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Find video protocols related to scientific articles indexed in Pubmed.
Unrevealing the interactive effects of climate change and oil contamination on lab-simulated estuarine benthic communities.
Glob Chang Biol
PUBLISHED: 07-22-2014
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There is growing concern that modifications to the global environment such as ocean acidification and increased ultraviolet radiation may interact with anthropogenic pollutants to adversely affect the future marine environment. Despite this, little is known about the nature of the potential risks posed by such interactions. Here, we performed a multifactorial microcosm experiment to assess the impact of ocean acidification, ultraviolet radiation B (UV-B) and oil hydrocarbon contamination on sediment chemistry, the microbial community (composition and function) and biochemical marker response of selected indicator species. We found that increased ocean acidification and oil contamination in the absence of UV-B will significantly alter bacterial composition by, among other changes, greatly reducing the relative abundance of Desulfobacterales, known to be important oil hydrocarbon degraders. Along with changes in bacterial composition, we identified concomitant shifts in the composition of aromatic hydrocarbons in the sediment and an increase in oxidative stress effects on our indicator species. Interestingly, our study identifies UV-B as a critical component in the interaction between these factors, since its presence alleviates harmful effects caused by the combination of reduced pH and oil pollution. The model system used here shows that the interactive effect of reduced pH and oil contamination can adversely affect the structure and functioning of sediment benthic communities, with the potential to exacerbate the toxicity of oil hydrocarbons in marine ecosystems. This article is protected by copyright. All rights reserved.
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Influence of environmental variables in the efficiency of phage therapy in aquaculture.
Microb Biotechnol
PUBLISHED: 05-20-2014
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Aquaculture facilities worldwide continue to experience significant economic losses because of disease caused by pathogenic bacteria, including multidrug-resistant strains. This scenario drives the search for alternative methods to inactivate pathogenic bacteria. Phage therapy is currently considered as a viable alternative to antibiotics for inactivation of bacterial pathogens in aquaculture systems. While phage therapy appears to represent a useful and flexible tool for microbiological decontamination of aquaculture effluents, the effect of physical and chemical properties of culture waters on the efficiency of this technology has never been reported. The present study aimed to evaluate the effect of physical and chemical properties of aquaculture waters (e.g. pH, temperature, salinity and organic matter content) on the efficiency of phage therapy under controlled experimental conditions in order to provide a basis for the selection of the most suitable protocol for subsequent experiments. A bioluminescent genetically transformed Escherichia coli was selected as a model microorganism to monitor real-time phage therapy kinetics through the measurement of bioluminescence, thus avoiding the laborious and time-consuming conventional method of counting colony-forming units (CFU). For all experiments, a bacterial concentration of ? 10(5) CFU ml(-1) and a phage concentration of ? 10(6-8) plaque forming unit ml(-1) were used. Phage survival was not significantly affected by the natural variability of pH (6.5-7.4), temperature (10-25 °C), salinity (0-30 g NaCl l(-1) ) and organic matter concentration of aquaculture waters in a temperate climate. Nonetheless, the efficiency of phage therapy was mostly affected by the variation of salinity and organic matter content. As the effectiveness of phage therapy increases with water salt content, this approach appears to be a suitable choice for marine aquaculture systems. The success of phage therapy may also be enhanced in non-marine systems through the addition of salt, whenever this option is feasible and does not affect the survival of aquatic species being cultured.
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Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons.
FEMS Microbiol. Ecol.
PUBLISHED: 05-13-2014
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In this study, two molecular techniques [denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing] were used to evaluate the composition of bacterial communities in salt marsh microhabitats [bulk sediment and sediment surrounding the roots (rhizosphere) of Halimione portulacoides and Sarcocornia perennis ssp. perennis] that have been differentially affected by oil hydrocarbon (OH) pollution. Both DGGE and pyrosequencing revealed that bacterial composition is structured by microhabitat. Rhizosphere sediment from both plant species revealed enrichment of operational taxonomic units closely related to Acidimicrobiales, Myxococcales and Sphingomonadales. The in silico metagenome analyses suggest that homologous genes related to OH degradation appeared to be more frequent in both plant rhizospheres than in bulk sediment. In summary, this study suggests that halophyte plant colonization is an important driver of hydrocarbonoclastic bacterial community composition in estuarine environments, which can be exploited for in situ phytoremediation of OH in salt marsh environments.
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Hydrocarbon contamination and plant species determine the phylogenetic and functional diversity of endophytic degrading bacteria.
Mol. Ecol.
PUBLISHED: 04-26-2014
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Salt marsh sediments are sinks for various anthropogenic contaminants, giving rise to significant environmental concern. The process of salt marsh plant survival in such environment is very intriguing and at the same time poorly understood. The plant–microbe interactions may play a key role in the process of environment and in planta detoxification.In this study, a combination of culture-dependent and culture-independent molecular approaches [enrichment cultures, polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), DNA sequencing] were used to investigate the effect of petroleum hydrocarbons (PH) contamination on the structure and function[polycyclic aromatic hydrocarbon (PAH) dioxygenase genes] of endophytic bacterial communities of salt marsh plant species (Halimione portulacoides and Sarcocornia perennis)in the estuarine system Ria de Aveiro (Portugal). Pseudomonads dominated the cultivable fraction of the endophytic communities in the enrichment cultures. In a set of fifty isolates tested, nine were positive for genes encoding for PAH dioxygenases (nahAc)and four were positive for plasmid carrying genes encoding PAH degradation enzymes(nahAc). Interestingly, these plasmids were only detected in isolates from most severely PH-polluted sites. The results revealed site-specific effects on endophytic communities,related to the level of PH contamination in the sediment, and plant-species-specific ‘imprints’ in community structure and in genes encoding for PAH dioxygenases. These results suggest a potential ecological role of bacterial plant symbiosis in the process of plant colonization in urban estuarine areas exposed to PH contamination.
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Optimization of preservation and processing of sea anemones for microbial community analysis using molecular tools.
Sci Rep
PUBLISHED: 03-31-2014
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For several years, knowledge on the microbiome associated with marine invertebrates was impaired by the challenges associated with the characterization of bacterial communities. With the advent of culture independent molecular tools it is possible to gain new insights on the diversity and richness of microorganisms associated with marine invertebrates. In the present study, we evaluated if different preservation and processing methodologies (prior to DNA extraction) can affect the bacterial diversity retrieved from snakelocks anemone Anemonia viridis. Denaturing gradient gel electrophoresis (DGGE) community fingerprints were used as proxy to determine the bacterial diversity retrieved (H'). Statistical analyses indicated that preservation significantly affects H'. The best approach to preserve and process A. viridis biomass for bacterial community fingerprint analysis was flash freezing in liquid nitrogen (preservation) followed by the use of a mechanical homogenizer (process), as it consistently yielded higher H'. Alternatively, biomass samples can be processed fresh followed by cell lyses using a mechanical homogenizer or mortar &pestle. The suitability of employing these two alternative procedures was further reinforced by the quantification of the 16S rRNA gene; no significant differences were recorded when comparing these two approaches and the use of liquid nitrogen followed by processing with a mechanical homogenizer.
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Microbe-Assisted Phytoremediation of Hydrocarbons in Estuarine Environments.
Microb. Ecol.
PUBLISHED: 03-13-2014
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Estuaries are sinks for various anthropogenic contaminants, such as petroleum hydrocarbons, giving rise to significant environmental concern. The demand for organisms and processes capable of degrading pollutants in a clean, effective, and less expensive process is of great importance. Phytoremedition approaches involving plant/bacteria interactions have been explored as an alternative, and halophyte vegetation has potential for use in phytoremedition of hydrocarbon contamination. Studies with plant species potentially suitable for microbe-assisted phytoremediation are widely represented in scientific literature. However, the in-depth understanding of the biological processes associated with the re-introduction of indigenous bacteria and plants and their performance in the degradation of hydrocarbons is still the limiting step for the application of these bioremediation solutions in a field context. The intent of the present review is to summarize the sources and effects of hydrocarbon contamination in estuarine environments, the strategies currently available for bioremediation (potential and limitations), and the perspectives of the use of halophyte plants in microbe-assisted phytoremediation approaches.
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Composition of Archaea in seawater, sediment, and sponges in the Kepulauan Seribu reef system, Indonesia.
Microb. Ecol.
PUBLISHED: 01-30-2014
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Coral reefs are among the most diverse and productive ecosystems in the world. Most research has, however, focused on eukaryotes such as corals and fishes. Recently, there has been increasing interest in the composition of prokaryotes, particularly those inhabiting corals and sponges, but these have mainly focused on bacteria. There have been very few studies of coral reef Archaea, despite the fact that Archaea have been shown to play crucial roles in nutrient dynamics, including nitrification and methanogenesis, of oligotrophic environments such as coral reefs. Here, we present the first study to assess Archaea in four different coral reef biotopes (seawater, sediment, and two sponge species, Stylissa massa and Xestospongia testudinaria). The archaeal community of both sponge species and sediment was dominated by Crenarchaeota, while the seawater community was dominated by Euryarchaeota. The biotope explained more than 72% of the variation in archaeal composition. The number of operational taxonomic units (OTUs) was highest in sediment and seawater biotopes and substantially lower in both sponge hosts. No "sponge-specific" archaeal OTUs were found, i.e., OTUs found in both sponge species but absent from nonhost biotopes. Despite both sponge species hosting phylogenetically distinct microbial assemblages, there were only minor differences in Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways. In contrast, most functional pathways differed significantly between microbiomes from sponges and nonhost biotopes including all energy metabolic pathways. With the exception of the methane and nitrogen metabolic pathway, all energy metabolic pathways were enriched in sponges when compared to nonhost biotopes.
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Habitat- and host-related variation in sponge bacterial symbiont communities in Indonesian waters.
FEMS Microbiol. Ecol.
PUBLISHED: 12-14-2013
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Marine lakes are unique ecosystems that contain isolated populations of marine organisms. Isolated from the surrounding marine habitat, many lakes house numerous endemic species. In this study, microbial communities of sponges inhabiting these lakes were investigated for the first time using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial richness and composition of two sponge species (Suberites diversicolor and Cinachyrella australiensis) inhabiting both marine lakes and adjacent open coastal systems. Host species and habitat explained almost 59% of the variation in bacterial composition. There was a significant difference in composition between both host species. Within S. diversicolor, there was little discernible difference between bacterial communities inside and outside lakes. The bacterial community of this species was, furthermore, dominated (63% of all sequences) by three very closely related alphaproteobacterial taxa identified as belonging to the recently described order Kiloniellales. Cinachyrella australiensis, in contrast, hosted markedly different bacterial communities inside and outside lakes with very few shared abundant taxa. Cinachyrella australiensis in open habitat only shared 9.4% of OTUs with C. australiensis in lake habitat. Bacteria were thus both highly species specific and, in the case of C. australiensis, habitat specific.
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Development and validation of an experimental life support system for assessing the effects of global climate change and environmental contamination on estuarine and coastal marine benthic communities.
Glob Chang Biol
PUBLISHED: 03-27-2013
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An experimental life support system (ELSS) was constructed to study the interactive effects of multiple stressors on coastal and estuarine benthic communities, specifically perturbations driven by global climate change and anthropogenic environmental contamination. The ELSS allows researchers to control salinity, pH, temperature, ultraviolet radiation (UVR), tidal rhythms and exposure to selected contaminants. Unlike most microcosms previously described, our system enables true independent replication (including randomization). In addition to this, it can be assembled using commercially available materials and equipment, thereby facilitating the replication of identical experimental setups in different geographical locations. Here, we validate the reproducibility and environmental quality of the system by comparing chemical and biological parameters recorded in our ELSS with those prevalent in the natural environment. Water, sediment microbial community and ragworm (the polychaete Hediste diversicolor) samples were obtained from four microcosms after 57 days of operation. In general, average concentrations of dissolved inorganic nutrients (NO3 (-) ; NH4 (+) and PO4 (-3) ) in the water column of the ELSS experimental control units were within the range of concentrations recorded in the natural environment. While some shifts in bacterial community composition were observed between in situ and ELSS sediment samples, the relative abundance of most metabolically active bacterial taxa appeared to be stable. In addition, ELSS operation did not significantly affect survival, oxidative stress and neurological biomarkers of the model organism Hediste diversicolor. The validation data indicate that this system can be used to assess independent or interactive effects of climate change and environmental contamination on benthic communities. Researchers will be able to simulate the effects of these stressors on processes driven by microbial communities, sediment and seawater chemistry and to evaluate potential consequences to sediment toxicity using model organisms such as Hediste diversicolor.
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Growth conditions influence UVB sensitivity and oxidative damage in an estuarine bacterial isolate.
Photochem. Photobiol. Sci.
PUBLISHED: 03-15-2013
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The dose-dependent variation of oxidative cellular damage imposed by UVB exposure in a representative estuarine bacterial strain, Pseudomonas sp. NT5I1.2B, was studied at different growth phases (mid-exponential, late-exponential, and stationary), growth temperatures (15 °C and 25 °C) and growth media (nutrient-rich Tryptic Soy Broth [TSB] and nutrient-poor M9). Survival and markers of oxidative damage (lipid peroxidation, protein carbonylation, DNA strand breakage, and DNA-protein cross-links) were monitored during exposure to increasing UVB doses (0-60 kJ m(-2)). Oxidative damage did not follow a clear linear dose-dependent pattern, particularly at high UVB doses (>10 kJ m(-2)), suggesting a dynamic interaction between damage induction and repair during irradiation and/or saturation of oxidative damage. Survival of stationary phase cells generally exceeded that of exponential phase cells by up to 33.5 times; the latter displayed enhanced levels of DNA-protein cross-links (up to 15.6-fold) and protein carbonylation (up to 6.0-fold). Survival of mid-exponential phase cells was generally higher at 15 °C than at 25 °C (up to 6.6-fold), which was accompanied by lower levels of DNA strand breaks (up to 4000-fold), suggesting a temperature effect on reactive oxygen species (ROS) generation and/or ROS interaction with cellular targets. Survival under medium-high UVB doses (>10 kJ m(-2)) was generally higher (up to 5.4-fold) in cells grown in TSB than in M9. These results highlight the influence of growth conditions preceding irradiation on the extent of oxidative damage induced by UVB exposure in bacteria.
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An ecotoxicological analysis of the sediment quality in a European Atlantic harbor emphasizes the current limitations of the Water Framework Directive.
Mar. Pollut. Bull.
PUBLISHED: 03-05-2013
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The "PortoNovo" project was developed to standardize the methodologies for water quality management in the port areas of coastal Atlantic regions to improve the Water Frame Directive (WFD) for these specific water bodies. Under this scope, water and sediment samples were collected from five sites within the Port of Aveiro, Portugal. According to the physical and chemical parameters that were analyzed (i.e., metals, total organic carbon, polychlorinated biphenyls and polycyclic aromatic hydrocarbons), the sediments were not considered at risk based on European sediment quality laws. However, the bioassays that were performed on the sediment samples (Microtox®) and the standardized acute toxicity test using the marine rotifer, Brachionus plicatilis, on sediment elutriates revealed higher toxicity levels. The use of bioassays to assess sediment quality clearly complements more conservative approaches and highlights current gaps within the WFD. The approach presented here can be easily transferred to other port areas for more reliable water quality management.
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Nucleic acid changes during photodynamic inactivation of bacteria by cationic porphyrins.
Bioorg. Med. Chem.
PUBLISHED: 02-27-2013
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Light activation of photosensitizing dyes in presence of molecular oxygen generates highly cytotoxic reactive oxygen species leading to cell inactivation. Nucleic acids are molecular targets of this photodynamic action but not considered the main cause of cell death. The in vivo effect of the photodynamic process on the intracellular nucleic acid content of Escherichia coli and Staphylococcus warneri was evaluated herein. Two cationic porphyrins (Tetra-Py(+)-Me and Tri-Py(+)-Me-PF) were used to photoinactivate E. coli (5.0?M; 10(8)cellsmL(-1)) and S. warneri (0.5?M; 10(8)cellsmL(-1)) upon white light irradiation at 4.0mWcm(-2) for 270min and 40min, respectively. Total nucleic acids were extracted from photosensitized bacteria after different times of irradiation and analyzed by agarose gel electrophoresis. The double-stranded DNA was quantified by fluorimetry and the porphyrin binding to bacteria was determined by spectrofluorimetry. E. coli was completely photoinactivated with both porphyrins (5.0?M), whereas S. warneri was only completely inactivated by Tri-Py(+)-Me-PF (0.5?M). The hierarchy of nucleic acid changes in E. coli was in the order: 23S rRNA>16S rRNA>genomic DNA. The nucleic acids of S. warneri were extensively reduced after 5min with Tri-Py(+)-Me-PF but almost unchanged with Tetra-Py(+)-Me after 40min of irradiation. The amount of Tri-Py(+)-Me-PF bound to E. coli after washing the cells is higher than Tetra-Py(+)-Me and the opposite was observed for S. warneri. The binding capacity of the photosensitizers is not directly related to the PDI efficiency or nucleic acid reduction and this reduction occurs in parallel with the decrease of surviving cells.
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Richness and composition of sediment bacterial assemblages in an Atlantic port environment.
Sci. Total Environ.
PUBLISHED: 02-07-2013
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In the present study, we assessed the bacterial richness and composition of sediment samples collected in and around the port of Aveiro, on the Atlantic coast of mainland Portugal. Sediment samples were collected in five locations: two within the port harbor, two in port areas along a channel adjacent to the harbor and one in a relatively undisturbed reference location. These areas were characterized as under high, medium and no port activity, respectively. In-depth, barcoded-pyrosequencing analysis indicated that port activity affects the composition and abundance of bacterial communities colonizing surface sediments. Sampling sites under the influence of port activities (channel and harbor) were associated with higher relative abundances of Desulfobacterales and a marked decline in the abundance of Flavobacteriia. In addition, there was a pronounced prevalence of operational taxonomic units (OTUs) in the port area that were closely related to hydrocarbon-degrading bacteria (Desulfococcus spp.), antifouling paint (bacterium strain WH6-7) and copper rich sediments (bacterium strain CanalPD16A). Here we provide evidence that specific phylotypes detected have the potential to be used as biomarkers and should be evaluated in future studies as proxies for sediment disturbance associated with port activity.
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Selective cultures for the isolation of biosurfactant producing bacteria: comparison of different combinations of environmental inocula and hydrophobic carbon sources.
Prep. Biochem. Biotechnol.
PUBLISHED: 02-06-2013
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The potential of estuarine microniches as reservoirs of biosurfactant-producing bacteria was evaluated by testing different combinations of inocula and hydrophobic carbon sources. Selective cultures using diesel, petroleum, or paraffin as hydrophobic carbon sources were prepared and inoculated with water from the surface microlayer, bulk sediments, and sediment of the rhizosphere of Halimione portulacoides. These inocula were compared regarding the frequency of biosurfactant-producing strains among selected isolates. The community structure of the selective cultures was profiled using denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene fragments at the end of the incubation. The DGGE profiles corresponding to the communities established in selective cultures at the end of the incubation revealed that communities were different in terms of structural diversity. The highest diversity was observed in the selective cultures containing paraffin (H () = 2.5). Isolates were obtained from the selective cultures (66) and tested for biosurfactant production by the atomized oil assay. Biosurfactant production was detected in 17 isolates identified as Microbacterium, Pseudomonas, Rhodococcus, and Serratia. The combination of estuarine surface microlayer (SML) water as inoculum and diesel as carbon source seems promising for the isolation of surfactant-producing bacteria. Supplemental materials are available for this article. Go to the publishers online edition of Preparative Biochemistry and Biotechnology to view the supplemental file.
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Contribution of chemical water properties to the differential responses of bacterioneuston and bacterioplankton to ultraviolet-B radiation.
FEMS Microbiol. Ecol.
PUBLISHED: 02-04-2013
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The surface microlayer (SML) is characterized by different physicochemical properties from underlying waters (UW). However, whether these differences in abiotic factors underlie the distinct sensitivity of bacterioneuston (i.e. SML bacteria) and bacterioplankton to environmental stressors remains to be addressed. We investigated the contribution of abiotic factors to the UV-B sensitivity of bacterioneuston and bacterioplankton. Nutrients (especially nitrogen and phosphate) emerged as important determinants of bacterial UV-B sensitivity. The role of particles, nutrients, and dissolved organic components on bacterial UV-B sensitivity was further evaluated using dilution cultures. Filtered samples were twofold more UV sensitive than unfiltered samples, suggesting a UV-protective effect of particles. High nutrient concentrations attenuated bacterial UV-B sensitivity (up to 40%), compared with unamended conditions, by influencing bacterial physiology and/or community composition. Suspending cells in natural water, particularly from the SML, also attenuated UV-B sensitivity (up to 23%), compared with suspension in an artificial mineral solution. Bioassays using Pseudomonas sp. strain NT5I1.2B revealed that chemical water properties influence UV-induced oxidative damage. UV-B sensitivity was associated with high cell-specific activities. The chemical environment of the SML and UW influences UV-B effects on the corresponding bacterial communities. Maintaining low cell activities might be advantageous in stressful environments, like the SML.
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Interactive effects of global climate change and pollution on marine microbes: the way ahead.
Ecol Evol
PUBLISHED: 01-25-2013
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Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future.
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Role of transition metals in UV-B-induced damage to bacteria.
Photochem. Photobiol.
PUBLISHED: 01-16-2013
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The purpose of this study was to explore the possible link between metals and UV-B-induced damage in bacteria. The effect of growth in the presence of enhanced concentrations of different transition metals (Co, Cu, Fe, Mn and Zn) on the UV-B sensitivity of a set of bacterial isolates was explored in terms of survival, activity and oxidative stress biomarkers (ROS generation, damage to DNA, lipid and proteins and activity of antioxidant enzymes). Metal amendment, particularly Fe, Cu and Mn, enhanced bacterial inactivation during irradiation by up to 35.8%. Amendment with Fe increased ROS generation during irradiation by 1.2-13.3%, DNA damage by 10.8-37.4% and lipid oxidative damage by 9.6-68.7%. Lipid damage during irradiation also increased after incubation with Cu and Co by up to 66.8% and 56.5% respectively. Mn amendment decreased protein carbonylation during irradiation by up to 44.2%. These results suggest a role of Fe, Co, Cu and Mn in UV-B-induced bacterial inactivation and the importance of metal homeostasis to limit the detrimental effects of ROS generated during irradiation.
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Photodynamic oxidation of Staphylococcus warneri membrane phospholipids: new insights based on lipidomics.
Rapid Commun. Mass Spectrom.
PUBLISHED: 01-11-2013
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The photodynamic process involves the combined use of light and a photosensitizer, which, in the presence of oxygen, originates cytotoxic species capable of oxidizing biological molecules, such as lipids. However, the effect of the photodynamic process in the bacterial phospholipid profile by a photosensitizer has never been reported. A lipidomic approach was used to study the photodynamic oxidation of membrane phospholipids of Staphylococcus warneri by a tricationic porphyrin [5,10,15-tris(1-methylpyridinium-4-yl)-20-(pentafluorophenyl)porphyrin triiodide, Tri-Py(+)-Me-PF].
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Molecular Analysis of Bacterial Communities and Detection of Potential Pathogens in a Recirculating Aquaculture System for Scophthalmus maximus and Solea senegalensis.
PLoS ONE
PUBLISHED: 01-01-2013
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The present study combined a DGGE and barcoded 16S rRNA pyrosequencing approach to assess bacterial composition in the water of a recirculating aquaculture system (RAS) with a shallow raceway system (SRS) for turbot (Scophthalmus maximus) and sole (Solea senegalensis). Barcoded pyrosequencing results were also used to determine the potential pathogen load in the RAS studied. Samples were collected from the water supply pipeline (Sup), fish production tanks (Pro), sedimentation filter (Sed), biofilter tank (Bio), and protein skimmer (Ozo; also used as an ozone reaction chamber) of twin RAS operating in parallel (one for each fish species). Our results revealed pronounced differences in bacterial community composition between turbot and sole RAS, suggesting that in the systems studied there is a strong species-specific effect on water bacterial communities. Proteobacteria was the most abundant phylum in the water supply and all RAS compartments. Other important taxonomic groups included the phylum Bacteriodetes. The saltwater supplied displayed a markedly lower richness and appeared to have very little influence on bacterial composition. The following potentially pathogenic species were detected: Photobacterium damselae in turbot (all compartments), Tenacibaculum discolor in turbot and sole (all compartments), Tenacibaculum soleae in turbot (all compartments) and sole (Pro, Sed and Bio), and Serratia marcescens in turbot (Sup, Sed, Bio and Ozo) and sole (only Sed) RAS. Despite the presence of these pathogens, no symptomatic fish were observed. Although we were able to identify potential pathogens, this approach should be employed with caution when monitoring aquaculture systems, as the required phylogenetic resolution for reliable identification of pathogens may not always be possible to achieve when employing 16S rRNA gene fragments.
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Can volatile organic metabolites be used to simultaneously assess microbial and mite contamination level in cereal grains and coffee beans?
PLoS ONE
PUBLISHED: 01-01-2013
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A novel approach based on headspace solid-phase microextraction (HS-SPME) combined with comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-ToFMS) was developed for the simultaneous screening of microbial and mite contamination level in cereals and coffee beans. The proposed approach emerges as a powerful tool for the rapid assessment of the microbial contamination level (ca. 70 min versus ca. 72 to 120 h for bacteria and fungi, respectively, using conventional plate counts), and mite contamination (ca. 70 min versus ca. 24 h). A full-factorial design was performed for optimization of the SPME experimental parameters. The methodology was applied to three types of rice (rough, brown, and white rice), oat, wheat, and green and roasted coffee beans. Simultaneously, microbiological analysis of the samples (total aerobic microorganisms, moulds, and yeasts) was performed by conventional plate counts. A set of 54 volatile markers was selected among all the compounds detected by GC×GC-ToFMS. Principal Component Analysis (PCA) was applied in order to establish a relationship between potential volatile markers and the level of microbial contamination. Methylbenzene, 3-octanone, 2-nonanone, 2-methyl-3-pentanol, 1-octen-3-ol, and 2-hexanone were associated to samples with higher microbial contamination level, especially in rough rice. Moreover, oat exhibited a high GC peak area of 2-hydroxy-6-methylbenzaldehyde, a sexual and alarm pheromone for adult mites, which in the other matrices appeared as a trace component. The number of mites detected in oat grains was correlated to the GC peak area of the pheromone. The HS-SPME/GC×GC-ToFMS methodology can be regarded as the basis for the development of a rapid and versatile method that can be applied in industry to the simultaneous assessment the level of microbiological contamination and for detection of mites in cereals grains and coffee beans.
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Ultracentrifugation as a direct method to concentrate viruses in environmental waters: virus-like particle enumeration as a new approach to determine the efficiency of recovery.
J Environ Monit
PUBLISHED: 11-24-2011
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Some health important enteric viruses are considered to be emerging waterborne pathogens and so the improvement of detection of these viruses in the aquatic environment is one of the most important steps in dealing with these pathogens. Since these viruses may be present in low numbers in water, it is necessary to concentrate water samples before viral detection. Although there are several methods to concentrate viruses in environmental waters, all present some drawbacks and consequently the method should be chosen that, despite its limitations, is adequate to achieve the aim of each study. As the effectiveness of the concentration methods is evaluated by determining the efficiency of viral recovery after concentration, it is important to use a simple and effective approach to evaluate their recovery efficiency. In this work ultracentrifugation, usually used as a secondary step for virus concentration, was evaluated as the main method to concentrate directly viruses in environmental water samples, using the microscopic enumeration of virus-like particles (VLP) as a new approach to estimate the efficiency of recovery. As the flocculation method is currently employed to concentrate viruses in environmental waters, it was also used in this study to assess the efficiency of the ultracentrifugation as the main viral concentration method in environmental waters. The results of this study indicate that ultracentrifugation is an adequate approach to concentrate viruses directly from environmental waters (recovery percentages between 66 and 72% in wastewaters and between 66 and 76% in recreational waters) and that the determination of VLP by epifluorescence microscopy is a simple, fast and cheap alternative approach to determine the recovery efficiency of the viral concentration methods.
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Bacteriophages with potential for inactivation of fish pathogenic bacteria: survival, host specificity and effect on bacterial community structure.
Mar Drugs
PUBLISHED: 09-22-2011
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Phage therapy may represent a viable alternative to antibiotics to inactivate fish pathogenic bacteria. Its use, however, requires the awareness of novel kinetics phenomena not applied to conventional drug treatments. The main objective of this work was to isolate bacteriophages with potential to inactivate fish pathogenic bacteria, without major effects on the structure of natural bacterial communities of aquaculture waters. The survival was determined in marine water, through quantification by the soft agar overlay technique. The host specificity was evaluated by cross infection. The ecological impact of phage addition on the structure of the bacterial community was evaluated by DGGE of PCR amplified 16S rRNA gene fragments. The survival period varied between 12 and 91 days, with a higher viability for Aeromonas salmonicida phages. The phages of Vibrio parahaemolyticus and of A. salmonicida infected bacteria of different families with a high efficacy of plating. The specific phages of pathogenic bacteria had no detectable impact on the structure of the bacterial community. In conclusion, V. parahaemolyticus and A. salmonicida phages show good survival time in marine water, have only a moderated impact on the overall bacterial community structure and the desired specificity for host pathogenic bacteria, being potential candidates for therapy of fish infectious diseases in marine aquaculture systems.
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Cnidarians as a source of new marine bioactive compounds--an overview of the last decade and future steps for bioprospecting.
Mar Drugs
PUBLISHED: 09-03-2011
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Marine invertebrates are rich sources of bioactive compounds and their biotechnological potential attracts scientific and economic interest worldwide. Although sponges are the foremost providers of marine bioactive compounds, cnidarians are also being studied with promising results. This diverse group of marine invertebrates includes over 11,000 species, 7500 of them belonging to the class Anthozoa. We present an overview of some of the most promising marine bioactive compounds from a therapeutic point of view isolated from cnidarians in the first decade of the 21st century. Anthozoan orders Alcyonacea and Gorgonacea exhibit by far the highest number of species yielding promising compounds. Antitumor activity has been the major area of interest in the screening of cnidarian compounds, the most promising ones being terpenoids (monoterpenoids, diterpenoids, sesquiterpenoids). We also discuss the future of bioprospecting for new marine bioactive compounds produced by cnidarians.
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Photodynamic inactivation of Penicillium chrysogenum conidia by cationic porphyrins.
Photochem. Photobiol. Sci.
PUBLISHED: 08-22-2011
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This work reports the photophysical and biological evaluation of five cationic porphyrins as photosensitizers (PS) for the photodynamic inactivation (PDI) of Penicillium chrysogenum conidia. Two different cationic porphyrin groups were synthesized from 5,10,15,20-tetrakis(4-pyridyl)porphyrin and 5,10,15,20-tetrakis(pentafluorophenyl)porphyrin. The photostability and singlet oxygen generation studies showed that these molecules are photostable and efficient singlet oxygen generators. PDI experiments of P. chrysogenum conidia conducted with 50 ?mol L(-1) of photosensitiser under white light at a fluence rate of 200 mW cm(-2) over 20 min showed that the most effective PS caused a 4.1 log reduction in the concentration of viable conidia. The present results show that porphyrins 1a and 1b are more efficient PSs than porphyrin 2a while porphyrins 1c and 2b show no inactivation of P. chrysogenum. It is also clear that the effectiveness of the molecule as PS for antifungal PDI is strongly related with the porphyrin substituent groups, and consequently their solubility in physiological media. The average amount of PS adsorbed per viable conidium was a determining factor in the photoinactivation efficiency and varied between the different studied PSs. Cationic PSs 1a and 1b might be promising anti-fungal PDI agents with potential applications in phytosanitation, biofilm control, bioremediation, and wastewater treatment.
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Applicability of photodynamic antimicrobial chemotherapy as an alternative to inactivate fish pathogenic bacteria in aquaculture systems.
Photochem. Photobiol. Sci.
PUBLISHED: 08-09-2011
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Aquaculture activities are increasing worldwide, stimulated by the progressive reduction of natural fish stocks in the oceans. However, these activities also suffer heavy production and financial losses resulting from fish infections caused by microbial pathogens, including multidrug resistant bacteria. Therefore, strategies to control fish infections are urgently needed, in order to make aquaculture industry more sustainable. Antimicrobial photodynamic therapy (aPDT) has emerged as an alternative to treat diseases and prevent the development of antibiotic resistance by pathogenic bacteria. The aim of this work was to evaluate the applicability of aPDT to inactivate pathogenic fish bacteria. To reach this objective a cationic porphyrin Tri-Py(+)-Me-PF was tested against nine pathogenic bacteria isolated from a semi-intensive aquaculture system and against the cultivable bacteria of the aquaculture system. The ecological impact of aPDT in the aquatic environment was also tested on the natural bacterial community, using the overall bacterial community structure and the cultivable bacteria as indicators. Photodynamic inactivation of bacterial isolates and of cultivable bacteria was assessed counting the number of colonies. The impact of aPDT in the overall bacterial community structure of the aquaculture water was evaluated by denaturing gel gradient electrophoresis (DGGE). The results showed that, in the presence of Tri-Py(+)-Me-PF, the growth of bacterial isolates was inhibited, resulting in a decrease of ?7-8 log after 60-270 min of irradiation. Cultivable bacteria were also considerably affected, showing decreases up to the detection limit (?2 log decrease on cell survival), but the inactivation rate varied significantly with the sampling period. The DGGE fingerprint analyses revealed changes in the bacterial community structure caused by the combination of aPDT and light. The results indicate that aPDT can be regarded as a new approach to control fish infections in aquaculture systems, but it is clearly more difficult to inactivate the complex natural bacterial communities of aquaculture waters than pure cultures of bacteria isolated from aquaculture systems. Considering the use of aPDT to inactivate pathogenic microbial community of aquaculture systems the monitoring of microorganisms is needed in order to select the most effective conditions.
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Mechanisms of photodynamic inactivation of a gram-negative recombinant bioluminescent bacterium by cationic porphyrins.
Photochem. Photobiol. Sci.
PUBLISHED: 07-29-2011
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Photodynamic therapy is a very promising approach to inactivate pathogenic microorganisms. The photodamage of cells involves reactive oxygen species (ROS) which are generated in situ by two main mechanisms (type I and/or type II). The mechanism responsible for the photoinactivation (PI) of a bioluminescent recombinant Escherichia coli, induced by three different cationic porphyrins, was identified in this work using a rapid method based on the monitoring of the metabolic activity of this bacterium. The inhibitory effect of the photodynamic process in the presence of a singlet oxygen quencher (sodium azide) or free radical scavengers (d-mannitol and l-cysteine) was evaluated by exposing bacterial suspensions with 0.5 ?M Tri-Py(+)-Me-PF, 5.0 ?M Tetra-Py(+)-Me or 5.0 ?M Tri-SPy(+)-Me-PF to white light. Strong bacterial protection was observed with sodium azide (100 mM) for the three cationic porphyrins. However, in the presence of Tri-Py(+)-Me-PF and Tetra-Py(+)-Me and the free radical scavengers (l-cysteine and d-mannitol) the reduction on the bacterial bioluminescence was significantly higher and similar to that obtained in their absence (5.4-6.0 log reduction). In the case of Tri-SPy(+)-Me-PF two distinct behaviours were observed when l-cysteine and d-mannitol were used as free radical scavengers: while the presence of l-cysteine (100 mM) lead to a bacterial protection similar to the one observed with sodium azide, in the presence of d-mannitol only a small protection was detected. The high inhibition of the PS activity by l-cysteine is not due to its radical scavenger ability but due to the singlet oxygen quenching by the sulfanyl group (-SH). In fact, the photodecomposition of 1,3-diphenylisobenzofuran in the presence of Tri-SPy(+)-Me-PF is completely suppressed when l-cysteine is present. The results obtained in this study suggest that singlet oxygen (type II mechanism) plays a very important role over free radicals (type I mechanism) on the PI process of the bioluminescent E. coli by Tri-Py(+)-Me-PF, Tetra-Py(+)-Me and Tri-SPy(+)-Me-PF. Although the use of scavengers is an adequate and simple approach to evaluate the relative importance of the two pathways, it is important to choose scavengers which do not interfere in both PI mechanisms. Sodium azide and d-mannitol seem to be good oxygen and free radical quenchers, respectively, to study the PI mechanisms by porphyrinic photosensitizers.
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Relation between bacterial activity in the surface microlayer and estuarine hydrodynamics.
FEMS Microbiol. Ecol.
PUBLISHED: 07-19-2011
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Bacterial communities of the surface microlayer (SML) of the estuary Ria de Aveiro (Portugal) were characterized in terms of abundance and activity during a 2-year survey at two sites with distinct hydrodynamic properties (marine and brackish water zones). The hydrodynamic conditions were simulated using a bidimensional numerical model and related to the microbiological observations. The pattern of variation of bacterial biomass productivity (BBP) was distinct between the two sampling sites. At the outer site, BBP was significantly lower at the SML, whereas at the inner site, it was significantly enhanced at the SML. Although the total bacterial abundance was similar in the SML and underlying water (UW), the fraction of cells attached to particles was significantly higher at the SML (two to three times). The integration of microbiological results with environmental and hydrological variables shows that strong currents in the marine zone promote the vertical mixing, inhibiting the establishment of an SML bacterial community distinct from that of UW. In contrast, in the brackish water zone, lower current velocities provide conditions for enhancing the bacterial activity in the enriched SML. Estuarine dynamics influence the distribution and activity of microorganisms at the SML and in the water column, with anticipated impacts for the carbon cycle in the estuarine environment.
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Evaluation of resistance development and viability recovery by a non-enveloped virus after repeated cycles of aPDT.
Antiviral Res.
PUBLISHED: 03-17-2011
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Nowadays, the emergence of drug resistant microorganisms is a public health concern. The antimicrobial photodynamic therapy (aPDT) has an efficient action against a wide range of microorganisms and can be viewed as an alternative approach for treating microbial infections. The aim of this study was to determine if a model target virus (T4-like bacteriophage), in the presence of the tricationic porphyrin 5,10,15-tris(1-methylpyridinium-4-yl)-20-(pentafluorophenyl)porphyrin tri-iodide (Tri-Py(+)-Me-PF), can develop resistance to aPDT and recover its viability after photodynamic treatments. To assess the development of aPDT resistance after repeated treatments, a suspension of T4-like bacteriophage was irradiated with white light (40 Wm(-2)) for 120 min in the presence of 5.0 ?M of Tri-Py(+)-Me-PF (99.99% of inactivation) and new phage suspensions were produced from the surviving phages, after each cycle of light exposure. The procedure was repeated ten times. To evaluate the recovery of viral viability after photoinactivation, a suspension of T4-like bacteriophage was irradiated with white light for 120 min in the presence of 5.0 ?M of Tri-Py(+)-Me-PF on five consecutive days. In each day, an aliquot of the irradiated suspension was plated and the number of lysis plaques was counted after 24, 48, 72, 96 and 120 h of dark incubation at 37 °C. The profile of bacteriophage photoinactivation did not change after ten consecutive cycles and no recovery of viability was detected after five accumulated cycles of photodynamic treatment. The results suggest that aPDT represents a valuable and promising alternative therapy to treat viral infections, overcoming the problem of microbial resistance.
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Photodynamic antimicrobial chemotherapy in aquaculture: photoinactivation studies of Vibrio fischeri.
PLoS ONE
PUBLISHED: 03-14-2011
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Photodynamic antimicrobial chemotherapy (PACT) combines light, a light-absorbing molecule that initiates a photochemical or photophysical reaction, and oxygen. The combined action of these three components originates reactive oxygen species that lead to microorganisms destruction. The aim was to evaluate the efficiency of PACT on Vibrio fischeri: 1) with buffer solution, varying temperature, pH, salinity and oxygen concentration values; 2) with aquaculture water, to reproduce photoinactivation (PI) conditions in situ.
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Evaluating seasonal dynamics of bacterial communities in marine fish aquaculture: a preliminary study before applying phage therapy.
J Environ Monit
PUBLISHED: 02-23-2011
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The increasing problem of antibiotic resistance in common pathogenic bacteria and the concern about the spreading of antibiotics in the environment bring the need to find new methods to control fish pathogens. Phage therapy represents a potential alternative to antibiotics, but its use in aquaculture requires a detailed understanding of bacterial communities, namely of fish pathogenic bacteria. Therefore, in this study the seasonal dynamics of the overall bacterial communities, microbiological water quality and disease-causing bacteria were followed in a marine aquaculture system of Ria de Aveiro (Portugal). Analysis of the bacterial diversity of the water samples by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments indicates that the bacterial community structure varied seasonally, showing a higher complexity during the warm season. The diversity of the main fish pathogenic bacteria, assessed by DGGE targeting the Vibrio genus, showed lower seasonal variation, with new dominating populations appearing mainly in the spring. Bacterial indicators, faecal coliforms and enterococci, enumerated by the filter-membrane method, also varied seasonally. The fluorescent in situ hybridization (FISH) results showed that the specific groups of bacteria varied during the study period and that the non-indigenous Enterobactereaceae family was the most abundant group followed by Vibrio and Aeromonas. The seasonal variation detected in terms of density and structure of total and pathogenic bacterial communities demonstrates the need for a careful monitoring of water through the year in order to select the suitable phages to inactivate fish pathogenic bacteria. The spring season seems to be the critical time period when phage therapy should be applied.
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Mangrove bacterial richness.
Commun Integr Biol
PUBLISHED: 02-21-2011
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Mangroves are complex and dynamic ecosystems varying in salinity, water level and nutrient availability; they also contain diverse and distinct microbial communities. Studies of microbes and their interactions with other ecosystem components (e.g., tree roots) are critical for our understanding of mangrove ecosystem functioning and remediation. Using a barcoding pyrosequencing approach, we previously noted the persistence of terrestrial bacterial populations on mangrove roots when nursery raised saplings were transplanted back to their natural environment. Here we go into further detail about the potential functional associations of bacterial guilds with distinct mangrove microhabitats including the rhizosphere. We also use a nonparametric richness estimator to show that estimated operational taxonomic unit (OTU) richness is more than twice that observed. In the transplant microhabitat, our estimate suggests that there are almost 7,000 OTUs for a sample size of 10,400 individual sequences with no sign of an asymptote, indicating that "true" richness for this microhabitat is substantially larger. Results on the number of bacterial OTUs should, however, be viewed with caution given that the barcoding pyrosequencing technique used can yield sequencing artifacts that may inflate richness estimates if not properly removed.
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A bacterial consortium isolated from an Icelandic fumarole displays exceptionally high levels of sulfate reduction and metals resistance.
J. Hazard. Mater.
PUBLISHED: 01-07-2011
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The soils of three fumaroles and one mining site, all with high metal content, were surveyed for the presence of metal-resistant sulfate-reducing bacteria and their potential application in the bioremediation of acid mine drainages. By means of selective soil enrichments a bacterial consortium was isolated from an Icelandic fumarole that displayed very high sulfate reduction in the presence of a mixture of 0.75 g/L of Fe, 0.20 g/L of Zn and 0.080 g/L of Cu. Under these conditions the bacterial consortium reduced 91% of the added 3.9 g/L of sulfate after 28 days, precipitating 100% of the Fe, 96% of the Zn and 97% of the Cu during the same time. Both total bacterial numbers and numbers of culturable sulfate-reducing bacteria remained unchanged when grown in media containing metals, suggesting low or absent inhibitory effects of the metals on the bacterial consortium. PCR-DGGE profiles of the sulfate reducing bacterial communities obtained from the Icelandic fumarole sample showed that bacterial diversity decreased significantly after metal addition: from the original 12 ribotypes only two were detected in the metal-tolerant culture. Phylogenetic analysis of 16S ribosomal RNA gene sequences revealed that these two ribotypes were affiliated with the genera Clostridium and Desulfovibrio, with C. subterminale, C. pascui, C. mesophilum and C. peptidovorans and D. desulfuricans identified as their closest relatives.
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Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia.
FEMS Microbiol. Ecol.
PUBLISHED: 08-31-2010
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In this study, the combination of culture enrichments and molecular tools was used to identify bacterial guilds, plasmids and functional genes potentially important in the process of petroleum hydrocarbon (PH) decontamination in mangrove microniches (rhizospheres and bulk sediment). In addition, we aimed to recover PH-degrading consortia (PHDC) for future use in remediation strategies. The PHDC were enriched with petroleum from rhizosphere and bulk sediment samples taken from a mangrove chronically polluted with oil hydrocarbons. Southern blot hybridization (SBH) assays of PCR amplicons from environmental DNA before enrichments resulted in weak positive signals for the functional gene types targeted, suggesting that PH-degrading genotypes and plasmids were in low abundance in the rhizosphere and bulk sediments. However, after enrichment, these genes were detected and strong microniche-dependent differences in the abundance and composition of hydrocarbonoclastic bacterial populations, plasmids (IncP-1?, IncP-1?, IncP-7 and IncP-9) and functional genes (naphthalene, extradiol and intradiol dioxygenases) were revealed by in-depth molecular analyses [PCR-denaturing gradient gel electrophoresis and hybridization (SBH and microarray)]. Our results suggest that, despite the low abundance of PH-degrading genes and plasmids in the environmental samples, the original bacterial composition of the mangrove microniches determined the structural and functional diversity of the PHDC enriched.
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Taking root: enduring effect of rhizosphere bacterial colonization in mangroves.
PLoS ONE
PUBLISHED: 07-16-2010
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Mangrove forests are of global ecological and economic importance, but are also one of the worlds most threatened ecosystems. Here we present a case study examining the influence of the rhizosphere on the structural composition and diversity of mangrove bacterial communities and the implications for mangrove reforestation approaches using nursery-raised plants.
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Effects of monospecific banks of salt marsh vegetation on sediment bacterial communities.
Microb. Ecol.
PUBLISHED: 04-19-2010
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The aim of this study was to understand if two species of salt marsh plants, widely distributed in European estuaries (Spartina maritima and Halimione portulacoides) differently influence the distribution, activity, and metabolic physiology of sediment bacterial communities in monospecific banks, in comparison with uncolonized sediment (control). Microbiological descriptors of abundance and activity were assessed along vertical profiles of sediments. Rates of activity of the extracellular enzymes beta-glucosidase, alpha-glucosidase, aminopeptidase, arylsulfatase, and phosphatase were generally higher in the vegetation banks in relation to control sediments where they were also less variable with depth. This is interpreted as an indirect effect related to supply of plant-derived polymeric substrates for bacterial growth. Parameters related to sediment texture (grain size, percent of fines or water content) showed significant relations with cell abundance or maximum hydrolysis rates, pointing to an indirect effect of plant colonization exerted through the modification of sediment physical properties. The profiles of utilization of sole-carbon-source (Biolog Ecoplates) showed that only the communities from the upper sediment layer of the S. maritima and the H. portulacoides banks exhibit consistent differences in terms of physiological profiles. Bacterial communities in control sediments exhibited the lowest physiological variability between surface and sub-surface communities. The results indicate that microbial colonization and organic matter decomposition are enhanced under the influence of salt marsh plants and confirm that plant coverage is a major determinant of the processes of organic matter recycling in intertidal estuarine sediments.
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Antimicrobial photodynamic therapy: study of bacterial recovery viability and potential development of resistance after treatment.
Mar Drugs
PUBLISHED: 01-06-2010
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Antimicrobial photodynamic therapy (aPDT) has emerged in the clinical field as a potential alternative to antibiotics to treat microbial infections. No cases of microbial viability recovery or any resistance mechanisms against it are yet known. 5,10,15-tris(1-Methylpyridinium-4-yl)-20-(pentafluorophenyl)-porphyrin triiodide (Tri-Py(+)-Me-PF) was used as photosensitizer. Vibrio fischeri and recombinant Escherichia coli were the studied bacteria. To determine the bacterial recovery after treatment, Tri-Py(+)-Me-PF (5.0 microM) was added to bacterial suspensions and the samples were irradiated with white light (40 W m(-2)) for 270 minutes. Then, the samples were protected from light, aliquots collected at different intervals and the bioluminescence measured. To assess the development of resistance after treatment, bacterial suspensions were exposed to white light (25 minutes), in presence of 5.0 microM of Tri-Py(+)-Me-PF (99.99% of inactivation) and plated. After the first irradiation period, surviving colonies were collected from the plate and resuspended in PBS. Then, an identical protocol was used and repeated ten times for each bacterium. The results suggest that aPDT using Tri-Py(+)-Me-PF represents a promising approach to efficiently destroy bacteria since after a single treatment these microorganisms do not recover their viability and after ten generations of partially photosensitized cells neither of the bacteria develop resistance to the photodynamic process.
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Phage therapy and photodynamic therapy: low environmental impact approaches to inactivate microorganisms in fish farming plants.
Mar Drugs
PUBLISHED: 05-21-2009
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Owing to the increasing importance of aquaculture to compensate for the progressive worldwide reduction of natural fish and to the fact that several fish farming plants often suffer from heavy financial losses due to the development of infections caused by microbial pathogens, including multidrug resistant bacteria, more environmentally-friendly strategies to control fish infections are urgently needed to make the aquaculture industry more sustainable. The aim of this review is to briefly present the typical fish farming diseases and their threats and discuss the present state of chemotherapy to inactivate microorganisms in fish farming plants as well as to examine the new environmentally friendly approaches to control fish infection namely phage therapy and photodynamic antimicrobial therapy.
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Rhizosphere communities of genetically modified zeaxanthin-accumulating potato plants and their parent cultivar differ less than those of different potato cultivars.
Appl. Environ. Microbiol.
PUBLISHED: 04-17-2009
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The effects of genetically modified (GM), zeaxanthin-accumulating potato plants on microbial communities in the rhizosphere were compared to the effects of different potato cultivars. Two GM lines and their parental cultivar, as well as four other potato cultivars, were grown in randomized field plots at two sites and in different years. Rhizosphere samples were taken at three developmental stages during plant growth and analyzed using denaturing gradient gel electrophoresis (DGGE) fingerprints of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria, Bacillus, Streptomycetaceae, Pseudomonas, gacA, Fungi, and Ascomycetes. In the bacterial DGGE gels analyzed, significant differences between the parental cultivar and the two GM lines were detected mainly for Actinobacteria but also for Betaproteobacteria and Streptomycetaceae, yet these differences occurred only at one site and in one year. Significant differences occurred more frequently for Fungi, especially Ascomycetes, than for bacteria. When all seven plant genotypes were compared, DGGE analysis revealed that different cultivars had a greater effect on both bacterial and fungal communities than genetic modification. The effects of genetic modification were detected mostly at the senescence developmental stage of the plants. The site was the overriding factor affecting microbial community structure compared to the plant genotype. In general, the fingerprints of the two GM lines were more similar to that of the parental cultivar, and the differences observed did not exceed natural cultivar-dependent variability.
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Occurrence and diversity of naphthalene dioxygenase genes in soil microbial communities from the Maritime Antarctic.
Environ. Microbiol.
PUBLISHED: 03-13-2009
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The diversity of naphthalene dioxygenase genes (ndo) in soil environments from the Maritime Antarctic was assessed, dissecting as well the influence of the two vascular plants that grow in the Antarctic: Deschampsia antarctica and Colobanthus quitensis. Total community DNA was extracted from bulk and rhizosphere soil samples from Jubany station and Potter Peninsula, South Shetland Islands. ndo genes were amplified by a nested PCR and analysed by denaturant gradient gel electrophoresis approach (PCR-DGGE) and cloning and sequencing. The ndo-DGGE fingerprints of oil-contaminated soil samples showed even and reproducible patterns, composed of four dominant bands. The presence of vascular plants did not change the relative abundance of ndo genotypes compared with bulk soil. For non-contaminated sites, amplicons were not obtained for all replicates and the variability among the fingerprints was comparatively higher, likely reflecting a lower abundance of ndo genes. The phylogenetic analyses showed that all sequences were affiliated to the nahAc genes closely related to those described for Pseudomonas species and related mobile genetic elements. This study revealed that a microdiversity of nahAc-like genes exists in microbial communities of Antarctic soils and quantitative PCR indicated that their relative abundance was increased in response to anthropogenic sources of pollution.
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Wavelength dependence of biological damage induced by UV radiation on bacteria.
Arch. Microbiol.
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The biological effects of UV radiation of different wavelengths (UVA, UVB and UVC) were assessed in nine bacterial isolates displaying different UV sensitivities. Biological effects (survival and activity) and molecular markers of oxidative stress [DNA strand breakage (DSB), generation of reactive oxygen species (ROS), oxidative damage to proteins and lipids, and the activity of antioxidant enzymes catalase and superoxide dismutase] were quantified and statistically analyzed in order to identify the major determinants of cell inactivation under the different spectral regions. Survival and activity followed a clear wavelength dependence, being highest under UVA and lowest under UVC. The generation of ROS, as well as protein and lipid oxidation, followed the same pattern. DNA damage (DSB) showed the inverse trend. Multiple stepwise regression analysis revealed that survival under UVA, UVB and UVC wavelengths was best explained by DSB, oxidative damage to lipids, and intracellular ROS levels, respectively.
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Contribution of reactive oxygen species to UV-B-induced damage in bacteria.
J. Photochem. Photobiol. B, Biol.
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The present work aimed to identify the reactive oxygen species (ROS) produced during UV-B exposure and their biochemical targets, in a set of bacterial isolates displaying different UV susceptibilities. For that, specific exogenous ROS scavengers (catalase/CAT, superoxide dismutase/SOD, sodium azide and mannitol) were used. Biological effects were assessed from total bacterial number, colony counts and heterotrophic activity (glucose uptake and respiration). DNA strand breakage, ROS generation, oxidative damage to proteins and lipids were used as markers of oxidative stress. Sodium azide conferred a statistically significant protection in terms of lipid oxidation and cell survival, suggesting that singlet oxygen might play an important role in UV-B induced cell inactivation. Mannitol exerted a significant protection against DNA strand breakage and protein carbonylation, assigning hydroxyl radicals to DNA and protein damage. The addition of exogenous CAT and SOD significantly protected the capacity for glucose uptake and respiration, suggesting that superoxide and H(2)O(2) are involved in the impairment of activity during UV-B exposure. The observation that amendment with ROS scavengers can sometimes also exert a pro-oxidant effect suggests that the intracellular oxidant status of the cell ultimately determines the efficiency of antioxidant defenses.
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Evidence for selective bacterial community structuring in the freshwater sponge Ephydatia fluviatilis.
Microb. Ecol.
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To understand the functioning of sponges, knowledge of the structure of their associated microbial communities is necessary. However, our perception of sponge-associated microbiomes remains mainly restricted to marine ecosystems. Here, we report on the molecular diversity and composition of bacteria in the freshwater sponge Ephydatia fluviatilis inhabiting the artificial lake Vinkeveense Plassen, Utrecht, The Netherlands. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints revealed that the apparent diversities within the domain Bacteria and the phylum Actinobacteria were lower in E. fluviatilis than in bulk water. Enrichment of specific PCR-DGGE bands in E. fluviatilis was detected. Furthermore, sponge- and bulk water-derived bacterial clone libraries differed with respect to bacterial community composition at the phylum level. E. fluviatilis-derived sequences were affiliated with six recognized phyla, i.e., Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes, Chlamydiae and Verrucomicrobia, in order of relative abundance; next to the uncultured candidate phylum TM7 and one deeply rooted bacterial lineage of undefined taxonomy (BLUT). Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla in the freshwater clone library whereas sequences affiliated with Planctomycetes, Verrucomicrobia, Acidobacteria and Armatimonadetes were found at lower frequencies. Fine-tuned phylogenetic inference showed no or negligible overlaps between the E. fluviatilis and water-derived phylotypes within bacterial taxa such as Alphaproteobacteria, Bacteroidetes and Actinobacteria. We also ascertained the status of two alphaproteobacterial lineages as freshwater sponge-specific phylogenetic clusters, and report on high distinctiveness of other E. fluviatilis specific phylotypes, especially within the Bacteroidetes, Planctomycetes and Chlamydia taxa. This study supports the contention that the composition and diversity of bacteria in E. fluviatilis is partially driven by the host organism.
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Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples.
Appl. Environ. Microbiol.
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Mangroves are complex ecosystems that regulate nutrient and sediment fluxes to the open sea. The importance of bacteria and fungi in regulating nutrient cycles has led to an interest in their diversity and composition in mangroves. However, very few studies have assessed Archaea in mangroves, and virtually nothing is known about whether mangrove rhizospheres affect archaeal diversity and composition. Here, we studied the diversity and composition of Archaea in mangrove bulk sediment and the rhizospheres of two mangrove trees, Rhizophora mangle and Laguncularia racemosa, using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing of archaeal 16S rRNA genes with a nested-amplification approach. DGGE profiles revealed significant structural differences between bulk sediment and rhizosphere samples, suggesting that roots of both mangrove species influence the sediment archaeal community. Nearly all of the detected sequences obtained with pyrosequencing were identified as Archaea, but most were unclassified at the level of phylum or below. Archaeal richness was, furthermore, the highest in the L. racemosa rhizosphere, intermediate in bulk sediment, and the lowest in the R. mangle rhizosphere. This study shows that rhizosphere microhabitats of R. mangle and L. racemosa, common plants in subtropical mangroves located in Rio de Janeiro, Brazil, hosted distinct archaeal assemblages.
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Isolation of surfactant-resistant pseudomonads from the estuarine surface microlayer.
J. Microbiol. Biotechnol.
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Bioremediation efforts often rely on the application of surfactants to enhance hydrocarbon bioavailability. However, synthetic surfactants can sometimes be toxic to degrading microorganisms, thus reducing the clearance rate of the pollutant. Therefore, surfactant-resistant bacteria can be an important tool for bioremediation efforts of hydrophobic pollutants, circumventing the toxicity of synthetic surfactants that often delay microbial bioremediation of these contaminants. In this study, we screened a natural surfactant-rich compartment, the estuarine surface microlayer (SML), for cultivable surfactant-resistant bacteria using selective cultures of sodium dodecyl sulfate (SDS) and cetyl trimethylammonium bromide (CTAB). Resistance to surfactants was evaluated by colony counts in solid media amended with critical micelle concentrations (CMC) of either surfactants, in comparison with non-amended controls. Selective cultures for surfactant-resistant bacteria were prepared in mineral medium also containing CMC concentrations of either CTAB or SDS. The surfactantresistant isolates obtained were tested by PCR for the Pseudomonas genus marker gacA gene and for the naphthalene-dioxygenase-encoding gene ndo. Isolates were also screened for biosurfactant production by the atomized oil assay. A high proportion of culturable bacterioneuston was tolerant to CMC concentrations of SDS or CTAB. The gacA-targeted PCR revealed that 64% of the isolates were Pseudomonads. Biosurfactant production in solid medium was detected in 9.4% of tested isolates, all affiliated with genus Pseudomonas. This study shows that the SML is a potential source of surfactant-resistant and biosurfactant-producing bacteria in which Pseudomonads emerge as a relevant group.
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Impact of organic and inorganic nanomaterials in the soil microbial community structure.
Sci. Total Environ.
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In this study the effect of organic and inorganic nanomaterials (NMs) on the structural diversity of the soil microbial community was investigated by Denaturing Gradient Gel Electrophoresis, after amplification with universal primers for the bacterial region V6-V8 of 16S rDNA. The polymers of carboxylmethyl-cellulose (CMC), of hydrophobically modified CMC (HM-CMC), and hydrophobically modified polyethylglycol (HM-PEG); the vesicles of sodium dodecyl sulphate/didodecyl dimethylammonium bromide (SDS/DDAB) and of monoolein/sodium oleate (Mo/NaO); titanium oxide (TiO(2)), titanium silicon oxide (TiSiO(4)), CdSe/ZnS quantum dots, gold nanorods, and Fe/Co magnetic fluid were the NMs tested. Soil samples were incubated, for a period of 30 days, after being spiked with NM suspensions previously characterized by Dynamic Light Scattering (DLS) or by an ultrahigh-resolution scanning electron microscope (SEM). The analysis of similarities (ANOSIM) of DGGE profiles showed that gold nanorods, TiO(2), CMC, HM-CMC, HM-PEG, and SDS/DDAB have significantly affected the structural diversity of the soil bacterial community.
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The UV responses of bacterioneuston and bacterioplankton isolates depend on the physiological condition and involve a metabolic shift.
FEMS Microbiol. Ecol.
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Bacteria from the surface microlayer (bacterioneuston) and underlying waters (bacterioplankton) were isolated upon exposure to UV-B radiation, and their individual UV sensitivity in terms of CFU numbers, activity (leucine and thymidine incorporation), sole-carbon source use profiles, repair potential (light-dependent and independent), and photoadaptation potential, under different physiological conditions, was compared. Colony counts were 11.5-16.2% more reduced by UV-B exposure in bacterioplankton isolates (P < 0.05). Inhibition of leucine incorporation in bacterioneuston isolates was 10.9-11.5% higher than in bacterioplankton (P < 0.05). These effects were accompanied by a shift in sole-carbon source use profiles, assessed with Biolog(®) EcoPlates, with a reduction in consumption of amines and amino acids and increased use of polymers, particularly in bacterioneuston isolates. Recovery under starvation was generally enhanced compared with nourished conditions, especially in bacterioneuston isolates. Overall, only insignificant increases in the induction of antibiotic resistant mutant phenotypes (Rif(R) and Nal(R) ) were observed. In general, a potential for photoadaptation could not be detected among the tested isolates. These results indicate that UV effects on bacteria are influenced by their physiological condition and are accompanied by a shift in metabolic profiles, more significant in bacterioneuston isolates, suggesting the presence of bacterial strains adapted to high UV levels in the SML.
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Phthalocyanine thio-pyridinium derivatives as antibacterial photosensitizers.
Photochem. Photobiol.
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This study describes the synthesis of three new tetra- and octa-thio-pyridinium phthalocyanine derivatives. PSs 3a and 4a were prepared from the tetramerization of phthalonitriles 1 and 2, respectively, whereas PS 5 was prepared from the nucleophilic substitution of the 8 beta fluor atoms of hexadecafluorophthalocyaninatozinc(II) by mercaptopyridine, followed by cationization. The recombinant bioluminescent Escherichia coli strain was used to assess, in real time, the photoinactivation efficiency of these cationic phthalocyanines, under white and red light. The cellular localization and uptake were also determined to assess the potential of the new phthalocyanines as antibacterial agents. Derivative 3a was the most effective PS, causing a 5 logs reduction in bioluminescence after 30 min of irradiation under white or red lights. The photoinactivation efficiency of the phthalocyanine 4a was similar (5 logs reduction in bioluminescence) to that of 3a when irradiated with white light, but the efficiency of inactivation was reduced (2.1 logs reduction in bioluminescence) under red light. The tetra-substituted phthalocyanine 3a also generates high amounts of singlet oxygen, does not aggregate in PBS and is highly fluorescent, which makes it an effective PS and a promising fluorescent labeling.
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Trends in the discovery of new marine natural products from invertebrates over the last two decades--where and what are we bioprospecting?
PLoS ONE
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It is acknowledged that marine invertebrates produce bioactive natural products that may be useful for developing new drugs. By exploring untapped geographical sources and/or novel groups of organisms one can maximize the search for new marine drugs to treat human diseases. The goal of this paper is to analyse the trends associated with the discovery of new marine natural products from invertebrates (NMNPI) over the last two decades. The analysis considers different taxonomical levels and geographical approaches of bioprospected species. Additionally, this research is also directed to provide new insights into less bioprospected taxa and world regions. In order to gather the information available on NMNPI, the yearly-published reviews of Marine Natural Products covering 1990-2009 were surveyed. Information on source organisms, specifically taxonomical information and collection sites, was assembled together with additional geographical information collected from the articles originally describing the new natural product. Almost 10000 NMNPI were discovered since 1990, with a pronounced increase between decades. Porifera and Cnidaria were the two dominant sources of NMNPI worldwide. The exception was polar regions where Echinodermata dominated. The majority of species that yielded the new natural products belong to only one class of each Porifera and Cnidaria phyla (Demospongiae and Anthozoa, respectively). Increased bioprospecting efforts were observed in the Pacific Ocean, particularly in Asian countries that are associated with the Japan Biodiversity Hotspot and the Kuroshio Current. Although results show comparably less NMNPI from polar regions, the number of new natural products per species is similar to that recorded for other regions. The present study provides information to future bioprospecting efforts addressing previously unexplored taxonomic groups and/or regions. We also highlight how marine invertebrates, which in some cases have no commercial value, may become highly valuable in the ongoing search for new drugs from the sea.
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Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing.
PLoS ONE
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Here, we use DGGE fingerprinting and barcoded pyrosequencing data, at six cut-off levels (85-100%), of all bacteria, Alphaproteobacteria and Betaproteobacteria to assess composition in the rhizosphere of nursery plants and nursery-raised transplants, native plants and bulk sediment in a mangrove habitat. When comparing compositional data based on DGGE fingerprinting and barcoded pyrosequencing at different cut-off levels, all revealed highly significant differences in composition among microhabitats. Procrustes superimposition revealed that ordination results using cut-off levels from 85-100% and DGGE fingerprint data were highly congruent with the standard 97% cut-off level. The various approaches revealed a primary gradient in composition from nursery to mangrove samples. The affinity between the nursery and transplants was greatest when using Betaproteobacteria followed by Alphaproteobacteria data. There was a distinct secondary gradient in composition from transplants to bulk sediment with native plants intermediate, which was most prevalent using all bacteria at intermediate cut-off levels (92-97%). Our results show that PCR-DGGE provides a robust and cost effective exploratory approach and is effective in distinguishing among a priori defined groups.
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Effects of UV-B radiation on the structural and physiological diversity of bacterioneuston and bacterioplankton.
Appl. Environ. Microbiol.
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The effects of UV radiation (UVR) on estuarine bacterioneuston and bacterioplankton were assessed in microcosm experiments. Bacterial abundance and DNA synthesis were more affected in bacterioplankton. Protein synthesis was more inhibited in bacterioneuston. Community analysis indicated that UVR has the potential to select resistant bacteria (e.g., Gammaproteobacteria), particularly abundant in bacterioneuston.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.