Rule-based simulation of temperate bacteriophage infection: Restriction–modification as a limiter to infection in bacterial populations

An individual-based model (IbM) for bacterial adaptation and evolution, COSMIC-Rules, has been employed to simulate interactions of virtual temperate bacteriophages (phages) and their bacterial hosts. Outcomes of infection mimic those of a phage such as lambda, which can enter either the lytic or lysogenic cycle, depending on the nutritional status of the host. Infection of different hosts possessing differing restriction and modification systems is also simulated. Phages restricted upon infection of one restricting host can be adapted (by host-controlled modification of the phage genome) and subsequently propagate with full efficiency on this host. However, such ability is lost if the progeny phages are passaged through a new host with a different restriction and modification system before attempted re-infection of the original restrictive host. The simulations show that adaptation and re-adaptation to a particular host-controlled restriction and modification system result in lower efficiency and delayed lysis of bacterial cells compared with infection of non-restricting host bacteria.     

Rule-based modelling of conjugative plasmid transfer and incompatibility

COSMIC-rules, an individual-based model for bacterial adaptation and evolution, has been used to study virtual transmission of plasmids within bacterial populations, in an environment varying between supportive and inhibitory. The simulations demonstrate spread of antibiotic resistance (R) plasmids, both compatible and incompatible, by the bacterial gene transfer process of conjugation. This paper describes the behaviour of virtual plasmids, their modes of exchange within bacterial populations and the impact of antibiotics, together with the rules governing plasmid transfer. Three case studies are examined: transfer of an R plasmid within an antibiotic-susceptible population, transfer of two incompatible R plasmids and transfer of two compatible R plasmids. R plasmid transfer confers antibiotic resistance on recipients. For incompatible plasmids, one or other plasmid could be maintained in bacterial cells and only that portion of the population acquiring the appropriate plasmid-encoded resistance survives exposure to the antibiotics. By contrast, the compatible plasmids transfer and mix freely within the bacterial population that survives in its entirety in the presence of the antibiotics. These studies are intended to inform models for examining adaptive evolution in bacteria. They provide proof of principle in simple systems as a platform for predicting the behaviour of bacterial populations in more complex situations, for example in response to changing environments or in multi-species bacterial assemblages.     

A random graph model of density thresholds in swarming cells

Swarming behaviour is a type of bacterial motility that has been found to be dependent on reaching a local density threshold of cells. With this in mind, the process through which cell‐to‐cell interactions develop and how an assembly of cells reaches collective motility becomes increasingly important to understand. Additionally, populations of cells and organisms have been modelled through graphs to draw insightful conclusions about population dynamics on a spatial level. In the present study, we make use of analogous random graph structures to model the formation of large chain subgraphs, representing interactions between multiple cells, as a random graph Markov process. Using numerical simulations and analytical results on how quickly paths of certain lengths are reached in a random graph process, metrics for intercellular interaction dynamics at the swarm layer that may be experimentally evaluated are proposed.     

Geographic structure of lineage associations in a plant-bacterial mutualism

Two species linked by a mutualistic relationship may evolve correlated population differentiation if there is long-term continuity of interactions between specific partners. This phenomenon was analyzed by multilocus enzyme electrophoresis on the annual legume Amphicarpaea bracteata and its nitrogen-fixing bacterial symbionts (Bradyrhizobium sp.) sampled from >20 sites over a 1000 km area. Three analyses indicated that genetic differentiation was correlated in the two organisms. First, the genetic distance between bacterial populations at each pair of sites was significantly positively related to the genetic distance between their host plant populations, as evaluated by the Mantel test. Second, a cluster analysis revealed that several divergent lineages were present both among plants and among bacteria. Bacterial lineages showed a highly nonrandom distribution across plant lineages that was consistent in each of two regions sampled. Finally, there were numerous cases where populations of the same plant lineage 1000 km apart harbored bacterial isolates with an identical multilocus genotype. Thus, despite recurrent opportunities for partner switching, particular genotypes of these two organisms associate consistently across multiple habitats throughout their geographic range.     

Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria–plasmid–phage interaction

Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities, bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here, we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage, SBW25φ2, and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria. We show that individually, both plasmids and phages impose selection leading to bacterial evolutionary responses that are distinct from bacterial populations evolving without MGEs, but that together, plasmids and phages impose conflicting selection on bacteria, constraining the evolutionary responses observed in pairwise interactions. Our findings highlight the likely difficulties of predicting evolutionary responses to multiple selective pressures from the observed evolutionary responses to each selective pressure alone. Understanding evolution in complex microbial communities comprising many species and MGEs will require that we go beyond studies of pairwise interactions.     

Simultaneous fluorescent gram staining and activity assessment of activated sludge bacteria

Wastewater treatment is one of the most important commercial biotechnological processes, and yet the component bacterial populations and their associated metabolic activities are poorly understood. The novel fluorescent dye hexidium iodide allows assessment of Gram status by differential absorption through bacterial cell walls. Differentiation between gram-positive and gram-negative wastewater bacteria was achieved after flow cytometric analysis. This study shows that the relative proportions of gram-positive and gram-negative bacterial cells identified by traditional microscopy and hexidium iodide staining were not significantly different. Dual staining of cells for Gram status and activity proved effective in analyzing mixtures of cultured bacteria and wastewater populations. Levels of highly active organisms at two wastewater treatment plants, both gram positive and gram negative, ranged from 1.5% in activated sludge flocs to 16% in the activated sludge fluid. Gram-positive organisms comprised <5% of the total bacterial numbers but accounted for 19 and 55% of the highly active organisms within flocs at the two plants. Assessment of Gram status and activity within activated sludge samples over a 4-day period showed significant differences over time. This method provides a rapid, quantitative measure of Gram status linked with in situ activity within wastewater systems.     

Human occupancy as a source of indoor airborne bacteria

Exposure to specific airborne bacteria indoors is linked to infectious and noninfectious adverse health outcomes. However, the sources and origins of bacteria suspended in indoor air are not well understood. This study presents evidence for elevated concentrations of indoor airborne bacteria due to human occupancy, and investigates the sources of these bacteria. Samples were collected in a university classroom while occupied and when vacant. The total particle mass concentration, bacterial genome concentration, and bacterial phylogenetic populations were characterized in indoor, outdoor, and ventilation duct supply air, as well as in the dust of ventilation system filters and in floor dust. Occupancy increased the total aerosol mass and bacterial genome concentration in indoor air PM(10) and PM(2.5) size fractions, with an increase of nearly two orders of magnitude in airborne bacterial genome concentration in PM(10). On a per mass basis, floor dust was enriched in bacterial genomes compared to airborne particles. Quantitative comparisons between bacterial populations in indoor air and potential sources suggest that resuspended floor dust is an important contributor to bacterial aerosol populations during occupancy. Experiments that controlled for resuspension from the floor implies that direct human shedding may also significantly impact the concentration of indoor airborne particles. The high content of bacteria specific to the skin, nostrils, and hair of humans found in indoor air and in floor dust indicates that floors are an important reservoir of human-associated bacteria, and that the direct particle shedding of desquamated skin cells and their subsequent resuspension strongly influenced the airborne bacteria population structure in this human-occupied environment. Inhalation exposure to microbes shed by other current or previous human occupants may occur in communal indoor environments.     

Simultaneous Fluorescent Gram Staining and Activity Assessment of Activated Sludge Bacteria

Wastewater treatment is one of the most important commercial biotechnological processes, and yet the component bacterial populations and their associated metabolic activities are poorly understood. The novel fluorescent dye hexidium iodide allows assessment of Gram status by differential absorption through bacterial cell walls. Differentiation between gram-positive and gram-negative wastewater bacteria was achieved after flow cytometric analysis. This study shows that the relative proportions of gram-positive and gram-negative bacterial cells identified by traditional microscopy and hexidium iodide staining were not significantly different. Dual staining of cells for Gram status and activity proved effective in analyzing mixtures of cultured bacteria and wastewater populations. Levels of highly active organisms at two wastewater treatment plants, both gram positive and gram negative, ranged from 1.5% in activated sludge flocs to 16% in the activated sludge fluid. Gram-positive organisms comprised <5% of the total bacterial numbers but accounted for 19 and 55% of the highly active organisms within flocs at the two plants. Assessment of Gram status and activity within activated sludge samples over a 4-day period showed significant differences over time. This method provides a rapid, quantitative measure of Gram status linked with in situ activity within wastewater systems.     

Diverse Microbiota Identified in Whole Intact Nest Chambers of the Red Mason Bee Osmia bicornis (Linnaeus 1758)

Microbial activity is known to have profound impact on bee ecology and physiology, both by beneficial and pathogenic effects. Most information about such associations is available for colony-building organisms, and especially the honey bee. There, active manipulations through worker bees result in a restricted diversity of microbes present within the colony environment. Microbial diversity in solitary bee nests remains unstudied, although their larvae face a very different situation compared with social bees by growing up in isolated compartments. Here, we assessed the microbiota present in nests and pre-adults of Osmia bicornis, the red mason bee, by culture-independent pyrosequencing. We found high bacterial diversity not comparable with honey bee colonies. We identified a variety of bacteria potentially with positive or negative interactions for bee larvae. However, most of the other diverse bacteria present in the nests seem to originate from environmental sources through incorporated nest building material and stored pollen. This diversity of microorganisms may cause severe larval mortality and require specific physiological or symbiotic adaptations against microbial threats. They may however also profit from such a diverse environment through gain of mutualistic partners. We conclude that further studies of microbiota interaction in solitary bees will improve the understanding of fitness components and populations dynamics.     

植物相关细菌基因组在细菌-植物之间相互作用研究中的作用

基因组以及后基因组研究可收集大量有用的生物学信息, 并使许多的生物体得以全面的认识。细菌基因组研究对于植物病原性及互生型细菌在细菌－植物之间相互作用提供了极为重要的信息, 尤其是Type-Ⅲ分泌系统(Type-Ⅲ secretion systems, TTSS)以及该系统在细菌－植物之间相互作用中的功能研究中具有举足轻重的作用。文章较为详细地阐述了当前植物相关细菌基因组学在细菌－植物研究中的作用,并分析了其未来研究的趋势。     

On Testing an Unspecified Function Through a Linear Mixed Effects Model with Multiple Variance Components

Summary We examine a generalized F ‐test of a nonparametric function through penalized splines and a linear mixed effects model representation. With a mixed effects model representation of penalized splines, we imbed the test of an unspecified function into a test of some fixed effects and a variance component in a linear mixed effects model with nuisance variance components under the null. The procedure can be used to test a nonparametric function or varying‐coefficient with clustered data, compare two spline functions, test the significance of an unspecified function in an additive model with multiple components, and test a row or a column effect in a two‐way analysis of variance model. Through a spectral decomposition of the residual sum of squares, we provide a fast algorithm for computing the null distribution of the test, which significantly improves the computational efficiency over bootstrap. The spectral representation reveals a connection between the likelihood ratio test (LRT) in a multiple variance components model and a single component model. We examine our methods through simulations, where we show that the power of the generalized F ‐test may be higher than the LRT, depending on the hypothesis of interest and the true model under the alternative. We apply these methods to compute the genome‐wide critical value and p ‐value of a genetic association test in a genome‐wide association study (GWAS), where the usual bootstrap is computationally intensive (up to 10⁸ simulations) and asymptotic approximation may be unreliable and conservative.     

Viruses' Life History: Towards a Mechanistic Basis of a Trade-Off between Survival and Reproduction among Phages

Life history theory accounts for variations in many traits involved in the reproduction and survival of living organisms, by determining the constraints leading to trade-offs among these different traits. The main life history traits of phages—viruses that infect bacteria—are the multiplication rate in the host, the survivorship of virions in the external environment, and their mode of transmission. By comparing life history traits of 16 phages infecting the bacteria Escherichia coli, we show that their mortality rate is constant with time and negatively correlated to their multiplication rate in the bacterial host. Even though these viruses do not age, this result is in line with the trade-off between survival and reproduction previously observed in numerous aging organisms. Furthermore, a multiple regression shows that the combined effects of two physical parameters, namely, the capsid thickness and the density of the packaged genome, account for 82% of the variation in the mortality rate. The correlations between life history traits and physical characteristics of virions may provide a mechanistic explanation of this trade-off. The fact that this trade-off is present in this very simple biological situation suggests that it might be a fundamental property of evolving entities produced under constraints. Moreover, such a positive correlation between mortality and multiplication reveals an underexplored trade-off in host–parasite interactions.     

Evolving Concepts of Bacterial Species

The same evolutionary forces that cause diversification in sexual eukaryotes are expected to cause diversification in bacteria. However, in bacteria, the wider variety of mechanisms for gene exchange (or lack thereof) increases the range of expected diversity patterns compared to those of sexual organisms. Two parallel concepts for bacterial speciation have developed, based on ecological divergence or barriers to recombination in turn. Recent evidence from DNA sequence data shows that both processes can generate independently evolving groups that are equivalent to sexual species and that represent separate arenas within which recombination (when it occurs), selection and drift occur. It remains unclear, however, how often different processes act in concert to generate simple units of diversity, or whether a more complex model of diversity is required, specifying hierarchical levels at which different cohesive processes operate. We advocate an integrative approach that evaluates the effects of multiple evolutionary forces on diversity patterns. There is also great potential for laboratory studies of bacterial evolution that test evolutionary mechanisms inferred from population genetic analyses of multi-locus and genome sequence data.     

Bacterial volatiles and their action potential

During the past few years, an increasing awareness concerning the emission of an unexpected high number of bacterial volatiles has been registered. Humans sense, intensively and continuously, microbial volatiles that are released during food transformation and fermentation, e.g., the aroma of wine and cheese. Recent investigations have clearly demonstrated that bacteria also employ their volatiles during interactions with other organisms in order to influence populations and communities. This review summarizes the presently known bioactive compounds and lists the wide panoply of effects possessed by organisms such as fungi, plants, animals, and bacteria. Because bacteria often emit highly complex volatile mixtures, the determination of biologically relevant volatiles remains in its infancy. Part of the future goal is to unravel the structure of these volatiles and their biosynthesis. Nevertheless, bacterial volatiles represent a source for new natural compounds that are interesting for man, since they can be used, for example, to improve human health or to increase the productivity of agricultural products.     

Interfaces between bacterial and eukaryotic "neuroecology"

The sensory capacity of bacteria and macroalgae (seaweeds) is limited with respect to many modalities (visual, auditory) common in "higher" organisms such as animals. Thus, we expect that other modalities, such as chemical signaling and sensing, would play particularly important roles in their sensory ecology. Here, we discuss two examples of chemical signaling in bacteria and seaweeds: (1) the role of chemical defenses and quorum-sensing (QS) regulatory systems in bacterial colonization and infection of the red alga Delisea pulchra and their ecological consequences, and (2) the regulation of dispersal and differentiation by nitric oxide (NO) in bacterial biofilms. Consistent with the goals of neuroecology, in both cases, we investigate the links between specific signal-mediated molecular mechanisms, and ecological outcomes, for populations or assemblages of bacteria or seaweeds. We conclude by suggesting that because of the fundamental role played by chemical signaling in bacteria, bacterial systems, either by themselves or in interactions with other organisms, have much to offer for understanding general issues in neuroecology. Thus, further integration of microbiology with the biology of eukaryotes would seem warranted and is likely to prove illuminating.     

Control of marine bacterioplankton populations: Measurement and significance of grazing

A variety of methods have been used to estimate the degree of control exercised upon marine bacterioplankton by grazing organisms. These include filtration or dilution of samples to reduce grazers, the use of specific inhibitors to prevent growth or grazing, and the use of artificial particles or radio-labelled bacteria as tracers for the natural bacterioplankton. Each of these techniques has drawbacks which may lead to under- or overestimates of grazing. In addition, they tell us little about which organisms are doing the grazing or the degree to which viruses or lytic bacteria compete with grazers for bacterial production. Because measurements of grazing and bacterioplankton growth rates are uncertain, exact comparisons are not presently possible. Thus measurements of bacterial and bacterivore abundance, concentrated on comparisons between seasons, on diel cycles and on spatial variations, have been used to evaluate mechanisms controlling bacterial populations. These give an idea of the degree of coupling between bacterial growth and bacterivore activity and of the time scales over which growth and grazing balance. Combined with laboratory studies of grazing, they currently provide the best insight into what controls populations of bacteria in the sea.     

Incorporating toxin hypothesis into a mathematical model of persister formation and dynamics

Biofilms are well known for their extreme tolerance to antibiotics. Recent experimental evidence has indicated the existence of a small fraction of specialized persister cells may be responsible for this tolerance. Although persister cells seem to exist in planktonic bacterial populations, within a biofilm the additional protection offered by the polymeric matrix allows persister cells to evade elimination and serve as a source for re-population. Whether persister cells develop through interactions with toxin/antitoxin modules or are senescent bacteria is an open question. In this investigation we contrast results of the analysis of a mathematical model of the toxin/antitoxin hypothesis for bacteria in a chemostat with results incorporating the senescence hypothesis. We find that the persister fraction of the population as a function of washout rate provides a viable distinction between the two hypotheses. We also give simulation results that indicate that a strategy of alternating dose/withdrawal disinfection can be effective in clearing the entire persister and susceptible populations of bacteria. This strategy was considered previously in analysis of a generic model of persister formation. We find that extending the model of persister formation to include the toxin/antitoxin interactions in a chemostat does not alter the qualitative results that success of the dosing strategy depends on the withdrawal time. While this treatment is restricted to planktonic bacterial populations, it serves as a framework for including persister cells in a spatially dependent biofilm model.