis, fecal 16S, and meta-transcriptomic analyses, as well as in vitro microbial interaction studies.

RESULTS

We show that bacterial swarmers are highly predictive of intestinal stress in mice and humans. We isolated a novel Enterobacter swarming strain, SM3, from mouse feces. SM3 and other known commensal swarmers, in contrast to their mutant strains, abrogated intestinal inflammation in mice. Treatment of colitic mice with SM3, but not its mutants, enriched beneficial fecal anaerobes belonging to the family of Bacteroidales S24-7. We observed SM3 swarming associated pathways in the in vivo fecal meta-transcriptomes. In vitro growth of S24-7 was enriched in presence of SM3 or its mutants; however, because SM3, but not mutants, induced S24-7 in vivo, we concluded that swarming plays an essential role in disseminating SM3 in vivo.

CONCLUSIONS

Overall, our work identified a new but counterintuitive paradigm in which intestinal stress allows for the emergence of swarming bacteria; however, these bacteria act to heal intestinal inflammation.

Design of nematic liquid crystals to control microscale dynamics

The dynamics of small particles, both living such as swimming bacteria and inanimate, such as colloidal spheres, has fascinated scientists for centuries. If one could learn how to control and streamline their chaotic motion, that would open technological opportunities in the transformation of stored or environmental energy into systematic motion, with applications in micro-robotics, transport of matter, guided morphogenesis. This review presents an approach to command microscale dynamics by replacing an isotropic medium with a liquid crystal. Orientational order and associated properties, such as elasticity, surface anchoring, and bulk anisotropy, enable new dynamic effects, ranging from the appearance and propagation of particle-like solitary waves to self-locomotion of an active droplet. By using photoalignment, the liquid crystal can be patterned into predesigned structures. In the presence of the electric field, these patterns enable the transport of solid and fluid particles through nonlinear electrokinetics rooted in anisotropy of conductivity and permittivity. Director patterns command the dynamics of swimming bacteria, guiding their trajectories, polarity of swimming, and distribution in space. This guidance is of a higher level of complexity than a simple following of the director by rod-like microorganisms. Namely, the director gradients mediate hydrodynamic interactions of bacteria to produce an active force and collective polar modes of swimming. The patterned director could also be engraved in a liquid crystal elastomer. When an elastomer coating is activated by heat or light, these patterns produce a deterministic surface topography. The director gradients define an activation force that shapes the elastomer in a manner similar to the active stresses triggering flows in active nematics. The patterned elastomer substrates could be used to define the orientation of cells in living tissues. The liquid-crystal guidance holds a major promise in achieving the goal of commanding microscale active flows.

Can dispersal be leveraged to improve microbial inoculant success?

Microorganisms have long been isolated from soils to develop microbial inoculants, with the goal of spiking them into new soils to augment target functions. However, establishment can be sporadic, and we assume that inoculants simply arrive at their destination. Here, we posit a need for integrating dispersal into inoculant development and deployment. We argue that consideration for an inoculant's dispersal ability, whether via active (e.g., chemotaxis) or passive (e.g., attachment to other organisms) means, and including methods of deployment that allow multiple establishment attempts could help increase the predictability of inoculant success. Dispersal can influence many key aspects of in-field survival, including the ability to escape stressors, seek favorable colonization sites, facilitate multiple establishment attempts, and engage in multikingdom interactions.

Sessile bacterium unlocks ability of surface motility through mutualistic interspecies interaction

In addition to their common planktonic lifestyle, bacteria frequently live in surface-associated habitats. Surface motility is essential for exploring these habitats for food sources. However, many bacteria are found on surfaces, even though they lack features required for migrating along surfaces. How these canonical non-motile bacteria adapt to the environmental fluctuations on surfaces remains unknown. Here, we report a previously unknown surface motility mode of the canonical non-motile bacterium, Dietzia sp. DQ12-45-1b, which is triggered by interaction with a dimorphic prosthecate bacterium, Glycocaulis alkaliphilus 6B-8T. Dietzia cells exhibits 'sliding'-like motility in an area where the strain Glycocaulis cells was pre-colonized with a sufficient density. Our analysis also demonstrates that Dietzia degrade n-alkanes and provide Glycocaulis with the resulting metabolites for survival, which in turn induced directional migration of Dietzia towards nutrient-rich environments. Such interaction-triggered migration was also found between Dietzia and Glycocaulis strains isolated from other habitats, suggesting that this mutualistic relationship ubiquitously occurs in natural environments. In conclusion, we propose a novel model for such a 'win-win' strategy, whereby non-motile bacteria pay metabolites to dimorphic prosthecate bacteria in return for migrating to seek for nutrients, which may represent a common strategy for canonically non-motile bacteria living on a surface.

Heterogeneous bacterial swarms with mixed lengths

Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly significant for understanding realistic bacterial swarms, which typically develop heterogeneities even when grown from a single cell. Here, mixed swarms of cells with different aspect ratios are studied both experimentally and in simulations. In contrast with previous theory, there is no macroscopic phase segregation. However, locally, long cells act as nucleation cites, around which aggregates of short, rapidly moving cells can form, resulting in enhanced swarming speeds. On the other hand, high fractions of long cells form a bottleneck for efficient swarming. Our results suggest a physical advantage for the spontaneous heterogeneity of bacterial swarm populations.

Hitchhiking Behavior in Bacteriophages Facilitates Phage Infection and Enhances Carrier Bacteria Colonization

Interactions between bacteriophages (phages) and biofilms remain poorly understood despite the broad implications for microbial ecology, water quality, and microbiome engineering. Here, we demonstrate that lytic coliphage PHH01 can hitchhike on carrier bacteria Bacillus cereus to facilitate its infection of host bacteria, Escherichia coli, in biofilms. Specifically, PHH01 could adsorb onto the flagella of B. cereus, and thus phage motility was increased, resulting in 4.36-fold more effective infection of E. coli in biofilm relative to free PHH01 alone. Moreover, phage infection mitigated interspecies competition and enhanced B. cereus colonization; the fraction of B. cereus in the final biofilm increased from 9% without phages to 43% with phages. The mutualistic relationship between the coliphage and carrier bacteria was substantiated by migration tests on an E. coli lawn: the conjugation of PHH01 and B. cereus enhanced B. cereus colonization by 6.54-fold compared to B. cereus alone (6.15 vs 0.94 cm² in 24 h) and PHH01 migration by 5.15-fold compared to PHH01 alone (10.3 vs 2.0 mm in 24 h). Metagenomic and electron microscopic analysis revealed that the phages of diverse taxonomies and different morphologies could be adsorbed by the flagella of B. cereus, suggesting hitchhiking on flagellated bacteria might be a widespread strategy in aquatic phage populations. Overall, our study highlights that hitchhiking behavior in phages can facilitate phage infection of biofilm bacteria, promote carrier bacteria colonization, and thus significantly influence biofilm composition, which holds promise for mediating biofilm functions and moderating associated risks.

Biofilm and swarming emergent behaviours controlled through the aid of biophysical understanding and tools

Bacteria can organise themselves into communities in the forms of biofilms and swarms. Through chemical and physical interactions between cells, these communities exhibit emergent properties that individual cells alone do not have. While bacterial communities have been mainly studied in the context of biochemistry and molecular biology, recent years have seen rapid advancements in the biophysical understanding of emergent phenomena through physical interactions in biofilms and swarms. Moreover, new technologies to control bacterial emergent behaviours by physical means are emerging in synthetic biology. Such technologies are particularly promising for developing engineered living materials (ELM) and devices and controlling contamination and biofouling. In this minireview, we overview recent studies unveiling physical and mechanical cues that trigger and affect swarming and biofilm development. In particular, we focus on cell shape, motion and density as the key parameters for mechanical cell-cell interactions within a community. We then showcase recent studies that use physical stimuli for patterning bacterial communities, altering collective behaviours and preventing biofilm formation. Finally, we discuss the future potential extension of biophysical and bioengineering research on microbial communities through computational modelling and deeper investigation of mechano-electrophysiological coupling.

Intermicrobial Hitchhiking: How Nonmotile Microbes Leverage Communal Motility

Motility allows many microbes to traverse their environment to find nutrient sources or escape unfavorable environments. However, some microbes are nonmotile and are restricted to their immediate conditions. Intriguingly, sporadic reports have demonstrated that many nonmotile microbes can utilize the motility machinery of other microbes in their vicinity. This form of transportation, called hitchhiking, has been observed with both prokaryotic and eukaryotic microbes. Importantly, many hitchhiking microbes are pathogenic to humans or plants. Here, we discuss reports of intermicrobial hitchhiking to generate a comprehensive view of hitchhiking mechanisms and how such interactions may influence human and plant health. We hypothesize that microbial hitchhiking is ubiquitous in nature and may become the subject of an independent subfield of research in microbiology.

Microbial Interactions Within Multiple-Strain Biological Control Agents Impact Soil-Borne Plant Disease

Major losses of crop yield and quality caused by soil-borne plant diseases have long threatened the ecology and economy of agriculture and forestry. Biological control using beneficial microorganisms has become more popular for management of soil-borne pathogens as an environmentally friendly method for protecting plants. Two major barriers limiting the disease-suppressive functions of biocontrol microbes are inadequate colonization of hosts and inefficient inhibition of soil-borne pathogen growth, due to biotic and abiotic factors acting in complex rhizosphere environments. Use of a consortium of microbial strains with disease inhibitory activity may improve the biocontrol efficacy of the disease-inhibiting microbes. The mechanisms of biological control are not fully understood. In this review, we focus on bacterial and fungal biocontrol agents to summarize the current state of the use of single strain and multi-strain biological control consortia in the management of soil-borne diseases. We discuss potential mechanisms used by microbial components to improve the disease suppressing efficacy. We emphasize the interaction-related factors to be considered when constructing multiple-strain biological control consortia and propose a workflow for assembling them by applying a reductionist synthetic community approach.

Adding a complex microbial agent twice to the composting of laying-hen manure promoted doxycycline degradation with a low risk on spreading tetracycline resistance genes

Poultry manure is a reservoir for antibiotics and antibiotic resistance genes and composting is an effective biological treatment for manure. This study explored the effect of using two methods of adding a complex microbial agent to the composting of laying-hen manure on doxycycline degradation and tetracycline resistance genes elimination. The results showed that incorporating a complex microbial agent at 0.8% (w/w) on the 0^th and 11th day (group MT2) effectively degraded doxycycline with a final degradation rate of 46.83 ± 0.55%. The half-life of doxycycline in this group was 21.90 ± 0.00 days and was significantly lower than that of group MT1 (1.6% (w/w) complex microbial agent added on the 0^th day) and group DT (compost without complex microbial agent). But there was no significant difference in the final degradation rate of doxycycline between group DT and group MT1. The addictive with the complex microbial agent changed the microbial community structure. Bacteroidetes, Firmicutes and Proteobacteria were the dominant phyla during composting. Aerococcus, Desemzia, Facklamia, Lactobacillus, Streptococcus, and Trichococcus were the bacteria related to the degradation of doxycycline. Moreover, the incorporation of a complex microbial agent could decrease the risk on spreading tetracycline resistance genes. The single addition promoted the elimination of tetM, whose possible hosts were Enterococcus, Lactobacillus, Staphylococcus, and Trichococcus. Adding the complex microbial agent twice promoted the elimination of tetX, which was related to the low abundance of Chryseobacterium, Flavobacterium and Neptunomonas in group MT2. Redundancy analysis showed that the bacterial community, residual doxycycline and physiochemical properties have a potential effect on the variation in tetracycline resistance genes levels. Overall, adding the complex microbial agent twice is an effective measure to degrade doxycycline.

Evolution of chemotactic hitchhiking

Bacteria typically reside in heterogeneous environments with various chemogradients where motile cells can gain an advantage over nonmotile cells. Since motility is energetically costly, cells must optimize their swimming speed and behaviour to maximize their fitness. Here, we investigate how cheating strategies might evolve where slow or nonmotile microbes exploit faster ones by sticking together and hitching a ride. Starting with physical and biological first principles, we computationally study the effects of sticking on the evolution of motility in a controlled chemostat environment. We find that stickiness allows for slow cheaters to dominate when chemoattractants are dispersed at intermediate distances. In this case, slow microbes exploit faster ones until they consume the population, leading to a tragedy of commons. For long races, slow microbes do gain an initial advantage from sticking, but eventually fall behind. Here, fast microbes are more likely to stick to other fast microbes and co-operate to increase their own population. We therefore conclude that whether the nature of the hitchhiking interaction is parasitic or mutualistic, depends on the chemoattractant distribution.

Bacterial surface motility is modulated by colony-scale flow and granular jamming

Microbes routinely face the challenge of acquiring territory and resources on wet surfaces. Cells move in large groups inside thin, surface-bound water layers, often achieving speeds of 30 µm s^-1 within this environment, where viscous forces dominate over inertial forces (low Reynolds number). The canonical Gram-positive bacterium Bacillus subtilis is a model organism for the study of collective migration over surfaces with groups exhibiting motility on length-scales three orders of magnitude larger than themselves within a few doubling times. Genetic and chemical studies clearly show that the secretion of endogenous surfactants and availability of free surface water are required for this fast group motility. Here, we show that: (i) water availability is a sensitive control parameter modulating an abiotic jamming-like transition that determines whether the group remains fluidized and therefore collectively motile, (ii) groups self-organize into discrete layers as they travel, (iii) group motility does not require proliferation, rather groups are pulled from the front, and (iv) flow within expanding groups is capable of moving material from the parent colony into the expanding tip of a cellular dendrite with implications for expansion into regions of varying nutrient content. Together, these findings illuminate the physical structure of surface-motile groups and demonstrate that physical properties, like cellular packing fraction and flow, regulate motion from the scale of individual cells up to length scales of centimetres.

Flower-like patterns in multi-species bacterial colonies

Diverse interactions among species within bacterial colonies lead to intricate spatiotemporal dynamics, which can affect their growth and survival. Here, we describe the emergence of complex structures in a colony grown from mixtures of motile and non-motile bacterial species on a soft agar surface. Time-lapse imaging shows that non-motile bacteria 'hitchhike' on the motile bacteria as the latter migrate outward. The non-motile bacteria accumulate at the boundary of the colony and trigger an instability that leaves behind striking flower-like patterns. The mechanism of the front instability governing this pattern formation is elucidated by a mathematical model for the frictional motion of the colony interface, with friction depending on the local concentration of the non-motile species. A more elaborate two-dimensional phase-field model that explicitly accounts for the interplay between growth, mechanical stress from the motile species, and friction provided by the non-motile species, fully reproduces the observed flower-like patterns.

Bacteria From the Multi-Contaminated Tinto River Estuary (SW, Spain) Show High Multi-Resistance to Antibiotics and Point to Paenibacillus spp. as Antibiotic-Resistance-Dissemination Players

Bacterial resistance to antibiotics is an ever-increasing phenomenon that, besides clinical settings, is generally assumed to be prevalent in environmental soils and waters. The analysis of bacteria resistant to each one of 11 antibiotics in waters and sediments of the Huelva’s estuary, a multi-contaminated environment, showed high levels of bacteria resistant mainly to Tm, among others. To further gain knowledge on the fate of multi-drug resistance (MDR) in environmental bacteria, 579 ampicillin-resistant bacteria were isolated tested for resistance to 10 antibiotics. 92.7% of the isolates were resistant to four or more antibiotic classes, indicating a high level of multi-resistance. 143 resistance profiles were found. The isolates with different MDR profiles and/or colony morphologies were phylogenetically ascribed based on 16S rDNA to phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, including 48 genera. Putative intrinsic resistance was detected in different phylogenetic groups including genera Altererythrobacter, Bacillus, Brevundimonas, Erythrobacter, Mesonia, Ochrobactrum, and Ponticaulis. Correlation of the presence of pairs of the non-intrinsic-resistances in phylogenetic groups based on the kappa index (κ) highlighted the co-habitation of some of the tested pairs at different phylogenetic levels. Maximum correlation (κ = 1.000) was found for pairs Cz^R/Tc^R in Betaproteobacteria, and Cc^R/Tc^R and Em^R/Sm^R in Sphingobacteriia at the class level, while at the genus level, was found for Cc^R/Tc^R and Nx^R/Tm^R in Mesonia, Cz^R/Tm^R and Em^R/Km^R in Paenibacillus, and Cc^R/Em^R and Rp^R/Tc^R in Pseudomonas. These results could suggest the existence of intra-class and intra-genus-transmissible genetic elements containing determinants for both members of each pair. Network analysis based on κ values higher than 0.4 indicated the sharing of paired resistances among several genera, many of them centered on the Paenibacillus node and raising the hypothesis of inter-genera transmission of resistances interconnected through members of this genus. This is the first time that a possible hotspot of resistance interchange in a particular environment may have been detected, opening up the possibility that one, or a few, bacterial members of the community could be important promoters of antibiotic resistance (AR) dissemination in this environment’s bacterial population. Further studies using the available isolates will likely give insights of the possible mechanisms and genetic elements involved.

Cellular heterogeneity results from indirect effects under metabolic tradeoffs

The emergence and maintenance of multicellularity requires the coexistence of diverse cellular populations displaying cooperative relationships. This enables long-term persistence of cellular consortia, particularly under environmental constraints that challenge cell survival. Toxic environments are known to trigger the formation of multicellular consortia capable of dealing with waste while promoting cell diversity as a way to overcome selection barriers. In this context, recent theoretical studies suggest that an environment containing both resources and toxic waste can promote the emergence of complex, spatially distributed proto-organisms exhibiting division of labour and higher-scale features beyond the cell-cell pairwise interactions. Some previous non-spatial models suggest that the presence of a growth inhibitor can trigger the coexistence of competitive species in an antibiotic-resistance context. In this paper, we further explore this idea using both mathematical and computational models taking the most fundamental features of the proto-organisms model interactions. It is shown that this resource-waste environmental context, in which both species are lethally affected by the toxic waste and metabolic tradeoffs are present, favours the maintenance of diverse populations. A spatial, stochastic extension confirms our basic results. The evolutionary and ecological implications of these results are outlined.

Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile

The ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil compartments and that most are dominated by a few dispersing taxa. Importantly, an increase in shared dispersers among the preferential flow paths of the clay till suggests that active dispersal plays a role in the successful colonization of these habitats.

This study assessed the dispersal of five bacterial communities from contrasting compartments along a fractured clay till depth profile comprising plow layer soil, preferential flow paths (biopores and the tectonic fractures below), and matrix sediments, down to 350 cm below the surface. A recently developed expansion of the porous surface model (PSM) was used to capture bacterial communities dispersing under controlled hydration conditions on a soil-like surface. All five communities contained bacteria capable of active dispersal under relatively low hydration conditions (−3.1 kPa). Further testing of the plow layer community revealed active dispersal even at matric potentials of −6.3 to −8.4 kPa, previously thought to be too dry for dispersal on the PSM. Using 16S rRNA gene amplicon sequencing, the dispersing communities were found to be less diverse than their corresponding total communities. The dominant dispersers in most compartments belonged to the genus Pseudomonas and, in the plow layer soil, to Rahnella as well. An exception to this was the dispersing community in the matrix at 350 cm below the surface, which was dominated by Pantoea. Hydrologically connected compartments shared proportionally more dispersing than nondispersing amplicon sequence variants (ASVs), suggesting that active dispersal is important for colonizing these compartments. These results highlight the importance of including soil profile heterogeneity when assessing the role of active dispersal and contribute to discerning the importance of active dispersal in the soil environment.

IMPORTANCE The ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil compartments and that most are dominated by a few dispersing taxa. Importantly, an increase in shared dispersers among the preferential flow paths of the clay till suggests that active dispersal plays a role in the successful colonization of these habitats.

Interspecies Social Spreading: Interaction between Two Sessile Soil Bacteria Leads to Emergence of Surface Motility

The wealth of studies on microbial communities has revealed the complexity and dynamics of the composition of communities in many ecological settings. Fewer studies probe the functional interactions of the community members. Function of the community as a whole may not be fully revealed by characterizing the individuals. In our two-species model community, we find an emergent trait resulting from the interaction of the soil bacteria Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48. Observation of emergent traits suggests there may be many functions of a community that are not predicted based on a priori knowledge of the community members. These types of studies will provide a more holistic understanding of microbial communities, allowing us to connect information about community composition with behaviors determined by interspecific interactions. These studies increase our ability to understand communities, such as the soil microbiome, plant-root microbiome, and human gut microbiome, with the final goal of being able to manipulate and rationally improve these communities.

Bacteria often live in complex communities in which they interact with other organisms. Consideration of the social environment of bacteria can reveal emergent traits and behaviors that would be overlooked by studying bacteria in isolation. Here we characterize a social trait which emerges upon interaction between the distantly related soil bacteria Pseudomonas fluorescens Pf0-1 and Pedobacter sp. strain V48. On hard agar, which is not permissive for motility of the monoculture of either species, coculture reveals an emergent phenotype that we term “interspecies social spreading,” where the mixed colony spreads across the hard surface. We show that initiation of social spreading requires close association between the two species of bacteria. Both species remain associated throughout the spreading colony, with reproducible and nonhomogenous patterns of distribution. The nutritional environment influences social spreading: no social behavior is observed under high-nutrient conditions, but low-nutrient conditions are insufficient to promote social spreading without high salt concentrations. This simple two-species consortium is a tractable model system that will facilitate mechanistic investigations of interspecies interactions and provide insight into emergent properties of interacting species. These studies will contribute to the broader knowledge of how bacterial interactions influence the functions of communities they inhabit.

IMPORTANCE The wealth of studies on microbial communities has revealed the complexity and dynamics of the composition of communities in many ecological settings. Fewer studies probe the functional interactions of the community members. Function of the community as a whole may not be fully revealed by characterizing the individuals. In our two-species model community, we find an emergent trait resulting from the interaction of the soil bacteria Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48. Observation of emergent traits suggests there may be many functions of a community that are not predicted based on a priori knowledge of the community members. These types of studies will provide a more holistic understanding of microbial communities, allowing us to connect information about community composition with behaviors determined by interspecific interactions. These studies increase our ability to understand communities, such as the soil microbiome, plant-root microbiome, and human gut microbiome, with the final goal of being able to manipulate and rationally improve these communities.

A statistical physics view of swarming bacteria

Bacterial swarming is a collective mode of motion in which cells migrate rapidly over surfaces, forming dynamic patterns of whirls and jets. This review presents a physical point of view of swarming bacteria, with an emphasis on the statistical properties of the swarm dynamics as observed in experiments. The basic physical principles underlying the swarm and their relation to contemporary theories of collective motion and active matter are reviewed and discussed in the context of the biological properties of swarming cells. We suggest a paradigm according to which bacteria have optimized some of their physical properties as a strategy for rapid surface translocation. In other words, cells take advantage of favorable physics, enabling efficient expansion that enhances survival under harsh conditions.

The propagation of active-passive interfaces in bacterial swarms

Propagating interfaces are ubiquitous in nature, underlying instabilities and pattern formation in biology and material science. Physical principles governing interface growth are well understood in passive settings; however, our understanding of interfaces in active systems is still in its infancy. Here, we study the evolution of an active-passive interface using a model active matter system, bacterial swarms. We use ultra-violet light exposure to create compact domains of passive bacteria within Serratia marcescens swarms, thereby creating interfaces separating motile and immotile cells. Post-exposure, the boundary re-shapes and erodes due to self-emergent collective flows. We demonstrate that the active-passive boundary acts as a diffuse interface with mechanical properties set by the flow. Intriguingly, interfacial velocity couples to local swarm speed and interface curvature, raising the possibility that an active analogue to classic Gibbs-Thomson-Stefan conditions may control this boundary propagation.

Cargo transport shapes the spatial organization of a microbial community

The human microbiome is an assemblage of diverse bacteria that interact with one another to form communities. Bacteria in a given community are arranged in a 3D matrix with many degrees of freedom. Snapshots of the community display well-defined structures, but the steps required for their assembly are not understood. Here, we show that this construction is carried out with the help of gliding bacteria. Gliding is defined as the motion of cells over a solid or semisolid surface without the necessity of growth or the aid of pili or flagella. Genomic analysis suggests that gliding bacteria are present in human microbial communities. We focus on Capnocytophaga gingivalis, which is present in abundance in the human oral microbiome. Tracking of fluorescently labeled single cells and of gas bubbles carried by fluid flow shows that swarms of C. gingivalis are layered, with cells in the upper layers moving more rapidly than those in the lower layers. Thus, cells also glide on top of one another. Cells of nonmotile bacterial species attach to the surface of C. gingivalis and are propelled as cargo. The cargo cell moves along the length of a C. gingivalis cell, looping from one pole to the other. Multicolor fluorescent spectral imaging of cells of different live but nonmotile bacterial species reveals their long-range transport in a polymicrobial community. A swarm of C. gingivalis transports some nonmotile bacterial species more efficiently than others and helps to shape the spatial organization of a polymicrobial community.

A Novel Microbial Culture Chamber Co-cultivation System to Study Algal-Bacteria Interactions Using Emiliania huxleyi and Phaeobacter inhibens as Model Organisms

Our understanding of microbial natural environments combines in situ experimentation with studies of specific interactions in laboratory-based setups. The purpose of this work was to develop, build and demonstrate the use of a microbial culture chamber enabling both in situ and laboratory-based studies. The design uses an enclosed chamber surrounded by two porous membranes that enables the comparison of growth of two separate microbial populations but allowing free exchange of small molecules. Initially, we tested if the presence of the macroalga Fucus vesiculosus inside the chamber affected colonization of the outer membranes by marine bacteria. The alga did indeed enrich the total population of colonizing bacteria by more than a factor of four. These findings lead us to investigate the effect of the presence of the coccolithophoric alga Emiliania huxleyi on attachment and biofilm formation of the marine bacterium Phaeobacter inhibens DSM17395. These organisms co-exist in the marine environment and have a well-characterized interdependence on secondary metabolites. P. inhibens attached in significantly higher numbers when having access to E. huxleyi as compared to when exposed to sterile media. The experiment was carried out using a wild type (wt) strain as well as a TDA-deficient strain of P. inhibens. The ability of the bacterium to produce the antibacterial compound, tropodithietic acid (TDA) influenced its attachment since the P. inhibens DSM17395 wt strain attached in higher numbers to a surface within the first 48 h of incubation with E. huxleyi as compared to a TDA-negative mutant. Whilst the attachment of the bacterium to a surface was facilitated by presence of the alga, however, we cannot conclude if this was directly affected by the algae or whether biofilm formation was dependent on the production of TDA by P. inhibens, which has been implied by previous studies. In the light of these results, other applications of immersed culture chambers are suggested.

Four domains: The fundamental unicell and Post-Darwinian Cognition-Based Evolution

Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication. Successive reiterations of the information cycle enact the informational architectures of the basic unicellular forms. From that base, inter-domain and cell-cell communications enable genetic and cellular variations through self-referential natural informational engineering and cellular niche construction. Holobionts are the exclusive endpoints of that self-referential cellular engineering as obligatory multicellular combinations of the essential Four Domains: Prokaryota, Archaea, Eukaryota and the Virome. Therefore, it is advocated that these Four Domains represent the perpetual object of the living circumstance rather than the visible macroorganic forms. In consequence, biology and its evolutionary development can be appraised as the continual defense of instantiated cellular self-reference. As the survival of cells is as dependent upon limitations and boundaries as upon any freedom of action, it is proposed that selection represents only one of many forms of cellular constraint that sustain self-referential integrity.

Novel Method Reveals a Narrow Phylogenetic Distribution of Bacterial Dispersers in Environmental Communities Exposed to Low-Hydration Conditions

In this study, we developed a method that provides profiles of community-level surface dispersal from environmental samples under controlled hydration conditions and enables us to isolate and uncover the diversity of the fastest bacterial dispersers. The method expands on the porous surface model (PSM), previously used to monitor the dispersal of individual bacterial strains in liquid films at the surface of a porous ceramic disc. The novel procedure targets complex communities and captures the dispersed bacteria on a solid medium for growth and detection. The method was first validated by distinguishing motile Pseudomonas putida and Flavobacterium johnsoniae strains from their nonmotile mutants. Applying the method to soil and lake water bacterial communities showed that community-scale dispersal declined as conditions became drier. However, for both communities, dispersal was detected even under low-hydration conditions (matric potential, -3.1 kPa) previously proven too dry for P. putida strain KT2440 motility. We were then able to specifically recover and characterize the fastest dispersers from the inoculated communities. For both soil and lake samples, 16S rRNA gene amplicon sequencing revealed that the fastest dispersers were substantially less diverse than the total communities. The dispersing fraction of the soil microbial community was dominated by Pseudomonas species cells, which increased in abundance under low-hydration conditions, while the dispersing fraction of the lake community was dominated by Aeromonas species cells and, under wet conditions (-0.5 kPa), also by Exiguobacterium species cells. The results gained in this study bring us a step closer to assessing the dispersal ability within complex communities under environmentally relevant conditions.IMPORTANCE Dispersal is a key process of bacterial community assembly, and yet, very few attempts have been made to assess bacterial dispersal at the community level, as the focus has previously been on pure-culture studies. A crucial factor for dispersal in habitats where hydration conditions vary, such as soils, is the thickness of the liquid films surrounding solid surfaces, but little is known about how the ability to disperse in such films varies within bacterial communities. Therefore, we developed a method to profile community dispersal and identify fast dispersers on a rough surface resembling soil surfaces. Our results suggest that within the motile fraction of a bacterial community, only a minority of the bacterial types are able to disperse in the thinnest liquid films. During dry periods, these efficient dispersers can gain a significant fitness advantage through their ability to colonize new habitats ahead of the rest of the community.

Modeling cooperating micro-organisms in antibiotic environment

Recent experiments with the bacteria Paenibacillus vortex reveal a remarkable strategy enabling it to cope with antibiotics by cooperating with a different bacterium—Escherichia coli. While P. vortex is a highly effective swarmer, it is sensitive to the antibiotic ampicillin. On the other hand, E. coli can degrade ampicillin but is non-motile when grown on high agar percentages. The two bacterial species form a shared colony in which E. coli is transported by P. vortex and E. coli detoxifies the ampicillin. The paper presents a simplified model, consisting of coupled reaction-diffusion equations, describing the development of ring patterns in the shared colony. Our results demonstrate some of the possible cooperative movement strategies bacteria utilize in order to survive harsh conditions. In addition, we explore the behavior of mixed colonies under new conditions such as antibiotic gradients, synchronization between colonies and possible dynamics of a 3-species system including P. vortex, E. coli and a carbon producing algae that provides nutrients under illuminated, nutrient poor conditions. The derived model was able to simulate an asymmetric relationship between two or three micro-organisms where cooperation is required for survival. Computationally, in order to avoid numerical artifacts due to symmetries within the discretizing grid, the model was solved using a second order Vectorizable Random Lattices method, which is developed as a finite volume scheme on a random grid.

Non-Equilibrium Assembly of Light-Activated Colloidal Mixtures

The collective phenomena exhibited by artificial active matter systems present novel routes to fabricating out-of-equilibrium microscale assemblies. Here, the crystallization of passive silica colloids into well-controlled 2D assemblies is shown, which is directed by a small number of self-propelled active colloids. The active colloids are titania-silica Janus particles that are propelled when illuminated by UV light. The strength of the attractive interaction and thus the extent of the assembled clusters can be regulated by the light intensity. A remarkably small number of the active colloids is sufficient to induce the assembly of the dynamic crystals. The approach produces rationally designed colloidal clusters and crystals with controllable sizes, shapes, and symmetries. This multicomponent active matter system offers the possibility of obtaining structures and assemblies that cannot be found in equilibrium systems.

Noncontact Cohesive Swimming of Bacteria in Two-Dimensional Liquid Films

Bacterial swimming in confined two-dimensional environments is ubiquitous in nature and in clinical settings. Characterizing individual interactions between swimming bacteria in 2D confinement will help to understand diverse microbial processes, such as bacterial swarming and biofilm formation. Here we report a novel motion pattern displayed by flagellated bacteria in 2D confinement: When two nearby cells align their moving directions, they tend to engage in cohesive swimming without direct cell body contact, as a result of hydrodynamic interaction but not flagellar intertwining. We further found that cells in cohesive swimming move with higher directional persistence, which can increase the effective diffusivity of cells by ∼3 times as predicted by computational modeling. As a conserved behavior for peritrichously flagellated bacteria, cohesive swimming in 2D confinement may be key to collective motion and self-organization in bacterial swarms; it may also promote bacterial dispersal in unsaturated soils and in interstitial space during infections.

Elements of biological oscillations in time and space

Oscillations in time and space are ubiquitous in nature and play critical roles in dynamic cellular processes. Although the molecular mechanisms underlying the generation of the dynamics are diverse, several distinct regulatory elements have been recognized as being critical in producing and modulating oscillatory dynamics. These include negative and positive feedback, time delay, nonlinearity in regulation, and random fluctuations ('noise'). Here we discuss the specific roles of these five elements in promoting or attenuating oscillatory dynamics, by drawing on insights from quantitative analyses of natural or synthetic biological networks.

Swimming bacteria promote dispersal of non-motile staphylococcal species

Swimming motility is considered a beneficial trait among bacterial species as it enables movement across fluid environments and augments invasion of tissues within the host. However, non-swimming bacteria also flourish in fluid habitats, but how they effectively spread and colonize distant ecological niches remains unclear. We show that non-motile staphylococci can gain motility by hitchhiking on swimming bacteria, leading to extended and directed motion with increased velocity. This phoretic interaction was observed between Staphylococcus aureus and Pseudomonas aeruginosa, Staphylococcus epidermidis and P. aeruginosa, as well as S. aureus and Escherichia coli, suggesting hitchhiking as a general translocation mechanism for non-motile staphylococcal species. By leveraging the motility of swimming bacteria, it was observed that staphylococci can colonize new niches that are less available in the absence of swimming carriers. This work highlights the importance of considering interactions between species within polymicrobial communities, in which bacteria can utilize each other as resources.

Antibiotic stress selects against cooperation in the pathogenic bacterium Pseudomonas aeruginosa

Cheats are a pervasive threat to public goods production in natural and human communities, as they benefit from the commons without contributing to it. Although ecological antagonisms such as predation, parasitism, competition, and abiotic environmental stress play key roles in shaping population biology, it is unknown how such stresses generally affect the ability of cheats to undermine cooperation. We used theory and experiments to address this question in the pathogenic bacterium, Pseudomonas aeruginosa Although public goods producers were selected against in all populations, our competition experiments showed that antibiotics significantly increased the advantage of nonproducers. Moreover, the dominance of nonproducers in mixed cultures was associated with higher resistance to antibiotics than in either monoculture. Mathematical modeling indicates that accentuated costs to producer phenotypes underlie the observed patterns. Mathematical analysis further shows how these patterns should generalize to other taxa with public goods behaviors. Our findings suggest that explaining the maintenance of cooperative public goods behaviors in certain natural systems will be more challenging than previously thought. Our results also have specific implications for the control of pathogenic bacteria using antibiotics and for understanding natural bacterial ecosystems, where subinhibitory concentrations of antimicrobials frequently occur.