RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere.

In aquatic systems, one of the non-destructive ways to quantify toxicity of contaminants to plants is to monitor changes in root exudation patterns. In aquatic conditions, monitoring and quantifying such changes are currently challenging because of dilution of root exudates in water phase and lack of suitable instrumentation to measure them. Exposure to pollutants would not only change the plant exudation, but also affect the microbial communities that surround the root zone, thereby changing the metabolic profiles of the rhizosphere. This study aims at developing a device, the RhizoFlowCell, which can quantify metabolic response of plants, as well as changes in the microbial communities, to give an estimate of the stress to which the rhizosphere is exposed. The usefulness of RhizoFlowCell is demonstrated using naphthalene as a test pollutant. Results show that RhizoFlowCell system is useful in quantifying the dynamic metabolic response of aquatic rhizosphere to determine ecosystem health.

Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity.

Networks of engineered waterways are critical in meeting the growing water demands in megacities. To capture and treat rainwater in an energy-efficient manner, approaches can be developed for such networks that use ecological services from microbial communities. Traditionally, engineered waterways were regarded as homogeneous systems with little responsiveness of ecological communities and ensuing processes. This study provides ecogenomics-derived key information to explain the complexity of urban aquatic ecosystems in well-managed watersheds with densely interspersed land-use patterns. Overall, sedimentary microbial communities had higher richness and evenness compared to the suspended communities in water phase. On the basis of PERMANOVA analysis, variation in structure and functions of microbial communities over space within same land-use type was not significant. In contrast, this difference was significant between different land-use types, which had similar chemical profiles. Of the 36 environmental parameters from spatial analysis, only three metals, namely potassium, copper and aluminum significantly explained between 7% and 11% of the variation in taxa and functions, based on distance-based linear models (DistLM). The ecogenomics approach adopted here allows the identification of key drivers of microbial communities and their functions at watershed-scale. These findings can be used to enhance microbial services, which are critical to develop ecologically friendly waterways in rapidly urbanizing environments.

Combination of synchrotron radiation-based Fourier transforms infrared microspectroscopy and confocal laser scanning microscopy to understand spatial heterogeneity in aquatic multispecies biofilms.

Understanding the spatial heterogeneity within environmental biofilms can provide an insight into compartmentalization of different functions in biofilm communities. We used a non-destructive and label-free method by combining Synchrotron Radiation-based Fourier Transform Infrared Microspectroscopy (SR-FTIR) with Confocal Laser Scanning Microscopy (CLSM) to distinguish the spatial chemical changes within multispecies biofilms grown from natural storm waters in flow cells. Among the different surfaces tested for biofilm growth and optimal imaging, mylar membranes were most suited and it enabled successful spatial infrared imaging of natural biofilms for obtaining reliable and interpretable FTIR spectra. Time series analysis of biofilm growth showed that influx of water during biofilm growth, results in significant changes in biofilm formation. Early biofilms showed active nutrient acquisition and desiccation tolerance mechanisms corresponding with accumulation of secreted proteins. Statistical approach used for the evaluation of chemical spectra allowed for clustering and classification of various regions of the biofilm. Microheterogeneity was observed in the polymeric components of the biofilm matrix, including cellulose, glycocalyx and dextran-like molecules. Fructan and glycan-rich regions were distinguishable and glycocalyx was abundant in the strongly adhering peripheral regions of biofilms. Inner core showed coexistence of oxygen dimers and ferrihydrite that will likely support growth of Fe (II)-oxidising bacteria. The combined SR-FTIR microspectroscopy and CSLM approach for complex natural biofilms described here will be useful both in understanding heterogeneity of matrix components and in correlating functions of juxtaposed microbial species in complex natural biofilms with physicochemical microenvironment to which they are exposed.

In situ removal of dissolved and suspended contaminants from a eutrophic pond using hybrid sand-filter.

In this study, in situ hybrid sand filters were designed to remove dissolved and suspended contaminants from eutrophic pond. Currently, there are no attempts made to eradicate dissolved as well as suspended contaminants from eutrophic water system in a single step. Monitoring studies revealed that examined pond contain high chlorophyll-a content (101.8 µg L(-1)), turbidity (39.5 NTU) and total dissolved solids concentration (0.04 g L(-1)). Samples were further exposed to extensive water quality analysis, which include examining physicochemical parameters (pH, conductivity, total dissolved solids, salinity, turbidity and chlorophyll-a), metals (Na, K, Ca, Mg, Al, Fe, Cu, Cd, Pb, Zn, Cr, and Ni) and anions (NO3, NO2, PO4, SO4, Cl, F and Br). To tackle pollutants, filtration system was designed to comprise of several components including fine sand, coarse sand/sorbent mix and gravel from top to bottom loaded in fiberglass tanks. All the filters (activated carbon, Sargassum and zeolite) completely removed algal biomass and showed potential to decrease pH during entire operational period of 20 h at 120 L h(-1). To examine the efficiency of filters in adverse conditions, the pond water was spiked with heavy metals (Cu, Cd, Pb, Zn, Cr, and Ni). Of the different filter systems, Sargassum-loaded filter performed exceedingly well with concentrations of heavy metals never exceeded the Environmental protection agency regulations for freshwater limits during total operational period. The total uptake capacities at the end of the fifth event were 24.9, 20.5, 0.58, 5.2, 0.091 and 2.8 mg/kg for Cr, Ni, Cu, Zn, Cd and Pb, respectively.

A bacterial quercetin oxidoreductase QuoA-mediated perturbation in the phenylpropanoid metabolic network increases lignification with a concomitant decrease in phenolamides in Arabidopsis.

Metabolic perturbations by a gain-of-function approach provide a means to alter steady states of metabolites and query network properties, while keeping enzyme complexes intact. A combination of genetic and targeted metabolomics approach was used to understand the network properties of phenylpropanoid secondary metabolism pathways. A novel quercetin oxidoreductase, QuoA, from Pseudomonas putida, which converts quercetin to naringenin, thus effectively reversing the biosynthesis of quercetin through a de novo pathway, was expressed in Arabidopsis thaliana. QuoA transgenic lines selected for low, medium, and high expression levels of QuoA RNA had corresponding levels of QuoA activity and hypocotyl coloration resulting from increased anthocyanin accumulation. Stems of all three QuoA lines had increased tensile strength resulting from increased lignification. Sixteen metabolic intermediates from anthocyanin, lignin, and shikimate pathways had increased accumulation, of which 11 paralleled QuoA expression levels in the transgenic lines. The concomitant upregulation of the above pathways was explained by a significant downregulation of the phenolamide pathway and its precursor, spermidine. In a tt6 mutant line, lignifications as well as levels of the lignin pathway metabolites were much lower than those of QuoA transgenic lines. Unlike QuoA lines, phenolamides and spermidine were not affected in the tt6 line. Taken together, these results suggest that phenolamide pathway plays a major role in directing metabolic intermediates into the lignin pathway. Metabolic perturbations were accompanied by downregulation of five genes associated with branch-point enzymes and upregulation of their corresponding products. These results suggest that gene-metabolite pairs are likely to be co-ordinately regulated at critical branch points. Thus, these perturbations by a gain-of-function approach have uncovered novel properties of the phenylpropanoid metabolic network.

datPAV--an online processing, analysis and visualization tool for exploratory investigation of experimental data.

SUMMARY: Data processing, analysis and visualization (datPAV) is an exploratory tool that allows experimentalist to quickly assess the general characteristics of the data. This platform-independent software is designed as a generic tool to process and visualize data matrices. This tool explores organization of the data, detect errors and support basic statistical analyses. Processed data can be reused whereby different step-by-step data processing/analysis workflows can be created to carry out detailed investigation. The visualization option provides publication-ready graphics. Applications of this tool are demonstrated at the web site for three cases of metabolomics, environmental and hydrodynamic data analysis. AVAILABILITY: datPAV is available free for academic use at http://www.sdwa.nus.edu.sg/datPAV/.

MetDAT: a modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation.

SUMMARY: Analysis of high throughput metabolomics experiments is a resource-intensive process that includes pre-processing, pre-treatment and post-processing at each level of experimental hierarchy. We developed an interactive user-friendly online software called Metabolite Data Analysis Tool (MetDAT) for mass spectrometry data. It offers a pipeline of tools for file handling, data pre-processing, univariate and multivariate statistical analyses, database searching and pathway mapping. Outputs are produced in the form of text and high-quality images in real-time. MetDAT allows users to combine data management and experiment-centric workflows for optimization of metabolomics methods and metabolite analysis. AVAILABILITY: MetDAT is available free for academic use from http://smbl.nus.edu.sg/METDAT2/. CONTACT: sanjay@nus.edu.sg

Serum tumor necrosis factor-alpha in Guillain-Barré syndrome and its relation to plasma exchange.

BACKGROUND: To correlate the serum tumor necrosis factor-alpha (TNFalpha) concentrations before, during and following plasma exchange in patients with Guillain-Barré syndrome (GBS). In this prospective study, 21 GBS patients were selected. Patients in clinical stages III to V were subjected to plasma exchange. The control group included equal numbers of age-matched patients with other neurological diseases and healthy voluntary blood donors. A sandwich ELISA method was applied to estimate serum TNFalpha concentrations in test and control groups. REVIEW SUMMARY: Twelve GBS patients had elevated serum TNFalpha levels that ranged between 74 and 182 pg/mL. All 12 GBS patients showed a steady decrease in the TNFalpha concentration following plasma exchange and also showed a positive correlation with neurological recovery. CONCLUSIONS: We conclude that serum TNFalpha concentrations are elevated in 57.1% of GBS patients and TNFalpha level decreases following plasma exchange.