Risk of Illness with Salmonella Spp. and Antibiotic-Resistant Salmonella sp. due to Consumption of Lettuce Irrigated with Water from La Ramada Irrigation District.

Despite heavy contamination of the Bogotá River with domestic and industrial waste, it remains vital for various purposes, including agricultural use at La Ramada Irrigation District. There are important concerns regarding pathogen concentrations in irrigation water at La Ramada, including the presence of antibiotic-resistant Salmonella spp. This study aimed to estimate the risk of Salmonella-related illness from consuming lettuce irrigated with Bogotá River water at La Ramada. We collected lettuce samples from 4 different sites, all irrigated with water from La Ramada. The methodology involved a process to detach Salmonella spp. from lettuce leaves, quantification through plate counts on SS agar, and establishment of antibiotic-resistant bacteria concentrations through growth on media supplemented with ampicillin or ciprofloxacin. The results showed concentrations of Salmonella spp. of 103.59,102.66, and 104.56 CFU/g lettuce at sites 1, 2, and 3, respectively, and ampicillin-resistant Salmonella spp. of 101.93, 101.31, and 102.07 CFU/g lettuce at sites 1, 2, and 3, respectively. No colonies were obtained from lettuce samples collected from site 4. Notably, we detected no isolates resistant to ciprofloxacin at any of the sites. Salmonella spp. concentrations varied greatly among sampling sites. Salmonella spp. concentrations were used to predict the daily probability of illness, with a probability of 0.59 (0.33 to 0.78, CI 95%) for Salmonella spp. and 0.3 (0.03 to 0.53, CI 95%) for ampicillin-resistant Salmonella spp.

Genomes of four Streptomyces strains reveal insights into putative new species and pathogenicity of scab-causing organisms.

Genomes of four Streptomyces isolates, two putative new species (Streptomyces sp. JH14 and Streptomyces sp. JH34) and two non thaxtomin-producing pathogens (Streptomyces sp. JH002 and Streptomyces sp. JH010) isolated from potato fields in Colombia were selected to investigate their taxonomic classification, their pathogenicity, and the production of unique secondary metabolites of Streptomycetes inhabiting potato crops in this region. The average nucleotide identity (ANI) value calculated between Streptomyces sp. JH34 and its closest relatives (92.23%) classified this isolate as a new species. However, Streptomyces sp. JH14 could not be classified as a new species due to the lack of genomic data of closely related strains. Phylogenetic analysis based on 231 single-copy core genes, confirmed that the two pathogenic isolates (Streptomyces sp. JH010 and JH002) belong to Streptomyces pratensis and Streptomyces xiamenensis, respectively, are distant from the most well-known pathogenic species, and belong to two different lineages. We did not find orthogroups of protein-coding genes characteristic of scab-causing Streptomycetes shared by all known pathogenic species. Most genes involved in biosynthesis of known virulence factors are not present in the scab-causing isolates (Streptomyces sp. JH002 and Streptomyces sp. JH010). However, Tat-system substrates likely involved in pathogenicity in Streptomyces sp. JH002 and Streptomyces sp. JH010 were identified. Lastly, the presence of a putative mono-ADP-ribosyl transferase, homologous to the virulence factor scabin, was confirmed in Streptomyces sp. JH002. The described pathogenic isolates likely produce virulence factors uncommon in Streptomyces species, including a histidine phosphatase and a metalloprotease potentially produced by Streptomyces sp. JH002, and a pectinesterase, potentially produced by Streptomyces sp. JH010. Biosynthetic gene clusters (BGCs) showed the presence of clusters associated with the synthesis of medicinal compounds and BGCs potentially linked to pathogenicity in Streptomyces sp. JH010 and JH002. Interestingly, BGCs that have not been previously reported were also found. Our findings suggest that the four isolates produce novel secondary metabolites and metabolites with medicinal properties.

Treatment of Wastewater, Phenols and Dyes Using Novel Magnetic Torus Microreactors and Laccase Immobilized on Magnetite Nanoparticles.

In this work, the design, manufacture, and testing of three different magnetic microreactors based on torus geometries (i.e., one-loop, two-horizontal-loop, and two-vertical-loop) is explored to increase the enzyme-based transformation of dyes by laccase bio-nanocomposites, improve the particle suspension, and promote the interaction of reagents. The laccase enzyme was covalently immobilized on amino-terminated silanized magnetite nanoparticles (laccase-magnetite). The optimal configuration for the torus microreactor and the applied magnetic field was evaluated in silico with the aid of the CFD and particle tracing modules of Comsol Multiphysics®. Eriochrome Black T (EBt) dye was tested as a biotransformation model at three different concentrations, i.e., 5 mg/L, 10 mg/L, and 20 mg/L. Phenol oxidation/removal was evaluated on artificial wastewater and real wastewater. The optimal catalytic performance of the bionanocomposite was achieved in the range of pH 4 to 4.5. A parabolic movement on the particles along the microchannels was induced by the magnetic field, which led to breaking the stability of the laminar flow and improving the mixing processes. Based on the simulation and experiments conducted with the three geometries, the two-vertical-loop microreactor demonstrated a better performance mainly due to larger dead zones and a longer residence time. Additionally, the overall dye removal efficiencies for this microreactor and the laccase-magnetite bionanocomposite were 98.05%, 93.87%, and 92.74% for the three evaluated concentrations. The maximum phenol oxidation with the laccase-magnetite treatment at low concentration for the artificial wastewater was 79.89%, while its phenol removal efficiency for a large volume of real wastewater was 17.86%. Treatments with real wastewater were carried out with a larger volume, equivalent to 200 biotransformation (oxidation) operating cycles of those carried out with dyes or phenol. Taken together, our results indicate that the novel microreactors introduced here have the potential to process wastewaters rich in contaminant dyes in continuous mode with efficiencies that are attractive for a potential large-scale operation. In this regard, future work will focus on finding the requirements for scaling-up the processes and evaluating the involved environmental impact indexes, economic performance, and different device geometries and processing schemes.

Enhanced biosorption of Cr(VI) using cotton fibers coated with chitosan - role of ester bonds.

We report on the role of ester bonds in the enhanced removal of hexavalent chromium from water using cotton fibers coated with chitosan. Adsorption capacities up to five times higher than those of the unmodified fibers were observed when the cotton fibers were exposed to an NaOH, followed by citric acid (0.97 M), and a chitosan solution (2%). We found that the use of NaOH favors the formation of ester bonds over amide bonds on the surface of the cotton fibers. This increase in the surface density of ester bonds generates an increase in the amount of exposed amino groups from the chitosan, hence increasing the removal capacity of the modified fibers. Experimental results also reveal that the adsorption is induced by the electrostatic attraction between the protonated amino groups on the surface and the negatively charged chromium ions in the water. Adsorption isotherms and kinetic studies indicated that the adsorption process fits the Langmuir and the Freundlich isotherm models as well as the pseudo-first and pseudo-second order kinetic models. These results can open a new avenue for the manufacturing of fibers with enhanced removal capacities for hexavalent chromium.

Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils.

Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA) were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community.

Risk of Illness with Salmonella due to Consumption of Raw Unwashed Vegetables Irrigated with Water from the Bogotá River.

The Bogotá River receives untreated wastewater from the city of Bogotá and many other towns. Downstream from Bogotá, water from the river is used for irrigation of crops. Concentrations of indicator organisms in the river are high, which is consistent with fecal contamination. To investigate the probability of illness due to exposure to enteric pathogens from the river, specifically Salmonella, we took water samples from the Bogotá River at six sampling locations in an area where untreated water from the river is used for irrigation of lettuce, broccoli, and cabbage. Salmonella concentrations were quantified by direct isolation and qPCR. Concentrations differed, depending on the quantification technique used, ranging between 107.7 and 109.9 number of copies of gene invA per L and 105.3 and 108.4 CFU/L, for qPCR and direct isolation, respectively. A quantitative microbial risk assessment model that estimates the daily risk of illness with Salmonella resulting from consuming raw unwashed vegetables irrigated with water from the Bogotá River was constructed using the Salmonella concentration data. The daily probability of illness from eating raw unwashed vegetables ranged between 0.62 and 0.85, 0.64 and 0.86, and 0.64 and 0.85 based on concentrations estimated by qPCR (0.47-0.85, 0.47-0.86, and 0.41-0.85 based on concentrations estimated by direct isolation) for lettuce, cabbage, and broccoli, respectively, which are all above the commonly propounded benchmark of 10-4 per year. Results obtained in this study highlight the necessity for appropriate wastewater treatment in the region, and emphasize the importance of postharvest practices, such as washing, disinfecting, and cooking.

Removal of sodium and chloride ions from aqueous solutions using fique fibers (Furcraea spp.).

Fique fibers obtained from the leaves of Furcraea spp., a highly abundant plant in the mountains of South America, may offer an alternative as biosorbents in desalination processes as they exhibit high removal capacities (13.26 meq/g for chloride ions and 15.52 meq/g for sodium ions) up to four times higher than exchange capacities commonly observed in synthetic resins. The ion removal capacity of the fibers was also found to be a function of the pH of the solution with the maximum removal of ions obtained at pH 8. Unlike most commercial ion exchange resins, our results suggest that fique fibers allow simultaneous removal of chloride and sodium ions.

Biodegradation of nitroglycerin in porous media and potential for bioaugmentation with Arthrobacter sp. strain JBH1.

Nitroglycerin (NG) is a toxic explosive found as a contaminant of soil and groundwater. Several microbial strains are capable of partially reducing the NG molecule to dinitro or mononitroesters. Recently, a strain capable of growing on NG as the sole source of carbon and nitrogen (Arthrobacter sp. strain JBH1) was isolated from contaminated soil. Despite the widespread presence of microbial strains capable of transforming NG in contaminated soils and sediments, the extent of NG biodegradation at contaminated sites is still unknown. In this study column experiments were conducted to investigate the extent of microbial degradation of NG in saturated porous media, specifically after bioaugmentation with JBH1. Initial experiments using sterile, low sorptivity sand, showed mineralization of NG after bioaugmentation with JBH1 in the absence of sources of carbon and nitrogen other than NG. Results could be modeled using a first order degradation rate of 0.14d(-1). Further experiments conducted using contaminated soil with high organic carbon content (highly sorptive) resulted in column effluents that did not contain NG although high dinitroester concentrations were observed. Bioaugmentation with JBH1 in sediments containing strains capable of partial transformation of NG resulted in complete mineralization of NG and faster degradation rates.

Key enzymes enabling the growth of Arthrobacter sp. strain JBH1 with nitroglycerin as the sole source of carbon and nitrogen.

Flavoprotein reductases that catalyze the transformation of nitroglycerin (NG) to dinitro- or mononitroglycerols enable bacteria containing such enzymes to use NG as the nitrogen source. The inability to use the resulting mononitroglycerols limits most strains to incomplete denitration of NG. Recently, Arthrobacter strain JBH1 was isolated for the ability to grow on NG as the sole source of carbon and nitrogen, but the enzymes and mechanisms involved were not established. Here, the enzymes that enable the Arthrobacter strain to incorporate NG into a productive pathway were identified. Enzyme assays indicated that the transformation of nitroglycerin to mononitroglycerol is NADPH dependent and that the subsequent transformation of mononitroglycerol is ATP dependent. Cloning and heterologous expression revealed that a flavoprotein catalyzes selective denitration of NG to 1-mononitroglycerol (1-MNG) and that 1-MNG is transformed to 1-nitro-3-phosphoglycerol by a glycerol kinase homolog. Phosphorylation of the nitroester intermediate enables the subsequent denitration of 1-MNG in a productive pathway that supports the growth of the isolate and mineralization of NG.

Growth of Arthrobacter sp. strain JBH1 on nitroglycerin as the sole source of carbon and nitrogen.

Arthrobacter sp. strain JBH1 was isolated from nitroglycerin-contaminated soil by selective enrichment. Detection of transient intermediates and simultaneous adaptation studies with potential intermediates indicated that the degradation pathway involves the conversion of nitroglycerin to glycerol via 1,2-dinitroglycerin and 1-mononitroglycerin, with concomitant release of nitrite. Glycerol then serves as the source of carbon and energy.

Effects of initial saturation on properties modification and displacement of tetrachloroethene with aqueous isobutanol.

Packed column experiments were conducted to study effects of initial saturation of tetrachloroethene (PCE) in the range of 1.0-14% pore volume (PV) on mobilization and downward migration of the non-aqueous phase liquid (NAPL) product upon contact with aqueous isobutanol ( approximately 10 vol.%). This study focused on the consequences of swelling beyond residual saturation. Columns were packed with mixtures of neat PCE, water and glass beads and waterflooded to establish a desired homogeneous residual saturation, and then flooded with aqueous isobutanol under controlled hydraulic conditions. Results showed a critical saturation of approximately 8% PV for these packed column experimental conditions. At low initial PCE saturations (<8% PV), experimental results showed reduced risk of NAPL-product migration upon contact with aqueous isobutanol. At higher initial PCE saturations (>8% PV), results showed NAPL-product mobilization and downward migration which was attributed to interfacial tension (IFT) reduction, swelling of the NAPL-product, and reduced density modification. Packed column results were compared with good agreement to theoretical predictions of NAPL-product mobilization using the total trapping number, N(T). In addition to the packed column study, preliminary batch experiments were conducted to study the effects of PCE volumetric fraction in the range of 0.5-20% on density, viscosity, and IFT modification as a function of time following contact with aqueous isobutanol ( approximately 10 vol.%). Modified NAPL-product fluid properties approached equilibrium within approximately 2 h of contact for density and viscosity. IFT reduction occurred immediately as expected. Measured fluid properties were compared with good agreement to theoretical equilibrium predictions based on UNIQUAC. Overall, this study demonstrates the importance of initial DNAPL saturation, and the associated risk of downward NAPL-product migration, in applying alcohol flooding for remediation of DNAPL contaminated ground water sites.

Dip-angle influence on areal DNAPL recovery by co-solvent flooding with and without pre-flooding.

A two-dimensional (2D) laboratory model was used to study effects of gravity on areal recovery of a representative dense non-aqueous phase liquid (DNAPL) contaminant by an alcohol pre-flood and co-solvent flood in dipping aquifers. Recent studies have demonstrated that injection of alcohol and co-solvent solutions can be used to reduce in-situ the density of DNAPL globules and displace the contaminant from the source zone. However, contact with aqueous alcohol reduces interfacial tension and causes DNAPL swelling, thus facilitating risk of uncontrolled downward DNAPL migration. The 2D laboratory model was operated with constant background gradient flow and a DNAPL spill was simulated using tetrachloroethene (PCE). The spill was dispersed to a trapped, immobile PCE saturation by a water flood. Areal PCE recovery was studied using a double-triangle well pattern to simulate a remediation scheme consisting of an alcohol pre-flood using aqueous isobutanol ( approximately 10% vol.) followed by a co-solvent flood using a solution of ethylene glycol (65%) and 1-propanol (35%). Experiments were conducted with the 2D model oriented in the horizontal plane and compared to experiments at the 15 degrees and 30 degrees dip-angle orientations. Injection was applied either in the downward or upward direction of flow. Experimental results were compared to theoretical predictions for flood front stability and used to evaluate effects of gravity on areal PCE recovery. Sensitivity experiments were performed to evaluate effects of the alcohol pre-flood on PCE areal recovery. For experiments conducted with the alcohol pre-flood and the 2D model oriented in the horizontal plane, results indicate that 89-93% of source zone PCE was recovered. With injection oriented downward, results indicate that areal PCE recovery was 70-77% for a 15 degrees dip angle and 57-59% for a 30 degrees dip angle. With injection oriented upward, results indicate that areal PCE recovery was 57-60% at the 30 degrees dip angle, which was similar to PCE recovery for injection in the downward flow direction. Lower areal PCE recovery at greater dip angles in either direction of flow was attributed to DNAPL swelling and migration, flood front instabilities and bypassing of the displaced fluid past the extraction wells during the alcohol pre-flood. Additional results demonstrate that the use of an alcohol pre-flood can be beneficial in improving DNAPL recovery in the horizontal orientation, but pre-flooding may reduce areal recovery efficiency in dip-angle orientations. This study also demonstrates the use of theoretical perturbation (fingering) analysis in predicting NAPL recovery efficiency for flooding processes in remediating aquifers with dip angles.