Division of Labor, Bet Hedging, and the Evolution of Mixed Biofilm Investment Strategies

Intrinsic antimicrobial resistance: Molecular biomaterials to combat microbial biofilms and bacterial persisters

The escalating rise in antimicrobial resistance (AMR) coupled with a declining arsenal of new antibiotics is imposing serious threats to global public health. A pervasive aspect of many acquired AMR infections is that the pathogenic microorganisms exist as biofilms, which are equipped with superior survival strategies. In addition, persistent and recalcitrant infections are seeded with bacterial persister cells at infection sites. Together, conventional antibiotic therapeutics often fail in the complete treatment of infections associated with bacterial persisters and biofilms. Novel therapeutics have been attempted to tackle AMR, biofilms, and persister-associated complex infections. This review focuses on the progress in designing molecular biomaterials and therapeutics to address acquired and intrinsic AMR, and the fundamental microbiology behind biofilms and persisters. Starting with a brief introduction of AMR basics and approaches to tackling acquired AMR, the emphasis is placed on various biomaterial approaches to combating intrinsic AMR, including (1) semi-synthetic antibiotics; (2) macromolecular or polymeric biomaterials mimicking antimicrobial peptides; (3) adjuvant effects in synergy; (4) nano-therapeutics; (5) nitric oxide-releasing antimicrobials; (6) antimicrobial hydrogels; (7) antimicrobial coatings. Particularly, the structure-activity relationship is elucidated in each category of these biomaterials. Finally, illuminating perspectives are provided for the future design of molecular biomaterials to bypass AMR and cure chronic multi-drug resistant (MDR) infections.

Insights on Pseudomonas aeruginosa Carbohydrate Binding from Profiles of Cystic Fibrosis Isolates Using Multivalent Fluorescent Glycopolymers Bearing Pendant Monosaccharides

Pseudomonas aeruginosa contributes to frequent, persistent, and, often, polymicrobial respiratory tract infections for individuals with cystic fibrosis (CF). Chronic CF infections lead to bronchiectasis and a shortened lifespan. P. aeruginosa expresses numerous adhesins, including lectins known to bind the epithelial cell and mucin glycoconjugates. Blocking carbohydrate-mediated host-pathogen and intra-biofilm interactions critical to the initiation and perpetuation of colonization offer promise as anti-infective treatment strategies. To inform anti-adhesion therapies, we profiled the monosaccharide binding of P. aeruginosa from CF and non-CF sources, and assessed whether specific bacterial phenotypic characteristics affected carbohydrate-binding patterns. Focusing at the cellular level, microscopic and spectrofluorometric tools permitted the solution-phase analysis of P. aeruginosa binding to a panel of fluorescent glycopolymers possessing distinct pendant monosaccharides. All P. aeruginosa demonstrated significant binding to glycopolymers specific for α-D-galactose, β-D-N-acetylgalactosamine, and β-D-galactose-3-sulfate. In each culture, a small subpopulation accounted for the binding. The carbohydrate anomeric configuration and sulfate ester presence markedly influenced binding. While this opportunistic pathogen from CF hosts presented with various colony morphologies and physiological activities, no phenotypic, physiological, or structural feature predicted enhanced or diminished monosaccharide binding. Important to anti-adhesive therapeutic strategies, these findings suggest that, regardless of phenotype or clinical source, P. aeruginosa maintain a small subpopulation that may readily associate with specific configurations of specific monosaccharides. This report provides insights into whole-cell P. aeruginosa carbohydrate-binding profiles and into the context within which successful anti-adhesive and/or anti-virulence anti-infective agents for CF must contend.

Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation during extreme cycles of feast and famine

Microbes are evolutionarily robust organisms capable of rapid adaptation to complex stress, which enables them to colonize harsh environments. In nature, microbes are regularly challenged by starvation, which is a particularly complex stress because resource limitation often co-occurs with changes in pH, osmolarity, and toxin accumulation created by metabolic waste. Often overlooked are the additional complications introduced by eventual resource replenishment, as successful microbes must withstand rapid environmental shifts before swiftly capitalizing on replenished resources to avoid invasion by competing species. To understand how microbes navigate trade-offs between growth and survival, ultimately adapting to thrive in environments with extreme fluctuations, we experimentally evolved 16 Escherichia coli populations for 900 days in repeated feast/famine conditions with cycles of 100-day starvation before resource replenishment. Using longitudinal population-genomic analysis, we found that evolution in response to extreme feast/famine is characterized by narrow adaptive trajectories with high mutational parallelism and notable mutational order. Genetic reconstructions reveal that early mutations result in trade-offs for biofilm and motility but trade-ups for growth and survival, as these mutations conferred positively correlated advantages during both short-term and long-term culture. Our results demonstrate how microbes can navigate the adaptive landscapes of regularly fluctuating conditions and ultimately follow mutational trajectories that confer benefits across diverse environments.

Metaphors as design tools for microbial consortia: An analysis of recent peer-reviewed literature

Single engineered microbial species cannot always conduct complex transformations, while complex, incompletely defined microbial consortia have heretofore been suited to a limited range of tasks. As biodesigners bridge this gap with intentionally designed microbial communities, they will, intentionally or otherwise, build communities that embody particular ideas about what microbial communities can and should be. Here, we suggest that metaphors-ideas about what microbial communities are like-are therefore important tools for designing synthetic consortia-based bioreactors. We identify a range of metaphors currently employed in peer-reviewed microbiome research articles, characterizing each through its potential structural implications and distinctive imagery. We present this metaphor catalogue in the interest of, first, making metaphors visible as design choices, second, enabling deliberate experimentation with them towards expanding the potential design space of the field, and third, encouraging reflection on the goals and values they embed.

Opportunities in optical and electrical single-cell technologies to study microbial ecosystems

New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.

A genetic switch controls Pseudomonas aeruginosa surface colonization

Efficient colonization of mucosal surfaces is essential for opportunistic pathogens like Pseudomonas aeruginosa, but how bacteria collectively and individually adapt to optimize adherence, virulence and dispersal is largely unclear. Here we identified a stochastic genetic switch, hecR-hecE, which is expressed bimodally and generates functionally distinct bacterial subpopulations to balance P. aeruginosa growth and dispersal on surfaces. HecE inhibits the phosphodiesterase BifA and stimulates the diguanylate cyclase WspR to increase c-di-GMP second messenger levels and promote surface colonization in a subpopulation of cells; low-level HecE-expressing cells disperse. The fraction of HecE+ cells is tuned by different stress factors and determines the balance between biofilm formation and long-range cell dispersal of surface-grown communities. We also demonstrate that the HecE pathway represents a druggable target to effectively counter P. aeruginosa surface colonization. Exposing such binary states opens up new ways to control mucosal infections by a major human pathogen.

A cryptic transcription factor regulates Caulobacter adhesin development

Alphaproteobacteria commonly produce an adhesin that is anchored to the exterior of the envelope at one cell pole. In Caulobacter crescentus this adhesin, known as the holdfast, facilitates attachment to solid surfaces and cell partitioning to air-liquid interfaces. An ensemble of two-component signal transduction (TCS) proteins controls C. crescentus holdfast biogenesis by indirectly regulating expression of HfiA, a potent inhibitor of holdfast synthesis. We performed a genetic selection to discover direct hfiA regulators that function downstream of the adhesion TCS system and identified rtrC, a hypothetical gene. rtrC transcription is directly activated by the adhesion TCS regulator, SpdR. Though its primary structure bears no resemblance to any defined protein family, RtrC binds and regulates dozens of sites on the C. crescentus chromosome via a pseudo-palindromic sequence. Among these binding sites is the hfiA promoter, where RtrC functions to directly repress transcription and thereby activate holdfast development. Either RtrC or SpdR can directly activate transcription of a second hfiA repressor, rtrB. Thus, environmental regulation of hfiA transcription by the adhesion TCS system is subject to control by an OR-gated type I coherent feedforward loop; these regulatory motifs are known to buffer gene expression against fluctuations in regulating signals. We have further assessed the functional role of rtrC in holdfast-dependent processes, including surface adherence to a cellulosic substrate and formation of pellicle biofilms at air-liquid interfaces. Strains harboring insertional mutations in rtrC have a diminished adhesion profile in a competitive cheesecloth binding assay and a reduced capacity to colonize pellicle biofilms in select media conditions. Our results add to an emerging understanding of the regulatory topology and molecular components of a complex bacterial cell adhesion control system.

Bet-hedging in innate and adaptive immune systems

Immune system evolution is shaped by the fitness costs and trade-offs associated with mounting an immune response. Costs that arise mainly as a function of the magnitude of investment, including energetic and immunopathological costs, are well-represented in studies of immune system evolution. Less well considered, however, are the costs of immune cell plasticity and specialization. Hosts in nature encounter a large diversity of microbes and parasites that require different and sometimes conflicting immune mechanisms for defense, but it takes precious time to recognize and correctly integrate signals for an effective polarized response. In this perspective, we propose that bet-hedging can be a viable alternative to plasticity in immune cell effector function, discuss conditions under which bet-hedging is likely to be an advantageous strategy for different arms of the immune system, and present cases from both innate and adaptive immune systems that suggest bet-hedging at play.

Challenges and opportunities for cheat therapy in the control of bacterial infections

Covering: 1999 to 2021Bacterial pathogens can be highly social, communicating and cooperating within multi-cellular groups to make us sick. The requirement for collective action in pathogens presents novel therapeutic avenues that seek to undermine cooperative behavior, what we call here 'cheat therapies'. We review two broad avenues of cheat therapy: first, the introduction of genetically engineered 'cheat' strains (bio-control cheats), and second the chemical induction of 'cheat' behavior in the infecting pathogens (chemical-control cheats). Both genetically engineered and chemically induced cheats can socially exploit the cooperative wildtype infection, reducing pathogen burden and the severity of disease. We review the costs and benefits of cheat therapies, highlighting advantages of evolutionary robustness and also the challenges of low to moderate efficacy, compared to conventional antibiotic treatments. We end with a summary of what we see as the most valuable next steps, focusing on adjuvant treatments and use as alternate therapies for mild, self-resolving infections - allowing the reservation of current and highly effective antibiotics for more critical patient needs.

Structured environments foster competitor coexistence by manipulating interspecies interfaces

Natural environments, like soils or the mammalian gut, frequently contain microbial consortia competing within a niche, wherein many species contain genetically encoded mechanisms of interspecies competition. Recent computational work suggests that physical structures in the environment can stabilize local competition between species that would otherwise be subject to competitive exclusion under isotropic conditions. Here we employ Lotka-Volterra models to show that interfacial competition localizes to physical structures, stabilizing competitive ecological networks of many species, even with significant differences in the strength of competitive interactions between species. Within a limited range of parameter space, we show that for stable communities the length-scale of physical structure inversely correlates with the width of the distribution of competitive fitness, such that physical environments with finer structure can sustain a broader spectrum of interspecific competition. These results highlight the potentially stabilizing effects of physical structure on microbial communities and lay groundwork for engineering structures that stabilize and/or select for diverse communities of ecological, medical, or industrial utility.

Raman Spectroscopy-Based Measurements of Single-Cell Phenotypic Diversity in Microbial Populations

Microbial cells that live in the same community can exist in different physiological and morphological states that change as a function of spatiotemporal variations in environmental conditions. This phenomenon is commonly known as phenotypic heterogeneity and/or diversity. Measuring this plethora of cellular expressions is needed to better understand and manage microbial processes. However, most tools to study phenotypic diversity only average the behavior of the sampled community. In this work, we present a way to quantify the phenotypic diversity of microbial samples by inferring the (bio)molecular profile of its constituent cells using Raman spectroscopy. We demonstrate how this tool can be used to quantify the phenotypic diversity that arises after the exposure of microbes to stress. Raman spectroscopy holds potential for the detection of stressed cells in bioproduction.

Microbial cells experience physiological changes due to environmental change, such as pH and temperature, the release of bactericidal agents, or nutrient limitation. This has been shown to affect community assembly and physiological processes (e.g., stress tolerance, virulence, or cellular metabolic activity). Metabolic stress is typically quantified by measuring community phenotypic properties such as biomass growth, reactive oxygen species, or cell permeability. However, bulk community measurements do not take into account single-cell phenotypic diversity, which is important for a better understanding and the subsequent management of microbial populations. Raman spectroscopy is a nondestructive alternative that provides detailed information on the biochemical makeup of each individual cell. Here, we introduce a method for describing single-cell phenotypic diversity using the Hill diversity framework of Raman spectra. Using the biomolecular profile of individual cells, we obtained a metric to compare cellular states and used it to study stress-induced changes. First, in two Escherichia coli populations either treated with ethanol or nontreated and then in two Saccharomyces cerevisiae subpopulations with either high or low expression of a stress reporter. In both cases, we were able to quantify single-cell phenotypic diversity and to discriminate metabolically stressed cells using a clustering algorithm. We also described how the lipid, protein, and nucleic acid compositions changed after the exposure to the stressor using information from the Raman spectra. Our results show that Raman spectroscopy delivers the necessary resolution to quantify phenotypic diversity within individual cells and that this information can be used to study stress-driven metabolic diversity in microbial populations.

IMPORTANCE Microbial cells that live in the same community can exist in different physiological and morphological states that change as a function of spatiotemporal variations in environmental conditions. This phenomenon is commonly known as phenotypic heterogeneity and/or diversity. Measuring this plethora of cellular expressions is needed to better understand and manage microbial processes. However, most tools to study phenotypic diversity only average the behavior of the sampled community. In this work, we present a way to quantify the phenotypic diversity of microbial samples by inferring the (bio)molecular profile of its constituent cells using Raman spectroscopy. We demonstrate how this tool can be used to quantify the phenotypic diversity that arises after the exposure of microbes to stress. Raman spectroscopy holds potential for the detection of stressed cells in bioproduction.

Phenotypic Parallelism during Experimental Adaptation of a Free-Living Bacterium to the Zebrafish Gut

Although animals encounter many bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. We used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association.

Although animals encounter a plethora of bacterial species throughout their lives, only a subset colonize vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. However, our understanding of how bacteria initiate symbioses with animal hosts remains underexplored, and this process is central to the assembly and function of gut bacterial communities. Therefore, we used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host by serially passaging replicate populations of Shewanella oneidensis through the intestines of larval zebrafish (Danio rerio). After approximately 200 bacterial generations, isolates from evolved populations improved their ability to colonize larval zebrafish during competition against their unpassaged ancestor. Genome sequencing revealed unique sets of mutations in the two evolved isolates exhibiting the highest mean competitive fitness. One isolate exhibited increased swimming motility and decreased biofilm formation compared to the ancestor, and we identified a missense mutation in the mannose-sensitive hemagglutinin pilus operon that is sufficient to increase fitness and reproduce these phenotypes. The second isolate exhibited enhanced swimming motility but unchanged biofilm formation, and here the genetic basis for adaptation is less clear. These parallel enhancements in motility and fitness resemble the behavior of a closely related Shewanella strain previously isolated from larval zebrafish and suggest phenotypic convergence with this isolate. Our results demonstrate that adaptation to the zebrafish gut is complex, with multiple evolutionary pathways capable of improving colonization, but that motility plays an important role during the onset of host association.

In silico bacteria evolve robust cooperaion via complex quorum-sensing strategies

Many species of bacteria collectively sense and respond to their social and physical environment via 'quorum sensing' (QS), a communication system controlling extracellular cooperative traits. Despite detailed understanding of the mechanisms of signal production and response, there remains considerable debate over the functional role(s) of QS: in short, what is it for? Experimental studies have found support for diverse functional roles: density sensing, mass-transfer sensing, genotype sensing, etc. While consistent with theory, these results cannot separate whether these functions were drivers of QS adaption, or simply artifacts or 'spandrels' of systems shaped by distinct ecological pressures. The challenge of separating spandrels from drivers of adaptation is particularly hard to address using extant bacterial species with poorly understood current ecologies (let alone their ecological histories). To understand the relationship between defined ecological challenges and trajectories of QS evolution, we used an agent-based simulation modeling approach. Given genetic mixing, our simulations produce behaviors that recapitulate features of diverse microbial QS systems, including coercive (high signal/low response) and generalized reciprocity (signal auto-regulation) strategists - that separately and in combination contribute to QS-dependent resilience of QS-controlled cooperation in the face of diverse cheats. We contrast our in silico results given defined ecological challenges with bacterial QS architectures that have evolved under largely unknown ecological contexts, highlighting the critical role of genetic constraints in shaping the shorter term (experimental evolution) dynamics of QS. More broadly, we see experimental evolution of digital organisms as a complementary tool in the search to understand the emergence of complex QS architectures and functions.

Small-Scale Heterogeneity in Drinking Water Biofilms

Biofilm heterogeneity has been characterized on various scales for both natural and engineered ecosystems. This heterogeneity has been attributed to spatial differences in environmental factors. Understanding their impact on localized biofilm heterogeneity in building plumbing systems is important for both management and representative sampling strategies. We assessed heterogeneity within the confined engineered ecosystem of a shower hose by high-resolution sampling (200 individual biofilm sections per hose) on varying scales (μm to m). We postulated that a biofilm grown on a single material under uniform conditions should be homogeneous in its structure, bacterial numbers, and community composition. A biofilm grown for 12 months under controlled laboratory conditions, showed homogeneity on large-scale. However, some small-scale heterogeneity was clearly observed. For example, biofilm thickness of cm-sections varied up to 4-fold, total cell concentrations (TCC) 3-fold, and relative abundance of dominant taxa up to 5-fold. A biofilm grown under real (i.e., uncontrolled) use conditions developed considerably more heterogeneity in all variables which was attributed to more discontinuity in environmental conditions. Interestingly, biofilm communities from both hoses showed comparably low diversity, with <400 taxa each, and only three taxa accounting for 57%, respectively, 73% of the community. This low diversity was attributed to a strong selective pressure, originating in migrating carbon from the flexible hoses as major carbon source. High-resolution sampling strategy enabled detailed analysis of spatial heterogeneity within an individual drinking water biofilm. This study gives insight into biofilm structure and community composition on cm-to m-scale and is useful for decision-making on sampling strategies in biofilm research and monitoring.

Multicellular behaviour enables cooperation in microbial cell aggregates

Oligosaccharides produced from the extracellular hydrolysis of biological materials can act as common goods that promote cooperative growth in microbial populations, whereby cell–cell aggregation increases both the per capita availability of resources and the per-cell growth rate. However, aggregation can also have detrimental consequences for growth, as gradients form within aggregates limiting the resource accessibility. We built a computational model, which predicts cooperation is restricted in dense cell aggregates larger than 10 µm because of the emergence of polymer and oligomer counter gradients. We compared these predictions to experiments performed with two well-studied alginate-degrading strains of Vibrio splendidus, which varied in their ability to secrete alginate lyase. We observed that both strains can form large aggregates (less than 50 µm), overcoming diffusion limitation by rearranging their internal structure. The stronger enzyme producer grew non-cooperatively and formed aggregates with internal channels that allowed exchange between the bulk environment and the aggregate, whereas the weak enzyme producer showed strongly cooperative growth and formed dense aggregates in which cells near the core mixed by active swimming. Our simulations suggest that the mixing and channelling reduce diffusion limitation and allow cells to uniformly grow in aggregates. Together, these data demonstrate that bacterial behaviour can help overcome competition imposed by resource gradients within cell aggregates.

This article is part of a discussion meeting issue ‘Single cell ecology’.

Trade-offs between gene expression, growth and phenotypic diversity in microbial populations

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Limitations in molecular resources for gene expression influence bacterial physiology.

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Bacteria optimise trade-offs between resource allocation and growth.

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Resource allocation plays a role in the emergence of phenotypic heterogeneity.

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Trade-offs between bet-hedging and growth can be harnessed in biotechnology.

Bacterial cells have a limited number of resources that can be allocated for gene expression. The intracellular competition for these resources has an impact on the cell physiology. Bacteria have evolved mechanisms to optimize resource allocation in a variety of scenarios, showing a trade-off between the resources used to maximise growth (e.g. ribosome synthesis) and the rest of cellular functions. Limitations in gene expression also play a role in generating phenotypic diversity, which is advantageous in fluctuating environments, at the expenses of decreasing growth rates. Our current understanding of these trade-offs can be exploited for biotechnological applications benefiting from the selective manipulation of the allocation of resources.

Heterogeneity in surface sensing suggests a division of labor in Pseudomonas aeruginosa populations

The second messenger signaling molecule cyclic diguanylate monophosphate (c-di-GMP) drives the transition between planktonic and biofilm growth in many bacterial species. Pseudomonas aeruginosa has two surface sensing systems that produce c-di-GMP in response to surface adherence. Current thinking in the field is that once cells attach to a surface, they uniformly respond by producing c-di-GMP. Here, we describe how the Wsp system generates heterogeneity in surface sensing, resulting in two physiologically distinct subpopulations of cells. One subpopulation has elevated c-di-GMP and produces biofilm matrix, serving as the founders of initial microcolonies. The other subpopulation has low c-di-GMP and engages in surface motility, allowing for exploration of the surface. We also show that this heterogeneity strongly correlates to surface behavior for descendent cells. Together, our results suggest that after surface attachment, P. aeruginosa engages in a division of labor that persists across generations, accelerating early biofilm formation and surface exploration.

Phenotypic Heterogeneity in Bacterial Quorum Sensing Systems

Quorum sensing is usually thought of as a collective behavior in which all members of a population partake. However, over the last decade, several reports of phenotypic heterogeneity in quorum sensing-related gene expression have been put forward, thus challenging this view. In the respective systems, cells of isogenic populations did not contribute equally to autoinducer production or target gene activation, and in some cases, the fraction of contributing cells was modulated by environmental factors. Here, we look into potential origins of these incidences and into how initial cell-to-cell variations might be amplified to establish distinct phenotypic heterogeneity. We furthermore discuss potential functions heterogeneity in bacterial quorum sensing systems could serve: as a preparation for environmental fluctuations (bet hedging), as a more cost-effective way of producing public goods (division of labor), as a loophole for genotypic cooperators when faced with non-contributing mutants (cheat protection), or simply as a means to fine-tune the output of the population as a whole (output modulation). We illustrate certain aspects of these recent developments with the model organisms Sinorhizobium meliloti, Sinorhizobium fredii and Bacillus subtilis, which possess quorum sensing systems of different complexity, but all show phenotypic heterogeneity therein.

The Many Facets of the Small Non-coding RNA RsaE (RoxS) in Metabolic Niche Adaptation of Gram-Positive Bacteria

Small regulatory RNAs (sRNAs) are increasingly recognized as players in the complex regulatory networks governing bacterial gene expression. RsaE (synonym RoxS) is an sRNA that is highly conserved in bacteria of the Bacillales order. Recent analyses in Bacillus subtilis, Staphylococcus aureus and Staphylococcus epidermidis identified RsaE/RoxS as a potent riboregulator of central carbon metabolism and energy balance with many molecular RsaE/RoxS functions and targets being shared across species. Similarities and species-specific differences in cellular processes modulated by RsaE/RoxS suggest that this sRNA plays a prominent role in the adaptation of Gram-positive bacteria to niches with varying nutrient availabilities and environmental cues. This review summarizes recent findings on the molecular function of RsaE/RoxS and its interaction with mRNA targets. Special emphasis will be on the integration of RsaE/RoxS into metabolic regulatory circuits and, derived from this, the role of RsaE/RoxS as a putative driver to generate phenotypic heterogeneity in bacterial populations. In this respect, we will particularly discuss heterogeneous RsaE expression in S. epidermidis biofilms and its possible contribution to metabolic niche diversification, programmed bacterial lysis and biofilm matrix production.

The small non-coding RNA RsaE influences extracellular matrix composition in Staphylococcus epidermidis biofilm communities

RsaE is a conserved small regulatory RNA (sRNA) which was previously reported to represent a riboregulator of central carbon flow and other metabolic pathways in Staphylococcus aureus and Bacillus subtilis. Here we show that RsaE contributes to extracellular (e)DNA release and biofilm-matrix switching towards polysaccharide intercellular adhesin (PIA) production in a hypervariable Staphylococcus epidermidis isolate. Transcriptome analysis through differential RNA sequencing (dRNA-seq) in combination with confocal laser scanning microscopy (CLSM) and reporter gene fusions demonstrate that S. epidermidis protein- and PIA-biofilm matrix producers differ with respect to RsaE and metabolic gene expression. RsaE is spatiotemporally expressed within S. epidermidis PIA-mediated biofilms, and its overexpression triggers a PIA biofilm phenotype as well as eDNA release in an S. epidermidis protein biofilm matrix-producing strain background. dRNA-seq and Northern blot analyses revealed RsaE to exist as a major full-length 100-nt transcript and a minor processed species lacking approximately 20 nucleotides at the 5'-end. RsaE processing results in expansion of the mRNA target spectrum. Thus, full-length RsaE interacts with S. epidermidis antiholin-encoding lrgA mRNA, facilitating bacterial lysis and eDNA release. Processed RsaE, however, interacts with the 5'-UTR of icaR and sucCD mRNAs, encoding the icaADBC biofilm operon repressor IcaR and succinyl-CoA synthetase of the tricarboxylic acid (TCA) cycle, respectively. RsaE augments PIA-mediated biofilm matrix production, most likely through activation of icaADBC operon expression via repression of icaR as well as by TCA cycle inhibition and re-programming of staphylococcal central carbon metabolism towards PIA precursor synthesis. Additionally, RsaE supports biofilm formation by mediating the release of eDNA as stabilizing biofilm matrix component. As RsaE itself is heterogeneously expressed within biofilms, we consider this sRNA to function as a factor favoring phenotypic heterogeneity and supporting division of labor in S. epidermidis biofilm communities.

Bacterial biofilms are highly organized structures which functionally emulate multicellular organisms, last but not least through heterogeneous gene expression patterns displayed by biofilm subpopulations. Here we analyzed the functions of the non-coding RNA RsaE in Staphylococcus epidermidis biofilm communities. RsaE exerted unexpected influences on S. epidermidis biofilm matrix composition by triggering localized eDNA release and facilitating PIA expression. RsaE accomplishes these effects by targeting mRNAs involved in bacterial lysis control, icaADBC expression and TCA cycle activity, with RsaE undergoing processing to exploit its full target potential. Interestingly, RsaE interaction with lysis-engaged lrgA mRNA is specific for S. epidermidis lrgA, but does not occur with lrgA mRNA from S. aureus, suggesting species-specific differences in staphylococcal lysis control. We speculate that RsaE-mediated bacterial lysis might represent a form of bacterial altruism contributing to biofilm structuring by providing nutrients to neighboring bacterial cells as well as by releasing eDNA as stabilizing biofilm matrix component. Due to its heterogeneous expression, we consider RsaE as a supporting factor that facilitates population diversity. Together, the data give insight into an unanticipated role of sRNAs as players in S. epidermidis biofilm organization.

Bacterial surface colonization, preferential attachment and fitness under periodic stress

Early bacterial surface colonization is not a random process wherein cells arbitrarily attach to surfaces and grow; but rather, attachment events, movement and cellular interactions induce non-random spatial organization. We have only begun to understand how the apparent self-organization affects the fitness of the population. A key factor contributing to fitness is the tradeoff between solitary-planktonic and aggregated surface-attached biofilm lifestyles. Though planktonic cells typically grow faster, bacteria in aggregates are more resistant to stress such as desiccation, antibiotics and predation. Here we ask if and to what extent informed surface-attachments improve fitness during early surface colonization under periodic stress conditions. We use an individual-based modeling approach to simulate foraging planktonic cells colonizing a surface under alternating wet-dry cycles. Such cycles are common in the largest terrestrial microbial habitats–soil, roots, and leaf surfaces–that are not constantly saturated with water and experience daily periods of desiccation stress. We compared different surface-attachment strategies, and analyzed the emerging spatio-temporal dynamics of surface colonization and population yield as a measure of fitness. We demonstrate that a simple strategy of preferential attachment (PA), biased to dense sites, carries a large fitness advantage over any random attachment across a broad range of environmental conditions–particularly under periodic stress.

A vast portion of bacterial life on Earth takes place on surfaces. In many of these surfaces cells collectively organize into biofilms that are known to provide them protection from various environmental stresses. Early bacterial colonization of surfaces, prior to the development of mature biofilm, is a critical stage during which cells attempt to establish a sustainable population. It is not a random process wherein cells arbitrarily attach to surfaces and grow to form micro-colonies. Rather, surface-attachments, movement and cellular interactions take place to yield non-random organization. Using computer simulations, based on individual-based modeling, we demonstrate that simple attachment strategies, where planktonic cells preferentially attach to existing surface-attached aggregates, may confer fitness advantage over random attachment. The advantage of preferential attachment is particularly substantial under periodic stress–a common characteristic of many natural microbial habitats. This is due to a more efficient recruitment of planktonic cells that accelerates the formation of stress-protected aggregates.

Structured environments fundamentally alter dynamics and stability of ecological communities

The dynamics and stability of ecological communities are intimately linked with the specific interactions-like cooperation or predation-between constituent species. In microbial communities, like those found in soils or the mammalian gut, physical anisotropies produced by fluid flow and chemical gradients impact community structure and ecological dynamics, even in structurally isotropic environments. Although natural communities existing in physically unstructured environments are rare, the role of environmental structure in determining community dynamics and stability remains poorly studied. To address this gap, we used modified Lotka-Volterra simulations of competitive microbial communities to characterize the effects of surface structure on community dynamics. We find that environmental structure has profound effects on communities, in a manner dependent on the specific pattern of interactions between community members. For two mutually competing species, eventual extinction of one competitor is effectively guaranteed in isotropic environments. However, addition of environmental structure enables long-term coexistence of both species via local "pinning" of competition interfaces, even when one species has a significant competitive advantage. In contrast, while three species competing in an intransitive loop (as in a game of rock-paper-scissors) coexist stably in isotropic environments, structural anisotropy disrupts the spatial patterns on which coexistence depends, causing chaotic population fluctuations and subsequent extinction cascades. These results indicate that the stability of microbial communities strongly depends on the structural environment in which they reside. Therefore, a more complete ecological understanding, including effective manipulation and interventions in natural communities of interest, must account for the physical structure of the environment.

Collapse of genetic division of labour and evolution of autonomy in pellicle biofilms

Closely related microorganisms often cooperate, but the prevalence and stability of cooperation between different genotypes remain debatable. Here, we track the evolution of pellicle biofilms formed through genetic division of labour and ask whether partially deficient partners can evolve autonomy. Pellicles of Bacillus subtilis rely on an extracellular matrix composed of exopolysaccharide (EPS) and the fibre protein TasA. In monocultures, ∆eps and ∆tasA mutants fail to form pellicles, but, facilitated by cooperation, they succeed in co-culture. Interestingly, cooperation collapses on an evolutionary timescale and ∆tasA gradually outcompetes its partner ∆eps. Pellicle formation can evolve independently from division of labour in ∆eps and ∆tasA monocultures, by selection acting on the residual matrix component, TasA or EPS, respectively. Using a set of interdisciplinary tools, we unravel that the TasA producer (∆eps) evolves via an unconventional but reproducible substitution in TasA that modulates the biochemical properties of the protein. Conversely, the EPS producer (ΔtasA) undergoes genetically variable adaptations, all leading to enhanced EPS secretion and biofilms with different biomechanical properties. Finally, we revisit the collapse of division of labour between Δeps and ΔtasA in light of a strong frequency versus exploitability trade-off that manifested in the solitarily evolving partners. We propose that such trade-off differences may represent an additional barrier to evolution of division of labour between genetically distinct microorganisms.

Parallel genetic adaptation across environments differing in mode of growth or resource availability

Evolution experiments have demonstrated high levels of genetic parallelism between populations evolving in identical environments. However, natural populations evolve in complex environments that can vary in many ways, likely sharing some characteristics but not others. Here, we ask whether shared selection pressures drive parallel evolution across distinct environments. We addressed this question in experimentally evolved populations founded from a clone of the bacterium Burkholderia cenocepacia. These populations evolved for 90 days (approximately 600 generations) under all combinations of high or low carbon availability and selection for either planktonic or biofilm modes of growth. Populations that evolved in environments with shared selection pressures (either level of carbon availability or mode of growth) were more genetically similar to each other than populations from environments that shared neither characteristic. However, not all shared selection pressures led to parallel evolution. Genetic parallelism between low-carbon biofilm and low-carbon planktonic populations was very low despite shared selection for growth under low-carbon conditions, suggesting that evolution in low-carbon environments may generate stronger trade-offs between biofilm and planktonic modes of growth. For all environments, a population's fitness in a particular environment was positively correlated with the genetic similarity between that population and the populations that evolved in that particular environment. Although genetic similarity was low between low-carbon environments, overall, evolution in similar environments led to higher levels of genetic parallelism and that genetic parallelism, in turn, was correlated with fitness in a particular environment.

Complex microbial systems across different levels of description

Complex biological systems offer a variety of interesting phenomena at the different physical scales. With increasing abstraction, details of the microscopic scales can often be extrapolated to average or typical macroscopic properties. However, emergent properties and cross-scale interactions can impede naïve abstractions and necessitate comprehensive investigations of these complex systems. In this review paper, we focus on microbial communities, and first, summarize a general hierarchy of relevant scales and description levels to understand these complex systems: (1) genetic networks, (2) single cells, (3) populations, and (4) emergent multi-cellular properties. Second, we employ two illustrating examples, microbial competition and biofilm formation, to elucidate how cross-scale interactions and emergent properties enrich the observed multi-cellular behavior in these systems. Finally, we conclude with pointing out the necessity of multi-scale investigations to understand complex biological systems and discuss recent investigations.

Altruism in a volatile world

The evolution of altruism-costly self-sacrifice in the service of others-has puzzled biologists since The Origin of Species. For half a century, attempts to understand altruism have developed around the concept that altruists may help relatives to have extra offspring in order to spread shared genes. This theory-known as inclusive fitness-is founded on a simple inequality termed Hamilton's rule. However, explanations of altruism have typically not considered the stochasticity of natural environments, which will not necessarily favour genotypes that produce the greatest average reproductive success. Moreover, empirical data across many taxa reveal associations between altruism and environmental stochasticity, a pattern not predicted by standard interpretations of Hamilton's rule. Here we derive Hamilton's rule with explicit stochasticity, leading to new predictions about the evolution of altruism. We show that altruists can increase the long-term success of their genotype by reducing the temporal variability in the number of offspring produced by their relatives. Consequently, costly altruism can evolve even if it has a net negative effect on the average reproductive success of related recipients. The selective pressure on volatility-suppressing altruism is proportional to the coefficient of variation in population fitness, and is therefore diminished by its own success. Our results formalize the hitherto elusive link between bet-hedging and altruism, and reveal missing fitness effects in the evolution of animal societies.