Growing reproducible biofilms with respect to structure and viable cell counts

Klebsiella pneumoniae AI-2 transporters mediate interspecies interactions and composition in a three-species biofilm community

Biofilms in nature often exist as communities. In this study, an experimental mixed-species community consisting of Pseudomonas aeruginosa, Pseudomonas protegens and Klebsiella pneumoniae was used to investigate how AI-2 transporters affect interspecies interactions and composition. The K. pneumoniae lsrB/lsrD deletion mutants had a 10-25-fold higher concentration of extracellular AI-2 compared to the wild-type. Although these deletion mutants produced monospecies biofilms of similar biomass, the substitution of these mutants for the parental strain significantly altered composition. Dual-species biofilm assays demonstrated that the changes in composition were due to the cumulative effect of pairwise interactions. It was further revealed that K. pneumoniae being present physically in the consortium was important in AI-2 mediating composition in the consortium, and that AI-2 transporters were crucial in achieving maximum biomass in the community. In conclusion, these findings demonstrate that AI-2 transporters mediate interspecies interactions and is important in maintaining the compositional equilibrium of the community.

Insulated Interlaced Surface Electrodes for Bacterial Inactivation and Detachment

Effective and stable antibiofouling surfaces and interfaces have long been of research interest. In this study, we designed, fabricated, and evaluated a surface coated with insulated interlaced electrodes for bacterial fouling reduction. The electrodes were printed Ag filaments of 100 μm width and 400 μm spacing over an area of 2 × 2 cm². The insulating Ag electrode coating material was polydimethylsiloxane (PDMS) or thermoplastic polyurethane (TPU) with a thickness of 10 to 40 μm. To evaluate the antibiofouling potential, E. coli inactivation after 2 min contact with the electrified surface and P. fluorescens detachment after 15 and 40 h growth were examined. The extent of bacterial inactivation was related to the insulating material, coating thickness, and applied voltage (magnitude and AC vs DC). A high bacterial inactivation (>98%) was achieved after only 2 min of treatment at 50 V AC and 10 kHz using a 10 μm TPU coating. P. fluorescens detachment after 15 and 40 h incubation in the absence of applied potential was completed with simultaneous cross-flow rinsing and AC application. Higher AC voltages and longer cross-flow rinsing times resulted in greater bacterial detachment with bacterial coverage able to be reduced to <1% after only 2 min of rinsing at 50 V AC and 10 kHz. Theoretical electric field analysis indicated that at 10 V the field strength penetrating the aqueous solution is nonuniform (∼16,000-20,000 V m^-1 for the 20 μm TPU) and suggests that dielectrophoresis plays a key role in bacterial detachment. The bacterial inactivation and detachment trends observed in this study indicate that this technique has merit for future antibiofouling surface development.

Biofilms vs. cities and humans vs. aliens - a tale of reproducibility in biofilms

Biofilms are complex and dynamic structures that include many more components than just viable cells. Therefore, the apparently simple goal of growing reproducible biofilms is often elusive. One of the challenges in defining reproducibility for biofilm research is that different research fields use a spectrum of parameters to define reproducibility for their particular application. For instance, is the researcher interested in achieving a similar population density, height of biofilm structures, or function of the biofilm in a certain ecosystem/industrial context? Within this article we categorize reproducibility into four different levels: level 1, no reproducibility; level 2, standard reproducibility; level 3, potential standard reproducibility; and level 4, total reproducibility. To better understand the need for these different levels of reproducibility, we expand on the 'cities of microbes' analogy for biofilms by imagining that a new civilization has reached the Earth's outskirts and starts studying the Earth's cities. This will provide a better sense of scale and illustrate how small details can impact profoundly on the growth and behavior of a biofilm and our understanding of reproducibility.

N-Acyl Homoserine Lactone-Mediated Quorum Sensing Regulates Species Interactions in Multispecies Biofilm Communities

Bacterial biofilms are important medically, environmentally and industrially and there is a need to understand the processes that govern functional synergy and dynamics of species within biofilm communities. Here, we have used a model, mixed-species biofilm community comprised of Pseudomonas aeruginosa PAO1, Pseudomonas protegens Pf-5 and Klebsiella pneumoniae KP1. This biofilm community displays higher biomass and increased resilience to antimicrobial stress conditions such as sodium dodecyl sulfate and tobramycin, compared to monospecies biofilm populations. P. aeruginosa is present at low proportions in the community and yet, it plays a critical role in community function, suggesting it acts as a keystone species in this community. To determine the factors that regulate community composition, we focused on P. aeruginosa because of its pronounced impact on community structure and function. Specifically, we evaluated the role of the N-acyl homoserine lactone (AHL) dependent quorum sensing (QS) system of P. aeruginosa PAO1, which regulates group behaviors including biofilm formation and the production of effector molecules. We found that mixed species biofilms containing P. aeruginosa QS mutants had significantly altered proportions of K. pneumoniae and P. protegens populations compared to mixed species biofilms with the wild type P. aeruginosa. Similarly, inactivation of QS effector genes, e.g. rhlA and pvdR, also governed the relative species proportions. While the absence of QS did not alter the proportions of the two species in dual species biofilms of P. aeruginosa and K. pneumoniae, it resulted in significantly lower proportions of P. aeruginosa in dual species biofilms with P. protegens. These observations suggest that QS plays an important role in modulating community biofilm structure and physiology and affects interspecific interactions.

Deciphering links between bacterial interactions and spatial organization in multispecies biofilms

Environmental microbes frequently live in multispecies biofilms where mutualistic relationships and co-evolution may occur, defining spatial organization for member species and overall community functions. In this context, intrinsic properties emerging from microbial interactions, such as efficient organization optimizing growth and activities in multispecies biofilms, may become the object of fitness selection. However, little is known on the nature of underlying interspecies interactions during establishment of a predictable spatial organization within multispecies biofilms. We present a comparative metatranscriptomic analysis of bacterial strains residing in triple-species and four-species biofilms, aiming at deciphering molecular mechanisms underpinning bacterial interactions responsible of the remarkably enhanced biomass production and associated typical spatial organization they display. Metatranscriptomic profiles concurred with changes in micro-site occupation in response to the addition/removal of a single species, being driven by both cooperation, competition, and facilitation processes. We conclude that the enhanced biomass production of the four-species biofilm is an intrinsic community property emerging from finely tuned space optimization achieved through concerted antagonistic and mutualistic interactions, where each species occupies a defined micro-site favoring its own growth. Our results further illustrate how molecular mechanisms can be better interpreted when supported by visual imaging of actual microscopic spatial organization, and we propose phenotypic adaptation selected by social interactions as molecular mechanisms stabilizing microbial communities.

Characterization of Mixed-Species Biofilm Formed by Vibrio parahaemolyticus and Listeria monocytogenes

Mixed-species biofilms are the predominant form of biofilms found in nature. Research on biofilms have typically concentrated on single species biofilms and this study expands the horizon of biofilm research, where the characterization and dynamic changes of mono and mixed-species biofilms formed by the pathogens, Vibrio parahaemolyticus and Listeria monocytogenes were investigated. Compared to mono-species biofilm, the biomass, bio-volume, and thickness of mixed-species biofilms were significantly lower, which were confirmed using crystal violet staining, confocal laser scanning microscopy and scanning electron microscopy. Further experimental analysis showed these variations might result from the reduction of bacterial numbers, the down-regulation of biofilm-regulated genes and loss of metabolic activity in mixed-species biofilm. In addition, V. parahaemolyticus was located primarily on the surface layers of the mixed-species biofilms thus accruing competitive advantage. This competitive advantage was evidenced in a higher V. parahaemolyticus population density in the mixed-species biofilms. The adhesion to surfaces of the mixed-species biofilms were also reduced due to lower concentrations of extracellular polysaccharide and protein when the structure of the mixed-species was examined using Raman spectral analysis, phenol-sulfuric acid method and Lowry method. Furthermore, the minimum biofilm inhibitory concentration to antibiotics obviously decreased when V. parahaemolyticus co-exited with L. monocytogenes. This study firstly elucidated the interactive behavior in biofilm development of two foodborne pathogens, and future studies for biofilm control and antibiotic therapy should take into account interactions in mixed-species biofilms.

Tracking bacteriome variation over time in Listeria monocytogenes-positive foci in food industry

The variation in microbial composition over time was assessed in biofilms formed in situ on selected non-food and food contact surfaces of meat and fish industries, previously identified as Listeria monocytogenes-positive foci. First, all samples were analysed for the detection and quantification of L. monocytogenes using ISO 11290-1 and ISO 11290-2 norms, respectively. Although the pathogen was initially detected in all samples, direct quantification was not possible. Psychrotrophic bacteria counts were among resident microbiota in meat industry samples (Mean_max = 6.14 log CFU/cm²) compared to those form fish industry (Mean_max = 5.85 log CFU/cm²). Visual analysis of the biofilms using epifluorescence microscopy revealed a trend to form microcolonies in which damaged/dead cells would act as anchoring structures. 16S rRNA gene metagenetic analysis demonstrated that, although Proteobacteria (71.37%) initially dominated the bacterial communities at one meat industry location, there was a dramatic shift in composition as the biofilms matured, where Actinobacteria (79.72%) became the major phylum present in later samples. This change was largely due to an increase of Nocardiaceae, Micrococcaceae and Microbacteriaceae. Nevertheless, for the other sampling location, the relative abundance of the dominating phylum (Firmicutes) remained consistent over the entire sampling period (Mean = 63.02%). In fish industry samples, Proteobacteria also initially dominated early on (90.69%) but subsequent sampling showed a higher diversity in which Bacteroidetes and Proteobacteria were the most abundant phyla accounting for the 48.04 and 37.98%, respectively by the last sampling period. Regardless of the location, the community profiles of the endpoint samples were similar to those reported previously. This demonstrated that in a given industrial setting there is a trend to establish a determinate biofilm structure due to the environmental factors and the constant incoming microbiota. This information could be used to improve the existing sanitisation protocols or for the design of novel strategies.

Micro-scale intermixing: a requisite for stable and synergistic co-establishment in a four-species biofilm

Microorganisms frequently coexist in complex multispecies communities, where they distribute non-randomly, reflective of the social interactions that occur. It is therefore important to understand how social interactions and local spatial organization influences multispecies biofilm succession. Here the localization of species pairs was analyzed in three dimensions in a reproducible four-species biofilm model, to study the impact of spatial positioning of individual species on the temporal development of the community. We found, that as the biofilms developed, species pairs exhibited distinct intermixing patterns unique to the four-member biofilms. Higher biomass and more intermixing were found in four-species biofilms compared to biofilms with fewer species. Intriguingly, in local regions within the four member biofilms where Microbacterium oxydans was scant, both biomass and intermixing of all species were lowered, compared to regions where M. oxydans was present at typical densities. Our data suggest that Xanthomonas retroflexus and M. oxydans, both low abundant biofilm-members, intermixed continuously during the development of the four-species biofilm, hereby facilitating their own establishment. In turn, this seems to have promoted distinct spatial organization of Stenotrophomonas rhizophila and Paenibacillus amylolyticus enabling enhanced growth of all four species. Here local intermixing of bacteria advanced the temporal development of a multi-species biofilm.

Quantifying the combined effects of pronase and benzalkonium chloride in removing late-stage Listeria monocytogenes-Escherichia coli dual-species biofilms

This work presents the assessment of the effectivity of a pronase (PRN)-benzalkonium chloride (BAC) sequential treatment in removing Listeria monocytogenes-Escherichia coli dual-species biofilms grown on stainless steel (SS) using fluorescence microscopy and plate count assays. The effects of PRN-BAC on the occupied area (OA) by undamaged cells in 168 h dual-species samples were determined using a first-order factorial design. Empirical equations significantly (r² = 0.927) described a negative individual effect of BAC and a negative interactive effect of PRN-BAC achieving OA reductions up to 46%. After treatment, high numbers of remaining attached and released viable and cultivable E. coli cells were detected in PRN-BAC combinations when low BAC concentrations were used. Therefore, at appropriate BAC doses, in addition to biofilm removal, sequential application of PRN and BAC represents an appealing strategy for pathogen control on SS surfaces while hindering the dispersion of live cells into the environment.

Low-abundant species facilitates specific spatial organization that promotes multispecies biofilm formation

Microorganisms frequently co-exist in matrix-embedded multispecies biofilms. Within biofilms, interspecies interactions influence the spatial organization of member species, which likely play an important role in shaping the development, structure and function of these communities. Here, a reproducible four-species biofilm, composed of Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus, was established to study the importance of individual species spatial organization during multispecies biofilm development. We found that the growth of species that are poor biofilm formers, M. oxydans and P. amylolyticus, were highly enhanced when residing in the four-species biofilm. Interestingly, the presence of the low-abundant M. oxydans (0.5% of biomass volume) was observed to trigger changes in the composition of the four-species community. The other three species were crucially needed for the successful inclusion of M. oxydans in the four-species biofilm, where X. retroflexus was consistently positioned in the top layer of the mature four-species biofilm. These findings suggest that low abundance key species can significantly impact the spatial organization and hereby stabilize the function and composition of complex microbiomes.

Removal of Listeria monocytogenes dual-species biofilms using combined enzyme-benzalkonium chloride treatments

The effects of pronase (PRN), cellulase (CEL) or DNaseI alone or combined with benzalkonium chloride (BAC) against Listeria monocytogenes-carrying biofilms were assayed. The best removal activity against L. monocytogenes-Escherichia coli biofilms was obtained using DNaseI followed by PRN and CEL. Subsequently, a modified logistic model was used to quantify the combined effects of PRN or DNaseI with BAC. A better BAC performance after PRN compared to DNaseI eradicating L. monocytogenes was observed. In E. coli the effects were the opposite. Finally, effects of DNaseI and DNaseI-BAC treatments were compared against two different L. monocytogenes-carrying biofilms. DNaseI-BAC was more effective against L. monocytogenes when co-cultured with E. coli. Nonetheless, comparing the removal effects after BAC addition, these were higher in mixed-biofilms with Pseudomonas fluorescens. However, a high number of released viable cells was observed after combined treatments. These results open new perspectives of enzymes as an anti-biofilm strategy for environmental pathogen control.

Epidemiology and Virulence of Klebsiella pneumoniae

Strains of Klebsiella pneumoniae are frequently opportunistic pathogens implicated in urinary tract and catheter-associated urinary-tract infections of hospitalized patients and compromised individuals. Infections are particularly difficult to treat since most clinical isolates exhibit resistance to several antibiotics leading to treatment failure and the possibility of systemic dissemination. Infections of medical devices such as urinary catheters is a major site of K. pneumoniae infections and has been suggested to involve the formation of biofilms on these surfaces. Over the last decade there has been an increase in research activity designed to investigate the pathogenesis of K. pneumoniae in the urinary tract. These investigations have begun to define the bacterial factors that contribute to growth and biofilm formation. Several virulence factors have been demonstrated to mediate K. pneumoniae infectivity and include, but are most likely not limited to, adherence factors, capsule production, lipopolysaccharide presence, and siderophore activity. The development of both in vitro and in vivo models of infection will lead to further elucidation of the molecular pathogenesis of K. pneumoniae. As for most opportunistic infections, the role of host factors as well as bacterial traits are crucial in determining the outcome of infections. In addition, multidrug-resistant strains of these bacteria have become a serious problem in the treatment of Klebsiella infections and novel strategies to prevent and inhibit bacterial growth need to be developed. Overall, the frequency, significance, and morbidity associated with K. pneumoniae urinary tract infections have increased over many years. The emergence of these bacteria as sources of antibiotic resistance and pathogens of the urinary tract present a challenging problem for the clinician in terms of management and treatment of individuals.

Semiquantitative Performance and Mechanism Evaluation of Carbon Nanomaterials as Cathode Coatings for Microbial Fouling Reduction

In this study, we examine bacterial attachment and survival on a titanium (Ti) cathode coated with various carbon nanomaterials (CNM): pristine carbon nanotubes (CNT), oxidized carbon nanotubes (O-CNT), oxidized-annealed carbon nanotubes (OA-CNT), carbon black (CB), and reduced graphene oxide (rGO). The carbon nanomaterials were dispersed in an isopropyl alcohol-Nafion solution and were then used to dip-coat a Ti substrate. Pseudomonas fluorescens was selected as the representative bacterium for environmental biofouling. Experiments in the absence of an electric potential indicate that increased nanoscale surface roughness and decreased hydrophobicity of the CNM coating decreased bacterial adhesion. The loss of bacterial viability on the noncharged CNM coatings ranged from 22% for CB to 67% for OA-CNT and was dependent on the CNM dimensions and surface chemistry. For electrochemical experiments, the total density and percentage of inactivation of the adherent bacteria were analyzed semiquantitatively as functions of electrode potential, current density, and hydrogen peroxide generation. Electrode potential and hydrogen peroxide generation were the dominant factors with regard to short-term (3-h) bacterial attachment and inactivation, respectively. Extended-time electrochemical experiments (12 h) indicated that in all cases, the density of total deposited bacteria increased almost linearly with time and that the rate of bacterial adhesion was decreased 8- to 10-fold when an electric potential was applied. In summary, this study provides a fundamental rationale for the selection of CNM as cathode coatings and electric potential to reduce microbial fouling.

The continuity of bacterial and physicochemical evolution: theory and experiments

The continuity of chemical and biological evolution, incorporating life's emergence, can be explored experimentally by energizing 'dead' bacterial biomacromolecules with nutrients under cycling physicochemical gradients. This approach arises from three evolutionary principles rooted in physical chemistry: (i) broken bacterial cells cannot spontaneously self-assemble into a living state without the supply of external energy - 2nd law of thermodynamics, (ii) the energy delivery must be cycling - the primary mechanism of chemical evolution at rotating planetary surfaces under solar irradiation, (iii) the cycling energy must act on chemical mixtures of high molecular diversity and crowding - provided by dead bacterial populations.

Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm

Most studies of biofilm biology have taken a reductionist approach, where single-species biofilms have been extensively investigated. However, biofilms in nature mostly comprise multiple species, where interspecies interactions can shape the development, structure and function of these communities differently from biofilm populations. Hence, a reproducible mixed-species biofilm comprising Pseudomonas aeruginosa, Pseudomonas protegens and Klebsiella pneumoniae was adapted to study how interspecies interactions affect biofilm development, structure and stress responses. Each species was fluorescently tagged to determine its abundance and spatial localization within the biofilm. The mixed-species biofilm exhibited distinct structures that were not observed in comparable single-species biofilms. In addition, development of the mixed-species biofilm was delayed 1-2 days compared with the single-species biofilms. Composition and spatial organization of the mixed-species biofilm also changed along the flow cell channel, where nutrient conditions and growth rate of each species could have a part in community assembly. Intriguingly, the mixed-species biofilm was more resistant to the antimicrobials sodium dodecyl sulfate and tobramycin than the single-species biofilms. Crucially, such community level resilience was found to be a protection offered by the resistant species to the whole community rather than selection for the resistant species. In contrast, community-level resilience was not observed for mixed-species planktonic cultures. These findings suggest that community-level interactions, such as sharing of public goods, are unique to the structured biofilm community, where the members are closely associated with each other.

Pulse-based non-thermal plasma (NTP) disrupts the structural characteristics of bacterial biofilms

Bacterial biofilms were constructed in vitro with two pathogenic strains of Pseudomonas aeruginosa and Staphylococcus aureus using a modified, novel sequential bioreactor system. The structure and stability of bacterial biofilms were evaluated following exposure to non-thermal plasma (NTP) discharge. Mathematical software was used to determine structural changes as biofilms grew over the course of 7 days. Statistical modeling was also performed to assess the ability of NTP to affect the development of the biofilms over different periods of time. Several structural characteristics were significantly affected by NTP discharge whereas others were unaffected. Changes in the three-dimensional structure of the biofilm following introduction of NTP was not limited to one period of development. The mechanism for this phenomenon is not understood but is likely to be a dual, synergistic effect due to the composition of the reactive species and other plasma-associated molecules isolated previously in the NTP discharge used in this study.

New trends in peptide-based anti-biofilm strategies: a review of recent achievements and bioinformatic approaches

Antimicrobial peptides (AMPs) have a broad spectrum of activity and unspecific mechanisms of action. Therefore, they are seen as valid alternatives to overcome clinically relevant biofilms and reduce the chance of acquired resistance. This paper reviews AMPs and anti-biofilm AMP-based strategies and discusses ongoing and future work. Recent studies report successful AMP-based prophylactic and therapeutic strategies, several databases catalogue AMP information and analysis tools, and novel bioinformatics tools are supporting AMP discovery and design. However, most AMP studies are performed with planktonic cultures, and most studies on sessile cells test AMPs on growing rather than mature biofilms. Promising preliminary synergistic studies have to be consubstantiated and the study of functionalized coatings with AMPs must be further explored. Standardized operating protocols, to enforce the repeatability and reproducibility of AMP anti-biofilm tests, and automated means of screening and processing the ever-expanding literature are still missing.

Biofilm image reconstruction for assessing structural parameters

The structure of biofilms can be numerically quantified from microscopy images using structural parameters. These parameters are used in biofilm image analysis to compare biofilms, to monitor temporal variation in biofilm structure, to quantify the effects of antibiotics on biofilm structure and to determine the effects of environmental conditions on biofilm structure. It is often hypothesized that biofilms with similar structural parameter values will have similar structures; however, this hypothesis has never been tested. The main goal was to test the hypothesis that the commonly used structural parameters can characterize the differences or similarities between biofilm structures. To achieve this goal (1) biofilm image reconstruction was developed as a new tool for assessing structural parameters, (2) independent reconstructions using the same starting structural parameters were tested to see how they differed from each other, (3) the effect of the original image parameter values on reconstruction success was evaluated, and (4) the effect of the number and type of the parameters on reconstruction success was evaluated. It was found that two biofilms characterized by identical commonly used structural parameter values may look different, that the number and size of clusters in the original biofilm image affect image reconstruction success and that, in general, a small set of arbitrarily selected parameters may not reveal relevant differences between biofilm structures.

Biofilm morphology as related to the porous media clogging

Aquifer recharge for the wastewater reuse has been considered and studied as a promising process to cope with the worldwide water scarcity. Soil clogging by an excessive growth of bacteria is often accompanied with the aquifer recharge. In this study, biofilm morphology and hydraulic conductivity were concurrently characterized at two flow rates and two levels of substrate concentrations. The experiments were conducted using a biofilm flow cell that was filled with glass beads. The biofilm images taken by confocal laser scanning microscopy (CLSM) were quantified by textural, areal, and fractal parameters. Hydraulic conductivity was monitored during the experiments. The flow velocity influenced the superficial morphology of biofilms and initial clogging time, while the substrate concentration affected biofilm density and clogging rate. Three different clogging mechanisms were suggested depending on the flow rate and substrate concentration: (1) clogging at a high flow rate can be accelerated by entrapped and accumulated biofilms, and can be easily eliminated by high shear force, (2) clogging at a low flow rate can be delayed for the time of local biofilm growths in the narrow pore necks, but the biofilm is rigid enough not to be sloughed, and (3) clogging in a solution with high substrate concentrations cannot be easily eliminated because of the growth of dense biofilms. The depicted biological clogging mechanisms will play a role in supporting studies about aquifer recharge.

High adsorption rate is detrimental to bacteriophage fitness in a biofilm-like environment

BACKGROUND

Bacterial biofilm is ubiquitous in nature. However, it is not clear how this crowded habitat would impact the evolution of bacteriophage (phage) life history traits. In this study, we constructed isogenic lambda phage strains that only differed in their adsorption rates, because of the presence/absence of extra side tail fibers or improved tail fiber J, and maker states. The high cell density and viscosity of the biofilm environment was approximated by the standard double-layer agar plate. The phage infection cycle in the biofilm environment was decomposed into three stages: settlement on to the biofilm surface, production of phage progeny inside the biofilm, and emigration of phage progeny out of the current focus of infection.

RESULTS

We found that in all cases high adsorption rate is beneficial for phage settlement, but detrimental to phage production (in terms of plaque size and productivity) and emigration out of the current plaque. Overall, the advantage of high adsorption accrued during settlement is more than offset by the disadvantages experienced during the production and emigration stages. The advantage of low adsorption rate was further demonstrated by the rapid emergence of low-adsorption mutant from a high-adsorption phage strain with the side tail fibers. DNA sequencing showed that 19 out of the 21 independent mutant clones have mutations in the stf gene, with the majority of them being single-nucleotide insertion/deletion mutations occurring in regions with homonucleotide runs.

CONCLUSION

We conclude that high mutation rate of the stf gene would ensure the existence of side tail fiber polymorphism, thus contributing to rapid adaptation of the phage population between diametrically different habitats of benthic biofilm and planktonic liquid culture. Such adaptability would also help to explain the maintenance of the stf gene in phage lambda's genome.

Toward automated analysis of biofilm architecture: bias caused by extraneous confocal laser scanning microscopy images

An increasing number of studies utilize confocal laser scanning microscopy (CLSM) for in situ visualization of biofilms and rely on the use of image analysis programs to extract quantitative descriptors of architecture. Recently, designed programs have begun incorporating procedures to automatically determine threshold values for three-dimensional CLSM image stacks. We have found that the automated threshold calculation is biased when a stack contains images lacking pixels of biological significance. Consequently, we have created the novel program Auto PHLIP-ML to resolve this bias by iteratively excluding extraneous images based on their area coverage of biomass. A procedure was developed to identify the optimal percent area coverage value used for extraneous image removal (PACVEIR). The optimal PACVEIR was defined to occur when the standard deviation of mean thickness, determined from replicate image stacks, was at a maximum, because it more accurately reflected inherent structural variation. Ten monoculture biofilms of either Ralstonia eutropha JMP228n::gfp or Acinetobacter sp. strain BD413 were tested to verify the routine. All biofilms exhibited an optimal PACVEIR between 0 and 1%. Prior to the exclusion of extraneous images, JMP228n::gfp appeared to develop more homogeneous biofilms than BD413. However, after the removal of extraneous images, JMP228n::gfp biofilms were found to form more heterogeneous biofilms. Similarly, JMP228n::gfp biofilms grown on glass surfaces vis-à-vis polyethylene membranes produced significantly different architectures after extraneous images had been removed but not when such images were included in threshold calculations. This study shows that the failure to remove extraneous images skewed a seemingly objective analysis of biofilm architecture and significantly altered statistically derived conclusions.

On the reproducibility of microcosm experiments - different community composition in parallel phototrophic biofilm microcosms

Phototrophic biofilms were cultivated simultaneously using the same inoculum in three identical flow-lane microcosms located in different laboratories. The growth rates of the biofilms were similar in the different microcosms, but denaturing gradient gel electrophoresis (DGGE) analysis of both 16S and 18S rRNA gene fragments showed that the communities developed differently in terms of species richness and community composition. One microcosm was dominated by Microcoleus and Phormidium species, the second microcosm was dominated by Synechocystis and Phormidium species, and the third microcosm was dominated by Microcoleus- and Planktothrix- affiliated species. No clear effect of light intensity on the cyanobacterial community composition was observed. In addition, DGGE profiles obtained from the cultivated biofilms showed a low resemblance with the profiles derived from the inoculum. These findings demonstrate that validation of reproducibility is essential for the use of microcosm systems in microbial ecology studies.

Can mushrooms fix atmospheric nitrogen?

It is generally reported that fungi like Pleurotus spp. can fix nitrogen (N2). The way they do it is still not clear. The present study hypothesized that only associations of fungi and diazotrophs can fix N2. This was tested in vitro. Pleurotus ostreatus was inoculated with a bradyrhizobial strain nodulating soybean and P. ostreatus with no inoculation was maintained as a control. At maximum mycelial colonization by the bradyrhizobial strain and biofilm formation, the cultures were subjected to acetylene reduction assay (ARA). Another set of the cultures was evaluated for growth and nitrogen accumulation. Nitrogenase activity was present in the biofilm, but not when the fungus or the bradyrhizobial strain was alone. A significant reduction in mycelial dry weight and a significant increase in nitrogen concentration were observed in the inoculated cultures compared to the controls. The mycelial weight reduction could be attributed to C transfer from the fungus to the bradyrhizobial strain, because of high C cost of biological N2 fixation. This needs further investigations using 14C isotopic tracers. It is clear from the present study that mushrooms alone cannot fix atmospheric N2. But when they are in association with diazotrophs, nitrogenase activity is detected because of the diazotrophic N2 fixation. It is not the fungus that fixes N2 as reported earlier. Effective N2 fixing systems, such as the present one, may be used to increase protein content of mushrooms. Our study has implications for future identification of as yet unidentified N2 systems occurring in the environment.

Quantifying biofilm structure: facts and fiction

There is no doubt among biofilm researchers that biofilm structure is important to many biofilm processes, such as the transport of nutrients to deeper layers of the biofilm. However, biofilm structure is an elusive term understood only qualitatively, and as such it cannot be directly correlated with any measurable parameters characterizing biofilm performance. To correlate biofilm structure with the parameters characterizing biofilm performance, such as the rate of nutrient transport within the space occupied by the biofilms, biofilm structure must first be quantified and expressed numerically on an appropriate scale. The task of extracting numerical parameters quantifying biofilm structure relies on using biofilm imaging and image analysis. Although defining parameters characterizing biofilm structure is relatively straightforward, and multiple parameters have been described in the computer science literature, interpreting the results of such analyses is not trivial. Existing computer software developed by several research groups, including ours, for the sole purpose of analyzing biofilm images helps quantify parameters from biofilm images but does nothing to help interpret the results of such analyses. Although computing structural parameters from biofilm images permits correlating biofilm structure with other biofilm processes, the meaning of the results is not obvious. The first step to understanding the quantification of biofilm structure, developing image analysis, methods to quantify information from biofilm images, has been made by several research groups. The next step is to explain the meaning of these analyses. This presentation explains the meaning of several parameters commonly used to characterize biofilm structure. It also reviews the authors' research and experience in quantifying biofilm structure and their attempts to quantitatively relate biofilm structure to fundamental biofilm processes.

A microcantilever-based pathogen detector

The ability to detect small amounts of materials, especially bacterial organisms, is important for medical diagnostics and national security issues. Engineered micromechanical systems provide one approach for constructing multifunctional, highly sensitive, real-time, immunospecific biological detectors. We present qualitative detection of specific Salmonella enterica strains using a functionalized silicon nitride microcantilever. Detection is achieved due to a change in the surface stress on the cantilever surface in situ upon binding of a small number of bacteria. Scanning electron micrographs indicate that less than 25 adsorbed bacteria are required for detection.

A computer investigation of chemically mediated detachment in bacterial biofilms

A three-dimensional computer model was used to evaluate the effect of chemically mediated detachment on biofilm development in a negligible-shear environment. The model, BacLAB, combines conventional diffusion-reaction equations for chemicals with a cellular automata algorithm to simulate bacterial growth, movement and detachment. BacLAB simulates the life cycle of a bacterial biofilm from its initial colonization of a surface to the development of a mature biofilm with cell areal densities comparable to those in the laboratory. A base model founded on well established transport equations that are easily adaptable to investigate conjectures at the biological level has been created. In this study, the conjecture of a detachment mechanism involving a bacterially produced chemical detachment factor in which high local concentrations of this detachment factor cause the bacteria to detach from the biofilm was examined. The results show that the often observed 'mushroom'-shaped structure can occur if detachment events create voids so that the remaining attached cells look like mushrooms.

Development of a standard test to assess the resistance of Staphylococcus aureus biofilm cells to disinfectants

A standardized disinfectant test for Staphylococcus aureus cells in biofilms was developed. Two disinfectants, the membrane-active compound benzalkonium chloride (BAC) and the oxidizing agent sodium hypochlorite, were used to evaluate the biofilm test. S. aureus formed biofilms on glass, stainless steel, and polystyrene in a simple system with constant nutrient flow that mimicked as closely as possible the conditions used in the current standard European disinfectant test (EN 1040). The biofilm that was formed on glass contained cell clumps and extracellular polysaccharides. The average surface coverage was 60%, and most (92%) of the biofilm cells were viable. Biofilm formation and biofilm disinfection in different experiments were reproducible. For biofilms exposed to BAC and hypochlorite the concentrations needed to achieve 4-log killing were 50 and 600 times higher, respectively, than the concentrations needed to achieve this level of killing with the European phase 1 suspension test cells. Our results show that a standardized disinfectant test for biofilm cells is a useful addition to the current standard tests.