Evolution of species interactions in a biofilm community

Rapid evolution of stability and productivity at the origin of a microbial mutualism

Mutualistic interactions are taxonomically and functionally diverse. Despite their ubiquity, however, the basic ecological and evolutionary processes underlying their origin and maintenance are poorly understood. A major reason for this is the lack of an experimentally tractable model system. We examine the evolution of an experimentally imposed obligate mutualism between sulfate-reducing and methanogenic microorganisms that have no known history of previous interaction. Twenty-four independent pairings (cocultures) of the bacterium Desulfovibrio vulgaris and the archaeon Methanococcus maripaludis were established and followed for 300 community doublings in two environments, one allowing for the development of a heterogeneous distribution of resources and the other not. Evolved cocultures grew up to 80% faster and were up to 30% more productive (biomass yield per mole of substrate) than the ancestors. The evolutionary process was marked by periods of significant instability leading to extinction of two of the cocultures, but it resulted in more stable, efficient, and productive mutualisms for most replicated pairings. Comparisons of evolved cocultures with those assembled from one evolved mutualist and one ancestral mutualist showed that evolution of both species contributed to improved productivity. Surprisingly, however, overall improvements in growth rate and yield were less than the sum of the individual contributions, suggesting antagonistic interactions between mutations from the coevolved populations. Physical constraints on the transfer of metabolites in the evolution environment affected the evolution of M. maripaludis, but not of D. vulgaris. Together, these results demonstrate that challenges can imperil nascent obligate mutualisms and demonstrate the evolutionary responses that enable their persistence and future evolution.

Bacterial competition: surviving and thriving in the microbial jungle

Most natural environments harbour a stunningly diverse collection of microbial species. In these communities, bacteria compete with their neighbours for space and resources. Laboratory experiments with pure and mixed cultures have revealed many active mechanisms by which bacteria can impair or kill other microorganisms. In addition, a growing body of theoretical and experimental population studies indicates that the interactions within and between bacterial species can have a profound impact on the outcome of competition in nature. The next challenge is to integrate the findings of these laboratory and theoretical studies and to evaluate the predictions that they generate in more natural settings.

Microbial metropolis

Microorganisms can form tightly knit communities such as biofilms. Many others include marine snow, anaerobic digester granules, the ginger beer plant and bacterial colonies. This chapter is devoted to a survey of the main properties of these communities, with an emphasis on biofilms. We start with attachment to surfaces and the nature of adhesion. The growing community then forms within a matrix, generally of organic macromolecules. Inevitably the environment within such a matrix is different from that outside. Organisms respond by forming crowd-detection and response units; these quorum sensing systems act as switches between planktonic life and the dramatically altered conditions found inside microbial aggregates. The community then matures and changes and may even fail and disappear. Antimicrobial resistance is discussed as an example of multicellular behavior. The multicellular lifestyle has been modeled mathematically and responded to powerful molecular biological techniques. Latterly, microbial systems have been used as models for fundamental evolutionary processes, mostly because of their high rates of reproduction and the ease of genetic manipulation. The life of most microbes is a duality between the yin of the community and the yang of planktonic existence. Sadly far less research has been devoted to adaptation to free-living forms than in the opposite direction.

E Unibus Plurum: genomic analysis of an experimentally evolved polymorphism in Escherichia coli

Microbial populations founded by a single clone and propagated under resource limitation can become polymorphic. We sought to elucidate genetic mechanisms whereby a polymorphism evolved in Escherichia coli under glucose limitation and persisted because of cross-feeding among multiple adaptive clones. Apart from a 29 kb deletion in the dominant clone, no large-scale genomic changes distinguished evolved clones from their common ancestor. Using transcriptional profiling on co-evolved clones cultured separately under glucose-limitation we identified 180 genes significantly altered in expression relative to the common ancestor grown under similar conditions. Ninety of these were similarly expressed in all clones, and many of the genes affected (e.g., mglBAC, mglD, and lamB) are in operons coordinately regulated by CRP and/or rpoS. While the remaining significant expression differences were clone-specific, 93% were exhibited by the majority clone, many of which are controlled by global regulators, CRP and CpxR. When transcriptional profiling was performed on adaptive clones cultured together, many expression differences that distinguished the majority clone cultured in isolation were absent, suggesting that CpxR may be activated by overflow metabolites removed by cross-feeding strains in co-culture. Relative to their common ancestor, shared expression differences among adaptive clones were partly attributable to early-arising shared mutations in the trans-acting global regulator, rpoS, and the cis-acting regulator, mglO. Gene expression differences that distinguished clones may in part be explained by mutations in trans-acting regulators malT and glpK, and in cis-acting sequences of acs. In the founder, a cis-regulatory mutation in acs (acetyl CoA synthetase) and a structural mutation in glpR (glycerol-3-phosphate repressor) likely favored evolution of specialists that thrive on overflow metabolites. Later-arising mutations that led to specialization emphasize the importance of compensatory rather than gain-of-function mutations in this system. Taken together, these findings underscore the importance of regulatory change, founder genotype, and the biotic environment in the adaptive evolution of microbes.

Experimental evolution of asexual species has shown that multiple genotypes can arise from a single ancestor and stably coexist (e unibus plurum). Although facilitated by environmental heterogeneity, this phenomenon also occurs in simple, homogeneous environments provisioned with a single limiting nutrient. We sought to discover genetic mechanisms that enabled an E. coli population founded by a single clone to become an interacting community composed of multiple clones. The founder of this population contained mutations that impair regulation of acetate and glycerol metabolism and likely favored the evolution of cross-feeding. Adaptive clones share cis- and trans-regulatory mutations shown elsewhere to enhance fitness under glucose limitation. Certain mutations that distinguish adaptive clones and underlie evolution of specialists were compensatory rather than gain-of-function, and all that we detected resulted in gene expression changes rather than protein structure changes. Evolved clones exhibited both common and clone-specific gene expression changes relative to their common ancestor; the pattern of gene expression in the dominant clone cultured alone differed from the pattern observed when it was cultured with variants feeding on its overflow metabolites. These findings illuminate the roles played by founder genotype, differential gene regulation, and the biotic environment in the adaptive evolution of bacteria.

Exploiting advances in imaging technology to study biofilms by applying multiphoton laser scanning microscopy as an imaging and manipulation tool

Biofilms are an important element of the natural ecosystems but can be detrimental in health care and industrial settings. To improve our ability to combat biofilms, we need to understand the processes that facilitate their formation and dispersal. One approach that has proven to be invaluable is to image biofilms as they grow. Here we describe tools and protocols to visualize biofilms with multiphoton laser scanning microscopy, compare this with single photon laser scanning confocal microscopy and highlight best working procedures. Furthermore, we describe how with multiphoton laser scanning microscopy the laser can be used to manipulate the biofilm, specifically to achieve localized bleaching, killing or ablation within the biofilm biomass. These applications open novel ways to study the dynamics of biofilm formation, regeneration and dispersal.

Mycoplasma pneumoniae and/or Chlamydophila pneumoniae inoculation causing different aggravations in cholesterol-induced atherosclerosis in apoE KO male mice

BACKGROUND

Chamydophila pneumoniae (CP) and/or Mycoplasma pneumoniae (MP) are two bacteria detected in vulnerable atheromas. In this study we aimed to analyze whether CP and/or MP aggravates atherosclerosis induced by cholesterol-enriched diet in C57BL/6 apoE KO male mice. Thirty male apoE KO mice aged eight weeks fed by a diet containing 1% cholesterol until 32 weeks of age were divided into four groups: the first was inoculated with CP (n = 7), the second with MP (n = 12), the third with both CP + MP (n = 5), and the fourth with saline (sham n = 6). The animals were re-inoculated at 36 weeks of age, and sacrificed at 40 weeks of age. Two ascending aorta and one aortic arch segments were sampled. In the most severely obstructed segment, vessel diameter, plaque height, percentage of luminal obstruction and the degree of adventitial inflammation were analyzed. The plaque area/intimal surface ratio was obtained by measuring all three segments. The adventitial inflammation was semiquantified (0 absent, 1 mild, 2 moderate, and 3 diffuse).

RESULTS

The mean and standard deviation of plaque height, % luminal obstruction, external diameter, the plaque area/intimal surface ratio and the adventitial inflammation values are the following for each group: MP (0.20 +/- 0.12 mm, 69 +/- 26%, 0.38 +/- 0.11 mm, 0.04 +/- 0.04 and 0.22 +/- 0.67), CP (0.23 +/- 0.08 mm, 90 +/- 26%, 0.37 +/- 0.08 mm, 0.04 +/- 0.03, and 0.44 +/- 0.53), MP + CP (18 +/- 0.08 mm, 84 +/- 4.0%, 0.35 +/- 0.25 mm, 0.03 +/- 0.03 and 1.33 +/- 0.82) and sham (0.08 +/- 0.09 mm, 42 +/- 46%, 0.30 +/- 0.10 mm, 0.02 +/- 0.03 and 0.71 +/- 0.76). A wider area of plaque/intimal surface was observed in MP + CP inoculated groups (p = 0.07 and 0.06) as well as an increased plaque height in CP (p = 0.01) in comparison with sham group. There was also an increased luminal obstruction (p = 0.047) in CP inoculated group in comparison to sham group. Adventitial inflammation in MP + CP inoculated group was higher than MP, CP and the sham groups (p = 0.02).

CONCLUSION

Inoculation of CP, MP or both agents in C57BL/6 apoE KO male mice caused aggravation of experimental atherosclerosis induced by cholesterol-enriched diet, with distinct characteristics. CP inoculation increased the plaque height with positive vessel remodeling and co-inoculation of MP + CP caused the highest adventitial inflammation measures.

Architectural analysis, viability assessment and growth kinetics of Candida albicans and Candida glabrata biofilms

The human fungal pathogen Candida is able to form biofilms in almost all the medical devices in current use. Indeed, biofilm formation is a major virulence attribute of microorganisms and account for a majority of human infections. Therefore, understanding processes appertaining to biofilm development is an important prerequisite for devising new strategies to prevent or eradicate biofilm-related infections. In the present study we used an array of both conventional and novel analytical tools to obtain a comprehensive view of Candida biofilm development. Enumeration of colony forming units, colorimetric (XTT) assay, Scanning Electron Microscopy (SEM) and novel Confocal Laser Scanning Microscopy (CLSM) coupled with COMSTAT software analyses were utilised to evaluate growth kinetics; architecture and viability of biofilms of a reference (ATCC) and a clinical strain each of two Candida species, C. albicans and C. glabrata. Biofilm growth kinetics on a polystyrene substrate was evaluated from the initial adhesion step (1.5 h) up to 72 h. These analyses revealed substantial inter- and intra-species differences in temporal organisation of Candida biofilm architecture, spatiality and cellular viability, while reaching maturity within a period of 48 h, on a polystyrene substrate. There were substantial differences in the growth kinetics upon methodology, although general trend seemed to be the same. Detailed architectural analysis provided by COMSTAT software corroborated the SEM and CSLM views. These analyses may provide a strong foundation for down stream molecular work of fungal biofilms.

Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA)

Microbial mats in sulfidic cave streams offer unique opportunities to study redox-based biogeochemical nutrient cycles. Previous work from Lower Kane Cave, Wyoming, USA, focused on the aerobic portion of microbial mats, dominated by putative chemolithoautotrophic, sulfur-oxidizing groups within the Epsilonproteobacteria and Gammaproteobacteria. To evaluate nutrient cycling and turnover within the whole mat system, a multidisciplinary strategy was used to characterize the anaerobic portion of the mats, including application of the full-cycle rRNA approach, the most probable number method, and geochemical and isotopic analyses. Seventeen major taxonomic bacterial groups and one archaeal group were retrieved from the anaerobic portions of the mats, dominated by Deltaproteobacteria and uncultured members of the Chloroflexi phylum. A nutrient spiraling model was applied to evaluate upstream to downstream changes in microbial diversity based on carbon and sulfur nutrient concentrations. Variability in dissolved sulfide concentrations was attributed to changes in the abundance of sulfide-oxidizing microbial groups and shifts in the occurrence and abundance of sulfate-reducing microbes. Gradients in carbon and sulfur isotopic composition indicated that released and recycled byproduct compounds from upstream microbial activities were incorporated by downstream communities. On the basis of the type of available chemical energy, the variability of nutrient species in a spiraling model may explain observed differences in microbial taxonomic affiliations and metabolic functions, thereby spatially linking microbial diversity to nutrient spiraling in the cave stream ecosystem.

Aggregatibacter actinomycetemcomitans builds mutualistic biofilm communities with Fusobacterium nucleatum and Veillonella species in saliva

Human oral bacterial pathogens grow in attached multispecies biofilm communities. Unattached cells are quickly removed by swallowing. Therefore, surface attachment is essential for growth, and we investigated multispecies community interactions resulting in mutualistic growth on saliva as the sole nutritional source. We used two model systems, saliva-coated transferable solid-phase polystyrene pegs (peg biofilms) and flow cells with saliva-coated glass surfaces. Fluorescent antibody staining and image analysis were used to quantify the biomass in flow cells, and quantitative real-time PCR with species-specific primers was used to quantify the biomass in peg biofilms. Veillonella sp. strain PK1910, Aggregatibacter actinomycetemcomitans JP2, and Fusobacterium nucleatum ATCC 10953 were unable to grow as single species in flow cells. Only A. actinomycetemcomitans grew after 36 h when peg biofilms remained submerged in saliva from the time of inoculation. Mixed-species coaggregates were used for two- and three-species inoculation. The biomass in two-species biofilms increased in both systems when Veillonella sp. strain PK1910 was present as one of the partners. Enhanced growth of all strains was observed in three-species biofilms in flow cells. Interestingly, in flow cells F. nucleatum and A. actinomycetemcomitans exhibited mutualism, and, although F. nucleatum was unable to grow with either of the other species in the peg system, F. nucleatum stimulated the growth of Veillonella sp. and together these two organisms increased the total biomass of A. actinomycetemcomitans in three-species peg biofilms. We propose that mutualistic two-species and multispecies oral biofilm communities form in vivo and that mutualism between commensal veillonellae and late colonizing pathogens, such as aggregatibacteria, contributes to the development of periodontal disease.

Intertwined interspecies relationships: approaches to untangle the microbial network

In nature, microorganisms live by interacting with each other. Microbiological studies that only consider pure cultures are not sufficient to adequately describe the natural behaviour of microbes. Several microbial interactions have been recognized to affect the growth or metabolism of others; e.g. syntrophic cometabolism, competition, production of inhibitors or activators, and predation. It is believed that third-party organisms easily affect the two-species relationships and these relationships form the basis of interspecies networks within microbial communities. A microbial network contributes to 'functional redundancy' or 'structural diversity' and the microbial communities effectively act as a multicellular organism. It is necessary to understand not only the physiological activity of members within microbial communities but also their roles to regulate the activity or population of others. To access the microbial network, we require (i) comprehensive determination of all possible interspecies relationships among microbes, (ii) knock-out experiments by which certain members can be removed or suppressed, and (iii) supplemental addition of microbes or activation of certain members. Microbial network studies have started using defined microbial communities, i.e. a mixed culture that is composed of three or four species. In order to expand these studies to microflora in nature, microbial ecology requires the help of mathematical biology.

Molecular characterization of Staphylococcus epidermidis strains isolated from a teaching hospital in Shanghai, China

Staphylococcus epidermidis is a leading cause of hospital-acquired infections, mostly associated with the use of medical devices in seriously ill or immunocompromised patients. Currently, the clonal characteristics of S. epidermidis in the hospital environment in China are unknown; neither is it known why these sequence types are easily disseminated in the hospital setting. In this study, multilocus sequence typing (MLST) was employed for the clonal analysis of 80 S. epidermidis isolates collected from patients with S. epidermidis infections. MLST revealed a total of 16 different sequence types among these isolates. ST2, which contained exclusively ica-positive, IS256-positive and biofilm-forming isolates, represented the majority of clinical strains tested. Of the S. epidermidis strains circulating in the hospital environment in China, as many as 96.25 % are resistant to meticillin. Four staphylococcal chromosomal cassette mec (SCCmec) types were identified among the total 80 S. epidermidis isolates, none of the strains carried an SCCmec I cassette. All of the ST2 isolates carried the SCCmec type III cassette. Taken together, the combination of biofilm-forming ability and antibiotic resistance helps ST2 become successfully established within nosocomial environments, and promotes the device-related infection and bacteraemia.

Insight into the microbial multicellular lifestyle via flow-cell technology and confocal microscopy

Biofilms are agglomerates of microorganisms surrounded by a self-produced extracellular matrix. During the last 10 years, there has been an increasing recognition of biofilms as a highly significant topic in microbiology with relevance for a variety of areas in our society including the environment, industry, and human health. Accordingly a number of biofilm model systems, molecular tools, microscopic techniques, and image analysis programs have been employed for the study of biofilms under controlled and reproducible conditions. Studies using confocal laser scanning microscopy (CLSM) of biofilms formed in flow-chamber experimental systems by genetically color-coded bacteria have provided detailed knowledge about biofilm developmental processes, cell differentiations, spatial organization, and function of laboratory-grown biofilms, in some cases down to the single cell level. In addition, the molecular mechanisms underlying the increased tolerance that biofilm cells often display towards antibiotic treatment are beginning to be unravelled.

Generational coexistence and ancestor's inhibition in bacterial populations

Generational coexistence in structured environments raises the possibility of a competition between ancestors and descendents. This type of kin competition, and in particular, the possibility that descendents might actively repress the ancestor's dominance, has been rarely considered in microbial evolutionary ecology. The recent discovery of the phenomenon of stationary-phase contact-dependent inhibition of bacterial ancestor cells by late descendents provides a new theoretical perspective to analyze intrapopulational evolutionary changes. The ancestor's inhibition effect might accelerate such changes, particularly when the descendents have acquired small adaptive advantages that are insufficient to rapidly displace the well-settled ancestors in a complex niche. Besides this effect of triggering selection of small genetic differences, the opportunities for intergenerational coexistence in bacteria, where ancestor's inhibition might occur, are reviewed in this work. A theoretical analysis is provided about the explanatory possibilities of the ancestor's inhibition effect in the controversies about intraspecific (in a large sense, including intrapopulational) genetic diversification, and the discontinuities observed in such processes, giving rise to the emergence of individualities and therefore differential units of selection.

Patterns and scales in gastrointestinal microbial ecology

The body surfaces of humans and other animals are colonized at birth by microorganisms. The majority of microbial residents on the human body exist within gastrointestinal (GI) tract communities, where they contribute to many aspects of host biology and pathobiology. Recent technological advances have expanded our ability to perceive the membership and physiologic traits of microbial communities along the GI tract. To translate this information into a mechanistic and practical understanding of host-microbe and microbe-microbe relationships, it is necessary to recast our conceptualization of the GI tract and its resident microbial communities in ecological terms. This review depicts GI microbial ecology in the context of 2 fundamental ecological concepts: (1) the patterns of biodiversity within the GI tract and (2) the scales of time, space, and environment within which we perceive those patterns. We show how this conceptual framework can be used to integrate our existing knowledge and identify important open questions in GI microbial ecology.

Fabrication of microbial biofilm arrays by geometric control of cell adhesion

This paper presents a technique for patterning arrays of microbial biofilms on a wide range of different substrates using thin polymer stencils. The stencils function as "scaffolds" that provide geometric control over cell adhesion on surfaces and confine biofilm growth to specific regions of a substrate. We demonstrate the fabrication of biofilm arrays with features (e.g., individual biofilms) as small as 50 microm in diameter with physiological characteristics that are reproducible. Biofilm arrays of a range of microorganisms can be produced using this technique, including: P. aeruginosa, B. subtilis, S. epidermidis, V. fischeri, E. coli, and C. albicans. This approach provides a simple, user-configurable, and relatively inexpensive method for growing biofilms in both static and flow conditions. The method described in this paper makes it possible to study the chemical, physical, and environmental factors that affect biofilm development in a statistically relevant and reproducible format.

Escherichia coli O157:H7 requires colonizing partner to adhere and persist in a capillary flow cell

The ability of a strain of waterborne Escherichia coli O157:H7 to colonize a glass flow cell and develop microcolonies when grown alone and with Pseudomonas aeruginosa PAO1 was examined. When introduced alone, planktonic E. coil were unable to attach to the glass surface. When introduced simultaneously with P. aeruginosa (co-inoculation), the two species coadhered to the surface. When E. coliwere introduced into a flow cell precolonized with a P. aeruginosa biofilm (precolonized), 10-fold more cells were retained than in the co-inoculated case. Both species were monitored nondestructively by time-lapse confocal microscopy, direct microscopy of the filtered effluent, and effluent plate counts. While more E. coli initially adhered in the precolonized system, E. coli microcolony formation occurred only in the co-inoculated system, where E. coil comprised 1% of the total surface-associated biovolume but greater than 50% of the biovolume near the edges of the flow cell. The hydrodynamics in the flow cell were evaluated using the finite volume analysis program CFX, revealing that shear stress was likely important in both initial attachment and steady-state colonization patterns. This research elucidates key factors which promote retention and subsequent biofilm development of E. coli 0157:H7.

INTRODUCTION

Bacteria exist in nature primarily in communities known as biofilms. These biofilms are usually characterized by differentiated structures, exhibit a different phenotype than their planktonic counterparts, and in nature most often consist of multispecies consortia (1, 2). An important process in shaping the formation and structure of some multispecies biofilms is the ability of certain species to coaggregate. In this process, planktonic cells adhere to genetically distinct cells in a biofilm or to other planktonic cells (3), thereby increasing biofilm formation. This process is growth-phase-dependent and is turned on and off by cells, suggestive that it may also play a role in dispersal and dissemination (4). Due to these and other complexities of the biofilm mode of growth, multiple species can coexist despite one organism having a much higher growth rate than another (5-7). In many cases, bacteria have been shown to gain a fitness advantage when residing in a mixed-species versus single-

Adaptive evolution in single species bacterial biofilms

Little is known about the dynamics of cellular growth, death, and evolution within bacterial biofilms. Here we show evidence of evolution within single-species biofilms in real time. Escherichia coli harvested from 22-day-old biofilms express a competitive advantage over cells incubated in biofilms for shorter periods of time. This advantage is manifested as the ability of aged cells to outcompete younger cells in the presence of a pre-existing biofilm, even though cells from older biofilms do not express an increased ability to form initial biofilms on a fresh, unoccupied surface. This phenomenon is similar to the growth advantage in stationary phase, or GASP, phenotype exhibited by planktonically grown cells when incubated under competitive conditions. The ability of bacteria in biofilms to show rapid heritable change has implications for our understanding of the adaptive abilities of biofilms in a wide variety of natural and man-made environments.

Enhancing the biofiltration of geosmin by seeding sand filter columns with a consortium of geosmin-degrading bacteria

Geosmin is a secondary metabolite that can be produced by many species of cyanobacteria and Actinomycetes. It imparts a musty/earthy taste and odour to drinking water which can result in consumer complaints and a general perception that there is a problem with the water quality. As geosmin is recalcitrant to conventional water treatment, processes are sought to ensure effective removal of this compound from potable water. Biological filtration (biofiltration) is an attractive option for geosmin removal as this compound has been shown to be biodegradable. However, effective biofiltration of geosmin can be site specific as it is highly dependent upon the types of organism present and there is often an extended acclimation period before efficient removals are achieved. We report here, a novel approach to enhance the biofiltration of geosmin by seeding sand filter columns with a bacterial consortium previously shown to be capable of effectively degrading geosmin. Geosmin removals of up to 75% were evident through sand columns which had been inoculated with the geosmin-degrading bacteria, when compared with non-inoculated sand columns where geosmin removals were as low as 25%. These low geosmin removals through the non-inoculated sand columns are consistent with previous studies and were attributed to physical/abiotic losses. The presence of an existing biofilm was shown to influence geosmin removal, as the biofilm allowed for greater attachment of the geosmin-degrading consortium (as determined by an ATP assay), and enhanced removals of geosmin. Minimal difference in geosmin removal was observed when the geosmin-degrading bacteria were inoculated into the sand columns containing either an active or inactive biofilm.

Dual fluorescence system for flow cytometric analysis of Escherichia coli transcriptional response in multi-species context

When studying interspecies interactions in a bacterial consortium, it may be desirable to analyze one species' transcriptional response as influenced by the other species. We developed a dual fluorescence system of Escherichia coli for Fluorescence-Activated Cell Sorter (FACS)-based analysis for such a purpose. First, we generated E. coli SCC1 strain, which constitutively expresses green fluorescent protein (GFP), but otherwise showed no observable difference from the parent strain MG1655 with respect to morphology, growth, and FACS-analyzed side- and forward-scatter profiles. Next, to analyze transcriptional response, plasmids carrying promoters of interest fused to a red fluorescent protein (AsRed2) reporter, were introduced into strain SCC1. Quantification of promoter activities of araB, lacZ, fadB and rpoE via AsRed2 reporter verified that the induction levels are similar between MG1655 and SCC1 strains. In mixtures and co-cultures, GFP expression of E. coli SCC1 allowed it to be separated from non-E. coli species by FACS to purity levels of 96.7-100.0%. When a mixture of E. coli SCC1 carrying promoter-AsRed2 fusion and a non-E. coli strain was analyzed by FACS, it enabled (i) distinction of E. coli SCC1 from the non-E. coli strain, (ii) analysis of the E. coli promoter activity via AsRed2 expression and (iii) identification of transcriptional heterogeneity within the E. coli population. Co-cultures of E. coli SCC1 with Klebsiella pneumoniae and/or Enterococcus faecalis analyzed by FACS showed that E. coli fadB and rpoE transcription were differentially influenced by partner species.

The developmental model of microbial biofilms: ten years of a paradigm up for review

For the past ten years, the developmental model of microbial biofilm formation has served as the major conceptual framework for biofilm research; however, the paradigmatic value of this model has begun to be challenged by the research community. Here, we critically evaluate recent data to determine whether biofilm formation satisfies the criteria requisite of a developmental system. We contend that the developmental model of biofilm formation must be approached as a model in need of further validation, rather than utilized as a platform on which to base empirical research and scientific inference. With this in mind, we explore the experimental approaches required to further our understanding of the biofilm phenotype, highlighting evolutionary and ecological approaches as a natural complement to rigorous mechanistic studies into the causal basis of biofilm formation. Finally, we discuss a second model of biofilm formation that serves as a counterpoint to our discussion of the developmental model. Our hope is that this article will provide a platform for discussion about the conceptual underpinnings of biofilm formation and the impact of such frameworks on shaping the questions we ask, and the answers we uncover, during our research into these microbial communities.

Incorporation of natural uncultivable Legionella pneumophila into potable water biofilms provides a protective niche against chlorination stress

Legionella pneumophila is a waterborne pathogen that has been isolated sporadically from drinking water distribution systems (DWDS). Resistance to disinfectants is mainly attributed to the association of cells with amoebae, but biofilms are also thought to provide some degree of protection. In the present work, a two-stage chemostat was used to form heterotrophic biofilms from drinking water to study the influence of chlorine on the presence of naturally occurring L. pneumophila. The pathogen was tracked in planktonic and sessile biofilm phases using standard culture recovery techniques for cultivable cells and a peptide nucleic acid fluorescence in situ hybridisation assay for total cells. The results showed that the total number of L. pneumophila cells in biofilms was not affected by the concentrations of chlorine tested, and the presence of L. pneumophila could not be detected by culturing. To restrict the outbreaks of disease caused by this bacterium, efforts need to be concentrated on preventing L. pneumophila from re-entering an infectious state by maintaining residual disinfectant levels through the entire DWDS network so that the resuscitation of cells via contact with amoebae is prevented.

Persistence mechanisms of conjugative plasmids

Are plasmids selfish parasitic DNA molecules or an integrated part of the bacterial genome? This chapter reviews the current understanding of the persistence mechanisms of conjugative plasmids harbored by bacterial cells and populations. The diversity and intricacy of mechanisms affecting the successful propagation and long-term continued existence of these extra-chromosomal elements is extensive. Apart from the accessory genetic elements that may provide plasmid-harboring cells a selective advantage, special focus is placed on the mechanisms conjugative plasmids employ to ensure their stable maintenance in the host cell. These importantly include the ability to self-mobilize in a process termed conjugative transfer, which may occur across species barriers. Other plasmid stabilizing mechanisms include the multimer resolution system, active partitioning, and post-segregational-killing of plasmid-free cells. Finally, various molecular adaptations of plasmids to better match the genetic background of their bacterial host cell will be described.

Species association increases biofilm resistance to chemical and mechanical treatments

The study of biofilm ecology and interactions might help to improve our understanding of their resistance mechanisms to control strategies. Concerns that the diversity of the biofilm communities can affect disinfection efficacy have led us to examine the effect of two antimicrobial agents on two important spoilage bacteria. Studies were conducted on single and dual species biofilms of Bacillus cereus and Pseudomonas fluorescens. Biofilms were formed on a stainless steel rotating device, in a bioreactor, at a constant Reynolds number of agitation (Re(A)). Biofilm phenotypic characterization showed significant differences, mainly in the metabolic activity and both extracellular proteins and polysaccharides content. Cetyl trimethyl ammonium bromide (CTAB) and glutaraldehyde (GLUT) solutions in conjunction with increasing Re(A) were used to treat biofilms in order to assess their ability to kill and remove biofilms. B. cereus and P. fluorescens biofilms were stratified in a layered structure with each layer having differential tolerance to chemical and mechanical stresses. Dual species biofilms and P. fluorescens single biofilms had both the highest resistance to removal when pre-treated with CTAB and GLUT, respectively. B. cereus biofilms were the most affected by hydrodynamic disturbance and the most susceptible to antimicrobials. Dual biofilms were more resistant to antimicrobials than each single species biofilm, with a significant proportion of the population remaining in a viable state after exposure to CTAB or GLUT. Moreover, the species association increased the proportion of viable cells of both bacteria, comparatively to the single species scenarios, enhancing each other's survival to antimicrobials and the biofilm shear stress stability.

The sociobiology of biofilms

Biofilms are densely packed communities of microbial cells that grow on surfaces and surround themselves with secreted polymers. Many bacterial species form biofilms, and their study has revealed them to be complex and diverse. The structural and physiological complexity of biofilms has led to the idea that they are coordinated and cooperative groups, analogous to multicellular organisms. We evaluate this idea by addressing the findings of microbiologists from the perspective of sociobiology, including theories of collective behavior (self-organization) and social evolution. This yields two main conclusions. First, the appearance of organization in biofilms can emerge without active coordination. That is, biofilm properties such as phenotypic differentiation, species stratification and channel formation do not necessarily require that cells communicate with one another using specialized signaling molecules. Second, while local cooperation among bacteria may often occur, the evolution of cooperation among all cells is unlikely for most biofilms. Strong conflict can arise among multiple species and strains in a biofilm, and spontaneous mutation can generate conflict even within biofilms initiated by genetically identical cells. Biofilms will typically result from a balance between competition and cooperation, and we argue that understanding this balance is central to building a complete and predictive model of biofilm formation.

Defined spatial structure stabilizes a synthetic multispecies bacterial community

This paper shows that for microbial communities, "fences make good neighbors." Communities of soil microorganisms perform critical functions: controlling climate, enhancing crop production, and remediation of environmental contamination. Microbial communities in the oral cavity and the gut are of high biomedical interest. Understanding and harnessing the function of these communities is difficult: artificial microbial communities in the laboratory become unstable because of "winner-takes-all" competition among species. We constructed a community of three different species of wild-type soil bacteria with syntrophic interactions using a microfluidic device to control spatial structure and chemical communication. We found that defined microscale spatial structure is both necessary and sufficient for the stable coexistence of interacting bacterial species in the synthetic community. A mathematical model describes how spatial structure can balance the competition and positive interactions within the community, even when the rates of production and consumption of nutrients by species are mismatched, by exploiting nonlinearities of these processes. These findings provide experimental and modeling evidence for a class of communities that require microscale spatial structure for stability, and these results predict that controlling spatial structure may enable harnessing the function of natural and synthetic multispecies communities in the laboratory.

Complementary cooperation between two syntrophic bacteria in pesticide degradation

Interactions between microbial species, including competition and mutualism, influence the abundance and distribution of the related species. For example, metabolic cooperation among multiple bacteria plays a major role in the maintenance of consortia. This study aims to clarify how two bacterial species coexist in a syntrophic association involving the degradation of the pesticide fenitrothion. To elucidate essential mechanisms for maintaining a syntrophic association, we employed a mathematical model based on an experimental study, because experiment cannot elucidate various conditions for two bacterial coexistence. We isolated fenitrothion-degrading Sphingomonas sp. TFEE and its metabolite of 3-methyl-4-nitrophenol (3M4N)-degrading Burkholderia sp. MN1 from a fenitrothion-treated soil microcosm. Neither bacterium can completely degrade fenitrothion alone, but they can utilize the second intermediate, methylhydroquinone (MHQ). Burkholderia sp. MN1 excretes a portion of MHQ during the degradation of 3M4N, from which Sphingomonas sp. TFEE carries out degradation to obtain carbon and energy. Based on experimental findings, we developed mathematical models that represent the syntrophic association involving the two bacteria. We found that the two bacteria are characterized by the mutualistic degradation of fenitrothion. Dynamics of two bacteria are determined by the degree of cooperation between two bacteria (i.e., supply of 3M4N by Sphingomonas sp. TFEE and excretion of MHQ by Burkholderia sp. MN1) and the initial population sizes. The syntrophic association mediates the coexistence of the two bacteria under the possibility of resource competition for MHQ, and robustly facilitates the maintenance of ecosystem function in terms of degrading xenobiotics. Thus, the mathematical analysis and numerical computations based on the experiment indicate the key mechanisms for coexistence of Sphingomonas sp. TFEE and Burkholderia sp. MN1 in syntrophic association involving fenitrothion degradation.

Functional analysis of aromatic biosynthetic pathways in Pseudomonas putida KT2440

Pseudomonas putida KT2440 is a non-pathogenic prototrophic bacterium with high potential for biotechnological applications. Despite all that is known about this strain, the biosynthesis of essential chemicals has not been fully analysed and auxotroph mutants are scarce. We carried out massive mini-Tn5 random mutagenesis and screened for auxotrophs that require aromatic amino acids. The biosynthesis of aromatic amino acids was analysed in detail including physical and transcriptional organization of genes, complementation assays and feeding experiments to establish pathway intermediates. There is a single pathway from chorismate leading to the biosynthesis of tryptophan, whereas the biosynthesis of phenylalanine and tyrosine is achieved through multiple convergent pathways. Genes for tryptophan biosynthesis are grouped in unlinked regions with the trpBA and trpGDE genes organized as operons and the trpI, trpE and trpF genes organized as single transcriptional units. The pheA and tyrA gene-encoding multifunctional enzymes for phenylalanine and tyrosine biosynthesis are linked in the chromosome and form an operon with the serC gene involved in serine biosynthesis. The last step in the biosynthesis of these two amino acids requires an amino transferase activity for which multiple tyrB-like genes are present in the host chromosome.

Prokaryote-eukaryote interactions identified by using Caenorhabditis elegans

Prokaryote-eukaryote interactions are ubiquitous and have important medical and environmental significance. Despite this, a paucity of data exists on the mechanisms and pathogenic consequences of bacterial-fungal encounters within a living host. We used the nematode Caenorhabditis elegans as a substitute host to study the interactions between two ecologically related and clinically troublesome pathogens, the prokaryote, Acinetobacter baumannii, and the eukaryote, Candida albicans. After co-infecting C. elegans with these organisms, we observed that A. baumannii inhibits filamentation, a key virulence determinant of C. albicans. This antagonistic, cross-kingdom interaction led to attenuated virulence of C. albicans, as determined by improved nematode survival when infected with both pathogens. In vitro coinfection assays in planktonic and biofilm environments supported the inhibitory effects of A. baumannii toward C. albicans, further showing a predilection of A. baumannii for C. albicans filaments. Interestingly, we demonstrate a likely evolutionary defense by C. albicans against A. baumannii, whereby C. albicans inhibits A. baumannii growth once a quorum develops. This counteroffensive is at least partly mediated by the C. albicans quorum-sensing molecule farnesol. We used the C. elegans-A. baumannii-C. albicans coinfection model to screen an A. baumannii mutant library, leading to the identification of several mutants attenuated in their inhibitory activity toward C. albicans. These findings present an extension to the current paradigm of studying monomicrobial pathogenesis in C. elegans and by use of genetic manipulation, provides a whole-animal model system to investigate the complex dynamics of a polymicrobial infection.

Endogenous oxidative stress produces diversity and adaptability in biofilm communities

Many bacterial species are capable of biofilm growth, in which cells live and replicate within multicellular community groups. Recent work shows that biofilm growth by a wide variety of bacterial species can generate genetic diversity in microbial populations. This finding is significant because the presence of diverse subpopulations can extend the range of conditions in which communities can thrive. Here, we used biofilms formed by the pathogen Pseudomonas aeruginosa to investigate how this population diversity is produced. We found that some cells within biofilms incur double-stranded DNA breaks caused by endogenous oxidative stress. Genetic variants then result when breaks are repaired by a mutagenic mechanism involving recombinatorial DNA repair genes. We hypothesized that the mutations produced could promote the adaptation of biofilm communities to changing conditions in addition to generating diversity. To test this idea, we exposed biofilms to an antibiotic and found that the oxidative stress-break repair mechanism increased the emergence of antibiotic-resistant bacteria. The diversity and adaptability produced by this mechanism could help biofilm communities survive in harsh environments.

Bacterial and fungal biofilm infections

Biofilms are communal structures of microorganisms encased in an exopolymeric coat that form on both natural and abiotic surfaces and have been associated with a variety of persistent infections that respond poorly to conventional antibiotic chemotherapy. Biofilm infections of certain indwelling medical devices by common pathogens such as staphylococci are not only associated with increased morbidity and mortality but are also significant contributors to the emergence and dissemination of antibiotic resistance traits in the nosocomial setting. Current treatment paradigms for biofilm-associated infections of semipermanent indwelling devices typically involve surgical replacement of the device combined with long-term antibiotic therapy and incur high health care costs. This review summarizes the existing data relating to the nature, prevalence, and treatment of biofilm-associated infections and highlights experimental approaches and therapies that are being pursued toward more effective treatments.

Heterogeneous selection in a spatially structured environment affects fitness tradeoffs of plasmid carriage in pseudomonads

Environmental conditions under which fitness tradeoffs of plasmid carriage are balanced to facilitate plasmid persistence remain elusive. Periodic selection for plasmid-encoded traits due to the spatial and temporal variation typical in most natural environments (such as soil particles, plant leaf and root surfaces, gut linings, and the skin) may play a role. However, quantification of selection pressures and their effects is difficult at a scale relevant to the bacterium in situ. The present work describes a novel experimental system for such fine-scale quantification, with conditions designed to mimic the mosaic of spatially variable selection pressures present in natural surface environments. The effects of uniform and spatially heterogeneous mercuric chloride (HgCl(2)) on the dynamics of a model community of plasmid-carrying, mercury-resistant (Hg(r)) and plasmid-free, mercury-sensitive (Hg(s)) pseudomonads were compared. Hg resulted in an increase in the surface area occupied by, and therefore an increase in the fitness of, Hg(r) bacteria relative to Hg(s) bacteria. Uniform and heterogeneous Hg distributions were demonstrated to result in different community structures by epifluorescence microscopy, with heterogeneous Hg producing spatially variable selection landscapes. The effects of heterogeneous Hg were only apparent at scales of a few hundred micrometers, emphasizing the importance of using appropriate analysis methods to detect effects of environmental heterogeneity on community dynamics. Heterogeneous Hg resulted in negative frequency-dependent selection for Hg(r) cells, suggesting that sporadic selection may facilitate the discontinuous distribution of plasmids through host populations in complex, structured environments.

Physiological heterogeneity in biofilms

Biofilms contain bacterial cells that are in a wide range of physiological states. Within a biofilm population, cells with diverse genotypes and phenotypes that express distinct metabolic pathways, stress responses and other specific biological activities are juxtaposed. The mechanisms that contribute to this genetic and physiological heterogeneity include microscale chemical gradients, adaptation to local environmental conditions, stochastic gene expression and the genotypic variation that occurs through mutation and selection. Here, we discuss the processes that generate chemical gradients in biofilms, the genetic and physiological responses of the bacteria as they adapt to these gradients and the techniques that can be used to visualize and measure the microscale physiological heterogeneities of bacteria in biofilms.

Fitness of isogenic colony morphology variants of Pseudomonas aeruginosa in murine airway infection

Chronic lung infections with Pseudomonas aeruginosa are associated with the diversification of the persisting clone into niche specialists and morphotypes, a phenomenon called 'dissociative behaviour'. To explore the potential of P. aeruginosa to change its morphotype by single step loss-of-function mutagenesis, a signature-tagged mini-Tn5 plasposon library of the cystic fibrosis airway isolate TBCF10839 was screened for colony morphology variants under nine different conditions in vitro. Transposon insertion into 1% of the genome changed colony morphology into eight discernable morphotypes. Half of the 55 targets encode features of primary or secondary metabolism whereby quinolone production was frequently affected. In the other half the transposon had inserted into genes of the functional categories transport, regulation or motility/chemotaxis. To mimic dissociative behaviour of isogenic strains in lungs, pools of 25 colony morphology variants were tested for competitive fitness in an acute murine airway infection model. Six of the 55 mutants either grew better or worse in vivo than in vitro, respectively. Metabolic proficiency of the colony morphology variant was a key determinant for survival in murine airways. The most common morphotype of self-destructive autolysis did unexpectedly not impair fitness. Transposon insertions into homologous genes of strain PAO1 did not reproduce the TBCF10839 mutant morphotypes for 16 of 19 examined loci pointing to an important role of the genetic background on colony morphology. Depending on the chosen P. aeruginosa strain, functional genome scans will explore other areas of the evolutionary landscape. Based on our discordant findings of mutant phenotypes in P. aeruginosa strains PAO1, PA14 and TBCF10839, we conclude that the current focus on few reference strains may miss modes of niche adaptation and dissociative behaviour that are relevant for the microevolution of complex traits in the wild.