Ecological succession and the competition-colonization trade-off in microbial communities.

BACKGROUND: During range expansion in spatially distributed habitats, organisms differ from one another in terms of their patterns of localization versus propagation. To exploit locations or explore the landscape? This is the competition-colonization trade-off, a dichotomy at the core of ecological succession. In bacterial communities, this trade-off is a fundamental mechanism towards understanding spatio-temporal fluxes in microbiome composition. RESULTS: Using microfluidics devices as structured bacterial habitats, we show that, in a synthetic two-species community of motile strains, Escherichia coli is a fugitive species, whereas Pseudomonas aeruginosa is a slower colonizer but superior competitor. We provide evidence highlighting the role of succession and the relevance of this trade-off in the community assembly of bacteria in spatially distributed patchy landscapes. Furthermore, aggregation-dependent priority effects enhance coexistence which is not possible in well-mixed environments. CONCLUSIONS: Our findings underscore the interplay between micron-scale landscape structure and dispersal in shaping biodiversity patterns in microbial ecosystems. Understanding this interplay is key to unleash the technological revolution of microbiome applications.

Comparative Study of the Solid-Liquid Interfacial Adsorption of Proteins in Their Native and Amyloid Forms.

The adhesive properties of amyloid fibers are thought to play a crucial role in various negative and positive aggregation processes, the study of which might help in their understanding and control. Amyloids have been prepared from two proteins, lysozyme and ß-lactoglobulin, as well as an Exendin-4 derivative miniprotein (E5). Thermal treatment was applied to form amyloids and their structure was verified by thioflavin T (ThT), 8-Anilino-1-naphthalenesulfonic acid (ANS) dye tests and electronic circular dichroism spectroscopy (ECD). Adsorption properties of the native and amyloid forms of the three proteins were investigated and compared using the mass-sensitive quartz crystal microbalance (QCM) technique. Due to the possible electrostatic and hydrophobic interactions, similar adsorbed amounts were found for the native or amyloid forms, while the structures of the adsorbed layers differed significantly. Native proteins formed smooth and dense adsorption layers. On the contrary, a viscoelastic, highly loose layer was formed in the presence of the amyloid forms, shown by increased motional resistance values determined by the QCM technique and also indicated by atomic force microscopy (AFM) and wettability measurements. The elongated structure and increased hydrophobicity of amyloids might contribute to this kind of aggregation.

Construction and Properties of Donor-Acceptor Stenhouse Adducts on Gold Surfaces.

The construction of a donor-acceptor Stenhouse adduct molecular layer on a gold surface is presented. To avoid the incompatibility of the thiol surface-binding group with the donor-acceptor polyene structure of the switch, an interfacial reaction approach was followed. Poly(dopamine)-supported gold nanoparticles on quartz slides were chosen as substrates, which was expected to facilitate both the interfacial reaction and the switching process by providing favorable steric conditions due to the curved particle surface. The reaction between the surface-bound donor half and the CF3-isoxazolone-based acceptor half was proved to be successful by X-ray photoelectron spectroscopy (XPS). However, UV-vis measurements suggested that a closed, cyclopentenone-containing structure of the switch formed on the surface irreversibly. Analysis of the wetting behavior of the surface revealed spontaneous water spreading that could be associated with conformational changes of the closed isomer.

Effects of ionic strength on the surface tension and nonequilibrium interfacial characteristics of poly(sodium styrenesulfonate)/dodecyltrimethylammonium bromide mixtures.

We rationalize the surface tension behavior and nonequilibrium interfacial characteristics of high molecular weight poly(sodium styrenesulfonate)/dodecyltrimethylammonium bromide (NaPSS/DTAB) mixtures with respect to the ionic strength. Excellent agreement is achieved between experimental data and our recent empirical model [Langmuir 2013, 29, 11554], which is based on the lack of colloidal stability of bulk aggregates in the phase separation region and has no free fitting parameters. We show that the size of a surface tension peak positioned at the edge of the phase separation region can be suppressed by the addition of inert electrolyte, which lowers the critical micelle concentration in relation to the phase separation region. Such manipulation of the peak is possible for the 100 ppm NaPSS/DTAB system because there is a high free surfactant concentration in the phase separation region. The close agreement of our model with the experimental data of samples in the phase separation region with respect to the ionic strength indicates that the surface tension behavior can be rationalized in terms of comprehensive precipitation regardless of whether there is a peak or not. The time scale of precipitation for the investigated system is on the order of one month, which emphasizes the need to understand the dynamic changes in the state of bulk aggregation in order to rationalize the surface properties of strongly interacting mixtures; steady state surface properties measured in the interim period will represent samples far from equilibrium. We show also that the surface properties of samples of low ionic strength outside the equilibrium phase separation region can be extreme opposites depending on the sample history, which is attributed to the generation of trapped nonequilibrium states. This work highlights the need to validate the underlying nature of oppositely charged polyelectrolyte/surfactant systems prior to the interpretation of experimental data within an equilibrium framework.

Examination of phacoemulsification tips after different numbers of cataract surgeries.

To compare unused phacoemulsification tips and those used different times with different techniques of cataract surgery (divide and conquer and chop), in vivo phacoemulsifications were performed with tips of different numbers of operation. These were compared with the same number of sterilized-only and unused tips with the help of an atomic force microscope. Comparison of roughness values (Sa, Sq), geometric and measurable flange length and surface was also performed (profile length %, area %). The differences between the parameters that can be measured during surgery (average ultrasound percentage, US ave %, Average Phaco Time, APT) were also analyzed. We found significant correlations between age and lens hardness (p = 0.0045), area % and APT (p = 0.03), between area % and US ave% (p = 0.03) and also between the two surgical techniques in terms of area% (p = 0.04) and US ave % (p < 0.01). Roughness increased with the number of uses. An increase in profile length% can be observed up to the twentieth operation. This can result from scratches and microscopic damages and also from abrasion and possible material additions on the surface of the needles. The divide and conquer technique causes less microscopic damage to the surface, and smaller average US energy is required during surgery.

Single-cell level LasR-mediated quorum sensing response of Pseudomonas aeruginosa to pulses of signal molecules.

Quorum sensing (QS) is a communication form between bacteria via small signal molecules that enables global gene regulation as a function of cell density. We applied a microfluidic mother machine to study the kinetics of the QS response of Pseudomonas aeruginosa bacteria to additions and withdrawals of signal molecules. We traced the fast buildup and the subsequent considerably slower decay of a population-level and single-cell-level QS response. We applied a mathematical model to explain the results quantitatively. We found significant heterogeneity in QS on the single-cell level, which may result from variations in quorum-controlled gene expression and protein degradation. Heterogeneity correlates with cell lineage history, too. We used single-cell data to define and quantitatively characterize the population-level quorum state. We found that the population-level QS response is well-defined. The buildup of the quorum is fast upon signal molecule addition. At the same time, its decay is much slower following signal withdrawal, and the quorum may be maintained for several hours in the absence of the signal. Furthermore, the quorum sensing response of the population was largely repeatable in subsequent pulses of signal molecules.

New method to predict the surface tension of complex synthetic and biological polyelectrolyte/surfactant mixtures.

Although the surface tension of complex mixtures determines the fate of many important natural processes, the property is notoriously difficult to interpret. Here we announce a new method that successfully predicts the surface tension of two synthetic and one biological polyelectrolyte/surfactant mixtures in the phase-separation region after dynamic changes in the bulk phase behavior have reached completion. The approach is based on the nonequilibrium framework of a lack of colloidal stability of bulk complexes in compositions around the charge match point of the oppositely charged components and requires as input parameters only the surface tension isotherm of the pure surfactant and some bulk measurements of the mixtures; no surface measurements of the mixtures are required. The complexity of the problem is reduced to a single empirical equation. This simplification in our understanding of the surface properties of strongly interacting mixtures involving macromolecules can lead to the optimization of applications involving synthetic polymers and biomacromolecules such as DNA at surfaces.

The interaction between mucin and poly(amino acid)s with controlled cationic group content in bulk phase and in thin layers.

The type and concentration of charged groups in polymers have a key role in mucoadhesive interactions. A series of cationic poly(amino acid)s with different charge densities was designed to unravel the correlation between chemical structure and mucin-polymer interactions. Colloidal interactions between the mucin protein and synthetic polyaspartamides were tested by dynamic light scattering, zeta potential measurements and turbidimetric titration as a function of polymer-to-mucin mass ratio. The mucoadhesive interactions displayed a strongly non-linear change with polymer composition. The attractive interactions between mucin and the polyaspartamides with at least 50 % cationic groups caused increased light scattering of dispersions due to the aggregation of mucin particles upon their charge reversal. Interactions were further analysed in a thin mucin layer to model life-like situations using a quartz crystal microbalance (QCM) in flow mode. Results pointed out that the fully cationic polyaspartamide is not necessarily superior to derivatives with lower cationic group content. The maximum of adsorbed mass of polymers on mucin was experienced at medium cationic group contents. This emphasizes the relevance of cationic polyaspartamides as mucoadhesive excipients due to their multiple functionalities and the possibility of fine-tuning their interactions with mucin via straightforward chemical steps.

Light-Induced and Thermal Isomerization of Azobenzenes on Immobilized Gold Nanoparticle Aggregates.

Morphologically different gold nanoparticle (AuNP) aggregates were prepared on macroscopic surfaces covered with a layer of polydopamine (PDA). The extent of particle aggregation and the particle size distribution could be controlled by the Au(III) reduction times, while the reduction process was triggered solely by the redox active polymer. Shorter reaction times led to smaller particles along with lower levels of aggregation, while longer reductions resulted in larger average particle diameter and heavier aggregation. The prepared surfaces were characterized by UV-Vis, AFM and KPFM techniques. These surfaces were used as solvent-free condensed phases to probe the photochemical and thermal isomerization processes of attached azobenzenes with different spacer lengths. Fast and reversible light-induced switching was observed in each case. The thermal cis-to-trans isomerization was found to be accelerated for particle-bound azobenzenes compared to those in solution.

Microfluidic Platforms Designed for Morphological and Photosynthetic Investigations of Chlamydomonas reinhardtii on a Single-Cell Level.

Chlamydomonas reinhardtii is a model organism of increasing biotechnological importance, yet, the evaluation of its life cycle processes and photosynthesis on a single-cell level is largely unresolved. To facilitate the study of the relationship between morphology and photochemistry, we established microfluidics in combination with chlorophyll a fluorescence induction measurements. We developed two types of microfluidic platforms for single-cell investigations: (i) The traps of the "Tulip" device are suitable for capturing and immobilizing single cells, enabling the assessment of their photosynthesis for several hours without binding to a solid support surface. Using this "Tulip" platform, we performed high-quality non-photochemical quenching measurements and confirmed our earlier results on bulk cultures that non-photochemical quenching is higher in ascorbate-deficient mutants (Crvtc2-1) than in the wild-type. (ii) The traps of the "Pot" device were designed for capturing single cells and allowing the growth of the daughter cells within the traps. Using our most performant "Pot" device, we could demonstrate that the FV/FM parameter, an indicator of photosynthetic efficiency, varies considerably during the cell cycle. Our microfluidic devices, therefore, represent versatile platforms for the simultaneous morphological and photosynthetic investigations of C. reinhardtii on a single-cell level.

Emergence of Resistant Escherichia coli Mutants in Microfluidic On-Chip Antibiotic Gradients.

Spatiotemporal structures and heterogeneities are common in natural habitats, yet their role in the evolution of antibiotic resistance is still to be uncovered. We applied a microfluidic gradient generator device to study the emergence of resistant bacteria in spatial ciprofloxacin gradients. We observed biofilm formation in regions with sub-inhibitory concentrations of antibiotics, which quickly expanded into the high antibiotic regions. In the absence of an explicit structure of the habitat, this multicellular formation led to a spatial structure of the population with local competition and limited migration. Therefore, such structures can function as amplifiers of selection and aid the spread of beneficial mutations. We found that the physical environment itself induces stress-related mutations that later prove beneficial when cells are exposed to antibiotics. This shift in function suggests that exaptation occurs in such experimental scenarios. The above two processes pave the way for the subsequent emergence of highly resistant specific mutations.

Viable protoplast formation of the coral endosymbiont alga Symbiodinium spp. in a microfluidics platform.

Symbiodiniaceae is an important dinoflagellate family which lives in endosymbiosis with reef invertebrates, including coral polyps, making them central to the holobiont. With coral reefs currently under extreme threat from climate change, there is a pressing need to improve our understanding on the stress tolerance and stress avoidance mechanisms of Symbiodinium spp. Reactive oxygen species (ROS) such as singlet oxygen are central players in mediating various stress responses; however, the detection of ROS using specific dyes is still far from definitive in intact Symbiodinium cells due to the hindrance of uptake of certain fluorescent dyes because of the presence of the cell wall. Protoplast technology provides a promising platform for studying oxidative stress with the main advantage of removed cell wall, however the preparation of viable protoplasts remains a significant challenge. Previous studies have successfully applied cellulose-based protoplast preparation in Symbiodiniaceae; however, the protoplast formation and regeneration process was found to be suboptimal. Here, we present a microfluidics-based platform which allowed protoplast isolation from individually trapped Symbiodinium cells, by using a precisely adjusted flow of cell wall digestion enzymes (cellulase and macerozyme). Trapped single cells exhibited characteristic changes in their morphology, cessation of cell division and a slight decrease in photosynthetic activity during protoplast formation. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Elevated flow rates in the microfluidic chambers resulted in somewhat faster protoplast formation; however, cell wall digestion at higher flow rates partially compromised photosynthetic activity. Physiologically competent protoplasts prepared from trapped cells in microfluidic chambers allowed for the first time the visualization of the intracellular localization of singlet oxygen (using Singlet Oxygen Sensor Green dye) in Symbiodiniaceae, potentially opening new avenues for studying oxidative stress.

Photoswitchable Macroscopic Solid Surfaces Based On Azobenzene-Functionalized Polydopamine/Gold Nanoparticle Composite Materials: Formation, Isomerization and Ligand Exchange.

The facile preparation of dynamic interfaces is presented based on the combination of photoisomerizable azobenzenes and polydopamine (PDA)/Au nanoparticle composite materials. Azobenzenes with different spacer lengths (C3 , C6 ) and surface-binding groups (SH, NH2 ) were synthesized. The polymer layer on macroscopic quartz surface was prepared by the facile aerobic autopolymerisation of dopamine hydrochloride under basic conditions. The presence of redox-active catechol moieties meant that gold nanoparticles were formed on the polymer surface. The obtained UV-Vis spectroscopic results confirmed that following their successful assembly, the switching of azobenzenes on PDA/Au was not affected by the surface binding group and the spacer length of the azobenzene molecules under the measurement conditions. Furthermore, facilitated by the curved nature of the Au particles, the surface-bound azobenzene layer could be reconstructed by ligand-exchange processes, and the photochemical characterization of the mixed layer was performed.

Application of Microfluidics in Experimental Ecology: The Importance of Being Spatial.

Microfluidics is an emerging technology that is used more and more in biology experiments. Its capabilities of creating precisely controlled conditions in cellular dimensions make it ideal to explore cell-cell and cell-environment interactions. Thus, a wide spectrum of problems in microbial ecology can be studied using engineered microbial habitats. Moreover, artificial microfluidic ecosystems can serve as model systems to test ecology theories and principles that apply on a higher level in the hierarchy of biological organization. In this mini review we aim to demonstrate the versatility of microfluidics and the diversity of its applications that help the advance of microbiology, and in more general, experimental ecology.

The impact of electrolyte on the aggregation of the complexes of hyperbranched poly(ethyleneimine) and sodium dodecyl sulfate.

The aggregation of the negatively charged complexes of hyperbranched poly(ethylenimine) (PEI) and sodium dodecyl sulfate (SDS) has been investigated at different sodium chloride (NaCl) concentrations using coagulation kinetics, electrophoretic mobility and dynamic light scattering measurements. The observed variation of the initial rate of coagulation with NaCl concentration indicates the formation of kinetically stable colloid dispersions in the investigated composition and pH range. These dispersions are electrostatically stabilized due to the adsorption of excess dodecyl sulfate ions on the surface of the polyelectrolyte/surfactant particles. Because of the enhanced adsorption of the anionic surfactant, the kinetic stability of the PEI/SDS dispersions increases with increasing SDS concentration and decreasing pH. Finally, we rationalize the effect of salt on the phase behavior and surface properties of polyelectrolyte/surfactant mixtures in terms of the salt-induced aggregation features of polyelectrolyte/surfactant particles.