Draft genome sequence of Enterobacter sp. strain EA-1, an electrochemically active microorganism isolated from tropical sediment

© 2018 Doyle et al. Enterobacter sp. strain EA-1 is an electrochemically active bacterium isolated from tropical sediment in Singapore. Here, the annotated draft genome assembly of the bacterium is reported. Whole-genome comparison indicates that Enterobacter sp. EA-1, along with a previously sequenced Enterobacter isolate from East Asia, forms a distinct clade within the Enterobacter genus

Mechanical properties of the superficial biofilm layer determine the architecture of biofilms

© 2016 The Royal Society of Chemistry. Cells in biofilms sense and interact with their environment through the extracellular matrix. The physicochemical properties of the matrix, particularly at the biofilm-environment interface, determine how cells respond to changing conditions. In this study we describe the application of atomic force microscopy and confocal imaging to probe in situ the mechanical properties of these interfacial regions and to elucidate how key matrix components can contribute to the physical sensing by the cells. We describe how the Young's modulus of microcolonies differs according to the size and morphology of microcolonies, as well as the flow rate. The Young's modulus increased as a function of microcolony diameter, which was correlated with the production of the polysaccharide Psl at later stages of maturation for hemispherical or mushroom shaped microcolonies. The Young's modulus of the periphery of the biofilm colony was however independent of the hydrodynamic shear. The morphology of the microcolonies also influenced interfacial or peripheral stiffness. Microcolonies with a diffuse morphology had a lower Young's modulus than isolated, circular ones and this phenomenon was due to a deficiency of Psl. In this way, changes in the specific polysaccharide components imbue the biofilm with distinct physical properties that may modulate the way in which bacteria perceive or respond to their environment. Further, the physical properties of the polysaccharides are closely linked to the specific architectures formed by the developing biofilm

Mechanical signatures of microbial biofilms in micropillar-embedded growth chambers

Biofilms are surface-attached communities of microorganisms embedded in an extracellular matrix and are essential for the cycling of organic matter in natural and engineered environments. They are also the leading cause of many infections, for example, those associated with chronic wounds and implanted medical devices. The extracellular matrix is a key biofilm component that determines its architecture and defines its physical properties. Herein, we used growth chambers embedded with micropillars to study the net mechanical forces (differential pressure) exerted during biofilm formation in situ. Pressure from the biofilm is transferred to the micropillars via the extracellular matrix, and reduction of major matrix components decreases the magnitude of micropillar deflections. The spatial arrangement of micropillar deflections caused by pressure differences in the different biofilm strains may potentially be used as mechanical signatures for biofilm characterization. Hence, we submit that micropillar-embedded growth chambers provide insights into the mechanical properties and dynamics of the biofilm and its matrix.Singapore. National Research Foundation (Singapore-MIT Alliance for Research and Technology (SMART)

From microhabitat ecohydraulics to an improved management of river catchments: bridging the gap between scales

[EN] Ecohydraulic studies in rivers range from local-scale studies, which target a better understanding of the mechanisms underlying biological responses to microhabitat hydraulics, to large-scale studies, which address the influence of hydro-morphological management on catchment biodiversity. A major challenge in the field is to bridge the gap between local- and large-scale studies, in order to base the large-scale physical management of rivers on general and transferable ecohydraulic processes. This Special Issue includes ten articles that illustrate progresses and difficulties to bridge this gap. It gathers microhabitat-scale studies focused on the identification of major ecohydraulic mechanisms, reach-scale studies that typically target generality and transferability across reaches, and examples of catchment-scale management based on general ecohydrological knowledge. The Special Issue illustrates how ecohydraulics have evolved to better integrate dynamic physical processes, ecological concepts and the consideration of ecosystem services. Although this remains challenging in practice, the Special Issue shows the need to integrate dynamic hydraulic descriptors of the environment for improving the cost-effectiveness of large-scale rivermanagement and restoration. These articles were presented at the 10th International Symposium on Ecohydraulics in Trondheim, Norway (2014), where the first symposium on ecohydraulics was organised 20 years before. The 10th issue of the symposium celebrated 20 years of ecohydraulic research and had about 300 delegates, giving 194 talks and presenting 86 posters.Harby, A.; Martinez-Capel, F.; Lamouroux, N. (2017). From microhabitat ecohydraulics to an improved management of river catchments: bridging the gap between scales. River Research and Applications. 33:189-191. doi:10.1002/rra.3114S18919133Anderson, D., Moggridge, H., Shucksmith, J. D., & Warren, P. H. (2015). Quantifying the Impact of Water Abstraction for Low Head ‘Run of the River’ Hydropower on Localized River Channel Hydraulics and Benthic Macroinvertebrates. River Research and Applications, 33(2), 202-213. doi:10.1002/rra.2992Doyle, M. W., Stanley, E. H., Strayer, D. L., Jacobson, R. B., & Schmidt, J. C. (2005). Effective discharge analysis of ecological processes in streams. Water Resources Research, 41(11). doi:10.1029/2005wr004222Egger, G., Politti, E., Lautsch, E., Benjankar, R. M., & Rood, S. B. (2016). Time and Intensity Weighted Indices of Fluvial Processes: a Case Study from the Kootenai River, USA. River Research and Applications, 33(2), 224-232. doi:10.1002/rra.2997Hailegeorgis, T. T., & Alfredsen, K. (2016). Regional Statistical and Precipitation-Runoff Modelling for Ecological Applications: Prediction of Hourly Streamflow in Regulated Rivers and Ungauged Basins. River Research and Applications, 33(2), 233-248. doi:10.1002/rra.3006Lamouroux, N., Pella, H., Snelder, T. H., Sauquet, E., Lejot, J., & Shankar, U. (2013). Uncertainty Models for Estimates of Physical Characteristics of River Segments Over Large Areas. JAWRA Journal of the American Water Resources Association, 50(1), 1-13. doi:10.1111/jawr.12101Harby, A., Martinez- Capel, F., & Lamouroux, N. (2017). From Microhabitat Ecohydraulics to an Improved Management of River Catchments: Bridging the gap Between Scales. River Research and Applications, 33(2), 189-191. doi:10.1002/rra.3114Martínez-Capel, F., García-López, L., & Beyer, M. (2016). Integrating Hydrological Modelling and Ecosystem Functioning for Environmental Flows in Climate Change Scenarios in the Zambezi River (Zambezi Region, Namibia). River Research and Applications, 33(2), 258-275. doi:10.1002/rra.3058Martínez-Fernández, V., González del Tánago, M., Maroto, J., & García de Jalón, D. (2016). Fluvial Corridor Changes Over Time in Regulated and Non-Regulated Rivers (Upper Esla River, NW Spain). River Research and Applications, 33(2), 214-223. doi:10.1002/rra.3032Mathews, R., & Richter, B. D. (2007). Application of the Indicators of Hydrologic Alteration Software in Environmental Flow Setting1. JAWRA Journal of the American Water Resources Association, 43(6), 1400-1413. doi:10.1111/j.1752-1688.2007.00099.xNoack, M., Ortlepp, J., & Wieprecht, S. (2016). An Approach to Simulate Interstitial Habitat Conditions During the Incubation Phase of Gravel-Spawning Fish. River Research and Applications, 33(2), 192-201. doi:10.1002/rra.3012Nzau Matondo, B., Benitez, J. P., Dierckx, A., Philippart, J. C., & Ovidio, M. (2016). Assessment of the Entering Stock, Migration Dynamics and Fish Pass Fidelity of European Eel in the Belgian Meuse River. River Research and Applications, 33(2), 292-301. doi:10.1002/rra.3034Parasiewicz P Castelli E Rogers J Vezza P Kapusta A 2017 Implementation of the natural flow paradigm to protect dwarf wedgemussel ( Alasmidonta heterodon ) in the upper Delaware River River Research and Applications 33 2 276 290 10.1002/rra.3112Rice, S. P., Little, S., Wood, P. J., Moir, H. J., & Vericat, D. (2010). The relative contributions of ecology and hydraulics to ecohydraulics. River Research and Applications, 26(4), 363-366. doi:10.1002/rra.1369Roy, M. L., Roy, A. G., & Legendre, P. (2010). The relations between ‘standard’ fluvial habitat variables and turbulent flow at multiple scales in morphological units of a gravel-bed river. River Research and Applications, 26(4), 439-455. doi:10.1002/rra.1281Seliger, C., Scheikl, S., Schmutz, S., Schinegger, R., Fleck, S., Neubarth, J., … Muhar, S. (2015). Hy:Con: A Strategic Tool For Balancing Hydropower Development And Conservation Needs. River Research and Applications, 32(7), 1438-1449. doi:10.1002/rra.2985Statzner, B., Gore, J. A., & Resh, V. H. (1988). Hydraulic Stream Ecology: Observed Patterns and Potential Applications. Journal of the North American Benthological Society, 7(4), 307-360. doi:10.2307/1467296Vowles, A. S., Eakins, L. R., Piper, A. T., Kerr, J. R., & Kemp, P. (2013). Developing Realistic Fish Passage Criteria: An Ecohydraulics Approach. Ecohydraulics, 143-156. doi:10.1002/9781118526576.ch

Matrix Polysaccharides and SiaD Diguanylate Cyclase Alter Community Structure and Competitiveness of Pseudomonas aeruginosa during Dual-Species Biofilm Development with Staphylococcus aureus

Copyright © 2018 Chew et al. Mixed-species biofilms display a number of emergent properties, including enhanced antimicrobial tolerance and communal metabolism. These properties may depend on interspecies relationships and the structure of the biofilm. However, the contribution of specific matrix components to emergent properties of mixed-species biofilms remains poorly understood. Using a dual-species biofilm community formed by the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus, we found that whilst neither Pel nor Psl polysaccharides, produced by P. aeruginosa, affect relative species abundance in mature P. aeruginosa and S. aureus biofilms, Psl production is associated with increased P. aeruginosa abundance and reduced S. aureus aggregation in the early stages of biofilm formation. Our data suggest that the competitive effect of Psl is not associated with its structural role in cross-linking the matrix and adhering to P. aeruginosa cells but is instead mediated through the activation of the diguanylate cyclase SiaD. This regulatory control was also found to be independent of the siderophore pyoverdine and Pseudomonas quinolone signal, which have previously been proposed to reduce S. aureus viability by inducing lactic acid fermentation-based growth. In contrast to the effect mediated by Psl, Pel reduced the effective crosslinking of the biofilm matrix and facilitated superdiffusivity in microcolony regions. These changes in matrix cross-linking enhance biofilm surface spreading and expansion of microcolonies in the later stages of biofilm development, improving overall dual-species biofilm growth and increasing biovolume severalfold. Thus, the biofilm matrix and regulators associated with matrix production play essential roles in mixed-species biofilm interactions.IMPORTANCE Bacteria in natural and engineered environments form biofilms that include many different species. Microorganisms rely on a number of different strategies to manage social interactions with other species and to access resources, build biofilm consortia, and optimize growth. For example, Pseudomonasaeruginosa and Staphylococcus aureus are biofilm-forming bacteria that coinfect the lungs of cystic fibrosis patients and diabetic and chronic wounds. P. aeruginosa is known to antagonize S. aureus growth. However, many of the factors responsible for mixed-species interactions and outcomes such as infections are poorly understood. Biofilm bacteria are encased in a self-produced extracellular matrix that facilitates interspecies behavior and biofilm development. In this study, we examined the poorly understood roles of the major matrix biopolymers and their regulators in mixed-species biofilm interactions and development

Dynamic Remodeling of Microbial Biofilms by Functionally Distinct Exopolysaccharides

Biofilms are densely populated communities of microbial cells protected and held together by a matrix of extracellular polymeric substances. The structure and rheological properties of the matrix at the microscale influence the retention and transport of molecules and cells in the biofilm, thereby dictating population and community behavior. Despite its importance, quantitative descriptions of the matrix microstructure and microrheology are limited. Here, particle-tracking microrheology in combination with genetic approaches was used to spatially and temporally study the rheological contributions of the major exopolysaccharides Pel and Psl in Pseudomonas aeruginosa biofilms. Psl increased the elasticity and effective cross-linking within the matrix, which strengthened its scaffold and appeared to facilitate the formation of microcolonies. Conversely, Pel reduced effective cross-linking within the matrix. Without Psl, the matrix becomes more viscous, which facilitates biofilm spreading. The wild-type biofilm decreased in effective cross-linking over time, which would be advantageous for the spreading and colonization of new surfaces. This suggests that there are regulatory mechanisms to control production of the exopolysaccharides that serve to remodel the matrix of developing biofilms. The exopolysaccharides were also found to have profound effects on the spatial organization and integration of P. aeruginosa in a mixed-species biofilm model of P. aeruginosa-Staphylococcus aureus. Pel was required for close association of the two species in mixed-species microcolonies. In contrast, Psl was important for P. aeruginosa to form single-species biofilms on top of S. aureus biofilms. Our results demonstrate that Pel and Psl have distinct physical properties and functional roles during biofilm formation.Singapore. National Research Foundation (Singapore Centre on Environmental Life Sciences Engineering (SCELSE))Nanyang Technological UniversityNational University of Singapore (Research Centre of Excellence Program)Singapore-MIT Alliance for Research and Technology (BioSystems and Micromechanics Program

From constrained stochastic processes to the nonlinear sigma model. Two old problems revisited

In this work a method is presented to derive the generating functional in path integral form for a system with an arbitrary number of degrees of freedom and constrained by general conditions. The method is applied to the case of the dynamics of an inextensible chain subjected to external forces. Next, the generating functional of the inextensible chain is computed assuming that the interactions are switched off. Finally, the generating functional of a two dimensional nonlinear sigma model with O(3) symmetry is derived exploiting its similarities with the model describing the dynamics of the inextensible chain.Comment: 20 pages, LaTeX + RevTeX, 1 figur

High-frequency pressure variations in the vicinity of a surface CO2 flux chamber

We report measurements of 2 Hz pressure fluctuations at and below the soil surface in the vicinity of a surface-based CO2 flux chamber. These measurements were part of a field experiment to examine the possible role of pressure pumping due to atmospheric pressure fluctuations on measurements of surface fluxes of CO2. Under the moderate wind speeds, warm temperatures, and dry soil conditions present at the time of our observations, the chamber had no effect on the pressure field in its near vicinity that could be detected above the level of natural pressure fluctuations in the vicinity. At frequencies at or \u3c2 Hz, pressure fluctuations easily penetrated the soil to depths of several cm with little attenuation. We conclude that the presence of the chamber does not introduce pressure perturbations that lead to biases in measurements of surface fluxes of CO2

Origin of Crack Tip Instabilities

This paper demonstrates that rapid fracture of ideal brittle lattices naturally involves phenomena long seen in experiment, but which have been hard to understand from a continuum point of view. These idealized models do not mimic realistic microstructure, but can be solved exactly and understood completely. First it is shown that constant velocity crack solutions do not exist at all for a range of velocities starting at zero and ranging up to about one quarter of the shear wave speed. Next it is shown that above this speed cracks are by and large linearly stable, but that at sufficiently high velocity they become unstable with respect to a nonlinear micro-cracking instability. The way this instability works itself out is related to the scenario known as intermittency, and the basic time scale which governs it is the inverse of the amount of dissipation in the model. Finally, we compare the theoretical framework with some new experiments in Plexiglas, and show that all qualitative features of the theory are mirrored in our experimental results.Comment: About fifty pages with lots of PostScript figure