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PubMed | Laboratory of Molecular Biology and Laboratory of Environmental Biotechnology
Type: | Journal: Journal of visualized experiments : JoVE | Year: 2015

The importance of microbial sulfate reduction relies on the various applications that it offers in environmental biotechnology. Engineered sulfate reduction is used in industrial wastewater treatment to remove large concentrations of sulfate along with the chemical oxygen demand (COD) and heavy metals. The most common approach to the process is with anaerobic bioreactors in which sulfidogenic sludge is obtained through adaptation of predominantly methanogenic granular sludge to sulfidogenesis. This process may take a long time and does not always eliminate the competition for substrate due to the presence of methanogens in the sludge. In this work, we propose a novel approach to obtain sulfidogenic sludge in which hydrothermal vents sediments are the original source of microorganisms. The microbial community developed in the presence of sulfate and volatile fatty acids is wide enough to sustain sulfate reduction over a long period of time without exhibiting inhibition due to sulfide. This protocol describes the procedure to generate the sludge from the sediments in an upflow anaerobic sludge blanket (UASB) type of reactor. Furthermore, the protocol presents the procedure to demonstrate the capability of the sludge to remove by reductive dechlorination a model of a highly toxic organic pollutant such as trichloroethylene (TCE). The protocol is divided in three stages: (1) the formation of the sludge and the determination of its sulfate reducing activity in the UASB, (2) the experiment to remove the TCE by the sludge, and (3) the identification of microorganisms in the sludge after the TCE reduction. Although in this case the sediments were taken from a site located in Mexico, the generation of a sulfidogenic sludge by using this procedure may work if a different source of sediments is taken since marine sediments are a natural pool of microorganisms that may be enriched in sulfate reducing bacteria.


Schernewski G.,Leibniz Institute for Baltic Sea Research | Fischer E.,Leibniz Institute for Baltic Sea Research | Huttula T.,University of Jyväskylä | Jost G.,Leibniz Institute for Baltic Sea Research | Ras M.,Laboratory of Environmental Biotechnology
Journal of Coastal Conservation | Year: 2012

Insufficient hygienic water quality and bathing prohibitions are still a serious problem in the Szczecin Lagoon (southern Baltic). In our study we focus on the southern lagoon coast and analyse the causes and consequences of high Escherichia coli bacteria concentrations. For this purpose we carry out laboratory experiments on the behaviour of E. coli in the lagoon, a literature review and apply a three-dimensional flow model together with a Lagrangian particle tracking routine. Three major E. coli sources, the Uecker river, the wetlands with cattle as well as sea gulls with bathing and fisheries were allocated, quantified and compiled into an emission scenario. This serves as input for transport simulations under different wind conditions and for the development of a spatial contamination map. Reasons for high E. coli concentrations in the lagoon are a permanent supply from different sources and the special environmental situation in the lagoon. The availability of organic matter, either in form of reed stems or as muddy sediments, has a positive effect on bacteria survival. Very important, too, are the prevailing wind and flow conditions, which cause water and organism transport in narrow ribbons along the coastline and promote near-shore accumulations. Even in our shallow lagoon, the application of a 3D-model is beneficial. Heavy rains are, very likely, responsible for the outstanding high total-coliform concentrations of 11,000 cfu/100 ml on August 21, 2006. The model system proved to be a valuable tool for spatial analysis and is suitable to support the development of bathing water profiles according to the EU Bathing Water Directive (2006/7/EC). © 2012 Springer Science+Business Media B.V.


Bruce T.,Laboratory of Environmental Biotechnology | Bruce T.,Federal University of Bahia | Leite F.G.,Laboratory of Environmental Biotechnology | Miranda M.,Federal University of Rio de Janeiro | And 4 more authors.
Archives of Microbiology | Year: 2016

Clostridium butyricum is widely used to produce organic solvents such as ethanol, butanol and acetone. We sequenced the entire genome of C. butyricum INCQS635 by using Ion Torrent technology. We found a high contribution of sequences assigned for carbohydrate subsystems (15–20 % of known sequences). Annotation based on protein-conserved domains revealed a higher diversity of glycoside hydrolases than previously found in C. acetobutylicum ATCC824 strain. More than 30 glycoside hydrolases (GH) families were found; families of GH involved in degradation of galactan, cellulose, starch and chitin were identified as most abundant (close to 50 % of all sequences assigned as GH) in C. butyricum INCQS635. KEGG metabolic pathways reconstruction allowed us to verify possible routes in the C. butyricum INCQS635 and C. acetobutylicum ATCC824 genomes. Metabolic pathways for ethanol synthesis are similar for both species, but alcohol dehydrogenase of C. butyricum INCQS635 and C. acetobutylicum ATCC824 was different. The genomic repertoire of C. butyricum is an important resource to underpin future studies towards improved solvents production. © 2015, Springer-Verlag Berlin Heidelberg.


Hernandez D.,Laboratory of Environmental Biotechnology | Rodriguez-Cabrera L.,Laboratory of Environmental Biotechnology | Valdes R.,Ave 31 be 158 and 190 | Moran T.,Laboratory of Environmental Biotechnology | And 5 more authors.
Journal of Agronomy | Year: 2013

Alternatives to Bacillus thuringiensis (Bt) pesticide crystal protein (Cry), such as vegetative phase insecticidal proteins (Vip), to combat insect in genetically-modified plants has being investigated to provide an insect resistance management additional tool. Likewise, this study aimed expressing and purifying Bt-Vip3Aal from an Escherichia coli strain for generating polyclonal rabbit antibodies to be then employed for Vip3Aal detection in genetically-transformed corn plants. To perform this subject, Vip3Aal was expressed in the JM-109 strain and purified by metal-chelate affinity chromatography. Next, a Dot-blot, Westem-blot and an enzyme-linked immunosorbent assay (BUSA) using Vip3Aal-specific polyclonal rabbit antibodies were carried out to detect Vip3Aal in genetically-modified com plant seeds and leaves, respectively. FR-Btl com plants transformed with CrylFal gene served as negative control. As results, Vip3Aal production method yielded up to 16 μ of purified Vip3Aal per fermentation supernatant milliliter, 50.4±4.0% recovery and 97.2±2.7% of SDS-PAGE purity. Vip3Aal amino acid sequence corresponded totally with expected sequence and Vip3Aal shown a high insecticidal (93.5±8.8%) at 2 fig mL-1 and immunogenicity capacity in rabbits (1:3000Q±4142). Vip3Aal quantification assays evidenced high specificity and sensitivity (1 ng mL-1 (Dot-blot) and 1 ng mL-1 (detection limit) 30 ng mL-1 (quantification limit)) in the ELISA. Quantification results were further corroborated through a biological assay using Spodoptera frugiperda and plant materials as insect diet supplements, where death rate ranged 68.7-7.0% in a doses dependent manner. Thus, these immunoassays can be successfully used to detect Vip3Aal, in the seeds and leaves allowing discrimination between modified-and non-modified-genetically com seeds and plants. © 2013 Asian Network for Scientific Information.


PubMed | Federal University of Rio de Janeiro and Laboratory of Environmental Biotechnology
Type: Journal Article | Journal: Archives of microbiology | Year: 2016

Clostridium butyricum is widely used to produce organic solvents such as ethanol, butanol and acetone. We sequenced the entire genome of C. butyricum INCQS635 by using Ion Torrent technology. We found a high contribution of sequences assigned for carbohydrate subsystems (15-20 % of known sequences). Annotation based on protein-conserved domains revealed a higher diversity of glycoside hydrolases than previously found in C. acetobutylicum ATCC824 strain. More than 30 glycoside hydrolases (GH) families were found; families of GH involved in degradation of galactan, cellulose, starch and chitin were identified as most abundant (close to 50 % of all sequences assigned as GH) in C. butyricum INCQS635. KEGG metabolic pathways reconstruction allowed us to verify possible routes in the C. butyricum INCQS635 and C. acetobutylicum ATCC824 genomes. Metabolic pathways for ethanol synthesis are similar for both species, but alcohol dehydrogenase of C. butyricum INCQS635 and C. acetobutylicum ATCC824 was different. The genomic repertoire of C. butyricum is an important resource to underpin future studies towards improved solvents production.

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