Colonial architecture in mixed species assemblages affects AHL mediated gene expression

Microbial interactions: ecology in a molecular perspective

The microorganism–microorganism or microorganism–host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial–host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community.

nDEP-driven cell patterning and bottom-up construction of cell aggregates using a new bioelectronic chip

Creating cell aggregates of controlled size and shape and patterning cells on substrates using a bottom-up approach constitutes important challenges for tissue-engineering applications and studies of cell-cell interactions. In this paper, we report nDEP (negative dielectrophoresis) driven assembly of cells as compact aggregates or onto defined areas using a new bioelectronic chip. This chip is composed of a quadripolar electrode array obtained using coplanar electrodes partially covered with a thin, micropatterned PDMS membrane. This thin PDMS layer was coated with poly-L-lysine and played the role of adhesive substrate for cell patterning. For the formation of detachable cell aggregates, the PDMS was not pretreated and cells were simply immobilized into assemblies maintained by cell-cell adhesion after the electric field removal. Cell viability after exposition to DEP buffer was also assessed, as well as cell spreading activity following DEP-driven assembly.

The presence and role of bacterial quorum sensing in activated sludge

Activated sludge used for wastewater treatment globally is composed of a high‐density microbial community of great biotechnological significance. In this study the presence and purpose of quorum sensing via N‐acylated‐l‐homoserine lactones (AHLs) in activated sludge was explored. The presence of N‐heptanoyl‐l‐homoserine lactone in organic extracts of sludge was demonstrated along with activation of a LuxR‐based AHL monitor strain deployed in sludge, indicating AHL‐mediated gene expression is active in sludge flocculates but not in the bulk aqueous phase. Bacterial isolates from activated sludge were screened for AHL production and expression of phenotypes commonly but not exclusively regulated by AHL‐mediated gene transcription. N‐acylated‐l‐homoserine lactone and exoenzyme production were frequently observed among the isolates. N‐acylated‐l‐homoserine lactone addition to sludge upregulated chitinase activity and an AHL‐ and chitinase‐producing isolate closely related to Aeromonas hydrophila was shown to respond to AHL addition with upregulation of chitinase activity. N‐acylated‐l‐homoserine lactones produced by this strain were identified and genes ahyI/R and chiA, encoding AHL production and response and chitinase activity respectively, were sequenced. These experiments provide insight into the relationship between AHL‐mediated gene expression and exoenzyme activity in activated sludge and may ultimately create opportunities to improve sludge performance.

Cellular dielectrophoresis: applications to the characterization, manipulation, separation and patterning of cells

Over the past decade, dielectrophoresis (DEP) has evolved into a powerful, robust and flexible method for cellular characterization, manipulation, separation and cell patterning. It is a field with widely varying disciplines, as it is quite common to see DEP integrated with a host of applications including microfluidics, impedance spectroscopy, tissue engineering, real-time PCR, immunoassays, stem-cell characterization, gene transfection and electroporation, just to name a few. The field is finally at the point where analytical and numerical polarization models can be used to adequately describe and characterize the dielectrophoretic behavior of cells, and there is ever increasing evidence demonstrating that electric fields can safely be used to manipulate cells without harm. As such, DEP is slowly making its way into the biological sciences. Today, DEP is being used to manipulate individual cells to specific regions of space for single-cell assays. DEP is able to separate rare cells from a heterogeneous cell suspension, where isolated cells can then be characterized and dynamically studied using nothing more than electric fields. However, there is need for a critical report to integrate the many new features of DEP for cellular applications. Here, a review of the basic theory and current applications of DEP, specifically for cells, is presented.

Construction by dielectrophoresis of microbial aggregates for the study of bacterial cell dormancy

A study of the effect of aggregate size on the resuscitation of dormant M. smegmatis was conducted by constructing cell aggregates with defined sizes and shapes using dielectrophoresis and monitoring the resuscitation process under controlled laboratorial conditions in a long-term cell feeding system. Differently sized cell aggregates were created on the surface of indium tin oxide coated microelectrodes, their heights and shapes controlled by the strength of the induced electric field and the shape of the microelectrodes. Both two-dimensional (ring-patterned) and three-dimensional cell aggregates were produced. The cell aggregates were maintained under sterile conditions at 37 degrees C for up to 14 days by continuously flushing Sauton's medium through the chamber. Resuscitation of dormant M. smegmatis was evaluated by the production of the fluorescent dye 5-cyano-2,3-ditolyltetrazolium chloride. The results confirm that the resuscitation of dormant M. smegmatis is triggered by the accumulation of a resuscitation promoting factor inside the aggregates by diffusion limitation.

Cell-cell signalling in bacteria: not simply a matter of quorum

Bacterial signalling known as quorum sensing (QS) relies on the synthesis of autoinducing signals throughout growth; when a threshold concentration is reached, these signals interact with a transcriptional regulator, allowing the expression of specific genes at a high cell density. One of the most studied intraspecies signalling is based on the use of N-acyl-homoserine lactones (AHL). Many factors other than cell density were shown to affect AHL accumulation and interfere with the QS signalling process. At the cellular level, the genetic determinants of QS are integrated in a complex regulatory network, including QS cascades and various transcriptional and post-transcriptional regulators that affect the synthesis of the AHL signal. In complex environments where bacteria exist, AHL do not accumulate at a constant rate; the diffusion and perception of the AHL signal outside bacterial cells can be compromised by abiotic environmental factors, by members of the bacterial community such as AHL-degrading bacteria and also by compounds produced by eukaryotes acting as an AHL mimic or inhibitor. This review aims to present all factors interfering with the AHL-mediated signalling process, at the levels of signal production, diffusion and perception.

Tissue engineering with electric fields: investigation of the shape of mammalian cell aggregates formed at interdigitated oppositely castellated electrodes

The shape of aggregates of cells formed by positive dielectrophoresis (DEP) at interdigitated oppositely castellated electrodes under different conditions was investigated and compared with calculations of the electric field gradient |nablaE(2)|, and the electric field E, and E(2). The results confirm that at low field strength the cells predominantly accumulate above the tips of the electrodes, but at higher electric field strengths the cells predominantly accumulate in the middle of the aggregate. For a given electrode size, a higher applied voltage significantly increases the aggregate footprint. Higher flow rates distort this pattern, with more cells accumulating at the electrodes that are upstream. Calculation of the electric field strength E, E(2) and the electric field strength gradient |nablaE(2)| in the interdigitated oppositely castellated electrode array shows that, at low flow rates, there is a strong correlation between the aggregate shape and the distribution of the electric field E and E(2), but not so between the aggregate shape and |nablaE(2)|. The results indicate that interparticle forces such as pearlchain formation strongly affect the aggregation process, but that, when positive DEP is used to make the aggregates, the distribution of the electric field E, or better E(2), can be used as a useful guide to the final aggregate shape.

The use of electric fields in tissue engineering: A review

The use of electric fields for measuring cell and tissue properties has a long history. However, the exploration of the use of electric fields in tissue engineering is only very recent. A review is given of the various methods by which electric fields may be used in tissue engineering, concentrating on the assembly of artificial tissues from its component cells using electrokinetics. A comparison is made of electrokinetic techniques with other physical cell manipulation techniques which can be used in the construction of artificial tissues.

Tissue engineering with electric fields: immobilization of mammalian cells in multilayer aggregates using dielectrophoresis

Positive dielectrophoresis can be used to create aggregates of animal cells with 3D architectures. It is shown that the cells, when pulled together into an aggregate by positive dielectrophoresis in a low-conductivity iso-osmotic solution, adhere to each other. The adherence of the cells to each other is non-specific and increases in time, and after 10-15 min becomes strong enough to immobilize the cells in the aggregate, enabling the ac electric field to be released, and the iso-osmotic buffer to be replaced by growth or other media. Cell viability is maintained. The new method of immobilization significantly simplifies the construction of aggregates of animal cells by dielectrophoresis, and increases the utility of dielectrophoresis in tissue engineering and related areas.

Acylated homoserine lactones in the environment: chameleons of bioactivity

Over the last 15 years, it has become increasingly apparent that a single class of compounds, the acylated homoserine lactones (AHLs), elicit effects on many levels of biological and ecological organization. Despite the fact that the distribution of AHL production in the prokaryotic phylogenetic tree is restricted to a small set of genera, representatives of these genera are abundant in the environment and are responsible for processes of much interest to humans. As well as driving interactions between clones, AHLs have been shown to mediate interactions between different species of bacteria and between bacteria and higher organisms, either through the phenotypes they regulate or directly through their own chemical behaviour. Understanding the biological activity of AHLs and the ecological consequences of these activities may provide us with an opportunity to manipulate the composition and function of complex biological assemblages. Ultimately, this broadens the biotechnological focus of AHL-based research beyond the attenuation of virulence in humans and plant pathogens.

Large scale dielectrophoretic construction of biofilms using textile technology

Arrays of microelectrodes for AC electrokinetic experiments were fabricated by weaving together stainless steel wires (weft) and flexible polyester yarn (warp) in a plain weave pattern. The cloth produced can be used to collect cells in low conductivity media by dielectrophoresis (DEP). The construction of model biofilms consisting of a yeast layer on top of a layer of M. luteus is demonstrated, using polyethylenimine (PEI) as the flocculating agent. This technique offers an alternative to the formation of biofilms at microelectrodes made by photolithography, and would allow the construction of biofilms with defined internal architectures by DEP at much larger scales than was possible previously. Furthermore, the flexibility of the cloth would also allow it to be distorted or folded into various shapes.

Does efficiency sensing unify diffusion and quorum sensing?

Quorum sensing faces evolutionary problems from non-producing or over-producing cheaters. Such problems are circumvented in diffusion sensing, an alternative explanation for quorum sensing. However, both explanations face the problems of signalling in complex environments such as the rhizosphere where, for example, the spatial distribution of cells can be more important for sensing than cell density, which we show by mathematical modelling. We argue that these conflicting concepts can be unified by a new hypothesis, efficiency sensing, and that some of the problems associated with signalling in complex environments, as well as the problem of maintaining honesty in signalling, can be avoided when the signalling cells grow in microcolonies.

Construction of artificially structured microbial consortia (ASMC) using dielectrophoresis: examining bacterial interactions via metabolic intermediates within environmental biofilms

The construction of artificial biofilms with defined internal architectures is described. Bacterial cells are suspended in a low conductivity medium, guided to specific areas in a microelectrode array by dielectrophoresis (DEP), and then immobilised using the flocculating agent poly(ethylenimine). Multispecies biofilms can be constructed by introducing different species at different times. The rapid construction of such biofilms with defined internal architectures provides, when combined with visual reporters of gene activity, a powerful new method for the investigation of the effects of the spatial organisation on interactions between bacterial species in biofilms. To demonstrate the utility of the technique as a method for investigating metabolic interactions in biofilms, aggregates were constructed from Acinetobacter sp. C6 and Pseudomonas putida::gfp. The Acinetobacter degrades benzyl alcohol, overproducing benzoate, which in turn is consumed by the Pseudomonas strain. The P. putida has a chromosomally expressed cassette encoding a gfp downstream of the promoter which controls degradation of benzoate, making the interaction between the two strains in the metabolism of benzyl alcohol visible by the production of green fluorescent protein (GFP). Microscopic observation of the biofilms, including the use of confocal laser scanning microscopy (CLSM), confirmed that metabolic exchange occurred. In addition, it was observed that the bacteria appear to have a preferred biofilm architecture, with P. putida in the bottom layer, and Acinetobacter at the top.